TY  - JOUR
A1  - Habel, Jan Christian
A1  - Ulrich, Werner
A1  - Eberle, Jonas
A1  - Schmitt, Thomas
T1  - Species community structures of Afrotropical butterflies differ depending on the monitoring method
JF  - Biodiversity and conservation
N2  - Standardised biodiversity assessment is crucial to understand community structures and population dynamics of animals. 
There exist various methods to monitor biodiversity. Approaches differ depending on the target species group and the aim of study, and show advantages and disadvantages. 
The obtained data and results are influenced by local environmental conditions and seasonal variability.
In a comparative approach, we studied butterfly diversity and community structure in the dryland savannah biome of south-eastern Kenya with two different methods, transect counts and bait trapping. 

We repeatedly collected data throughout the dry and rainy seasons, in both near natural and anthropogenically influenced landscapes. Significantly more species and individuals were recorded by transect counts than by bait trapping, though the larger and more mobile Nymphalid species (and in particular representatives of the genus Charaxes) were comparatively overrepresented in traps. 

The transect data revealed much more pronounced effects of land-use and seasonality than the trap data. These results show that the choice of data collection methods must depend on the general research question, habitat conditions and season. To study the relative variation of species diversity and abundance, the collection of a fraction of the total species diversity might be sufficient. 

However, if the focus is on a largely complete recording of species diversity, the use of various collection methods is essential. More specifically, our data clearly demonstrate that transect counts represent a reasonable method for assessing butterfly diversity for the African dryland savannah region, but fails to fully capture occurrences of all species. Bait trapping can be used only as a supplementary method for assessing some few highly mobile low-density species.
KW  - monitoring
KW  - transect count
KW  - bait trap
KW  - population dynamic
KW  - disturbance
KW  - seasonality
Y1  - 2022
U6  - https://doi.org/10.1007/s10531-021-02332-2
SN  - 0960-3115
SN  - 1572-9710
VL  - 31
IS  - 1
SP  - 245
EP  - 259
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Mbebi, Alain J.
A1  - Breitler, Jean-Christophe
A1  - Bordeaux, M'elanie
A1  - Sulpice, Ronan
A1  - McHale, Marcus
A1  - Tong, Hao
A1  - Toniutti, Lucile
A1  - Castillo, Jonny Alonso
A1  - Bertrand, Benoit
A1  - Nikoloski, Zoran
T1  - A comparative analysis of genomic and phenomic predictions of growth-related traits in 3-way coffee hybrids
JF  - G3: Genes, genomes, genetics
N2  - Genomic prediction has revolutionized crop breeding despite remaining issues of transferability of models to unseen environmental conditions and environments. Usage of endophenotypes rather than genomic markers leads to the possibility of building phenomic prediction models that can account, in part, for this challenge. Here, we compare and contrast genomic prediction and phenomic prediction models for 3 growth-related traits, namely, leaf count, tree height, and trunk diameter, from 2 coffee 3-way hybrid populations exposed to a series of treatment-inducing environmental conditions. The models are based on 7 different statistical methods built with genomic markers and ChlF data used as predictors. This comparative analysis demonstrates that the best-performing phenomic prediction models show higher predictability than the best genomic prediction models for the considered traits and environments in the vast majority of comparisons within 3-way hybrid populations. In addition, we show that phenomic prediction models are transferrable between conditions but to a lower extent between populations and we conclude that chlorophyll a fluorescence data can serve as alternative predictors in statistical models of coffee hybrid performance. Future directions will explore their combination with other endophenotypes to further improve the prediction of growth-related traits for crops.
KW  - genomic prediction
KW  - phenomic prediction
KW  - 3-way coffee hybrids
KW  - chlorophyll a fluorescence
KW  - GenPred
KW  - Shared Data Resource
Y1  - 2022
U6  - https://doi.org/10.1093/g3journal/jkac170
SN  - 2160-1836
VL  - 12
IS  - 9
PB  - Genetics Soc. of America
CY  - Pittsburgh, PA
ER  - 
TY  - JOUR
A1  - Heim, Birgit
A1  - Lisovski, Simeon
A1  - Wieczorek, Mareike
A1  - Morgenstern, Anne
A1  - Juhls, Bennet
A1  - Shevtsova, Iuliia
A1  - Kruse, Stefan
A1  - Boike, Julia
A1  - Fedorova, Irina
A1  - Herzschuh, Ulrike
T1  - Spring snow cover duration and tundra greenness in the Lena Delta, Siberia
BT  - two decades of MODIS satellite time series (2001-2021)
JF  - Environmental research letters
N2  - The Lena Delta in Siberia is the largest delta in the Arctic and as a snow-dominated ecosystem particularly vulnerable to climate change. 
Using the two decades of MODerate resolution Imaging Spectroradiometer satellite acquisitions, this study investigates interannual and spatial variability of snow-cover duration and summer vegetation vitality in the Lena Delta. 

We approximated snow by the application of the normalized difference snow index and vegetation greenness by the normalized difference vegetation index (NDVI). We consolidated the analyses by integrating reanalysis products on air temperature from 2001 to 2021, and air temperature, ground temperature, and the date of snow-melt from time-lapse camera (TLC) observations from the Samoylov observatory located in the central delta. 
We extracted spring snow-cover duration determined by a latitudinal gradient. The 'regular year' snow-melt is transgressing from mid-May to late May within a time window of 10 days across the delta. 
We calculated yearly deviations per grid cell for two defined regions, one for the delta, and one focusing on the central delta. We identified an ensemble of early snow-melt years from 2012 to 2014, with snow-melt already starting in early May, and two late snow-melt years in 2004 and 2017, with snow-melt starting in June. In the times of TLC recording, the years of early and late snow-melt were confirmed. 

In the three summers after early snow-melt, summer vegetation greenness showed neither positive nor negative deviations. Whereas, vegetation greenness was reduced in 2004 after late snow-melt together with the lowest June monthly air temperature of the time series record. Since 2005, vegetation greenness is rising, with maxima in 2018 and 2021. 
The NDVI rise since 2018 is preceded by up to 4 degrees C warmer than average June air temperature. The ongoing operation of satellite missions allows to monitor a wide range of land surface properties and processes that will provide urgently needed data in times when logistical challenges lead to data gaps in land-based observations in the rapidly changing Arctic.
KW  - Arctic vegetation
KW  - tundra
KW  - snow cover duration
KW  - NDVI
KW  - NDSI
KW  - MODIS
KW  - Lena Delta
Y1  - 2022
U6  - https://doi.org/10.1088/1748-9326/ac8066
SN  - 1748-9326
VL  - 17
IS  - 8
PB  - IOP Publ. Ltd.
CY  - Bristol
ER  - 
TY  - JOUR
A1  - Montes-Osuna, Nuria
A1  - Cernava, Tomislav
A1  - Gomez-Lama Cabanas, Carmen
A1  - Berg, Gabriele
A1  - Mercado-Blanco, Jesus
T1  - Identification of volatile organic compounds emitted by two beneficial endophytic pseudomonas strains from olive roots
JF  - Plants
N2  - The production of volatile organic compounds (VOCs) represents a promising strategy of plant-beneficial bacteria to control soil-borne phytopathogens. 
Pseudomonas sp. PICF6 and Pseudomonas simiae PICF7 are two indigenous inhabitants of olive roots displaying effective biological control against Verticillium dahliae. Additionally, strain PICF7 is able to promote the growth of barley and Arabidopsis thaliana, VOCs being involved in the growth of the latter species. 

In this study, the antagonistic capacity of these endophytic bacteria against relevant phytopathogens (Verticillium spp., Rhizoctonia solani, Sclerotinia sclerotiorum and Fusarium oxysporum f.sp. lycopersici) was assessed. Under in vitro conditions, PICF6 and PICF7 were only able to antagonize representative isolates of V. dahliae and V. longisporum. Remarkably, both strains produced an impressive portfolio of up to twenty VOCs, that included compounds with reported antifungal (e.g., 1-undecene, (methyldisulfanyl) methane and 1-decene) or plant growth promoting (e.g., tridecane, 1-decene) activities. Moreover, their volatilomes differed strongly in the absence and presence of V. dahliae. 

For example, when co incubated with the defoliating pathotype of V. dahliae, the antifungal compound 4-methyl-2,6-bis(2-methyl-2-propanyl)phenol was produced. Results suggest that volatiles emitted by these endophytes may differ in their modes of action, and that potential benefits for the host needs further investigation in planta.
KW  - biological control agents
KW  - olive rhizobacteria
KW  - Pseudomonas sp
KW  - PICF6
KW  - Pseudomonas simiae PICF7
KW  - root endophytes
KW  - Verticillium dahliae
KW  - volatilome
Y1  - 2022
U6  - https://doi.org/10.3390/plants11030318
SN  - 2223-7747
VL  - 11
IS  - 3
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Manna, Vincenzo
A1  - Zoccarato, Luca
A1  - Banchi, Elisa
A1  - Arnosti, Carol
A1  - Grossart, Hans-Peter
A1  - Celussi, Mauro
T1  - Linking lifestyle and foraging strategies of marine bacteria
BT  - selfish behaviour of particle-attached bacteria in the northern Adriatic Sea
JF  - Environmental microbiology reports
N2  - Microbe-mediated enzymatic hydrolysis of organic matter entails the production of hydrolysate, the recovery of which may be more or less efficient. The selfish uptake mechanism, recently discovered, allows microbes to hydrolyze polysaccharides and take up large oligomers, which are then degraded in the periplasmic space. By minimizing the hydrolysate loss, selfish behaviour may be profitable for free-living cells dwelling in a patchy substrate landscape. However, selfish uptake seems to be tailored to algal-derived polysaccharides, abundant in organic particles, suggesting that particle-attached microbes may use this strategy. We tracked selfish polysaccharides uptake in surface microbial communities of the northeastern Mediterranean Sea, linking the occurrence of this processing mode with microbial lifestyle. Additionally, we set up fluorescently labelled polysaccharides incubations supplying phytodetritus to investigate a 'pioneer' scenario for particle-attached microbes. Under both conditions, selfish behaviour was almost exclusively carried out by particle-attached microbes, suggesting that this mechanism may represent an advantage in the race for particle exploitation. Our findings shed light on the selfish potential of particle-attached microbes, suggesting multifaceted foraging strategies exerted by particle colonizers.
Y1  - 2022
U6  - https://doi.org/10.1111/1758-2229.13059
SN  - 1758-2229
VL  - 14
IS  - 4
SP  - 549
EP  - 558
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Minutillo, Serena A.
A1  - Ruano-Rosa, David
A1  - Abdelfattah, Ahmed
A1  - Schena, Leonardo
A1  - Malacrino, Antonino
T1  - The fungal microbiome of wheat flour includes potential mycotoxin producers
JF  - Foods
N2  - Consumers are increasingly demanding higher quality and safety standards for the products they consume, and one of this is wheat flour, the basis of a wide variety of processed products. This major component in the diet of many communities can be contaminated by microorganisms before the grain harvest, or during the grain storage right before processing. These microorganisms include several fungal species, many of which produce mycotoxins, secondary metabolites that can cause severe acute and chronic disorders. Yet, we still know little about the overall composition of fungal communities associated with wheat flour. In this study, we contribute to fill this gap by characterizing the fungal microbiome of different types of wheat flour using culture-dependent and -independent techniques. Qualitatively, these approaches suggested similar results, highlighting the presence of several fungal taxa able to produce mycotoxins. In-vitro isolation of fungal species suggest a higher frequency of Penicillium, while metabarcoding suggest a higher abundance of Alternaria. This discrepancy might reside on the targeted portion of the community (alive vs. overall) or in the specific features of each technique. Thus, this study shows that commercial wheat flour hosts a wide fungal diversity with several taxa potentially representing concerns for consumers, aspects that need more attention throughout the food production chain.
KW  - Penicillium
KW  - Alternaria
KW  - post-harvest
KW  - metabarcoding
Y1  - 2022
U6  - https://doi.org/10.3390/foods11050676
SN  - 2304-8158
VL  - 11
IS  - 5
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Wassermann, Birgit
A1  - Abdelfattah, Ahmed
A1  - Wicaksono, Wisnu Adi
A1  - Kusstatscher, Peter
A1  - Müller, Henry
A1  - Cernava, Tomislav
A1  - Goertz, Simon
A1  - Rietz, Steffen
A1  - Abbadi, Amine
A1  - Berg, Gabriele
T1  - The Brassica napus seed microbiota is cultivar-specific and transmitted via paternal breeding lines
JF  - Microbial biotechnology
N2  - Seed microbiota influence germination and plant health and have the potential to improve crop performance, but the factors that determine their structure and functions are still not fully understood. 
Here, we analysed the impact of plant-related and external factors on seed endophyte communities of 10 different oilseed rape (Brassica napus L.) cultivars from 26 field sites across Europe. 

All seed lots harboured a high abundance and diversity of endophytes, which were dominated by six genera: Ralstonia, Serratia, Enterobacter, Pseudomonas, Pantoea, and Sphingomonas. 

The cultivar was the main factor explaining the variations in bacterial diversity, abundance and composition. In addition, the latter was significantly influenced by diverse biotic and abiotic factors, for example host germination rates and disease resistance against Plasmodiophora brassicae. 
A set of bacterial biomarkers was identified to discriminate between characteristics of the seeds, for example Sphingomonas for improved germination and Brevundimonas for disease resistance. 
Application of a Bayesian community approach suggested vertical transmission of seed endophytes, where the paternal parent plays a major role and might even determine the germination performance of the offspring. 

This study contributes to the understanding of seed microbiome assembly and underlines the potential of the microbiome to be implemented in crop breeding and biocontrol programmes.
Y1  - 2022
U6  - https://doi.org/10.1111/1751-7915.14077
SN  - 1751-7915
VL  - 15
IS  - 9
SP  - 2379
EP  - 2390
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Dreymann, Nico
A1  - Wuensche, Julia
A1  - Sabrowski, Wiebke
A1  - Moeller, Anja
A1  - Czepluch, Denise
A1  - Vu Van, Dana
A1  - Füssel, Susanne
A1  - Menger, Marcus M.
T1  - Inhibition of Human Urokinase-Type Plasminogen Activator (uPA) Enzyme Activity and Receptor Binding by DNA Aptamers as Potential Therapeutics through Binding to the Different Forms of uPA
JF  - International journal of molecular sciences
N2  - Urokinase-type plasminogen activator is widely discussed as a marker for cancer prognosis and diagnosis and as a target for cancer therapies. Together with its receptor, uPA plays an important role in tumorigenesis, tumor progression and metastasis. In the present study, systematic evolution of ligands by exponential enrichment (SELEX) was used to select single-stranded DNA aptamers targeting different forms of human uPA. Selected aptamers allowed the distinction between HMW-uPA and LMW-uPA, and therefore, presumably, have different binding regions. Here, uPAapt-02-FR showed highly affine binding with a K-D of 0.7 nM for HMW-uPA and 21 nM for LMW-uPA and was also able to bind to pro-uPA with a K-D of 14 nM. Furthermore, no cross-reactivity to mouse uPA or tissue-type plasminogen activator (tPA) was measured, demonstrating high specificity. Suppression of the catalytic activity of uPA and inhibition of uPAR-binding could be demonstrated through binding with different aptamers and several of their truncated variants. Since RNA aptamers are already known to inhibit uPA-uPAR binding and other pathological functions of the uPA system, these aptamers represent a novel, promising tool not only for detection of uPA but also for interfering with the pathological functions of the uPA system by additionally inhibiting uPA activity.
KW  - biomarker
KW  - cancer
KW  - cancer therapy
KW  - DNA aptamer
KW  - microscale thermophoresis (MST)
KW  - SELEX
KW  - surface plasmon resonance spectroscopy (SPR)
KW  - uPA
KW  - uPAR
KW  - urokinase
Y1  - 2022
U6  - https://doi.org/10.3390/ijms23094890
SN  - 1661-6596
SN  - 1422-0067
VL  - 23
IS  - 9
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Zhang, Kai
A1  - Hu, Jiege
A1  - Yang, Shuai
A1  - Xu, Wei
A1  - Wang, Zhichao
A1  - Zhuang, Peiwen
A1  - Grossart, Hans-Peter
A1  - Luo, Zhuhua
T1  - Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1
JF  - Journal of hazardous materials
N2  - Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.
KW  - Impranil PU degradation
KW  - Lipase
KW  - Cutinase
KW  - HsbA
KW  - Fatty acid degradation
Y1  - 2022
U6  - https://doi.org/10.1016/j.jhazmat.2022.129406
SN  - 0304-3894
SN  - 1873-3336
VL  - 437
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Raffeiner, Margot
A1  - Üstün, Suayib
A1  - Guerra, Tiziana
A1  - Spinti, Daniela
A1  - Fitzner, Maria
A1  - Sonnewald, Sophia
A1  - Baldermann, Susanne
A1  - Börnke, Frederik
T1  - The Xanthomonas type-III effector XopS stabilizes CaWRKY40a to regulate defense responses and stomatal immunity in pepper (Capsicum annuum)
JF  - The plant cell
N2  - As a critical part of plant immunity, cells that are attacked by pathogens undergo rapid transcriptional reprogramming to minimize virulence. Many bacterial phytopathogens use type III effector (T3E) proteins to interfere with plant defense responses, including this transcriptional reprogramming. Here, we show that Xanthomonas outer protein S (XopS), a T3E of Xanthomonas campestris pv. vesicatoria (Xcv), interacts with and inhibits proteasomal degradation of WRKY40, a transcriptional regulator of defense gene expression. Virus-induced gene silencing of WRKY40 in pepper (Capsicum annuum) enhanced plant tolerance to Xcv infection, indicating that WRKY40 represses immunity. Stabilization of WRKY40 by XopS reduces the expression of its targets, which include salicylic acid-responsive genes and the jasmonic acid signaling repressor JAZ8. Xcv bacteria lacking XopS display significantly reduced virulence when surface inoculated onto susceptible pepper leaves. XopS delivery by Xcv, as well as ectopic expression of XopS in Arabidopsis thaliana or Nicotiana benthamiana, prevented stomatal closure in response to bacteria and biotic elicitors. Silencing WRKY40 in pepper or N. benthamiana abolished XopS's ability to prevent stomatal closure. This suggests that XopS interferes with both preinvasion and apoplastic defense by manipulating WRKY40 stability and downstream gene expression, eventually altering phytohormone crosstalk to promote pathogen proliferation.
Y1  - 2022
U6  - https://doi.org/10.1093/plcell/koac032
SN  - 1040-4651
SN  - 1532-298X
VL  - 34
IS  - 5
SP  - 1684
EP  - 1708
PB  - Oxford Univ. Press
CY  - Cary
ER  - 
TY  - JOUR
A1  - Hannigan, Sara
A1  - Nendel, Claas
A1  - Krull, Marcos
T1  - Effects of temperature on the movement and feeding behaviour of the large lupine beetle, Sitona gressorius
JF  - Journal of pest science
N2  - Even though the effects of insect pests on global agricultural productivity are well recognised, little is known about movement and dispersal of many species, especially in the context of global warming. This work evaluates how temperature and light conditions affect different movement metrics and the feeding rate of the large lupine beetle, an agricultural pest responsible for widespread damage in leguminous crops. By using video recordings, the movement of 384 beetles was digitally analysed under six different temperatures and light conditions in the laboratory. Bayesian linear mixed-effect models were used to analyse the data. Furthermore, the effects of temperature on the daily diffusion coefficient of beetles were estimated by using hidden Markov models and random walk simulations. Results of this work show that temperature, light conditions, and beetles' weight were the main factors affecting the flight probability, displacement, time being active and the speed of beetles. Significant variations were also observed in all evaluated metrics. On average, beetles exposed to light conditions and higher temperatures had higher mean speed and flight probability. However, beetles tended to stay more active at higher temperatures and less active at intermediate temperatures, around 20 degrees C. Therefore, both the diffusion coefficient and displacement of beetles were lower at intermediate temperatures. These results show that the movement behaviour and feeding rates of beetles can present different relationships in the function of temperature. It also shows that using a single diffusion coefficient for insects in spatially explicit models may lead to over- or underestimation of pest spread.
KW  - Agricultural pests
KW  - Diffusion
KW  - Hidden Markov models
KW  - Movement ecology
Y1  - 2022
U6  - https://doi.org/10.1007/s10340-022-01510-7
SN  - 1612-4758
SN  - 1612-4766
SP  - 389
EP  - 402
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Hilgers, Leon
A1  - Hartmann, Stefanie
A1  - Pfaender, Jobst
A1  - Lentge-Maass, Nora
A1  - Marwoto, Ristiyanti M.
A1  - von Rintelen, Thomas
A1  - Hofreiter, Michael
T1  - Evolutionary divergence and radula diversification in two ecomorphs from an adaptive radiation of freshwater snails
JF  - Genes
N2  - (1) Background: 
Adaptive diversification of complex traits plays a pivotal role in the evolution of organismal diversity. In the freshwater snail genus Tylomelania, adaptive radiations were likely promoted by trophic specialization via diversification of their key foraging organ, the radula.

(2) Methods: 
To investigate the molecular basis of radula diversification and its contribution to lineage divergence, we used tissue-specific transcriptomes of two sympatric Tylomelania sarasinorum ecomorphs.

(3) Results: 
We show that ecomorphs are genetically divergent lineages with habitat-correlated abundances. Sequence divergence and the proportion of highly differentially expressed genes are significantly higher between radula transcriptomes compared to the mantle and foot. However, the same is not true when all differentially expressed genes or only non-synonymous SNPs are considered. Finally, putative homologs of some candidate genes for radula diversification (hh, arx, gbb) were also found to contribute to trophic specialization in cichlids and Darwin's finches.

