@article{WeyhenmeyerMackayStockwelletal.2017, author = {Weyhenmeyer, Gesa A. and Mackay, Murray and Stockwell, Jason D. and Thiery, Wim and Grossart, Hans-Peter and Augusto-Silva, Petala B. and Baulch, Helen M. and de Eyto, Elvira and Hejzlar, Josef and Kangur, Kuelli and Kirillin, Georgiy and Pierson, Don C. and Rusak, James A. and Sadro, Steven and Woolway, R. Iestyn}, title = {Citizen science shows systematic changes in the temperature difference between air and inland waters with global warming}, series = {Scientific reports}, volume = {7}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep43890}, pages = {9}, year = {2017}, abstract = {Citizen science projects have a long history in ecological studies. The research usefulness of such projects is dependent on applying simple and standardized methods. Here, we conducted a citizen science project that involved more than 3500 Swedish high school students to examine the temperature difference between surface water and the overlying air (T-w-T-a) as a proxy for sensible heat flux (Q(H)). If Q(H) is directed upward, corresponding to positive T-w-T-a, it can enhance CO2 and CH4 emissions from inland waters, thereby contributing to increased greenhouse gas concentrations in the atmosphere. The students found mostly negative T-w-T-a across small ponds, lakes, streams/rivers and the sea shore (i.e. downward Q(H)), with T-w-T-a becoming increasingly negative with increasing T-a. Further examination of T-w-T-a using high-frequency temperature data from inland waters across the globe confirmed that T-w-T-a is linearly related to T-a. Using the longest available high-frequency temperature time series from Lake Erken, Sweden, we found a rapid increase in the occasions of negative T-w-T-a with increasing annual mean T-a since 1989. From these results, we can expect that ongoing and projected global warming will result in increasingly negative T-w-T-a, thereby reducing CO2 and CH4 transfer velocities from inland waters into the atmosphere.}, language = {en} } @article{McGinnisFluryTangetal.2017, author = {McGinnis, Daniel F. and Flury, Sabine and Tang, Kam W. and Grossart, Hans-Peter}, title = {Porewater methane transport within the gas vesicles of diurnally migrating Chaoborus spp.}, series = {Scientific reports}, volume = {7}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/srep44478}, pages = {7}, year = {2017}, abstract = {Diurnally-migrating Chaoborus spp. reach populations of up to 130,000 individuals m-2 in lakes up to 70 meters deep on all continents except Antarctica. Linked to eutrophication, migrating Chaoborus spp. dwell in the anoxic sediment during daytime and feed in the oxic surface layer at night. Our experiments show that by burrowing into the sediment, Chaoborus spp. utilize the high dissolved gas partial pressure of sediment methane to inflate their tracheal sacs. This mechanism provides a significant energetic advantage that allows the larvae to migrate via passive buoyancy rather than more energy-costly swimming. The Chaoborus spp. larvae, in addition to potentially releasing sediment methane bubbles twice a day by entering and leaving the sediment, also transport porewater methane within their gas vesicles into the water column, resulting in a flux of 0.01-2 mol m-2 yr-1 depending on population density and water depth. Chaoborus spp. emerging annually as flies also result in 0.1-6 mol m-2 yr-1 of carbon export from the system. Finding the tipping point in lake eutrophication enabling this methane-powered migration mechanism is crucial for ultimately reconstructing the geographical expansion of Chaoborus spp., and the corresponding shifts in the lake's biogeochemistry, carbon cycling and food web structure.}, language = {en} } @article{IonescuBizicKarnataketal.2022, author = {Ionescu, Danny and Bizic, Mina and Karnatak, Rajat and Musseau, Camille L. and Onandia, Gabriela and Kasada, Minoru and Berger, Stella A. and Nejstgaard, Jens Christian and Ryo, Masahiro and Lischeid, Gunnar and Gessner, Mark O. and Wollrab, Sabine and Grossart, Hans-Peter}, title = {From microbes to mammals: Pond biodiversity homogenization across different land-use types in an agricultural landscape}, series = {Ecological monographs}, volume = {92}, journal = {Ecological monographs}, number = {3}, publisher = {Wiley}, address = {Hoboken}, issn = {0012-9615}, doi = {10.1002/ecm.1523}, pages = {28}, year = {2022}, abstract = {Local biodiversity patterns are expected to strongly reflect variation in topography, land use, dispersal boundaries, nutrient supplies, contaminant spread, management practices, and other anthropogenic influences. Contrary to this expectation, studies focusing on specific taxa revealed a biodiversity homogenization effect in areas subjected to long-term intensive industrial agriculture. We investigated whether land use affects biodiversity levels and community composition (alpha- and beta-diversity) in 67 kettle holes (KH) representing small aquatic islands embedded in the patchwork matrix of a largely agricultural landscape comprising grassland, forest, and arable fields. These KH, similar to millions of standing water bodies of glacial origin, spread across northern Europe, Asia, and North America, are physico-chemically diverse and differ in the degree of coupling with their surroundings. We assessed aquatic and sediment biodiversity patterns of eukaryotes, Bacteria, and Archaea in relation to environmental features of the KH, using deep-amplicon-sequencing of environmental DNA (eDNA). First, we asked whether deep sequencing of eDNA provides a representative picture of KH aquatic biodiversity across the Bacteria, Archaea, and eukaryotes. Second, we investigated if and to what extent KH biodiversity is influenced by the surrounding land use. We hypothesized that richness and community composition will greatly differ in KH from agricultural land use compared with KH in grasslands and forests. Our data show that deep eDNA amplicon sequencing is useful for in-depth assessments of cross-domain biodiversity comprising both micro- and macro-organisms, but has limitations with respect to single-taxa conservation studies. Using this broad method, we show that sediment eDNA, integrating several years to decades, depicts the history of agricultural land-use intensification. Aquatic biodiversity was best explained by seasonality, whereas land-use type explained little of the variation. We concluded that, counter to our hypothesis, land use intensification coupled with landscape wide nutrient enrichment (including atmospheric deposition), groundwater connectivity between KH and organismal (active and passive) dispersal in the tight network of ponds, resulted in a biodiversity homogenization in the KH water, leveling off today's detectable differences in KH biodiversity between land-use types. These findings have profound implications for measures and management strategies to combat current biodiversity loss in agricultural landscapes worldwide.}, language = {en} } @article{HornickBachCrawfurdetal.2017, author = {Hornick, Thomas and Bach, Lennart T. and Crawfurd, Katharine J. and Spilling, Kristian and Achterberg, Eric P. and Woodhouse, Jason Nicholas and Schulz, Kai G. and Brussaard, Corina P. D. and Riebesell, Ulf and Grossart, Hans-Peter}, title = {Ocean acidification impacts bacteria-phytoplankton coupling at low-nutrient conditions}, series = {Biogeosciences}, volume = {14}, journal = {Biogeosciences}, number = {1}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1726-4170}, doi = {10.5194/bg-14-1-2017}, pages = {1 -- 15}, year = {2017}, abstract = {The oceans absorb about a quarter of the annually produced anthropogenic atmospheric carbon dioxide (CO2), resulting in a decrease in surface water pH, a process termed ocean acidification (OA). Surprisingly little is known about how OA affects the physiology of heterotrophic bacteria or the coupling of heterotrophic bacteria to phytoplankton when nutrients are limited. Previous experiments were, for the most part, undertaken during productive phases or following nutrient additions designed to stimulate algal blooms. Therefore, we performed an in situ large-volume mesocosm (similar to 55 m(3)) experiment in the Baltic Sea by simulating different fugacities of CO2 (fCO(2)) extending from present to future conditions. The study was conducted in July-August after the nominal spring bloom, in order to maintain low-nutrient conditions throughout the experiment. This resulted in phytoplankton communities dominated by small-sized functional groups (picophytoplankton). There was no consistent fCO(2)-induced effect on bacterial protein production (BPP), cell-specific BPP (csBPP) or biovolumes (BVs) of either free-living (FL) or particle-associated (PA) heterotrophic bacteria, when considered as individual components (univariate analyses). Permutational Multivariate Analysis of Variance (PERMANOVA) revealed a significant effect of the fCO(2) treatment on entire assemblages of dissolved and particulate nutrients, metabolic parameters and the bacteria-phytoplankton community. However, distance-based linear modelling only identified fCO(2) as a factor explaining the variability observed amongst the microbial community composition, but not for explaining variability within the metabolic parameters. This suggests that fCO(2) impacts on microbial metabolic parameters occurred indirectly through varying physicochemical parameters and microbial species composition. Cluster analyses examining the co-occurrence of different functional groups of bacteria and phytoplankton further revealed a separation of the four fCO(2)-treated mesocosms from both control mesocosms, indicating that complex trophic interactions might be altered in a future acidified ocean. Possible consequences for nutrient cycling and carbon export are still largely unknown, in particular in a nutrient-limited ocean.}, language = {en} } @article{XiaoLiuWangetal.2020, author = {Xiao, Shangbin and Liu, Liu and Wang, Wei and Lorke, Andreas and Woodhouse, Jason Nicholas and Grossart, Hans-Peter}, title = {A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water}, series = {Hydrology and earth system sciences : HESS}, volume = {24}, journal = {Hydrology and earth system sciences : HESS}, number = {7}, publisher = {European Geosciences Union (EGU) ; Copernicus}, address = {Munich}, issn = {1027-5606}, doi = {10.5194/hess-24-3871-2020}, pages = {3871 -- 3880}, year = {2020}, abstract = {Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95\%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6\% and a measurement accuracy of 0.5\% for CH4. A similar performance was observed for dissolved CO2 (t(95\%) = 10 s, equilibration ratio 67.1 \%). An equilibration ratio as high as 91.8\% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.}, language = {en} } @article{HokeWoodhouseZoccaratoetal.2020, author = {Hoke, Alexa and Woodhouse, Jason Nicholas and Zoccarato, Luca and McCarthy, Valerie and de Eyto, Elvira and Caldero-Pascual, Maria and Geffroy, Ewan and Dillane, Mary and Grossart, Hans-Peter and Jennings, Eleanor}, title = {Impacts of extreme weather events on bacterial community composition of a temperate humic lake}, series = {Water}, volume = {12}, journal = {Water}, number = {10}, publisher = {MDPI}, address = {Basel}, issn = {2073-4441}, doi = {10.3390/w12102757}, pages = {19}, year = {2020}, abstract = {Extreme weather events are projected to increase in frequency and intensity as climate change continues. Heterotrophic bacteria play a critical role in lake ecosystems, yet little research has been done to determine how they are affected by such extremes. The purpose of this study was to use high-throughput sequencing to explore the bacterial community composition of a humic oligotrophic lake on the North Atlantic Irish coast and to assess the impacts on composition dynamics related to extreme weather events. Samples for sequencing were collected from Lough Feeagh on a fortnightly basis from April to November 2018. Filtration was used to separate free-living and particle-associated bacterial communities and amplicon sequencing was performed for the 16S rRNA V4 region. Two named storms, six high discharge events, and one drought period occurred during the sampling period. These events had variable, context-dependent effects on bacterial communities in Lough Feeagh. The particle-associated community was found to be more likely to respond to physical changes, such as mixing, while the free-living population responded to changes in nutrient and carbon concentrations. Generally, however, the high stability of the bacterial community observed in Lough Feeagh suggests that the bacterial community is relatively resilient to extreme weather events.}, language = {en} } @article{SchellenbergReichertHardtetal.2020, author = {Schellenberg, Johannes and Reichert, Jessica and Hardt, Martin and Klingelh{\"o}fer, Ines and Morlock, Gertrud and Schubert, Patrick and Bižić, Mina and Grossart, Hans-Peter and K{\"a}mpfer, Peter and Wilke, Thomas and Glaeser, Stefanie P.}, title = {The bacterial microbiome of the long-term aquarium cultured high-microbial abundance sponge Haliclona cnidata}, series = {Frontiers in Marine Science}, volume = {7}, journal = {Frontiers in Marine Science}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {2296-7745}, doi = {10.3389/fmars.2020.00266}, pages = {20}, year = {2020}, abstract = {Marine sponges host highly diverse but specific bacterial communities that provide essential functions for the sponge holobiont, including antimicrobial defense. Here, we characterized the bacterial microbiome of the marine sponge Haliclona cnidata that has been in culture in an artificial marine aquarium system. We tested the hypotheses (1) that the long-term aquarium cultured sponge H. cnidata is tightly associated with a typical sponge bacterial microbiota and (2) that the symbiotic Bacteria sustain bioactivity under harmful environmental conditions to facilitate holobiont survival by preventing pathogen invasion. Microscopic and phylogenetic analyses of the bacterial microbiota revealed that H. cnidata represents a high microbial abundance (HMA) sponge with a temporally stable bacterial community that significantly shifts with changing aquarium conditions. A 4-week incubation experiment was performed in small closed aquarium systems with antibiotic and/or light exclusion treatments to reduce the total bacterial and photosynthetically active sponge-associated microbiota to a treatment-specific resilient community. While the holobiont was severely affected by the experimental treatment (i.e., bleaching of the sponge, reduced bacterial abundance, shifted bacterial community composition), the biological defense and bacterial community interactions (i.e., quorum sensing activity) remained intact. 16S rRNA gene amplicon sequencing revealed a resilient community of 105 bacterial taxa, which remained in the treated sponges. These 105 taxa accounted for a relative abundance of 72-83\% of the bacterial sponge microbiota of non-treated sponge fragments that have been cultured under the same conditions. We conclude that a sponge-specific resilient community stays biologically active under harmful environmental conditions, facilitating the resilience of the holobiont. In H. cnidata, bacteria are located in bacteriocytes, which may have contributed to the observed phenomenon.}, language = {en} } @article{FerreraSarmentoPriscuetal.2017, author = {Ferrera, Isabel and Sarmento, Hugo and Priscu, John C. and Chiuchiolo, Amy and Gonzalez, Jose M. and Grossart, Hans-Peter}, title = {Diversity and Distribution of Freshwater Aerobic Anoxygenic Phototrophic Bacteria across a Wide Latitudinal Gradient}, series = {Frontiers in microbiology}, volume = {8}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2017.00175}, pages = {12}, year = {2017}, abstract = {Aerobic anoxygenic phototrophs (AAPs) have been shown to exist in numerous marine and brackish environments where they are hypothesized to play important ecological roles. Despite their potential significance, the study of freshwater AAPs is in its infancy and limited to local investigations. Here, we explore the occurrence, diversity and distribution of AAPs in lakes covering a wide latitudinal gradient: Mongolian and German lakes located in temperate regions of Eurasia, tropical Great East African lakes, and polar permanently ice-covered Antarctic lakes. Our results show a widespread distribution of AAPs in lakes with contrasting environmental conditions and confirm that this group is composed of different members of the Alpha- and Betaproteobacteria. While latitude does not seem to strongly influence AAP abundance, clear patterns of community structure and composition along geographic regions were observed as indicated by a strong macro-geographical signal in the taxonomical composition of AAPs. Overall, our results suggest that the distribution patterns of freshwater AAPs are likely driven by a combination of small-scale environmental conditions (specific of each lake and region) and large-scale geographic factors (climatic regions across a latitudinal gradient).}, language = {en} } @article{SchornSalmanCarvalhoLittmannetal.2019, author = {Schorn, Sina and Salman-Carvalho, Verena and Littmann, Sten and Ionescu, Danny and Grossart, Hans-Peter and Cypionka, Heribert}, title = {Cell architecture of the giant sulfur bacterium achromatium oxaliferum}, series = {FEMS Microbiology Ecology}, volume = {96}, journal = {FEMS Microbiology Ecology}, number = {2}, publisher = {Oxford University Press}, address = {Oxford}, issn = {1574-6941}, doi = {10.1093/femsec/fiz200}, pages = {1 -- 8}, year = {2019}, abstract = {Achromatium oxaliferum is a large sulfur bacterium easily recognized by large intracellular calcium carbonate bodies. Although these bodies often fill major parts of the cells' volume, their role and specific intracellular location are unclear. In this study, we used various microscopy and staining techniques to identify the cell compartment harboring the calcium carbonate bodies. We observed that Achromatium cells often lost their calcium carbonate bodies, either naturally or induced by treatments with diluted acids, ethanol, sodium bicarbonate and UV radiation which did not visibly affect the overall shape and motility of the cells (except for UV radiation). The water-soluble fluorescent dye fluorescein easily diffused into empty cavities remaining after calcium carbonate loss. Membranes (stained with Nile Red) formed a network stretching throughout the cell and surrounding empty or filled calcium carbonate cavities. The cytoplasm (stained with FITC and SYBR Green for nucleic acids) appeared highly condensed and showed spots of dissolved Ca2+ (stained with Fura-2). From our observations, we conclude that the calcium carbonate bodies are located in the periplasm, in extra-cytoplasmic pockets of the cytoplasmic membrane and are thus kept separate from the cell's cytoplasm. This periplasmic localization of the carbonate bodies might explain their dynamic formation and release upon environmental changes.}, language = {en} } @article{MasigolKhodaparastMostowfizadehGhalamfarsaetal.2020, author = {Masigol, Hossein and Khodaparast, Seyed Akbar and Mostowfizadeh-Ghalamfarsa, Reza and Rojas-Jimenez, Keilor and Woodhouse, Jason Nicholas and Neubauer, Darshan and Grossart, Hans-Peter}, title = {Taxonomical and functional diversity of Saprolegniales in Anzali lagoon, Iran}, series = {Aquatic Ecology}, volume = {54}, journal = {Aquatic Ecology}, number = {1}, publisher = {Springer Science}, address = {Dordrecht}, issn = {1573-5125}, doi = {10.1007/s10452-019-09745-w}, pages = {323 -- 336}, year = {2020}, abstract = {Studies on the diversity, distribution and ecological role of Saprolegniales (Oomycota) in freshwater ecosystems are currently receiving attention due to a greater understanding of their role in carbon cycling in various aquatic ecosystems. In this study, we characterized several Saprolegniales species isolated from Anzali lagoon, Gilan province, Iran, using morphological and molecular methods. Four species of Saprolegnia were identified, including S. anisospora and S. diclina as first reports for Iran, as well as Achlya strains, which were closely related to A. bisexualis, A. debaryana and A. intricata. Evaluation of the ligno-, cellulo- and chitinolytic activities was performed using plate assay methods. Most of the Saprolegniales isolates were obtained in autumn, and nearly 50\% of the strains showed chitinolytic and cellulolytic activities. However, only a few Saprolegniales strains showed lignolytic activities. This study has important implications for better understanding the ecological niche of oomycetes, and to differentiate them from morphologically similar, but functionally different aquatic fungi in freshwater ecosystems.