TY - JOUR A1 - Zoccarato, Luca A1 - Sher, Daniel A1 - Miki, Takeshi A1 - Segre, Daniel A1 - Grossart, Hans-Peter T1 - A comparative whole-genome approach identifies bacterial traits for marine microbial interactions JF - Communications biology N2 - 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. Y1 - 2022 U6 - https://doi.org/10.1038/s42003-022-03184-4 SN - 2399-3642 VL - 5 IS - 1 PB - Springer Nature CY - Berlin ER - TY - JOUR A1 - Xiao, Shangbin A1 - Liu, Liu A1 - Wang, Wei A1 - Lorke, Andreas A1 - Woodhouse, Jason Nicholas A1 - Grossart, Hans-Peter T1 - A Fast-Response Automated Gas Equilibrator (FaRAGE) for continuous in situ measurement of CH4 and CO2 dissolved in water JF - Hydrology and earth system sciences : HESS N2 - 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. Y1 - 2020 U6 - https://doi.org/10.5194/hess-24-3871-2020 SN - 1027-5606 SN - 1607-7938 VL - 24 IS - 7 SP - 3871 EP - 3880 PB - European Geosciences Union (EGU) ; Copernicus CY - Munich ER - TY - JOUR A1 - Ilicic, Doris A1 - Woodhouse, Jason Nicholas A1 - Karsten, Ulf A1 - Zimmermann, Jonas A1 - Wichard, Thomas A1 - Quartino, Maria Liliana A1 - Campana, Gabriela Laura A1 - Livenets, Alexandra A1 - Van den Wyngaert, Silke A1 - Grossart, Hans-Peter T1 - Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones JF - Frontiers in microbiology N2 - Aquatic ecosystems are frequently overlooked as fungal habitats, although there is increasing evidence that their diversity and ecological importance are greater than previously considered. Aquatic fungi are critical and abundant components of nutrient cycling and food web dynamics, e.g., exerting top-down control on phytoplankton communities and forming symbioses with many marine microorganisms. However, their relevance for microphytobenthic communities is almost unexplored. In the light of global warming, polar regions face extreme changes in abiotic factors with a severe impact on biodiversity and ecosystem functioning. Therefore, this study aimed to describe, for the first time, fungal diversity in Antarctic benthic habitats along the salinity gradient and to determine the co-occurrence of fungal parasites with their algal hosts, which were dominated by benthic diatoms. Our results reveal that Ascomycota and Chytridiomycota are the most abundant fungal taxa in these habitats. We show that also in Antarctic waters, salinity has a major impact on shaping not just fungal but rather the whole eukaryotic community composition, with a diversity of aquatic fungi increasing as salinity decreases. Moreover, we determined correlations between putative fungal parasites and potential benthic diatom hosts, highlighting the need for further systematic analysis of fungal diversity along with studies on taxonomy and ecological roles of Chytridiomycota. KW - Antarctica KW - aquatic fungi KW - Chytridiomycota KW - phytoplankton host KW - salinity gradient KW - Illumina amplicon sequencing KW - Carlini Station Y1 - 2022 U6 - https://doi.org/10.3389/fmicb.2022.805694 SN - 1664-302X IS - 13 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Ilicic, Doris A1 - Grossart, Hans-Peter T1 - Basal parasitic fungi in marine food webs-a mystery yet to unravel JF - Journal of Fungi N2 - Although aquatic and parasitic fungi have been well known for more than 100 years, they have only recently received increased awareness due to their key roles in microbial food webs and biogeochemical cycles. There is growing evidence indicating that fungi inhabit a wide range of marine habitats, from the deep sea all the way to surface waters, and recent advances in molecular tools, in particular metagenome approaches, reveal that their diversity is much greater and their ecological roles more important than previously considered. Parasitism constitutes one of the most widespread ecological interactions in nature, occurring in almost all environments. Despite that, the diversity of fungal parasites, their ecological functions, and, in particular their interactions with other microorganisms remain largely speculative, unexplored and are often missing from current theoretical concepts in marine ecology and biogeochemistry. In this review, we summarize and discuss recent research avenues on parasitic fungi and their ecological potential in marine