@article{PohankovaHlavinkaKersebaumetal.2022, author = {Pohankov{\´a}, Eva and Hlavinka, Petr and Kersebaum, Kurt-Christian and Rodr{\´i}guez, Alfredo and Balek, Jan and Bednař{\´i}k, Martin and Dubrovsk{\´y}, Martin and Gobin, Anne and Hoogenboom, Gerrit and Moriondo, Marco and Nendel, Claas and Olesen, J{\o}rgen E. E. and R{\"o}tter, Reimund Paul and Ruiz-Ramos, Margarita and Shelia, Vakhtang and Stella, Tommaso and Hoffmann, Munir Paul and Tak{\´a}č, Jozef and Eitzinger, Josef and Dibari, Camilla and Ferrise, Roberto and Bl{\´a}hov{\´a}, Monika and Trnka, Miroslav}, title = {Expected effects of climate change on the production and water use of crop rotation management reproduced by crop model ensemble for Czech Republic sites}, series = {European journal of agronomy}, volume = {134}, journal = {European journal of agronomy}, publisher = {Elsevier}, address = {Amsterdam}, issn = {1161-0301}, doi = {10.1016/j.eja.2021.126446}, pages = {27}, year = {2022}, abstract = {Crop rotation, fertilization and residue management affect the water balance and crop production and can lead to different sensitivities to climate change. To assess the impacts of climate change on crop rotations (CRs), the crop model ensemble (APSIM,AQUACROP, CROPSYST, DAISY, DSSAT, HERMES, MONICA) was used. The yields and water balance of two CRs with the same set of crops (winter wheat, silage maize, spring barley and winter rape) in a continuous transient run from 1961 to 2080 were simulated. CR1 was without cover crops and without manure application. Straw after the harvest was exported from the fields. CR2 included cover crops, manure application and crop residue retention left on field. Simulations were performed using two soil types (Chernozem, Cambisol) within three sites in the Czech Republic, which represent temperature and precipitation gradients for crops in Central Europe. For the description of future climatic conditions, seven climate scenarios were used. Six of them had increasing CO \& nbsp;concentrations according RCP 8.5, one had no CO2 increase in the future. The output of an ensemble expected higher productivity by 0.82 t/ha/year and 2.04 t/ha/year for yields and aboveground biomass in the future (2051-2080). However, if the direct effect of a CO2 increase is not considered, the average yields for lowlands will be lower. Compared to CR1, CR2 showed higher average yields of 1.26 t/ha/year for current climatic conditions and 1.41 t/ha/year for future climatic conditions. For the majority of climate change scenarios, the crop model ensemble agrees on the projected yield increase in C3 crops in the future for CR2 but not for CR1. Higher agreement for future yield increases was found for Chernozem, while for Cambisol, lower yields under dry climate scenarios are expected. For silage maize, changes in simulated yields depend on locality. If the same hybrid will be used in the future, then yield reductions should be expected within lower altitudes. The results indicate the potential for higher biomass production from cover crops, but CR2 is associated with almost 120 mm higher evapotranspiration compared to that of CR1 over a 5-year cycle for lowland stations in the future, which in the case of the rainfed agriculture could affect the long-term soil water balance. This could affect groundwater replenishment, especially for locations with fine textured soils, although the findings of this study highlight the potential for the soil water-holding capacity to buffer against the adverse weather conditions.}, language = {en} } @article{WangHeWangetal.2022, author = {Wang, Enli and He, Di and Wang, Jing and Lilley, Julianne M. and Christy, Brendan and Hoffmann, Munir P. and O'Leary, Garry and Hatfield, Jerry L. and Ledda, Luigi and Deligios, Paola A. and Grant, Brian and Jing, Qi and Nendel, Claas and Kage, Henning and Qian, Budong and Rezaei, Ehsan Eyshi and Smith, Ward and Weymann, Wiebke and Ewert, Frank}, title = {How reliable are current crop models for simulating growth and seed yield of canola across global sites and under future climate change?}, series = {Climatic change}, volume = {172}, journal = {Climatic change}, number = {1-2}, publisher = {Springer Nature}, address = {Dordrecht}, issn = {0165-0009}, doi = {10.1007/s10584-022-03375-2}, pages = {22}, year = {2022}, abstract = {To better understand how climate change might influence global canola production, scientists from six countries have completed the first inter-comparison of eight crop models for simulating growth and seed yield of canola, based on experimental data from six sites across five countries. A sensitivity analysis was conducted with a combination of five levels of atmospheric CO2 concentrations, seven temperature changes, five precipitation changes, together with five nitrogen application rates. Our results were in several aspects different from those of previous model inter-comparison studies for wheat, maize, rice, and potato crops. A partial model calibration only on phenology led to very poor simulation of aboveground biomass and seed yield of canola, even from the ensemble median or mean. A full calibration with additional data of leaf area index, biomass, and yield from one treatment at each site reduced simulation error of seed yield from 43.8 to 18.0\%, but the uncertainty in simulation results remained large. Such calibration (with data from one treatment) was not able to constrain model parameters to reduce simulation uncertainty across the wide range of environments. Using a multi-model ensemble mean or median reduced the uncertainty of yield simulations, but the simulation error remained much larger than observation errors, indicating no guarantee that the ensemble mean/median would predict the correct responses. Using multi-model ensemble median, canola yield was projected to decline with rising temperature (2.5-5.7\% per degrees C), but to increase with increasing CO2 concentration (4.6-8.3\% per 100-ppm), rainfall (2.1-6.1\% per 10\% increase), and nitrogen rates (1.3-6.0\% per 10\% increase) depending on locations. Due to the large uncertainty, these results need to be treated with caution. We further discuss the need to collect new data to improve modelling of several key physiological processes of canola for increased confidence in future climate impact assessments.