Environmental microbiology最新文献

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Genetic diversity of the banana Fusarium wilt pathogen in Cuba and across Latin America and the Caribbean 古巴以及整个拉丁美洲和加勒比地区香蕉镰刀菌枯萎病病原体的遗传多样性。
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-23 DOI: 10.1111/1462-2920.16636
Einar Martínez-de la Parte, Luis Pérez-Vicente, David E. Torres, Anouk van Westerhoven, Harold J. G. Meijer, Michael F. Seidl, Gert H. J. Kema
{"title":"Genetic diversity of the banana Fusarium wilt pathogen in Cuba and across Latin America and the Caribbean","authors":"Einar Martínez-de la Parte,&nbsp;Luis Pérez-Vicente,&nbsp;David E. Torres,&nbsp;Anouk van Westerhoven,&nbsp;Harold J. G. Meijer,&nbsp;Michael F. Seidl,&nbsp;Gert H. J. Kema","doi":"10.1111/1462-2920.16636","DOIUrl":"10.1111/1462-2920.16636","url":null,"abstract":"<p>Fusarium wilt of bananas (FWB) is a severe plant disease that leads to substantial losses in banana production worldwide. It remains a major concern for Cuban banana cultivation. The disease is caused by members of the soil-borne <i>Fusarium oxysporum</i> species complex. However, the genetic diversity among <i>Fusarium</i> species infecting bananas in Cuba has remained largely unexplored. In our comprehensive survey, we examined symptomatic banana plants across all production zones in the country, collecting 170 <i>Fusarium</i> isolates. Leveraging genotyping-by-sequencing and whole-genome comparisons, we investigated the genetic diversity within these isolates and compared it with a global <i>Fusarium</i> panel. Notably, typical FWB symptoms were observed in Bluggoe cooking bananas and Pisang Awak subgroups across 14 provinces. Our phylogenetic analysis revealed that <i>F. purpurascens</i>, <i>F. phialophorum</i>, and <i>F. tardichlamydosporum</i> are responsible for FWB in Cuba, with <i>F. tardichlamydosporum</i> dominating the population. Furthermore, we identified between five and seven distinct genetic clusters, with <i>F. tardichlamydosporum</i> isolates forming at least two subgroups. This finding underscores the high genetic diversity of <i>Fusarium</i> spp. contributing to FWB in the Americas. Our study sheds light on the population genetic structure and diversity of the FWB pathogen in Cuba and the broader Latin American and Caribbean regions.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16636","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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 “Preventing multiresistance: New insights for managing fungal adaptation” 防止多重抗性:管理真菌适应性的新见解"。
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-23 DOI: 10.1111/1462-2920.16641
{"title":"Correction to “Preventing multiresistance: New insights for managing fungal adaptation”","authors":"","doi":"10.1111/1462-2920.16641","DOIUrl":"10.1111/1462-2920.16641","url":null,"abstract":"<p>Ballu, A., Ugazio, C., Duplaix, C., Noly, A., Wullschleger, J., Torriani, S.F.F., Dérédec A., Carpentier F., Walker A.S. (2024) Preventing multi-resistance: new insights for managing fungal adaptation. <i>Environmental Microbiology</i>, 26(4), e16614. Available from: https://doi.org/10.1111/1462-2920.16614</p><p>In the title, the text “Preventing multi-resistance: New insights for managing fungal adaptation” was incorrect. This should have read: “Preventing multiple resistance above all: New insights for managing fungal adaptation.”</p><p>This has been corrected in the online version of the article.</p><p>We apologize for this error.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16641","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141087353","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks 不同弧菌基因组上携带 Zot 毒素的噬菌体:利用多层网络进行综合评估。
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-23 DOI: 10.1111/1462-2920.16654
Esteban F. Soto, Melissa Alegría, Felipe Sepúlveda, Katherine García, Gastón Higuera, Daniel Castillo, Francisco E. Fontúrbel, Roberto Bastías
{"title":"Prophages carrying Zot toxins on different Vibrio genomes: A comprehensive assessment using multilayer networks","authors":"Esteban F. Soto,&nbsp;Melissa Alegría,&nbsp;Felipe Sepúlveda,&nbsp;Katherine García,&nbsp;Gastón Higuera,&nbsp;Daniel Castillo,&nbsp;Francisco E. Fontúrbel,&nbsp;Roberto Bastías","doi":"10.1111/1462-2920.16654","DOIUrl":"10.1111/1462-2920.16654","url":null,"abstract":"<p>Vibrios, a group of bacteria that are among the most abundant in marine environments, include several species such as <i>Vibrio cholerae</i> and <i>Vibrio parahaemolyticus</i>, which can be pathogenic to humans. Some species of <i>Vibrio</i> contain prophages within their genomes. These prophages can carry genes that code for toxins, such as the zonula occludens toxin (Zot), which contribute to bacterial virulence. Understanding the association between different <i>Vibrio</i> species, prophages and Zot genes can provide insights into their ecological interactions. In this study, we evaluated 4619 <i>Vibrio</i> genomes from 127 species to detect the presence of prophages carrying the Zot toxin. We found 2030 potential prophages with <i>zot</i>-like genes in 43 <i>Vibrio</i> species, showing a non-random association within a primarily modular interaction network. Some prophages, such as CTX or Vf33, were associated with specific species. In contrast, prophages phiVCY and VfO3K6 were found in 28 and 20 <i>Vibrio</i> species, respectively. We also identified six clusters of Zot-like sequences in prophages, with the ZOT2 cluster being the most frequent, present in 34 <i>Vibrio</i> species. This analysis helps to understand the distribution patterns of <i>zot</i>-containing prophages across Vibrio genomes and the potential routes of Zot-like toxin dissemination.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141080926","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Genome analysis and description of Tunturibacter gen. nov. expands the diversity of Terriglobia in tundra soils Tunturibacter gen. nov. 的基因组分析和描述扩大了苔原土壤中 Terriglobia 的多样性。
