TY - JOUR A1 - Muro, Javier A1 - Linstädter, Anja A1 - Magdon, Paul A1 - Woellauer, Stephan A1 - Männer, Florian A. A1 - Schwarz, Lisa-Maricia A1 - Ghazaryan, Gohar A1 - Schultz, Johannes A1 - Malenovsky, Zbynek A1 - Dubovyk, Olena T1 - Predicting plant biomass and species richness in temperate grasslands across regions, time, and land management with remote sensing and deep learning JF - Remote sensing of environment : an interdisciplinary journal N2 - Spatial predictions of biomass production and biodiversity at regional scale in grasslands are critical to evaluate the effects of management practices across environmental gradients. New generations of remote sensing sensors and machine learning approaches can predict these grassland characteristics with varying accuracy. However, such studies frequently fail to cover a sufficiently broad range of environmental conditions, and their prediction models are often case-specific. To address this gap, we have modelled above-ground biomass and species richness in 150 spatially independent grassland plots of three geographical regions in Germany. These regions follow a North-South climate gradient and differ in soil types, topography, elevation, climatic conditions, historical contexts, and management intensities. The predictors tested in this study are Sentinel-1 backscatter, Sentinel-2 time series of surface reflectance along with derived vegetation indices and Rao's Q, and a set of topoedaphic variables. We compared the performance of a feed-forward deep neural network (DNN) with a random forest (RF) regression algorithm. The DNN achieved the best estimations of biomass (r2 = 0.45) when trained with Sentinel-2 surface reflectance only. Moreover, the DNN showed a higher generalizability than RF during spatial cross-validations (i.e., calibrating and validating in different regions, r2 = 0.38 vs. 0.26). Species richness pre-dictions by both algorithms improved when the full time series of Sentinel-2 surface reflectance values were used (highest r2 = 0.42 achieved by the DNN), but both performed poorly during spatial cross-validations. Overall, the DNN-based models were more robust than RF models, showed a lower bias and lower systematic error, and required fewer inputs. Explainability analysis indicated that red-edge and near infrared information from May and October was the most relevant to predict species richness. This study presents an important step forward in generating robust spatially explicit predictions of grassland attributes and biodiversity variables across large areas, environmental gradients, and phenological stages. KW - Sentinel-1 KW - biodiversity KW - Machine learning KW - Modelling KW - Rao ?s Q; KW - Sentinel-2 Y1 - 2022 U6 - https://doi.org/10.1016/j.rse.2022.113262 SN - 0034-4257 SN - 1879-0704 VL - 282 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Flemer, Burkhardt A1 - Gulati, Sneha A1 - Bergna, Alessandro A1 - Rändler, Manuela A1 - Cernava, Tomislav A1 - Witzel, Katja A1 - Berg, Gabriele A1 - Grosch, Rita T1 - Biotic and abiotic stress factors induce microbiome shifts and enrichment of distinct beneficial bacteria in tomato roots JF - Phytobiomes journal N2 - Crops are often simultaneously threatened by abiotic and biotic stress factors but the stress response of the plant holobiont is not well understood, despite the high importance of this response to ensure future plant production. Therefore, the aim of this study was to assess the impact of individual and combined abiotic (ionic and osmotic) and biotic ( Verticillium dahliae and Fusarium oxysporum) stress factors on plant performance and on the bacterial composition of the root endosphere in tomato. Structure and function of the microbiota was analyzed by 16S ribosomal RNA gene amplicon sequencing and a complementary cultivation approach, including in vitro and in vivo assays. Under all stress conditions, tomato growth and photosynthetic activity was reduced. Combined abiotic stressors with F. oxysporum but not with V. dahliae infection led to an additive negative effect on plant performance. All stress conditions induced a microbiome shift, and changed the relative abundance of phyla such as Firmicutes and classes of Proteobacteria. Endophytes identified as Bacillus, Paenibacillus, and Microbacterium spp. showed tolerance to abiotic stress conditions and plant beneficial effects. Stressor-specific enrichments of beneficial bacteria in the root were discovered (e.g., Paenibacillus in roots infected with F. oxysporum and Microbacterium in roots infected with V. dahliae). Interestingly, endophytes that were able to promote plant growth were obtained only from roots exposed to individual biotic and combined abiotic and biotic stress conditions but not individual abiotic stressors. Our study revealed stressor-specific enrichment of beneficial bacteria in tomato roots, which has implications for novel plant protection strategies. KW - combined stress factors KW - Fusarium KW - microbiome KW - osmotic stress KW - salinity KW - soilborne pathogens KW - Verticillium Y1 - 2022 U6 - https://doi.org/10.1094/PBIOMES-10-21-0067-R SN - 2471-2906 VL - 6 IS - 4 SP - 276 EP - 289 PB - American Phytopathological Society CY - St. Paul ER - TY - JOUR A1 - Roeleke, Manuel A1 - Schlägel, Ulrike E. A1 - Gallagher, Cara A1 - Pufelski, Jan A1 - Blohm, Torsten A1 - Nathan, Ran A1 - Toledo, Sivan A1 - Jeltsch, Florian A1 - Voigt, Christian C. T1 - Insectivorous bats form mobile sensory networks to optimize prey localization: The case of the common noctule bat JF - Proceedings of the National Academy of Sciences of the United States of America N2 - Animals that depend on ephemeral, patchily