}, language = {en} } @article{McHuronAdamczakArnouldetal.2022, author = {McHuron, Elizabeth A. and Adamczak, Stephanie and Arnould, John P. Y. and Ashe, Erin and Booth, Cormac and Bowen, W. Don and Christiansen, Fredrik and Chudzinska, Magda and Costa, Daniel P. and Fahlman, Andreas and Farmer, Nicholas A. and Fortune, Sarah M. E. and Gallagher, Cara A. and Keen, Kelly A. and Madsen, Peter T. and McMahon, Clive R. and Nabe-Nielsen, Jacob and Noren, Dawn P. and Noren, Shawn R. and Pirotta, Enrico and Rosen, David A. S. and Speakman, Cassie N. and Villegas-Amtmann, Stella and Williams, Rob}, title = {Key questions in marine mammal bioenergetics}, series = {Conservation physiology}, volume = {10}, journal = {Conservation physiology}, number = {1}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {2051-1434}, doi = {10.1093/conphys/coac055}, pages = {17}, year = {2022}, abstract = {Bioenergetic approaches are increasingly used to understand how marine mammal populations could be affected by a changing and disturbed aquatic environment. There remain considerable gaps in our knowledge of marine mammal bioenergetics, which hinder the application of bioenergetic studies to inform policy decisions. We conducted a priority-setting exercise to identify high-priority unanswered questions in marine mammal bioenergetics, with an emphasis on questions relevant to conservation and management. Electronic communication and a virtual workshop were used to solicit and collate potential research questions from the marine mammal bioenergetic community. From a final list of 39 questions, 11 were identified as 'key'questions because they received votes from at least 50\% of survey participants. Key questions included those related to energy intake (prey landscapes, exposure to human activities) and expenditure (field metabolic rate, exposure to human activities, lactation, time-activity budgets), energy allocation priorities, metrics of body condition and relationships with survival and reproductive success and extrapolation of data from one species to another. Existing tools to address key questions include labelled water, animal-borne sensors, mark-resight data from long-term research programs, environmental DNA and unmanned vehicles. Further validation of existing approaches and development of new methodologies are needed to comprehensively address some key questions, particularly for cetaceans. The identification of these key questions can provide a guiding framework to set research priorities, which ultimately may yield more accurate information to inform policies and better conserve marine mammal populations.}, language = {en} } @article{SporbertJakubkaBucheretal.2022, author = {Sporbert, Maria and Jakubka, Desiree and Bucher, Solveig Franziska and Hensen, Isabell and Freiberg, Martin and Heubach, Katja and K{\"o}nig, Andreas and Nordt, Birgit and Plos, Carolin and Blinova, Ilona and Bonn, Aletta and Knickmann, Barbara and Koubek, Tom{\´a}š and Linst{\"a}dter, Anja and Maškov{\´a}, Tereza and Primack, Richard B. and Rosche, Christoph and Shah, Manzoor A. and Stevens, Albert-Dieter and Tielb{\"o}rger, Katja and Tr{\"a}ger, Sabrina and Wirth, Christian and R{\"o}mermann, Christine}, title = {Functional traits influence patterns in vegetative and reproductive plant phenology - a multi-botanical garden study}, series = {New phytologist}, volume = {235}, journal = {New phytologist}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0028-646X}, doi = {10.1111/nph.18345}, pages = {2199 -- 2210}, year = {2022}, abstract = {Phenology has emerged as key indicator of the biological impacts of climate change, yet the role of functional traits constraining variation in herbaceous species' phenology has received little attention. Botanical gardens are ideal places in which to investigate large numbers of species growing under common climate conditions. We ask whether interspecific variation in plant phenology is influenced by differences in functional traits. We recorded onset, end, duration and intensity of initial growth, leafing out, leaf senescence, flowering and fruiting for 212 species across five botanical gardens in Germany. We measured functional traits, including plant height, absolute and specific leaf area, leaf dry matter content, leaf carbon and nitrogen content and seed mass and accounted for species' relatedness. Closely related species showed greater similarities in timing of phenological events than expected by chance, but species' traits had a high degree of explanatory power, pointing to paramount importance of species' life-history strategies. Taller plants showed later timing of initial growth, and flowered, fruited and underwent leaf senescence later. Large-leaved species had shorter flowering and fruiting durations. Taller, large-leaved species differ in their phenology and are more competitive than smaller, small-leaved species. We assume climate warming will change plant communities' competitive hierarchies with consequences for biodiversity.