}, language = {en} } @article{ZhangHuYangetal.2022, author = {Zhang, Kai and Hu, Jiege and Yang, Shuai and Xu, Wei and Wang, Zhichao and Zhuang, Peiwen and Grossart, Hans-Peter and Luo, Zhuhua}, title = {Biodegradation of polyester polyurethane by the marine fungus Cladosporium halotolerans 6UPA1}, series = {Journal of hazardous materials}, volume = {437}, journal = {Journal of hazardous materials}, publisher = {Elsevier}, address = {Amsterdam}, issn = {0304-3894}, doi = {10.1016/j.jhazmat.2022.129406}, pages = {10}, year = {2022}, abstract = {Lack of degradability and the accumulation of polymeric wastes increase the risk for the health of the environment. Recently, recycling of polymeric waste materials becomes increasingly important as raw materials for polymer synthesis are in short supply due to the rise in price and supply chain disruptions. As an important polymer, polyurethane (PU) is widely used in modern life, therefore, PU biodegradation is desirable to avoid its accumulation in the environment. In this study, we isolated a fungal strain Cladosporium halotolerans from the deep sea which can grow in mineral medium with a polyester PU (Impranil DLN) as a sole carbon source. Further, we demonstrate that it can degrade up to 80\% of Impranil PU after 3 days of incubation at 28 celcius by breaking the carbonyl groups (1732 cm(-1)) and C-N-H bonds (1532 cm(-1) and 1247 cm(-1)) as confirmed by Fourier-transform infrared (FTIR) spectroscopy analysis. Gas chromatography-mass spectrometry (GC-MS) analysis revealed polyols and alkanes as PU degradation intermediates, indicating the hydrolysis of ester and urethane bonds. Esterase and urease activities were detected in 7 days-old cultures with PU as a carbon source. Transcriptome analysis showed a number of extracellular protein genes coding for enzymes such as cutinase, lipase, peroxidase and hydrophobic surface binding proteins A (HsbA) were expressed when cultivated on Impranil PU. The yeast two-hybrid assay revealed that the hydrophobic surface binding protein ChHsbA1 directly interacts with inducible esterases, ChLip1 (lipase) and ChCut1 (cutinase). Further, the KEGG pathway for "fatty acid degradation " was significantly enriched in Impranil PU inducible genes, indicating that the fungus may use the degradation intermediates to generate energy via this pathway. Taken together, our data indicates secretion of both esterase and hydrophobic surface binding proteins by C. halotolerans plays an important role in Impranil PU absorption and subsequent degradation. Our study provides a mechanistic insight into Impranil PU biodegradation by deep sea fungi and provides the basis for future development of biotechnological PU recycling.}, language = {en} } @article{HuangQiaoXuetal.2021, author = {Huang, Lixing and Qiao, Ying and Xu, Wei and Gong, Linfeng and He, Rongchao and Qi, Weilu and Gao, Qiancheng and Cai, Hongyan and Grossart, Hans-Peter and Yan, Qingpi}, title = {Full-length transcriptome}, series = {Frontiers in immunology}, volume = {12}, journal = {Frontiers in immunology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-3224}, doi = {10.3389/fimmu.2021.737332}, pages = {18}, year = {2021}, abstract = {Fish is considered as a supreme model for clarifying the evolution and regulatory mechanism of vertebrate immunity. However, the knowledge of distinct immune cell populations in fish is still limited, and further development of techniques advancing the identification of fish immune cell populations and their functions are required. Single cell RNA-seq (scRNA-seq) has provided a new approach for effective in-depth identification and characterization of cell subpopulations. Current approaches for scRNA-seq data analysis usually rely on comparison with a reference genome and hence are not suited for samples without any reference genome, which is currently very common in fish research. Here, we present an alternative, i.e. scRNA-seq data analysis with a full-length transcriptome as a reference, and evaluate this approach on samples from Epinephelus coioides-a teleost without any published genome. We show that it reconstructs well most of the present transcripts in the scRNA-seq data achieving a sensitivity equivalent to approaches relying on genome alignments of related species. Based on cell heterogeneity and known markers, we characterized four cell types: T cells, B cells, monocytes/macrophages (Mo/M phi) and NCC (non-specific cytotoxic cells). Further analysis indicated the presence of two subsets of Mo/M phi including M1 and M2 type, as well as four subsets in B cells, i.e. mature B cells, immature B cells, pre B cells and early-pre B cells. Our research will provide new clues for understanding biological characteristics, development and function of immune cell populations of teleost. Furthermore, our approach provides a reliable alternative for scRNA-seq data analysis in teleost for which no reference genome is currently available.}, language = {en} } @article{PerkinsSantosRoseetal.2022, author = {Perkins, Anita K. and Santos, Isaac R. and Rose, Andrew L. and Schulz, Kai G. and Grossart, Hans-Peter and Eyre, Bradley D. and Kelaher, Brendan P. and Oakes, Joanne M.}, title = {Production of dissolved carbon and alkalinity during macroalgal wrack degradation on beaches}, series = {Biogeochemistry}, volume = {160}, journal = {Biogeochemistry}, number = {2}, publisher = {Springer}, address = {Dordrecht}, issn = {0168-2563}, doi = {10.1007/s10533-022-00946-4}, pages = {159 -- 175}, year = {2022}, abstract = {Marine macroalgae are a key primary producer in coastal ecosystems, but are often overlooked in blue carbon inventories. Large quantities of macroalgal detritus deposit on beaches, but the fate of wrack carbon (C) is little understood. If most of the wrack carbon is respired back to CO2, there would be no net carbon sequestration. However, if most of the wrack carbon is converted to bicarbonate (alkalinity) or refractory DOC, wrack deposition would represent net carbon sequestration if at least part of the metabolic products (e.g., reduced Fe and S) are permanently removed (i.e., long-term burial) and the DOC is not remineralised. To investigate the release of macroalgal C via porewater and its potential to contribute to C sequestration (blue carbon), we monitored the degradation of Ecklonia radiata in flow-through mesocosms simulating tidal flushing on sandy beaches. Over 60 days, 81\% of added E. radiata organic matter (OM) decomposed. Per 1 mol of detritus C, the degradation produced 0.48 +/- 0.34 mol C of dissolved organic carbon (DOC) (59\%) and 0.25 +/- 0.07 mol C of dissolved inorganic carbon (DIC) (31\%) in porewater, and a small amount of CO2 (0.3 +/- 0.0 mol C; ca. 3\%) which was emitted to the atmosphere. A significant amount of carbonate alkalinity was found in porewater, equating to 33\% (0.27 +/- 0.05 mol C) of the total degraded C. The degradation occurred in two phases. In the first phase (days 0-3), 27\% of the OM degraded, releasing highly reactive DOC. In the second phase (days 4-60), the labile DOC was converted to DIC. The mechanisms underlying E. radiata degradation were sulphate reduction and ammonification. It is likely that the carbonate alkalinity was primarily produced through sulphate reduction. The formation of carbonate alkalinity and semi-labile or refractory DOC from beach wrack has the potential to play an overlooked role in coastal carbon cycling and contribute to marine carbon sequestration.}, language = {en} } @article{BizicIonescuKarnataketal.2022, author = {Bizic, Mina and Ionescu, Danny and Karnatak, Rajat and Musseau, Camille L. and Onandia, Gabriela and Berger, Stella A. and Nejstgaard, Jens C. and Lischeid, Gunnar and Gessner, Mark O. and Wollrab, Sabine and Grossart, Hans-Peter}, title = {Land-use type temporarily affects active pond community structure but not gene expression patterns}, series = {Molecular ecology}, volume = {31}, journal = {Molecular ecology}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0962-1083}, doi = {10.1111/mec.16348}, pages = {1716 -- 1734}, year = {2022}, abstract = {Changes in land use and agricultural intensification threaten biodiversity and ecosystem functioning of small water bodies. We studied 67 kettle holes (KH) in an agricultural landscape in northeastern Germany using landscape-scale metatranscriptomics to understand the responses of active bacterial, archaeal and eukaryotic communities to land-use type. These KH are proxies of the millions of small standing water bodies of glacial origin spread across the northern hemisphere. Like other landscapes in Europe, the study area has been used for intensive agriculture since the 1950s. In contrast to a parallel environmental DNA study that suggests the homogenization of biodiversity across KH, conceivably resulting from long-lasting intensive agriculture, land-use type affected the structure of the active KH communities during spring crop fertilization, but not a month later. This effect was more pronounced for eukaryotes than for bacteria. In contrast, gene expression patterns did not differ between months or across land-use types, suggesting a high degree of functional redundancy across the KH communities. Variability in gene expression was best explained by active bacterial and eukaryotic community structures, suggesting that these changes in functioning are primarily driven by interactions between organisms. Our results indicate that influences of the surrounding landscape result in temporary changes in the activity of different community members. Thus, even in KH where biodiversity has been homogenized, communities continue to respond to land management. This potential needs to be considered when developing sustainable management options for restoration purposes and for successful mitigation of further biodiversity loss in agricultural landscapes.}, language = {en} } @article{AichnerDubbertKieletal.2022, author = {Aichner, Bernhard and Dubbert, David and Kiel, Christine and Kohnert, Katrin and Ogashawara, Igor and Jechow, Andreas and Harpenslager, Sarah-Faye and H{\"o}lker, Franz and Nejstgaard, Jens Christian and Grossart, Hans-Peter and Singer, Gabriel and Wollrab, Sabine and Berger, Stella Angela}, title = {Spatial and seasonal patterns of water isotopes in northeastern German lakes}, series = {Earth system science data : ESSD}, volume = {14}, journal = {Earth system science data : ESSD}, number = {4}, publisher = {Copernicus}, address = {G{\"o}ttingen}, issn = {1866-3508}, doi = {10.5194/essd-14-1857-2022}, pages = {1857 -- 1867}, year = {2022}, abstract = {Water stable isotopes (delta O-18 and delta H-2) were analyzed in samples collected in lakes, associated with riverine systems in northeastern Germany, throughout 2020. The dataset (Aichner et al., 2021; https://doi.org/10.1594/PANGAEA.935633) is derived from water samples collected at (a) lake shores (sampled in March and July 2020), (b) buoys which were temporarily installed in deep parts of the lake (sampled monthly from March to October 2020), (c) multiple spatially distributed spots in four selected lakes (in September 2020), and (d) the outflow of Muggelsee (sampled biweekly from March 2020 to January 2021). At shores, water was sampled with a pipette from 40-60 cm below the water surface and directly transferred into a measurement vial, while at buoys a Limnos water sampler was used to obtain samples from 1 m below the surface. Isotope analysis was conducted at IGB Berlin, using a Picarro L2130-i cavity ring-down spectrometer, with a measurement uncertainty of < 0.15 parts per thousand (delta O-18) and < 0.0 parts per thousand (delta H-2). The data give information about the vegetation period and the full seasonal isotope amplitude in the sampled lakes and about spatial isotope variability in different branches of the associated riverine systems.}, language = {en} } @article{VillalbaKarnatakGrossartetal.2022, author = {Villalba, Luis Alberto and Karnatak, Rajat and Grossart, Hans-Peter and Wollrab, Sabine}, title = {Flexible habitat choice of pelagic bacteria increases system stability and energy flow through the microbial loop}, series = {Limnology and oceanography : L \& O}, volume = {67}, journal = {Limnology and oceanography : L \& O}, number = {6}, publisher = {Wiley-Blackwell}, address = {Oxford [u.a.]}, issn = {0024-3590}, doi = {10.1002/lno.12091}, pages = {1402 -- 1415}, year = {2022}, abstract = {Pelagic bacteria can be classified into free-living and particle-attached life modes, which either dwell in the water column or attach to suspended particles. Bacteria with a generalist life style, however, can actively shift between these two habitats. Globally increasing densities of natural and artificial particles enhance habitat heterogeneity, with potential consequences for system stability and trophic transfer through aquatic food webs. To better decipher the dynamics of microbial communities, we investigated the influence of adaptive vs. fixed habitat choice on species coexistence for a simplified bacterial community by analyzing a corresponding food web model, consisting of two specialist bacterial prey species (free and attached), a generalist bacterial prey species with the ability to shift between both habitats, and two protist predators, specialized on either water or particle compartment. For simplicity we assume a shared resource pool, considering particles only for colonization but not as a source for nutrients or carbon, that is, inert particles like microplastics or inorganic sediments. The model predicts coexistence on a cyclic attractor between fixed and flexible bacteria, if the costs for adaptive habitat choice can be balanced by adaptation speed. The presence of adaptive prey dampens predator-prey cycle amplitudes, contributing to system stabilization resulting in higher mean predator biomass compared to specialist prey only. Thus, in pelagic microbial systems, flexible habitat choice at the prey level has important implications for system stability and magnitude of energy flow through the microbial loop.}, language = {en} } @article{HiltGrossartMcGinnisetal.2022, author = {Hilt, Sabine and Grossart, Hans-Peter and McGinnis, Daniel F. and Keppler, Frank}, title = {Potential role of submerged macrophytes for oxic methane production in aquatic ecosystems}, series = {Limnology and oceanography}, journal = {Limnology and oceanography}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, doi = {10.1002/lno.12095}, pages = {13}, year = {2022}, abstract = {Methane (CH4) from aquatic ecosystems contributes to about half of total global CH4 emissions to the atmosphere. Until recently, aquatic biogenic CH4 production was exclusively attributed to methanogenic archaea living under anoxic or suboxic conditions in sediments, bottom waters, and wetlands. However, evidence for oxic CH4 production (OMP) in freshwater, brackish, and marine habitats is increasing. Possible sources were found to be driven by various planktonic organisms supporting different OMP mechanisms. Surprisingly, submerged macrophytes have been fully ignored in studies on OMP, yet they are key components of littoral zones of ponds, lakes, and coastal systems. High CH4 concentrations in these zones have been attributed to organic substrate production promoting classic methanogenesis in the absence of oxygen. Here, we review existing studies and argue that, similar to terrestrial plants and phytoplankton, macroalgae and submerged macrophytes may directly or indirectly contribute to CH4 formation in oxic waters. We propose several potential direct and indirect mechanisms: (1) direct production of CH4; (2) production of CH4 precursors and facilitation of their bacterial breakdown or chemical conversion; (3) facilitation of classic methanogenesis; and (4) facilitation of CH4 ebullition. As submerged macrophytes occur in many freshwater and marine habitats, they are important in global carbon budgets and can strongly vary in their abundance due to seasonal and boom-bust dynamics. Knowledge on their contribution to OMP is therefore essential to gain a better understanding of spatial and temporal dynamics of CH4 emissions and thus to substantially reduce current uncertainties when estimating global CH4 emissions from aquatic ecosystems.}, language = {en} } @article{MannaZoccaratoBanchietal.2022, author = {Manna, Vincenzo and Zoccarato, Luca and Banchi, Elisa and Arnosti, Carol and Grossart, Hans-Peter and Celussi, Mauro}, title = {Linking lifestyle and foraging strategies of marine bacteria}, series = {Environmental microbiology reports}, volume = {14}, journal = {Environmental microbiology reports}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.13059}, pages = {549 -- 558}, year = {2022}, abstract = {Microbe-mediated enzymatic hydrolysis of organic matter entails the production of hydrolysate, the recovery of which may be more or less efficient. The selfish uptake mechanism, recently discovered, allows microbes to hydrolyze polysaccharides and take up large oligomers, which are then degraded in the periplasmic space. By minimizing the hydrolysate loss, selfish behaviour may be profitable for free-living cells dwelling in a patchy substrate landscape. However, selfish uptake seems to be tailored to algal-derived polysaccharides, abundant in organic particles, suggesting that particle-attached microbes may use this strategy. We tracked selfish polysaccharides uptake in surface microbial communities of the northeastern Mediterranean Sea, linking the occurrence of this processing mode with microbial lifestyle. Additionally, we set up fluorescently labelled polysaccharides incubations supplying phytodetritus to investigate a 'pioneer' scenario for particle-attached microbes. Under both conditions, selfish behaviour was almost exclusively carried out by particle-attached microbes, suggesting that this mechanism may represent an advantage in the race for particle exploitation. Our findings shed light on the selfish potential of particle-attached microbes, suggesting multifaceted foraging strategies exerted by particle colonizers.}, language = {en} } @article{IlicicGrossart2022, author = {Ilicic, Doris and Grossart, Hans-Peter}, title = {Basal parasitic fungi in marine food webs-a mystery yet to unravel}, series = {Journal of Fungi}, volume = {8}, journal = {Journal of Fungi}, number = {2}, publisher = {MDPI}, address = {Basel}, issn = {2309-608X}, doi = {10.3390/jof8020114}, pages = {16}, year = {2022}, abstract = {Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research.}, 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{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{ZoccaratoSherMikietal.2022, author = {Zoccarato, Luca and Sher, Daniel and Miki, Takeshi and Segre, Daniel and Grossart, Hans-Peter}, title = {A comparative whole-genome approach identifies bacterial traits for marine microbial interactions}, series = {Communications biology}, volume = {5}, journal = {Communications biology}, number = {1}, publisher = {Springer Nature}, address = {Berlin}, issn = {2399-3642}, doi = {10.1038/s42003-022-03184-4}, pages = {13}, year = {2022}, abstract = {Luca Zoccarato, Daniel Sher et al. leverage publicly available bacterial genomes from marine and other environments to examine traits underlying microbial interactions. Their results provide a valuable resource to investigate clusters of functional and linked traits to better understand marine bacteria community assembly and dynamics. Microbial interactions shape the structure and function of microbial communities with profound consequences for biogeochemical cycles and ecosystem health. Yet, most interaction mechanisms are studied only in model systems and their prevalence is unknown. To systematically explore the functional and interaction potential of sequenced marine bacteria, we developed a trait-based approach, and applied it to 473 complete genomes (248 genera), representing a substantial fraction of marine microbial communities. We identified genome functional clusters (GFCs) which group bacterial taxa with common ecology and life history. Most GFCs revealed unique combinations of interaction traits, including the production of siderophores (10\% of genomes), phytohormones (3-8\%) and different B vitamins (57-70\%). Specific GFCs, comprising Alpha- and Gammaproteobacteria, displayed more interaction traits than expected by chance, and are thus predicted to preferentially interact synergistically and/or antagonistically with bacteria and phytoplankton. Linked trait clusters (LTCs) identify traits that may have evolved to act together (e.g., secretion systems, nitrogen metabolism regulation and B vitamin transporters), providing testable hypotheses for complex mechanisms of microbial interactions. Our approach translates multidimensional genomic information into an atlas of marine bacteria and their putative functions, relevant for understanding the fundamental rules that govern community assembly and dynamics.}, language = {en} } @article{TolomeevDubovskayaKirillinetal.2022, author = {Tolomeev, Aleksandr P. and Dubovskaya, Olga P. and Kirillin, Georgiy and Buseva, Zhanna and Kolmakova, Olesya and Grossart, Hans-Peter and Tang, Kam W. and Gladyšev, Michail I.}, title = {Degradation of dead cladoceran zooplankton and their contribution to organic carbon cycling in stratified lakes}, series = {Journal of plankton research}, volume = {44}, journal = {Journal of plankton research}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0142-7873}, doi = {10.1093/plankt/fbac023}, pages = {386 -- 400}, year = {2022}, abstract = {The contribution of dead zooplankton biomass to carbon cycle in aquatic ecosystems is practically unknown. Using abundance data of zooplankton in water column and dead zooplankton in sediment traps in Lake Stechlin, an ecological-mathematical model was developed to simulate the abundance and sinking of zooplankton carcasses and predict the related release of labile organic matter (LOM) into the water column. We found species-specific differences in mortality rate of the dominant zooplankton: Daphnia cucullata, Bosmina coregoni and Diaphanosoma brachyurum (0.008, 0.129 and 0.020 day(-1), respectively) and differences in their carcass sinking velocities in metalimnion (and hypolimnion): 2.1 (7.64), 14.0 (19.5) and 1.1 (5.9) m day(-1), respectively. Our model simulating formation and degradation processes of dead zooplankton predicted a bimodal distribution of the released LOM: epilimnic and metalimnic peaks of comparable intensity, ca. 1 mg DW m(-3) day(-1). Maximum degradation of carcasses up to ca. 1.7 mg DW m(-3) day(-1) occurred in the density gradient zone of metalimnion. LOM released from zooplankton carcasses into the surrounding water may stimulate microbial activity and facilitate microbial degradation of more refractory organic matter; therefore, dead zooplankton are expected to be an integral part of water column carbon source/sink dynamics in stratified lakes.