Subhadeep Chowdhury, Hugo Berthelot, Corentin Baudet, David González-Santana, Christian Furbo Reeder, Stéphane L'Helguen, Jean-François Maguer, Carolin R Löscher, Arvind Singh, Stéphane Blain, Nicolas Cassar, Sophie Bonnet, Hélène Planquette, Mar Benavides
{"title":"Fronts divide diazotroph communities in the Southern Indian Ocean.","authors":"Subhadeep Chowdhury, Hugo Berthelot, Corentin Baudet, David González-Santana, Christian Furbo Reeder, Stéphane L'Helguen, Jean-François Maguer, Carolin R Löscher, Arvind Singh, Stéphane Blain, Nicolas Cassar, Sophie Bonnet, Hélène Planquette, Mar Benavides","doi":"10.1093/femsec/fiae095","DOIUrl":"10.1093/femsec/fiae095","url":null,"abstract":"<p><p>Dinitrogen (N2) fixation represents a key source of reactive nitrogen in marine ecosystems. While the process has been rather well-explored in low latitudes of the Atlantic and Pacific Oceans, other higher latitude regions and particularly the Indian Ocean have been chronically overlooked. Here, we characterize N2 fixation and diazotroph community composition across nutrient and trace metals gradients spanning the multifrontal system separating the oligotrophic waters of the Indian Ocean subtropical gyre from the high nutrient low chlorophyll waters of the Southern Ocean. We found a sharp contrasting distribution of diazotroph groups across the frontal system. Notably, cyanobacterial diazotrophs dominated north of fronts, driving high N2 fixation rates (up to 13.96 nmol N l-1 d-1) with notable peaks near the South African coast. South of the fronts non-cyanobacterial diazotrophs prevailed without significant N2 fixation activity being detected. Our results provide new crucial insights into high latitude diazotrophy in the Indian Ocean, which should contribute to improved climate model parameterization and enhanced constraints on global net primary productivity projections.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11245648/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141590092","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Anna Shoemaker, Andrew Maritan, Su Cosar, Sylvia Nupp, Ana Menchaca, Thomas Jackson, Aria Dang, Bonnie K Baxter, Daniel R Colman, Eric C Dunham, Eric S Boyd
{"title":"Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah.","authors":"Anna Shoemaker, Andrew Maritan, Su Cosar, Sylvia Nupp, Ana Menchaca, Thomas Jackson, Aria Dang, Bonnie K Baxter, Daniel R Colman, Eric C Dunham, Eric S Boyd","doi":"10.1093/femsec/fiae105","DOIUrl":"10.1093/femsec/fiae105","url":null,"abstract":"<p><p>Little is known of primary production in dark hypersaline ecosystems despite the prevalence of such environments on Earth today and throughout its geologic history. Here, we generated and analyzed metagenome-assembled genomes (MAGs) organized as operational taxonomic units (OTUs) from three depth intervals along a 30-cm sediment core from the north arm of Great Salt Lake, Utah. The sediments and associated porewaters were saturated with NaCl, exhibited redox gradients with depth, and harbored nitrogen-depleted organic carbon. Metabolic predictions of MAGs representing 36 total OTUs recovered from the core indicated that communities transitioned from aerobic and heterotrophic at the surface to anaerobic and autotrophic at depth. Dark CO2 fixation was detected in sediments and the primary mode of autotrophy was predicted to be via the Wood-Ljungdahl pathway. This included novel hydrogenotrophic acetogens affiliated with the bacterial class Candidatus Bipolaricaulia. Minor populations were dependent on the Calvin cycle and the reverse tricarboxylic acid cycle, including in a novel Thermoplasmatota MAG. These results are interpreted to reflect the favorability of and selectability for populations that operate the lowest energy requiring CO2-fixation pathway known, the Wood-Ljungdahl pathway, in anoxic and hypersaline conditions that together impart a higher energy demand on cells.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11287216/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758032","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mari Vanharanta, Mariano Santoro, Cristian Villena-Alemany, Jonna Piiparinen, Kasia Piwosz, Hans-Peter Grossart, Matthias Labrenz, Kristian Spilling