(4) Conclusions: 
Our results are in line with diversifying selection on the radula driving Tylomelania ecomorph divergence and indicate that some molecular pathways may be especially prone to adaptive diversification, even across phylogenetically distant animal groups.
KW  - speciation
KW  - adaptive radiation
KW  - molluscs
KW  - RNAseq
KW  - regulatory evolution
KW  - trophic specialization
Y1  - 2022
U6  - https://doi.org/10.3390/genes13061029
SN  - 2073-4425
VL  - 13
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Perkins, Anita K.
A1  - Santos, Isaac R.
A1  - Rose, Andrew L.
A1  - Schulz, Kai G.
A1  - Grossart, Hans-Peter
A1  - Eyre, Bradley D.
A1  - Kelaher, Brendan P.
A1  - Oakes, Joanne M.
T1  - Production of dissolved carbon and alkalinity during macroalgal wrack degradation on beaches
BT  - a mesocosm experiment with implications for blue carbon
JF  - Biogeochemistry
N2  - Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration.
KW  - Tidal pumping
KW  - Organic matter degradation
KW  - Carbon cycle
KW  - Mineralisation
KW  - Porewater exchange
KW  - Submarine groundwater discharge
Y1  - 2022
U6  - https://doi.org/10.1007/s10533-022-00946-4
SN  - 0168-2563
SN  - 1573-515X
VL  - 160
IS  - 2
SP  - 159
EP  - 175
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Huß, Sebastian
A1  - Judd, Rika Siedah
A1  - Koper, Kaan
A1  - Maeda, Hiroshi A.
A1  - Nikoloski, Zoran
T1  - An automated workflow that generates atom mappings for large-scale metabolic models and its application to Arabidopsis thaliana
JF  - The plant journal
N2  - Quantification of reaction fluxes of metabolic networks can help us understand how the integration of different metabolic pathways determines cellular functions. Yet, intracellular fluxes cannot be measured directly but are estimated with metabolic flux analysis (MFA), which relies on the patterns of isotope labeling of metabolites in the network. The application of MFA also requires a stoichiometric model with atom mappings that are currently not available for the majority of large-scale metabolic network models, particularly of plants. While automated approaches such as the Reaction Decoder Toolkit (RDT) can produce atom mappings for individual reactions, tracing the flow of individual atoms of the entire reactions across a metabolic model remains challenging. Here we establish an automated workflow to obtain reliable atom mappings for large-scale metabolic models by refining the outcome of RDT, and apply the workflow to metabolic models of Arabidopsis thaliana. We demonstrate the accuracy of RDT through a comparative analysis with atom mappings from a large database of biochemical reactions, MetaCyc. We further show the utility of our automated workflow by simulating N-15 isotope enrichment and identifying nitrogen (N)-containing metabolites which show enrichment patterns that are informative for flux estimation in future N-15-MFA studies of A. thaliana. The automated workflow established in this study can be readily expanded to other species for which metabolic models have been established and the resulting atom mappings will facilitate MFA and graph-theoretic structural analyses with large-scale metabolic networks.
KW  - atom mapping
KW  - genome-scale metabolic model
KW  - isotopic labeling
KW  - metabolic
KW  - flux analysis
KW  - technical advance
Y1  - 2022
U6  - https://doi.org/10.1111/tpj.15903
SN  - 0960-7412
SN  - 1365-313X
VL  - 111
IS  - 5
SP  - 1486
EP  - 1500
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Ostermann-Miyashita, Emu-Felicitas
A1  - König, Hannes J.
A1  - Pernat, Nadja
A1  - Bellingrath-Kimura, Sonoko Dorothea
A1  - Hibler, Sophia
A1  - Kiffner, Christian
T1  - Knowledge of returning wildlife species and willingness to participate in citizen science projects among wildlife park visitors in Germany
JF  - People and nature
N2  - Successful conservation efforts have led to recent increases of large mammals such as European bison Bison bonasus, moose Alces alces and grey wolf Canis lupus and their return to former habitats in central Europe. 
While embraced by some, the recovery of these species is a controversial topic and holds potential for human-wildlife conflicts. 
Involving the public has been suggested to be an effective method for monitoring wildlife and mitigating associated conflicts. 
To assess two interrelated prerequisites for engaging people in Citizen Science (CS)-knowledge of returning species and respondents' readiness to participate in CS activities for monitoring and managing these species-we conducted a survey (questionnaire) in two wildlife parks located in different states of Germany. 
Based on 472 complete questionnaires, we developed generalized linear models to understand how sociodemographic variables and exposure to the species affected visitors' knowledge of each species, and to investigate if sociodemographic variables and knowledge influenced the likelihood of visitors to participate in CS activities. 
Almost all visitors were aware of the returning wolf population, while knowledge and awareness about bison and moose were significantly lower. 
Knowledge of the two herbivores differed geographically (higher knowledge of moose in the north-eastern state), possibly indicating a positive association between exposure to the species and knowledge. 
However, models generally performed poorly in predicting knowledge about wildlife, suggesting that such specific knowledge is insufficiently explained by sociodemographic variables. Our model, which explained stated willingness in CS indicated that younger participants and those with higher knowledge scores in the survey were more willing to engage in CS activities. 
Overall, our analyses highlight how exposure to large mammals, knowledge about wildlife and human demographics are interrelated-insights that are helpful for effectively recruiting citizen scientists for wildlife conservation. 
Read the free Plain Language Summary for this article on the Journal blog.
KW  - environmental awareness
KW  - human-animal relationships
KW  - human-wildlife conflicts
KW  - social-ecological system
KW  - wildlife conservation
KW  - wildlife knowledge
Y1  - 2022
U6  - https://doi.org/10.1002/pan3.10379
SN  - 2575-8314
VL  - 4
IS  - 5
SP  - 1201
EP  - 1215
PB  - British Ecological Society; Wiley
CY  - London; Hoboken, NJ
ER  - 
TY  - JOUR
A1  - Potente, Giacomo
A1  - Léveillé-Bourret, Étienne
A1  - Yousefi, Narjes
A1  - Choudhury, Rimjhim Roy
A1  - Keller, Barbara
A1  - Diop, Seydina Issa
A1  - Duijsings, Daniël
A1  - Pirovano, Walter
A1  - Lenhard, Michael
A1  - Szövényi, Péter
A1  - Conti, Elena
T1  - Comparative genomics elucidates the origin of a supergene controlling floral heteromorphism
JF  - Molecular biology and evolution : MBE
N2  - Supergenes are nonrecombining genomic regions ensuring the coinheritance of multiple, coadapted genes. Despite the importance of supergenes in adaptation, little is known on how they originate. A classic example of supergene is the S locus controlling heterostyly, a floral heteromorphism occurring in 28 angiosperm families. In Primula, heterostyly is characterized by the cooccurrence of two complementary, self-incompatible floral morphs and is controlled by five genes clustered in the hemizygous, ca. 300-kb S locus. Here, we present the first chromosome-scale genome assembly of any heterostylous species, that of Primula veris (cowslip). By leveraging the high contiguity of the P. veris assembly and comparative genomic analyses, we demonstrated that the S-locus evolved via multiple, asynchronous gene duplications and independent gene translocations. Furthermore, we discovered a new whole-genome duplication in Ericales that is specific to the Primula lineage. We also propose a mechanism for the origin of S-locus hemizygosity via nonhomologous recombination involving the newly discovered two pairs of CFB genes flanking the S locus. Finally, we detected only weak signatures of degeneration in the S locus, as predicted for hemizygous supergenes. The present study provides a useful resource for future research addressing key questions on the evolution of supergenes in general and the S locus in particular: How do supergenes arise? What is the role of genome architecture in the evolution of complex adaptations? Is the molecular architecture of heterostyly supergenes across angiosperms similar to that of Primula?
KW  - genome architecture
KW  - supergene
KW  - heterostyly
KW  - evolutionary genomics
KW  - chromosome-scale genome assembly
KW  - primula
Y1  - 2022
U6  - https://doi.org/10.1093/molbev/msac035
SN  - 0737-4038
SN  - 1537-1719
VL  - 39
IS  - 2
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Lucena-Perez, María
A1  - Bazzicalupo, Enrico
A1  - Paijmans, Johanna
A1  - Kleinman-Ruiz, Daniel
A1  - Dalén, Love
A1  - Hofreiter, Michael
A1  - Delibes, Miguel
A1  - Clavero, Miguel
A1  - Godoy, José A.
T1  - Ancient genome provides insights into the history of Eurasian lynx in Iberia and Western Europe
JF  - Quaternary science reviews : the international multidisciplinary research and review journal
N2  - The Eurasian lynx (Lynx lynx) is one of the most widely distributed felids in the world. However, most of its populations started to decline a few millennia ago. Historical declines have been especially severe in Europe, and particularly in Western Europe, from where the species disappeared in the last few centuries. Here, we analyze the genome of an Eurasian lynx inhabiting the Iberian Peninsula 2500 ya, to gain insights into the phylogeographic position and genetic status of this extinct population. Also, we contextualize previous ancient data in the light of new phylogeographic studies of the species. Our results suggest that the Iberian population is part of an extinct European lineage closely related to the current Carpathian-Baltic lineages. Also, this sample holds the lowest diversity reported for the species so far, and similar to that of the highly endangered Iberian lynx. A combination of historical factors, such as a founder effect while colonizing the peninsula, together with intensified human impacts during the Holocene in the Cantabrian strip, could have led to a genetic impoverishment of the population and precipitated its extinction. Mitogenomic lineages distribution in space and time support the long-term coexistence of several lineages of Eurasian lynx in Western Europe with fluctuating ranges. While mitochondrial sequences related to the lineages currently found in Balkans and Caucasus were predominant during the Pleistocene, those more closely related to the lineage currently distributed in Central Europe prevailed during the Holocene. The use of ancient genomics has proven to be a useful tool to understand the biogeographic pattern of the Eurasian lynx in the past.
Y1  - 2022
U6  - https://doi.org/10.1016/j.quascirev.2022.107518
SN  - 0277-3791
SN  - 1873-457X
VL  - 285
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Escalante, Ignacio
A1  - Dominguez, Marisol
A1  - Gomez-Ruiz, Daisy Alejandra
A1  - Machado, Glauco
T1  - Benefits and costs of mixed-species aggregations in Harvestmen (Arachnida: Opiliones)
JF  - Frontiers in ecology and evolution
N2  - Many animals form aggregations with individuals of the same species (single-species aggregations, SSA). Less frequently, individuals may also aggregate with individuals of other species (mixed-species aggregations, MSA). Although the benefits and costs of SSA have been intensively studied, the same is not true for MSA. Here, we first review the cases of MSA in harvestmen, an arachnid order in which the records of MSA are more frequent than other arthropod orders. We then propose several benefits and costs of MSA in harvestmen, and contrast them with those of SSA. Second, using field-gathered data we describe gregariousness in seven species of Prionostemma harvestmen from Costa Rica. These species form MSA, but individuals are also found solitarily or in SSA. We tested one possible benefit and one possible cost of gregariousness in Prionostemma harvestmen. Regarding the benefit, we hypothesized that individuals missing legs would be more exposed to predation than eight-legged individuals and thus they should be found preferentially in aggregations, where they would be more protected from predators. Our data, however, do not support this hypothesis. Regarding the cost, we hypothesized that gregariousness increases the chances of parasitism. We found no support for this hypothesis either because both mite prevalence and infestation intensity did not differ between solitary or aggregated individuals. Additionally, the type of aggregation (SSA or MSA) was not associated with the benefit or the cost we explored. This lack of effect may be explained by the fluid membership of the aggregations, as we found high turnover over time in the number of individuals and species composition of the aggregations. In conclusion, we hope our review and empirical data stimulate further studies on MSA, which remains one of the most elusive forms of group living in animals.
KW  - alarm signals
KW  - aggregation size
KW  - autotomy
KW  - chemical defenses
KW  - dilution
KW  - effect
KW  - ectoparasitism
KW  - group living
KW  - roosting site
Y1  - 2022
U6  - https://doi.org/10.3389/fevo.2021.766323
SN  - 2296-701X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Krumbholz, Julia
A1  - Ishida, Keishi
A1  - Baunach, Martin
A1  - Teikari, Jonna
A1  - Rose, Magdalena M.
A1  - Sasso, Severin
A1  - Hertweck, Christian
A1  - Dittmann, Elke
T1  - Deciphering chemical mediators regulating specialized metabolism in a symbiotic cyanobacterium
JF  - Angewandte Chemie : a journal of the Gesellschaft Deutscher Chemiker. International edition
N2  - Genomes of cyanobacteria feature a variety of cryptic biosynthetic pathways for complex natural products, but the peculiarities limiting the discovery and exploitation of the metabolic dark matter are not well understood. Here we describe the discovery of two cell density-dependent chemical mediators, nostoclide and nostovalerolactone, in the symbiotic model strain Nostoc punctiforme, and demonstrate their pronounced impact on the regulation of specialized metabolism. Through transcriptional, bioinformatic and labeling studies we assigned two adjacent biosynthetic gene clusters to the biosynthesis of the two polyketide mediators. Our findings provide insight into the orchestration of specialized metabolite production and give lessons for the genomic mining and high-titer production of cyanobacterial bioactive compounds.
KW  - Biosynthesis
KW  - Cyanobacteria
KW  - Genomic Mining
KW  - Quorum Sensing
KW  - Specialized
KW  - Metabolism
Y1  - 2022
U6  - https://doi.org/10.1002/anie.202204545
SN  - 1433-7851
SN  - 1521-3773
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Li, Chenzhi
A1  - Postl, Alexander K.
A1  - Böhmer, Thomas
A1  - Cao, Xianyong
A1  - Dolman, Andrew M.
A1  - Herzschuh, Ulrike
T1  - Harmonized chronologies of a global late Quaternary pollen dataset (LegacyAge 1.0)
JF  - Earth system science data : ESSD
N2  - We present a chronology framework named LegacyAge 1.0 containing harmonized chronologies for 2831 pollen records (downloaded from the Neotoma Paleoecology Database and the supplementary Asian datasets) together with their age control points and metadata in machine-readable data formats.  
All chronologies use the Bayesian framework implemented in Bacon version 2.5.3. Optimal parameter settings of priors (accumulation.shape, memory.strength, memory.mean, accumulation.rate, and thickness) were identified based on information in the original publication or iteratively after preliminary model inspection. 
The most common control points for the chronologies are radiocarbon dates (86.1 %), calibrated by the latest calibration curves (IntCal20 and SHCal20 for the terrestrial radiocarbon dates in the Northern Hemisphere and Southern Hemisphere and Marine20 for marine materials). 
The original publications were consulted when dealing with outliers and inconsistencies. Several major challenges when setting up the chronologies included the waterline issue (18.8% of records), reservoir effect (4.9 %), and sediment deposition discontinuity (4.4 %). 
Finally, we numerically compare the LegacyAge 1.0 chronologies to those published in the original publications and show that the reliability of the chronologies of 95.4% of records could be improved according to our assessment. 
Our chronology framework and revised chronologies provide the opportunity to make use of the ages and age uncertainties in synthesis studies of, for example, pollen-based vegetation and climate change. 
The LegacyAge 1.0 dataset, including metadata, datings, harmonized chronologies, and R code used, is openaccess and available at PANGAEA (https://doi.org/10.1594/PANGAEA.933132; Li et al., 2021) and Zenodo (https://doi.org/10.5281/zenodo.5815192; Li et al., 2022), respectively.
Y1  - 2022
U6  - https://doi.org/10.5194/essd-14-1331-2022
SN  - 1866-3508
SN  - 1866-3516
VL  - 14
IS  - 3
SP  - 1331
EP  - 1343
PB  - Copernics Publications
CY  - Katlenburg-Lindau
ER  - 
TY  - JOUR
A1  - Irob, Katja
A1  - Blaum, Niels
A1  - Baldauf, Selina
A1  - Kerger, Leon
A1  - Strohbach, Ben
A1  - Kanduvarisa, Angelina
A1  - Lohmann, Dirk
A1  - Tietjen, Britta
T1  - Browsing herbivores improve the state and functioning of savannas
BT  - A model assessment of alternative land-use strategies
JF  - Ecology and evolution
N2  - Changing climatic conditions and unsustainable land use are major threats to savannas worldwide. Historically, many African savannas were used intensively for livestock grazing, which contributed to widespread patterns of bush encroachment across savanna systems. To reverse bush encroachment, it has been proposed to change the cattle-dominated land use to one dominated by comparatively specialized browsers and usually native herbivores. However, the consequences for ecosystem properties and processes remain largely unclear. We used the ecohydrological, spatially explicit model EcoHyD to assess the impacts of two contrasting, herbivore land-use strategies on a Namibian savanna: grazer- versus browser-dominated herbivore communities. We varied the densities of grazers and browsers and determined the resulting composition and diversity of the plant community, total vegetation cover, soil moisture, and water use by plants. Our results showed that plant types that are less palatable to herbivores were best adapted to grazing or browsing animals in all simulated densities. Also, plant types that had a competitive advantage under limited water availability were among the dominant ones irrespective of land-use scenario. Overall, the results were in line with our expectations: under high grazer densities, we found heavy bush encroachment and the loss of the perennial grass matrix. Importantly, regardless of the density of browsers, grass cover and plant functional diversity were significantly higher in browsing scenarios. Browsing herbivores increased grass cover, and the higher total cover in turn improved water uptake by plants overall. We concluded that, in contrast to grazing-dominated land-use strategies, land-use strategies dominated by browsing herbivores, even at high herbivore densities, sustain diverse vegetation communities with high cover of perennial grasses, resulting in lower erosion risk and bolstering ecosystem services.
KW  - browsing
KW  - ecohydrology
KW  - land use
KW  - plant community
KW  - savanna
KW  - wildlife
KW  - management
Y1  - 2022
U6  - https://doi.org/10.1002/ece3.8715
SN  - 2045-7758
VL  - 12
IS  - 3
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Ghafarian, Fatemeh
A1  - Wieland, Ralf
A1  - Lüttschwager, Dietmar
A1  - Nendel, Claas
T1  - Application of extreme gradient boosting and Shapley Additive explanations to predict temperature regimes inside forests from standard open-field meteorological data
JF  - Environmental modelling & software with environment data news
N2  - Forest microclimate can buffer biotic responses to summer heat waves, which are expected to become more extreme under climate warming. Prediction of forest microclimate is limited because meteorological observation standards seldom include situations inside forests. 
We use eXtreme Gradient Boosting - a Machine Learning technique - to predict the microclimate of forest sites in Brandenburg, Germany, using seasonal data comprising weather features. 
The analysis was amended by applying a SHapley Additive explanation to show the interaction effect of variables and individualised feature attributions. 
We evaluate model performance in comparison to artificial neural networks, random forest, support vector machine, and multi-linear regression. 
After implementing a feature selection, an ensemble approach was applied to combine individual models for each forest and improve robustness over a given single prediction model. 
The resulting model can be applied to translate climate change scenarios into temperatures inside forests to assess temperature-related ecosystem services provided by forests.
KW  - cooling effect
KW  - machine learning
KW  - ensemble method
KW  - ecosystem services
Y1  - 2022
U6  - https://doi.org/10.1016/j.envsoft.2022.105466
SN  - 1364-8152
SN  - 1873-6726
VL  - 156
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Mitzscherling, Julia
A1  - MacLean, Joana
A1  - Lipus, Daniel
A1  - Bartholomäus, Alexander
A1  - Mangelsdorf, Kai
A1  - Lipski, André
A1  - Roddatis, Vladimir
A1  - Liebner, Susanne
A1  - Wagner, Dirk
T1  - Nocardioides alcanivorans sp. nov., a novel hexadecane-degrading species isolated from plastic waste
JF  - International journal of systematic and evolutionary microbiology
N2  - Strain NGK65(T), a novel hexadecane degrading, non-motile, Gram-positive, rod-to-coccus shaped, aerobic bacterium, was isolated from plastic polluted soil sampled at a landfill. 
Strain NGK65(T) hydrolysed casein, gelatin, urea and was catalase-positive. It optimally grew at 28 degrees C. in 0-1% NaCl and at pH 7.5-8.0. Glycerol, D-glucose, arbutin, aesculin, salicin, potassium 5-ketogluconate. sucrose, acetate, pyruvate and hexadecane were used as sole carbon sources. 
The predominant membrane fatty acids were iso-C-16:0 followed by iso-C(17:)0 and C-18:1 omega 9c. The major polar lipids were phosphatidylglycerol, phosphatidylethanolamine, phosphatidylinositol and hydroxyphosphatidylinositol. 
The cell-wall peptidoglycan type was A3 gamma, with LL-diaminopimelic acid and glycine as the diagnostic amino acids. MK 8 (H-4) was the predominant menaquinone. Phylogenetic analysis based on 16S rRNA gene sequences indicated that strain NGK65(T) belongs to the genus Nocardioides (phylum Actinobacteria). appearing most closely related to Nocardioides daejeonensis MJ31(T) (98.6%) and Nocardioides dubius KSL-104(T) (98.3%). 
The genomic DNA G+C content of strain NGK65(T) was 68.2%. 
Strain NGK65(T) and the type strains of species involved in the analysis had average nucleotide identity values of 78.3-71.9% as well as digital DNA-DNA hybridization values between 22.5 and 19.7%, which clearly indicated that the isolate represents a novel species within the genus Nocardioides. 
Based on phenotypic and molecular characterization, strain NGK65(T) can clearly be differentiated from its phylogenetic neighbours to establish a novel species, for which the name Nocardioides alcanivorans sp. nov. is proposed. 
The type strain is NGK65(T) (=DSM 113112(T)=NCCB 100846(T)).
KW  - Nocardioides alcanivorans
KW  - hexadecane
KW  - plastic degradation
KW  - terrestrial
KW  - plastisphere
KW  - bacteria
Y1  - 2022
U6  - https://doi.org/10.1099/ijsem.0.005319
SN  - 1466-5026
SN  - 1466-5034
VL  - 72
IS  - 4
PB  - Microbiology Society
CY  - London
ER  - 
TY  - JOUR
A1  - Hilt, Sabine
A1  - Grossart, Hans-Peter
A1  - McGinnis, Daniel F.
A1  - Keppler, Frank
T1  - Potential role of submerged macrophytes for oxic methane production in aquatic ecosystems
JF  - Limnology and oceanography
N2  - Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.
Y1  - 2022
U6  - https://doi.org/10.1002/lno.12095
SN  - 0024-3590
SN  - 1939-5590
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Pan, Xuefeng
A1  - Sarhan, Radwan Mohamed
A1  - Kochovski, Zdravko
A1  - Chen, Guosong
A1  - Taubert, Andreas
A1  - Mei, Shilin
A1  - Lu, Yan
T1  - Template synthesis of dual-functional porous MoS2 nanoparticles with photothermal conversion and catalytic properties
JF  - Nanoscale
N2  - Advanced catalysis triggered by photothermal conversion effects has aroused increasing interest due to its huge potential in environmental purification. 
In this work, we developed a novel approach to the fast degradation of 4-nitrophenol (4-Nip) using porous MoS2 nanoparticles as catalysts, which integrate the intrinsic catalytic property of MoS2 with its photothermal conversion capability. 
Using assembled polystyrene-b-poly(2-vinylpyridine) block copolymers as soft templates, various MoS 2 particles were prepared, which exhibited tailored morphologies (e.g., pomegranate-like, hollow, and open porous structures). 
The photothermal conversion performance of these featured particles was compared under near-infrared (NIR) light irradiation. 
Intriguingly, when these porous MoS2 particles were further employed as catalysts for the reduction of 4-Nip, the reaction rate constant was increased by a factor of 1.5 under NIR illumination. 
We attribute this catalytic enhancement to the open porous architecture and light-to-heat conversion performance of the MoS2 particles. This contribution offers new opportunities for efficient photothermal-assisted catalysis.
Y1  - 2022
U6  - https://doi.org/10.1039/d2nr01040b
SN  - 2040-3372
VL  - 14
IS  - 18
SP  - 6888
EP  - 6901
PB  - RSC Publ. (Royal Society of Chemistry)
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Hagemann, Justus
A1  - Conejero, Carles
A1  - Stillfried, Milena
A1  - Mentaberre, Gregorio
A1  - Castillo-Contreras, Raquel
A1  - Fickel, Jörns
A1  - Lopez-Olvera, Jorge Ramón
T1  - Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain
JF  - The science of the total environment : an international journal for scientific research into the environment and its relationship with man
N2  - Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. 
However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. 
Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. 
The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. 
A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. 
This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. 
The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. 
Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. 
These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. 
The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.
KW  - gene flow
KW  - island population
KW  - population genetics
KW  - sus scrofa
KW  - synurbisation
KW  - urban ecology
Y1  - 2022
U6  - https://doi.org/10.1016/j.scitotenv.2022.155126
SN  - 0048-9697
SN  - 1879-1026
VL  - 833
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Ralevski, Alexandra
A1  - Apelt, Federico
A1  - Olas, Justyna Jadwiga
A1  - Müller-Röber, Bernd
A1  - Rugarli, Elena I.
A1  - Kragler, Friedrich
A1  - Horvath, Tamas L.
T1  - Plant mitochondrial FMT and its mammalian homolog CLUH controls development and behavior in Arabidopsis and locomotion in mice
JF  - Cellular and molecular life sciences
N2  - Mitochondria in animals are associated with development, as well as physiological and pathological behaviors. Several conserved mitochondrial genes exist between plants and higher eukaryotes. Yet, the similarities in mitochondrial function between plant and animal species is poorly understood. Here, we show that FMT (FRIENDLY MITOCHONDRIA) from Arabidopsis thaliana, a highly conserved homolog of the mammalian CLUH (CLUSTERED MITOCHONDRIA) gene family encoding mitochondrial proteins associated with developmental alterations and adult physiological and pathological behaviors, affects whole plant morphology and development under both stressed and normal growth conditions. FMT was found to regulate mitochondrial morphology and dynamics, germination, and flowering time. It also affects leaf expansion growth, salt stress responses and hyponastic behavior, including changes in speed of hyponastic movements. Strikingly, Cluh(+/-) heterozygous knockout mice also displayed altered locomotive movements, traveling for shorter distances and had slower average and maximum speeds in the open field test. These observations indicate that homologous mitochondrial genes may play similar roles and affect homologous functions in both plants and animals.
KW  - Arabidopsis thaliana
KW  - Mitochondria
KW  - FMT
KW  - Hyponasty
KW  - Mice
KW  - CLUH;
KW  - Locomotion
Y1  - 2022
U6  - https://doi.org/10.1007/s00018-022-04382-3
SN  - 1420-682X
SN  - 1420-9071
VL  - 79
IS  - 6
PB  - Springer International Publishing AG
CY  - Cham (ZG)
ER  - 
TY  - JOUR
A1  - Leins, Johannes A.
A1  - Grimm, Volker
A1  - Drechsler, Martin
T1  - Large-scale PVA modeling of insects in cultivated grasslands
BT  - the role of dispersal in mitigating the effects of management schedules under climate change
JF  - Ecology and evolution
N2  - In many species, dispersal is decisive for survival in a changing climate. Simulation models for population dynamics under climate change thus need to account for this factor. Moreover, large numbers of species inhabiting agricultural landscapes are subject to disturbances induced by human land use. We included dispersal in the HiLEG model that we previously developed to study the interaction between climate change and agricultural land use in single populations. Here, the model was parameterized for the large marsh grasshopper (LMG) in cultivated grasslands of North Germany to analyze (1) the species development and dispersal success depending on the severity of climate change in subregions, (2) the additional effect of grassland cover on dispersal success, and (3) the role of dispersal in compensating for detrimental grassland mowing. Our model simulated population dynamics in 60-year periods (2020-2079) on a fine temporal (daily) and high spatial (250 x 250 m(2)) scale in 107 subregions, altogether encompassing a range of different grassland cover, climate change projections, and mowing schedules. We show that climate change alone would allow the LMG to thrive and expand, while grassland cover played a minor role. Some mowing schedules that were harmful to the LMG nevertheless allowed the species to moderately expand its range. Especially under minor climate change, in many subregions dispersal allowed for mowing early in the year, which is economically beneficial for farmers. More severe climate change could facilitate LMG expansion to uninhabited regions but would require suitable mowing schedules along the path. These insights can be transferred to other species, given that the LMG is considered a representative of grassland communities. For more specific predictions on the dynamics of other species affected by climate change and land use, the publicly available HiLEG model can be easily adapted to the characteristics of their life cycle.
KW  - bilinear interpolation
KW  - climate change
KW  - dispersal success
KW  - land use
KW  - large marsh grasshopper
KW  - spatially explicit model
Y1  - 2022
U6  - https://doi.org/10.1002/ece3.9063
SN  - 2045-7758
VL  - 12
IS  - 7
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Ghafarian, Fatemeh
A1  - Wieland, Ralf
A1  - Nendel, Claas
T1  - Estimating the Evaporative Cooling Effect of Irrigation within and above Soybean Canopy
JF  - Water
N2  - Vegetation with an adequate supply of water might contribute to cooling the land surface around it through the latent heat flux of transpiration. This study investigates the potential estimation of evaporative cooling at plot scale, using soybean as example. Some of the plants' physiological parameters were monitored and sampled at weekly intervals. A physics-based model was then applied to estimate the irrigation-induced cooling effect within and above the canopy during the middle and late season of the soybean growth period. We then examined the results of the temperature changes at a temporal resolution of ten minutes between every two irrigation rounds. During the middle and late season of growth, the cooling effects caused by evapotranspiration within and above the canopy were, on average, 4.4 K and 2.9 K, respectively. We used quality indicators such as R-squared (R-2) and mean absolute error (MAE) to evaluate the performance of the model simulation. The performance of the model in this study was better above the canopy (R-2 = 0.98, MAE = 0.3 K) than below (R-2 = 0.87, MAE = 0.9 K) due to the predefined thermodynamic condition used to estimate evaporative cooling. Moreover, the study revealed that canopy cooling contributes to mitigating heat stress conditions during the middle and late seasons of crop growth.
KW  - canopy cooling effects
KW  - shading cooling
KW  - canopy-air temperature
KW  - energy
KW  - balance
KW  - the Penman-Monteith equation
Y1  - 2022
U6  - https://doi.org/10.3390/w14030319
SN  - 2073-4441
VL  - 14
IS  - 3
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Milles, Alexander Benedikt
A1  - Dammhahn, Melanie
A1  - Jeltsch, Florian
A1  - Schlägel, Ulrike
A1  - Grimm, Volker
T1  - Fluctuations in density-dependent selection drive the evolution of a pace-of-life syndrome within and between populations
JF  - The American naturalist : a bi-monthly journal devoted to the advancement and correlation of the biological sciences
N2  - The pace-of-life syndrome (POLS) hypothesis posits that suites of traits are correlated along a slow-fast continuum owing to life history trade-offs. Despite widespread adoption, environmental conditions driving the emergence of POLS remain unclear. A recently proposed conceptual framework of POLS suggests that a slow-fast continuum should align to fluctuations in density-dependent selection. We tested three key predictions made by this framework with an ecoevolutionary agent-based population model. Selection acted on responsiveness (behavioral trait) to interpatch resource differences and the reproductive investment threshold (life history trait). Across environments with density fluctuations of different magnitudes, we observed the emergence of a common axis of trait covariation between and within populations (i.e., the evolution of a POLS). Slow-type (fast-type) populations with high (low) responsiveness and low (high) reproductive investment threshold were selected at high (low) population densities and less (more) intense and frequent density fluctuations. In support of the predictions, fast-type populations contained a higher degree of variation in traits and were associated with higher intrinsic reproductive rate (r(0)) and higher sensitivity to intraspecific competition (gamma), pointing to a universal trade-off. While our findings support that POLS aligns with density-dependent selection, we discuss possible mechanisms that may lead to alternative evolutionary pathways.
KW  - pace-of-life syndrome
KW  - density dependence
KW  - life history
KW  - trait
KW  - variation
KW  - model
KW  - personality
Y1  - 2022
U6  - https://doi.org/10.1086/718473
SN  - 0003-0147
SN  - 1537-5323
VL  - 199
IS  - 4
SP  - E124
EP  - E139
PB  - Univ. of Chicago Press
CY  - Chicago
ER  - 
TY  - JOUR
A1  - Stanke, Sandra
A1  - Wenger, Christian
A1  - Bier, Frank Fabian
A1  - Hölzel, Ralph
T1  - AC electrokinetic immobilization of influenza virus
JF  - Electrophoresis : microfluids & proteomics