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-22 DOI: 10.1111/1462-2920.16640
Adriana Messyasz, Minna K. Männistö, Lee J. Kerkhof, Max M. Häggblom
{"title":"Genome analysis and description of Tunturibacter gen. nov. expands the diversity of Terriglobia in tundra soils","authors":"Adriana Messyasz,&nbsp;Minna K. Männistö,&nbsp;Lee J. Kerkhof,&nbsp;Max M. Häggblom","doi":"10.1111/1462-2920.16640","DOIUrl":"10.1111/1462-2920.16640","url":null,"abstract":"<p>Increased temperatures in Arctic tundra ecosystems are leading to higher microbial respiration rates of soil organic matter, resulting in the release of carbon dioxide and methane. To understand the effects of this microbial activity, it is important to better characterize the diverse microbial communities in Arctic soil. Our goal is to refine our understanding of the phylogenetic diversity of <i>Terriglobia</i>, a common but elusive group within the <i>Acidobacteriota</i> phylum. This will help us link this diversity to variations in carbon and nitrogen usage patterns. We used long-read Oxford Nanopore MinION sequences in combination with metagenomic short-read sequences to assemble complete <i>Acidobacteriota</i> genomes. This allowed us to build multi-locus phylogenies and annotate pangenome markers to distinguish <i>Acidobacteriota</i> strains from several tundra soil isolates. We identified a phylogenetic cluster containing four new species previously associated with <i>Edaphobacter lichenicola</i>. We conclude that this cluster represents a new genus, which we have named <i>Tunturibacter</i>. We describe four new species: <i>Tunturibacter lichenicola</i> comb. nov., <i>Tunturibacter empetritectus</i> sp. nov., <i>Tunturibacter gelidoferens</i> sp. nov., and <i>Tunturibacter psychrotolerans</i> sp. nov. By uncovering new species and strains within the <i>Terriglobia</i> and improving the accuracy of their phylogenetic placements, we hope to enhance our understanding of this complex phylum and shed light on the mechanisms that shape microbial communities in polar soils.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16640","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141075627","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands 瑞士泥炭地微生物群落结构的调节因素是栖息地条件而非苔藓成分
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-17 DOI: 10.1111/1462-2920.16631
Rachel Korn, Christian Berg, Louis-Félix Bersier, Sarah M. Gray, Gerhard G. Thallinger
{"title":"Habitat conditions and not moss composition mediate microbial community structure in Swiss peatlands","authors":"Rachel Korn,&nbsp;Christian Berg,&nbsp;Louis-Félix Bersier,&nbsp;Sarah M. Gray,&nbsp;Gerhard G. Thallinger","doi":"10.1111/1462-2920.16631","DOIUrl":"https://doi.org/10.1111/1462-2920.16631","url":null,"abstract":"<p>Peatlands, one of the oldest ecosystems, globally store significant amounts of carbon and freshwater. However, they are under severe threat from human activities, leading to changes in water, nutrient and temperature regimes in these delicate systems. Such shifts can trigger a substantial carbon flux into the atmosphere and diminish the water-holding capacity of peatlands. Microbes associated with moss in peatlands play a crucial role in providing these ecosystem services, which are at risk due to global change. Therefore, understanding the factors influencing microbial composition and function is vital. Our study focused on five peatlands along an altitudinal gradient in Switzerland, where we sampled moss on hummocks containing <i>Sarracenia purpurea</i>. Structural equation modelling revealed that habitat condition was the primary predictor of community structure and directly influenced other environmental variables. Interestingly, the microbial composition was not linked to the local moss species identity. Instead, microbial communities varied significantly between sites due to differences in acidity levels and nitrogen availability. This finding was also mirrored in a co-occurrence network analysis, which displayed a distinct distribution of indicator species for acidity and nitrogen availability. Therefore, peatland conservation should take into account the critical habitat characteristics of moss-associated microbial communities.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16631","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140952717","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Critical steps in an environmental metaproteomics workflow 环境元蛋白质组学工作流程的关键步骤
