FEMS microbiology ecology最新文献_第10页

Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning. 温带二叠纪湖泊中小型原生生物和自由生活细菌群落的时空变化：代谢标码和机器学习的启示。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-07-12 DOI: 10.1093/femsec/fiae104

Michał Karlicki, Anna Bednarska, Paweł Hałakuc, Kacper Maciszewski, Anna Karnkowska

{"title":"Spatio-temporal changes of small protist and free-living bacterial communities in a temperate dimictic lake: insights from metabarcoding and machine learning.","authors":"Michał Karlicki, Anna Bednarska, Paweł Hałakuc, Kacper Maciszewski, Anna Karnkowska","doi":"10.1093/femsec/fiae104","DOIUrl":"10.1093/femsec/fiae104","url":null,"abstract":"Microbial communities, which include prokaryotes and protists, play an important role in aquatic ecosystems and influence ecological processes. To understand these communities, metabarcoding provides a powerful tool to assess their taxonomic composition and track spatio-temporal dynamics in both marine and freshwater environments. While marine ecosystems have been extensively studied, there is a notable research gap in understanding eukaryotic microbial communities in temperate lakes. Our study addresses this gap by investigating the free-living bacteria and small protist communities in Lake Roś (Poland), a dimictic temperate lake. Metabarcoding analysis revealed that both the bacterial and protist communities exhibit distinct seasonal patterns that are not necessarily shaped by dominant taxa. Furthermore, machine learning and statistical methods identified crucial amplicon sequence variants (ASVs) specific to each season. In addition, we identified a distinct community in the anoxic hypolimnion. We have also shown that the key factors shaping the composition of analysed community are temperature, oxygen, and silicon concentration. Understanding these community structures and the underlying factors is important in the context of climate change potentially impacting mixing patterns and leading to prolonged stratification.","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/PMC11302952/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141747856","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}

引用次数: 0

Editorial: thematic issue on microbial ecotoxicology. 编辑：微生物生态毒理学专题。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-07-12 DOI: 10.1093/femsec/fiae097

Stéphane Vuilleumier, Lise Barthelmebs, Natàlia Corcoll, Marina Hery, Dimitrios G Karpouzas, Lukas Y Wick

引用次数: 0

The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics. 具有不同植物生长特性的 51 个马铃薯栽培品种的根瘤微生物群。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-07-12 DOI: 10.1093/femsec/fiae088

Benoit Renaud Martins, Viviane Radl, Krzysztof Treder, Dorota Michałowska, Karin Pritsch, Michael Schloter

{"title":"The rhizosphere microbiome of 51 potato cultivars with diverse plant growth characteristics.","authors":"Benoit Renaud Martins, Viviane Radl, Krzysztof Treder, Dorota Michałowska, Karin Pritsch, Michael Schloter","doi":"10.1093/femsec/fiae088","DOIUrl":"10.1093/femsec/fiae088","url":null,"abstract":"Rhizosphere microbial communities play a substantial role in plant productivity. We studied the rhizosphere bacteria and fungi of 51 distinct potato cultivars grown under similar greenhouse conditions using a metabarcoding approach. As expected, individual cultivars were the most important determining factor of the rhizosphere microbial composition; however, differences were also obtained when grouping cultivars according to their growth characteristics. We showed that plant growth characteristics were related to deterministic and stochastic assembly processes of bacterial and fungal communities, respectively. The bacterial genera Arthrobacter and Massilia (known to produce indole acetic acid and siderophores) exhibited greater relative abundance in high- and medium-performing cultivars. Bacterial co-occurrence networks were larger in the rhizosphere of these cultivars and were characterized by a distinctive combination of plant beneficial Proteobacteria and Actinobacteria along with a module of diazotrophs namely Azospira, Azoarcus, and Azohydromonas. Conversely, the network within low-performing cultivars revealed the lowest nodes, hub taxa, edges density, robustness, and the highest average path length resulting in reduced microbial associations, which may potentially limit their effectiveness in promoting plant growth. Our findings established a clear pattern between plant productivity and the rhizosphere microbiome composition and structure for the investigated potato cultivars, offering insights for future management practices.","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/PMC11242454/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141261289","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}

引用次数: 0

Fronts divide diazotroph communities in the Southern Indian Ocean. 南印度洋的重氮营养群落被锋面分割。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-07-12 DOI: 10.1093/femsec/fiae095

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":"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.","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}

引用次数: 0

Wood-Ljungdahl pathway encoding anaerobes facilitate low-cost primary production in hypersaline sediments at Great Salt Lake, Utah. 编码厌氧菌的伍德-荣格达尔途径促进了犹他州大盐湖超盐沉积物中的低成本初级生产。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-07-12 DOI: 10.1093/femsec/fiae105

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":"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.","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}

引用次数: 0

Correction to: Alpine soil microbial ecology in a changing world. 更正：不断变化的世界中的高山土壤微生物生态学。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-07-12 DOI: 10.1093/femsec/fiae085

引用次数: 0

Microbial remineralization processes during postspring-bloom with excess phosphate available in the northern Baltic Sea. 波罗的海北部春暖花开后磷酸盐过剩时的微生物再矿化过程。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-07-12 DOI: 10.1093/femsec/fiae103

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":"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.","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}

引用次数: 0

Genomic analysis of Salmonella bacteriophages revealed multiple endolysin ORFs and importance of ligand-binding site of receptor-binding protein. 噬菌体沙门氏菌的基因组分析揭示了多个内溶素 ORF 和受体结合蛋白配体结合位点的重要性。

IF 4.2 3区生物学

FEMS microbiology ecology Pub Date : 2024-06-17 DOI: 10.1093/femsec/fiae079

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":"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.","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}

引用次数: 0

Organizing a global list of cyanobacteria and algae from soil biocrusts evidenced great geographic and taxonomic gaps. 从土壤生物簇中整理出的蓝藻和藻类全球清单显示出巨大的地理和分类差距。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-06-17 DOI: 10.1093/femsec/fiae086

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":"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.","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}

引用次数: 0

The microgeo: an R package rapidly displays the biogeography of soil microbial community traits on maps. microgeo：一个 R 软件包，可在地图上快速显示土壤微生物群落的生物地理特征。

IF 3.5 3区生物学

FEMS microbiology ecology Pub Date : 2024-06-17 DOI: 10.1093/femsec/fiae087

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":"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.","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}

引用次数: 0