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  1. Free, publicly-accessible full text available November 12, 2025
  2. van_der_Hooft, Justin_J J (Ed.)
    ABSTRACT <p><italic>Microcystis</italic>spp. are renowned for producing the hepatotoxin microcystin in freshwater cyanobacterial harmful algal blooms around the world, threatening drinking water supplies and public and environmental health. However,<italic>Microcystis</italic>genomes also harbor numerous biosynthetic gene clusters (BGCs) encoding the biosynthesis of other secondary metabolites, including many with toxic properties. Most of these BGCs are uncharacterized and currently lack links to biosynthesis products. However, recent field studies show that many of these BGCs are abundant and transcriptionally active in natural communities, suggesting potentially important yet unknown roles in bloom ecology and water quality. Here, we analyzed 21 xenic<italic>Microcystis</italic>cultures isolated from western Lake Erie to investigate the diversity of the biosynthetic potential of this genus. Through metabologenomic and<italic>in silico</italic>approaches, we show that these<italic>Microcystis</italic>strains contain variable BGCs, previously observed in natural populations, and encode distinct metabolomes across cultures. Additionally, we find that the majority of metabolites and gene clusters are uncharacterized, highlighting our limited understanding of the chemical repertoire of<italic>Microcystis</italic>spp. Due to the complex metabolomes observed in culture, which contain a wealth of diverse congeners as well as unknown metabolites, these results underscore the need to deeply explore and identify secondary metabolites produced by<italic>Microcystis</italic>beyond microcystins to assess their impacts on human and environmental health.</p><sec><title>IMPORTANCE

    The genusMicrocystisforms dense cyanobacterial harmful algal blooms (cyanoHABs) and can produce the toxin microcystin, which has been responsible for drinking water crises around the world. While microcystins are of great concern,Microcystisalso produces an abundance of other secondary metabolites that may be of interest due to their potential for toxicity, ecological importance, or pharmaceutical applications. In this study, we combine genomic and metabolomic approaches to study the genes responsible for the biosynthesis of secondary metabolites as well as the chemical diversity of produced metabolites inMicrocystisstrains from the Western Lake Erie Culture Collection. This unique collection comprisesMicrocystisstrains that were directly isolated from western Lake Erie, which experiences substantial cyanoHAB events annually and has had negative impacts on drinking water, tourism, and industry.

     
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    Free, publicly-accessible full text available July 23, 2025
  3. Free, publicly-accessible full text available November 1, 2025
  4. Stedman, Kenneth M (Ed.)
    ABSTRACT <p>Here, we report on the raw and coassembled metatranscriptomes of 39 Lake Erie surface (1.0 m) water samples collected over a 2-day diel period encompassing episodic weather and bloom events. Preliminary taxonomic annotations and read mappings revealed that<italic>Microcystis</italic>spp. accounted for up to ~47% of the transcriptionally active community.</p></sec> </div> <a href='#' class='show open-abstract' style='margin-left:10px;'>more »</a> <a href='#' class='hide close-abstract' style='margin-left:10px;'>« less</a> <div class="actions" style="padding-left:10px;"> <span class="reader-count"> Free, publicly-accessible full text available November 12, 2025</span> </div> </div><div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemscope itemtype="http://schema.org/TechArticle"> <div class="item-info"> <div class="title"> <a href="https://par.nsf.gov/biblio/10565411-metagenomics-reveals-spatial-variation-cyanobacterial-composition-function-biosynthetic-potential-winam-gulf-lake-victoria-kenya" itemprop="url"> <span class='span-link' itemprop="name">Metagenomics reveals spatial variation in cyanobacterial composition, function, and biosynthetic potential in the Winam Gulf, Lake Victoria, Kenya</span> </a> </div> <div> <strong> <a class="misc external-link" href="https://doi.org/10.1128/aem.01507-24" target="_blank" title="Link to document DOI">https://doi.org/10.1128/aem.01507-24  <span class="fas fa-external-link-alt"></span></a> </strong> </div> <div class="metadata"> <span class="authors"> <span class="author" itemprop="author">Hart, Lauren N</span> <span