N2  - The use of alternating current (AC) electrokinetic forces, like dielectrophoresis and AC electroosmosis, as a simple and fast method to immobilize sub-micrometer objects onto nanoelectrode arrays is presented. Due to its medical relevance, the influenza virus is chosen as a model organism. One of the outstanding features is that the immobilization of viral material to the electrodes can be achieved permanently, allowing subsequent handling independently from the electrical setup. Thus, by using merely electric fields, we demonstrate that the need of prior chemical surface modification could become obsolete. The accumulation of viral material over time is observed by fluorescence microscopy. The influences of side effects like electrothermal fluid flow, causing a fluid motion above the electrodes and causing an intensity gradient within the electrode array, are discussed. Due to the improved resolution by combining fluorescence microscopy with deconvolution, it is shown that the viral material is mainly drawn to the electrode edge and to a lesser extent to the electrode surface. Finally, areas of application for this functionalization technique are presented.
KW  - AC electrokinetics
KW  - AC electroosmosis
KW  - dielectrophoresis
KW  - influenza virus
KW  - nanoelectrodes
Y1  - 2022
U6  - https://doi.org/10.1002/elps.202100324
SN  - 0173-0835
SN  - 1522-2683
VL  - 43
IS  - 12
SP  - 1309
EP  - 1321
PB  - Wiley-Blackwell
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Tong, Hao
A1  - Nankar, Amol N.
A1  - Liu, Jintao
A1  - Todorova, Velichka
A1  - Ganeva, Daniela
A1  - Grozeva, Stanislava
A1  - Tringovska, Ivanka
A1  - Pasev, Gancho
A1  - Radeva-Ivanova, Vesela
A1  - Gechev, Tsanko
A1  - Kostova, Dimitrina
A1  - Nikoloski, Zoran
T1  - Genomic prediction of morphometric and colorimetric traits in Solanaceous fruits
JF  - Horticulture research
N2  - Selection of high-performance lines with respect to traits of interest is a key step in plant breeding. Genomic prediction allows to determine the genomic estimated breeding values of unseen lines for trait of interest using genetic markers, e.g. single-nucleotide polymorphisms (SNPs), and machine learning approaches, which can therefore shorten breeding cycles, referring to genomic selection (GS). Here, we applied GS approaches in two populations of Solanaceous crops, i.e. tomato and pepper, to predict morphometric and colorimetric traits. The traits were measured by using scoring-based conventional descriptors (CDs) as well as by Tomato Analyzer (TA) tool using the longitudinally and latitudinally cut fruit images. The GS performance was assessed in cross-validations of classification-based and regression-based machine learning models for CD and TA traits, respectively. The results showed the usage of TA traits and tag SNPs provide a powerful combination to predict morphology and color-related traits of Solanaceous fruits. The highest predictability of 0.89 was achieved for fruit width in pepper, with an average predictability of 0.69 over all traits. The multi-trait GS models are of slightly better predictability than single-trait models for some colorimetric traits in pepper. While model validation performs poorly on wild tomato accessions, the usage as many as one accession per wild species in the training set can increase the transferability of models to unseen populations for some traits (e.g. fruit shape for which predictability in unseen scenario increased from zero to 0.6). Overall, GS approaches can assist the selection of high-performance Solanaceous fruits in crop breeding.
Y1  - 2022
U6  - https://doi.org/10.1093/hr/uhac072
SN  - 2052-7276
VL  - 9
PB  - Oxford Univ. Press
CY  - Cary
ER  - 
TY  - JOUR
A1  - Sabrowski, Wiebke
A1  - Dreymann, Nico
A1  - Möller, Anja
A1  - Czepluch, Denise
A1  - Albani, Patricia P.
A1  - Theodoridis, Dimitrios
A1  - Menger, Marcus M.
T1  - The use of high-affinity polyhistidine binders as masking probes for the selection of an NDM-1 specific aptamer
JF  - Scientific reports
N2  - The emergence of carbapenemase-producing multi-drug resistant Enterobacteriaceae poses a dramatic, world-wide health risk. Limited treatment options and a lack of easy-to-use methods for the detection of infections with multi-drug resistant bacteria leave the health-care system with a fast-growing challenge. Aptamers are single stranded DNA or RNA molecules that bind to their targets with high affinity and specificity and can therefore serve as outstanding detection probes. However, an effective aptamer selection process is often hampered by non-specific binding. When selections are carried out against recombinant proteins, purification tags (e.g. polyhistidine) serve as attractive side targets, which may impede protein target binding. In this study, aptamer selection was carried out against N-terminally hexa-histidine tagged New Delhi metallo-ss-lactamase 1. After 14 selection rounds binding to polyhistidine was detected rather than to New Delhi metallo-ss-lactamase 1. Hence, the selection strategy was changed. As one aptamer candidate showed remarkable binding affinity to polyhistidine, it was used as a masking probe and selection was restarted from selection round 10. Finally, after three consecutive selection rounds, an aptamer with specific binding properties to New Delhi metallo-ss-lactamase 1 was identified. This aptamer may serve as a much-needed detection probe for New Delhi metallo-ss-lactamase 1 expressing Enterobacteriaceae.
Y1  - 2022
U6  - https://doi.org/10.1038/s41598-022-12062-2
SN  - 2045-2322
VL  - 12
IS  - 1
PB  - Macmillan Publishers Limited, part of Springer Nature
CY  - London
ER  - 
TY  - JOUR
A1  - Haueis, Lisa
A1  - Stech, Marlitt
A1  - Kubick, Stefan
T1  - A Cell-free Expression Pipeline for the Generation and Functional Characterization of Nanobodies
JF  - Frontiers in Bioengineering and Biotechnology
N2  - Cell-free systems are well-established platforms for the rapid synthesis, screening, engineering and modification of all kinds of recombinant proteins ranging from membrane proteins to soluble proteins, enzymes and even toxins. Also within the antibody field the cell-free technology has gained considerable attention with respect to the clinical research pipeline including antibody discovery and production. Besides the classical full-length monoclonal antibodies (mAbs), so-called "nanobodies" (Nbs) have come into focus. A Nb is the smallest naturally-derived functional antibody fragment known and represents the variable domain (VHH, similar to 15 kDa) of a camelid heavy-chain-only antibody (HCAb). Based on their nanoscale and their special structure, Nbs display striking advantages concerning their production, but also their characteristics as binders, such as high stability, diversity, improved tissue penetration and reaching of cavity-like epitopes. The classical way to produce Nbs depends on the use of living cells as production host. Though cell-based production is well-established, it is still time-consuming, laborious and hardly amenable for high-throughput applications. Here, we present for the first time to our knowledge the synthesis of functional Nbs in a standardized mammalian cell-free system based on Chinese hamster ovary (CHO) cell lysates. Cell-free reactions were shown to be time-efficient and easy-to-handle allowing for the "on demand" synthesis of Nbs. Taken together, we complement available methods and demonstrate a promising new system for Nb selection and validation.
KW  - cell-free protein synthesis
KW  - In vitro transcription
KW  - translation
KW  - nanobody
KW  - VHH
KW  - camelid
KW  - CHO cell lysate
Y1  - 2022
U6  - https://doi.org/10.3389/fbioe.2022.896763
SN  - 2296-4185
VL  - 10
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Andersson, Matilda L.
A1  - Scharnweber, Inga Kristin
A1  - Eklöv, Peter
T1  - The interaction between metabolic rate, habitat choice, and resource use in a polymorphic freshwater species
JF  - Ecology and evolution
N2  - Resource polymorphism is common across taxa and can result in alternate ecotypes with specific morphologies, feeding modes, and behaviors that increase performance in a specific habitat. This can result in high intraspecific variation in the expression of specific traits and the extent to which these traits are correlated within a single population. Although metabolic rate influences resource acquisition and the overall pace of life of individuals it is not clear how metabolic rate interacts with the larger suite of traits to ultimately determine individual fitness. We examined the relationship between metabolic rates and the major differences (habitat use, morphology, and resource use) between littoral and pelagic ecotypes of European perch (Perca fluviatilis) from a single lake in Central Sweden. Standard metabolic rate (SMR) was significantly higher in pelagic perch but did not correlate with resource use or morphology. Maximum metabolic rate (MMR) was not correlated with any of our explanatory variables or with SMR. Aerobic scope (AS) showed the same pattern as SMR, differing across habitats, but contrary to expectations, was lower in pelagic perch. This study helps to establish a framework for future experiments further exploring the drivers of intraspecific differences in metabolism. In addition, since metabolic rates scale with temperature and determine predator energy requirements, our observed differences in SMR across habitats will help determine ecotype-specific vulnerabilities to climate change and differences in top-down predation pressure across habitats.
KW  - intraspecific variation
KW  - metabolic rate
KW  - morphometrics
KW  - Perca
KW  - fluviatilis
KW  - plasticity
KW  - resource use
KW  - respirometry
KW  - stable isotopes
Y1  - 2022
U6  - https://doi.org/10.1002/ece3.9129
SN  - 2045-7758
VL  - 12
IS  - 8
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Scheffler, Christiane
A1  - Hermanussen, Michael
T1  - Reply to the letter titled:  "Pathologizing normal height or identifying chronic malnutrition: Public health concerns of calling stunting normal" / by Nafis Faizi,  Mohd Yasir Zubair and Fazeelah Tasleem'. -  New York, NY [u.a.] : Wiley Interscience. - 2022. - (American Journal of Human Biology : the Official Journal of the Human Biology Council, 16 Feb 2022. - 34(2022) 5 ). - https://doi.org/10.1002/ajhb.23735
JF  - American journal of human biology : the official journal of the Human Biology Association
Y1  - 2022
U6  - https://doi.org/10.1002/ajhb.23741
SN  - 1520-6300
VL  - 34
IS  - 5
PB  - Wiley Interscience
CY  - New York, NY [u.a.]
ER  - 
TY  - JOUR
A1  - Berg-Mohnicke, Michael
A1  - Nendel, Claas
T1  - A case for object capabilities as the foundation of a distributed environmental model and simulation infrastructure
JF  - Environmental modelling & software with environment data news
N2  - With the advent of increasingly powerful computational architectures, scientists use these possibilities to create simulations of ever-increasing size and complexity. Large-scale simulations of environmental systems require huge amounts of resources. Managing these in an operational way becomes increasingly complex and difficult to handle for individual scientists. State-of-the-art simulation infrastructures usually provide the necessary re-sources in a centralised setup, which often results in an all-or-nothing choice for the user. Here, we outline an alternative approach to handling this complexity, while rendering the use of high-performance hardware and large datasets still possible. It retains a number of desirable properties: (i) a decentralised structure, (ii) easy sharing of resources to promote collaboration and (iii) secure access to everything, including natural delegation of authority across levels and system boundaries. We show that the object capability paradigm will cover these issues, and present the first steps towards developing a simulation infrastructure based on these principles.
KW  - Cap'n proto
KW  - Scientific collaboration
KW  - Co -development
KW  - Communication
KW  - protocol
KW  - Object capability
Y1  - 2022
U6  - https://doi.org/10.1016/j.envsoft.2022.105471
SN  - 1364-8152
SN  - 1873-6726
VL  - 156
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Çabuk, Uğur
A1  - Ünlü, Ercan Selçuk
T1  - A combined de novo assembly approach increases the quality of prokaryotic draft genomes
JF  - Folia microbiologica : international journal for general, environmental and applied microbiology, and immunology
N2  - Next-generation sequencing methods provide comprehensive data for the analysis of structural and functional analysis of the genome. The draft genomes with low contig number and high N50 value can give insight into the structure of the genome as well as provide information on the annotation of the genome. In this study, we designed a pipeline that can be used to assemble prokaryotic draft genomes with low number of contigs and high N50 value. We aimed to use combination of two de novo assembly tools (SPAdes and IDBA-Hybrid) and evaluate the impact of this approach on the quality metrics of the assemblies. The followed pipeline was tested with the raw sequence data with short reads (< 300) for a total of 10 species from four different genera. To obtain the final draft genomes, we firstly assembled the sequences using SPAdes to find closely related organism using the extracted 16 s rRNA from it. IDBA-Hybrid assembler was used to obtain the second assembly data using the closely related organism genome. SPAdes assembler tool was implemented using the second assembly, produced by IDBA-hybrid as a hint. The results were evaluated using QUAST and BUSCO. The pipeline was successful for the reduction of the contig numbers and increasing the N50 statistical values in the draft genome assemblies while preserving the coverage of the draft genomes.
KW  - De novo assembly
KW  - Prokaryotes
KW  - Bacteria
KW  - NGS
KW  - Short reads
KW  - Draft genome
Y1  - 2022
U6  - https://doi.org/10.1007/s12223-022-00980-7
SN  - 0015-5632
SN  - 1874-9356
VL  - 67
SP  - 801
EP  - 810
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Olimi, Expedito
A1  - Kusstatscher, Peter
A1  - Wicaksono, Wisnu Adi
A1  - Abdelfattah, Ahmed
A1  - Cernava, Tomislav
A1  - Berg, Gabriele
T1  - Insights into the microbiome assembly during different growth stages and storage of strawberry plants
JF  - Environmental microbiome
N2  - Background: Microbiome assembly was identified as an important factor for plant growth and health, but this process is largely unknown, especially for the fruit microbiome. Therefore, we analyzed strawberry plants of two cultivars by focusing on microbiome tracking during the different growth stages and storage using amplicon sequencing, qPCR, and microscopic approaches. <br /> Results: Strawberry plants carried a highly diverse microbiome, therein the bacterial families Sphingomonadaceae (25%), Pseudomonadaceae (17%), and Burkholderiaceae (11%); and the fungal family Mycosphaerella (45%) were most abundant. All compartments were colonized by high number of bacteria and fungi (10(7)-10(10) marker gene copies per g fresh weight), and were characterized by high microbial diversity (6049 and 1501 ASVs); both were higher for the belowground samples than in the phyllosphere. Compartment type was the main driver of microbial diversity, structure, and abundance (bacterial: 45%; fungal: 61%) when compared to the cultivar (1.6%; 2.2%). Microbiome assembly was strongly divided for belowground habitats and the phyllosphere; only a low proportion of the microbiome was transferred from soil via the rhizosphere to the phyllosphere. During fruit development, we observed the highest rates of microbial transfer from leaves and flowers to ripe fruits, where most of the bacteria occured inside the pulp. In postharvest fruits, microbial diversity decreased while the overall abundance increased. Developing postharvest decay caused by Botrytis cinerea decreased the diversity as well, and induced a reduction of potentially beneficial taxa. <br /> Conclusion: Our findings provide insights into microbiome assembly in strawberry plants and highlight the importance of microbe transfer during fruit development and storage with potential implications for food health and safety.
KW  - Fragaria x ananassa
KW  - Microbiome assembly
KW  - Fruit pathogens
KW  - Bacterial
KW  - communities
KW  - Fungal communities
KW  - Amplicon sequencing
KW  - CLSM
Y1  - 2022
U6  - https://doi.org/10.1186/s40793-022-00415-3
SN  - 2524-6372
VL  - 17
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Weyrich, Alexandra
A1  - Guerrero-Altamirano, Tania P.
A1  - Yasar, Selma
A1  - Czirjak, Gábor-Árpád
A1  - Wachter, Bettina
A1  - Fickel, Jörns
T1  - First Steps towards the development of epigenetic biomarkers in female cheetahs (Acinonyx jubatus)
JF  - Life : open access journal
N2  - Free-ranging cheetahs (Acinonyx jubatus) are generally healthy, whereas cheetahs under human care, such as those in zoological gardens, suffer from ill-defined infectious and degenerative pathologies. These differences are only partially explained by husbandry management programs because both groups share low genetic diversity. However, mounting evidence suggests that physiological differences between populations in different environments can be tracked down to differences in epigenetic signatures. Here, we identified differentially methylated regions (DMRs) between free-ranging cheetahs and conspecifics in zoological gardens and prospect putative links to pathways relevant to immunity, energy balance and homeostasis. Comparing epigenomic DNA methylation profiles obtained from peripheral blood mononuclear cells (PBMCs) from eight free-ranging female cheetahs from Namibia and seven female cheetahs living in zoological gardens within Europe, we identified DMRs of which 22 were hypermethylated and 23 hypomethylated. Hypermethylated regions in cheetahs under human care were located in the promoter region of a gene involved in host-pathogen interactions (KLC1) and in an intron of a transcription factor relevant for the development of pancreatic beta-cells, liver, and kidney (GLIS3). The most canonical mechanism of DNA methylation in promoter regions is assumed to repress gene transcription. Taken together, this could indicate that hypermethylation at the promoter region of KLC1 is involved in the reduced immunity in cheetahs under human care. This approach can be generalized to characterize DNA methylation profiles in larger cheetah populations under human care with a more granular longitudinal data collection, which, in the future, could be used to monitor the early onset of pathologies, and ultimately translate into the development of biomarkers with prophylactic and/or therapeutic potential.
KW  - animals under human care
KW  - captivity
KW  - carnivore
KW  - DNA methylation;
KW  - felidae
KW  - free-ranging
KW  - wildlife
Y1  - 2022
U6  - https://doi.org/10.3390/life12060920
SN  - 2075-1729
VL  - 12
IS  - 6
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Li, Shuang
A1  - Abdulkadir, Nafi'u
A1  - Schattenberg, Florian
A1  - da Rocha, Ulisses Nunes
A1  - Grimm, Volker
A1  - Müller, Susann
A1  - Liu, Zishu
T1  - Stabilizing microbial communities by looped mass transfer
JF  - Proceedings of the National Academy of Sciences of the United States of America : PNAS
N2  - Building and changing a microbiome at will and maintaining it over hundreds of generations has so far proven challenging. Despite best efforts, complex microbiomes appear to be susceptible to large stochastic fluctuations. Current capabilities to assemble and control stable complex microbiomes are limited. Here, we propose a looped mass transfer design that stabilizes microbiomes over long periods of time. Five local microbiomes were continuously grown in parallel for over 114 generations and connected by a loop to a regional pool. Mass transfer rates were altered and microbiome dynamics were monitored using quantitative high-throughput flow cytometry and taxonomic sequencing of whole communities and sorted subcommunities. Increased mass transfer rates reduced local and temporal variation in microbiome assembly, did not affect functions, and overcame stochasticity, with all microbiomes exhibiting high constancy and increasing resistance. Mass transfer synchronized the structures of the five local microbiomes and nestedness of certain cell types was eminent. Mass transfer increased cell number and thus decreased net growth rates mu'. Subsets of cells that did not show net growth mu'SCx were rescued by the regional pool R and thus remained part of the microbiome. The loop in mass transfer ensured the survival of cells that would otherwise go extinct, even if they did not grow in all local microbiomes or grew more slowly than the actual dilution rate D would allow. The rescue effect, known from metacommunity theory, was the main stabilizing mechanism leading to synchrony and survival of subcommunities, despite differences in cell physiological properties, including growth rates.
KW  - microbial ecology
KW  - metacommunity assembly
KW  - stability
KW  - microbial
KW  - community cytometry
KW  - single-cell analytics
Y1  - 2022
U6  - https://doi.org/10.1073/pnas.2117814119
SN  - 1091-6490
VL  - 119
IS  - 17
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Lischeid, Gunnar
A1  - Webber, Heidi
A1  - Sommer, Michael
A1  - Nendel, Claas
A1  - Ewert, Frank
T1  - Machine learning in crop yield modelling
BT  - A powerful tool, but no surrogate for science
JF  - Agricultural and forest meteorology
N2  - Provisioning a sufficient stable source of food requires sound knowledge about current and upcoming threats to agricultural production. To that end machine learning approaches were used to identify the prevailing climatic and soil hydrological drivers of spatial and temporal yield variability of four crops, comprising 40 years yield data each from 351 counties in Germany. Effects of progress in agricultural management and breeding were subtracted from the data prior the machine learning modelling by fitting smooth non-linear trends to the 95th percentiles of observed yield data. An extensive feature selection approach was followed then to identify the most relevant predictors out of a large set of candidate predictors, comprising various soil and meteorological data. Particular emphasis was placed on studying the uniqueness of identified key predictors. Random Forest and Support Vector Machine models yielded similar although not identical results, capturing between 50% and 70% of the spatial and temporal variance of silage maize, winter barley, winter rapeseed and winter wheat yield. Equally good performance could be achieved with different sets of predictors. Thus identification of the most reliable models could not be based on the outcome of the model study only but required expert's judgement. Relationships between drivers and response often exhibited optimum curves, especially for summer air temperature and precipitation. In contrast, soil moisture clearly proved less relevant compared to meteorological drivers. In view of the expected climate change both excess precipitation and the excess heat effect deserve more attention in breeding as well as in crop modelling.
KW  - Crop modelling
KW  - Machine learning
KW  - Random forests
KW  - Support vector
KW  - machine
KW  - Feature selection
KW  - Equivocality
Y1  - 2021
U6  - https://doi.org/10.1016/j.agrformet.2021.108698
SN  - 0168-1923
SN  - 1873-2240
VL  - 312
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Agarwal, Saloni
A1  - Warmt, Christian
A1  - Henkel, Jörg
A1  - Schrick, Livia
A1  - Nitsche, Andreas
A1  - Bier, Frank Fabian
T1  - Lateral flow-based nucleic acid detection of SARS-CoV-2 using enzymatic incorporation of biotin-labeled dUTP for POCT use
JF  - Analytical and bioanalytical chemistry : a merger of Fresenius' journal of analytical chemistry, Analusis and Quimica analitica
N2  - The degree of detrimental effects inflicted on mankind by the COVID-19 pandemic increased the need to develop ASSURED (Affordable, Sensitive, Specific, User-friendly, Rapid and Robust, Equipment-free, and Deliverable) POCT (point of care testing) to overcome the current and any future pandemics. Much effort in research and development is currently advancing the progress to overcome the diagnostic pressure built up by emerging new pathogens. LAMP (loop-mediated isothermal amplification) is a well-researched isothermal technique for specific nucleic acid amplification which can be combined with a highly sensitive immunochromatographic readout via lateral flow assays (LFA). Here we discuss LAMP-LFA robustness, sensitivity, and specificity for SARS-CoV-2 N-gene detection in cDNA and clinical swab-extracted RNA samples. The LFA readout is designed to produce highly specific results by incorporation of biotin and FITC labels to 11-dUTP and LF (loop forming forward) primer, respectively. The LAMP-LFA assay was established using cDNA for N-gene with an accuracy of 95.65%. To validate the study, 82 SARS-CoV-2-positive RNA samples were tested. Reverse transcriptase (RT)-LAMP-LFA was positive for the RNA samples with an accuracy of 81.66%; SARS-CoV-2 viral RNA was detected by RT-LAMP-LFA for as low as CT-33. Our method reduced the detection time to 15 min and indicates therefore that RT-LAMP in combination with LFA represents a promising nucleic acid biosensing POCT platform that combines with smartphone based semi-quantitative data analysis.
KW  - Point of care testing (POCT)
KW  - Lateral flow assay (LFA)
KW  - COVID-19
KW  - Reverse transcription loop-mediated isothermal amplification (RT-LAMP);
KW  - SARS-CoV-2 N-gene
Y1  - 2022
U6  - https://doi.org/10.1007/s00216-022-03880-4
SN  - 1618-2642
SN  - 1618-2650
VL  - 414
IS  - 10
SP  - 3177
EP  - 3186
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Laun, Konstantin
A1  - Duffus, Benjamin R.
A1  - Wahlefeld, Stefan
A1  - Katz, Sagie
A1  - Belger, Dennis Heinz
A1  - Hildebrandt, Peter
A1  - Mroginski, Maria Andrea
A1  - Leimkühler, Silke
A1  - Zebger, Ingo
T1  - Infrared spectroscopy flucidates the inhibitor binding sites in a metal-dependent formate dehydrogenase
JF  - Chemistry - a European journal
N2  - Biological carbon dioxide (CO2) reduction is an important step by which organisms form valuable energy-richer molecules required for further metabolic processes. The Mo-dependent formate dehydrogenase (FDH) from Rhodobacter capsulatus catalyzes reversible formate oxidation to CO2 at a bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor. To elucidate potential substrate binding sites relevant for the mechanism, we studied herein the interaction with the inhibitory molecules azide and cyanate, which are isoelectronic to CO2 and charged as formate. We employed infrared (IR) spectroscopy in combination with density functional theory (DFT) and inhibition kinetics. One distinct inhibitory molecule was found to bind to either a non-competitive or a competitive binding site in the secondary coordination sphere of the active site. Site-directed mutagenesis of key amino acid residues in the vicinity of the bis-MGD cofactor revealed changes in both non-competitive and competitive binding, whereby the inhibitor is in case of the latter interaction presumably bound between the cofactor and the adjacent Arg587.
KW  - CO2 reduction
KW  - DFT
KW  - formate oxidation
KW  - inhibition kinetics
KW  - IR
KW  - spectroscopy
KW  - molybdoenzyme
Y1  - 2022
U6  - https://doi.org/10.1002/chem.202201091
SN  - 0947-6539
SN  - 1521-3765
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Cordeiro, Andre M.
A1  - Andrade, Luis
A1  - Monteiro, Catarina C.
A1  - Leitao, Guilherme
A1  - Wigge, Philip Anthony
A1  - Saibo, Nelson J. M.
T1  - Phytochrome-interacting factors
BT  - a promising tool to improve crop productivity
JF  - Journal of experimental botany
N2  - Review exploring the regulation of PHYTOCHROME-INTERACTING FACTORS by light, their role in abiotic stress tolerance and plant architecture, and their influence on crop productivity. 
Light is a key determinant for plant growth, development, and ultimately yield. Phytochromes, red/far-red photoreceptors, play an important role in plant architecture, stress tolerance, and productivity. In the model plant Arabidopsis, it has been shown that PHYTOCHROME-INTERACTING FACTORS (PIFs; bHLH transcription factors) act as central hubs in the integration of external stimuli to regulate plant development. Recent studies have unveiled the importance of PIFs in crops. They are involved in the modulation of plant architecture and productivity through the regulation of cell division and elongation in response to different environmental cues. These studies show that different PIFs have overlapping but also distinct functions in the regulation of plant growth. Therefore, understanding the molecular mechanisms by which PIFs regulate plant development is crucial to improve crop productivity under both optimal and adverse environmental conditions. In this review, we discuss current knowledge of PIFs acting as integrators of light and other signals in different crops, with particular focus on the role of PIFs in responding to different environmental conditions and how this can be used to improve crop productivity.
KW  - Cold
KW  - drought
KW  - grain size
KW  - heat
KW  - light signaling
KW  - phytochrome
KW  - PIF
KW  - plant architecture
KW  - plant breeding
KW  - plant yield
KW  - salinity
Y1  - 2022
U6  - https://doi.org/10.1093/jxb/erac142
SN  - 0022-0957
SN  - 1460-2431
VL  - 73
IS  - 12
SP  - 3881
EP  - 3897
PB  - Oxford Univ. Press
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Aichner, Bernhard
A1  - Dubbert, David
A1  - Kiel, Christine
A1  - Kohnert, Katrin
A1  - Ogashawara, Igor
A1  - Jechow, Andreas
A1  - Harpenslager, Sarah-Faye
A1  - Hölker, Franz
A1  - Nejstgaard, Jens Christian
A1  - Grossart, Hans-Peter
A1  - Singer, Gabriel
A1  - Wollrab, Sabine
A1  - Berger, Stella Angela
T1  - Spatial and seasonal patterns of water isotopes in northeastern German lakes
JF  - Earth system science data : ESSD
N2  - Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.
Y1  - 2022
U6  - https://doi.org/10.5194/essd-14-1857-2022
SN  - 1866-3508
SN  - 1866-3516
VL  - 14
IS  - 4
SP  - 1857
EP  - 1867
PB  - Copernicus
CY  - Göttingen
ER  - 
TY  - JOUR
A1  - Prüfer, Mareike
A1  - Wenger, Christian
A1  - Bier, Frank Fabian
A1  - Laux, Eva-Maria
A1  - Hölzel, Ralph
T1  - Activity of AC electrokinetically immobilized horseradish peroxidase
JF  - Electrophoresis : microfluidics, nanoanalysis & proteomics
N2  - Dielectrophoresis (DEP) is an AC electrokinetic effect mainly used to manipulate cells. Smaller particles, like virions, antibodies, enzymes, and even dye molecules can be immobilized by DEP as well. In principle, it was shown that enzymes are active after immobilization by DEP, but no quantification of the retained activity was reported so far. In this study, the activity of the enzyme horseradish peroxidase (HRP) is quantified after immobilization by DEP. For this, HRP is immobilized on regular arrays of titanium nitride ring electrodes of 500 nm diameter and 20 nm widths. The activity of HRP on the electrode chip is measured with a limit of detection of 60 fg HRP by observing the enzymatic turnover of Amplex Red and H2O2 to fluorescent resorufin by fluorescence microscopy. The initial activity of the permanently immobilized HRP equals up to 45% of the activity that can be expected for an ideal monolayer of HRP molecules on all electrodes of the array. Localization of the immobilizate on the electrodes is accomplished by staining with the fluorescent product of the enzyme reaction. The high residual activity of enzymes after AC field induced immobilization shows the method's suitability for biosensing and research applications.
KW  - AC electrokinetics
KW  - dielectrophoresis
KW  - enzyme activity
KW  - immobilization;
KW  - nanoelectrodes
Y1  - 2022
U6  - https://doi.org/10.1002/elps.202200073
SN  - 0173-0835
SN  - 1522-2683
SP  - 1920
EP  - 1933
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Kiemel, Katrin
A1  - De Cahsan, Binia
A1  - Paraskevopoulou, Sofia
A1  - Weithoff, Guntram
A1  - Tiedemann, Ralph
T1  - Mitochondrial genomes of the freshwater monogonont rotifer Brachionus fernandoi and of two additional B. calyciflorus sensu stricto lineages from Germany and the USA (Rotifera, Brachionidae)
JF  - Mitochondrial DNA. Part B-Resources
N2  - The Brachionus calyciflorus species complex was recently subdivided into four species, but genetic resources to resolve phylogenetic relationships within this complex are still lacking. We provide two complete mitochondrial (mt) genomes from B. calyciflorus sensu stricto (Germany, USA) and the mt coding sequences (cds) from a German B. fernandoi. Phylogenetic analysis placed our B. calyciflorus sensu stricto strains close to the published genomes of B. calyciflorus, forming the putative sister species to B. fernandoi. Global representatives of B. calyciflorus sensu stricto (i.e. Europe, USA, and China) are genetically closer related to each other than to B. fernandoi (average pairwise nucleotide diversity 0.079 intraspecific vs. 0.254 interspecific).
KW  - Mitogenome
KW  - cryptic species
KW  - Brachionus calyciflorus s
KW  - Brachionus
KW  - fernandoi
KW  - monogonont rotifer
Y1  - 2022
U6  - https://doi.org/10.1080/23802359.2022.2060765
SN  - 2380-2359
VL  - 7
IS  - 4
SP  - 646
EP  - 648
PB  - Routledge, Taylor & Francis Group
CY  - Abingdon
ER  - 
TY  - JOUR
A1  - Kernecker, Maria
A1  - Fienitz, Meike
A1  - Nendel, Claas
A1  - Paetzig, Marlene
A1  - Walzl, Karin Pirhofer
A1  - Raatz, Larissa
A1  - Schmidt, Martin
A1  - Wulf, Monika
A1  - Zscheischler, Jana
T1  - Transition zones across agricultural field boundaries for integrated landscape research and management of biodiversity and yields
JF  - Ecological solutions and evidence
N2  - Biodiversity conservation and agricultural production have been largely framed as separate goals for landscapes in the discourse on land use. Although there is an increasing tendency to move away from this dichotomy in theory, the tendency is perpetuated by the spatially explicit approaches used in research and management practice. Transition zones (TZ) have previously been defined as areas where two adjacent fields or patches interact, and so they occur abundantly throughout agricultural landscapes. Biodiversity patterns in TZ have been extensively studied, but their relationship to yield patterns and social-ecological dimensions has been largely neglected. Focusing on European, temperate agricultural landscapes, we outline three areas of research and management that together demonstrate how TZ might be used to facilitate an integrated landscape approach: (i) plant and animal species' use and response to boundaries and the resulting effects on yield, for a deeper understanding of how landscape structure shapes quantity and quality of TZ; (ii) local knowledge on field or patch-level management and its interactions with biodiversity and yield in TZ, and (iii) conflict prevention and collaborative management across land-use boundaries.
KW  - ecotones
KW  - field boundaries
KW  - functional traits
KW  - landscape complexity;
KW  - land-use conflicts
KW  - local knowledge
KW  - spillovers
Y1  - 2022
U6  - https://doi.org/10.1002/2688-8319.12122
SN  - 2688-8319
VL  - 3
IS  - 1
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Palma-Vera, Sergio E.
A1  - Reyer, Henry
A1  - Langhammer, Martina
A1  - Reinsch, Norbert
A1  - Derezanin, Lorena
A1  - Fickel, Jörns
A1  - Qanbari, Saber
A1  - Weitzel, Joachim M.
A1  - Franzenburg, Soeren
A1  - Hemmrich-Stanisak, Georg
A1  - Schön, Jennifer
T1  - Genomic characterization of the world's longest selection experiment in mouse reveals the complexity of polygenic traits
JF  - BMC Biology
N2  - Background
Long-term selection experiments are a powerful tool to understand the genetic background of complex traits. The longest of such experiments has been conducted in the Research Institute for Farm Animal Biology (FBN), generating extreme mouse lines with increased fertility, body mass, protein mass and endurance. For >140 generations, these lines have been maintained alongside an unselected control line, representing a valuable resource for understanding the genetic basis of polygenic traits. However, their history and genomes have not been reported in a comprehensive manner yet. Therefore, the aim of this study is to provide a summary of the breeding history and phenotypic traits of these lines along with their genomic characteristics. We further attempt to decipher the effects of the observed line-specific patterns of genetic variation on each of the selected traits. 