}, language = {en} } @article{VatovaRubinGrossartetal.2022, author = {Vatova, Mariyana and Rubin, Conrad and Grossart, Hans-Peter and Goncalves, Susana C. and Schmidt, Susanne I. and Jarić, Ivan}, title = {Aquatic fungi: largely neglected targets for conservation}, series = {Frontiers in ecology and the environment}, volume = {20}, journal = {Frontiers in ecology and the environment}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {1540-9295}, doi = {10.1002/fee.2495}, pages = {207 -- 209}, year = {2022}, language = {en} } @phdthesis{Hempel2024, author = {Hempel, Elisabeth}, title = {Resolving the evolutionary history of two hippotragin antelopes using archival and ancient DNA}, doi = {10.25932/publishup-64771}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-647718}, school = {Universit{\"a}t Potsdam}, pages = {xii, 224}, year = {2024}, abstract = {African antelopes are iconic but surprisingly understudied in terms of their genetics, especially when it comes to their evolutionary history and genetic diversity. The age of genomics provides an opportunity to investigate evolution using whole nuclear genomes. Decreasing sequencing costs enable the recovery of multiple loci per genome, giving more power to single specimen analyses and providing higher resolution insights into species and populations that can help guide conservation efforts. This age of genomics has only recently begun for African antelopes. Many African bovids have a declining population trend and hence, are often endangered. Consequently, contemporary samples from the wild are often hard to collect. In these cases, ex situ samples from contemporary captive populations or in the form of archival or ancient DNA (aDNA) from historical museum or archaeological/paleontological specimens present a great research opportunity with the latter two even offering a window to information about the past. However, the recovery of aDNA is still considered challenging from regions with prevailing climatic conditions that are deemed adverse for DNA preservation like the African continent. This raises the question if DNA recovery from fossils as old as the early Holocene from these regions is possible. This thesis focuses on investigating the evolutionary history and genetic diversity of two species: the addax (Addax nasomaculatus) and the blue antelope (Hippotragus leucophaeus). The addax is critically endangered and might even already be extinct in the wild, while the blue antelope became extinct ~1800 AD, becoming the first extinct large African mammal species in historical times. Together, the addax and the blue antelope can inform us about current and past extinction events and the knowledge gained can help guide conservation efforts of threatened species. The three studies used ex situ samples and present the first nuclear whole genome data for both species. The addax study used historical museum specimens and a contemporary sample from a captive population. The two studies on the blue antelope used mainly historical museum specimens but also fossils, and resulted in the recovery of the oldest paleogenome from Africa at that time. The aim of the first study was to assess the genetic diversity and the evolutionary history of the addax. It found that the historical wild addax population showed only limited phylogeographic structuring, indicating that the addax was a highly mobile and panmictic population and suggesting that the current European captive population might be missing the majority of the historical mitochondrial diversity. It also found the nuclear and mitochondrial diversity in the addax to be rather low compared to other wild ungulate species. Suggestions on how to best save the remaining genetic diversity are presented. The European zoo population was shown to exhibit no or only minor levels of inbreeding, indicating good prospects for the restoration of the species in the wild. The trajectory of the addax's effective population size indicated a major bottleneck in the late Pleistocene and a low effective population size well before recent human impact led to the species being critically endangered today. The second study set out to investigate the identities of historical blue antelope specimens using aDNA techniques. Results showed that six out of ten investigated specimens were misidentified, demonstrating the blue antelope to be one of the scarcest mammal species in historical natural history collections, with almost no bone reference material. The preliminary analysis of the mitochondrial genomes suggested a low diversity and hence low population size at the time of the European colonization of southern Africa. Study three presents the results of the analyses of two blue antelope nuclear genomes, one ~200 years old and another dating to the early Holocene, 9,800-9,300 cal years BP. A fossil-calibrated phylogeny dated the divergence time of the three historically extant Hippotragus species to ~2.86 Ma and demonstrated the blue and the sable antelope (H. niger) to be sister species. In addition, ancient gene flow from the roan (H. equinus) into the blue antelope was detected. A comparison with the roan and the sable antelope indicated that the blue antelope had a much lower nuclear diversity, suggesting a low population size since at least the early Holocene. This concurs with findings from the fossil record that show a considerable decline in abundance after the Pleistocene-Holocene transition. Moreover, it suggests that the blue antelope persisted throughout the Holocene regardless of a low population size, indicating that human impact in the colonial era was a major factor in the blue antelope's extinction. This thesis uses aDNA analyses to provide deeper insights into the evolutionary history and genetic diversity of the addax and the blue antelope. Human impact likely was the main driver of extinction in the blue antelope, and is likely the main factor threatening the addax today. This thesis demonstrates the value of ex situ samples for science and conservation, and suggests to include genetic data for conservation assessments of species. It further demonstrates the beneficial use of aDNA for the taxonomic identification of historically important specimens in natural history collections. Finally, the successful retrieval of a paleogenome from the early Holocene of Africa using shotgun sequencing shows that DNA retrieval from samples of that age is possible from regions generally deemed unfavorable for DNA preservation, opening up new research opportunities. All three studies enhance our knowledge of African antelopes, contributing to the general understanding of African large mammal evolution and to the conservation of these and similarly threatened species.}, language = {en} } @phdthesis{Kueken2020, author = {K{\"u}ken, Anika}, title = {Predictions from constraint-based approaches including enzyme kinetics}, school = {Universit{\"a}t Potsdam}, pages = {116, A-16, B-7, C-8}, year = {2020}, abstract = {The metabolic state of an organism reflects the entire phenotype that is jointly affected by genetic and environmental changes. Due to the complexity of metabolism, system-level modelling approaches have become indispensable tools to obtain new insights into biological functions. In particular, simulation and analysis of metabolic networks using constraint-based modelling approaches have helped the analysis of metabolic fluxes. However, despite ongoing improvements in prediction of reaction flux through a system, approaches to directly predict metabolite concentrations from large-scale metabolic networks remain elusive. In this thesis, we present a computational approach for inferring concentration ranges from genome-scale metabolic models endowed with mass action kinetics. The findings specify a molecular mechanism underling facile control of concentration ranges for components in large-scale metabolic networks. Most importantly, an extended version of the approach can be used to predict concentration ranges without knowledge of kinetic parameters, provided measurements of concentrations in a reference state. We show that the approach is applicable with large-scale kinetic and stoichiometric metabolic models of organisms from different kingdoms of life. By challenging the predictions of concentration ranges in the genome-scale metabolic network of Escherichia coli with real-world data sets, we further demonstrate the prediction power and limitations of the approach. To predict concentration ranges in other species, e.g. model plant species Arabidopsis thaliana, we would rely on estimates of kinetic parameters (i.e. enzyme catalytic rates) since plant-specific enzyme catalytic rates are poorly documented. Using the constraint-based approach of Davidi et al. for estimation of enzyme catalytic rates, we obtain values for 168 plant enzymes. The approach depends on quantitative proteomics data and flux estimates obtained from constraint-based model of plant leaf metabolism integrating maximal rates of selected enzymes, plant-specific constraints on fluxes through canonical pathways, and growth measurements from Arabidopsis thaliana rosette under ten conditions. We demonstrate a low degree of plant enzyme saturation, supported by the agreement between concentrations of nicotinamide adenine dinucleotide, adenosine triphosphate, and glyceraldehyde 3-phosphate, based on our maximal in vivo catalytic rates, and available quantitative metabolomics data. Hence, our results show genome-wide estimation for plant-specific enzyme catalytic rates is feasible. These can now be readily employed to study resource allocation, to predict enzyme and metabolite concentrations using recent constrained-based modelling approaches. Constraint-based methods do not directly account for kinetic mechanisms and corresponding parameters. Therefore, a number of workflows have already been proposed to approximate reaction kinetics and to parameterize genome-scale kinetic models. We present a systems biology strategy to build a fully parameterized large-scale model of Chlamydomonas reinhardtii accounting for microcompartmentalization in the chloroplast stroma. Eukaryotic algae comprise a microcompartment, the pyrenoid, essential for the carbon concentrating mechanism (CCM) that improves their photosynthetic performance. Since the experimental study of the effects of microcompartmentation on metabolic pathways is challenging, we employ our model to investigate compartmentation of fluxes through the Calvin-Benson cycle between pyrenoid and stroma. Our model predicts that ribulose-1,5-bisphosphate, the substrate of Rubisco, and 3-phosphoglycerate, its product, diffuse in and out of the pyrenoid. We also find that there is no major diffusional barrier to metabolic flux between the pyrenoid and stroma. Therefore, our computational approach represents a stepping stone towards understanding of microcompartmentalized CCM in other organisms. This thesis provides novel strategies to use genome-scale metabolic networks to predict and integrate metabolite concentrations. Therefore, the presented approaches represent an important step in broadening the applicability of large-scale metabolic models to a range of biotechnological and medical applications.}, language = {en} } @article{KuekenNikoloski2019, author = {K{\"u}ken, Anika and Nikoloski, Zoran}, title = {Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways}, series = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, volume = {179}, journal = {Plant physiology : an international journal devoted to physiology, biochemistry, cellular and molecular biology, biophysics and environmental biology of plants}, number = {3}, publisher = {American Society of Plant Physiologists}, address = {Rockville}, issn = {0032-0889}, doi = {10.1104/pp.18.01273}, pages = {894 -- 906}, year = {2019}, abstract = {Successfully designed and implemented plant-specific synthetic metabolic pathways hold promise to increase crop yield and nutritional value. Advances in synthetic biology have already demonstrated the capacity to design artificial biological pathways whose behavior can be predicted and controlled in microbial systems. However, the transfer of these advances to model plants and crops faces the lack of characterization of plant cellular pathways and increased complexity due to compartmentalization and multicellularity. Modern computational developments provide the means to test the feasibility of plant synthetic metabolic pathways despite gaps in the accumulated knowledge of plant metabolism. Here, we provide a succinct systematic review of optimization-based and retrobiosynthesis approaches that can be used to design and in silico test synthetic metabolic pathways in large-scale plant context-specific metabolic models. In addition, by surveying the existing case studies, we highlight the challenges that these approaches face when applied to plants. Emphasis is placed on understanding the effect that metabolic designs can have on native metabolism, particularly with respect to metabolite concentrations and thermodynamics of biochemical reactions. In addition, we discuss the computational developments that may help to transform the identified challenges into opportunities for plant synthetic biology.}, language = {en} } @misc{KoenigWeigeltTayloretal.2020, author = {K{\"o}nig, Christian and Weigelt, Patrick and Taylor, Amanda and Stein, Anke and Dawson, Wayne and Essl, Franz and Pergl, Jan and Pyšek, Petr and Kleunen, Mark van and Winter, Marten and Chatelain, Cyrille and Wieringa, Jan J. and Krestov, Pavel and Kreft, Holger}, title = {Source pools and disharmony of the world's island floras}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1}, issn = {1866-8372}, doi = {10.25932/publishup-52510}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-525101}, pages = {14}, year = {2020}, abstract = {Island disharmony refers to the biased representation of higher taxa on islands compared to their mainland source regions and represents a central concept in island biology. Here, we develop a generalizable framework for approximating these source regions and conduct the first global assessment of island disharmony and its underlying drivers. We compiled vascular plant species lists for 178 oceanic islands and 735 mainland regions. Using mainland data only, we modelled species turnover as a function of environmental and geographic distance and predicted the proportion of shared species between each island and mainland region. We then quantified the over- or under-representation of families on individual islands (representational disharmony) by contrasting the observed number of species against a null model of random colonization from the mainland source pool, and analysed the effects of six family-level functional traits on the resulting measure. Furthermore, we aggregated the values of representational disharmony per island to characterize overall taxonomic bias of a given flora (compositional disharmony), and analysed this second measure as a function of four island biogeographical variables. Our results indicate considerable variation in representational disharmony both within and among plant families. Examples of generally over-represented families include Urticaceae, Convolvulaceae and almost all pteridophyte families. Other families such as Asteraceae and Orchidaceae were generally under-represented, with local peaks of over-representation in known radiation hotspots. Abiotic pollination and a lack of dispersal specialization were most strongly associated with an insular over-representation of families, whereas other family-level traits showed minor effects. With respect to compositional disharmony, large, high-elevation islands tended to have the most disharmonic floras. Our results provide important insights into the taxon- and island-specific drivers of disharmony. The proposed framework allows overcoming the limitations of previous approaches and provides a quantitative basis for incorporating functional and phylogenetic approaches into future studies of island disharmony.}, language = {en} } @phdthesis{Kindermann2024, author = {Kindermann, Liana}, title = {Trees, shrubs, and land-use change}, doi = {10.25932/publishup-64894}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-648943}, school = {Universit{\"a}t Potsdam}, pages = {X, 186}, year = {2024}, abstract = {The global drylands cover nearly half of the terrestrial surface and are home to more than two billion people. In many drylands, ongoing land-use change transforms near-natural savanna vegetation to agricultural land to increase food production. In Southern Africa, these heterogenous savanna ecosystems are also recognized as habitats of many protected animal species, such as elephant, lion and large herds of diverse herbivores, which are of great value for the tourism industry. Here, subsistence farmers and livestock herder communities often live in close proximity to nature conservation areas. Although these land-use transformations are different regarding the future they aspire to, both processes, nature conservation with large herbivores and agricultural intensification, have in common, that they change the vegetation structure of savanna ecosystems, usually leading to destruction of trees, shrubs and the woody biomass they consist of. Such changes in woody vegetation cover and biomass are often regarded as forms of land degradation and forest loss. Global forest conservation approaches and international programs aim to stop degradation processes, also to conserve the carbon bound within wood from volatilization into earth's atmosphere. In search for mitigation options against global climate change savannas are increasingly discussed as potential carbon sinks. Savannas, however, are not forests, in that they are naturally shaped by and adapted to disturbances, such as wildfires and herbivory. Unlike in forests, disturbances are necessary for stable, functioning savanna ecosystems and prevent these ecosystems from forming closed forest stands. Their consequently lower levels of carbon storage in woody vegetation have long been the reason for savannas to be overlooked as a potential carbon sink but recently the question was raised if carbon sequestration programs (such as REDD+) could also be applied to savanna ecosystems. However, heterogenous vegetation structure and chronic disturbances hamper the quantification of carbon stocks in savannas, and current procedures of carbon storage estimation entail high uncertainties due to methodological obstacles. It is therefore challenging to assess how future land-use changes such as agricultural intensification or increasing wildlife densities will impact the carbon storage balance of African drylands. In this thesis, I address the research gap of accurately quantifying carbon storage in vegetation and soils of disturbance-prone savanna ecosystems. I further analyse relevant drivers for both ecosystem compartments and their implications for future carbon storage under land-use change. Moreover, I show that in savannas different carbon storage pools vary in their persistence to disturbance, causing carbon bound in shrub vegetation to be most likely to experience severe losses under land-use change while soil organic carbon stored in subsoils is least likely to be impacted by land-use change in the future. I start with summarizing conventional approaches to carbon storage assessment and where and for which reasons they fail to accurately estimated savanna ecosystem carbon storage. Furthermore, I outline which future-making processes drive land-use change in Southern Africa along two pathways of land-use transformation and how these are likely to influence carbon storage. In the following chapters, I propose a new method of carbon storage estimation which is adapted to the specific conditions of disturbance-prone ecosystems and demonstrate the advantages of this approach in relation to existing forestry methods. Specifically, I highlight sources for previous over- and underestimation of savanna carbon stocks which the proposed methodology resolves. In the following chapters, I apply the new method to analyse impacts of land-use change on carbon storage in woody vegetation in conjunction with the soil compartment. With this interdisciplinary approach, I can demonstrate that indeed both, agricultural intensification and nature conservation with large herbivores, reduce woody carbon storage above- and belowground, but partly sequesters this carbon into the soil organic carbon stock. I then quantify whole-ecosystem carbon storage in different ecosystem compartments (above- and belowground woody carbon in shrubs and trees, respectively, as well as topsoil and subsoil organic carbon) of two savanna vegetation types (scrub savanna and savanna woodland). Moreover, in a space-for-time substitution I analyse how land-use changes impact carbon storage in each compartment and in the whole ecosystem. Carbon storage compartments are found to differ in their persistence to land-use change with carbon bound in shrub biomass being least persistent to future changes and subsoil organic carbon being most stable under changing land-use. I then explore which individual land-use change effects act as drivers of carbon storage through Generalized Additive Models (GAMs) and uncover non-linear effects, especially of elephant browsing, with implications for future carbon storage. In the last chapter, I discuss my findings in the larger context of this thesis and discuss relevant implications for land-use change and future-making decisions in rural Africa.