class="sep">; </span><span class="author" itemprop="author">Zepernick, Brittany N</span> <span class="sep">; </span><span class="author" itemprop="author">Natwora, Kaela E</span> <span class="sep">; </span><span class="author" itemprop="author">Brown, Katelyn M</span> <span class="sep">; </span><span class="author" itemprop="author">Obuya, Julia Akinyi</span> <span class="sep">; </span><span class="author" itemprop="author">Lomeo, Davide</span> <span class="sep">; </span><span class="author" itemprop="author">Barnard, Malcolm A</span> <span class="sep">; </span><span class="author" itemprop="author">Okech, Eric O</span> <span class="sep">; </span><span class="author" itemprop="author">Kiledal, E Anders</span> <span class="sep">; </span><span class="author" itemprop="author">Den_Uyl, Paul A</span> <span class="sep">; </span><span class="author">et al</span></span> <span class="year">( <time itemprop="datePublished" datetime="2025-01-08">January 2025</time> , Applied and Environmental Microbiology) </span> </div> <span class="editors"> <span class="editor" itemprop="editor">Biddle, Jennifer F</span> (Ed.) </span> <div style="cursor: pointer;-webkit-line-clamp: 5;" class="abstract" itemprop="description"> <title>ABSTRACT

    The Winam Gulf in the Kenyan region of Lake Victoria experiences prolific, year-round cyanobacterial harmful algal blooms (cyanoHABs) which pose threats to human, livestock, and ecosystem health. To our knowledge, there is limited molecular research on the gulf’s cyanoHABs, and thus, the strategies employed for survival and proliferation by toxigenic cyanobacteria in this region remain largely unexplored. Here, we used metagenomics to analyze the Winam Gulf’s cyanobacterial composition, function, and biosynthetic potential.Dolichospermumwas the dominant bloom-forming cyanobacterium, co-occurring withMicrocystisat most sites.MicrocystisandPlanktothrixwere more abundant in shallow and turbid sites. Metagenome-assembled genomes (MAGs) ofDolichospermumharbored nitrogen fixation genes, suggesting diazotrophy as a potential mechanism supporting the proliferation ofDolichospermumin the nitrogen-limited gulf. Over 300 biosynthetic gene clusters (BGCs) putatively encoding the synthesis of toxins and other secondary metabolites were identified across the gulf, even at sites where there were no visible cyanoHAB events. Almost all BGCs identified had no known synthesis product, indicating a diverse and novel biosynthetic repertoire capable of synthesizing harmful or potentially therapeutic metabolites.MicrocystisMAGs containedmcygenes encoding the synthesis of hepatotoxic microcystins which are a concern for drinking water safety. These findings illustrate the spatial variation of bloom-forming cyanobacteria in the Winam Gulf and their available strategies to dominate different ecological niches. This study underscores the need for further use of genomic techniques to elucidate the dynamics and mitigate the potentially harmful effects of cyanoHABs and their associated toxins on human, environmental, and economic health.

     
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    Free, publicly-accessible full text available January 8, 2026
  5. Newton, Irene_L G (Ed.)
    ABSTRACT <p>We report 40 metagenomic libraries collected from the Winam Gulf of Lake Victoria during May–July of 2022–2023 and an additional eight opportunistic libraries from adjacent Lakes Simbi, Naivasha, and regional river systems. The sampling period captured cyanobacterial bloom events – shedding insight onto community composition and genomic potential.</p></sec> </div> <a href='#' class='show open-abstract' style='margin-left:10px;'>more »</a> <a href='#' class='hide close-abstract' style='margin-left:10px;'>« less</a> <div class="actions" style="padding-left:10px;"> <span class="reader-count"> Free, publicly-accessible full text available November 12, 2025</span> </div> </div><div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemscope itemtype="http://schema.org/TechArticle"> <div class="item-info"> <div class="title"> <a href="https://par.nsf.gov/biblio/10430307-response-comment-models-predict-planned-phosphorus-load-reduction-make-lake-erie-more-toxic" itemprop="url"> <span class='span-link' itemprop="name">Response to Comment on “Models predict planned phosphorus load reduction will make Lake Erie more toxic”</span> </a> </div> <div> <strong> <a class="misc external-link" href="https://doi.org/10.1126/science.ade2277" target="_blank" title="Link to document DOI">https://doi.org/10.1126/science.ade2277  <span class="fas fa-external-link-alt"></span></a> </strong> </div> <div class="metadata"> <span class="authors"> <span class="author" itemprop="author">Hellweger, Ferdi L.