distributed prey often use public information to locate resource patches. The use of public information can lead to the aggregation of foragers at prey patches, a mechanism known as local enhancement. However, when ephemeral resources are distributed over large areas, foragers may also need to increase search efficiency, and thus apply social strategies when sampling the landscape. While sensory networks of visually oriented animals have already been confirmed, we lack an understanding of how acoustic eavesdropping adds to the formation of sensory networks. Here we radio-tracked a total of 81 aerial-hawking bats at very high spatiotemporal resolution during five sessions over 3 y, recording up to 19 individuals simultaneously. Analyses of interactive flight behavior provide conclusive evidence that bats form temporary mobile sensory networks by adjusting their movements to neighboring conspecifics while probing the airspace for prey. Complementary agent-based simulations confirmed that the observed movement patterns can lead to the formation of mobile sensory networks, and that bats located prey faster when networking than when relying only on local enhancement or searching solitarily. However, the benefit of networking diminished with decreasing group size. The combination of empirical analyses and simulations elucidates how animal groups use acoustic information to efficiently locate unpredictable and ephemeral food patches. Our results highlight that declining local populations of social foragers may thus suffer from Allee effects that increase the risk of collapses under global change scenarios, like insect decline and habitat degradation. KW - automated radio tracking KW - ephemerality KW - group foraging KW - simulation KW - sociality Y1 - 2022 U6 - https://doi.org/10.1073/pnas.2203663119 SN - 0027-8424 SN - 1091-6490 VL - 119 IS - 33 PB - National Acad. of Sciences CY - Washington ER - TY - JOUR A1 - Orf, Isabel A1 - Tenenboim, Hezi A1 - Omranian, Nooshin A1 - Nikoloski, Zoran A1 - Fernie, Alisdair R. A1 - Lisec, Jan A1 - Brotman, Yariv A1 - Bromke, Mariusz A. T1 - Transcriptomic and metabolomic analysis of a Pseudomonas-resistant versus a susceptible Arabidopsis accession JF - International journal of molecular sciences N2 - Accessions of one plant species may show significantly different levels of susceptibility to stresses. The Arabidopsis thaliana accessions Col-0 and C24 differ significantly in their resistance to the pathogen Pseudomonas syringae pv. tomato (Pst). To help unravel the underlying mechanisms contributing to this naturally occurring variance in resistance to Pst, we analyzed changes in transcripts and compounds from primary and secondary metabolism of Col-0 and C24 at different time points after infection with Pst. Our results show that the differences in the resistance of Col-0 and C24 mainly involve mechanisms of salicylic-acid-dependent systemic acquired resistance, while responses of jasmonic-acid-dependent mechanisms are shared between the two accessions. In addition, arginine metabolism and differential activity of the biosynthesis pathways of aliphatic glucosinolates and indole glucosinolates may also contribute to the resistance. Thus, this study highlights the difference in the defense response strategies utilized by different genotypes. KW - Arabidopsis KW - Pseudomonas syringae pv. tomato KW - resistance KW - systems approach Y1 - 2022 U6 - https://doi.org/10.3390/ijms232012087 SN - 1422-0067 VL - 23 IS - 20 PB - MDPI CY - Basel ER - TY - JOUR A1 - Wang, Jun A1 - Chen, Xiaowen A1 - Hou, Xin A1 - Wang, Jingan A1 - Yue, Wucheng A1 - Huang, Shu A1 - Xu, Gangchun A1 - Yan, Jizhou A1 - Lu, Guoqing A1 - Hofreiter, Michael A1 - Li, Chenhong A1 - Wang, Chenghui T1 - "Omics" data unveil early molecular response underlying limb regeneration in the Chinese mitten crab, Eriocheir sinensis JF - Science Advances N2 - Limb regeneration is a fascinating and medically interesting trait that has been well preserved in arthropod lineages, particularly in crustaceans. However, the molecular mechanisms underlying arthropod limb regeneration remain largely elusive. The Chinese mitten crab Eriocheir sinensis shows strong regenerative capacity, a trait that has likely allowed it to become a worldwide invasive species. Here, we report a chromosome-level genome of E. sinensis as well as large-scale transcriptome data during the limb regeneration process. Our results reveal that arthropod -specific genes involved in signal transduction, immune response, histone methylation, and cuticle development all play fundamental roles during the regeneration process. Particularly, Innexin2-mediated signal transduction likely facilitates the early stage of the regeneration process, while an effective crustacean-specific prophenoloxidase system (ProPo-AS) plays crucial roles in the initial immune response. Collectively, our findings uncover novel genetic pathways pertaining to arthropod limb regeneration and provide valuable resources for studies on regeneration from a comparative perspective. Y1 - 2022 U6 - https://doi.org/10.1126/sciadv.abl4642 SN - 2375-2548 VL - 8 IS - 37 PB - American Assoc. for the Advancement of Science CY - Washington, DC [u.a.] ER - TY - JOUR A1 - Gao, Qiancheng A1 - Ma, Xiaowan A1 - Wang, Zhichao A1 - Chen, Haisheng A1 - Luo, Yu A1 - Wu, Bi A1 - Qi, Shanni A1 - Lin, Miaozhen A1 - Tian, Jing A1 - Qiao, Ying A1 - Grossart, Hans-Peter A1 - Xu, Wei A1 - Huang, Lixing T1 - Seasonal variation, virulence gene and antibiotic resistance of Vibrio in a semi-enclosed bay with mariculture (Dongshan Bay, Southern China) JF - Marine pollution bulletin : the international journal for