}, language = {en} } @article{ZwickelKahlRychliketal.2018, author = {Zwickel, Theresa and Kahl, Sandra and Rychlik, Michael and M{\"u}ller, Marina E. H.}, title = {Chemotaxonomy of Mycotoxigenic Small-Spored Alternaria Fungi}, series = {Frontiers in microbiology}, volume = {9}, journal = {Frontiers in microbiology}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2018.01368}, pages = {20}, year = {2018}, abstract = {Necrotrophic as well as saprophytic small-spored Altemaria (A.) species are annually responsible for major losses of agricultural products, such as cereal crops, associated with the contamination of food and feedstuff with potential health-endangering Altemaria toxins. Knowledge of the metabolic capabilities of different species-groups to form mycotoxins is of importance for a reliable risk assessment. 93 Altemaria strains belonging to the four species groups Alternaria tenuissima, A. arborescens, A. altemata, and A. infectoria were isolated from winter wheat kernels harvested from fields in Germany and Russia and incubated under equal conditions. Chemical analysis by means of an HPLC-MS/MS multi-Alternaria-toxin-method showed that 95\% of all strains were able to form at least one of the targeted 17 non-host specific Altemaria toxins. Simultaneous production of up to 15 (modified) Altemaria toxins by members of the A. tenuissima, A. arborescens, A. altemata species-groups and up to seven toxins by A. infectoria strains was demonstrated. Overall tenuazonic acid was the most extensively formed mycotoxin followed by alternariol and alternariol mono methylether, whereas altertoxin I was the most frequently detected toxin. Sulfoconjugated modifications of alternariol, alternariol mono methylether, altenuisol and altenuene were frequently determined. Unknown perylene quinone derivatives were additionally detected. Strains of the species-group A. infectoria could be segregated from strains of the other three species-groups due to significantly lower toxin levels and the specific production of infectopyrone. Apart from infectopyrone, alterperylenol was also frequently produced by 95\% of the A. infectoria strains. Neither by the concentration nor by the composition of the targeted Altemaria toxins a differentiation between the species-groups A. altemata, A. tenuissima and A. arborescens was possible.}, language = {en} } @article{NeiberKahlWiggeringetal.2019, author = {Neiber, Marco Thomas and Kahl, Sandra and Wiggering, Benedikt and Glaubrecht, Matthias}, title = {Adding the West-African riverine component}, series = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, volume = {4674}, journal = {Zootaxa : an international journal of zootaxonomy ; a rapid international journal for animal taxonomists}, number = {3}, publisher = {Magnolia Press}, address = {Auckland}, issn = {1175-5326}, doi = {10.11646/zootaxa.4674.3.1}, pages = {301 -- 328}, year = {2019}, abstract = {While Africa's lacustrine gastropod fauna, in particular of Lake Tanganyika, has received much attention, the continent's riverine malacofauna has long been neglected. Pseudocleopatra is a relatively poorly known paludomid gastropod genus with species found throughout the lower reaches of the West African Volta and Congo rivers. In the course of ongoing systematic revisions of African paludomids, we present here a morphometric analysis and revision of the recent species assigned to the genus, i.e., P. togoensis, P. voltana, P. dartevellei and P. bennikei, to improve taxonomic acuity for this group. We use available museum material for geometric morphometrics, multivariate ratio analysis and comparisons of radular and opercular characters. Our results demonstrate that the four recent species of Pseudocleopatra are clearly distinguishable on the basis of ratios of shell measurements as well as radular and opercular characters. Pseudocleopatra has generic-level synapomorphies including: concentric opercula with relatively large paucispiral nuclei, and rachidian radular teeth with usually 13-20 cusps. On the basis of this characterisation, the nominal species Cleopatra broecki is transferred to Pseudocleopatra. Additionally, the nominal taxon P. bennikei is synonymized with P. broecki n. comb. The phylogenetic relationships of Pseudocleopatra are currently unknown, but the observed tendency of some fossil taxa assigned to Pseudocleopatra towards thalassoidism, i.e., the resemblance to marine gastropods, has led to the hypothesis that some of the thalassoid endemics in Lake Tanganyika may have originated from or be related to Pseudocleopatra. Should this hypothesis be correct, which is in need of testing by molecular genetic methods when suitable samples become available, Pseudocleopatra may play a crucial role in understanding of the evolution of thalassoidism in African Paludomidae.}, language = {en} } @article{KahlLenhardJoshi2019, author = {Kahl, Sandra and Lenhard, Michael and Joshi, Jasmin Radha}, title = {Compensatory mechanisms to climate change in the widely distributed species Silene vulgaris}, series = {The journal of ecology}, volume = {107}, journal = {The journal of ecology}, number = {4}, publisher = {Wiley}, address = {Hoboken}, issn = {0022-0477}, doi = {10.1111/1365-2745.13133}, pages = {1918 -- 1930}, year = {2019}, abstract = {The adaptation of plants to future climatic conditions is crucial for their survival. Not surprisingly, phenotypic responses to climate change have already been observed in many plant populations. These responses may be due to evolutionary adaptive changes or phenotypic plasticity. Especially plant species with a wide geographic range are either expected to show genetic differentiation in response to differing climate conditions or to have a high phenotypic plasticity. We investigated phenotypic responses and plasticity as an estimate of the adaptive potential in the widespread species Silene vulgaris. In a greenhouse experiment, 25 European populations covering a geographic range from the Canary Islands to Sweden were exposed to three experimental precipitation and two temperature regimes mimicking a possible climate-change scenario for central Europe. We hypothesized that southern populations have a better performance under high temperature and drought conditions, as they are already adapted to a comparable environment. We found that our treatments significantly influenced the plants, but did not reveal a latitudinal difference in response to climate treatments for most plant traits. Only flower number showed a stronger plasticity in northern European populations (e.g. Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation treatment. Synthesis. The significant treatment response in Silene vulgaris, independent of population origin - except for the number of flowers produced - suggests a high degree of universal phenotypic plasticity in this widely distributed species. This reflects the likely adaptation strategy of the species and forms the basis for a successful survival strategy during upcoming climatic changes. However, as flower number, a strongly fitness-related trait, decreased more strongly in northern populations under a climate-change scenario, there might be limits to adaptation even in this widespread, plastic species.}, language = {en} } @article{BornhorstSeyfried2021, author = {Bornhorst, Dorothee and Seyfried, Salim}, title = {Strong as a hippo's heart}, series = {Frontiers in cell and developmental biology}, volume = {9}, journal = {Frontiers in cell and developmental biology}, publisher = {Frontiers Media}, address = {Lausanne, Schweiz}, issn = {2296-634X}, doi = {10.3389/fcell.2021.731101}, pages = {1 -- 10}, year = {2021}, abstract = {The heart is comprised of multiple tissues that contribute to its physiological functions. During development, the growth of myocardium and endocardium is coupled and morphogenetic processes within these separate tissue layers are integrated. Here, we discuss the roles of mechanosensitive Hippo signaling in growth and morphogenesis of the zebrafish heart. Hippo signaling is involved in defining numbers of cardiac progenitor cells derived from the secondary heart field, in restricting the growth of the epicardium, and in guiding trabeculation and outflow tract formation. Recent work also shows that myocardial chamber dimensions serve as a blueprint for Hippo signaling-dependent growth of the endocardium. Evidently, Hippo pathway components act at the crossroads of various signaling pathways involved in embryonic zebrafish heart development. Elucidating how biomechanical Hippo signaling guides heart morphogenesis has direct implications for our understanding of cardiac physiology and pathophysiology.}, language = {en} } @article{SzangoliesRohwaederJeltsch2022, author = {Szangolies, Leonna and Rohw{\"a}der, Marie-Sophie and Jeltsch, Florian}, title = {Single large AND several small habitat patches}, series = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, volume = {65}, journal = {Basic and applied ecology : Journal of the Gesellschaft f{\"u}r {\"O}kologie}, publisher = {Elsevier}, address = {M{\"u}nchen}, issn = {1439-1791}, doi = {10.1016/j.baae.2022.09.004}, pages = {16 -- 27}, year = {2022}, abstract = {The debate whether single large or several small (SLOSS) patches benefit biodiversity has existed for decades, but recent literature provides increasing evidence for the importance of small habitats. Possible beneficial mechanisms include reduced presence of preda-tors and competitors in small habitat areas or specific functions such as stepping stones for dispersal. Given the increasing amount of studies highlighting individual behavioral differences that may influence these functions, we hypothesize that the advantage of small versus large habitat patches not only depends on patch functionality but also on the presence of animal personalities (i.e., risk-tolerant vs. risk-averse). Using an individual-based, spatially-explicit community model, we analyzed the diversity of mammal communities in landscapes consisting of a few large habitat islands interspersed with different amounts and sizes of small habitat patches. Within these heterogeneous environments, individuals compete for resources and form home-ranges, with only risk-tolerant individuals using habitat edges. Results show that when risk-tolerant individuals exist, small patches increase species diversity. A strong peak occurs at approximately 20\% habitat cover in small patches when those small habitats are only used for foraging but not for breeding and home-range core position. Additional usage as stepping stones for juvenile dispersal further increases species persistence. Over-all, our results reveal that a combination of a few large and several small habitat patches promotes biodiversity by enhancing land-scape heterogeneity. Here, heterogeneity is created by pronounced differences in habitat functionality, increasing edge density, and variability in habitat use by different behavioral types. The finding that a combination of single large AND several small (SLASS) patches is needed for effective biodiversity preservation has implications for advancing landscape conservation. Particularly in struc-turally poor agricultural areas, modern technology enables precise management with the opportunity to create small foraging habitats by excluding less profitable agricultural land from cultivation.}, language = {en} } @article{BanerjeeSilvaLipowskyetal.2022, author = {Banerjee, Pallavi and Silva, Daniel Varon and Lipowsky, Reinhard and Santer, Mark}, title = {The importance of side branches of glycosylphosphatidylinositol anchors}, series = {Glycobiology}, volume = {32}, journal = {Glycobiology}, number = {11}, publisher = {Oxford Univ. Press}, address = {Cary}, issn = {0959-6658}, doi = {10.1093/glycob/cwac037}, pages = {933 -- 948}, year = {2022}, abstract = {Many proteins are anchored to the cell surface of eukaryotes using a unique family of glycolipids called glycosylphosphatidylinositol (GPI) anchors. These glycolipids also exist without a covalently bound protein, in particular on the cell surfaces of protozoan parasites where they are densely populated. GPIs and GPI-anchored proteins participate in multiple cellular processes such as signal transduction, cell adhesion, protein trafficking and pathogenesis of Malaria, Toxoplasmosis, Trypanosomiasis and prion diseases, among others. All GPIs share a common conserved glycan core modified in a cell-dependent manner with additional side glycans or phosphoethanolamine residues. Here, we use atomistic molecular dynamic simulations and perform a systematic study to evaluate the structural properties of GPIs with different side chains inserted in lipid bilayers. Our results show a flop-down orientation of GPIs with respect to the membrane surface and the presentation of the side chain residues to the solvent. This finding agrees well with experiments showing the role of the side residues as active epitopes for recognition of GPIs by macrophages and induction of GPI-glycan-specific immune responses. Protein-GPI interactions were investigated by attaching parasitic GPIs to Green Fluorescent Protein. GPIs are observed to recline on the membrane surface and pull down the attached protein close to the membrane facilitating mutual contacts between protein, GPI and the lipid bilayer. This model is efficient in evaluating the interaction of GPIs and GPI-anchored proteins with membranes and can be extended to study other parasitic GPIs and proteins and develop GPI-based immunoprophylaxis to treat infectious diseases.}, language = {en} } @article{KuekenTrevesNikoloski2023, author = {K{\"u}ken, Anika and Treves, Haim and Nikoloski, Zoran}, title = {A simulation-free constrained regression approach for flux estimation in isotopically nonstationary metabolic flux analysis with applications in microalgae}, series = {Frontiers in plant science : FPLS}, volume = {14}, journal = {Frontiers in plant science : FPLS}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-462X}, doi = {10.3389/fpls.2023.1140829}, pages = {12}, year = {2023}, abstract = {Introduction Flux phenotypes from different organisms and growth conditions allow better understanding of differential metabolic networks functions. Fluxes of metabolic reactions represent the integrated outcome of transcription, translation, and post-translational modifications, and directly affect growth and fitness. However, fluxes of intracellular metabolic reactions cannot be directly measured, but are estimated via metabolic flux analysis (MFA) that integrates data on isotope labeling patterns of metabolites with metabolic models. While the application of metabolomics technologies in photosynthetic organisms have resulted in unprecedented data from 13CO2-labeling experiments, the bottleneck in flux estimation remains the application of isotopically nonstationary MFA (INST-MFA). INST-MFA entails fitting a (large) system of coupled ordinary differential equations, with metabolite pools and reaction fluxes as parameters. Here, we focus on the Calvin-Benson cycle (CBC) as a key pathway for carbon fixation in photosynthesizing organisms and ask if approaches other than classical INST-MFA can provide reliable estimation of fluxes for reactions comprising this pathway. Methods First, we show that flux estimation with the labeling patterns of all CBC intermediates can be formulated as a single constrained regression problem, avoiding the need for repeated simulation of time-resolved labeling patterns. Results We then compare the flux estimates of the simulation-free constrained regression approach with those obtained from the classical INST-MFA based on labeling patterns of metabolites from the microalgae Chlamydomonas reinhardtii, Chlorella sorokiniana and Chlorella ohadii under different growth conditions. Discussion Our findings indicate that, in data-rich scenarios, simulation-free regression-based approaches provide a suitable alternative for flux estimation from classical INST-MFA since we observe a high qualitative agreement (rs=0.89) to predictions obtained from INCA, a state-of-the-art tool for INST-MFA.}, language = {en} } @article{WojcikCeulemansGaedke2021, author = {Wojcik, Laurie Anne Myriam and Ceulemans, Ruben and Gaedke, Ursula}, title = {Functional diversity buffers the effects of a pulse perturbation on the dynamics of tritrophic food webs}, series = {Ecology and Evolution}, volume = {11}, journal = {Ecology and Evolution}, number = {22}, publisher = {John Wiley \& Sons, Inc.}, address = {Hoboken (New Jersey)}, issn = {2045-7758}, doi = {10.1002/ece3.8214}, pages = {15639 -- 15663}, year = {2021}, abstract = {Biodiversity decline causes a loss of functional diversity, which threatens ecosystems through a dangerous feedback loop: This loss may hamper ecosystems' ability to buffer environmental changes, leading to further biodiversity losses. In this context, the increasing frequency of human-induced excessive loading of nutrients causes major problems in aquatic systems. Previous studies investigating how functional diversity influences the response of food webs to disturbances have mainly considered systems with at most two functionally diverse trophic levels. We investigated the effects of functional diversity on the robustness, that is, resistance, resilience, and elasticity, using a tritrophic—and thus more realistic—plankton food web model. We compared a non-adaptive food chain with no diversity within the individual trophic levels to a more diverse food web with three adaptive trophic levels. The species fitness differences were balanced through trade-offs between defense/growth rate for prey and selectivity/half-saturation constant for predators. We showed that the resistance, resilience, and elasticity of tritrophic food webs decreased with larger perturbation sizes and depended on the state of the system when the perturbation occurred. Importantly, we found that a more diverse food web was generally more resistant and resilient but its elasticity was context-dependent. Particularly, functional diversity reduced the probability of a regime shift toward a non-desirable alternative state. The basal-intermediate interaction consistently determined the robustness against a nutrient pulse despite the complex influence of the shape and type of the dynamical attractors. This relationship was strongly influenced by the diversity present and the third trophic level. Overall, using a food web model of realistic complexity, this study confirms the destructive potential of the positive feedback loop between biodiversity loss and robustness, by uncovering mechanisms leading to a decrease in resistance, resilience, and potentially elasticity as functional diversity declines.}, language = {en} } @misc{ZwickelKahlKlaffkeetal.2017, author = {Zwickel, Theresa and Kahl, Sandra and Klaffke, Horst and Rychlik, Michael and M{\"u}ller, Marina E. H.}, title = {Spotlight on the underdogs}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-400438}, pages = {17}, year = {2017}, abstract = {Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 °C, 25 °C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 °C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions}, language = {en} } @article{RomeroMujalliRochowKahletal.2021, author = {Romero Mujalli, Daniel and Rochow, Markus and Kahl, Sandra and Paraskevopoulou, Sofia and Folkertsma, Remco and Jeltsch, Florian and Tiedemann, Ralph}, title = {Adaptive and nonadaptive plasticity in changing environments}, series = {Ecology and evolution}, volume = {11}, journal = {Ecology and evolution}, number = {11}, publisher = {John Wiley \& Sons, Inc.}, address = {New Jersey}, issn = {2045-7758}, doi = {10.1002/ece3.7485}, pages = {6341 -- 6357}, year = {2021}, abstract = {Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype-phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.