</span> <span class="sep">; </span><span class="author" itemprop="author">Schampera, Charlotte</span> <span class="sep">; </span><span class="author" itemprop="author">Martin, Robbie M.</span> <span class="sep">; </span><span class="author" itemprop="author">Eigemann, Falk</span> <span class="sep">; </span><span class="author" itemprop="author">Smith, Derek J.</span> <span class="sep">; </span><span class="author" itemprop="author">Dick, Gregory J.</span> <span class="sep">; </span><span class="author" itemprop="author">Wilhelm, Steven W.</span> </span> <span class="year">( <time itemprop="datePublished" datetime="2022-11-11">November 2022</time> , Science) </span> </div> <div style="cursor: pointer;-webkit-line-clamp: 5;" class="abstract" itemprop="description"> Huisman et al . claim that our model is poorly supported or contradicted by other studies and the predictions are “seriously flawed.” We show their criticism is based on an incomplete selection of evidence, misinterpretation of data, or does not actually refute the model. Like all ecosystem models, our model has simplifications and uncertainties, but it is better than existing approaches hat ignore biology and do not predict toxin concentration. </div> <a href='#' class='show open-abstract' style='margin-left:10px;'>more »</a> <a href='#' class='hide close-abstract' style='margin-left:10px;'>« less</a> <div class="actions" style="padding-left:10px;"> <span class="reader-count"> <a class="misc external-link" href="https://doi.org/10.1126/science.ade2277" target="_blank" title="Link to document DOI" data-ostiid="10430307"> Full Text Available <span class="fas fa-external-link-alt"></span> </a> </span> </div> </div><div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemscope itemtype="http://schema.org/TechArticle"> <div class="item-info"> <div class="title"> <a href="https://par.nsf.gov/biblio/10410107-uptake-phytoplankton-derived-carbon-cobalamins-novel-acidobacteria-genera-microcystis-blooms-inferred-from-metagenomic-metatranscriptomic-evidence" itemprop="url"> <span class='span-link' itemprop="name">Uptake of Phytoplankton-Derived Carbon and Cobalamins by Novel Acidobacteria Genera in Microcystis Blooms Inferred from Metagenomic and Metatranscriptomic Evidence</span> </a> </div> <div> <strong> <a class="misc external-link" href="https://doi.org/10.1128/aem.01803-21" target="_blank" title="Link to document DOI">https://doi.org/10.1128/aem.01803-21  <span class="fas fa-external-link-alt"></span></a> </strong> </div> <div class="metadata"> <span class="authors"> <span class="author" itemprop="author">Smith, Derek J.</span> <span class="sep">; </span><span class="author" itemprop="author">Kharbush, Jenan J.</span> <span class="sep">; </span><span class="author" itemprop="author">Kersten, Roland D.</span> <span class="sep">; </span><span class="author" itemprop="author">Dick, Gregory J.</span> </span> <span class="year">( <time itemprop="datePublished" datetime="2022-07-26">July 2022</time> , Applied and Environmental Microbiology) </span> </div> <span class="editors"> <span class="editor" itemprop="editor">Glass, Jennifer B.</span> (Ed.) </span> <div style="cursor: pointer;-webkit-line-clamp: 5;" class="abstract" itemprop="description"> ABSTRACT Interactions between bacteria and phytoplankton can influence primary production, community composition, and algal bloom development. However, these interactions are poorly described for many consortia, particularly for freshwater bloom-forming cyanobacteria. Here, we assessed the gene content and expression of two uncultivated Acidobacteria from Lake Erie Microcystis blooms. These organisms were targeted because they were previously identified as important catalase producers in Microcystis blooms, suggesting that they protect Microcystis from H 2 O 2 . Metatranscriptomics revealed that both Acidobacteria transcribed genes for uptake of organic compounds that are known cyanobacterial products and exudates, including lactate, glycolate, amino acids, peptides, and cobalamins. Expressed genes for amino acid metabolism and peptide transport and degradation suggest that use of amino acids and peptides by Acidobacteria may regenerate nitrogen for cyanobacteria and other organisms. The Acidobacteria genomes lacked genes for biosynthesis of cobalamins but expressed genes for its transport and remodeling. This indicates that the Acidobacteria obtained cobalamins externally, potentially from