Results
Over the course of >140 generations, selection on the control line has given rise to two extremely fertile lines (>20 pups per litter each), two giant growth lines (one lean, one obese) and one long-distance running line. Whole genome sequencing analysis on 25 animals per line revealed line-specific patterns of genetic variation among lines, as well as high levels of homozygosity within lines. This high degree of distinctiveness results from the combined effects of long-term continuous selection, genetic drift, population bottleneck and isolation. Detection of line-specific patterns of genetic differentiation and structural variation revealed multiple candidate genes behind the improvement of the selected traits. 

Conclusions
The genomes of the Dummerstorf trait-selected mouse lines display distinct patterns of genomic variation harbouring multiple trait-relevant genes. Low levels of within-line genetic diversity indicate that many of the beneficial alleles have arrived to fixation alongside with neutral alleles. This study represents the first step in deciphering the influence of selection and neutral evolutionary forces on the genomes of these extreme mouse lines and depicts the genetic complexity underlying polygenic traits.
KW  - Mouse
KW  - Fertility
KW  - Body mass
KW  - Endurance
KW  - Selective breeding
KW  - Genetic
KW  - drift
KW  - Bottleneck
KW  - Whole genome sequencing
KW  - Single-nucleotide
KW  - polymorphism
KW  - Structural variation
Y1  - 2022
U6  - https://doi.org/10.1186/s12915-022-01248-9
SN  - 1741-7007
VL  - 20
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Bapolisi, Alain Murhimalika
A1  - Kielb, Patrycja
A1  - Bekir, Marek
A1  - Lehnen, Anne-Catherine
A1  - Radon, Christin
A1  - Laroque, Sophie
A1  - Wendler, Petra
A1  - Müller-Werkmeister, Henrike
A1  - Hartlieb, Matthias
T1  - Antimicrobial polymers of linear and bottlebrush architecture
BT  - Probing the membrane interaction and physicochemical properties
JF  - Macromolecular rapid communications : publishing the newsletters of the European Polymer Federation
N2  - Polymeric antimicrobial peptide mimics are a promising alternative for the future management of the daunting problems associated with antimicrobial resistance. However, the development of successful antimicrobial polymers (APs) requires careful control of factors such as amphiphilic balance, molecular weight, dispersity, sequence, and architecture. While most of the earlier developed APs focus on random linear copolymers, the development of APs with advanced architectures proves to be more potent. It is recently developed multivalent bottlebrush APs with improved antibacterial and hemocompatibility profiles, outperforming their linear counterparts. Understanding the rationale behind the outstanding biological activity of these newly developed antimicrobials is vital to further improving their performance. This work investigates the physicochemical properties governing the differences in activity between linear and bottlebrush architectures using various spectroscopic and microscopic techniques. Linear copolymers are more solvated, thermo-responsive, and possess facial amphiphilicity resulting in random aggregations when interacting with liposomes mimicking Escheria coli membranes. The bottlebrush copolymers adopt a more stable secondary conformation in aqueous solution in comparison to linear copolymers, conferring rapid and more specific binding mechanism to membranes. The advantageous physicochemical properties of the bottlebrush topology seem to be a determinant factor in the activity of these promising APs.
KW  - antimicrobial polymers
KW  - bottlebrush copolymers
KW  - liposomes
KW  - membrane
KW  - interactions
KW  - quartz crystal microbalance
Y1  - 2022
U6  - https://doi.org/10.1002/marc.202200288
SN  - 1521-3927
SN  - 1022-1336
VL  - 43
IS  - 19
PB  - Wiley-VCH
CY  - Weinheim
ER  - 
TY  - JOUR
A1  - Azcorra, Hugo
A1  - Dickinson, Federico
A1  - Mendez-Dominguez, Nina
A1  - Mumm, Rebekka
A1  - Valentín, Graciela
T1  - Development of birthweight and length for gestational age and sex references in Yucatan, Mexico
JF  - American journal of human biology : the official journal of the Human Biology Council
N2  - Objective To develop sex- and gestational age specific reference percentiles and curves for birth weight and length for Yucatec neonates using data from birth registers of infants born during 2015-2019. Material and methods Observational, descriptive, epidemiologic study in a 5-year period including every registered birth in the state of Yucatan, Mexico using birth registries. A total of 158 432 live, physically healthy singletons (76 442 females and 81 990 males) between 25 and 42 weeks of gestation were included in the analysis. We used the LMS method to construct smoothed reference centiles (3rd, 10th, 25th, 50th, 75th, 95th, and 97th) and curves for males and females separately. Results Mean maternal age was 26 (SD = 6.22) years. Fifty-two percent of births occurred by vaginal delivery, 37% were firstborn and similar proportions were second (33%) and third or more (30%) born. 5.5% of newborns included in the references corresponds to neonates born before 37 weeks of gestation (5.9% boys and 5.1% girls). In both sexes, the percentage of infants with a birthweight less than 2500 g was 6.7%. The birthweight at the 50th percentile for males and females at 40 weeks of gestation in this cohort was 3256 and 3167 g, respectively, and the corresponding values for birth length were 50.23 and 49.84 cm (mean differences between sexes: 89 g and 0.40 cm, respectively). Conclusion The reference percentile and curves developed in this study are useful for research purposes and can help health practitioners to assess the biological status of infants born in Yucatan.
Y1  - 2022
U6  - https://doi.org/10.1002/ajhb.23732
SN  - 1042-0533
SN  - 1520-6300
VL  - 34
IS  - 6
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Ehrlich, Elias
A1  - Thygesen, Uffe Høgsbro
A1  - Kiørboe, Thomas
T1  - Evolution of toxins as a public good in phytoplankton
JF  - Proceedings of the Royal Society of London : B, Biological sciences
N2  - Toxic phytoplankton blooms have increased in many waterbodies worldwide with well-known negative impacts on human health, fisheries and ecosystems. However, why and how phytoplankton evolved toxin production is still a puzzling question, given that the producer that pays the costs often shares the benefit with other competing algae and thus provides toxins as a 'public good' (e.g. damaging a common competitor or predator). Furthermore, blooming phytoplankton species often show a high intraspecific variation in toxicity and we lack an understanding of what drives the dynamics of coexisting toxic and non-toxic genotypes. Here, by using an individual-based two-dimensional model, we show that small-scale patchiness of phytoplankton strains caused by demography can explain toxin evolution in phytoplankton with low motility and the maintenance of genetic diversity within their blooms. This patchiness vanishes for phytoplankton with high diffusive motility, suggesting different evolutionary pathways for different phytoplankton groups. In conclusion, our study reveals that small-scale spatial heterogeneity, generated by cell division and counteracted by diffusive cell motility and turbulence, can crucially affect toxin evolution and eco-evolutionary dynamics in toxic phytoplankton species. This contributes to a better understanding of conditions favouring toxin production and the evolution of public goods in asexually reproducing organisms in general.
KW  - toxic algal blooms
KW  - evolution of cooperation
KW  - coexistence
KW  - patchiness in
KW  - phytoplankton
KW  - eco-evolutionary feedback
KW  - spatial pattern formation
Y1  - 2022
U6  - https://doi.org/10.1098/rspb.2022.0393
SN  - 0962-8452
SN  - 1471-2954
VL  - 289
IS  - 1977
PB  - Royal Society
CY  - London
ER  - 
TY  - JOUR
A1  - Eccard, Jana
A1  - Mendes Ferreira, Clara
A1  - Peredo Arce, Andres
A1  - Dammhahn, Melanie
T1  - Top-down effects of foraging decisions on local, landscape and regional biodiversity of resources (DivGUD)
JF  - Ecology letters
N2  - Foraging by consumers acts as a biotic filtering mechanism for biodiversity at the trophic level of resources. Variation in foraging behaviour has cascading effects on abundance, diversity, and functional trait composition of the community of resource species. Here we propose diversity at giving-up density (DivGUD), i.e. when foragers quit exploiting a patch, as a novel concept and simple measure quantifying cascading effects at multiple spatial scales. In experimental landscapes with an assemblage of plant seeds, patch residency of wild rodents decreased local alpha-DivGUD (via elevated mortality of species with large seeds) and regional gamma-DivGUD, while dissimilarity among patches in a landscape (beta-DivGUD) increased. By linking theories of adaptive foraging behaviour with community ecology, DivGUD allows to investigate cascading indirect predation effects, e.g. the ecology-of-fear framework, feedbacks between functional trait composition of resource species and consumer communities, and effects of inter-individual differences among foragers on the biodiversity of resource communities.
KW  - biodiversity
KW  - cascading effects
KW  - foraging behaviour
KW  - functional traits
KW  - giving-up density
KW  - landscape of fear
KW  - optimal foraging
KW  - patch use
Y1  - 2022
U6  - https://doi.org/10.1111/ele.13901
SN  - 1461-0248
VL  - 25
IS  - 1
SP  - 3
EP  - 16
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Perrella, Giorgio
A1  - Bäurle, Isabel
A1  - van Zanten, Martijn
T1  - Epigenetic regulation of thermomorphogenesis and heat stress tolerance
JF  - New phytologist : international journal of plant science
N2  - Many environmental conditions fluctuate and organisms need to respond effectively. This is especially true for temperature cues that can change in minutes to seasons and often follow a diurnal rhythm. Plants cannot migrate and most cannot regulate their temperature. Therefore, a broad array of responses have evolved to deal with temperature cues from freezing to heat stress. A particular response to mildly elevated temperatures is called thermomorphogenesis, a suite of morphological adaptations that includes thermonasty, formation of thin leaves and elongation growth of petioles and hypocotyl. Thermomorphogenesis allows for optimal performance in suboptimal temperature conditions by enhancing the cooling capacity. When temperatures rise further, heat stress tolerance mechanisms can be induced that enable the plant to survive the stressful temperature, which typically comprises cellular protection mechanisms and memory thereof. Induction of thermomorphogenesis, heat stress tolerance and stress memory depend on gene expression regulation, governed by diverse epigenetic processes. In this Tansley review we update on the current knowledge of epigenetic regulation of heat stress tolerance and elevated temperature signalling and response, with a focus on thermomorphogenesis regulation and heat stress memory. In particular we highlight the emerging role of H3K4 methylation marks in diverse temperature signalling pathways.
KW  - chromatin remodelling
KW  - elevated temperature
KW  - epigenetics
KW  - heat stress
KW  - histone modification
KW  - memory
KW  - temperature response
KW  - thermomorphogenesis
Y1  - 2022
U6  - https://doi.org/10.1111/nph.17970
SN  - 0028-646X
SN  - 1469-8137
VL  - 234
IS  - 4
SP  - 1144
EP  - 1160
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Berg, Gabriele
A1  - Cernava, Tomislav
T1  - The plant microbiota signature of the Anthropocene as a challenge for microbiome research
JF  - Microbiome
N2  - Background: 
One promise of the recently presented microbiome definition suggested that, in combination with unifying concepts and standards, microbiome research could be important for solving new challenges associated with anthropogenic-driven changes in various microbiota. With this commentary we want to further elaborate this suggestion, because we noticed specific signatures in microbiota affected by the Anthropocene.