}, language = {en} } @phdthesis{Kahl2022, author = {Kahl, Sandra}, title = {Evolutionary adaptive responses to rapid climate change in plants}, doi = {10.25932/publishup-55648}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-556483}, school = {Universit{\"a}t Potsdam}, pages = {127}, year = {2022}, abstract = {The ongoing climate change is altering the living conditions for many organisms on this planet at an unprecedented pace. Hence, it is crucial for the survival of species to adapt to these changing conditions. In this dissertation Silene vulgaris is used as a model organism to understand the adaption strategies of widely distributed plant species to the current climate change. Especially plant species that possess a wide geographic range are expected to have a high phenotypic plasticity or to show genetic differentiation in response to the different climate conditions they grow in. However, they are often underrepresented in research. In the greenhouse experiment presented in this thesis, I examined the phenotypic responses and plasticity in S. vulgaris to estimate its' adaptation potential. Seeds from 25 wild European populations were collected along a latitudinal gradient and grown in a greenhouse under three different precipitation (65 mm, 75 mm, 90 mm) and two different temperature regimes (18°C, 21°C) that resembled a possible climate change scenario for central Europe. Afterwards different biomass and fecundity-related plant traits were measured. The treatments significantly influenced the plants but did not reveal a latitudinal difference in response to climate treatments for most plant traits. The number of flowers per individual however, showed a stronger plasticity in northern European populations (e.g., Swedish populations) where numbers decreased more drastically with increased temperature and decreased precipitation. To gain an even deeper understanding of the adaptation of S. vulgaris to climate change it is also important to reveal the underlying phylogeny of the sampled populations. Therefore, I analysed their population genetic structure through whole genome sequencing via ddRAD. The sequencing revealed three major genetic clusters in the S. vulgaris populations sampled in Europe: one cluster comprised Southern European populations, one cluster Western European populations and another cluster contained central European populations. A following analysis of experimental trait responses among the clusters to the climate-change scenario showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate-change scenario. In addition to the potential geographic and genetic adaptation differences to climate change this dissertation also deals with the response differences between the sexes in S. vulgaris. As a gynodioecious species populations of S. vulgaris consist of female and hermaphrodite individuals and the sexes can differ in their morphological traits which is known as sexual dimorphism. As climate change is becoming an important factor influencing plant morphology it remains unclear if and how different sexes may respond in sexually dimorphic species. To examine this question the sex of each individual plant was determined during the greenhouse experiment and the measured plant traits were analysed accordingly. In general, hermaphrodites had a higher number of flowers but a lower number of leaves than females. With regards to the climate change treatment, I found that hermaphrodites showed a milder negative response to higher temperatures in the number of flowers produced and in specific leaf area (SLA) compared to females. Synthesis - The significant treatment response in Silene vulgaris, independent of population origin in most traits suggests a high degree of universal phenotypic plasticity. Also, the three European intraspecific genetic lineages detected showed comparable parallel response patterns in half of the traits suggesting considerable phenotypic plasticity. Hence, plasticity might represent a possible adaptation strategy of this widely distributed species during ongoing and future climatic changes. The results on sexual dimorphism show that females and hermaphrodites are differing mainly in their number of flowers and females are affected more strongly by the experimental climate-change scenario. These results provide a solid knowledge basis on the sexual dimorphism in S. vulgaris under climate change, but further research is needed to determine the long-term impact on the breeding system for the species. In summary this dissertation provides a comprehensive insight into the adaptation mechanisms and consequences of a widely distributed and gynodioecious plant species and leverages our understanding of the impact of anthropogenic climate change on plants.}, language = {en} } @misc{KahlKappelJoshietal.2021, author = {Kahl, Sandra and Kappel, Christian and Joshi, Jasmin Radha and Lenhard, Michael}, title = {Phylogeography of a widely distributed plant species reveals cryptic genetic lineages with parallel phenotypic responses to warming and drought conditions}, series = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Zweitver{\"o}ffentlichungen der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, issn = {1866-8372}, doi = {10.25932/publishup-53003}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-530035}, pages = {13986 -- 14002}, year = {2021}, abstract = {To predict how widely distributed species will perform under future climate change, it is crucial to understand and reveal their underlying phylogenetics. However, detailed information about plant adaptation and its genetic basis and history remains scarce and especially widely distributed species receive little attention despite their putatively high adaptability. To examine the adaptation potential of a widely distributed species, we sampled the model plant Silene vulgaris across Europe. In a greenhouse experiment, we exposed the offspring of these populations to a climate change scenario for central Europe and revealed the population structure through whole-genome sequencing. Plants were grown under two temperatures (18°C and 21°C) and three precipitation regimes (65, 75, and 90 mm) to measure their response in biomass and fecundity-related traits. To reveal the population genetic structure, ddRAD sequencing was employed for a whole-genome approach. We found three major genetic clusters in S. vulgaris from Europe: one cluster comprising Southern European populations, one cluster of Western European populations, and another cluster containing central European populations. Population genetic diversity decreased with increasing latitude, and a Mantel test revealed significant correlations between FST and geographic distances as well as between genetic and environmental distances. Our trait analysis showed that the genetic clusters significantly differed in biomass-related traits and in the days to flowering. However, half of the traits showed parallel response patterns to the experimental climate change scenario. Due to the differentiated but parallel response patterns, we assume that phenotypic plasticity plays an important role for the adaptation of the widely distributed species S. vulgaris and its intraspecific genetic lineages.}, language = {en} } @misc{RomeroMujalliRochowKahletal.2021, author = {Romero-Mujalli, Daniel and Rochow, Markus and Kahl, Sandra and Paraskevopoulou, Sofia and Folkertsma, Remco and Jeltsch, Florian and Tiedemann, Ralph}, title = {Adaptive and nonadaptive plasticity in changing environments: Implications for sexual species with different life history strategies}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1170}, issn = {1866-8372}, doi = {10.25932/publishup-52320}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-523201}, pages = {19}, year = {2021}, abstract = {Populations adapt to novel environmental conditions by genetic changes or phenotypic plasticity. Plastic responses are generally faster and can buffer fitness losses under variable conditions. Plasticity is typically modeled as random noise and linear reaction norms that assume simple one-to- one genotype-phenotype maps and no limits to the phenotypic response. Most studies on plasticity have focused on its effect on population viability. However, it is not clear, whether the advantage of plasticity depends solely on environmental fluctuations or also on the genetic and demographic properties (life histories) of populations. Here we present an individual-based model and study the relative importance of adaptive and nonadaptive plasticity for populations of sexual species with different life histories experiencing directional stochastic climate change. Environmental fluctuations were simulated using differentially autocorrelated climatic stochasticity or noise color, and scenarios of directiona climate change. Nonadaptive plasticity was simulated as a random environmental effect on trait development, while adaptive plasticity as a linear, saturating, or sinusoidal reaction norm. The last two imposed limits to the plastic response and emphasized flexible interactions of the genotype with the environment. Interestingly, this assumption led to (a) smaller phenotypic than genotypic variance in the population (many-to- one genotype-phenotype map) and the coexistence of polymorphisms, and (b) the maintenance of higher genetic variation—compared to linear reaction norms and genetic determinism—even when the population was exposed to a constant environment for several generations. Limits to plasticity led to genetic accommodation, when costs were negligible, and to the appearance of cryptic variation when limits were exceeded. We found that adaptive plasticity promoted population persistence under red environmental noise and was particularly important for life histories with low fecundity. Populations produing more offspring could cope with environmental fluctuations solely by genetic changes or random plasticity, unless environmental change was too fast.}, language = {en} } @article{ZwickelKahlKlaffkeetal.2016, author = {Zwickel, Theresa and Kahl, Sandra and Klaffke, Horst and Rychlik, Michael and M{\"u}ller, Marina E. H.}, title = {Spotlight on the Underdogs-An Analysis of Underrepresented Alternaria Mycotoxins Formed Depending on Varying Substrate, Time and Temperature Conditions}, series = {Toxins}, volume = {8}, journal = {Toxins}, publisher = {MDPI}, address = {Basel}, issn = {2072-6651}, doi = {10.3390/toxins8110344}, pages = {570 -- 583}, year = {2016}, abstract = {Alternaria (A.) is a genus of widespread fungi capable of producing numerous, possibly health-endangering Alternaria toxins (ATs), which are usually not the focus of attention. The formation of ATs depends on the species and complex interactions of various environmental factors and is not fully understood. In this study the influence of temperature (7 degrees C, 25 degrees C), substrate (rice, wheat kernels) and incubation time (4, 7, and 14 days) on the production of thirteen ATs and three sulfoconjugated ATs by three different Alternaria isolates from the species groups A. tenuissima and A. infectoria was determined. High-performance liquid chromatography coupled with tandem mass spectrometry was used for quantification. Under nearly all conditions, tenuazonic acid was the most extensively produced toxin. At 25 degrees C and with increasing incubation time all toxins were formed in high amounts by the two A. tenuissima strains on both substrates with comparable mycotoxin profiles. However, for some of the toxins, stagnation or a decrease in production was observed from day 7 to 14. As opposed to the A. tenuissima strains, the A. infectoria strain only produced low amounts of ATs, but high concentrations of stemphyltoxin III. The results provide an essential insight into the quantitative in vitro AT formation under different environmental conditions, potentially transferable to different field and storage conditions.}, language = {en} } @phdthesis{AriasAndres2018, author = {Arias Andr{\´e}s, Mar{\´i}a de Jes{\´u}s}, title = {Microbial gene exchange on microplastic particles}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-417241}, school = {Universit{\"a}t Potsdam}, pages = {94}, year = {2018}, abstract = {Plastic pollution is ubiquitous on the planet since several millions of tons of plastic waste enter aquatic ecosystems each year. Furthermore, the amount of plastic produced is expected to increase exponentially shortly. The heterogeneity of materials, additives and physical characteristics of plastics are typical of these emerging contaminants and affect their environmental fate in marine and freshwaters. Consequently, plastics can be found in the water column, sediments or littoral habitats of all aquatic ecosystems. Most of this plastic debris will fragment as a product of physical, chemical and biological forces, producing particles of small size. These particles (< 5mm) are known as "microplastics" (MP). Given their high surface-to-volume ratio, MP stimulate biofouling and the formation of biofilms in aquatic systems. As a result of their unique structure and composition, the microbial communities in MP biofilms are referred to as the "Plastisphere." While there is increasing data regarding the distinctive composition and structure of the microbial communities that form part of the plastisphere, scarce information exists regarding the activity of microorganisms in MP biofilms. This surface-attached lifestyle is often associated with the increase in horizontal gene transfer (HGT) among bacteria. Therefore, this type of microbial activity represents a relevant function worth to be analyzed in MP biofilms. The horizontal exchange of mobile genetic elements (MGEs) is an essential feature of bacteria. It accounts for the rapid evolution of these prokaryotes and their adaptation to a wide variety of environments. The process of HGT is also crucial for spreading antibiotic resistance and for the evolution of pathogens, as many MGEs are known to contain antibiotic resistance genes (ARGs) and genetic determinants of pathogenicity. In general, the research presented in this Ph.D. thesis focuses on the analysis of HGT and heterotrophic activity in MP biofilms in aquatic ecosystems. The primary objective was to analyze the potential of gene exchange between MP bacterial communities vs. that of the surrounding water, including bacteria from natural aggregates. Moreover, the thesis addressed the potential of MP biofilms for the proliferation of biohazardous bacteria and MGEs from wastewater treatment plants (WWTPs) and associated with antibiotic resistance. Finally, it seeks to prove if the physiological profile of MP biofilms under different limnological conditions is divergent from that of the water communities. Accordingly, the thesis is composed of three independent studies published in peer-reviewed journals. The two laboratory studies were performed using both model and environmental microbial communities. In the field experiment, natural communities from freshwater ecosystems were examined. In Chapter I, the inflow of treated wastewater into a temperate lake was simulated with a concentration gradient of MP particles. The effects of MP on the microbial community structure and the occurrence of integrase 1 (int 1) were followed. The int 1 is a marker associated with mobile genetic elements and known as a proxy for anthropogenic effects on the spread of antimicrobial resistance genes. During the experiment, the abundance of int1 increased in the plastisphere with increasing MP particle concentration, but not in the surrounding water. In addition, the microbial community on MP was more similar to the original wastewater community with increasing microplastic concentrations. Our results show that microplastic particles indeed promote persistence of standard indicators of microbial anthropogenic pollution in natural waters. In Chapter II, the experiments aimed to compare the permissiveness of aquatic bacteria towards model antibiotic resistance plasmid pKJK5, between communities that form biofilms on MP vs. those that are free-living. The frequency of plasmid transfer in bacteria associated with MP was higher when compared to bacteria that are free-living or in natural aggregates. Moreover, comparison increased gene exchange occurred in a broad range of phylogenetically-diverse bacteria. The results indicate a different activity of HGT in MP biofilms, which could affect the ecology of aquatic microbial communities on a global scale and the spread of antibiotic resistance. Finally, in Chapter III, physiological measurements were performed to assess whether microorganisms on MP had a different functional diversity from those in water. General heterotrophic activity such as oxygen consumption was compared in microcosm assays with and without MP, while diversity and richness of heterotrophic activities were calculated by using Biolog® EcoPlates. Three lakes with different nutrient statuses presented differences in MP-associated biomass build up. Functional diversity profiles of MP biofilms in all lakes differed from those of the communities in the surrounding water, but only in the oligo-mesotrophic lake MP biofilms had a higher functional richness compared to the ambient water. The results support that MP surfaces act as new niches for aquatic microorganisms and can affect global carbon dynamics of pelagic environments. Overall, the experimental works presented in Chapters I and II support a scenario where MP pollution affects HGT dynamics among aquatic bacteria. Among the consequences of this alteration is an increase in the mobilization and transfer efficiency of ARGs. Moreover, it supposes that changes in HGT can affect the evolution of bacteria and the processing of organic matter, leading to different catabolic profiles such as demonstrated in Chapter III. The results are discussed in the context of the fate and magnitude of plastic pollution and the importance of HGT for bacterial evolution and the microbial loop, i.e., at the base of aquatic food webs. The thesis supports a relevant role of MP biofilm communities for the changes observed in the aquatic microbiome as a product of intense human intervention.}, language = {en} } @phdthesis{Liu2020, author = {Liu, Qi}, title = {Influence of CO2 degassing on microbial community distribution and activity in the Hartoušov degassing system, western Eger Rift (Czech Republic)}, doi = {10.25932/publishup-47534}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-475341}, school = {Universit{\"a}t Potsdam}, pages = {146}, year = {2020}, abstract = {The Cheb Basin (CZ) is a shallow Neogene intracontinental basin located in the western Eger Rift. The Cheb Basin is characterized by active seismicity and diffuse degassing of mantle-derived CO2 in mofette fields. Within the Cheb Basin, the Hartoušov mofette field shows a daily CO2 flux of 23-97 tons. More than 99\% of CO2 released over an area of 0.35 km2. Seismic active periods have been observed in 2000 and 2014 in the Hartoušov mofette field. Due to the active geodynamic processes, the Cheb Basin is considered to be an ideal region for the continental deep biosphere research focussing on the interaction of biological processes with geological processes. To study the influence of CO2 degassing on microbial community in the surface and subsurface environments, two 3-m shallow drillings and a 108.5-m deep scientific drilling were conducted in 2015 and 2016 respectively. Additionally, the fluid retrieved from the deep drilling borehole was also recovered. The different ecosystems were compared regarding their geochemical properties, microbial abundances, and microbial community structures. The geochemistry of the mofette is characterized by low pH, high TOC, and sulfate contents while the subsurface environment shows a neutral pH, and various TOC and sulfate contents in different lithological settings. Striking differences in the microbial community highlight the substantial impact of elevated CO2 concentrations and high saline groundwater on microbial processes. In general, the microorganisms had low abundance in the deep subsurface sediment compared with the shallow mofette. However, within the mofette and the deep subsurface sediment, the abundance of microbes does not show a typical decrease with depth, indicating that the uprising CO2-rich groundwater has a strong influence on the microbial communities via providing sufficient substrate for anaerobic chemolithoautotrophic microorganisms. Illumina MiSeq sequencing of the 16S rRNA genes and multivariate statistics reveals that the pH strongly influences the microbial community composition in the mofette, while the subsurface microbial community is significantly influenced by the groundwater which motivated by the degassing CO2. Acidophilic microorganisms show a much higher relative abundance in the mofette. Meanwhile, the OTUs assigned to family Comamonadaceae are the dominant taxa which characterize the subsurface communities. Additionally, taxa involved in sulfur cycling characterizing the microbial communities in both mofette and CO2 dominated subsurface environments. Another investigated important geo-bio interaction is the influence of the seismic activity. During seismic events, released H2 may serve as the electron donor for microbial hydrogenotrophic processes, such as methanogenesis. To determine whether the seismic events can potentially trigger methanogenesis by the elevated geogenic H2 concentration, we performed laboratory simulation experiments with sediments retrieved from the drillings. The simulation results indicate that after the addition of hydrogen, substantial amounts of methane were produced in incubated mofette sediments and deep subsurface sediments. The methanogenic hydrogenotrophic genera Methanobacterium was highly enriched during the incubation. The modeling of the in-situ observation of the earthquake swarm period in 2000 at the Novy Kostel focal area/Czech Republic and our laboratory simulation experiments reveals a close relation between seismic activities and microbial methane production via earthquake-induced H2 release. We thus conclude that H2 - which is released during seismic activity - can potentially trigger methanogenic activity in the deep subsurface. Based on this conclusion, we further hypothesize that the hydrogenotrophic early life on Earth was boosted by the Late Heavy Bombardment induced seismic activity in approximately 4.2 to 3.8 Ga.}, language = {en} } @misc{WurzbacherFuchsAttermeyeretal.2017, author = {Wurzbacher, Christian and Fuchs, Andrea and Attermeyer, Katrin and Frindte, Katharina and Grossart, Hans-Peter and Hupfer, Michael and Casper, Peter and Monaghan, Michael T.