Microcystis , which has a complete gene repertoire for pseudocobalamin biosynthesis; expressed them in field samples; and produced pseudocobalamin in axenic culture. Both Acidobacteria were detected in Microcystis blooms worldwide. Together, the data support the hypotheses that uncultured and previously unidentified Acidobacteria taxa exchange metabolites with phytoplankton during harmful cyanobacterial blooms and influence nitrogen available to phytoplankton. Thus, novel Acidobacteria may play a role in cyanobacterial physiology and bloom development. IMPORTANCE Interactions between heterotrophic bacteria and phytoplankton influence competition and successions between phytoplankton taxa, thereby influencing ecosystem-wide processes such as carbon cycling and algal bloom development. The cyanobacterium Microcystis forms harmful blooms in freshwaters worldwide and grows in buoyant colonies that harbor other bacteria in their phycospheres. Bacteria in the phycosphere and in the surrounding community likely influence Microcystis physiology and ecology and thus the development of freshwater harmful cyanobacterial blooms. However, the impacts and mechanisms of interaction between bacteria and Microcystis are not fully understood. This study explores the mechanisms of interaction between Microcystis and uncultured members of its phycosphere in situ with population genome resolution to investigate the cooccurrence of Microcystis and freshwater Acidobacteria in blooms worldwide. </div> <a href='#' class='show open-abstract' style='margin-left:10px;'>more »</a> <a href='#' class='hide close-abstract' style='margin-left:10px;'>« less</a> <div class="actions" style="padding-left:10px;"> <span class="reader-count"> <a class="misc external-link" href="https://doi.org/10.1128/aem.01803-21" target="_blank" title="Link to document DOI" data-ostiid="10410107"> Full Text Available <span class="fas fa-external-link-alt"></span> </a> </span> </div> </div><div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemscope itemtype="http://schema.org/TechArticle"> <div class="item-info"> <div class="title"> <a href="https://par.nsf.gov/biblio/10376404-response-model-assumptions-limit-implications-nitrogen-phosphorus-management-need-move-beyond-phosphorus-biomass-toxin-doctrine" itemprop="url"> <span class='span-link' itemprop="name">Response to “Model assumptions limit implications for nitrogen and phosphorus management”: The need to move beyond the phosphorus = biomass = toxin doctrine</span> </a> </div> <div> <strong> <a class="misc external-link" href="https://doi.org/10.1016/j.jglr.2022.10.001" target="_blank" title="Link to document DOI">https://doi.org/10.1016/j.jglr.2022.10.001  <span class="fas fa-external-link-alt"></span></a> </strong> </div> <div class="metadata"> <span class="authors"> <span class="author" itemprop="author">Wilhelm, Steven W.</span> <span class="sep">; </span><span class="author" itemprop="author">Hellweger, Ferdi L.</span> <span class="sep">; </span><span class="author" itemprop="author">Martin, Robbie M.</span> <span class="sep">; </span><span class="author" itemprop="author">Schampera, Charlotte</span> <span class="sep">; </span><span class="author" itemprop="author">Eigemann, Falk</span> <span class="sep">; </span><span class="author" itemprop="author">Smith, Derek J.</span> <span class="sep">; </span><span class="author" itemprop="author">Dick, Gregory J.</span> </span> <span class="year">( <time itemprop="datePublished" datetime="2022-10-01">October 2022</time> , Journal of Great Lakes Research) </span> </div> <div class="actions" style="padding-left:10px;"> <span class="reader-count"> <a class="misc external-link" href="https://doi.org/10.1016/j.jglr.2022.10.001" target="_blank" title="Link to document DOI" data-ostiid="10376404"> Full Text Available <span class="fas fa-external-link-alt"></span> </a> </span> </div> </div><div class="clearfix"></div> </div> </li> <li> <div class="article item document" itemscope itemtype="http://schema.org/TechArticle"> <div class="item-info"> <div class="title"> <a href="https://par.nsf.gov/biblio/10417648-sulfur-cycling-connects-microbiomes-biogeochemistry-deep-sea-hydrothermal-plumes" itemprop="url"> <span class='span-link' itemprop="name">Sulfur cycling connects microbiomes and biogeochemistry in deep-sea hydrothermal plumes</span> </a> </div> <div> <strong> <a class="misc external-link" href="https://doi.org/10.1038/s41396-023-01421-0" target="_blank" title="Link to document DOI">https://doi.org/10.1038/s41396-023-01421-0  <span class="fas fa-external-link-alt"></span></a> </strong> </div> <div class="metadata"> <span class="authors"> <span class="author" itemprop="author">Zhou, Zhichao</span> <span class="sep">; </span><span class="author" itemprop="author">Tran, Patricia Q.