}, language = {en} } @article{VencesKoehlerCrottinietal.2022, author = {Vences, Miguel and K{\"o}hler, J{\"o}rn and Crottini, Angelica and Hofreiter, Michael and Hutter, Carl R. and du Preez, Louis and Preick, Michaela and Rakotoarison, Andolalao and Rancilhac, Lo{\"i}s and Raselimanana, Achille P. and Rosa, Gon{\c{c}}alo M. and Scherz, Mark D. and Glaw, Frank}, title = {An integrative taxonomic revision and redefinition of Gephyromantis (Laurentomantis) malagasius based on archival DNA analysis reveals four new mantellid frog species from Madagascar}, series = {Vertebrate zoology}, volume = {72}, journal = {Vertebrate zoology}, publisher = {Senckenberg Gesellschaft f{\"u}r Naturforschung}, address = {Frankfurt am Main}, issn = {1864-5755}, doi = {10.3897/vz.72.e78830}, pages = {271 -- 309}, year = {2022}, abstract = {The subgenus Laurentomantis in the genus Gephyromantis contains some of the least known amphibian species of Madagascar. The six currently valid nominal species are rainforest frogs known from few individuals, hampering a full understanding of the species diversity of the clade. We assembled data on specimens collected during field surveys over the past 30 years and integrated analysis of mitochondrial and nuclear-encoded genes of 88 individuals, a comprehensive bioacoustic analysis, and morphological comparisons to delimit a minimum of nine species-level lineages in the subgenus. To clarify the identity of the species Gephyromantis malagasius, we applied a target-enrichment approach to a sample of the 110 year old holotype of Microphryne malagasia Methuen and Hewitt, 1913 to assign this specimen to a lineage based on a mitochondrial DNA barcode. The holotype clustered unambiguously with specimens previously named G. ventrimaculatus. Consequently we propose to consider Trachymantis malagasia ventrimaculatus Angel, 1935 as a junior synonym of Gephyromantis malagasius. Due to this redefinition of G. malagasius, no scientific name is available for any of the four deep lineages of frogs previously subsumed under this name, all characterized by red color ventrally on the hindlimbs. These are here formally named as Gephyromantis fiharimpe sp. nov., G. matsilo sp. nov., G. oelkrugi sp. nov., and G. portonae sp. nov. The new species are distinguishable from each other by genetic divergences of >4\% uncorrected pairwise distance in a fragment of the 16S rRNA marker and a combination of morphological and bioacoustic characters. Gephyromantis fiharimpe and G. matsilo occur, respectively, at mid-elevations and lower elevations along a wide stretch of Madagascar's eastern rainforest band, while G. oelkrugi and G. portonae appear to be more range-restricted in parts of Madagascar's North East and Northern Central East regions. Open taxonomic questions surround G. horridus, to which we here assign specimens from Montagne d'Ambre and the type locality Nosy Be; and G. ranjomavo, which contains genetically divergent populations from Marojejy, Tsaratanana, and Ampotsidy.}, language = {en} } @article{EsmaeilishirazifardUsherTrimetal.2022, author = {Esmaeilishirazifard, Elham and Usher, Louise and Trim, Carol and Denise, Hubert and Sangal, Vartul and Tyson, Gregory H. and Barlow, Axel and Redway, Keith F. and Taylor, John D. and Kremyda-Vlachou, Myrto and Davies, Sam and Loftus, Teresa D. and Lock, Mikaella M. G. and Wright, Kstir and Dalby, Andrew and Snyder, Lori A. S. and Wuster, Wolfgang and Trim, Steve and Moschos, Sterghios A.}, title = {Bacterial adaptation to venom in snakes and arachnida}, series = {Microbiology spectrum}, volume = {10}, journal = {Microbiology spectrum}, number = {3}, publisher = {American Society for Microbiology}, address = {Birmingham, Ala.}, issn = {2165-0497}, doi = {10.1128/spectrum.02408-21}, pages = {16}, year = {2022}, abstract = {Notwithstanding their 3 to 5\% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75\% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Animal venoms are considered sterile sources of antimicrobial compounds with strong membrane-disrupting activity against multidrug-resistant bacteria. However, venomous bite wound infections are common in developing nations. Investigating the envenomation organ and venom microbiota of five snake and two spider species, we observed venom community structures that depend on the host venomous animal species and evidenced recovery of viable microorganisms from black-necked spitting cobra (Naja nigricollis) and Indian ornamental tarantula (Poecilotheria regalis) venoms. Among the bacterial isolates recovered from N. nigricollis, we identified two venom-resistant, novel sequence types of Enterococcus faecalis whose genomes feature 16 virulence genes, indicating infectious potential, and 45 additional genes, nearly half of which improve bacterial membrane integrity. Our findings challenge the dogma of venom sterility and indicate an increased primary infection risk in the clinical management of venomous animal bite wounds. IMPORTANCE Notwithstanding their 3 to 5\% mortality, the 2.7 million envenomation-related injuries occurring annually-predominantly across Africa, Asia, and Latin America-are also major causes of morbidity. Venom toxin-damaged tissue will develop infections in some 75\% of envenomation victims, with E. faecalis being a common culprit of disease; however, such infections are generally considered to be independent of envenomation. Here, we provide evidence on venom microbiota across snakes and arachnida and report on the convergent evolution mechanisms that can facilitate adaptation to black-necked cobra venom in two independent E. faecalis strains, easily misidentified by biochemical diagnostics. Therefore, since inoculation with viable and virulence gene-harboring bacteria can occur during envenomation, acute infection risk management following envenomation is warranted, particularly for immunocompromised and malnourished victims in resource-limited settings. These results shed light on how bacteria evolve for survival in one of the most extreme environments on Earth and how venomous bites must be also treated for infections.