}, title = {Shifts among Eukaryota, Bacteria, and Archaea define the vertical organization of a lake sediment}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1111}, issn = {1866-8372}, doi = {10.25932/publishup-43196}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-431965}, pages = {18}, year = {2017}, abstract = {Background Lake sediments harbor diverse microbial communities that cycle carbon and nutrients while being constantly colonized and potentially buried by organic matter sinking from the water column. The interaction of activity and burial remained largely unexplored in aquatic sediments. We aimed to relate taxonomic composition to sediment biogeochemical parameters, test whether community turnover with depth resulted from taxonomic replacement or from richness effects, and to provide a basic model for the vertical community structure in sediments. Methods We analyzed four replicate sediment cores taken from 30-m depth in oligo-mesotrophic Lake Stechlin in northern Germany. Each 30-cm core spanned ca. 170 years of sediment accumulation according to 137Cs dating and was sectioned into layers 1-4 cm thick. We examined a full suite of biogeochemical parameters and used DNA metabarcoding to examine community composition of microbial Archaea, Bacteria, and Eukaryota. Results Community β-diversity indicated nearly complete turnover within the uppermost 30 cm. We observed a pronounced shift from Eukaryota- and Bacteria-dominated upper layers (<5 cm) to Bacteria-dominated intermediate layers (5-14 cm) and to deep layers (>14 cm) dominated by enigmatic Archaea that typically occur in deep-sea sediments. Taxonomic replacement was the prevalent mechanism in structuring the community composition and was linked to parameters indicative of microbial activity (e.g., CO2 and CH4 concentration, bacterial protein production). Richness loss played a lesser role but was linked to conservative parameters (e.g., C, N, P) indicative of past conditions. Conclusions By including all three domains, we were able to directly link the exponential decay of eukaryotes with the active sediment microbial community. The dominance of Archaea in deeper layers confirms earlier findings from marine systems and establishes freshwater sediments as a potential low-energy environment, similar to deep sea sediments. We propose a general model of sediment structure and function based on microbial characteristics and burial processes. An upper "replacement horizon" is dominated by rapid taxonomic turnover with depth, high microbial activity, and biotic interactions. A lower "depauperate horizon" is characterized by low taxonomic richness, more stable "low-energy" conditions, and a dominance of enigmatic Archaea.}, language = {en} } @misc{GubelitGrossart2020, author = {Gubelit, Yulia I. and Grossart, Hans-Peter}, title = {New Methods, New Concepts}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {969}, issn = {1866-8372}, doi = {10.25932/publishup-47428}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-474286}, pages = {13}, year = {2020}, abstract = {Microbial interactions play an essential role in aquatic ecosystems and are of the great interest for both marine and freshwater ecologists. Recent development of new technologies and methods allowed to reveal many functional mechanisms and create new concepts. Yet, many fundamental aspects of microbial interactions have been almost exclusively studied for marine pelagic and benthic ecosystems. These studies resulted in a formulation of the Black Queen Hypothesis, a development of the phycosphere concept for pelagic communities, and a realization of microbial communication as a key mechanism for microbial interactions. In freshwater ecosystems, especially for periphyton communities, studies focus mainly on physiology, biodiversity, biological indication, and assessment, but the many aspects of microbial interactions are neglected to a large extent. Since periphyton plays a great role for aquatic nutrient cycling, provides the basis for water purification, and can be regarded as a hotspot of microbial biodiversity, we highlight that more in-depth studies on microbial interactions in periphyton are needed to improve our understanding on functioning of freshwater ecosystems. In this paper we first present an overview on recent concepts (e.g., the "Black Queen Hypothesis") derived from state-of-the-art OMICS methods including metagenomics, metatranscriptomics, and metabolomics. We then point to the avenues how these methods can be applied for future studies on biodiversity and the ecological role of freshwater periphyton, a yet largely neglected component of many freshwater ecosystems.}, language = {en} } @misc{KettnerOberbeckmannLabrenzetal.2019, author = {Kettner, Marie Therese and Oberbeckmann, Sonja and Labrenz, Matthias and Grossart, Hans-Peter}, title = {The Eukaryotic Life on Microplastics in Brackish Ecosystems}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {741}, issn = {1866-8372}, doi = {10.25932/publishup-43499}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434996}, pages = {10}, year = {2019}, abstract = {Microplastics (MP) constitute a widespread contaminant all over the globe. Rivers and wastewater treatment plants (WWTP) transport annually several million tons of MP into freshwaters, estuaries and oceans, where they provide increasing artificial surfaces for microbial colonization. As knowledge on MP-attached communities is insufficient for brackish ecosystems, we conducted exposure experiments in the coastal Baltic Sea, an in-flowing river and a WWTP within the drainage basin. While reporting on prokaryotic and fungal communities from the same set-up previously, we focus here on the entire eukaryotic communities. Using high-throughput 18S rRNA gene sequencing, we analyzed the eukaryotes colonizing on two types of MP, polyethylene and polystyrene, and compared them to the ones in the surrounding water and on a natural surface (wood). More than 500 different taxa across almost all kingdoms of the eukaryotic tree of life were identified on MP, dominated by Alveolata, Metazoa, and Chloroplastida. The eukaryotic community composition on MP was significantly distinct from wood and the surrounding water, with overall lower diversity and the potentially harmful dinoflagellate Pfiesteria being enriched on MP. Co-occurrence networks, which include prokaryotic and eukaryotic taxa, hint at possibilities for dynamic microbial interactions on MP. This first report on total eukaryotic communities on MP in brackish environments highlights the complexity of MP-associated biofilms, potentially leading to altered microbial activities and hence changes in ecosystem functions.}, language = {en} } @misc{RojasJimenezRieckWurzbacheretal.2019, author = {Rojas-Jimenez, Keilor and Rieck, Angelika and Wurzbacher, Christian and J{\"u}rgens, Klaus and Labrenz, Matthias and Grossart, Hans-Peter}, title = {A Salinity Threshold Separating Fungal Communities in the Baltic Sea}, series = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam Mathematisch-Naturwissenschaftliche Reihe}, number = {739}, issn = {1866-8372}, doi = {10.25932/publishup-43493}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-434937}, pages = {9}, year = {2019}, abstract = {Salinity is a significant factor for structuring microbial communities, but little is known for aquatic fungi, particularly in the pelagic zone of brackish ecosystems. In this study, we explored the diversity and composition of fungal communities following a progressive salinity decline (from 34 to 3 PSU) along three transects of ca. 2000 km in the Baltic Sea, the world's largest estuary. Based on 18S rRNA gene sequence analysis, we detected clear changes in fungal community composition along the salinity gradient and found significant differences in composition of fungal communities established above and below a critical value of 8 PSU. At salinities below this threshold, fungal communities resembled those from freshwater environments, with a greater abundance of Chytridiomycota, particularly of the orders Rhizophydiales, Lobulomycetales, and Gromochytriales. At salinities above 8 PSU, communities were more similar to those from marine environments and, depending on the season, were dominated by a strain of the LKM11 group (Cryptomycota) or by members of Ascomycota and Basidiomycota. Our results highlight salinity as an important environmental driver also for pelagic fungi, and thus should be taken into account to better understand fungal diversity and ecological function in the aquatic realm.}, language = {en} } @phdthesis{Perillon2017, author = {P{\´e}rillon, C{\´e}cile}, title = {The effect of groundwater on benthic primary producers and their interaction}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-406883}, school = {Universit{\"a}t Potsdam}, pages = {XVII, 180}, year = {2017}, abstract = {In littoral zones of lakes, multiple processes determine lake ecology and water quality. Lacustrine groundwater discharge (LGD), most frequently taking place in littoral zones, can transport or mobilize nutrients from the sediments and thus contribute significantly to lake eutrophication. Furthermore, lake littoral zones are the habitat of benthic primary producers, namely submerged macrophytes and periphyton, which play a key role in lake food webs and influence lake water quality. Groundwater-mediated nutrient-influx can potentially affect the asymmetric competition between submerged macrophytes and periphyton for light and nutrients. While rooted macrophytes have superior access to sediment nutrients, periphyton can negatively affect macrophytes by shading. LGD may thus facilitate periphyton production at the expense of macrophyte production, although studies on this hypothesized effect are missing. The research presented in this thesis is aimed at determining how LGD influences periphyton, macrophytes, and the interactions between these benthic producers. Laboratory experiments were combined with field experiments and measurements in an oligo-mesotrophic hard water lake. In the first study, a general concept was developed based on a literature review of the existing knowledge regarding the potential effects of LGD on nutrients and inorganic and organic carbon loads to lakes, and the effect of these loads on periphyton and macrophytes. The second study includes a field survey and experiment examining the effects of LGD on periphyton in an oligotrophic, stratified hard water lake (Lake Stechlin). This study shows that LGD, by mobilizing phosphorus from the sediments, significantly promotes epiphyton growth, especially at the end of the summer season when epilimnetic phosphorus concentrations are low. The third study focuses on the potential effects of LGD on submerged macrophytes in Lake Stechlin. This study revealed that LGD may have contributed to an observed change in macrophyte community composition and abundance in the shallow littoral areas of the lake. Finally, a laboratory experiment was conducted which mimicked the conditions of a seepage lake. Groundwater circulation was shown to mobilize nutrients from the sediments, which significantly promoted periphyton growth. Macrophyte growth was negatively affected at high periphyton biomasses, confirming the initial hypothesis. More generally, this thesis shows that groundwater flowing into nutrient-limited lakes may import or mobilize nutrients. These nutrients first promote periphyton, and subsequently provoke radical changes in macrophyte populations before finally having a possible influence on the lake's trophic state. Hence, the eutrophying effect of groundwater is delayed and, at moderate nutrient loading rates, partly dampened by benthic primary producers. The present research emphasizes the importance and complexity of littoral processes, and the need to further investigate and monitor the benthic environment. As present and future global changes can significantly affect LGD, the understanding of these complex interactions is required for the sustainable management of lake water quality.}, language = {en} } @misc{MantzoukiLuerlingFastneretal.2018, author = {Mantzouki, Evanthia and L{\"u}rling, Miquel and Fastner, Jutta and Domis, Lisette Nicole de Senerpont and Wilk-Wo{\'{z}}niak, Elżbieta and Koreiviene, Judita and Seelen, Laura and Teurlincx, Sven and Verstijnen, Yvon and Krztoń, Wojciech and Walusiak, Edward and Karosienė, Jūratė and Kasperovičienė, Jūratė and Savadova, Ksenija and Vitonytė, Irma and Cillero-Castro, Carmen and Budzyńska, Agnieszka and Goldyn, Ryszard and Kozak, Anna and Rosińska, Joanna and Szeląg-Wasielewska, Elżbieta and Domek, Piotr and Jakubowska-Krepska, Natalia and Kwasizur, Kinga and Messyasz, Beata and Pełechata, Aleksandra and Pełechaty, Mariusz and Kokocinski, Mikolaj and Garc{\´i}a-Murcia, Ana and Real, Monserrat and Romans, Elvira and Noguero-Ribes, Jordi and Duque, David Parre{\~n}o and Fern{\´a}ndez-Mor{\´a}n, El{\´i}sabeth and Karakaya, Nusret and H{\"a}ggqvist, Kerstin and Beklioğlu, Meryem and Filiz, Nur and Levi, Eti E. and Iskin, Uğur and Bezirci, Gizem and Tav{\c{s}}anoğlu, {\"U}lk{\"u} Nihan and {\"O}zhan, Koray and Gkelis, Spyros and Panou, Manthos and Fakioglu, {\"O}zden and Avagianos, Christos and Kaloudis, Triantafyllos and {\c{C}}elik, Kemal and Yilmaz, Mete and Marc{\´e}, Rafael and Catal{\´a}n, Nuria and Bravo, Andrea G. and Buck, Moritz and Colom-Montero, William and Mustonen, Kristiina and Pierson, Don and Yang, Yang and Raposeiro, Pedro M. and Gon{\c{c}}alves, V{\´i}tor and Antoniou, Maria G. and Tsiarta, Nikoletta and McCarthy, Valerie and Perello, Victor C. and Feldmann, T{\~o}nu and Laas, Alo and Panksep, Kristel and Tuvikene, Lea and Gagala, Ilona and Mankiewicz-Boczek, Joana and Yağc{\i}, Meral Apayd{\i}n and {\c{C}}{\i}nar, Şakir and {\c{C}}apk{\i}n, Kadir and Yağc{\i}, Abdulkadir and Cesur, Mehmet and Bilgin, Fuat and Bulut, Cafer and Uysal, Rahmi and Obertegger, Ulrike and Boscaini, Adriano and Flaim, Giovanna and Salmaso, Nico and Cerasino, Leonardo and Richardson, Jessica and Visser, Petra M. and Verspagen, Jolanda M. H. and Karan, T{\"u}nay and Soylu, Elif Neyran and Mara{\c{s}}l{\i}oğlu, Faruk and Napi{\´o}rkowska-Krzebietke, Agnieszka and Ochocka, Agnieszka and Pasztaleniec, Agnieszka and Ant{\~a}o-Geraldes, Ana M. and Vasconcelos, Vitor and Morais, Jo{\~a}o and Vale, Micaela and K{\"o}ker, Latife and Ak{\c{c}}aalan, Reyhan and Albay, Meri{\c{c}} and Maronić, Dubravka Špoljarić and Stević, Filip and Pfeiffer, Tanja Žuna and Fonvielle, Jeremy Andre and Straile, Dietmar and Rothhaupt, Karl-Otto and Hansson, Lars-Anders and Urrutia-Cordero, Pablo and Bl{\´a}ha, Luděk and Geriš, Rodan and Fr{\´a}nkov{\´a}, Mark{\´e}ta and Ko{\c{c}}er, Mehmet Ali Turan and Alp, Mehmet Tahir and Remec-Rekar, Spela and Elersek, Tina and Triantis, Theodoros and Zervou, Sevasti-Kiriaki and Hiskia, Anastasia and Haande, Sigrid and Skjelbred, Birger and Madrecka, Beata and Nemova, Hana and Drastichova, Iveta and Chomova, Lucia and Edwards, Christine and Sevindik, Tuğba Ongun and Tunca, Hatice and {\"O}nem, Bur{\c{c}}in and Aleksovski, Boris and Krstić, Svetislav and Vucelić, Itana Bokan and Nawrocka, Lidia and Salmi, Pauliina and Machado-Vieira, Danielle and Oliveira, Alinne Gurj{\~a}o De and Delgado-Mart{\´i}n, Jordi and Garc{\´i}a, David and Cereijo, Jose Lu{\´i}s and Gom{\`a}, Joan and Trapote, Mari Carmen and Vegas-Vilarr{\´u}bia, Teresa and Obrador, Biel and Grabowska, Magdalena and Karpowicz, Maciej and Chmura, Damian and {\´U}beda, B{\´a}rbara and G{\´a}lvez, Jos{\´e} {\´A}ngel and {\"O}zen, Arda and Christoffersen, Kirsten Seestern and Warming, Trine Perlt and Kobos, Justyna and Mazur-Marzec, Hanna and P{\´e}rez-Mart{\´i}nez, Carmen and Ramos-Rodr{\´i}guez, Elo{\´i}sa and Arvola, Lauri and Alcaraz-P{\´a}rraga, Pablo and Toporowska, Magdalena and Pawlik-Skowronska, Barbara and Nied{\'{z}}wiecki, Michał and Pęczuła, Wojciech and Leira, Manel and Hern{\´a}ndez, Armand and Moreno-Ostos, Enrique and Blanco, Jos{\´e} Mar{\´i}a and Rodr{\´i}guez, Valeriano and Montes-P{\´e}rez, Jorge Juan and Palomino, Roberto L. and Rodr{\´i}guez-P{\´e}rez, Estela and Carballeira, Rafael and Camacho, Antonio and Picazo, Antonio and Rochera, Carlos and Santamans, Anna C. and Ferriol, Carmen and Romo, Susana and Soria, Juan Miguel and Dunalska, Julita and Sieńska, Justyna and Szymański, Daniel and Kruk, Marek and Kostrzewska-Szlakowska, Iwona and Jasser, Iwona and Žutinić, Petar and Udovič, Marija Gligora and Plenković-Moraj, Anđelka and Frąk, Magdalena and Bańkowska-Sobczak, Agnieszka and Wasilewicz, Michał and {\"O}zkan, Korhan and Maliaka, Valentini and Kangro, Kersti and Grossart, Hans-Peter and Paerl, Hans W. and Carey, Cayelan C. and Ibelings, Bas W.}, title = {Temperature effects explain continental scale distribution of cyanobacterial toxins}, series = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, journal = {Postprints der Universit{\"a}t Potsdam : Mathematisch-Naturwissenschaftliche Reihe}, number = {1105}, issn = {1866-8372}, doi = {10.25932/publishup-42790}, url = {http://nbn-resolving.de/urn:nbn:de:kobv:517-opus4-427902}, pages = {26}, year = {2018}, abstract = {Insight into how environmental change determines the production and distribution of cyanobacterial toxins is necessary for risk assessment. Management guidelines currently focus on hepatotoxins (microcystins). Increasing attention is given to other classes, such as neurotoxins (e.g., anatoxin-a) and cytotoxins (e.g., cylindrospermopsin) due to their potency. Most studies examine the relationship between individual toxin variants and environmental factors, such as nutrients, temperature and light. In summer 2015, we collected samples across Europe to investigate the effect of nutrient and temperature gradients on the variability of toxin production at a continental scale. Direct and indirect effects of temperature were the main drivers of the spatial distribution in the toxins produced by the cyanobacterial community, the toxin concentrations and toxin quota. Generalized linear models showed that a Toxin Diversity Index (TDI) increased with latitude, while it decreased with water stability. Increases in TDI were explained through a significant increase in toxin variants such as MC-YR, anatoxin and cylindrospermopsin, accompanied by a decreasing presence of MC-LR. While global warming continues, the direct and indirect effects of increased lake temperatures will drive changes in the distribution of cyanobacterial toxins in Europe, potentially promoting selection of a few highly toxic species or strains.}, language = {en} } @article{BjornerasWeyhenmeyerEvansetal.2017, author = {Bjorneras, C. and Weyhenmeyer, G. A. and Evans, C. D. and Gessner, M. O. and Grossart, Hans-Peter and Kangur, K. and Kokorite, I. and Kortelainen, P. and Laudon, H. and Lehtoranta, J. and Lottig, N. and Monteith, D. T. and Noges, P. and Noges, T. and Oulehle, F. and Riise, G. and Rusak, J. A. and Raike, A. and Sire, J. and Sterling, S. and Kritzberg, E. S.}, title = {Widespread Increases in Iron Concentration in European and North American Freshwaters}, series = {Global biogeochemical cycles}, volume = {31}, journal = {Global biogeochemical cycles}, publisher = {American Geophysical Union}, address = {Washington}, issn = {0886-6236}, doi = {10.1002/2017GB005749}, pages = {1488 -- 1500}, year = {2017}, abstract = {Recent reports of increasing iron (Fe) concentrations in freshwaters are of concern, given the fundamental role of Fe in biogeochemical processes. Still, little is known about the frequency and geographical distribution of Fe trends or about the underlying drivers. We analyzed temporal trends of Fe concentrations across 340 water bodies distributed over 10 countries in northern Europe and North America in order to gain a clearer understanding of where, to what extent, and why Fe concentrations are on the rise. We found that Fe concentrations have significantly increased in 28\% of sites, and decreased in 4\%, with most positive trends located in northern Europe. Regions with rising Fe concentrations tend to coincide with those with organic carbon (OC) increases. Fe and OC increases may not be directly mechanistically linked, but may nevertheless be responding to common regional-scale drivers such as declining sulfur deposition or hydrological changes. A role of hydrological factors was supported by covarying trends in Fe and dissolved silica, as these elements tend to stem from similar soil depths. A positive relationship between Fe increases and conifer cover suggests that changing land use and expanded forestry could have contributed to enhanced Fe export, although increases were also observed in nonforested areas. We conclude that the phenomenon of increasing Fe concentrations is widespread, especially in northern Europe, with potentially significant implications for wider ecosystem biogeochemistry, and for the current browning of freshwaters.