{"title":"Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea.","authors":"Mari Vanharanta, Mariano Santoro, Cristian Villena-Alemany, Jonna Piiparinen, Kasia Piwosz, Hans-Peter Grossart, Matthias Labrenz, Kristian Spilling","doi":"10.1093/femsec/fiae103","DOIUrl":"10.1093/femsec/fiae103","url":null,"abstract":"<p><p>The phosphorus (P) concentration is increasing in parts of the Baltic Sea following the spring bloom. The fate of this excess P-pool is an open question, and here we investigate the role of microbial degradation processes in the excess P assimilation phase. During a 17-day-long mesocosm experiment in the southwest Finnish archipelago, we examined nitrogen, phosphorus, and carbon acquiring extracellular enzyme activities in three size fractions (<0.2, 0.2-3, and >3 µm), bacterial abundance, production, community composition, and its predicted metabolic functions. The mesocosms received carbon (C) and nitrogen (N) amendments individually and in combination (NC) to distinguish between heterotrophic and autotrophic processes. Alkaline phosphatase activity occurred mainly in the dissolved form and likely contributed to the excess phosphate conditions together with grazing. At the beginning of the experiment, peptidolytic and glycolytic enzymes were mostly produced by free-living bacteria. However, by the end of the experiment, the NC-treatment induced a shift in peptidolytic and glycolytic activities and degradation of phosphomonoesters toward the particle-associated fraction, likely as a consequence of higher substrate availability. This would potentially promote retention of nutrients in the surface as opposed to sedimentation, but direct sedimentation measurements are needed to verify this hypothesis.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11302951/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747855","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Correction to: Alpine soil microbial ecology in a changing world.","authors":"","doi":"10.1093/femsec/fiae085","DOIUrl":"10.1093/femsec/fiae085","url":null,"abstract":"","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":"100 8","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-07-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11271679/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141758033","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Mustafa Guzel, Aysenur Yucefaydali, Segah Yetiskin, Aysu Deniz, Osman Yaşar Tel, Mustafa Akçelik, Yeşim Soyer
{"title":"Genomic analysis of Salmonella bacteriophages revealed multiple endolysin ORFs and importance of ligand-binding site of receptor-binding protein.","authors":"Mustafa Guzel, Aysenur Yucefaydali, Segah Yetiskin, Aysu Deniz, Osman Yaşar Tel, Mustafa Akçelik, Yeşim Soyer","doi":"10.1093/femsec/fiae079","DOIUrl":"10.1093/femsec/fiae079","url":null,"abstract":"<p><p>Salmonella is a prevalent foodborne pathogen causing millions of global cases annually. Antimicrobial resistance is a growing public health concern, leading to search for alternatives like bacteriophages. A total of 97 bacteriophages, isolated from cattle farms (n = 48), poultry farms (n = 37), and wastewater (n = 5) samples in Türkiye, were subjected to host-range analysis using 36 Salmonella isolates with 18 different serotypes. The broadest host range belonged to an Infantis phage (MET P1-091), lysing 28 hosts. A total of 10 phages with the widest host range underwent further analysis, revealing seven unique genomes (32-243 kb), including a jumbophage (>200 kb). Except for one with lysogenic properties, none of them harbored virulence or antibiotic resistance genes, making them potential Salmonella reducers in different environments. Examining open reading frames (ORFs) of endolysin enzymes revealed surprising findings: five of seven unique genomes contained multiple endolysin ORFs. Despite sharing same endolysin sequences, phages exhibited significant differences in host range. Detailed analysis unveiled diverse receptor-binding protein sequences, with similar structures but distinct ligand-binding sites. These findings emphasize the importance of ligand-binding sites of receptor-binding proteins. Additionally, bacterial reduction curve and virulence index revealed that Enteritidis phages inhibit bacterial growth even at low concentrations, unlike Infantis and Kentucky phages.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11180984/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179250","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Luana Soares Dal-Ferro, Arthur Schenider, Dabny Goulart Missiaggia, Libério Junio Silva, Adaíses Simone Maciel-Silva, Cleber Cunha Figueredo
{"title":"Organizing a global list of cyanobacteria and algae from soil biocrusts evidenced great geographic and taxonomic gaps.","authors":"Luana Soares Dal-Ferro, Arthur Schenider, Dabny Goulart Missiaggia, Libério Junio Silva, Adaíses Simone Maciel-Silva, Cleber Cunha Figueredo","doi":"10.1093/femsec/fiae086","DOIUrl":"10.1093/femsec/fiae086","url":null,"abstract":"<p><p>Biocrusts determine soil stability and resiliency, with a special role played by oxygenic photoautotrophic microorganisms in these communities. We evaluated temporal and geographic trends in studies focused on these microorganisms in biocrusts. Two databases were surveyed to obtain scientific articles published from 1998 to 2020 containing the terms 'biocrusts,' 