ecosystems, e.g., the fungal shunt, and emphasize the need for further research. KW - basal fungi KW - parasites KW - Chytridiomycota KW - Rozellomycota KW - food web KW - biological carbon pump Y1 - 2022 U6 - https://doi.org/10.3390/jof8020114 SN - 2309-608X VL - 8 IS - 2 PB - MDPI CY - Basel ER - TY - JOUR A1 - Numberger, Daniela A1 - Ganzert, Lars A1 - Zoccarato, Luca A1 - Mühldorfer, Kristin A1 - Sauer, Sascha A1 - Grossart, Hans-Peter A1 - Greenwood, Alex D. T1 - Characterization of bacterial communities in wastewater with enhanced taxonomic resolution by full-length 16S rRNA sequencing JF - Scientific reports N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-46015-z SN - 2045-2322 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Srivastava, Abhishek A1 - Murugaiyan, Jayaseelan A1 - Garcia, Juan A. L. A1 - De Corte, Daniele A1 - Hoetzinger, Matthias A1 - Eravci, Murat A1 - Weise, Christoph A1 - Kumar, Yadhu A1 - Roesler, Uwe A1 - Hahn, Martin W. A1 - Grossart, Hans-Peter T1 - Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes JF - Frontiers in Microbiology N2 - Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection. KW - DNA modification KW - gene expression KW - freshwater heterotrophic bacteria KW - UV radiation KW - purifying selection Y1 - 2020 U6 - https://doi.org/10.3389/fmicb.2020.544785 SN - 1664-302X VL - 11 PB - Frontiers Media CY - Lausanne ER - TY - JOUR A1 - Günthel, Marco A1 - Donis, Daphne A1 - Kirillin, Georgiy A1 - Ionescu, Danny A1 - Bizic, Mina A1 - McGinnis, Daniel F. A1 - Grossart, Hans-Peter A1 - Tang, Kam W. T1 - Contribution of oxic methane production to surface methane emission in lakes and its global importance JF - Nature Communications N2 - Recent discovery of oxic methane production in sea and lake waters, as well as wetlands, demands re-thinking of the global methane cycle and re-assessment of the contribution of oxic waters to atmospheric methane emission. Here we analysed system-wide sources and sinks of surface-water methane in a temperate lake. Using a mass balance analysis, we show that internal methane production in well-oxygenated surface water is an important source for surface-water methane during the stratified period. Combining our results and literature reports, oxic methane contribution to emission follows a predictive function of littoral sediment area and surface mixed layer volume. The contribution of oxic methane source(s) is predicted to increase with lake size, accounting for the majority (>50%) of surface methane emission for lakes with surface areas >1 km(2). Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-13320-0 SN - 2041-1723 VL - 10 PB - Nature Publishing Group UK CY - London ER - TY - GEN A1 - Numberger, Daniela A1 - Dreier, Carola A1 - Vullioud, Colin A1 - Gabriel, Guelsah A1 - Greenwood, Alex D. A1 - Grossart, Hans-Peter T1 - Correction: Recovery of influenza A viruses from lake water and sediments by experimental inoculation (vol 14, e0216880, 2019) T2 - PLoS one Y1 - 2019 U6 - https://doi.org/10.1371/journal.pone.0218882 SN - 1932-6203 VL - 14 IS - 6 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Lundgreen, Regitze B. C. A1 - Jaspers, Cornelia A1 - Traving, Sachia J. A1 - Ayala, Daniel J. A1 - Lombard, Fabien A1 - Grossart, Hans-Peter A1 - Nielsen, Torkel G. A1 - Munk, Peter A1 - Riemann, Lasse T1 - Eukaryotic and cyanobacterial communities associated with marine snow particles in the oligotrophic Sargasso Sea JF - Scientific reports N2 - 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. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-45146-7 SN - 2045-2322 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Huang, Lixing A1 - Qiao, Ying A1 - Xu, Wei A1 - Gong, Linfeng A1 - He, Rongchao A1 - Qi, Weilu A1 - Gao, Qiancheng A1 - Cai, Hongyan A1 - Grossart, Hans-Peter A1 - Yan, Qingpi T1 - Full-length transcriptome BT - a reliable alternative for single-cell RNA-seq analysis in the spleen of teleost without reference genome JF - Frontiers in immunology N2 - 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. KW - scRNA-seq KW - full-length transcriptome KW - immune cell population KW - teleost KW - infection Y1 - 2021 U6 - https://doi.org/10.3389/fimmu.2021.737332 SN - 1664-3224 VL - 12 PB - Frontiers Media CY - Lausanne ER -