}, language = {en} } @article{LischkeMehnerHiltetal.2017, author = {Lischke, Betty and Mehner, Thomas and Hilt, Sabine and Attermeyer, Katrin and Brauns, Mario and Brothers, Soren M. and Grossart, Hans-Peter and Koehler, Jan and Scharnweber, Inga Kristin and Gaedke, Ursula}, title = {Benthic carbon is inefficiently transferred in the food webs of two eutrophic shallow lakes}, series = {Freshwater biology}, volume = {62}, journal = {Freshwater biology}, publisher = {Wiley}, address = {Hoboken}, issn = {0046-5070}, doi = {10.1111/fwb.12979}, pages = {1693 -- 1706}, year = {2017}, abstract = {The sum of benthic autotrophic and bacterial production often exceeds the sum of pelagic autotrophic and bacterial production, and hence may contribute substantially to whole-lake carbon fluxes, especially in shallow lakes. Furthermore, both benthic and pelagic autotrophic and bacterial production are highly edible and of sufficient nutritional quality for animal consumers. We thus hypothesised that pelagic and benthic transfer efficiencies (ratios of production at adjacent trophic levels) in shallow lakes should be similar. We performed whole ecosystem studies in two shallow lakes (3.5ha, mean depth 2m), one with and one without submerged macrophytes, and quantified pelagic and benthic biomass, production and transfer efficiencies for bacteria, phytoplankton, epipelon, epiphyton, macrophytes, zooplankton, macrozoobenthos and fish. We expected higher transfer efficiencies in the lake with macrophytes, because these provide shelter and food for macrozoobenthos and may thus enable a more efficient conversion of basal production to consumer production. In both lakes, the majority of the whole-lake autotrophic and bacterial production was provided by benthic organisms, but whole-lake primary consumer production mostly relied on pelagic autotrophic and bacterial production. Consequently, transfer efficiency of benthic autotrophic and bacterial production to macrozoobenthos production was an order of magnitude lower than the transfer efficiency of pelagic autotrophic and bacterial production to rotifer and crustacean production. Between-lake differences in transfer efficiencies were minor. We discuss several aspects potentially causing the unexpectedly low benthic transfer efficiencies, such as the food quality of producers, pelagic-benthic links, oxygen concentrations in the deeper lake areas and additional unaccounted consumer production by pelagic and benthic protozoa and meiobenthos at intermediate or top trophic levels. None of these processes convincingly explain the large differences between benthic and pelagic transfer efficiencies. Our data indicate that shallow eutrophic lakes, even with a major share of autotrophic and bacterial production in the benthic zone, can function as pelagic systems with respect to primary consumer production. We suggest that the benthic autotrophic production was mostly transferred to benthic bacterial production, which remained in the sediments, potentially cycling internally in a similar way to what has previously been described for the microbial loop in pelagic habitats. Understanding the energetics of whole-lake food webs, including the fate of the substantial benthic bacterial production, which is either mineralised at the sediment surface or permanently buried, has important implications for regional and global carbon cycling.}, language = {en} } @article{AttermeyerGrossartFluryetal.2017, author = {Attermeyer, Katrin and Grossart, Hans-Peter and Flury, Sabine and Premke, Katrin}, title = {Bacterial processes and biogeochemical changes in the water body of kettle holes - mainly driven by autochthonous organic matter?}, series = {Aquatic sciences : research across boundaries}, volume = {79}, journal = {Aquatic sciences : research across boundaries}, publisher = {Springer}, address = {Basel}, issn = {1015-1621}, doi = {10.1007/s00027-017-0528-1}, pages = {675 -- 687}, year = {2017}, abstract = {Kettle holes are small inland waters formed from glacially-created depressions often situated in agricultural landscapes. Due to their high perimeter-to-area ratio facilitating a high aquatic-terrestrial coupling, kettle holes can accumulate high concentrations of organic carbon and nutrients, fueling microbial activities and turnover rates. Thus, they represent hotspots of carbon turnover in the landscape, but their bacterial activities and controlling factors have not been well investigated. Therefore, we aimed to assess the relative importance of various environmental factors on bacterial and biogeochemical processes in the water column of kettle holes and to disentangle their variations. In the water body of ten kettle holes in north-eastern Germany, we measured several physico-chemical and biological parameters such as carbon quantity and quality, as well as bacterial protein production (BP) and community respiration (CR) in spring, early summer and autumn 2014. Particulate organic matter served as an indicator of autochthonous production and represented an important parameter to explain variations in BP and CR. This notion is supported by qualitative absorbance indices of dissolved molecules in water samples and C: N ratios of the sediments, which demonstrate high fractions of autochthonous organic matter (OM) in the studied kettle holes. In contrast, dissolved chemical parameters were less important for bacterial activities although they revealed strong differences throughout the growing season. Pelagic bacterial activities and dynamics might thus be regulated by autochthonous OM in kettle holes implying a control of important biogeochemical processes by internal primary production rather than facilitated exchange with the terrestrial surrounding due to a high perimeter-to-area ratio.}, language = {en} } @article{WurzbacherAttermeyerKettneretal.2017, author = {Wurzbacher, Christian and Attermeyer, Katrin and Kettner, Marie Therese and Flintrop, Clara and Warthmann, Norman and Hilt, Sabine and Grossart, Hans-Peter and Monaghan, Michael T.}, title = {DNA metabarcoding of unfractionated water samples relates phyto-, zoo- and bacterioplankton dynamics and reveals a single-taxon bacterial bloom}, series = {Environmental microbiology reports}, volume = {9}, journal = {Environmental microbiology reports}, publisher = {Wiley}, address = {Hoboken}, issn = {1758-2229}, doi = {10.1111/1758-2229.12540}, pages = {383 -- 388}, year = {2017}, abstract = {Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. Here we tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. Significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a 3-month period in spring were found. Patterns followed the same trend as plankton estimates measured using traditional microscopic methods. The bloom of a conditionally rare bacterial taxon belonging to Arcicella was characterized, which rapidly came to dominate the whole lake ecosystem and would have remained unnoticed without metabarcoding. The data demonstrate the potential of universal DNA metabarcoding applied to unfractionated samples for providing a more holistic view of plankton communities.}, language = {en} } @article{HornakKasalickySimeketal.2017, author = {Hornak, Karel and Kasalicky, Vojtech and Simek, Karel and Grossart, Hans-Peter}, title = {Strain-specific consumption and transformation of alga-derived dissolved organic matter by members of the Limnohabitans-C and Polynucleobacter-B clusters of Betaproteobacteria}, series = {Environmental microbiology}, volume = {19}, journal = {Environmental microbiology}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.13900}, pages = {4519 -- 4535}, year = {2017}, abstract = {We investigated changes in quality and quantity of extracellular and biomass-derived organic matter (OM) from three axenic algae (genera Rhodomonas, Chlamydomonas, Coelastrum) during growth of Limnohabitans parvus, Limnohabitans planktonicus and Polynucleobacter acidiphobus representing important clusters of freshwater planktonic Betaproteobacteria. Total extracellular and biomass-derived OM concentrations from each alga were approximately 20 mg l(-1) and 1 mg l(-1) respectively, from which up to 9\% could be identified as free carbohydrates, polyamines, or free and combined amino acids. Carbohydrates represented 54\%-61\% of identified compounds of the extracellular OM from each alga. In biomass-derived OM of Rhodomonas and Chlamydomonas 71\%-77\% were amino acids and polyamines, while in that of Coelastrum 85\% were carbohydrates. All bacteria grew on alga-derived OM of Coelastrum, whereas only Limnohabitans strains grew on OM from Rhodomonas and Chlamydomonas. Bacteria consumed 24\%-76\% and 38\%-82\% of all identified extracellular and biomass-derived OM compounds respectively, and their consumption was proportional to the concentration of each OM compound in the different treatments. The bacterial biomass yield was higher than the total identifiable OM consumption indicating that bacteria also utilized other unidentified alga-derived OM compounds. Bacteria, however, also produced specific OM compounds suggesting enzymatic polymer degradation or de novo exudation.}, language = {en} } @article{KettnerRojasJimenezOberbeckmannetal.2017, author = {Kettner, Marie Therese and Rojas-Jimenez, Keilor and Oberbeckmann, Sonja and Labrenz, Matthias and Grossart, Hans-Peter}, title = {Microplastics alter composition of fungal communities in aquatic ecosystems}, series = {Environmental microbiology}, volume = {19}, journal = {Environmental microbiology}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.13891}, pages = {4447 -- 4459}, year = {2017}, abstract = {Despite increasing concerns about microplastic (MP) pollution in aquatic ecosystems, there is insufficient knowledge on how MP affect fungal communities. In this study, we explored the diversity and community composition of fungi attached to polyethylene (PE) and polystyrene (PS) particles incubated in different aquatic systems in north-east Germany: the Baltic Sea, the River Warnow and a wastewater treatment plant. Based on next generation 18S rRNA gene sequencing, 347 different operational taxonomic units assigned to 81 fungal taxa were identified on PE and PS. The MP-associated communities were distinct from fungal communities in the surrounding water and on the natural substrate wood. They also differed significantly among sampling locations, pointing towards a substrate and location specific fungal colonization. Members of Chytridiomycota, Cryptomycota and Ascomycota dominated the fungal assemblages, suggesting that both parasitic and saprophytic fungi thrive in MP biofilms. Thus, considering the worldwide increasing accumulation of plastic particles as well as the substantial vector potential of MP, especially these fungal taxa might benefit from MP pollution in the aquatic environment with yet unknown impacts on their worldwide distribution, as well as biodiversity and food web dynamics at large.}, language = {en} } @article{AmalfitanoCornoEckertetal.2017, author = {Amalfitano, Stefano and Corno, Gianluca and Eckert, Ester and Fazi, Stefano and Ninio, Shira and Callieri, Cristiana and Grossart, Hans-Peter and Eckert, Werner}, title = {Tracing particulate matter and associated microorganisms in freshwaters}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {800}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-017-3260-x}, pages = {145 -- 154}, year = {2017}, abstract = {Sediment resuspension represents a key process in all natural aquatic systems, owing to its role in nutrient cycling and transport of potential contaminants. Although suspended solids are generally accepted as an important quality parameter, current monitoring programs cover quantitative aspects only. Established methodologies do not provide information on origin, fate, and risks associated with uncontrolled inputs of solids in waters. Here we discuss the analytical approaches to assess the occurrence and ecological relevance of resuspended particulate matter in freshwaters, with a focus on the dynamics of associated contaminants and microorganisms. Triggered by the identification of specific physical-chemical traits and community structure of particle-associated microorganisms, recent findings suggest that a quantitative determination of microorganisms can be reasonably used to trace the origin of particulate matter by means of nucleic acid-based assays in different aquatic systems.}, language = {en} } @article{TangFluryGrossartetal.2017, author = {Tang, Kam W. and Flury, Sabine and Grossart, Hans-Peter and McGinnis, Daniel F.}, title = {The Chaoborus pump: Migrating phantom midge larvae sustain hypolimnetic oxygen deficiency and nutrient internal loading in lakes}, series = {Water research}, volume = {122}, journal = {Water research}, publisher = {Elsevier}, address = {Oxford}, issn = {0043-1354}, doi = {10.1016/j.watres.2017.05.058}, pages = {36 -- 41}, year = {2017}, abstract = {Hypolimnetic oxygen demand in lakes is often assumed to be driven mainly by sediment microbial processes, while the role of Chaoborus larvae, which are prevalent in eutrophic lakes with hypoxic to anoxic bottoms, has been overlooked. We experimentally measured the respiration rates of C flavicans at different temperatures yielding a Q(10) of 1.44-1.71 and a respiratory quotient of 0.84-0.98. Applying the experimental data in a system analytical approach, we showed that migrating Chaoborus larvae can significantly add to the water column and sediment oxygen demand, and contribute to the observed linear relationship between water column respiration and depth. The estimated phosphorus excretion by Chaoborus in sediment is comparable in magnitude to the required phosphorus loading for eutrophication. Migrating Chaoborus larvae thereby essentially trap nutrients between the water column and the sediment, and this continuous internal loading of nutrients would delay lake remediation even when external inputs are stopped. (C) 2017 Elsevier Ltd. All rights reserved.}, language = {en} } @article{IonescuBizicIonescuDeMaioetal.2017, author = {Ionescu, Danny and Bizic-Ionescu, Mina and De Maio, Nicola and Cypionka, Heribert and Grossart, Hans-Peter}, title = {Community-like genome in single cells of the sulfur bacterium Achromatium oxaliferum}, series = {Nature Communications}, volume = {8}, journal = {Nature Communications}, publisher = {Nature Publ. Group}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-017-00342-9}, pages = {9193 -- 9205}, year = {2017}, language = {en} } @article{KaylerPremkeGessleretal.2019, author = {Kayler, Zachary E. and Premke, Katrin and Gessler, Arthur and Gessner, Mark O. and Griebler, Christian and Hilt, Sabine and Klemedtsson, Leif and Kuzyakov, Yakov and Reichstein, Markus and Siemens, Jan and Totsche, Kai-Uwe and Tranvik, Lars and Wagner, Annekatrin and Weitere, Markus and Grossart, Hans-Peter}, title = {Integrating Aquatic and Terrestrial Perspectives to Improve Insights Into Organic Matter Cycling at the Landscape Scale}, series = {Frontiers in Earth Science}, volume = {7}, journal = {Frontiers in Earth Science}, publisher = {Frontiers Research Foundation}, address = {Lausanne}, issn = {2296-6463}, doi = {10.3389/feart.2019.00127}, pages = {14}, year = {2019}, abstract = {Across a landscape, aquatic-terrestrial interfaces within and between ecosystems are hotspots of organic matter (OM) mineralization. These interfaces are characterized by sharp spatio-temporal changes in environmental conditions, which affect OM properties and thus control OM mineralization and other transformation processes. Consequently, the extent of OM movement at and across aquatic-terrestrial interfaces is crucial in determining OM turnover and carbon (C) cycling at the landscape scale. Here, we propose expanding current concepts in aquatic and terrestrial ecosystem sciences to comprehensively evaluate OM turnover at the landscape scale. We focus on three main concepts toward explaining OM turnover at the landscape scale: the landscape spatiotemporal context, OM turnover described by priming and ecological stoichiometry, and anthropogenic effects as a disruptor of natural OM transfer magnitudes and pathways. A conceptual framework is introduced that allows for discussing the disparities in spatial and temporal scales of OM transfer, changes in environmental conditions, ecosystem connectivity, and microbial-substrate interactions. The potential relevance of priming effects in both terrestrial and aquatic systems is addressed. For terrestrial systems, we hypothesize that the interplay between the influx of OM, its corresponding elemental composition, and the elemental demand of the microbial communities may alleviate spatial and metabolic thresholds. In comparison, substrate level OM dynamics may be substantially different in aquatic systems due to matrix effects that accentuate the role of abiotic conditions, substrate quality, and microbial community dynamics. We highlight the disproportionate impact anthropogenic activities can have on OM cycling across the landscape. This includes reversing natural OM flows through the landscape, disrupting ecosystem connectivity, and nutrient additions that cascade across the landscape. This knowledge is crucial for a better understanding of OM cycling in a landscape context, in particular since terrestrial and aquatic compartments may respond differently to the ongoing changes in climate, land use, and other anthropogenic interferences.}, language = {en} } @article{LundgreenJaspersTravingetal.2019, author = {Lundgreen, Regitze B. C. and Jaspers, Cornelia and Traving, Sachia J. and Ayala, Daniel J. and Lombard, Fabien and Grossart, Hans-Peter and Nielsen, Torkel G. and Munk, Peter and Riemann, Lasse}, title = {Eukaryotic and cyanobacterial communities associated with marine snow particles in the oligotrophic Sargasso Sea}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-45146-7}, pages = {12}, year = {2019}, abstract = {Marine snow aggregates represent heterogeneous agglomerates of dead and living organic matter. Composition is decisive for their sinking rates, and thereby for carbon flux to the deep sea. For oligotrophic oceans, information on aggregate composition is particularly sparse. To address this, the taxonomic composition of aggregates collected from the subtropical and oligotrophic Sargasso Sea (Atlantic Ocean) was characterized by 16S and 18S rRNA gene sequencing. Taxonomy assignment was aided by a collection of the contemporary plankton community consisting of 75 morphologically and genetically identified plankton specimens. The diverse rRNA gene reads of marine snow aggregates, not considering Trichodesmium puffs, were dominated by copepods (52\%), cnidarians (21\%), radiolarians (11\%), and alveolates (8\%), with sporadic contributions by cyanobacteria, suggesting a different aggregate composition than in eutrophic regions. Composition linked significantly with sampling location but not to any measured environmental parameters or plankton biomass composition. Nevertheless, indicator and network analyses identified key roles of a few rare taxa. This points to complex regulation of aggregate composition, conceivably affected by the environment and plankton characteristics. The extent to which this has implications for particle densities, and consequently for sinking rates and carbon sequestration in oligotrophic waters, needs further interrogation.}, language = {en} } @article{MasigolKhodaparastWoodhouseetal.2019, author = {Masigol, Hossein and Khodaparast, Seyed Akbar and Woodhouse, Jason Nicholas and Rojas Jim{\´e}nez, Keilor and Fonvielle, Jeremy Andre and Rezakhani, Forough and Mostowfizadeh-Ghalamfarsa, Reza and Neubauer, Darshan and Goldhammer, Tobias and Grossart, Hans-Peter}, title = {The contrasting roles of aquatic fungi and oomycetes in the degradation and transformation of polymeric organic matter}, series = {Limnology and oceanography}, volume = {64}, journal = {Limnology and oceanography}, number = {6}, publisher = {Wiley}, address = {Hoboken}, issn = {0024-3590}, pages = {2662 -- 2678}, year = {2019}, abstract = {Studies on the ecological role of fungi and, to a lesser extent, oomycetes, are receiving increasing attention, mainly due to their participation in the cycling of organic matter in aquatic ecosystems. To unravel their importance in humification processes, we isolated several strains of fungi and oomycetes from Anzali lagoon, Iran. We then performed taxonomic characterization by morphological and molecular methods, analyzed the ability to degrade several polymeric substrates, performed metabolic fingerprinting with Ecoplates, and determined the degradation of humic substances (HS) using liquid chromatography-organic carbon detection. Our analyses highlighted the capacity of aquatic fungi to better degrade a plethora of organic molecules, including complex polymers. Specifically, we were able to demonstrate not only the utilization of these complex polymers, but also the role of fungi in the production of HS. In contrast, oomycetes, despite some morphological and physiological similarities with aquatic fungi, exhibited a propensity toward opportunism, quickly benefitting from the availability of small organic molecules, while exhibiting sensitivity toward more complex polymers. Despite their contrasting roles, our study highlights the importance of both oomycetes and fungi in aquatic organic matter transformation and cycling with potential implications for the global carbon cycle.}, language = {en} } @article{NumbergerGanzertZoccaratoetal.2019, author = {Numberger, Daniela and Ganzert, Lars and Zoccarato, Luca and M{\"u}hldorfer, Kristin and Sauer, Sascha and Grossart, Hans-Peter and Greenwood, Alex D.