}, language = {en} } @article{RiemannRahavPassowetal.2022, author = {Riemann, Lasse and Rahav, Eyal and Passow, Uta and Grossart, Hans-Peter and de Beer, Dirk and Klawonn, Isabell and Eichner, Meri and Benavides, Mar and Bar-Zeev, Edo}, title = {Planktonic aggregates as hotspots for heterotrophic diazotrophy: the plot thickens}, series = {Frontiers in microbiology}, volume = {13}, journal = {Frontiers in microbiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2022.875050}, pages = {9}, year = {2022}, abstract = {Biological dinitrogen (N-2) fixation is performed solely by specialized bacteria and archaea termed diazotrophs, introducing new reactive nitrogen into aquatic environments. Conventionally, phototrophic cyanobacteria are considered the major diazotrophs in aquatic environments. However, accumulating evidence indicates that diverse non-cyanobacterial diazotrophs (NCDs) inhabit a wide range of aquatic ecosystems, including temperate and polar latitudes, coastal environments and the deep ocean. NCDs are thus suspected to impact global nitrogen cycling decisively, yet their ecological and quantitative importance remain unknown. Here we review recent molecular and biogeochemical evidence demonstrating that pelagic NCDs inhabit and thrive especially on aggregates in diverse aquatic ecosystems. Aggregates are characterized by reduced-oxygen microzones, high C:N ratio (above Redfield) and high availability of labile carbon as compared to the ambient water. We argue that planktonic aggregates are important loci for energetically-expensive N-2 fixation by NCDs and propose a conceptual framework for aggregate-associated N-2 fixation. Future studies on aggregate-associated diazotrophy, using novel methodological approaches, are encouraged to address the ecological relevance of NCDs for nitrogen cycling in aquatic environments.}, language = {en} } @article{SchulteMeucciStoofLeichsenringetal.2022, author = {Schulte, Luise and Meucci, Stefano and Stoof-Leichsenring, Kathleen R. and Heitkam, Tony and Schmidt, Nicola and von Hippel, Barbara and Andreev, Andrei A. and Diekmann, Bernhard and Biskaborn, Boris and Wagner, Bernd and Melles, Martin and Pestryakova, Lyudmila A. and Alsos, Inger G. and Clarke, Charlotte and Krutovsky, Konstantin and Herzschuh, Ulrike}, title = {Larix species range dynamics in Siberia since the Last Glacial captured from sedimentary ancient DNA}, series = {Communications biology}, volume = {5}, journal = {Communications biology}, number = {1}, publisher = {Springer Nature}, address = {London}, issn = {2399-3642}, doi = {10.1038/s42003-022-03455-0}, pages = {11}, year = {2022}, abstract = {Climate change is expected to cause major shifts in boreal forests which are in vast areas of Siberia dominated by two species of the deciduous needle tree larch (Larix). The species differ markedly in their ecosystem functions, thus shifts in their respective ranges are of global relevance. However, drivers of species distribution are not well understood, in part because paleoecological data at species level are lacking. This study tracks Larix species distribution in time and space using target enrichment on sedimentary ancient DNA extracts from eight lakes across Siberia. We discovered that Larix sibirica, presently dominating in western Siberia, likely migrated to its northern distribution area only in the Holocene at around 10,000 years before present (ka BP), and had a much wider eastern distribution around 33 ka BP. Samples dated to the Last Glacial Maximum (around 21 ka BP), consistently show genotypes of L. gmelinii. Our results suggest climate as a strong determinant of species distribution in Larix and provide temporal and spatial data for species projection in a changing climate. Using ancient sedimentary DNA from up to 50 kya, dramatic distributional shifts are documented in two dominant boreal larch species, likely guided by environmental changes suggesting climate as a strong determinant of species distribution.}, language = {en} } @article{LopezSanchezBarethBoltenetal.2021, author = {L{\´o}pez-S{\´a}nchez, Aida and Bareth, Georg and Bolten, Andreas and Rose, Laura E. and Mansfeldt, Tim and Sapp, Melanie and Linst{\"a}dter, Anja}, title = {Effects of declining oak vitality on ecosystem multifunctionality}, series = {Forest ecology and management}, volume = {484}, journal = {Forest ecology and management}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0378-1127}, doi = {10.1016/j.foreco.2021.118927}, pages = {12}, year = {2021}, abstract = {Mediterranean oak woodlands are currently facing unprecedented degradation threats from oak decline. The Iberian oak decline "Seca", related to Phytophthora infection, causes crown defoliation that may adversely affect ecosystem services (ESs). We aim to improve our understanding of how Seca-induced declines in crown foliation affect the provision of multiple ecosystem services from understory vegetation. We selected holm (Quercus ilex) and cork oak (Q. suber) trees in a Spanish oak woodland and evaluated three proxies of canopy effects. One proxy (crown defoliation) solely captured Seca-dependent effects, one proxy solely captured Seca-independent effects (tree dimensions such as diameter and height), while the third proxy (tree vigor) captured overall canopy effects. We then used the best-performing proxies to assess canopy effects on key ecosystem services (ESs) such as aboveground net primary production (ANPP), grass and legume biomass, species diversity, litter decomposition rates, and a combined index of ecosystem multifunctionality.
We found that both types of canopy effects (i.e. Seca-dependent and Seca-independent effects) were related, indicating that ANPP was disproportionally more affected by Seca when defoliated trees were large. Responses of other ESs were mostly not significant, although lower species diversity was found under trees with intermediate vigor. Our results underline that a Seca-related decline in canopy density triggered a homogenization of ecosystem service delivery on the ecosystem scale. The ecosystem functions (EFs) under trees of low vigor are similar to that in adjacent open microsites indicating that the presence of vigorous (i.e. old and vital) trees is critical for maintaining EFs at a landscape level. Our results also highlight the importance of quantifying not only defoliation but also tree dimensions as both factors jointly and interactively modify canopy effects on ecosystem multifunctionality.