'algae,' and 'cyanobacteria.' Although interest in biocrusts has increased recently, their ecological importance is still little explored. The scientific articles that mentioned a species list of cyanobacteria and/or algae revealed a very heterogeneous geographic distribution of research. Biocrusts have not been explored in many regions and knowledge in the tropics, where these communities showed high species richness, is limited. Geographic gaps were detected and more detailed studies are needed, mainly where biocrust communities are threatened by anthropogenic impacts. Aiming to address these knowledge gaps, we assembled a taxonomic list of all algae and cyanobacteria found in these articles, including information on their occurrence and ecology. This review is an updated global taxonomic survey of biocrusts, which importantly reveals their high species richness of oxygenic photoautotrophic microorganisms. We believe this database will be useful to future research by providing valuable taxonomic and biogeographic information regarding algae and cyanobacteria in biocrusts.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11221558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179256","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Chaonan Li, Chi Liu, Hankang Li, Haijun Liao, Lin Xu, Minjie Yao, Xiangzhen Li
{"title":"The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps.","authors":"Chaonan Li, Chi Liu, Hankang Li, Haijun Liao, Lin Xu, Minjie Yao, Xiangzhen Li","doi":"10.1093/femsec/fiae087","DOIUrl":"10.1093/femsec/fiae087","url":null,"abstract":"<p><p>Many R packages provide statistical approaches for elucidating the diversity of soil microbes, yet they still struggle to visualize microbial traits on a geographical map. This creates challenges in interpreting microbial biogeography on a regional scale, especially when the spatial scale is large or the distribution of sampling sites is uneven. Here, we developed a lightweight, flexible, and user-friendly R package called microgeo. This package integrates many functions involved in reading, manipulating, and visualizing geographical boundary data; downloading spatial datasets; and calculating microbial traits and rendering them onto a geographical map using grid-based visualization, spatial interpolation, or machine learning. Using this R package, users can visualize any trait calculated by microgeo or other tools on a map and can analyze microbiome data in conjunction with metadata derived from a geographical map. In contrast to other R packages that statistically analyze microbiome data, microgeo provides more-intuitive approaches in illustrating the biogeography of soil microbes on a large geographical scale, serving as an important supplement to statistically driven comparisons and facilitating the biogeographic analysis of publicly accessible microbiome data at a large spatial scale in a more convenient and efficient manner. The microgeo R package can be installed from the Gitee (https://gitee.com/bioape/microgeo) and GitHub (https://github.com/ChaonanLi/microgeo) repositories. Detailed tutorials for the microgeo R package are available at https://chaonanli.github.io/microgeo.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11212663/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141310413","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Ashwana D Fricker, Tianming Yao, Stephen R Lindemann, Gilberto E Flores
{"title":"Enrichment and characterization of human-associated mucin-degrading microbial consortia by sequential passage.","authors":"Ashwana D Fricker, Tianming Yao, Stephen R Lindemann, Gilberto E Flores","doi":"10.1093/femsec/fiae078","DOIUrl":"10.1093/femsec/fiae078","url":null,"abstract":"<p><p>Mucin is a glycoprotein secreted throughout the mammalian gastrointestinal tract that can support endogenous microorganisms in the absence of complex polysaccharides. While several mucin-degrading bacteria have been identified, the interindividual differences in microbial communities capable of metabolizing this complex polymer are not well described. To determine whether community assembly on mucin is deterministic across individuals or whether taxonomically distinct but functionally similar mucin-degrading communities are selected across fecal inocula, we used a 10-day in vitro sequential batch culture fermentation from three human donors with mucin as the sole carbon source. For each donor, 16S rRNA gene amplicon sequencing was used to characterize microbial community succession, and the short-chain fatty acid profile was determined from the final community. All three communities reached a steady-state by day 7 in which the community composition stabilized. Taxonomic comparisons amongst communities revealed that one of the final communities had Desulfovibrio, another had Akkermansia, and all three shared other members, such as Bacteroides. Metabolic output differences were most notable for one of the donor's communities, with significantly less production of acetate and propionate than the other two communities. These findings demonstrate the feasibility of developing stable mucin-degrading communities with shared and unique taxa. Furthermore, the mechanisms and efficiencies of mucin degradation across individuals are important for understanding how this community-level process impacts human health.