}, title = {Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing}, series = {Scientific reports}, volume = {9}, journal = {Scientific reports}, publisher = {Nature Publ. Group}, address = {London}, issn = {2045-2322}, doi = {10.1038/s41598-019-46015-z}, pages = {14}, year = {2019}, abstract = {Wastewater treatment is crucial to environmental hygiene in urban environments. However, wastewater treatment plants (WWTPs) collect chemicals, organic matter, and microorganisms including pathogens and multi-resistant bacteria from various sources which may be potentially released into the environment via WWTP effluent. To better understand microbial dynamics in WWTPs, we characterized and compared the bacterial community of the inflow and effluent of a WWTP in Berlin, Germany using full-length 16S rRNA gene sequences, which allowed for species level determination in many cases and generally resolved bacterial taxa. Significantly distinct bacterial communities were identified in the wastewater inflow and effluent samples. Dominant operational taxonomic units (OTUs) varied both temporally and spatially. Disease associated bacterial groups were efficiently reduced in their relative abundance from the effluent by the WWTP treatment process, except for Legionella and Leptospira species which demonstrated an increase in relative proportion from inflow to effluent. This indicates that WWTPs, while effective against enteric bacteria, may enrich and release other potentially pathogenic bacteria into the environment. The taxonomic resolution of full-length 16S rRNA genes allows for improved characterization of potential pathogenic taxa and other harmful bacteria which is required to reliably assess health risk.}, language = {en} } @article{NumbergerDreierVullioudetal.2019, author = {Numberger, Daniela and Dreier, Carole and Vullioud, Colin and Gabriel, G{\"u}lsah and Greenwood, Alex D. and Grossart, Hans-Peter}, title = {Recovery of influenza a viruses from lake water and sediments by experimental inoculation}, series = {PLoS one}, volume = {14}, journal = {PLoS one}, number = {5}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0216880}, pages = {13}, year = {2019}, abstract = {Influenza A viruses (IAV) are zoonotic pathogens relevant to human, domestic animal and wildlife health. Many avian IAVs are transmitted among waterfowl via a faecal-oral-route. Therefore, environmental water where waterfowl congregate may play an important role in the ecology and epidemiology of avian IAV. Water and sediment may sustain and transmit virus among individuals or species. It is unclear at what concentrations waterborne viruses are infectious or remain detectable. To address this, we performed lake water and sediment dilution experiments with varying concentrations or infectious doses of four IAV strains from seal, turkey, duck and gull. To test for infectivity of the IAV strains in a concentration dependent manner, we applied cultivation to specific pathogen free (SPF) embryonated chicken eggs and Madin-Darby Canine Kidney (MDCK) cells. IAV recovery was more effective from embryonated chicken eggs than MDCK cells for freshwater lake dilutions, whereas, MDCK cells were more effective for viral recovery from sediment samples. Low infectious dose (1 PFU/200 mu L) was sufficient in most cases to detect and recover IAV from lake water dilutions. Sediment required higher initial infectious doses (>= 100 PFU/200 mu L).}, language = {en} } @article{TangBackhausRiemannetal.2019, author = {Tang, Kam W. and Backhaus, Liv and Riemann, Lasse and Koski, Marja and Grossart, Hans-Peter and Munk, Peter and Nielsen, Torkel Gissel}, title = {Copepod carcasses in the subtropical convergence zone of the Sargasso Sea}, series = {Journal of plankton research}, volume = {41}, journal = {Journal of plankton research}, number = {4}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0142-7873}, doi = {10.1093/plankt/fbz038}, pages = {549 -- 560}, year = {2019}, abstract = {The oligotrophic subtropical gyre covers a vast area of the Atlantic Ocean. Decades of time-series monitoring have generated detailed temporal information about zooplankton species and abundances at fixed locations within the gyre, but their live/dead status is often omitted, especially in the dynamic subtropical convergence zone (STCZ) where the water column stratification pattern can change considerably across the front as warm and cold water masses converge. We conducted a detailed survey in the North Atlantic STCZ and showed that over 85\% of the copepods were typically concentrated in the upper 200 m. Copepod carcasses were present in all samples and their proportional numerical abundances increased with depth, reaching up to 91\% at 300-400 m. Overall, 14-19\% of the copepods within the upper 200 m were carcasses. Shipboard experiments showed that during carcass decomposition, microbial respiration increased, and the bacterial community associated with the carcasses diverged from that in the ambient water. Combining field and experimental data, we estimated that decomposing copepod carcasses constitute a negligible oxygen sink in the STCZ, but sinking carcasses may represent an overlooked portion of the passive carbon sinking flux and should be incorporated in future studies of carbon flux in this area.}, language = {en} } @article{RojasJimenezGrossartCordesetal.2020, author = {Rojas-Jimenez, Keilor and Grossart, Hans-Peter and Cordes, Erik and Cort{\´e}s, Jorge}, title = {Fungal Communities in Sediments Along a Depth Gradient in the Eastern Tropical Pacific}, series = {Frontiers in Microbiology}, volume = {11}, journal = {Frontiers in Microbiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.575207}, pages = {9}, year = {2020}, abstract = {Deep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3,474 m) in two transects of about 1,500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63\% of all fungal sequences: the yeast Metschnikowia (49.4\%), Rhizophydium (6.9\%), and Cladosporium (6.7\%). We distinguished a cluster composed mainly by yeasts, and a second cluster by filamentous fungi, but we were unable to detect a strong effect of depth and the overlying water temperature, salinity, dissolved oxygen (DO), and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.}, language = {en} } @misc{GrossartVandenWyngaertKagamietal.2019, author = {Grossart, Hans-Peter and Van den Wyngaert, Silke and Kagami, Maiko and Wurzbacher, Christian and Cunliffe, Michael and Rojas-Jimenz, Keilor}, title = {Fungi in aquatic ecosystems}, series = {Nature reviews. Microbiology}, volume = {17}, journal = {Nature reviews. Microbiology}, number = {6}, publisher = {Nature Publ. Group}, address = {Basingstoke}, issn = {1740-1526}, doi = {10.1038/s41579-019-0175-8}, pages = {339 -- 354}, year = {2019}, abstract = {Fungi are phylogenetically and functionally diverse ubiquitous components of almost all ecosystems on Earth, including aquatic environments stretching from high montane lakes down to the deep ocean. Aquatic ecosystems, however, remain frequently overlooked as fungal habitats, although fungi potentially hold important roles for organic matter cycling and food web dynamics. Recent methodological improvements have facilitated a greater appreciation of the importance of fungi in many aquatic systems, yet a conceptual framework is still missing. In this Review, we conceptualize the spatiotemporal dimensions, diversity, functions and organismic interactions of fungi in structuring aquatic food webs. We focus on currently unexplored fungal diversity, highlighting poorly understood ecosystems, including emerging artificial aquatic habitats.}, language = {en} } @misc{NumbergerDreierVullioudetal.2019, author = {Numberger, Daniela and Dreier, Carola and Vullioud, Colin and Gabriel, Guelsah and Greenwood, Alex D. and Grossart, Hans-Peter}, title = {Correction: Recovery of influenza A viruses from lake water and sediments by experimental inoculation (vol 14, e0216880, 2019)}, series = {PLoS one}, volume = {14}, journal = {PLoS one}, number = {6}, publisher = {PLoS}, address = {San Fransisco}, issn = {1932-6203}, doi = {10.1371/journal.pone.0218882}, pages = {1}, year = {2019}, language = {en} } @article{TiegsCostelloIskenetal.2019, author = {Tiegs, Scott D. and Costello, David M. and Isken, Mark W. and Woodward, Guy and McIntyre, Peter B. and Gessner, Mark O. and Chauvet, Eric and Griffiths, Natalie A. and Flecker, Alex S. and Acuna, Vicenc and Albarino, Ricardo and Allen, Daniel C. and Alonso, Cecilia and Andino, Patricio and Arango, Clay and Aroviita, Jukka and Barbosa, Marcus V. M. and Barmuta, Leon A. and Baxter, Colden V. and Bell, Thomas D. C. and Bellinger, Brent and Boyero, Luz and Brown, Lee E. and Bruder, Andreas and Bruesewitz, Denise A. and Burdon, Francis J. and Callisto, Marcos and Canhoto, Cristina and Capps, Krista A. and Castillo, Maria M. and Clapcott, Joanne and Colas, Fanny and Colon-Gaud, Checo and Cornut, Julien and Crespo-Perez, Veronica and Cross, Wyatt F. and Culp, Joseph M. and Danger, Michael and Dangles, Olivier and de Eyto, Elvira and Derry, Alison M. and Diaz Villanueva, Veronica and Douglas, Michael M. and Elosegi, Arturo and Encalada, Andrea C. and Entrekin, Sally and Espinosa, Rodrigo and Ethaiya, Diana and Ferreira, Veronica and Ferriol, Carmen and Flanagan, Kyla M. and Fleituch, Tadeusz and Shah, Jennifer J. Follstad and Frainer, Andre and Friberg, Nikolai and Frost, Paul C. and Garcia, Erica A. and Lago, Liliana Garcia and Garcia Soto, Pavel Ernesto and Ghate, Sudeep and Giling, Darren P. and Gilmer, Alan and Goncalves, Jose Francisco and Gonzales, Rosario Karina and Graca, Manuel A. S. and Grace, Mike and Grossart, Hans-Peter and Guerold, Francois and Gulis, Vlad and Hepp, Luiz U. and Higgins, Scott and Hishi, Takuo and Huddart, Joseph and Hudson, John and Imberger, Samantha and Iniguez-Armijos, Carlos and Iwata, Tomoya and Janetski, David J. and Jennings, Eleanor and Kirkwood, Andrea E. and Koning, Aaron A. and Kosten, Sarian and Kuehn, Kevin A. and Laudon, Hjalmar and Leavitt, Peter R. and Lemes da Silva, Aurea L. and Leroux, Shawn J. and Leroy, Carri J. and Lisi, Peter J. and MacKenzie, Richard and Marcarelli, Amy M. and Masese, Frank O. and Mckie, Brendan G. and Oliveira Medeiros, Adriana and Meissner, Kristian and Milisa, Marko and Mishra, Shailendra and Miyake, Yo and Moerke, Ashley and Mombrikotb, Shorok and Mooney, Rob and Moulton, Tim and Muotka, Timo and Negishi, Junjiro N. and Neres-Lima, Vinicius and Nieminen, Mika L. and Nimptsch, Jorge and Ondruch, Jakub and Paavola, Riku and Pardo, Isabel and Patrick, Christopher J. and Peeters, Edwin T. H. M. and Pozo, Jesus and Pringle, Catherine and Prussian, Aaron and Quenta, Estefania and Quesada, Antonio and Reid, Brian and Richardson, John S. and Rigosi, Anna and Rincon, Jose and Risnoveanu, Geta and Robinson, Christopher T. and Rodriguez-Gallego, Lorena and Royer, Todd V. and Rusak, James A. and Santamans, Anna C. and Selmeczy, Geza B. and Simiyu, Gelas and Skuja, Agnija and Smykla, Jerzy and Sridhar, Kandikere R. and Sponseller, Ryan and Stoler, Aaron and Swan, Christopher M. and Szlag, David and Teixeira-de Mello, Franco and Tonkin, Jonathan D. and Uusheimo, Sari and Veach, Allison M. and Vilbaste, Sirje and Vought, Lena B. M. and Wang, Chiao-Ping and Webster, Jackson R. and Wilson, Paul B. and Woelfl, Stefan and Xenopoulos, Marguerite A. and Yates, Adam G. and Yoshimura, Chihiro and Yule, Catherine M. and Zhang, Yixin X. and Zwart, Jacob A.}, title = {Global patterns and drivers of ecosystem functioning in rivers and riparian zones}, series = {Science Advances}, volume = {5}, journal = {Science Advances}, number = {1}, publisher = {American Assoc. for the Advancement of Science}, address = {Washington}, issn = {2375-2548}, doi = {10.1126/sciadv.aav0486}, pages = {8}, year = {2019}, abstract = {River ecosystems receive and process vast quantities of terrestrial organic carbon, the fate of which depends strongly on microbial activity. Variation in and controls of processing rates, however, are poorly characterized at the global scale. In response, we used a peer-sourced research network and a highly standardized carbon processing assay to conduct a global-scale field experiment in greater than 1000 river and riparian sites. We found that Earth's biomes have distinct carbon processing signatures. Slow processing is evident across latitudes, whereas rapid rates are restricted to lower latitudes. Both the mean rate and variability decline with latitude, suggesting temperature constraints toward the poles and greater roles for other environmental drivers (e.g., nutrient loading) toward the equator. These results and data set the stage for unprecedented "next-generation biomonitoring" by establishing baselines to help quantify environmental impacts to the functioning of ecosystems at a global scale.}, language = {en} } @article{KolmakovaGladyshevFonvielleetal.2019, author = {Kolmakova, Olesya V. and Gladyshev, Michail I. and Fonvielle, Jeremy Andre and Ganzert, Lars and Hornick, Thomas and Grossart, Hans-Peter}, title = {Effects of zooplankton carcasses degradation on freshwater bacterial community composition and implications for carbon cycling}, series = {Environmental microbiology}, volume = {21}, journal = {Environmental microbiology}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1462-2912}, doi = {10.1111/1462-2920.14418}, pages = {34 -- 49}, year = {2019}, abstract = {Non-predatory mortality of zooplankton provides an abundant, yet, little studied source of high quality labile organic matter (LOM) in aquatic ecosystems. Using laboratory microcosms, we followed the decomposition of organic carbon of fresh C-13-labelled Daphnia carcasses by natural bacterioplankton. The experimental setup comprised blank microcosms, that is, artificial lake water without any organic matter additions (B), and microcosms either amended with natural humic matter (H), fresh Daphnia carcasses (D) or both, that is, humic matter and Daphnia carcasses (HD). Most of the carcass carbon was consumed and respired by the bacterial community within 15 days of incubation. A shift in the bacterial community composition shaped by labile carcass carbon and by humic matter was observed. Nevertheless, we did not observe a quantitative change in humic matter degradation by heterotrophic bacteria in the presence of LOM derived from carcasses. However, carcasses were the main factor driving the bacterial community composition suggesting that the presence of large quantities of dead zooplankton might affect the carbon cycling in aquatic ecosystems. Our results imply that organic matter derived from zooplankton carcasses is efficiently remineralized by a highly specific bacterial community, but does not interfere with the bacterial turnover of more refractory humic matter.}, language = {en} } @article{BatistaWoodhouseGrossartetal.2018, author = {Batista, A. M. M. and Woodhouse, Jason Nicholas and Grossart, Hans-Peter and Giani, A.}, title = {Methanogenic archaea associated to Microcystis sp. in field samples and in culture}, series = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, volume = {831}, journal = {Hydrobiologia : acta hydrobiologica, hydrographica, limnologica et protistologica}, number = {1}, publisher = {Springer}, address = {Dordrecht}, issn = {0018-8158}, doi = {10.1007/s10750-018-3655-3}, pages = {163 -- 172}, year = {2018}, abstract = {Cyanobacterial mass developments impact the community composition of heterotrophic microorganisms with far-reaching consequences for biogeochemical and energy cycles of freshwater ecosystems including reservoirs. Here we sought to evaluate the temporal stability of methanogenic archaea in the water column and further scrutinize their associations with cyanobacteria. Monthly samples were collected from October 2009 to December 2010 in hypereutrophic Pampulha reservoir with permanently blooming cyanobacteria, and from January to December 2011 in oligotrophic Volta Grande reservoir with only sporadic cyanobacteria incidence. The presence of archaea in cyanobacterial cultures was investigated by screening numerous strains of Microcystis spp. from these reservoirs as well as from lakes in Europe, Asia, and North-America. We consistently determined the occurrence of archaea, in particular methanogenic archaea, in both reservoirs throughout the year. However, archaea were only associated with two strains (Microcystis sp. UFMG 165 and UFMG 175) recently isolated from these reservoirs. These findings do not implicate archaea in the occurrence of methane in the epilimnion of inland waters, but rather serve to highlight the potential of microhabitats associated with particles, including phytoplankton, to shelter unique microbial communities.}, language = {en} } @misc{BlockDenfeldStockwelletal.2019, author = {Block, Benjamin D. and Denfeld, Blaize A. and Stockwell, Jason D. and Flaim, Giovanna and Grossart, Hans-Peter and Knoll, Lesley B. and Maier, Dominique B. and North, Rebecca L. and Rautio, Milla and Rusak, James A. and Sadro, Steve and Weyhenmeyer, Gesa A. and Bramburger, Andrew J. and Branstrator, Donn K. and Salonen, Kalevi and Hampton, Stephanie E.}, title = {The unique methodological challenges of winter limnology}, series = {Limnology and Oceanography: Methods}, volume = {17}, journal = {Limnology and Oceanography: Methods}, number = {1}, publisher = {Wiley}, address = {Hoboken}, issn = {1541-5856}, doi = {10.1002/lom3.10295}, pages = {42 -- 57}, year = {2019}, abstract = {Winter is an important season for many limnological processes, which can range from biogeochemical transformations to ecological interactions. Interest in the structure and function of lake ecosystems under ice is on the rise. Although limnologists working at polar latitudes have a long history of winter work, the required knowledge to successfully sample under winter conditions is not widely available and relatively few limnologists receive formal training. In particular, the deployment and operation of equipment in below 0 degrees C temperatures pose considerable logistical and methodological challenges, as do the safety risks of sampling during the ice-covered period. Here, we consolidate information on winter lake sampling and describe effective methods to measure physical, chemical, and biological variables in and under ice. We describe variation in snow and ice conditions and discuss implications for sampling logistics and safety. We outline commonly encountered methodological challenges and make recommendations for best practices to maximize safety and efficiency when sampling through ice or deploying instruments in ice-covered lakes. Application of such practices over a broad range of ice-covered lakes will contribute to a better understanding of the factors that regulate lakes during winter and how winter conditions affect the subsequent ice-free period.}, language = {en} } @article{StegerKimGanzertetal.2019, author = {Steger, Kristin and Kim, Amy Taeyen and Ganzert, Lars and Grossart, Hans-Peter and Smart, David R.}, title = {Floodplain soil and its bacterial composition are strongly affected by depth}, series = {FEMS microbiology ecology}, volume = {95}, journal = {FEMS microbiology ecology}, number = {3}, publisher = {Oxford Univ. Press}, address = {Oxford}, issn = {0168-6496}, doi = {10.1093/femsec/fiz014}, pages = {11}, year = {2019}, abstract = {We studied bacterial abundance and community structure of five soil cores using high-throughput sequencing of the 16S rRNA gene. Shifts in the soil bacterial composition were more pronounced within a vertical profile than across the landscape. Soil organic carbon (SOC) and nitrogen (N) concentrations decreased exponentially with soil depth and revealed a buried carbon-rich horizon between 0.8 and 1.3 m across all soil cores. This buried horizon was phylogenetically similar to its surrounding subsoils supporting the idea that the type of carbon, not necessarily the amount of carbon was driving the apparent similarities. In contrast to other studies, Nitrospirae was one of our major phyla with relatively high abundances throughout the soil profile except for the surface soil. Although depth is the major driver shaping soil bacterial community structure, positive correlations with SOC and N concentrations, however, were revealed with the bacterial abundance of Acidobacteria, one of the major, and Gemmatimonadetes, one of the minor phyla in our study. Our study showed that bacterial diversity in soils below 2.0 m can be still as high if not higher than in the above laying subsurface soil suggesting that various bacteria throughout the soil profile influence major biogeochemical processes in floodplain soils.}, language = {en} } @misc{AriasAndresRojasJimenezGrossart2018, author = {Arias-Andres, Maria and Rojas-Jimenez, Keilor and Grossart, Hans-Peter}, title = {Collateral effects of microplastic pollution on aquatic microorganisms}, series = {Trends in Analytical Chemistry}, volume = {112}, journal = {Trends in Analytical Chemistry}, publisher = {Elsevier}, address = {Oxford}, issn = {0165-9936}, doi = {10.1016/j.trac.2018.11.041}, pages = {234 -- 240}, year = {2018}, abstract = {Microplastics (MP) provide a unique and extensive surface for microbial colonization in aquatic ecosystems. The formation of microorganism-microplastic complexes, such as biofilms, maximizes the degradation of organic matter and horizontal gene transfer. In this context, MP affect the structure and function of microbial communities, which in turn render the physical and chemical fate of MP. This new paradigm generates challenges for microbiology, ecology, and ecotoxicology. Dispersal of MP is concomitant with that of their associated microorganisms and their mobile genetic elements, including antibiotic resistance genes, islands of pathogenicity, and diverse metabolic pathways. Functional changes in aquatic microbiomes can alter carbon metabolism and food webs, with unknown consequences on higher organisms or human microbiomes and hence health. Here, we examine a variety of effects of MP pollution from the microbial ecology perspective, whose repercussions on aquatic ecosystems begin to be unraveled. (C) 2018 Elsevier B.V. All rights reserved.}, language = {en} }