}, language = {en} } @article{DunkerBoydDurkaetal.2022, author = {Dunker, Susanne and Boyd, Matthew and Durka, Walter and Erler, Silvio and Harpole, W. Stanley and Henning, Silvia and Herzschuh, Ulrike and Hornick, Thomas and Knight, Tiffany and Lips, Stefan and M{\"a}der, Patrick and Švara, Elena Motivans and Mozarowski, Steven and Rakosy, Demetra and R{\"o}mermann, Christine and Schmitt-Jansen, Mechthild and Stoof-Leichsenring, Kathleen and Stratmann, Frank and Treudler, Regina and Virtanen, Risto and Wendt-Potthoff, Katrin and Wilhelm, Christian}, title = {The potential of multispectral imaging flow cytometry for environmental monitoring}, series = {Cytometry part A}, volume = {101}, journal = {Cytometry part A}, number = {9}, publisher = {Wiley}, address = {Hoboken}, issn = {1552-4922}, doi = {10.1002/cyto.a.24658}, pages = {782 -- 799}, year = {2022}, abstract = {Environmental monitoring involves the quantification of microscopic cells and particles such as algae, plant cells, pollen, or fungal spores. Traditional methods using conventional microscopy require expert knowledge, are time-intensive and not well-suited for automated high throughput. Multispectral imaging flow cytometry (MIFC) allows measurement of up to 5000 particles per second from a fluid suspension and can simultaneously capture up to 12 images of every single particle for brightfield and different spectral ranges, with up to 60x magnification. The high throughput of MIFC has high potential for increasing the amount and accuracy of environmental monitoring, such as for plant-pollinator interactions, fossil samples, air, water or food quality that currently rely on manual microscopic methods. Automated recognition of particles and cells is also possible, when MIFC is combined with deep-learning computational techniques. Furthermore, various fluorescence dyes can be used to stain specific parts of the cell to highlight physiological and chemical features including: vitality of pollen or algae, allergen content of individual pollen, surface chemical composition (carbohydrate coating) of cells, DNA- or enzyme-activity staining. Here, we outline the great potential for MIFC in environmental research for a variety of research fields and focal organisms. In addition, we provide best practice recommendations.}, language = {en} } @article{GrohDiamantopoulosDuanetal.2022, author = {Groh, Jannis and Diamantopoulos, Efstathios and Duan, Xiaohong and Ewert, Frank and Heinlein, Florian and Herbst, Michael and Holbak, Maja and Kamali, Bahareh and Kersebaum, Kurt-Christian and Kuhnert, Matthias and Nendel, Claas and Priesack, Eckart and Steidl, J{\"o}rg and Sommer, Michael and P{\"u}tz, Thomas and Vanderborght, Jan and Vereecken, Harry and Wallor, Evelyn and Weber, Tobias K. D. and Wegehenkel, Martin and Weiherm{\"u}ller, Lutz and Gerke, Horst H.}, title = {Same soil, different climate: Crop model intercomparison on translocated lysimeters}, series = {Vadose zone journal}, volume = {21}, journal = {Vadose zone journal}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1539-1663}, doi = {10.1002/vzj2.20202}, pages = {25}, year = {2022}, abstract = {Crop model intercomparison studies have mostly focused on the assessment of predictive capabilities for crop development using weather and basic soil data from the same location. Still challenging is the model performance when considering complex interrelations between soil and crop dynamics under a changing climate. The objective of this study was to test the agronomic crop and environmental flux-related performance of a set of crop models. The aim was to predict weighing lysimeter-based crop (i.e., agronomic) and water-related flux or state data (i.e., environmental) obtained for the same soil monoliths that were taken from their original environment and translocated to regions with different climatic conditions, after model calibration at the original site. Eleven models were deployed in the study. The lysimeter data (2014-2018) were from the Dedelow (Dd), Bad Lauchstadt (BL), and Selhausen (Se) sites of the TERENO (TERrestrial ENvironmental Observatories) SOILCan network. Soil monoliths from Dd were transferred to the drier and warmer BL site and the wetter and warmer Se site, which allowed a comparison of similar soil and crop under varying climatic conditions. The model parameters were calibrated using an identical set of crop- and soil-related data from Dd. Environmental fluxes and crop growth of Dd soil were predicted for conditions at BL and Se sites using the calibrated models. The comparison of predicted and measured data of Dd lysimeters at BL and Se revealed differences among models. At site BL, the crop models predicted agronomic and environmental components similarly well. Model performance values indicate that the environmental components at site Se were better predicted than agronomic ones. The multi-model mean was for most observations the better predictor compared with those of individual models. For Se site conditions, crop models failed to predict site-specific crop development indicating that climatic conditions (i.e., heat stress) were outside the range of variation in the data sets considered for model calibration. For improving predictive ability of crop models (i.e., productivity and fluxes), more attention should be paid to soil-related data (i.e., water fluxes and system states) when simulating soil-crop-climate interrelations in changing climatic conditions.