Results: 
Here, we discuss this based on a review of available literature and our own research targeting exemplarily the plant microbiome. It is not only crucial for plants themselves but also linked to planetary health. We suggest that different human activities are commonly linked to a shift of diversity and evenness of the plant microbiota, which is also characterized by a decrease of host specificity, and an increase of r-strategic microbes, pathogens, and hypermutators. The resistome, anchored in the microbiome, follows this shift by an increase of specific antimicrobial resistance (AMR) mechanisms as well as an increase of plasmid-associated resistance genes. This typical microbiome signature of the Anthropocene is often associated with dysbiosis and loss of resilience, and leads to frequent pathogen outbreaks. Although several of these observations are already confirmed by meta-studies, this issue requires more attention in upcoming microbiome studies. 

Conclusions: 
Our commentary aims to inspire holistic studies for the development of solutions to restore and save microbial diversity for ecosystem functioning as well as the closely connected planetary health.
Y1  - 2022
U6  - https://doi.org/10.1186/s40168-021-01224-5
SN  - 2049-2618
VL  - 10
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Stripp, Sven T.
A1  - Duffus, Benjamin R.
A1  - Fourmond, Vincent
A1  - Leger, Christophe
A1  - Leimkühler, Silke
A1  - Hirota, Shun
A1  - Hu, Yilin
A1  - Jasniewski, Andrew
A1  - Ogata, Hideaki
A1  - Ribbe, Markus W.
T1  - Second and outer coordination sphere effects in nitrogenase, hydrogenase, formate dehydrogenase, and CO dehydrogenase
JF  - Chemical reviews : CR
N2  - Gases like H-2, N-2, CO2, and CO are increasingly recognized as critical feedstock in "green" energy conversion and as sources of nitrogen and carbon for the agricultural and chemical sectors. However, the industrial transformation of N-2, CO2, and CO and the production of H-2 require significant energy input, which renders processes like steam reforming and the Haber-Bosch reaction economically and environmentally unviable. Nature, on the other hand, performs similar tasks efficiently at ambient temperature and pressure, exploiting gas-processing metalloenzymes (GPMs) that bind low-valent metal cofactors based on iron, nickel, molybdenum, tungsten, and sulfur. Such systems are studied to understand the biocatalytic principles of gas conversion including N-2 fixation by nitrogenase and H-2 production by hydrogenase as well as CO2 and CO conversion by formate dehydrogenase, carbon monoxide dehydrogenase, and nitrogenase. In this review, we emphasize the importance of the cofactor/protein interface, discussing how second and outer coordination sphere effects determine, modulate, and optimize the catalytic activity of GPMs. These may comprise ionic interactions in the second coordination sphere that shape the electron density distribution across the cofactor, hydrogen bonding changes, and allosteric effects. In the outer coordination sphere, proton transfer and electron transfer are discussed, alongside the role of hydrophobic substrate channels and protein structural changes. Combining the information gained from structural biology, enzyme kinetics, and various spectroscopic techniques, we aim toward a comprehensive understanding of catalysis beyond the first coordination sphere.
Y1  - 2022
U6  - https://doi.org/10.1021/acs.chemrev.1c00914
SN  - 0009-2665
SN  - 1520-6890
VL  - 122
IS  - 14
SP  - 11900
EP  - 11973
PB  - American Chemical Society
CY  - Washington, DC
ER  - 
TY  - JOUR
A1  - Delker, Carolin
A1  - Quint, Marcel
A1  - Wigge, Philip Anthony
T1  - Recent advances in understanding thermomorphogenesis signaling
JF  - Current opinion in plant biology
N2  - Plants show remarkable phenotypic plasticity and are able to adjust their morphology and development to diverse environmental stimuli. Morphological acclimation responses to elevated ambient temperatures are collectively termed thermomorphogenesis. In Arabidopsis thaliana, morphological changes are coordinated to a large extent by the transcription factor PHYTOCHROME-INTERACTING FACTOR 4 (PIF4), which in turn is regulated by several thermosensing mechanisms and modulators. Here, we review recent advances in the identification of factors that regulate thermomorphogenesis of Arabidopsis seedlings by affecting PIF4 expression and PIF4 activity. We summarize newly identified thermosensing mechanisms and highlight work on the emerging topic of organ- and tissue-specificity in the regulation of thermomorphogenesis.
Y1  - 2022
U6  - https://doi.org/10.1016/j.pbi.2022.102231
SN  - 1369-5266
SN  - 1879-0356
VL  - 68
PB  - Elsevier
CY  - London
ER  - 
TY  - JOUR
A1  - Ristow, Michael
A1  - Panitsa, Maria
A1  - Meyer, Stefan
A1  - Bergmeier, Erwin
T1  - Factors of detection deficits in vascular plant inventories - an island case study
JF  - Diversity
N2  - The degree of completeness of large-scale floristic inventories is often difficult to judge. We compared prior vascular plant species inventories of the Mediterranean island of Limnos (North Aegean, Greece) with 231 recent records from 2016-2021. Together with the recent records, the known number of vascular plant species on the island is 960 native taxa, 63 established neophytes, and 27 species of as yet casual status for a total of 1050 taxa. We looked at a number of traits (plant family, size, flower color, perceptibility, habitat, reproduction period, rarity, and status) to investigate whether they were overrepresented in the dataset of the newly found taxa. Overrepresentation was found in some plant families (e.g., Poaceae and Chenopodiaceae) and for traits such as hydrophytic life form, unobtrusive flower color, coastal as well as agricultural and ruderal habitats, and late (summer/autumn) reproduction period. Apart from the well-known fact of esthetic bias, we found evidence for ecological and perceptibility biases. Plant species inventories based on prior piecemeal collated data should focus on regionally specific species groups and underrepresented and rare habitats.
KW  - Aegean flora
KW  - floristic survey
KW  - Mediterranean island
KW  - perceptibility
KW  - habitat
KW  - plant traits
KW  - rarity
Y1  - 2022
U6  - https://doi.org/10.3390/d14040303
SN  - 1424-2818
VL  - 14
IS  - 4
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Scharf, Christina
A1  - Weinelt, Ferdinand Anton
A1  - Schroeder, Ines
A1  - Paal, Michael
A1  - Weigand, Michael
A1  - Zoller, Michael
A1  - Irlbeck, Michael
A1  - Kloft, Charlotte
A1  - Briegel, Josef
A1  - Liebchen, Uwe
T1  - Does the cytokine adsorber CytoSorb (R) reduce vancomycin exposure in critically ill patients with sepsis or septic shock?
BT  - a prospective observational study
JF  - Annals of intensive care
N2  - Background: 
Hemadsorption of cytokines is used in critically ill patients with sepsis or septic shock. Concerns have been raised that the cytokine adsorber CytoSorb (R) unintentionally adsorbs vancomycin. This study aimed to quantify vancomycin elimination by CytoSorb (R) . 

Methods: 
Critically ill patients with sepsis or septic shock receiving continuous renal replacement therapy and CytoSorb (R) treatment during a prospective observational study were included in the analysis. Vancomycin pharmacokinetics was characterized using population pharmacokinetic modeling. Adsorption of vancomycin by the CytoSorb (R) was investigated as linear or saturable process. The final model was used to derive dosing recommendations based on stochastic simulations. 

Results:
20 CytoSorb (R) treatments in 7 patients (160 serum samples/24 during CytoSorb (R)-treatment, all continuous infusion) were included in the study. A classical one-compartment model, including effluent flow rate of the continuous hemodialysis as linear covariate on clearance, best described the measured concentrations (without CytoSorb (R)). Significant adsorption with a linear decrease during CytoSorb (R) treatment was identified (p <0.0001) and revealed a maximum increase in vancomycin clearance of 291% (initially after CytoSorb (R) installation) and a maximum adsorption capacity of 572 mg. For a representative patient of our cohort a reduction of the area under the curve (AUC) by 93 mg/L*24 h during CytoSorb (R) treatment was observed. The additional administration of 500 mg vancomycin over 2 h during CytoSorb (R) attenuated the effect and revealed a negligible reduction of the AUC by 4 mg/L*24h.