marine environmental scientists, engineers, administrators, politicians and lawyers N2 - In this study, the virulence genes, antibiotic resistance of culturable Vibrio and the environmental factors affecting Vibrio abundance were analyzed in four seasons in DongShan Bay with different intensity of aquaculture practice. A total of 253 bacteria isolates were obtained, of which 177 Vibrio strains belonged to 26 species. Annual Vibrio abundance in this region ranged from 20 to 11,600 CFU mL(-1) and the most significant positive correlation occurred with temperature. Detection of 9 different Vibrio virulence genes revealed that most isolates contained atypical virulence genes in addition to the typical ones. In particular, virulence genes of hemolysin such as tdh, trh, and hlyA (6.32 %, 15.52 %, and 11.30 %) showed different degrees of horizontal gene transfer (HGT). In our antibiotic resistance test, the multiple antibiotic resistance (MAR) index of the isolates ranged from 0.01 to 0.03 in different seasons, and three MAR Vibrio strains were detected. Overall, our study sheds new light on the spatial distribution patterns and the occurrence of virulence genes and antibiotics resistance Vibrio iso-lated from a subtropical bay with intensive aquaculture. Our study provides a suitable microbial quality sur-veillance in a mariculture impacted coastal environment. It will help to establish effective disease prevention measures in this area and provide useful guidance and support for formulating local antibiotics use policies. KW - Vibrio community dynamics KW - Virulence genes KW - Multiple antibiotic KW - resistance KW - Aquaculture KW - Food-borne diseases KW - Marine ecological KW - environment Y1 - 2022 U6 - https://doi.org/10.1016/j.marpolbul.2022.114112 SN - 0025-326X SN - 1879-3363 VL - 184 PB - Elsevier Science CY - Amsterdam [u.a.] ER - TY - JOUR A1 - Zhou, Yaqi A1 - Wang, Hongkai A1 - Xu, Sunde A1 - Liu, Kai A1 - Qi, Hao A1 - Wang, Mengcen A1 - Chen, Xiaoyulong A1 - Berg, Gabriele A1 - Ma, Zhonghua A1 - Cernava, Tomislav A1 - Chen, Yun T1 - Bacterial-fungal interactions under agricultural settings: from physical to chemical interactions JF - Stress biology N2 - Bacteria and fungi are dominant members of environmental microbiomes. Various bacterial-fungal interactions (BFIs) and their mutual regulation are important factors for ecosystem functioning and health. Such interactions can be highly dynamic, and often require spatiotemporally resolved assessments to understand the interplay which ranges from antagonism to mutualism. Many of these interactions are still poorly understood, especially in terms of the underlying chemical and molecular interplay, which is crucial for inter-kingdom communication and interference. BFIs are highly relevant under agricultural settings; they can be determinative for crop health. Advancing our knowledge related to mechanisms underpinning the interactions between bacteria and fungi will provide an extended basis for biological control of pests and pathogens in agriculture. Moreover, it will facilitate a better understanding of complex microbial community networks that commonly occur in nature. This will allow us to determine factors that are crucial for community assembly under different environmental conditions and pave the way for constructing synthetic communities for various biotechnological applications. Here, we summarize the current advances in the field of BFIs with an emphasis on agriculture. KW - bacterial-fungal interactions KW - biological control KW - synthetic communities KW - secondary metabolites Y1 - 2022 U6 - https://doi.org/10.1007/s44154-022-00046-1 SN - 2731-0450 VL - 2 IS - 1 PB - Springer Nature, Northwest A&F University CY - Singapore, Yangling ER - TY - JOUR A1 - Höfs, Soraya A1 - Huelague, Deniz A1 - Bennet, Francesca A1 - Carl, Peter A1 - Flemig, Sabine A1 - Schmid, Thomas A1 - Schenk, Jorg A. A1 - Hodoroaba, Vasile-Dan A1 - Schneider, Rudolf J. T1 - Electrochemical immunomagnetic Ochratoxin A sensing BT - steps forward in the application of 3,3’,5,5’-Tetramethylbenzidine in amperometric assays JF - ChemElectroChem N2 - Electrochemical methods offer great promise in meeting the demand for user-friendly on-site devices for monitoring important parameters. The food industry often runs own lab procedures, for example, for mycotoxin analysis, but it is a major goal to simplify analysis, linking analytical methods with smart technologies. Enzyme-linked immunosorbent assays, with photometric detection of 3,3',5,5'-tetramethylbenzidine (TMB), form a good basis for sensitive detection. To provide a straightforward approach for the miniaturization of the detection step, we have studied the pitfalls of the electrochemical TMB detection. By cyclic voltammetry it was found that the TMB electrochemistry is strongly dependent on the pH and the electrode material. A stable electrode response to TMB could be achieved at pH 1 on gold electrodes. We created a smartphone-based, electrochemical, immunomagnetic assay for the detection of ochratoxin A in real samples, providing a solid basis for sensing of further analytes. KW - amperometry KW - cyclic voltammetry KW - immunoassays KW - screen-printed electrodes KW - 3,3′,5,5′-tetramethylbenzidine Y1 - 2021 U6 - https://doi.org/10.1002/celc.202100446 SN - 2196-0216 VL - 8 IS - 13 SP - 2597 EP - 2606 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Razaghi-Moghadam, Zahra A1 - Sokolowska, Ewelina A1 - Sowa, Marcin A. A1 - Skirycz, Aleksandra A1 - Nikoloski, Zoran T1 - Combination of network and molecule structure accurately predicts competitive inhibitory interactions JF - Computational and structural