}, language = {en} } @article{CaoChenTianetal.2022, author = {Cao, Xianyong and Chen, Jianhui and Tian, Fang and Xu, Qinghai and Herzschuh, Ulrike and Telford, Richard and Huang, Xiaozhong and Zheng, Zhuo and Shen, Caiming and Li, Wenjia}, title = {Long-distance modern analogues bias results of pollen-based precipitation reconstructions}, series = {Science bulletin}, volume = {67}, journal = {Science bulletin}, number = {11}, publisher = {Elsevier}, address = {Amsterdam}, issn = {2095-9273}, doi = {10.1016/j.scib.2022.01.003}, pages = {1115 -- 1117}, year = {2022}, language = {en} } @article{SedaghatmehrThirumalaikumarKamranfaretal.2021, author = {Sedaghatmehr, Mastoureh and Thirumalaikumar, Venkatesh P. and Kamranfar, Iman and Schulz, Karina and M{\"u}ller-R{\"o}ber, Bernd and Sampathkumar, Arun and Balazadeh, Salma}, title = {Autophagy complements metalloprotease FtsH6 in degrading plastid heat shock protein HSP21 during heat stress recovery}, series = {The journal of experimental botany : an official publication of the Society for Experimental Biology and of the Federation of European Societies of Plant Physiology}, volume = {72}, journal = {The journal of experimental botany : an official publication of the Society for Experimental Biology and of the Federation of European Societies of Plant Physiology}, number = {21}, publisher = {Oxford University Press}, address = {Oxford}, issn = {0022-0957}, doi = {10.1093/jxb/erab304}, pages = {7498 -- 7513}, year = {2021}, abstract = {Moderate and temporary heat stresses prime plants to tolerate, and survive, a subsequent severe heat stress. Such acquired thermotolerance can be maintained for several days under normal growth conditions, and can create a heat stress memory. We recently demonstrated that plastid-localized small heat shock protein 21 ( HSP21) is a key component of heat stress memory in Arabidopsis thaliana. A sustained high abundance of HSP21 during the heat stress recovery phase extends heat stress memory. The level of HSP21 is negatively controlled by plastid-localized metalloprotease FtsH6 during heat stress recovery. Here, we demonstrate that autophagy, a cellular recycling mechanism, exerts additional control over HSP21 degradation. Genetic and chemical disruption of both metalloprotease activity and autophagy trigger superior HSP21 accumulation, thereby improving memory. Furthermore, we provide evidence that autophagy cargo receptor ATG8-INTERACTING PROTEIN1 (ATI1) is associated with heat stress memory. ATI1 bodies co-localize with both autophagosomes and HSP21, and their abundance and transport to the vacuole increase during heat stress recovery. Together, our results provide new insights into the module for control of the regulation of heat stress memory, in which two distinct protein degradation pathways act in concert to degrade HSP21, thereby enabling cells to recover from the heat stress effect at the cost of reducing the heat stress memory.}, language = {en} } @article{VandenWyngaertGanzertSetoetal.2022, author = {Van den Wyngaert, Silke and Ganzert, Lars and Seto, Kensuke and Rojas-Jimenez, Keilor and Agha, Ramsy and Berger, Stella A. and Woodhouse, Jason and Padisak, Judit and Wurzbacher, Christian and Kagami, Maiko and Grossart, Hans-Peter}, title = {Seasonality of parasitic and saprotrophic zoosporic fungi: linking sequence data to ecological traits}, series = {ISME journal}, volume = {16}, journal = {ISME journal}, number = {9}, publisher = {Springer Nature}, address = {London}, issn = {1751-7362}, doi = {10.1038/s41396-022-01267-y}, pages = {2242 -- 2254}, year = {2022}, abstract = {Zoosporic fungi of the phylum Chytridiomycota (chytrids) regularly dominate pelagic fungal communities in freshwater and marine environments. Their lifestyles range from obligate parasites to saprophytes. Yet, linking the scarce available sequence data to specific ecological traits or their host ranges constitutes currently a major challenge. We combined 28 S rRNA gene amplicon sequencing with targeted isolation and sequencing approaches, along with cross-infection assays and analysis of chytrid infection prevalence to obtain new insights into chytrid diversity, ecology, and seasonal dynamics in a temperate lake. Parasitic phytoplankton-chytrid and saprotrophic pollen-chytrid interactions made up the majority of zoosporic fungal reads. We explicitly demonstrate the recurrent dominance of parasitic chytrids during frequent diatom blooms and saprotrophic chytrids during pollen rains. Distinct temporal dynamics of diatom-specific parasitic clades suggest mechanisms of coexistence based on niche differentiation and competitive strategies. The molecular and ecological information on chytrids generated in this study will aid further exploration of their spatial and temporal distribution patterns worldwide. To fully exploit the power of environmental sequencing for studies on chytrid ecology and evolution, we emphasize the need to intensify current isolation efforts of chytrids and integrate taxonomic and autecological data into long-term studies and experiments.}, language = {en} } @article{GorinScherzKorostetal.2021, author = {Gorin, Vladislav A. and Scherz, Mark D. and Korost, Dmitry V. and Poyarkov, Nikolay A.}, title = {Consequences of parallel miniaturisation in Microhylinae (Anura, Microhylidae), with the description of a new genus of diminutive South East Asian frogs}, series = {Zoosystematics and evolution : Mitteilungen aus dem Museum f{\"u}r Naturkunde in Berlin}, volume = {97}, journal = {Zoosystematics and evolution : Mitteilungen aus dem Museum f{\"u}r Naturkunde in Berlin}, number = {1}, publisher = {Pensoft Publishers}, address = {Sofia}, issn = {1860-0743}, doi = {10.3897/zse.97.57968}, pages = {21 -- 54}, year = {2021}, abstract = {The genus Microhyla Tschudi, 1838 includes 52 species and is one of the most diverse genera of the family Microhylidae, being the most species-rich taxon of the Asian subfamily Microhylinae. The recent, rapid description of numerous new species of Microhyla with complex phylogenetic relationships has made the taxonomy of the group especially challenging. Several recent phylogenetic studies suggested paraphyly of Microhyla with respect to Glyphoglossus Gunther, 1869, and revealed three major phylogenetic lineages of mid-Eocene origin within this assemblage. However, comprehensive works assessing morphological variation among and within these lineages are absent. In the present study we investigate the generic taxonomy of Microhyla-Glyphoglossus assemblage based on a new phylogeny including 57 species, comparative morphological analysis of skeletons from cleared-and-stained specimens for 23 species, and detailed descriptions of generalized osteology based on volume-rendered micro-CT scans for five speciesal-together representing all major lineages within the group. The results confirm three highly divergent and well-supported clades that correspond with external and osteological morphological characteristics, as well as respective geographic distribution. Accordingly, acknowledging ancient divergence between these lineages and their significant morphological differentiation, we propose to consider these three lineages as distinct genera: Microhyla sensu stricto, Glyphoglossus, and a newly described genus, Nanohyla gen. nov.