Conclusion: 
We recommend the infusion of 500 mg vancomycin over 2 h during CytoSorb (R) treatment to avoid subtherapeutic concentrations.
KW  - Vancomycin
KW  - Critically ill patients
KW  - CytoSorb (R)
KW  - Sepsis;
KW  - Pharmacokinetics
KW  - Adsorption
Y1  - 2022
U6  - https://doi.org/10.1186/s13613-022-01017-5
SN  - 2110-5820
VL  - 12
IS  - 1
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Voigt, Christian C.
A1  - Kaiser, Klara
A1  - Look, Samantha
A1  - Scharnweber, Inga Kristin
A1  - Scholz, Carolin
T1  - Wind turbines without curtailment produce large numbers of bat fatalities throughout their lifetime
BT  - a call against ignorance and neglect
JF  - Global ecology and conservation
N2  - Bats are protected by national and international legislation in European countries, yet many species, particularly migratory aerial insectivores, collide with wind turbines which counteracts conservation efforts. Within the European Union it is legally required to curtail the operation of wind turbines at periods of high bat activity, yet this is not practiced at old wind turbines. Based on data from the national carcass repository in Germany and from our own carcass searches at a wind park with three turbines west of Berlin, we evaluated the magnitude of bat casualties at old, potentially poor-sited wind turbines operating without curtailment. We report 88 documented bat carcasses collected by various searchers over the 20-year operation period of this wind park from 2001 to 2021. Common noctule bats (Nyctalus noctula) and common pipistrelles (Pipistrellus pipistrellus) were most often found dead at these turbines. Our search campaign in August and September 2021 yielded a total of 18 carcasses. We estimated that at least 209 bats were likely killed during our field survey, yielding more than 70 casualties/wind turbine or 39 casualties/ MW in two months. Since our campaign covered only part of the migration season, we consider this value as an underestimate. The 20-year period of the wind park emphasises the substantial impact old turbines may have on bat individuals and populations when operating without curtailments. We call for reconsidering the operation procedures of old wind turbines to stop the continuous loss of bats in Germany and other countries where turbine curtailments are even less practiced than in Germany.
KW  - green-green dilemma
KW  - wind energy bat conflict
KW  - wildlife casualties
Y1  - 2022
U6  - https://doi.org/10.1016/j.gecco.2022.e02149
SN  - 2351-9894
VL  - 37
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Pohle, Lara
A1  - Hosoya, Georg
A1  - Pohle, Jennifer
A1  - Meyer-Jenßen, Lars
T1  - The relationship between early childhood teachers' instructional quality and children's mathematics development
JF  - Learning and instruction : the journal of the European Association for Research on Learning and Instruction
N2  - This study examined how early childhood (EC) teachers' instructional quality predicted children's development in mathematics across two measurement occasions. Therefore, EC teachers' (n = 25) instructional quality was assessed using one standardized observation instrument covering both domain-specific and general aspects of instructional quality. Additionally, data on children's (n = 208) outcome in early number skills was collected applying a standardized test. Multilevel structural equation modeling was used accounting for nested data. Children's age and the average size of preschool groups were controlled for. Results revealed that EC teachers' instructional quality predicted children's development but was not associated with their initial achievement. The findings suggest that instruments covering domain-specific and general aspects might be helpful in order to measure EC teachers' instructional quality in mathematics and predict children's learning growth. Understanding the mechanisms between instructional quality and children's development may help EC teachers to enhance their math teaching in practice.
KW  - Early childhood education
KW  - Early childhood teachers
KW  - Instructional
KW  - quality
KW  - Early mathematics development
Y1  - 2022
U6  - https://doi.org/10.1016/j.learninstruc.2022.101636
SN  - 0959-4752
SN  - 1873-3263
VL  - 82
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Andrade, Luis
A1  - Lu, Yunlong
A1  - Cordeiro, Andre
A1  - Costa, João M. F.
A1  - Wigge, Philip Anthony
A1  - Saibo, Nelson J. M.
A1  - Jaeger, Katja E.
T1  - The evening complex integrates photoperiod signals to control flowering in rice
JF  - Proceedings of the National Academy of Sciences of the United States of America : PNAS
N2  - Plants use photoperiodism to activate flowering in response to a particular daylength. In rice, flowering is accelerated in short-day conditions, and even a brief exposure to light during the dark period (night-break) is sufficient to delay flowering. Although many of the genes involved in controlling flowering in rice have been uncovered, how the long- and short-day flowering pathways are integrated, and the mechanism of photoperiod perception is not understood. While many of the signaling components controlling photoperiod-activated flowering are conserved between Arabidopsis and rice, flowering in these two systems is activated by opposite photoperiods. Here we establish that photoperiodism in rice is controlled by the evening complex (EC). We show that mutants in the EC genes LUX ARRYTHMO (LUX) and EARLY FLOWERING3 (ELF3) paralogs abolish rice flowering. We also show that the EC directly binds and suppresses the expression of flowering repressors, including PRR37 and Ghd7. We further demonstrate that light acts via phyB to cause a rapid and sustained posttranslational modification of ELF3-1. Our results suggest a mechanism by which the EC is able to control both long- and short-day flowering pathways.
KW  - rice
KW  - flowering
KW  - ELF3
KW  - LUX
KW  - Evening Complex
Y1  - 2022
U6  - https://doi.org/10.1073/pnas.2122582119
SN  - 0027-8424
SN  - 1091-6490
VL  - 119
IS  - 26
PB  - National Acad. of Sciences
CY  - Washington
ER  - 
TY  - JOUR
A1  - Wendering, Philipp
A1  - Nikoloski, Zoran
T1  - COMMIT
BT  - Consideration of metabolite leakage and community composition improves microbial community reconstructions
JF  - PLoS Computational Biology : a new community journal / publ. by the Public Library of Science (PLoS) in association with the International Society for Computational Biology (ISCB)
N2  - Composition and functions of microbial communities affect important traits in diverse hosts, from crops to humans. Yet, mechanistic understanding of how metabolism of individual microbes is affected by the community composition and metabolite leakage is lacking. Here, we first show that the consensus of automatically generated metabolic reconstructions improves the quality of the draft reconstructions, measured by comparison to reference models. We then devise an approach for gap filling, termed COMMIT, that considers metabolites for secretion based on their permeability and the composition of the community. By applying COMMIT with two soil communities from the Arabidopsis thaliana culture collection, we could significantly reduce the gap-filling solution in comparison to filling gaps in individual reconstructions without affecting the genomic support. Inspection of the metabolic interactions in the soil communities allows us to identify microbes with community roles of helpers and beneficiaries. Therefore, COMMIT offers a versatile fully automated solution for large-scale modelling of microbial communities for diverse biotechnological applications. <br /> Author summaryMicrobial communities are important in ecology, human health, and crop productivity. However, detailed information on the interactions within natural microbial communities is hampered by the community size, lack of detailed information on the biochemistry of single organisms, and the complexity of interactions between community members. Metabolic models are comprised of biochemical reaction networks based on the genome annotation, and can provide mechanistic insights into community functions. Previous analyses of microbial community models have been performed with high-quality reference models or models generated using a single reconstruction pipeline. However, these models do not contain information on the composition of the community that determines the metabolites exchanged between the community members. In addition, the quality of metabolic models is affected by the reconstruction approach used, with direct consequences on the inferred interactions between community members. Here, we use fully automated consensus reconstructions from four approaches to arrive at functional models with improved genomic support while considering the community composition. We applied our pipeline to two soil communities from the Arabidopsis thaliana culture collection, providing only genome sequences. Finally, we show that the obtained models have 90% genomic support and demonstrate that the derived interactions are corroborated by independent computational predictions.
Y1  - 2022
U6  - https://doi.org/10.1371/journal.pcbi.1009906
SN  - 1553-734X
SN  - 1553-7358
VL  - 18
IS  - 3
PB  - Public Library of Science
CY  - San Fransisco
ER  - 
TY  - JOUR
A1  - Zhang, Shanshan
A1  - Liu, Yue
A1  - Machatschek, Rainhard Gabriel
A1  - Lendlein, Andreas
T1  - Ultrathin collagen type I films formed at the air-water interface
JF  - MRS advances : a journal of the Materials Research Society (MRS)
N2  - Collagen-based biomaterials with oriented fibrils have shown great application potential in medicine. However, it is still challenging to control the type I collagen fibrillogenesis in ultrathin films. Here, we report an approach to produce cohesive and well-organized type I collagen ultrathin films of about 10 nm thickness using the Langmuir-Blodgett technique. Ellipsometry, rheology, and Brewster angle microscopy are applied to investigate in situ how the molecules behave at the air-water interface, both at room temperature and 37 degrees C. The interfacial storage modulus observed at room temperature vanishes upon heating, indicating the existence and disappearance of the network structure in the protein nanosheet. The films were spanning over holes as large as 1 mm diameter when transferred at room temperature, proving the strong cohesive interactions. A highly aligned and fibrillar structure was observed by atomic force microscopy (AFM) and optical microscopy.
Y1  - 2022
U6  - https://doi.org/10.1557/s43580-021-00160-8
SN  - 2059-8521
VL  - 7
IS  - 4
SP  - 56
EP  - 62
PB  - Springer Nature Switzerland AG
CY  - Cham
ER  - 
TY  - JOUR
A1  - Fujihara, Kenji M.
A1  - Zhang, Bonnie Z.
A1  - Jackson, Thomas D.
A1  - Ogunkola, Moses
A1  - Nijagal, Brunda
A1  - Milne, Julia V.
A1  - Sallman, David A.
A1  - Ang, Ching-Seng
A1  - Nikolic, Iva
A1  - Kearney, Conor J.
A1  - Hogg, Simon J.
A1  - Cabalag, Carlos S.
A1  - Sutton, Vivien R.
A1  - Watt, Sally
A1  - Fujihara, Asuka T.
A1  - Trapani, Joseph A.
A1  - Simpson, Kaylene J.
A1  - Stojanovski, Diana
A1  - Leimkühler, Silke
A1  - Haupt, Sue
A1  - Phillips, Wayne A.
A1  - Clemons, Nicholas J.
T1  - Eprenetapopt triggers ferroptosis, inhibits NFS1 cysteine desulfurase, and synergizes with serine and glycine dietary restriction
JF  - Science Advances
N2  - The mechanism of action of eprenetapopt (APR-246, PRIMA-1MET) as an anticancer agent remains unresolved, al-though the clinical development of eprenetapopt focuses on its reported mechanism of action as a mutant-p53 reactivator. Using unbiased approaches, this study demonstrates that eprenetapopt depletes cellular antioxidant glutathione levels by increasing its turnover, triggering a nonapoptotic, iron-dependent form of cell death known as ferroptosis. Deficiency in genes responsible for supplying cancer cells with the substrates for de novo glutathione synthesis (SLC7A11, SHMT2, and MTHFD1L), as well as the enzymes required to synthesize glutathione (GCLC and GCLM), augments the activity of eprenetapopt. Eprenetapopt also inhibits iron-sulfur cluster biogenesis by limit-ing the cysteine desulfurase activity of NFS1, which potentiates ferroptosis and may restrict cellular proliferation. The combination of eprenetapopt with dietary serine and glycine restriction synergizes to inhibit esophageal xenograft tumor growth. These findings reframe the canonical view of eprenetapopt from a mutant-p53 reactivator to a ferroptosis inducer.
Y1  - 2022
U6  - https://doi.org/10.1126/sciadv.abm9427
SN  - 2375-2548
VL  - 8
IS  - 37
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  - 
TY  - JOUR
A1  - Fiorini, Vanina D.
A1  - Domínguez, Marisol
A1  - Reboreda, Juan C.
A1  - Swaddle, John P.
T1  - A recent invasive population of the European starling sturnus vulgaris has lower genetic diversity and higher fluctuating asymmetry than primary invasive and native populations
JF  - Biological invasions : unique international journal uniting scientists in the broad field of biological invasions
N2  - Fluctuating asymmetries (FA) are small stress-induced random deviations from perfect symmetry that arise during the development of bilaterally symmetrical traits. One of the factors that can reduce developmental stability of the individuals and cause FA at a population level is the loss of genetic variation. Populations of founding colonists frequently have lower genetic variation than their ancestral populations that could be reflected in a higher level of FA. The European starling (Sturnus vulgaris) is native to Eurasia and was introduced successfully in the USA in 1890 and Argentina in 1983. In this study, we documented the genetic diversity and FA of starlings from England (ancestral population), USA (primary introduction) and Argentina (secondary introduction). We predicted the Argentinean starlings would have the highest level of FA and lowest genetic diversity of the three populations. We captured wild adult European starlings in England, USA, and Argentina, measured their mtDNA diversity and allowed them to molt under standardized conditions to evaluate their FA of primary feathers. For genetic analyses, we extracted DNA from blood samples of individuals from Argentina and USA and from feather samples from individuals from England and sequenced the mitochondrial control region. Starlings in Argentina showed the highest composite FA and exhibited the lowest haplotype and nucleotide diversity. The USA population showed a level of FA and genetic diversity similar to the native population. Therefore, the level of asymmetry and genetic diversity found among these populations was consistent with our predictions based on their invasion history.
KW  - Exotic bird species
KW  - Fluctuating asymmetry
KW  - Genetic variability
KW  - Sturnus
KW  - vulgaris
Y1  - 2022
U6  - https://doi.org/10.1007/s10530-021-02653-x
SN  - 1387-3547
SN  - 1573-1464
VL  - 24
IS  - 2
SP  - 437
EP  - 448
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Baral, Hans Otto
A1  - Rönsch, Peter
A1  - Richter, Udo
A1  - Urban, Alexander
A1  - Kruse, Julia
A1  - Bemmann, Martin
A1  - Kummer, Volker
A1  - Javier Valencia, Francisco
A1  - Huth, Wolfgang
T1  - Schroeteria decaisneana, S. poeltii, and Ciboria ploettneriana (Sclerotiniaceae, Helotiales, Ascomycota), three parasites on Veronica seeds
BT  - first report of teleomorphs in Schroeteria
JF  - Mycological progress : international journal of the German Mycological Society
N2  - Ciboria ploettneriana, Schroeteria decaisneana, and S. poeltii produce morphologically very similar apothecia emerging from fallen stromatized seeds of Veronica spp., the former two on V. hederifolia agg. in temperate central Europe and S. poeltii on V. cymbalaria in mediterranean southern Europe. They are described and illustrated in detail based on fresh collections or moist chamber cultures of infected seeds. A key is provided to differentiate the three species from their teleomorphs. For the first time, connections between two teleomorphs and two Schroeteria anamorphs are reported. Members of the anamorph-typified genus Schroeteria are known as host-specific plant parasites that infect seeds of different Veronica spp. In earlier times, they were classified in the Ustilaginales (Basidiomycota), but since more than 30 years, they are referred to as false smut fungi producing smut-like chlamydospores, based on light microscopic and ultrastructural studies which referred them to the Sclerotiniaceae (Helotiales). During the present study, rDNA sequences were obtained for the first time from chlamydospores of Schroeteria bornmuelleri (on V. rubrifolia), S. decaisneana (on V. hederifolia), S. delastrina (generic type, on V. arvensis), and S. poeltii (on V. cymbalaria) and from apothecia of C. ploettneriana, S. decaisneana, and S. poeltii. As a result, the anamorph-teleomorph connection could be established for S. decaisneana and S. poeltii by a 100% ITS similarity, whereas C. ploettneriana could not be connected to a smut-like anamorph. Ciboria ploettneriana in the here-redefined sense clustered in our combined phylogenetic analyses of ITS and LSU in relationship of Sclerotinia s.l., Botrytis, and Myriosclerotinia rather than Ciboria, but its placement was not supported. Its affiliation in Ciboria was retained until a better solution is found. Also Schroeteria poeltii clustered unresolved in this relationship but with a much higher molecular distance. The remaining three Schroeteria spp. formed a strongly supported monophyletic group, here referred to as "Schroeteria core clade", which clustered with medium to high support as a sister clade of Monilinia jezoensis, a member of the Monilinia alpina group of section Disjunctoriae. We observed ITS distances of 5-6.3% among members of the Schroeteria core clade, but 13.8-14.7% between this clade and S. poeltii, which appears to be correlated with the deviating chlamydospore morphology of S. poeltii. Despite its apparent paraphyly, Schroeteria is accepted here in a wide sense as a genus distinct from Monilinia, particularly because of its very special anamorphs. A comparable heterogeneity in rDNA analyses was observed in Monilinia and other genera of Sclerotiniaceae. Such apparent heterogeneity should be met with skepticism, however, because the inclusion of protein-coding genes in phylogenetic analyses resulted in a monophyletic genus Monilinia. More sclerotiniaceous taxa should be analysed for protein-coding genes in the future, including Schroeteria. Four syntype specimens of Ciboria ploettneriana in B were reexamined in the present study, revealing a mixture of the two species growing on V. hederifolia agg. Based on its larger ascospores in comparison with S. decaisneana, a lectotype is proposed for C. ploettneriana.
KW  - anamorph-teleomorph connection
KW  - plant parasite
KW  - false smut fungi
KW  - seed
KW  - infection
KW  - Veronica hederifolia
KW  - Veronica cymbalaria
Y1  - 2022
U6  - https://doi.org/10.1007/s11557-021-01742-4
SN  - 1617-416X
SN  - 1861-8952
VL  - 21
IS  - 1
SP  - 359
EP  - 407
PB  - Springer
CY  - Berlin ; Heidelberg
ER  - 
TY  - JOUR
A1  - Hermanussen, Michael
A1  - Erofeev, Sergei
A1  - Scheffler, Christiane
T1  - The socio-endocrine regulation of human growth
JF  - Acta paediatrica : nurturing the child
N2  - Aim Growth is a multifarious phenomenon that has been studied by nutritionists, economists, paediatric endocrinologists; archaeologists, child psychologists and other experts. Yet, a unifying theory of understanding growth regulation is still lacking. Method Critical review of the literature. Results We summarise evidence linking social competition and its effect on hierarchies in social structures, with the neuronal networks of the ventromedial hypothalamus and body size. The endocrine signalling system regulating growth hormone, Insulin-like-Growth-Factor1 and skeletal growth, is well conserved in the evolution of vertebrata for some 400 million years. The link between size and status permits adaptive plasticity, competitive growth and strategic growth adjustments also in humans. Humans perceive size as a signal of dominance with tallness being favoured and particularly prevalent in the upper social classes. Conclusion Westernised societies are competitive. People are tall, and "open to change." Social values include striving for status and prestige implying socio-economic domination. We consider the transition of political and social values following revolutions and civil wars, as key elements that interact with the evolutionarily conserved neuroendocrine competence for adaptive developmental plasticity, overstimulate the hypothalamic growth regulation and finally lead to the recent historic increases in average height.
KW  - competitive growth
KW  - developmental plasticity
KW  - evolution
KW  - growth
KW  - hormone-releasing hormone
KW  - strategic growth adjustments
Y1  - 2022
U6  - https://doi.org/10.1111/apa.16504
SN  - 0803-5253
SN  - 1651-2227
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Apriyanto, Ardha
A1  - Compart, Julia
A1  - Zimmermann, Vincent
A1  - Alseekh, Saleh
A1  - Fernie, Alisdair R.
A1  - Fettke, Jörg
T1  - Indication that starch and sucrose are biomarkers for oil yield in oil palm (Elaeis guineensis Jacq.)
JF  - Food chemistry
N2  - Oil palm (Elaeis guineensis Jacq.) is the most productive oil-producing crop per hectare of land. The oil that accumulates in the mesocarp tissue of the fruit is the highest observed among fruit-producing plants. A comparative analysis between high-, medium-, and low-yielding oil palms, particularly during fruit development, revealed unique characteristics. Metabolomics analysis was able to distinguish accumulation patterns defining of the various developmental stages and oil yield. Interestingly, high- and medium-yielding oil palms exhibited substantially increased sucrose levels compared to low-yielding palms. In addition, parameters such as starch granule morphology, granule size, total starch content, and starch chain length distribution (CLD) differed significantly among the oil yield categories with a clear correlation between oil yield and various starch parameters. These results provide new insights into carbohydrate and starch metabolism for biosynthesis of oil palm fruits, indicating that starch and sucrose can be used as novel, easy-to-analyze, and reliable biomarker for oil yield.
KW  - carbohydrate
KW  - mesocarp
KW  - metabolites
KW  - oil palm
KW  - oil yield
KW  - sucrose;
KW  - starch
Y1  - 2022
U6  - https://doi.org/10.1016/j.foodchem.2022.133361
SN  - 0308-8146
SN  - 1873-7072
VL  - 393
PB  - Elsevier
CY  - New York, NY [u.a.]
ER  - 
TY  - JOUR
A1  - Gutschmann, Björn
A1  - Simões, Matilde Maldonado
A1  - Schiewe, Thomas
A1  - Schröter, Edith S.
A1  - Münzberg, Marvin
A1  - Neubauer, Peter
A1  - Bockisch, Anika
A1  - Riedel, Sebastian Lothar Stefan
T1  - Continuous feeding strategy for polyhydroxyalkanoate production from solid waste animal fat at laboratory- and pilot-scale
JF  - Microbial biotechnology / Society for Applied Microbiology
N2  - Bioconversion of waste animal fat (WAF) to polyhydroxyalkanoates (PHAs) is an approach to lower the production costs of these plastic alternatives. However, the solid nature of WAF requires a tailor-made process development. In this study, a double-jacket feeding system was built to thermally liquefy the WAF to employ a continuous feeding strategy. During laboratory-scale cultivations with Ralstonia eutropha Re2058/pCB113, 70% more PHA (45 g(PHA) L-1) and a 75% higher space-time yield (0.63 g(PHA) L-1 h(-1)) were achieved compared to previously reported fermentations with solid WAF. During the development process, growth and PHA formation were monitored in real-time by in-line photon density wave spectroscopy. The process robustness was further evaluated during scale-down fermentations employing an oscillating aeration, which did not alter the PHA yield although cells encountered periods of oxygen limitation. Flow cytometry with propidium iodide staining showed that more than two-thirds of the cells were viable at the end of the cultivation and viability was even little higher in the scale-down cultivations. Application of this feeding system at 150-L pilot-scale cultivation yielded in 31.5 g(PHA) L-1, which is a promising result for the further scale-up to industrial scale.
Y1  - 2022
U6  - https://doi.org/10.1111/1751-7915.14104
SN  - 1751-7915
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Sauter, Tilman
A1  - Kratz, Karl
A1  - Farhan, Muhammad
A1  - Heuchel, Matthias
A1  - Lendlein, Andreas
T1  - Design and fabrication of fiber mesh actuators
JF  - Applied materials today
N2  - Soft actuator performance can be tuned by chemistry or mechanical manipulation, but this adjustability is limited especially in view of their growing technological relevance. Inspired from textile engineering, we designed and fabricated fiber mesh actuators and introduced new features like anisotropic behavior and soft-tissue like elastic deformability. Design criteria for the meshes are the formation of fiber bundles, the angle between fiber bundles in different stacked layers and covalent crosslinks forming within and between fibers at their interfacial contact areas. Through crosslinking the interfiber bond strength increased from a bond transmitting neither axial nor rotational loads (pin joint) to a bond strength capable of both (welded joint). For non-linear elastic stiffening, stacked fiber bundles with four embracing fibers were created forming microstructural rhombus shapes. Loading the rhombus diagonally allowed generation of “soft tissue”-like mechanics. By adjustment of stacking angles, the point of strong increase in stress is tuned. While the highest stresses are observed in aligned and crosslinked fiber mats along the direction of the fiber, the strongest shape-memory actuation behavior is found in randomly oriented fiber mats. Fiber mesh actuators controlled by temperature are of high significance as soft robot skins and as for active patches supporting tissue regeneration.
Y1  - 2022
U6  - https://doi.org/10.1016/j.apmt.2022.101562
SN  - 2352-9407
VL  - 29
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Foerster, Verena
A1  - Asrat, Asfawossen
A1  - Ramsey, Christopher Bronk
A1  - Brown, Erik T.
A1  - Chapot, Melissa S.
A1  - Deino, Alan
A1  - Düsing, Walter
A1  - Grove, Matthew
A1  - Hahn, Annette
A1  - Junginger, Annett
A1  - Kaboth-Bahr, Stefanie
A1  - Lane, Christine S.
A1  - Opitz, Stephan
A1  - Noren, Anders
A1  - Roberts, Helen M.
A1  - Stockhecke, Mona
A1  - Tiedemann, Ralph
A1  - Vidal, Celine M.
A1  - Vogelsang, Ralf
A1  - Cohen, Andrew S.
A1  - Lamb, Henry F.
A1  - Schaebitz, Frank
A1  - Trauth, Martin H.
T1  - Pleistocene climate variability in eastern Africa influenced hominin evolution
JF  - Nature geoscience
N2  - Despite more than half a century of hominin fossil discoveries in eastern Africa, the regional environmental context of hominin evolution and dispersal is not well established due to the lack of continuous palaeoenvironmental records from one of the proven habitats of early human populations, particularly for the Pleistocene epoch. Here we present a 620,000-year environmental record from Chew Bahir, southern Ethiopia, which is proximal to key fossil sites. Our record documents the potential influence of different episodes of climatic variability on hominin biological and cultural transformation. The appearance of high anatomical diversity in hominin groups coincides with long-lasting and relatively stable humid conditions from similar to 620,000 to 275,000 years bp (episodes 1-6), interrupted by several abrupt and extreme hydroclimate perturbations. A pattern of pronounced climatic cyclicity transformed habitats during episodes 7-9 (similar to 275,000-60,000 years bp), a crucial phase encompassing the gradual transition from Acheulean to Middle Stone Age technologies, the emergence of Homo sapiens in eastern Africa and key human social and cultural innovations. Those accumulative innovations plus the alignment of humid pulses between northeastern Africa and the eastern Mediterranean during high-frequency climate oscillations of episodes 10-12 (similar to 60,000-10,000 years bp) could have facilitated the global dispersal of H. sapiens.
KW  - Evolutionary ecology
KW  - Limnology
KW  - Palaeoclimate
Y1  - 2022
U6  - https://doi.org/10.1038/s41561-022-01032-y
SN  - 1752-0894
SN  - 1752-0908
VL  - 15
IS  - 10
SP  - 805
EP  - 811
PB  - Nature Publ. Group
CY  - London
ER  - 
TY  - JOUR
A1  - Jia, Weihan
A1  - Anslan, Sten
A1  - Chen, Fahu
A1  - Cao, Xianyong
A1  - Dong, Hailiang
A1  - Dulias, Katharina
A1  - Gu, Zhengquan
A1  - Heinecke, Liv
A1  - Jiang, Hongchen
A1  - Kruse, Stefan
A1  - Kang, Wengang
A1  - Li, Kai
A1  - Liu, Sisi
A1  - Liu, Xingqi
A1  - Liu, Ying
A1  - Ni, Jian
A1  - Schwalb, Antje
A1  - Stoof-Leichsenring, Kathleen R.
A1  - Shen, Wei
A1  - Tian, Fang
A1  - Wang, Jing
A1  - Wang, Yongbo
A1  - Wang, Yucheng
A1  - Xu, Hai
A1  - Yang, Xiaoyan
A1  - Zhang, Dongju
A1  - Herzschuh, Ulrike
T1  - Sedimentary ancient DNA reveals past ecosystem and biodiversity changes on the Tibetan Plateau: overview and prospects
JF  - Quaternary science reviews : the international multidisciplinary research and review journal
N2  - Alpine ecosystems on the Tibetan Plateau are being threatened by ongoing climate warming and intensified human activities. Ecological time-series obtained from sedimentary ancient DNA (sedaDNA) are essential for understanding past ecosystem and biodiversity dynamics on the Tibetan Plateau and their responses to climate change at a high taxonomic resolution. Hitherto only few but promising studies have been published on this topic. The potential and limitations of using sedaDNA on the Tibetan Plateau are not fully understood. Here, we (i) provide updated knowledge of and a brief introduction to the suitable archives, region-specific taphonomy, state-of-the-art methodologies, and research questions of sedaDNA on the Tibetan Plateau; (ii) review published and ongoing sedaDNA studies from the Tibetan Plateau; and (iii) give some recommendations for future sedaDNA study designs. Based on the current knowledge of taphonomy, we infer that deep glacial lakes with freshwater and high clay sediment input, such as those from the southern and southeastern Tibetan Plateau, may have a high potential for sedaDNA studies. Metabarcoding (for microorganisms and plants), metagenomics (for ecosystems), and hybridization capture (for prehistoric humans) are three primary sedaDNA approaches which have been successfully applied on the Tibetan Plateau, but their power is still limited by several technical issues, such as PCR bias and incompleteness of taxonomic reference databases. Setting up high-quality and open-access regional taxonomic reference databases for the Tibetan Plateau should be given priority in the future. To conclude, the archival, taphonomic, and methodological conditions of the Tibetan Plateau are favorable for performing sedaDNA studies. More research should be encouraged to address questions about long-term ecological dynamics at ecosystem scale and to bring the paleoecology of the Tibetan Plateau into a new era.
KW  - Sedimentary ancient DNA (sedaDNA)
KW  - Tibetan Plateau
KW  - Environmental DNA
KW  - Taphonomy
KW  - Ecosystem
KW  - Biodiversity
KW  - Paleoecology
KW  - Paleogeography
Y1  - 2022
U6  - https://doi.org/10.1016/j.quascirev.2022.107703
SN  - 0277-3791
SN  - 1873-457X
VL  - 293
PB  - Elsevier
CY  - Oxford
ER  - 
TY  - JOUR
A1  - Reinhard, Johanna E.
A1  - Geißler, Katja
A1  - Blaum, Niels
T1  - Grass and ground dwelling beetle community responses to holistic and wildlife grazing management using a cross-fence comparison in Western Kalahari rangeland, Namibia
JF  - Journal of insect conservation : an international journal devoted to the conservation of insects and related invertebrates
N2  - Savannahs are often branded by livestock grazing with resulting land degradation. Holistic management of livestock was proposed to contribute to biodiversity conservation by simulating native wildlife grazing behaviour. This study attempts the comparison of the impact of a holistic management regime to a wildlife grazing management regime on grass and ground-dwelling beetle species diversity on neighboring farms in Namibian rangeland. Results show that the response of biodiversity in species richness and composition to holistic management of livestock differs substantially from wildlife grazing with a positive impact. From a total of 39 identified species of ground-dwelling beetles (Coleoptera: Tenebrionidae, Carabidae) from 29 genera, eight species were found to be indicators for holistic management of livestock and three were found to be indicators for wildlife grazed rangeland. Observations suggest that holistic management of livestock may contribute to biodiversity conservation, but the differential effect of grazing management on species assemblages suggests that livestock grazing cannot replace native wildlife herbivory. Implications for insect conservation An adaptive management strategy such as holistic management used in this study shows the potential to support high beetle biodiversity. Holistic management of livestock thus aspects in favour for a sustainable form of grazing management for insect conservation even though it does not functionally replace grazing by native wildlife.
KW  - Beetle conservation
KW  - Land use management
KW  - Biodiversity
KW  - Insect conservation
KW  - Wildlife management
Y1  - 2022
U6  - https://doi.org/10.1007/s10841-022-00410-6
SN  - 1366-638X
SN  - 1572-9753
VL  - 26
SP  - 711
EP  - 720
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Bognár, Zsófia
A1  - Supala, Eszter
A1  - Yarman, Aysu
A1  - Zhang, Xiaorong
A1  - Bier, Frank Fabian
A1  - Scheller, Frieder W.
A1  - Gyurcsanyi, Róbert E.
T1  - Peptide epitope-imprinted polymer microarrays for selective protein recognition
BT  - application for SARS-CoV-2 RBD protein
JF  - Chemical science / RSC, Royal Society of Chemistry
N2  - We introduce a practically generic approach for the generation of epitope-imprinted polymer-based microarrays for protein recognition on surface plasmon resonance imaging (SPRi) chips. The SPRi platform allows the subsequent rapid screening of target binding kinetics in a multiplexed and label-free manner. The versatility of such microarrays, both as synthetic and screening platform, is demonstrated through developing highly affine molecularly imprinted polymers (MIPs) for the recognition of the receptor binding domain (RBD) of SARS-CoV-2 spike protein. A characteristic nonapeptide GFNCYFPLQ from the RBD and other control peptides were microspotted onto gold SPRi chips followed by the electrosynthesis of a polyscopoletin nanofilm to generate in one step MIP arrays. A single chip screening of essential synthesis parameters, including the surface density of the template peptide and its sequence led to MIPs with dissociation constants (K-D) in the lower nanomolar range for RBD, which exceeds the affinity of RBD for its natural target, angiotensin-convertase 2 enzyme. Remarkably, the same MIPs bound SARS-CoV-2 virus like particles with even higher affinity along with excellent discrimination of influenza A (H3N2) virus. While MIPs prepared with a truncated heptapeptide template GFNCYFP showed only a slightly decreased affinity for RBD, a single mismatch in the amino acid sequence of the template, i.e. the substitution of the central cysteine with a serine, fully suppressed the RBD binding.
Y1  - 2021
U6  - https://doi.org/10.1039/d1sc04502d
SN  - 2041-6539
VL  - 13
IS  - 5
SP  - 1263
EP  - 1269
PB  - Royal Society of Chemistry
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Schulte, Luise
A1  - Li, Chenzhi
A1  - Lisovski, Simeon
A1  - Herzschuh, Ulrike
T1  - Forest-permafrost feedbacks and glacial refugia help explain the unequal distribution of larch across continents
JF  - Journal of biogeography
N2  - Aim: The continental-scale distribution of plant functional types, such as evergreen and summergreen needle-leaf forest, is assumed to be determined by contemporary climate. However, the distribution of summergreen needle-leaf forest of larch (Larix Mill.) differs markedly between the continents, despite relatively similar climatic conditions. The reasons for these differences are little understood. Our aim is to identify potential triggers and drivers of the current distribution patterns by comparing species' bioclimatic niches, glacial refugia and postglacial recolonization patterns.

