@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{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{IlicicWoodhouseKarstenetal.2022, author = {Ilicic, Doris and Woodhouse, Jason Nicholas and Karsten, Ulf and Zimmermann, Jonas and Wichard, Thomas and Quartino, Maria Liliana and Campana, Gabriela Laura and Livenets, Alexandra and Van den Wyngaert, Silke and Grossart, Hans-Peter}, title = {Antarctic Glacial Meltwater Impacts the Diversity of Fungal Parasites Associated With Benthic Diatoms in Shallow Coastal Zones}, series = {Frontiers in microbiology}, journal = {Frontiers in microbiology}, number = {13}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2022.805694}, pages = {12}, year = {2022}, abstract = {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.}, 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{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{SrivastavaMurugaiyanGarciaetal.2020, author = {Srivastava, Abhishek and Murugaiyan, Jayaseelan and Garcia, Juan A. L. and De Corte, Daniele and Hoetzinger, Matthias and Eravci, Murat and Weise, Christoph and Kumar, Yadhu and Roesler, Uwe and Hahn, Martin W. and Grossart, Hans-Peter}, title = {Combined Methylome, Transcriptome and Proteome Analyses Document Rapid Acclimatization of a Bacterium to Environmental Changes}, series = {Frontiers in Microbiology}, volume = {11}, journal = {Frontiers in Microbiology}, publisher = {Frontiers Media}, address = {Lausanne}, issn = {1664-302X}, doi = {10.3389/fmicb.2020.544785}, pages = {21}, year = {2020}, abstract = {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.}, language = {en} } @article{GuenthelDonisKirillinetal.2019, author = {G{\"u}nthel, Marco and Donis, Daphne and Kirillin, Georgiy and Ionescu, Danny and Bizic, Mina and McGinnis, Daniel F. and Grossart, Hans-Peter and Tang, Kam W.}, title = {Contribution of oxic methane production to surface methane emission in lakes and its global importance}, series = {Nature Communications}, volume = {10}, journal = {Nature Communications}, publisher = {Nature Publishing Group UK}, address = {London}, issn = {2041-1723}, doi = {10.1038/s41467-019-13320-0}, pages = {10}, year = {2019}, abstract = {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).}, 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{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{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} }