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":4.2,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11180985/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141093252","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
{"title":"Clean your own house first: integrating sustainability into microbiology labs.","authors":"Priscilla Carrillo-Barragan","doi":"10.1093/femsec/fiae084","DOIUrl":"10.1093/femsec/fiae084","url":null,"abstract":"<p><p>Microbiology laboratories are pivotal hubs for exploring the potential of microorganisms and addressing global challenges. Particularly, Environmental Microbiology facilities hold substantial influence in advancing knowledge and capabilities crucial for achieving the United Nations Sustainable Development Goals. This raises the imperative of integrating sustainable practices to mitigate the environmental impact of research activities and foster a culture of responsibility. Such an approach not only aligns with global sustainability objectives but also catalyses innovative, eco-conscious methodologies in scientific research aimed at tackling pressing environmental issues. Concerns regarding the environmental footprint of laboratory practices have stimulated innovative improvements within the scientific community, ranging from resource-efficient initiatives to the management of essential commodities like water and energy. This perspective discusses specific areas where microbiology laboratories can enhance their sustainability efforts, drawing on reports and case studies of pioneering groups. Additionally, it explores potential collaborators to support these endeavours and emphasises the pivotal role of early career researchers in driving this transition. By initiating discussions and sparking curiosity within the environmental microbial community, this commentary seeks to propel the microbial ecology field toward a greener future, starting from within the laboratory environment.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11210500/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179306","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
William S Pearman, Grant A Duffy, Neil J Gemmell, Sergio E Morales, Ceridwen I Fraser
{"title":"Long-distance movement dynamics shape host microbiome richness and turnover.","authors":"William S Pearman, Grant A Duffy, Neil J Gemmell, Sergio E Morales, Ceridwen I Fraser","doi":"10.1093/femsec/fiae089","DOIUrl":"10.1093/femsec/fiae089","url":null,"abstract":"<p><p>Host-associated microbial communities are shaped by host migratory movements. These movements can have contrasting impacts on microbiota, and understanding such patterns can provide insight into the ecological processes that contribute to community diversity. Furthermore, long-distance movements to new environments are anticipated to occur with increasing frequency due to host distribution shifts resulting from climate change. Understanding how hosts transport their microbiota with them could be of importance when examining biological invasions. Although microbial community shifts are well-documented, the underlying mechanisms that lead to the restructuring of these communities remain relatively unexplored. Using literature and ecological simulations, we develop a framework to elucidate the major factors that lead to community change. We group host movements into two types-regular (repeated/cyclical migratory movements, as found in many birds and mammals) and irregular (stochastic/infrequent movements that do not occur on a cyclical basis, as found in many insects and plants). Ecological simulations and prior research suggest that movement type and frequency, alongside environmental exposure (e.g. internal/external microbiota) are key considerations for understanding movement-associated community changes. From our framework, we derive a series of testable hypotheses, and suggest means to test them, to facilitate future research into host movement and microbial community dynamics.</p>","PeriodicalId":12312,"journal":{"name":"FEMS microbiology ecology","volume":" ","pages":""},"PeriodicalIF":3.5,"publicationDate":"2024-06-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11212666/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141300417","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}