}, language = {en} } @article{SchmidtReilJeskeetal.2021, author = {Schmidt, Sabrina and Reil, Daniela and Jeske, Kathrin and Drewes, Stephan and Rosenfeld, Ulrike and Fischer, Stefan and Spierling, Nastasja G. and Labutin, Anton and Heckel, Gerald and Jacob, Jens and Ulrich, Rainer G. and Imholt, Christian}, title = {Spatial and temporal dynamics and molecular evolution of Tula orthohantavirus in German vole populations}, series = {Viruses / Molecular Diversity Preservation International (MDPI)}, volume = {13}, journal = {Viruses / Molecular Diversity Preservation International (MDPI)}, number = {6}, publisher = {MDPI}, address = {Basel}, issn = {1999-4915}, doi = {10.3390/v13061132}, pages = {17}, year = {2021}, abstract = {Tula orthohantavirus (TULV) is a rodent-borne hantavirus with broad geographical distribution in Europe. Its major reservoir is the common vole (Microtus arvalis), but TULV has also been detected in closely related vole species. Given the large distributional range and high amplitude population dynamics of common voles, this host-pathogen complex presents an ideal system to study the complex mechanisms of pathogen transmission in a wild rodent reservoir. We investigated the dynamics of TULV prevalence and the subsequent potential effects on the molecular evolution of TULV in common voles of the Central evolutionary lineage. Rodents were trapped for three years in four regions of Germany and samples were analyzed for the presence of TULV-reactive antibodies and TULV RNA with subsequent sequence determination. The results show that individual (sex) and population-level factors (abundance) of hosts were significant predictors of local TULV dynamics. At the large geographic scale, different phylogenetic TULV clades and an overall isolation-by-distance pattern in virus sequences were detected, while at the small scale (<4 km) this depended on the study area. In combination with an overall delayed density dependence, our results highlight that frequent, localized bottleneck events for the common vole and TULV do occur and can be offset by local recolonization dynamics.}, language = {en} } @article{BelluardoScherzSantosetal.2022, author = {Belluardo, Francesco and Scherz, Mark D. and Santos, Barbara and Andreone, Franco and Antonelli, Alexandre and Glaw, Frank and Munoz-Pajares, A. Jesus and Randrianirina, Jasmin E. and Raselimanana, Achille P. and Vences, Miguel and Crottini, Angelica}, title = {Molecular taxonomic identification and species-level phylogeny of the narrow-mouthed frogs of the genus Rhombophryne (Anura: Microhylidae: Cophylinae) from Madagascar}, series = {Systematics and biodiversity}, volume = {20}, journal = {Systematics and biodiversity}, number = {1}, publisher = {Routledge, Taylor \& Francis Group}, address = {Abingdon}, issn = {1477-2000}, doi = {10.1080/14772000.2022.2039320}, pages = {1 -- 13}, year = {2022}, abstract = {The study of diamond frogs (genus Rhombophryne, endemic to Madagascar) has been historically hampered by the paucity of available specimens, because of their low detectability in the field. Over the last 10 years, 13 new taxa have been described, and 20 named species are currently recognized. Nevertheless, undescribed diversity within the genus is probably large, calling for a revision of the taxonomic identification of published records and an update of the known distribution of each lineage. Here we generate DNA sequences of the mitochondrial 16S rRNA gene of all specimens available to us, revise the genetic data from public databases, and report all deeply divergent mitochondrial lineages of Rhombophryne identifiable from these data. We also generate a multi-locus dataset (including five mitochondrial and eight nuclear markers; 9844 bp) to infer a species-level phylogenetic hypothesis for the diversification of this genus and revise the distribution of each lineage. We recognize a total of 10 candidate species, two of which are identified here for the first time. The genus Rhombophryne is here proposed to be divided into six main species groups, and phylogenetic relationships among some of them are not fully resolved. These frogs are primarily distributed in northern Madagascar, and most species are known from only few localities. A previous record of this genus from the Tsingy de Bemaraha (western Madagascar) is interpreted as probably due to a mislabelling and should not be considered further unless confirmed by new data. By generating this phylogenetic hypothesis and providing an updated distribution of each lineage, our findings will facilitate future species descriptions, pave the way for evolutionary studies, and provide valuable information for the urgent conservation of diamond frogs.