biotechnology journal N2 - Mining of metabolite-protein interaction networks facilitates the identification of design principles underlying the regulation of different cellular processes. However, identification and characterization of the regulatory role that metabolites play in interactions with proteins on a genome-scale level remains a pressing task. Based on availability of high-quality metabolite-protein interaction networks and genome-scale metabolic networks, here we propose a supervised machine learning approach, called CIRI that determines whether or not a metabolite is involved in a competitive inhibitory regulatory interaction with an enzyme. First, we show that CIRI outperforms the naive approach based on a structural similarity threshold for a putative competitive inhibitor and the substrates of a metabolic reaction. We also validate the performance of CIRI on several unseen data sets and databases of metabolite-protein interactions not used in the training, and demonstrate that the classifier can be effectively used to predict competitive inhibitory interactions. Finally, we show that CIRI can be employed to refine predictions about metabolite-protein interactions from a recently proposed PROMIS approach that employs metabolomics and proteomics profiles from size exclusion chromatography in E. coli to predict metaboliteprotein interactions. Altogether, CIRI fills a gap in cataloguing metabolite-protein interactions and can be used in directing future machine learning efforts to categorize the regulatory type of these interactions. KW - Metabolite-protein interactions KW - Genome-scale metabolic models KW - Supervised machine learning Y1 - 2021 U6 - https://doi.org/10.1016/j.csbj.2021.04.012 SN - 2001-0370 VL - 19 SP - 2170 EP - 2178 PB - Research Network of Computational and Structural Biotechnology (RNCSB) CY - Gotenburg ER - TY - JOUR A1 - Habel, Jan Christian A1 - Schmitt, Thomas A1 - Gros, Patrick A1 - Ulrich, Werner T1 - Breakpoints in butterfly decline in Central Europe over the last century JF - The science of the total environment : an international journal for scientific research into the environment and its relationship with man N2 - Recent studies indicated severe decline of insect diversity and abundance across major parts of Central Europe. Theoretical studies showed that the drivers behind biodiversity loss vary considerably over time. However, these scenarios so far have been insufficiently approved by long-term and large-scale data. In this study we analysed the temporal trends of butterflies and Zygaenid moths across the federal state of Salzburg, northern Austria, from 1920 to 2019. Our study area covers a large variety of habitats and altitudes. Various changes of land use and intensification occurred during and shortly before our studied period, with a first wave of habitat destruction starting in the late 19th century, followed by the deterioration of habitat quality since the mid-20th century. We used 59,870 presence-only data of 168 butterfly and burnet moth species. Each of these species was classified according to ecological characteristics. Break point analyses for non-linear temporal trends in the community composition returned two major time windows. These time windows coincide with periods characterized by severe habitat destruction and the deterioration of habitat quality due to agricultural intensification. We found significant reductions of the proportion of species requiring specific habitats since 1920 and until today. We identified additional break points for species requiring high habitat qualities, endangered butterfly species, and sedentary species, particularly after a main break point in the 1960s. Our findings underline that, apart from habitat destruction, the deterioration of habitat quality is a main driver of biodiversity loss in general. Therefore, nature conservation should focus on maintaining the highest possible habitat quality. KW - biodiversity crisis KW - time series KW - species community assembly KW - species richness KW - relative abundance KW - trait assemblages KW - break points KW - multiple drivers Y1 - 2022 U6 - https://doi.org/10.1016/j.scitotenv.2022.158315 SN - 0048-9697 SN - 1879-1026 VL - 851 IS - Part 2 PB - Elsevier Science CY - Amsterdam ER - TY - JOUR A1 - Glaw, Frank A1 - Kohler, Jorn A1 - Hawlitschek, Oliver A1 - Ratsoavina, Fanomezana M. A1 - Rakotoarison, Andolalao A1 - Scherz, Mark D. A1 - Vences, Miguel T1 - Extreme miniaturization of a new amniote vertebrate and insights into the evolution of genital size in chameleons JF - Scientific reports N2 - Evolutionary reduction of adult body size (miniaturization) has profound consequences for organismal biology and is an important subject of evolutionary research. Based on two individuals we describe a new, extremely miniaturized chameleon, which may be the world's smallest reptile species. The male holotype of Brookesia nana sp. nov. has a snout-vent length of 13.5 mm (total length 21.6 mm) and has large, apparently fully developed hemipenes, making it apparently the smallest mature male amniote ever recorded. The female paratype measures 19.2 mm snout-vent length (total length 28.9 mm) and a micro-CT scan revealed developing eggs in the body cavity, likewise indicating sexual maturity. The new chameleon is only known from a degraded montane rainforest in northern Madagascar and might be threatened by extinction. Molecular phylogenetic analyses place it as sister to B. karchei, the largest species in the clade of miniaturized Brookesia species, for which we resurrect Evoluticauda Angel, 1942 as subgenus name. The genetic divergence of B. nana sp. nov. is rather