Location: Northern hemisphere.

Taxon: Species of the genus Larix (Mill.).

Methods: We compare species distribution and dominance using species ranges and sites of dominance, as well as their occurrence on modelled permafrost extent, and active layer thickness (ALT). We compare the bioclimatic niches and calculate the niche overlap between species, using the same data in addition to modern climate data. We synthesize pollen, macrofossil and ancient DNA palaeo-evidence of past Larix occurrences of the last 60,000 years and track differences in distribution patterns through time.

Results: Bioclimatic niches show large overlaps between Asian larch species and American Larix laricina. The distribution across various degrees of permafrost extent is distinctly different for Asian L. gmelinii and L. cajanderi compared to the other species, whereas the distribution on different depths of ALT is more similar among Asian and American species. Northern glacial refugia for Larix are only present in eastern Asia and Alaska.

Main Conclusion: The dominance of summergreen larches in Asia, where evergreen conifers dominate most of the rest of the boreal forests, is dependent on the interaction of several factors which allows Asian L. gmelinii and L. cajanderi to dominate where these factors coincide. These factors include the early postglacial spread out of northern glacial refugia in the absence of competitors as well as a positive feedback mechanism between frozen ground and forest.
KW  - bioclimatic niche
KW  - glacial refugia
KW  - larch
KW  - Larix
KW  - permafrost
KW  - phylogeography
KW  - postglacial recolonization
Y1  - 2022
U6  - https://doi.org/10.1111/jbi.14456
SN  - 0305-0270
SN  - 1365-2699
VL  - 49
IS  - 10
SP  - 1825
EP  - 1838
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Biermann, Robin Tim
A1  - Bach, Linh T.
A1  - Kläring, Hans-Peter
A1  - Baldermann, Susanne
A1  - Börnke, Frederik
A1  - Schwarz, Dietmar
T1  - Discovering tolerance-A computational approach to assess abiotic stress tolerance in tomato under greenhouse conditions
JF  - Frontiers in sustainable food systems
N2  - Modern plant cultivars often possess superior growth characteristics, but within a limited range of environmental conditions. Due to climate change, crops will be exposed to distressing abiotic conditions more often in the future, out of which heat stress is used as example for this study. To support identification of tolerant germplasm and advance screening techniques by a novel multivariate evaluation method, a diversity panel of 14 tomato genotypes, comprising Mediterranean landraces of Solanum lycopersicum, the cultivar "Moneymaker" and Solanum pennellii LA0716, which served as internal references, was assessed toward their tolerance against long-term heat stress. After 5 weeks of growth, young tomato plants were exposed to either control (22/18 degrees C) or heat stress (35/25 degrees C) conditions for 2 weeks. Within this period, water consumption, leaf angles and leaf color were determined. Additionally, gas exchange and leaf temperature were investigated. Finally, biomass traits were recorded. The resulting multivariate dataset on phenotypic plasticity was evaluated to test the hypothesis, that more tolerant genotypes have less affected phenotypes upon stress adaptation. For this, a cluster-analysis-based approach was developed that involved a principal component analysis (PCA), dimension reduction and determination of Euclidean distances. These distances served as measure for the phenotypic plasticity upon heat stress. Statistical evaluation allowed the identification and classification of homogeneous groups consisting each of four putative more or less heat stress tolerant genotypes. The resulting classification of the internal references as "tolerant" highlights the applicability of our proposed tolerance assessment model. PCA factor analysis on principal components 1-3 which covered 76.7% of variance within the phenotypic data, suggested that some laborious measure such as the gas exchange might be replaced with the determination of leaf temperature in larger heat stress screenings. Hence, the overall advantage of the presented method is rooted in its suitability of both, planning and executing screenings for abiotic stress tolerance using multivariate phenotypic data to overcome the challenge of identifying abiotic stress tolerant plants from existing germplasms and promote sustainable agriculture for the future.
KW  - abiotic stress
KW  - breeding
KW  - heat stress
KW  - phenotyping
KW  - Solanum
KW  - lycopersicum
KW  - screening
KW  - stress tolerance
Y1  - 2022
U6  - https://doi.org/10.3389/fsufs.2022.878013
SN  - 2571-581X
VL  - 6
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Klauschies, Toni
A1  - Isanta-Navarro, Jana
T1  - The joint effects of salt and 6PPD contamination on a freshwater herbivore
JF  - The science of the total environment : an international journal for scientific research into the environment and its relationship with man
N2  - Using sodium chloride (NaCl) for de-icing roads is known to have severe consequences on freshwater organisms when washed into water bodies. N-(1,3-dimethylbutyl)-N '-phenyl-p-phenylenediamine, also known as 6PPD, is an antiozonant mainly found in automobile tire rubber to prevent ozone mediated cracking or wear-out. Especially the ozonated derivate, 6PPD-quinone, which is washed into streams after storm events, has been found to be toxic for coho salmon. Studies on other freshwater organisms could not confirm those findings, pointing towards distinct species-specific differences. Storm events result in greater run-offs from all water-soluble contaminants into freshwater bodies, potentially enhancing the concentrations of both chloride and 6PPD during winter. Here we show that these two contaminants have synergistic negative effects on the population growth of the rotifer Brachionus calyciflorus, a common freshwater herbivore. Hence, while only high concentrations of 6PPD and even higher concentrations of 6PPD-quinone, beyond environmentally relevant concentrations, had lethal effects on rotifers, the addition of NaCl enhanced the sensitivity of the rotifers towards the application of 6PPD so that their negative effects were more pronounced at lower concentrations. Similarly, 6PPD increased the lethal effect of NaCl. Our results support the species-specific toxicity of 6PPD and demonstrate a synergistic effect of the antiozonant on the toxicity of other environmentally relevant stressors, such as road salt contamination.
KW  - Anthropogenic impact
KW  - Car tire rubber
KW  - Environmental stressor
KW  - Rotifer
KW  - Sodium chloride
KW  - 6PPD quinone
Y1  - 2022
U6  - https://doi.org/10.1016/j.scitotenv.2022.154675
SN  - 0048-9697
SN  - 1879-1026
VL  - 829
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Kruse, Stefan
A1  - Herzschuh, Ulrike
T1  - Regional opportunities for tundra conservation in the next 1000 years
JF  - eLife
N2  - The biodiversity of tundra areas in northern high latitudes is threatened by invasion of forests under global warming. However, poorly understood nonlinear responses of the treeline ecotone mean the timing and extent of tundra losses are unclear, but policymakers need such information to optimize conservation efforts. Our individual-based model LAVESI, developed for the Siberian tundra-taiga ecotone, can help improve our understanding. Consequently, we simulated treeline migration trajectories until the end of the millennium, causing a loss of tundra area when advancing north. Our simulations reveal that the treeline follows climate warming with a severe, century-long time lag, which is overcompensated by infilling of stands in the long run even when temperatures cool again. Our simulations reveal that only under ambitious mitigation strategies (relative concentration pathway 2.6) will ~30% of original tundra areas remain in the north but separated into two disjunct refugia.
KW  - Larix gmelinii
KW  - Larix cajanderi
KW  - nonlinear response
KW  - treeline ecotone
KW  - tundra
KW  - Ecology
KW  - Short Report
Y1  - 2022
U6  - https://doi.org/10.7554/eLife.75163
SN  - 2050-084X
VL  - 11
PB  - eLife Sciences Publications
CY  - Cambridge
ER  - 
TY  - JOUR
A1  - Hoffmann, Julia
A1  - Hölker, Franz
A1  - Eccard, Jana
T1  - Welcome to the dark side
BT  - partial nighttime illumination affects night-and daytime foraging behavior of a small mammal
JF  - Frontiers in ecology and evolution
N2  - Differences in natural light conditions caused by changes in moonlight are known to affect perceived predation risk in many nocturnal prey species. As artificial light at night (ALAN) is steadily increasing in space and intensity, it has the potential to change movement and foraging behavior of many species as it might increase perceived predation risk and mask natural light cycles. We investigated if partial nighttime illumination leads to changes in foraging behavior during the night and the subsequent day in a small mammal and whether these changes are related to animal personalities. We subjected bank voles to partial nighttime illumination in a foraging landscape under laboratory conditions and in large grassland enclosures under near natural conditions. We measured giving-up density of food in illuminated and dark artificial seed patches and video recorded the movement of animals. While animals reduced number of visits to illuminated seed patches at night, they increased visits to these patches at the following day compared to dark seed patches. Overall, bold individuals had lower giving-up densities than shy individuals but this difference increased at day in formerly illuminated seed patches. Small mammals thus showed carry-over effects on daytime foraging behavior due to ALAN, i.e., nocturnal illumination has the potential to affect intra- and interspecific interactions during both night and day with possible changes in personality structure within populations and altered predator-prey dynamics.
KW  - light pollution
KW  - inter-individual differences
KW  - animal personality
KW  - Myodes glareolus
KW  - ALAN
Y1  - 2022
U6  - https://doi.org/10.3389/fevo.2021.779825
SN  - 2296-701X
VL  - 9
PB  - Frontiers Media
CY  - Lausanne
ER  - 
TY  - JOUR
A1  - Iltis, Peter W.
A1  - Frahm, Jens
A1  - Voit, Dirk
A1  - Wood, Danielle
A1  - Taylor, Scott
T1  - Oral cavity movements of the tongue during large interval slurs in high-level horn players br a descriptive study
JF  - Medical problems of performing artists
N2  - OBJECTIVE: 
Recent publications describing lingual movement strategies within the oral cavity of brass players have established the existence of efficient and predictable movement patterns in healthy performers for a variety of performance tasks. In this study we extend the research to include the playing of large interval slurs in horn players. 

METHODS: 
Real-time MRI films at 40-msec resolution were simultaneously obtained in the sagittal
and coronal planes in 9 professional horn players as they performed 2 repetitions each of 3 slur sequences spanning 1 octave, 1 octave + 3rd, and 1 octave + 5th at a mezzo forte dynamic level. Nine profile lines were overlaid on the images allowing the measurement of dorsal tongue edge movement using a customized MATLAB toolkit. Movement along lines representing the anterior, middle, and posterior oral cavity in the sagittal plane, as well as the vertical height of an air channel observed in the coronal plane, are reported. 

RESULTS: 
Both sagittal and coronal views demonstrate patterned tongue movements that narrow and widen the air channel during ascending and descending slurs, respectively. The magnitude of these movements is greater during larger intervals, though not perfectly consistent within each slur sequence. Additionally, the tongue position during notes
tends to drift in the direction of the subsequent note in each sequence. We suggest that the observed movements may help to modulate air speed through the lips, possible attenuating embouchure muscle tension changes by assisting changes in lip vibration frequency.
Y1  - 2022
U6  - https://doi.org/10.21091/mppa.2022.2014
SN  - 0885-1158
SN  - 1938-2766
VL  - 3
IS  - 2
SP  - 89
EP  - 97
PB  - Science & Medicine, Inc.
CY  - Narberth
ER  - 
TY  - JOUR
A1  - Kiemel, Katrin
A1  - Gurke, Marie
A1  - Paraskevopoulou, Sofia
A1  - Havenstein, Katja
A1  - Weithoff, Guntram
A1  - Tiedemann, Ralph
T1  - Variation in heat shock protein 40 kDa relates to divergence in thermotolerance among cryptic rotifer species
JF  - Scientific reports
N2  - Genetic divergence and the frequency of hybridization are central for defining species delimitations, especially among cryptic species where morphological differences are merely absent. Rotifers are known for their high cryptic diversity and therefore are ideal model organisms to investigate such patterns. Here, we used the recently resolved Brachionus calyciflorus species complex to investigate whether previously observed between species differences in thermotolerance and gene expression are also reflected in their genomic footprint. We identified a Heat Shock Protein gene (HSP 40 kDa) which exhibits cross species pronounced sequence variation. This gene exhibits species-specific fixed sites, alleles, and sites putatively under positive selection. These sites are located in protein binding regions involved in chaperoning and may therefore reflect adaptive diversification. By comparing three genetic markers (ITS, COI, HSP 40 kDa), we revealed hybridization events between the cryptic species. The low frequency of introgressive haplotypes/alleles suggest a tight, but not fully impermeable boundary between the cryptic species.
Y1  - 2022
U6  - https://doi.org/10.1038/s41598-022-27137-3
SN  - 2045-2322
VL  - 12
IS  - 1
PB  - Macmillan Publishers Limited
CY  - London
ER  - 
TY  - JOUR
A1  - Villalba, Luis Alberto
A1  - Karnatak, Rajat
A1  - Grossart, Hans-Peter
A1  - Wollrab, Sabine
T1  - Flexible habitat choice of pelagic bacteria increases system stability and energy flow through the microbial loop
JF  - Limnology and oceanography : L & O
N2  - Pelagic bacteria can be classified into free-living and particle-attached life modes, which either dwell in the water column or attach to suspended particles. Bacteria with a generalist life style, however, can actively shift between these two habitats. Globally increasing densities of natural and artificial particles enhance habitat heterogeneity, with potential consequences for system stability and trophic transfer through aquatic food webs. To better decipher the dynamics of microbial communities, we investigated the influence of adaptive vs. fixed habitat choice on species coexistence for a simplified bacterial community by analyzing a corresponding food web model, consisting of two specialist bacterial prey species (free and attached), a generalist bacterial prey species with the ability to shift between both habitats, and two protist predators, specialized on either water or particle compartment. For simplicity we assume a shared resource pool, considering particles only for colonization but not as a source for nutrients or carbon, that is, inert particles like microplastics or inorganic sediments. The model predicts coexistence on a cyclic attractor between fixed and flexible bacteria, if the costs for adaptive habitat choice can be balanced by adaptation speed. The presence of adaptive prey dampens predator-prey cycle amplitudes, contributing to system stabilization resulting in higher mean predator biomass compared to specialist prey only. Thus, in pelagic microbial systems, flexible habitat choice at the prey level has important implications for system stability and magnitude of energy flow through the microbial loop.
Y1  - 2022
U6  - https://doi.org/10.1002/lno.12091
SN  - 0024-3590
SN  - 1939-5590
VL  - 67
IS  - 6
SP  - 1402
EP  - 1415
PB  - Wiley-Blackwell
CY  - Oxford [u.a.]
ER  - 
TY  - JOUR
A1  - Ilicic, Doris
A1  - Grossart, Hans-Peter
T1  - Basal parasitic fungi in marine food webs-a mystery yet to unravel
JF  - Journal of Fungi
N2  - Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.
KW  - basal fungi
KW  - parasites
KW  - Chytridiomycota
KW  - Rozellomycota
KW  - food web
KW  - biological carbon pump
Y1  - 2022
U6  - https://doi.org/10.3390/jof8020114
SN  - 2309-608X
VL  - 8
IS  - 2
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Emary, Clive
A1  - Malchow, Anne-Kathleen
T1  - Stability-instability transition in tripartite merged ecological networks
JF  - Journal of mathematical biology
N2  - Although ecological networks are typically constructed based on a single type of interaction, e.g. trophic interactions in a food web, a more complete picture of ecosystem composition and functioning arises from merging networks of multiple interaction types. In this work, we consider tripartite networks constructed by merging two bipartite networks, one mutualistic and one antagonistic. Taking the interactions within each sub-network to be distributed randomly, we consider the stability of the dynamics of the network based on the spectrum of its community matrix. In the asymptotic limit of a large number of species, we show that the spectrum undergoes an eigenvalue phase transition, which leads to an abrupt destabilisation of the network as the ratio of mutualists to antagonists is increased. We also derive results that show how this transition is manifest in networks of finite size, as well as when disorder is introduced in the segregation of the two interaction types. Our random-matrix results will serve as a baseline for understanding the behaviour of merged networks with more realistic structures and/or more detailed dynamics.
KW  - Random matrices
KW  - Phase transition
KW  - Random eigenvalues
KW  - Population dynamics
KW  - Community matrix
KW  - Ecological network
Y1  - 2022
U6  - https://doi.org/10.1007/s00285-022-01783-7
SN  - 0303-6812
SN  - 1432-1416
VL  - 85
IS  - 3
PB  - Springer
CY  - Heidelberg
ER  - 
TY  - JOUR
A1  - Parry, Victor
A1  - Schlägel, Ulrike E.
A1  - Tiedemann, Ralph
A1  - Weithoff, Guntram
T1  - Behavioural responses of defended and undefended prey to their predator
BT  - a case study of rotifera
JF  - Biology : open access journal
N2  - Many animals that have to cope with predation have evolved mechanisms to reduce their predation risk. One of these mechanisms is change in morphology, for example, the development of spines. These spines are induced, when mothers receive chemical signals of a predator (kairomones) and their daughters are then equipped with defensive spines. We studied the behaviour of a prey and its predator when the prey is either defended or undefended. We used common aquatic micro-invertebrates, the rotifers Brachionus calyciflorus (prey) and Asplanchna brightwellii (predator) as experimental animals. We found that undefended prey increased its swimming speed in the presence of the predator. The striking result was that the defended prey did not respond to the predator's presence. This suggests that defended prey has a different response behaviour to a predator than undefended conspecifics. Our study provides further insights into complex zooplankton predator-prey interactions. Predation is a strong species interaction causing severe harm or death to prey. Thus, prey species have evolved various defence strategies to minimize predation risk, which may be immediate (e.g., a change in behaviour) or transgenerational (morphological defence structures). We studied the behaviour of two strains of a rotiferan prey (Brachionus calyciflorus) that differ in their ability to develop morphological defences in response to their predator Asplanchna brightwellii. Using video analysis, we tested: (a) if two strains differ in their response to predator presence and predator cues when both are undefended; (b) whether defended individuals respond to live predators or their cues; and (c) if the morphological defence (large spines) per se has an effect on the swimming behaviour. We found a clear increase in swimming speed for both undefended strains in predator presence. However, the defended specimens responded neither to the predator presence nor to their cues, showing that they behave indifferently to their predator when they are defended. We did not detect an effect of the spines on the swimming behaviour. Our study demonstrates a complex plastic behaviour of the prey, not only in the presence of their predator, but also with respect to their defence status.
KW  - animal behaviour
KW  - transgenerational response
KW  - Brachionus calyciflorus
KW  - Asplanchna brightwellii
KW  - video analysis
Y1  - 2022
U6  - https://doi.org/10.3390/biology11081217
SN  - 2079-7737
VL  - 11
IS  - 8
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Kiemel, Katrin
A1  - Weithoff, Guntram
A1  - Tiedemann, Ralph
T1  - DNA metabarcoding reveals impact of local recruitment, dispersal, and hydroperiod on assembly of a zooplankton metacommunity
JF  - Molecular ecology
N2  - Understanding the environmental impact on the assembly of local communities in relation to their spatial and temporal connectivity is still a challenge in metacommunity ecology. This study aims to unravel underlying metacommunity processes and environmental factors that result in observed zooplankton communities. Unlike most metacommunity studies, we jointly examine active and dormant zooplankton communities using a DNA metabarcoding approach to overcome limitations of morphological species identification. We applied two-fragment (COI and 18S) metabarcoding to monitor communities of 24 kettle holes over a two-year period to unravel (i) spatial and temporal connectivity of the communities, (ii) environmental factors influencing local communities, and (iii) dominant underlying metacommunity processes in this system. We found a strong separation of zooplankton communities from kettle holes of different hydroperiods (degree of permanency) throughout the season, while the community composition within single kettle holes did not differ between years. Species richness was primarily dependent on pH and permanency, while species diversity (Shannon Index) was influenced by kettle hole location. Community composition was impacted by kettle hole size and surrounding field crops. Environmental processes dominated temporal and spatial processes. Sediment communities showed a different composition compared to water samples but did not differ between ephemeral and permanent kettle holes. Our results suggest that communities are mainly structured by environmental filtering based on pH, kettle hole size, surrounding field crops, and permanency. Environmental filtering based on specific conditions in individual kettle holes seems to be the dominant process in community assembly in the studied zooplankton metacommunity.
KW  - bulk DNA
KW  - dispersal
KW  - DNA-metabarcoding
KW  - environmental filtering;
KW  - metacommunity
KW  - zooplankton
Y1  - 2022
U6  - https://doi.org/10.1111/mec.16627
SN  - 0962-1083
SN  - 1365-294X
VL  - 32
IS  - 23
PB  - Wiley
CY  - Hoboken
ER  - 
TY  - JOUR
A1  - Herzschuh, Ulrike
A1  - Böhmer, Thomas
A1  - Li, Chenzhi
A1  - Cao, Xianyong
A1  - Hébert, Raphaël
A1  - Dallmeyer, Anne
A1  - Telford, Richard J.
A1  - Kruse, Stefan
T1  - Reversals in temperature-precipitation correlations in the Northern Hemisphere extratropics during the Holocene
JF  - Geophysical research letters
N2  - Future precipitation levels remain uncertain because climate models have struggled to reproduce observed variations in temperature-precipitation correlations. Our analyses of Holocene proxy-based temperature-precipitation correlations and hydrological sensitivities from 2,237 Northern Hemisphere extratropical pollen records reveal a significant latitudinal dependence and temporal variations among the early, middle, and late Holocene. These proxy-based variations are largely consistent with patterns obtained from transient climate simulations (TraCE21k). While high latitudes and subtropical monsoon areas show mainly stable positive correlations throughout the Holocene, the mid-latitude pattern is temporally and spatially more variable. In particular, we identified a reversal from positive to negative temperature-precipitation correlations in the eastern North American and European mid-latitudes from the early to mid-Holocene that mainly related to slowed down westerlies and a switch to moisture-limited convection under a warm climate. Our palaeoevidence of past temperature-precipitation correlation shifts identifies those regions where simulating past and future precipitation levels might be particularly challenging.
Y1  - 2022
U6  - https://doi.org/10.1029/2022GL099730
SN  - 0094-8276
SN  - 1944-8007
VL  - 49
IS  - 22
PB  - American Geophysical Union
CY  - Washington
ER  - 
TY  - JOUR
A1  - Mumm, Rebekka
A1  - Scheffler, Christiane
A1  - Hermanussen, Michael
T1  - Locally structured correlation (LSC) plots describe inhomogeneity in normally distributed correlated bivariate variables
JF  - Archives of public health = Archives belges de santé publique = Belgisch archief voor volksgezondheid
N2  - Background
The association between bivariate variables may not necessarily be homogeneous throughout the whole range of the variables. We present a new technique to describe inhomogeneity in the association of bivariate variables. 