</span> <span class="sep">; </span><span class="author" itemprop="author">Adams, Alyssa M.</span> <span class="sep">; </span><span class="author" itemprop="author">Kieft, Kristopher</span> <span class="sep">; </span><span class="author" itemprop="author">Breier, John A.</span> <span class="sep">; </span><span class="author" itemprop="author">Fortunato, Caroline S.</span> <span class="sep">; </span><span class="author" itemprop="author">Sheik, Cody S.</span> <span class="sep">; </span><span class="author" itemprop="author">Huber, Julie A.</span> <span class="sep">; </span><span class="author" itemprop="author">Li, Meng</span> <span class="sep">; </span><span class="author" itemprop="author">Dick, Gregory J.</span> <span class="sep">; </span><span class="author">et al</span></span> <span class="year">( <time itemprop="datePublished" datetime="2023-01-01">January 2023</time> , The ISME Journal) </span> </div> <div style="cursor: pointer;-webkit-line-clamp: 5;" class="abstract" itemprop="description"> Abstract In globally distributed deep-sea hydrothermal vent plumes, microbiomes are shaped by the redox energy landscapes created by reduced hydrothermal vent fluids mixing with oxidized seawater. Plumes can disperse over thousands of kilometers and their characteristics are determined by geochemical sources from vents, e.g., hydrothermal inputs, nutrients, and trace metals. However, the impacts of plume biogeochemistry on the oceans are poorly constrained due to a lack of integrated understanding of microbiomes, population genetics, and geochemistry. Here, we use microbial genomes to understand links between biogeography, evolution, and metabolic connectivity, and elucidate their impacts on biogeochemical cycling in the deep sea. Using data from 36 diverse plume samples from seven ocean basins, we show that sulfur metabolism defines the core microbiome of plumes and drives metabolic connectivity in the microbial community. Sulfur-dominated geochemistry influences energy landscapes and promotes microbial growth, while other energy sources influence local energy landscapes. We further demonstrated the consistency of links among geochemistry, function, and taxonomy. Amongst all microbial metabolisms, sulfur transformations had the highest MW-score, a measure of metabolic connectivity in microbial communities. Additionally, plume microbial populations have low diversity, short migration history, and gene-specific sweep patterns after migrating from background seawater. Selected functions include nutrient uptake, aerobic oxidation, sulfur oxidation for higher energy yields, and stress responses for adaptation. Our findings provide the ecological and evolutionary bases of change in sulfur-driven microbial communities and their population genetics in adaptation to changing geochemical gradients in the oceans. </div> <a href='#' class='show open-abstract' style='margin-left:10px;'>more »</a> <a href='#' class='hide close-abstract' style='margin-left:10px;'>« less</a> <div class="actions" style="padding-left:10px;"> <span class="reader-count"> <a class="misc external-link" href="https://doi.org/10.1038/s41396-023-01421-0" target="_blank" title="Link to document DOI" data-ostiid="10417648"> Full Text Available <span class="fas fa-external-link-alt"></span> </a> </span> </div> </div><div class="clearfix"></div> </div> </li> </ol> <div id="pagination-lower" style=""> <div class="pull-right" style="line-height: 30px;"> <div class="btn-group pagination nomargin"> <a href="#" class="btn btn-sm btn-default noborderradius" disabled="disabled">«<span class="hidden-xs"> Prev</span></a> <a class="dropdown-toggle btn btn-sm btn-default paging-dropdown hidden-xs noborderradius" href="#" data-toggle="dropdown"><span class="caret"></span><span class="sr-only">Select page number</span></a> <div class="dropdown-menu pull-right paging-slider-dropdown" style="padding: 15px;"> <small> <div class="text-muted" style="line-height:20px;"><label for="pagination-sel-sptag-2">Go to page: <span class="paging-target">1</span> of <span class="paging-max">4</span></label></div> <div> <table> <tr> <td valign="top"> <input id="pagination-sel-sptag-2" data-range="" value="1" min="1" max="4" name="pagination-sel" type="range" class="pagination-sel noborderradius" style="height:26px;padding:0px;margin-right:5px; 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