strong (9.914.9% to all other Evoluticauda species in the 16S rRNA gene). A comparative study of genital length in Malagasy chameleons revealed a tendency for the smallest chameleons to have the relatively largest hemipenes, which might be a consequence of a reversed sexual size dimorphism with males substantially smaller than females in the smallest species. The miniaturized males may need larger hemipenes to enable a better mechanical fit with female genitals during copulation. Comprehensive studies of female genitalia are needed to test this hypothesis and to better understand the evolution of genitalia in reptiles. Y1 - 2021 U6 - https://doi.org/10.1038/s41598-020-80955-1 SN - 2045-2322 VL - 11 IS - 1 PB - Springer Nature CY - Berlin ER - TY - JOUR A1 - Wicaksono, Wisnu Adi A1 - Egamberdieva, Dilfuza A1 - Berg, Christian A1 - Mora, Maximilian A1 - Kusstatscher, Peter A1 - Cernava, Tomislav A1 - Berg, Gabriele T1 - Function-based rhizosphere assembly along a gradient of desiccation in the former Aral Sea JF - mSystems N2 - The desiccation of the Aral Sea represents one of the largest human-made environmental regional disasters. The salt- and toxin-enriched dried-out basin provides a natural laboratory for studying ecosystem functioning and rhizosphere assembly under extreme anthropogenic conditions. Here, we investigated the prokaryotic rhizosphere communities of the native pioneer plant Suaeda acuminata (C.A.Mey.) Moq. in comparison to bulk soil across a gradient of desiccation (5, 10, and 40 years) by metagenome and amplicon sequencing combined with quantitative PCR (qPCR) analyses. The rhizosphere effect was evident due to significantly higher bacterial abundances but less diversity in the rhizosphere compared to bulk soil. Interestingly, in the highest salinity (5 years of desiccation), rhizosphere functions were mainly provided by archaeal communities. Along the desiccation gradient, we observed a significant change in the rhizosphere microbiota, which was reflected by (i) a decreasing archaeon-bacterium ratio, (ii) replacement of halophilic archaea by specific plant-associated bacteria, i.e., Alphaproteobacteria and Actinobacteria, and (iii) an adaptation of specific, potentially plant-beneficial biosynthetic pathways. In general, both bacteria and archaea were found to be involved in carbon cycling and fixation, as well as methane and nitrogen metabolism. Analysis of metagenome-assembled genomes (MAGs) showed specific signatures for production of osmoprotectants, assimilatory nitrate reduction, and transport system induction. Our results provide evidence that rhizosphere assembly by cofiltering specific taxa with distinct traits is a mechanism which allows plants to thrive under extreme conditions. Overall, our findings highlight a function-based rhizosphere assembly, the importance of plant-microbe interactions in salinated soils, and their exploitation potential for ecosystem restoration approaches.IMPORTANCE The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. Here, we investigated bacterial and archaeal communities in the rhizosphere of pioneer plants by combining classic molecular methods with amplicon sequencing as well as metagenomics for functional insights. By implementing a desiccation gradient, we observed (i) remarkable differences in the archaeon-bacterium ratio of plant rhizosphere samples, (ii) replacement of archaeal indicator taxa during succession, and (iii) the presence of specific, potentially plant-beneficial biosynthetic pathways in archaea present during the early stages. In addition, our results provide hitherto-undescribed insights into the functional redundancy between plant-associated archaea and bacteria. The desertification of the Aral Sea basin in Uzbekistan and Kazakhstan represents one of the most serious anthropogenic environmental disasters of the last century. Since the 1960s, the world's fourth-largest inland body of water has been constantly shrinking, which has resulted in an extreme increase of salinity accompanied by accumulation of many hazardous and carcinogenic substances, as well as heavy metals, in the dried-out basin. KW - Aral Sea KW - microbiome KW - desiccation KW - nutrient cycling KW - soil microorganisms KW - revegetation KW - archaea KW - bacteria KW - metagenome Y1 - 2022 U6 - https://doi.org/10.1128/msystems.00739-22 SN - 2379-5077 VL - 7 IS - 6 PB - American Society for Microbiology CY - Washington, DC ER - TY - JOUR A1 - Vyse, Stuart A. A1 - Herzschuh, Ulrike A1 - Pfalz, Gregor A1 - Pestryakova, Lyudmila A. A1 - Diekmann, Bernhard A1 - Nowaczyk, Norbert A1 - Biskaborn, Boris K. T1 - Sediment and carbon accumulation in a glacial lake in Chukotka (Arctic Siberia) during the Late Pleistocene and Holocene BT - combining hydroacoustic profiling and down-core analyses JF - Biogeosciences N2 - Lakes act as important sinks for inorganic and organic sediment components. However, investigations of sedimentary carbon budgets within glacial lakes are currently absent from Arctic Siberia. The aim of this paper is to provide the first reconstruction of accumulation rates, sediment and carbon budgets from a lacustrine sediment core from Lake Rauchuagytgyn, Chukotka (Arctic Siberia). We combined multiple sediment biogeochemical and sedimentological parameters from a radiocarbon-dated 6.5m sediment core with lake basin hydroacoustic data to derive sediment stratigraphy, sediment volumes and infill budgets. Our results distinguished three principal sediment and carbon accumulation regimes that could be identified across all measured environmental proxies including early Marine Isotope Stage 2 (MIS2) (ca. 29-23.4 ka cal BP), mid-MIS2-early MIS1 (ca. 23.4-11.69 ka cal BP) and the Holocene (ca. 11.69-present). Estimated organic carbon accumulation rates (OCARs) were higher within Holocene sediments (average 3.53 gOCm(-2) a(-1)) than Pleistocene sediments (average 1.08 gOCm(-2) a(-1)) and are similar to those calculated for boreal lakes from Quebec and Finland and Lake Baikal but significantly lower than Siberian thermokarst lakes and Alberta glacial lakes. Using a bootstrapping approach, we estimated the total organic carbon pool to be 0.26 +/- 0.02 Mt and a total sediment pool of 25.7 +/- 1.71 Mt within a hydroacoustically derived sediment volume of ca. 32 990 557m(3). The total organic carbon pool is substantially smaller than Alaskan yedoma, thermokarst lake sediments and Alberta glacial lakes but shares similarities with Finnish boreal lakes. Temporal variability in sediment and carbon accumulation dynamics at Lake Rauchuagytgyn is controlled predominantly by palaeoclimate variation that regulates lake ice-cover dynamics and catchment glacial, fluvial and permafrost processes through time. These processes, in turn, affect catchment and within-lake primary productivity as well as catchment soil development. Spatial differences compared to other lake systems at a trans-regional scale likely relate to the high-latitude, mountainous location of Lake Rauchuagytgyn. Y1 - 2021 U6 - https://doi.org/10.5194/bg-18-4791-2021 SN - 1726-4170 SN - 1726-4189 VL - 18 IS - 16 SP - 4791 EP - 4816 PB - Copernicus CY - Katlenburg-Lindau ER - TY - JOUR A1 - Sedaghatmehr, Mastoureh A1 - Stüwe, Benno A1 - Müller-Röber, Bernd A1 - Balazadeh, Salma T1 - Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6 JF - Journal of experimental botany N2 - The transcription factor HSFA2 fine-tunes a balance between prolongation and resetting of thermomemory in Arabidopsis via the regulation of both memory-supporting and memory-resetting genes. Plants 'memorize' stressful events and protect themselves from future, often more severe, stresses. To maximize growth after stress, plants 'reset' or 'forget' memories of stressful situations, which requires an intricate balance between stress memory formation and the degree of forgetfulness. HEAT SHOCK PROTEIN 21 (HSP21) encodes a small heat shock protein in plastids of Arabidopsis thaliana. HSP21 functions as a key component of thermomemory, which requires a sustained elevated level of HSP21 during recovery from heat stress. A heat-induced metalloprotease, filamentation temperature-sensitive H6 (FtsH6), degrades HSP21 to its pre-stress abundance, thereby resetting memory during the recovery phase. The transcription factor heat shock factor A2 (HSFA2) activates downstream genes essential for mounting thermomemory, acting as a positive regulator in the process. Here, using a yeast one-hybrid screen, we identify HSFA2 as an upstream transactivator of the resetting element FtsH6. Constitutive and inducible overexpression of HSFA2 increases expression of FtsH6, whereas it is drastically reduced in the hsfa2 knockout mutant. Chromatin immunoprecipitation reveals in planta binding of HSFA2 to the FtsH6 promoter. Importantly, overexpression of HSFA2 improves thermomemory more profoundly in ftsh6 than wild-type plants. Thus, by activating both memory-supporting and memory-resetting genes, HSFA2 acts as a cellular homeostasis factor during thermomemory. KW - Arabidopsis thaliana KW - FtsH6 KW - heat stress KW - HSFA2 KW - HSP21 KW - thermomemory; KW - thermorecovery Y1 - 2022 U6 - https://doi.org/10.1093/jxb/erac257 SN - 0022-0957 SN - 1460-2431 VL - 73 IS - 18 SP - 6394 EP - 6404 PB - Oxford Univ. Press CY - Oxford ER - TY - JOUR A1 - Baumas, Chloe M. J. A1 - Le Moigne, Frédéric A. C. A1 - Garel, Marc A1 - Bhairy, Nagib A1 - Guasco, Sophie A1 - Riou, Virginie A1 - Armougom, Fabrice A1 - Grossart, Hans-Peter A1 - Tamburini, Christian T1 - Mesopelagic microbial carbon production correlates with diversity across different marine particle fractions JF - The ISME journal : multidisciplinary journal of microbial ecology N2 - The vertical flux of marine snow particles significantly reduces atmospheric carbon dioxide concentration. In the mesopelagic zone, a large proportion of the organic carbon carried by sinking particles dissipates thereby escaping long term sequestration. Particle associated prokaryotes are largely responsible for such organic carbon loss. However, links between this important ecosystem flux and ecological processes such as community development of prokaryotes on different particle fractions (sinking vs. non-sinking) are yet virtually unknown. This prevents accurate predictions of mesopelagic organic carbon loss in response to changing ocean dynamics. Using combined measurements of prokaryotic heterotrophic production rates and species richness in the North Atlantic, we reveal that carbon loss rates and associated microbial richness are drastically different with particle fractions. Our results demonstrate a strong negative correlation between prokaryotic carbon losses and species richness. Such a trend may be related to prokaryotes detaching from fast-sinking particles constantly enriching non-sinking associated communities in the mesopelagic zone. Existing global scale data suggest this negative correlation is a widespread feature of mesopelagic microbes. Y1 - 2021 U6 - https://doi.org/10.1038/s41396-020-00880-z SN - 1751-7362 SN - 1751-7370 VL - 15 IS - 6 SP - 1695 EP - 1708 PB - Nature Publishing Group CY - Basingstoke ER - TY - JOUR A1 - Hirschberg, Stefan A1 - Bauer, Hannes A1 - Kamhieh-Milz, Julian A1 - Ringel, Frauke A1 - Harms, Christoph A1 - Eddin, Omar Kamal A1 - Pruss, Axel A1 - Hanack, Katja A1 - Schulze-Forster, Kai T1 - SARS-CoV-2 virus-like particles (VLPs) specifically detect humoral immune reactions in an ELISA-Based Platform JF - Antibodies N2 - A key in controlling the SARS-CoV-2 pandemic is the assessment of the immune status of the population. We explored the utility of SARS-CoV-2 virus-like particles (VLPs) as antigens to detect specific humoral immune reactions in an enzyme-linked immunosorbent assay (ELISA). For this purpose, SARS-CoV-2 VLPs were produced from an engineered cell line and characterized by Western blot, ELISA, and nanoparticle tracking analysis. Subsequently, we collected 42 serum samples from before the pandemic (2014), 89 samples from healthy subjects, and 38 samples from vaccinated subjects. Seventeen samples were collected less than three weeks after infection, and forty-four samples more than three weeks after infection. All serum samples were characterized for their reactivity with VLPs and the SARS-CoV-2 N- and S-protein. Finally, we compared the performance of the VLP-based ELISA with a certified in vitro diagnostic device (IVD). In the applied set of samples, we determined a sensitivity of 95.5% and a specificity of 100% for the certified IVD. There were seven samples with an uncertain outcome. Our VLP-ELISA demonstrated a superior performance, with a sensitivity of 97.5%, a specificity of 100%, and only three uncertain outcomes. This result warrants further research to develop a certified IVD based on SARS-CoV-2 VLPs as an antigen. KW - virus-like particle (VLP) KW - SARS-CoV-2 in vitro diagnostic device (IVD) KW - enzyme-linked immunosorbent assay (ELISA) KW - immune reaction KW - antibodies Y1 - 2022 U6 - https://doi.org/10.3390/antib11040076 SN - 2073-4468 VL - 11 IS - 4 PB - MDPI CY - Basel ER - TY - JOUR A1 - Dreymann, Nico A1 - Sabrowski, Wiebke A1 - Danso, Jennifer A1 - Menger, Marcus T1 - Aptamer-based sandwich assay formats for detection and discrimination of human high- and low-molecular-weight uPA for cancer prognosis and diagnosis JF - Cancers / Molecular Diversity Preservation International (MDPI) N2 - Simple Summary Urokinase-type plasminogen activator (urokinase, uPA) is a widely discussed biomarker for cancer prognosis and diagnosis. The gold standard for the determination of protein biomarkers in physiological samples is the enzyme-linked immunosorbent assay (ELISA). Here, antibodies are used to detect the specific protein. In our study, recently published urokinase aptamers were tested for their use in a sandwich assay format as alternative specific recognition elements. Different aptamer combinations were used for the detection of uPA in a sandwich-assay format and a combination of aptamers and antibodies additionally allowed the differentiation of human high and low molecular weight- (HMW- and LMW-) uPA. Hence, uPA aptamers offer a valuable alternative as specific recognition elements for analytical purposes. Since aptamers are easy to synthesize and modify, they can be used as a cost-effective alternative in sandwich assay formats for the detection of uPA in physiological samples. Abstract Urokinase-type plasminogen activator (urokinase, uPA) is a frequently discussed biomarker for prognosis, diagnosis, and recurrence of cancer. In a previous study, we developed ssDNA aptamers that bind to different forms of human urokinase, which are therefore assumed to have different binding regions. In this study, we demonstrate the development of aptamer-based sandwich assays that use different combinations of these aptamers to detect high molecular weight- (HMW-) uPA in a micro titer plate format. By combining aptamers and antibodies, it was possible to distinguish between HMW-uPA and low molecular weight- (LMW-) uPA. For the best performing aptamer combination, we calculated the limit of detection (LOD) and limit of quantification (LOQ) in spiked buffer and urine samples with an LOD up to 50 ng/mL and 138 ng/mL, respectively. To show the specificity and sequence dependence of the reporter aptamer uPAapt-02-FR, we have identified key nucleotides within the sequence that are important for specific folding and binding to uPA using a fluorescent dye-linked aptamer assay (FLAA). Since uPA is a much-discussed marker for prognosis and diagnosis in various types of cancers, these aptamers and their use in a micro titer plate assay format represent a novel, promising tool for the detection of uPA and for possible diagnostic applications. KW - ALISA KW - aptamer KW - biomarker KW - cancer prognosis KW - early stage cancer detection KW - ELONA KW - sandwich assay KW - uPA KW - urokinase Y1 - 2022 U6 - https://doi.org/10.3390/cancers14215222 SN - 2072-6694 VL - 14 IS - 21 PB - MDPI CY - Basel ER - TY - JOUR A1 - Scholz, Stella A1 - Kerestetzopoulou, Sofia A1 - Wiebach, Vincent A1 - Schnegotzki, Romina A1 - Schmid, Bianca A1 - Reyna-Gonzalez, Emmanuel A1 - Ding, Ling A1 - Süssmuth, Roderich D. A1 - Dittmann, Elke A1 - Baunach, Martin T1 - One-Pot chemoenzymatic synthesis of microviridin analogs containing functional tags JF - ChemBioChem : an official journal of the EFMC N2 - Microviridins are a prominent family of ribosomally synthesized and posttranslationally modified peptides (RiPPs) featuring characteristic lactone and lactam rings. Their unusual cage-like architecture renders them highly potent serine protease inhibitors of which individual variants specifically inhibit different types of proteases of pharmacological interest. While posttranslational modifications are key for the stability and bioactivity of RiPPs, additional attractive properties can be introduced by functional tags. To date - although highly desirable - no method has been reported to