Methods
We consider the correlation of two normally distributed random variables. The 45 degrees diagonal through the origin of coordinates represents the line on which all points would lie if the two variables completely agreed. If the two variables do not completely agree, the points will scatter on both sides of the diagonal and form a cloud. In case of a high association between the variables, the band width of this cloud will be narrow, in case of a low association, the band width will be wide. The band width directly relates to the magnitude of the correlation coefficient. We then determine the Euclidean distances between the diagonal and each point of the bivariate correlation, and rotate the coordinate system clockwise by 45 degrees. The standard deviation of all Euclidean distances, named "global standard deviation", reflects the band width of all points along the former diagonal. Calculating moving averages of the standard deviation along the former diagonal results in "locally structured standard deviations" and reflect patterns of "locally structured correlations (LSC)". LSC highlight inhomogeneity of bivariate correlations. We exemplify this technique by analyzing the association between body mass index (BMI) and hip circumference (HC) in 6313 healthy East German adults aged 18 to 70 years. 

Results
The correlation between BMI and HC in healthy adults is not homogeneous. LSC is able to identify regions where the predictive power of the bivariate correlation between BMI and HC increases or decreases, and highlights in our example that slim people have a higher association between BMI and HC than obese people.

Conclusion
Locally structured correlations (LSC) identify regions of higher or lower than average correlation between two normally distributed variables.
KW  - Standard deviation
KW  - Locally structured standard deviation
KW  - Locally
KW  - structured correlation
KW  - Variance
Y1  - 2022
U6  - https://doi.org/10.1186/s13690-021-00748-4
SN  - 0778-7367
SN  - 2049-3258
VL  - 80
IS  - 1
PB  - BMC
CY  - London
ER  - 
TY  - JOUR
A1  - Dallmeyer, Anne
A1  - Kleinen, Thomas
A1  - Claussen, Martin
A1  - Weitzel, Nils
A1  - Cao, Xianyong
A1  - Herzschuh, Ulrike
T1  - The deglacial forest conundrum
JF  - Nature Communications
N2  - How fast the Northern Hemisphere (NH) forest biome tracks strongly warming climates is largely unknown. Regional studies reveal lags between decades and millennia. Here we report a conundrum: Deglacial forest expansion in the NH extra-tropics occurs approximately 4000 years earlier in a transient MPI-ESM1.2 simulation than shown by pollen-based biome reconstructions. Shortcomings in the model and the reconstructions could both contribute to this mismatch, leaving the underlying causes unresolved. The simulated vegetation responds within decades to simulated climate changes, which agree with pollen-independent reconstructions. Thus, we can exclude climate biases as main driver for differences. Instead, the mismatch points at a multi-millennial disequilibrium of the NH forest biome to the climate signal. Therefore, the evaluation of time-slice simulations in strongly changing climates with pollen records should be critically reassessed. Our results imply that NH forests may be responding much slower to ongoing climate changes than Earth System Models predict. <br /> Deglacial forest expansion in the Northern Hemisphere poses a conundrum: Model results agree with the climate signal but are several millennia ahead of reconstructed forest dynamics. The underlying causes remain unsolved.
Y1  - 2022
U6  - https://doi.org/10.1038/s41467-022-33646-6
SN  - 2041-1723
VL  - 13
IS  - 1
PB  - Nature Publishing Group UK
CY  - [London]
ER  - 
TY  - JOUR
A1  - Li, Zhen
A1  - Wang, Yongbo
A1  - Herzschuh, Ulrike
A1  - Cao, Xianyong
A1  - Ni, Jian
A1  - Zhao, Yan
T1  - Pollen-based biome reconstruction on the Qinghai-Tibetan Plateau during the past 15,000 years
JF  - Palaeogeography, palaeoclimatology, palaeoecology : an international journal for the geo-sciences
N2  - Reconstruction of past vegetation change is critical for better understanding the potential impact of future global change on the fragile alpine ecosystems of the Qinghai-Tibetan Plateau (QTP). In this paper, pollen assemblages comprising 58 records from the QTP, spanning the past 15 kyrs, were collected to reconstruct biome compositions using a standard approach. Six forest biomes were identified mainly on the southeastern plateau, exhibiting a pattern of gradual expansion along the eastern margin during early to mid-Holocene times. The alpine meadow biome was separately identified based on an updated scheme, and showed notable westward expansions towards lower latitudes and higher altitudes during early Holocene times. Consistent patterns of migration could also be identified for the alpine steppe biome, which moved eastward during the late Holocene after 4 ka. As the dominant biome type, temperate steppe was distributed widely over the QTP with minor migration patterns, except for a progressive expansion to lower altitudes in the late Holocene times. The desert biome was inferred mainly as covering the northwestern plateau and the Qaidam Basin, in relatively restricted areas. The spatial distribution of the reconstructed biomes represent the large-scale vegetation gradient on the QTP. Monsoonal precipitation expressed predominant controls on the development of alpine ecosystems, while the variations in desert vegetation responded to regional moisture brought by the mid-latitude Westerlies. Temperature changes played relatively minor roles in the variations of alpine vegetation, but exerted more significant impacts on the forest biomes.
KW  - biomization
KW  - pollen
KW  - vegetation migration
KW  - Qinghai-Tibetan Plateau
KW  - holocene
Y1  - 2022
U6  - https://doi.org/10.1016/j.palaeo.2022.111190
SN  - 0031-0182
SN  - 1872-616X
VL  - 604
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Jänicke, Clemens
A1  - Goddard, Adam
A1  - Stein, Susanne
A1  - Steinmann, Horst-Henning
A1  - Lakes, Tobia
A1  - Nendel, Claas
A1  - Müller, Daniel
T1  - Field-level land-use data reveal heterogeneous crop sequences with distinct regional differences in Germany
JF  - European journal of agronomy
N2  - Crop cultivation intensifies globally, which can jeopardize biodiversity and the resilience of cropping systems. We investigate changes in crop rotations as one intensification metric for half of the croplands in Germany with annual field-level land-use data from 2005 to 2018. We proxy crop rotations with crop sequences and compare how these sequences changed among three seven-year periods. The results reveal an overall high diversity of crop sequences in Germany. Half of the cropland has crop sequences with four or more crops within a seven-year period, while continuous cultivation of the same crop is present on only 2% of the cropland. Larger farms tend to have more diverse crop sequences and organic farms have lower shares of cereal crops. In three federal states, crop rotations became less structurally diverse over time, i.e. the number of crops and the number of changes between crops decreased. In one state, structural diversity increased and the proportion of monocropping decreased. The functional diversity of the crop sequences, which measures the share of winter and spring crops as well as the share of leaf and cereal crops per sequence, remained largely stable. Trends towards cereal-or leaf -crop dominated sequences varied between the states, and no clear overall dynamic could be observed. However, the share of winter crops per sequence decreased in all four federal states. Quantifying the dynamics of crop sequences at the field level is an important metric of land-use intensity and can reveal the patterns of land-use intensification.
KW  - crop production
KW  - crop rotation
KW  - cropping diversity
KW  - IACS
KW  - intensification
KW  - land-use intensity
Y1  - 2022
U6  - https://doi.org/10.1016/j.eja.2022.126632
SN  - 1161-0301
SN  - 1873-7331
VL  - 141
PB  - Elsevier
CY  - Amsterdam
ER  - 
TY  - JOUR
A1  - Wicaksono, Wisnu Adi
A1  - Braun, Maria
A1  - Bernhardt, Jörg
A1  - Riedel, Katharina
A1  - Cernava, Tomislav
A1  - Berg, Gabriele
T1  - Trade-off for survival
BT  - microbiome response to chemical exposure combines activation of intrinsic resistances and adapted metabolic activity
JF  - Environment international : a journal of science, technology, health, monitoring and policy
N2  - The environmental micmbiota is increasingly exposed to chemical pollution. While the emergence of multi-resistant pathogens is recognized as a global challenge, our understanding of antimicrobial resistance (AMR) development from native microbiomes and the risks associated with chemical exposure is limited. By implementing a lichen as a bioindicator organism and model for a native microbiome, we systematically examined responses towards antimicrobials (colistin, tetracycline, glyphosate, and alkylpyrazine). Despite an unexpectedly high resilience, we identified potential evolutionary consequences of chemical exposure in terms of composition and functioning of native bacterial communities. Major shifts in bacterial composition were observed due to replacement of naturally abundant taxa; e.g. Chthoniobacterales by Pseudomonadales. A general response, which comprised activation of intrinsic resistance and parallel reduction of metabolic activity at RNA and protein levels was deciphered by a multi-omics approach. Targeted analyses of key taxa based on metagenome-assembled genomes reflected these responses but also revealed diversified strategies of their players. Chemical-specific responses were also observed, e.g., glyphosate enriched bacterial r-strategists and activated distinct ARGs. Our work demonstrates that the high resilience of the native micmbiota toward antimicrobial exposure is not only explained by the presence of antibiotic resistance genes but also adapted metabolic activity as a trade-off for survival. Moreover, our results highlight the importance of native microbiomes as important but so far neglected AMR reservoirs. We expect that this phenomenon is representative for a wide range of environmental microbiota exposed to chemicals that potentially contribute to the emergence of antibiotic-resistant bacteria from natural environments.
Y1  - 2022
U6  - https://doi.org/10.1016/j.envint.2022.107474
SN  - 1873-6750
VL  - 168
PB  - Elsevier Science
CY  - Amsterdam [u.a.]
ER  - 
TY  - JOUR
A1  - Radosavljevic, Boris
A1  - Lantuit, Hugues
A1  - Knoblauch, Christian
A1  - Couture, Nicole
A1  - Herzschuh, Ulrike
A1  - Fritz, Michael
T1  - Arctic nearshore sediment dynamics - an example from Herschel Island - Qikiqtaruk, Canada
JF  - Journal of marine science and engineering
N2  - Increasing arctic coastal erosion rates imply a greater release of sediments and organic matter into the coastal zone. With 213 sediment samples taken around Herschel Island-Qikiqtaruk, Canadian Beaufort Sea, we aimed to gain new insights on sediment dynamics and geochemical properties of a shallow arctic nearshore zone. Spatial characteristics of nearshore sediment texture (moderately to poorly sorted silt) are dictated by hydrodynamic processes, but ice-related processes also play a role. We determined organic matter (OM) distribution and inferred the origin and quality of organic carbon by C/N ratios and stable carbon isotopes delta C-13. The carbon content was higher offshore and in sheltered areas (mean: 1.0 wt.%., S.D.: 0.9) and the C/N ratios also showed a similar spatial pattern (mean: 11.1, S.D.: 3.1), while the delta C-13 (mean: -26.4 parts per thousand VPDB, S.D.: 0.4) distribution was more complex. We compared the geochemical parameters of our study with terrestrial and marine samples from other studies using a bootstrap approach. Sediments of the current study contained 6.5 times and 1.8 times less total organic carbon than undisturbed and disturbed terrestrial sediments, respectively. Therefore, degradation of OM and separation of carbon pools take place on land and continue in the nearshore zone, where OM is leached, mineralized, or transported beyond the study area.
KW  - permafrost
KW  - Arctic Ocean
KW  - stable carbon isotopes
KW  - nitrogen
KW  - sediment
KW  - chemistry
KW  - sediment dynamics
KW  - Beaufort Sea
KW  - grain size
Y1  - 2022
U6  - https://doi.org/10.3390/jmse10111589
SN  - 2077-1312
VL  - 10
IS  - 11
PB  - MDPI
CY  - Basel
ER  - 
TY  - JOUR
A1  - Tebbe, Jonas
A1  - Ottensmann, Meinolf
A1  - Havenstein, Katja
A1  - Efstratiou, Artemis
A1  - Lenz, Tobias L.
A1  - Caspers, Barbara A.
A1  - Forcada, Jaume
A1  - Tiedemann, Ralph
A1  - Hoffman, Joseph
T1  - Intronic primers reveal unexpectedly high major histocompatibility complex diversity in Antarctic fur seals
JF  - Scientific reports
N2  - The major histocompatibility complex (MHC) is a group of genes comprising one of the most important components of the vertebrate immune system. Consequently, there has been much interest in characterising MHC variation and its relationship with fitness in a variety of species. Due to the exceptional polymorphism of MHC genes, careful PCR primer design is crucial for capturing all of the allelic variation present in a given species. We therefore developed intronic primers to amplify the full-length 267 bp protein-coding sequence of the MHC class II DQB exon 2 in the Antarctic fur seal. We then characterised patterns of MHC variation among mother-offspring pairs from two breeding colonies and detected 19 alleles among 771 clone sequences from 56 individuals. The distribution of alleles within and among individuals was consistent with a single-copy, classical DQB locus showing Mendelian inheritance. Amino acid similarity at the MHC was significantly associated with genome-wide relatedness, but no relationship was found between MHC heterozygosity and genome-wide heterozygosity. Finally, allelic diversity was several times higher than reported by a previous study based on partial exon sequences. This difference appears to be related to allele-specific amplification bias, implying that primer design can strongly impact the inference of MHC diversity.
Y1  - 2022
U6  - https://doi.org/10.1038/s41598-022-21658-7
SN  - 2045-2322
VL  - 12
IS  - 1
PB  - Nature Publishing Group
CY  - London
ER  - 
TY  - JOUR
A1  - Hébert, Raphaël
A1  - Herzschuh, Ulrike
A1  - Laepple, Thomas
T1  - Millennial-scale climate variability over land overprinted by ocean temperature fluctuations
JF  - Nature geoscience
N2  - Variations in regional temperature have widespread implications for society, but our understanding of the amplitude and origin of long-term natural variability is insufficient for accurate regional projections. This is especially the case for terrestrial temperature variability, which is currently thought to be weak over long timescales. By performing spectral analysis on climate reconstructions, produced using sedimentary pollen records from the Northern Hemisphere over the last 8,000 years, coupled with instrumental data, we provide a comprehensive estimate of regional temperature variability from annual to millennial timescales. We show that short-term random variations are overprinted by strong ocean-driven climate variability on multi-decadal and longer timescales. This may cause substantial and potentially unpredictable regional climatic shifts in the coming century, in contrast to the relatively muted and homogeneous warming projected by climate models. Due to the marine influence, regions characterized by stable oceanic climate at sub-decadal timescales experience stronger long-term variability, and continental regions with higher sub-decadal variability show weaker long-term variability. This fundamental relationship between the timescales provides a unique insight into the emergence of a marine-driven low-frequency regime governing terrestrial climate variability and sets the basis to project the amplitude of temperature fluctuations on multi-decadal timescales and longer. 

Temperature variability over land is enhanced by ocean temperature fluctuations on millennial timescales, with implications for regional-scale climate change, according to an analysis of Northern Hemisphere proxy records and observations.
Y1  - 2022
U6  - https://doi.org/10.1038/s41561-022-01056-4
SN  - 1752-0894
SN  - 1752-0908
VL  - 15
IS  - 11
SP  - 899
PB  - Nature portfolio
CY  - Berlin
ER  - 
TY  - JOUR
A1  - Nathan, Ran
A1  - Monk, Christopher T.
A1  - Arlinghaus, Robert
A1  - Adam, Timo
A1  - Alós, Josep
A1  - Assaf, Michael
A1  - Baktoft, Henrik
A1  - Beardsworth, Christine E.
A1  - Bertram, Michael G.
A1  - Bijleveld, Allert
A1  - Brodin, Tomas
A1  - Brooks, Jill L.
A1  - Campos-Candela, Andrea
A1  - Cooke, Steven J.
A1  - Gjelland, Karl O.
A1  - Gupte, Pratik R.
A1  - Harel, Roi
A1  - Hellstrom, Gustav
A1  - Jeltsch, Florian
A1  - Killen, Shaun S.
A1  - Klefoth, Thomas
A1  - Langrock, Roland
A1  - Lennox, Robert J.
A1  - Lourie, Emmanuel
A1  - Madden, Joah R.
A1  - Orchan, Yotam
A1  - Pauwels, Ine S.
A1  - Riha, Milan
A1  - Röleke, Manuel
A1  - Schlägel, Ulrike
A1  - Shohami, David
A1  - Signer, Johannes
A1  - Toledo, Sivan
A1  - Vilk, Ohad
A1  - Westrelin, Samuel
A1  - Whiteside, Mark A.
A1  - Jaric, Ivan
T1  - Big-data approaches lead to an increased understanding of the ecology of animal movement
JF  - Science
N2  - Understanding animal movement is essential to elucidate how animals interact, survive, and thrive in a changing world. Recent technological advances in data collection and management have transformed our understanding of animal "movement ecology" (the integrated study of organismal movement), creating a big-data discipline that benefits from rapid, cost-effective generation of large amounts of data on movements of animals in the wild. These high-throughput wildlife tracking systems now allow more thorough investigation of variation among individuals and species across space and time, the nature of biological interactions, and behavioral responses to the environment. Movement ecology is rapidly expanding scientific frontiers through large interdisciplinary and collaborative frameworks, providing improved opportunities for conservation and insights into the movements of wild animals, and their causes and consequences.
Y1  - 2022
U6  - https://doi.org/10.1126/science.abg1780
SN  - 0036-8075
SN  - 1095-9203
VL  - 375
IS  - 6582
SP  - 734
EP  - +
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  - 
TY  - JOUR
A1  - Nakamura, Yasunori
A1  - Steup, Martin
A1  - Colleoni, Christophe
A1  - Iglesias, Alberto A.
A1  - Bao, Jinsong
A1  - Fujita, Naoko
A1  - Tetlow, Ian
T1  - Molecular regulation of starch metabolism
JF  - Plant molecular biology : an international journal of fundamental research and genetic engineering
Y1  - 2022
U6  - https://doi.org/10.1007/s11103-022-01253-0
SN  - 0167-4412
SN  - 1573-5028
VL  - 108
IS  - 4-5
SP  - 289
EP  - 290
PB  - Springer
CY  - Dordrecht
ER  - 
TY  - JOUR
A1  - Küken, Anika
A1  - Langary, Damoun
A1  - Nikoloski, Zoran
T1  - The hidden simplicity of metabolic networks is revealed by multireaction dependencies
JF  - Science Advances
N2  - Understanding the complexity of metabolic networks has implications for manipulation of their functions. The complexity of metabolic networks can be characterized by identifying multireaction dependencies that are challenging to determine due to the sheer number of combinations to consider. Here, we propose the concept of concordant complexes that captures multireaction dependencies and can be efficiently determined from the algebraic structure and operational constraints of metabolic networks. The concordant complexes imply the existence of concordance modules based on which the apparent complexity of 12 metabolic networks of organisms from all kingdoms of life can be reduced by at least 78%. A comparative analysis against an ensemble of randomized metabolic networks shows that the metabolic network of Escherichia coli contains fewer concordance modules and is, therefore, more tightly coordinated than expected by chance. Together, our findings demonstrate that metabolic networks are considerably simpler than what can be perceived from their structure alone.
Y1  - 2022
U6  - https://doi.org/10.1126/sciadv.abl6962
SN  - 2375-2548
VL  - 8
IS  - 13
PB  - American Assoc. for the Advancement of Science
CY  - Washington
ER  -