}, language = {en} } @article{GarbulowskiSmolinskaCabuketal.2022, author = {Garbulowski, Mateusz and Smolinska, Karolina and {\c{C}}abuk, Uğur and Yones, Sara A. and Celli, Ludovica and Yaz, Esma Nur and Barrenas, Fredrik and Diamanti, Klev and Wadelius, Claes and Komorowski, Jan}, title = {Machine learning-based analysis of glioma grades reveals co-enrichment}, series = {Cancers}, volume = {14}, journal = {Cancers}, number = {4}, publisher = {MDPI}, address = {Basel}, issn = {2072-6694}, doi = {10.3390/cancers14041014}, pages = {19}, year = {2022}, abstract = {Simple Summary Gliomas are heterogenous types of cancer, therefore the therapy should be personalized and targeted toward specific pathways. We developed a methodology that corrected strong batch effects from The Cancer Genome Atlas datasets and estimated glioma grade-specific co-enrichment mechanisms using machine learning. Our findings created hypotheses for annotations, e.g., pathways, that should be considered as therapeutic targets. Gliomas develop and grow in the brain and central nervous system. Examining glioma grading processes is valuable for improving therapeutic challenges. One of the most extensive repositories storing transcriptomics data for gliomas is The Cancer Genome Atlas (TCGA). However, such big cohorts should be processed with caution and evaluated thoroughly as they can contain batch and other effects. Furthermore, biological mechanisms of cancer contain interactions among biomarkers. Thus, we applied an interpretable machine learning approach to discover such relationships. This type of transparent learning provides not only good predictability, but also reveals co-predictive mechanisms among features. In this study, we corrected the strong and confounded batch effect in the TCGA glioma data. We further used the corrected datasets to perform comprehensive machine learning analysis applied on single-sample gene set enrichment scores using collections from the Molecular Signature Database. Furthermore, using rule-based classifiers, we displayed networks of co-enrichment related to glioma grades. Moreover, we validated our results using the external glioma cohorts. We believe that utilizing corrected glioma cohorts from TCGA may improve the application and validation of any future studies. Finally, the co-enrichment and survival analysis provided detailed explanations for glioma progression and consequently, it should support the targeted treatment.}, language = {en} } @article{AgarwalHamidizadehBier2023, author = {Agarwal, Saloni and Hamidizadeh, Mojdeh and Bier, Frank Fabian}, title = {Detection of reverse transcriptase LAMP-amplified nucleic acid from oropharyngeal viral swab samples using biotinylated DNA probes through a lateral flow assay}, series = {Biosensors : open access journal}, volume = {13}, journal = {Biosensors : open access journal}, number = {11}, publisher = {MDPI}, address = {Basel}, issn = {2079-6374}, doi = {10.3390/bios13110988}, pages = {15}, year = {2023}, abstract = {This study focuses on three key aspects: (a) crude throat swab samples in a viral transport medium (VTM) as templates for RT-LAMP reactions; (b) a biotinylated DNA probe with enhanced specificity for LFA readouts; and (c) a digital semi-quantification of LFA readouts. Throat swab samples from SARS-CoV-2 positive and negative patients were used in their crude (no cleaning or pre-treatment) forms for the RT-LAMP reaction. The samples were heat-inactivated but not treated for any kind of nucleic acid extraction or purification. The RT-LAMP (20 min processing time) product was read out by an LFA approach using two labels: FITC and biotin. FITC was enzymatically incorporated into the RT-LAMP amplicon with the LF-LAMP primer, and biotin was introduced using biotinylated DNA probes, specifically for the amplicon region after RT-LAMP amplification. This assay setup with biotinylated DNA probe-based LFA readouts of the RT-LAMP amplicon was 98.11\% sensitive and 96.15\% specific. The LFA result was further analysed by a smartphone-based IVD device, wherein the T-line intensity was recorded. The LFA T-line intensity was then correlated with the qRT-PCR Ct value of the positive swab samples. A digital semi-quantification of RT-LAMP-LFA was reported with a correlation coefficient of R2 = 0.702. The overall RT-LAMP-LFA assay time was recorded to be 35 min with a LoD of three RNA copies/µL (Ct-33). With these three advancements, the nucleic acid testing-point of care technique (NAT-POCT) is exemplified as a versatile biosensor platform with great potential and applicability for the detection of pathogens without the need for sample storage, transportation, or pre-processing.}, language = {en} } @article{NumbergerZoccaratoWoodhouseetal.2022, author = {Numberger, Daniela and Zoccarato, Luca and Woodhouse, Jason Nicholas and Ganzert, Lars and Sauer, Sascha and Garc{\´i}a M{\´a}rquez, Jaime Ricardo and Domisch, Sami and Grossart, Hans-Peter and Greenwood, Alex}, title = {Urbanization promotes specific bacteria in freshwater microbiomes including potential pathogens}, series = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, volume = {845}, journal = {The science of the total environment : an international journal for scientific research into the environment and its relationship with man}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0048-9697}, doi = {10.1016/j.scitotenv.2022.157321}, pages = {13}, year = {2022}, abstract = {Freshwater ecosystems are characterized by complex and highly dynamic microbial communities that are strongly structured by their local environment and biota. Accelerating urbanization and growing city populations detrimentally alter freshwater environments. To determine differences in freshwater microbial communities associated with urban-ization, full-length 16S rRNA gene PacBio sequencing was performed in a case study from surface waters and sedi-ments from a wastewater treatment plant, urban and rural lakes in the Berlin-Brandenburg region, Northeast Germany. Water samples exhibited highly habitat specific bacterial communities with multiple genera showing clear urban signatures. We identified potentially harmful bacterial groups associated with environmental parameters specific to urban habitats such as Alistipes, Escherichia/Shigella, Rickettsia and Streptococcus. We demonstrate that urban-ization alters natural microbial communities in lakes and, via simultaneous warming and eutrophication and creates favourable conditions that promote specific bacterial genera including potential pathogens. Our findings are evidence to suggest an increased potential for long-term health risk in urbanized waterbodies, at a time of rapidly expanding global urbanization. The results highlight the urgency for undertaking mitigation measures such as targeted lake restoration projects and sustainable water management efforts.}, language = {en} }