incorporate functional tags in microviridin scaffolds or the overarching class of graspetides. In this study, a chemoenzymatic in vitro platform is used to introduce functional tags in various microviridin variants yielding biotinylated, dansylated or propargylated congeners. This straightforward approach paves the way for customized protease inhibitors with built-in functionalities that can help to unravel the still elusive ecological roles and targets of this remarkable class of compounds and to foster applications based on protease inhibition. KW - chemoenzymatic synthesis KW - protease inhibitors KW - microviridins KW - RiPPs KW - synthetic biology Y1 - 2022 U6 - https://doi.org/10.1002/cbic.202200345 SN - 1439-4227 SN - 1439-7633 VL - 23 IS - 20 PB - Wiley-VCH CY - Weinheim ER - TY - JOUR A1 - Heinze, Johannes A1 - Krumpholz, Laura A1 - Blaum, Niels A1 - Hoefgen, Rainer A1 - Ogden, Michael T1 - Shoot herbivory by grasshoppers has stronger effects on root morphology than clipping JF - Plant ecology : an international journal N2 - Studies investigating the effect of aboveground herbivory on plants often use clipping to simulate the effects of herbivores, for practical reasons. However, herbivore movements and transfer of oral secretions during herbivory may cause a different response in plant physiology and morphology compared to clipping. While studies have compared effects of real herbivory vs. clipping on biomass production, plant physiology, and shoot morphology, no study has compared such effects on root morphology. Therefore, we investigated the effect of herbivory by grasshoppers, herbivory simulated by clipping, and no herbivory on root morphological traits of ten grassland plant species. Root morphological traits were differently affected by the two herbivory treatments. Grasshopper herbivory significantly changed root morphology toward thinner roots with increased specific root length and root area, and decreased root tissue density compared to untreated control plants. Clipping had mostly similar, but weaker effects on root morphology than grasshopper herbivory. On the species level, grasshopper herbivory led to strongest changes in root morphology in almost all cases. In contrast, depending on the species, clipping resulted in varying root morphological trait values similar to grasshopper-damaged plants, or in some cases, more closely aligned with control plants. Though clipping was partly able to mimic the effects of herbivory by grasshoppers, results also indicate that, depending on the species, grasshopper herbivory had different but mostly stronger effects. We, therefore, recommend that future studies apply herbivory with real herbivores to better reflect natural responses in plants and related processes that root morphological traits mediate. KW - root morphology KW - root traits KW - clipping KW - herbivory KW - grasshopper Y1 - 2022 U6 - https://doi.org/10.1007/s11258-022-01259-0 SN - 1385-0237 SN - 1573-5052 VL - 223 IS - 9 SP - 1069 EP - 1078 PB - Springer Science + Business Media B.V. CY - Dordrecht ER - TY - JOUR A1 - Schödl, Isabel A1 - Odemer, Richard A1 - Becher, Matthias A. A1 - Berg, Stefan A1 - Otten, Christoph A1 - Grimm, Volker A1 - Groeneveld, Jürgen T1 - Simulation of Varroa mite control in honey bee colonies without synthetic acaricides: demonstration of Good Beekeeping Practice for Germany in the BEEHAVE model JF - Ecology and evolution N2 - The BEEHAVE model simulates the population dynamics and foraging activity of a single honey bee colony (Apis mellifera) in great detail. Although it still makes numerous simplifying assumptions, it appears to capture a wide range of empirical observations. It could, therefore, in principle, also be used as a tool in beekeeper education, as it allows the implementation and comparison of different management options. Here, we focus on treatments aimed at controlling the mite Varroa destructor. However, since BEEHAVE was developed in the UK, mite treatment includes the use of a synthetic acaricide, which is not part of Good Beekeeping Practice in Germany. A practice that consists of drone brood removal from April to June, treatment with formic acid in August/September, and treatment with oxalic acid in November/December. We implemented these measures, focusing on the timing, frequency, and spacing between drone brood removals. The effect of drone brood removal and acid treatment, individually or in combination, on a mite-infested colony was examined. We quantify the efficacy of Varroa mite control as the reduction of mites in treated bee colonies compared to untreated bee colonies. We found that drone brood removal was very effective, reducing mites by 90% at the end of the first simulation year after the introduction of mites. This value was significantly higher than the 50-67% reduction expected by bee experts and confirmed by empirical studies. However, literature reports varying percent reductions in mite numbers from 10 to 85% after drone brood removal. The discrepancy between model results, empirical data, and expert estimates indicate that these three sources should be reviewed and refined, as all are based on simplifying assumptions. These results and the adaptation of BEEHAVE to the Good Beekeeping Practice are a decisive step forward for the future use of BEEHAVE in beekeeper education in Germany and anywhere where organic acids and drone brood removal are utilized. KW - acaricides KW - BEEHAVE KW - beekeeping KW - drones KW - education KW - honey bees KW - modelling KW - pest control KW - Varroa mite Y1 - 2022 U6 - https://doi.org/10.1002/ece3.9456 SN - 2045-7758 VL - 12 IS - 11 PB - John Wiley & Sons, Inc. ER -