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-17 DOI: 10.1111/1462-2920.16637
Daniel J. Nebauer, Leanne A. Pearson, Brett A. Neilan
{"title":"Critical steps in an environmental metaproteomics workflow","authors":"Daniel J. Nebauer,&nbsp;Leanne A. Pearson,&nbsp;Brett A. Neilan","doi":"10.1111/1462-2920.16637","DOIUrl":"10.1111/1462-2920.16637","url":null,"abstract":"<p>Environmental metaproteomics is a rapidly advancing field that provides insights into the structure, dynamics, and metabolic activity of microbial communities. As the field is still maturing, it lacks consistent workflows, making it challenging for non-expert researchers to navigate. This review aims to introduce the workflow of environmental metaproteomics. It outlines the standard practices for sample collection, processing, and analysis, and offers strategies to overcome the unique challenges presented by common environmental matrices such as soil, freshwater, marine environments, biofilms, sludge, and symbionts. The review also highlights the bottlenecks in data analysis that are specific to metaproteomics samples and provides suggestions for researchers to obtain high-quality datasets. It includes recent benchmarking studies and descriptions of software packages specifically built for metaproteomics analysis. The article is written without assuming the reader's familiarity with single-organism proteomic workflows, making it accessible to those new to proteomics or mass spectrometry in general. This primer for environmental metaproteomics aims to improve accessibility to this exciting technology and empower researchers to tackle challenging and ambitious research questions. While it is primarily a resource for those new to the field, it should also be useful for established researchers looking to streamline or troubleshoot their metaproteomics experiments.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16637","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140954337","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates 大环境梯度河流中氧化亚氮还原剂的生物地理学及其对排放率的影响
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-16 DOI: 10.1111/1462-2920.16622
Sibo Zhang, Xinghui Xia, Leilei Yu, Shaoda Liu, Xiaokang Li, Junfeng Wang, Yue Zheng, Lanfang Han, Qian Tan, Zhifeng Yang
{"title":"Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates","authors":"Sibo Zhang,&nbsp;Xinghui Xia,&nbsp;Leilei Yu,&nbsp;Shaoda Liu,&nbsp;Xiaokang Li,&nbsp;Junfeng Wang,&nbsp;Yue Zheng,&nbsp;Lanfang Han,&nbsp;Qian Tan,&nbsp;Zhifeng Yang","doi":"10.1111/1462-2920.16622","DOIUrl":"https://doi.org/10.1111/1462-2920.16622","url":null,"abstract":"<p>Microbial communities that reduce nitrous oxide (N<sub>2</sub>O) are divided into two clades, <i>nosZ</i>I and <i>nosZ</i>II. These clades significantly differ in their ecological niches and their implications for N<sub>2</sub>O emissions in terrestrial environments. However, our understanding of N<sub>2</sub>O reducers in aquatic systems is currently limited. This study investigated the relative abundance and diversity of <i>nosZ</i>I- and <i>nosZ</i>II-type N<sub>2</sub>O reducers in rivers and their impact on N<sub>2</sub>O emissions. Our findings revealed that stream sediments possess a high capacity for N<sub>2</sub>O reduction, surpassing N<sub>2</sub>O production under high N<sub>2</sub>O/NO<sub>3</sub>- ratio conditions. This study, along with others in freshwater systems, demonstrated that <i>nosZ</i>I marginally dominates more often in rivers. While microbes containing either <i>nosZ</i>I and <i>nosZ</i>II were crucial in reducing N<sub>2</sub>O emissions, the net contribution of <i>nosZ</i>II-containing microbes was more significant. This can be attributed to the <i>nir</i> gene co-occurring more frequently with the <i>nosZ</i>I gene than with the <i>nosZ</i>II gene. The diversity within each clade also played a role, with <i>nosZ</i>II species being more likely to function as N<sub>2</sub>O sinks in streams with higher N<sub>2</sub>O concentrations. Overall, our findings provide a foundation for a better understanding of the biogeography of stream N<sub>2</sub>O reducers and their effects on N<sub>2</sub>O emissions.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140952963","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization 研究盐化后盐的特异性对淡水微生物群落和功能潜力的影响
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-16 DOI: 10.1111/1462-2920.16628
Jonathon B. Van Gray, Paul Ayayee
{"title":"Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization","authors":"Jonathon B. Van Gray,&nbsp;Paul Ayayee","doi":"10.1111/1462-2920.16628","DOIUrl":"https://doi.org/10.1111/1462-2920.16628","url":null,"abstract":"<p>The degradation of freshwater systems by salt pollution is a threat to global freshwater resources. Salinization is commonly identified by increased specific conductance (conductivity), a proxy for salt concentrations. However, conductivity fails to account for the diversity of salts entering freshwaters and the potential implications this has on microbial communities and functions. We tested 4 types of salt pollution—MgCl<sub>2</sub>, MgSO<sub>4</sub>, NaCl, and Na<sub>2</sub>SO<sub>4</sub>—on bacterial taxonomic and functional α-, β-diversity of communities originating from streams in two distinct localities (Nebraska [NE] and Ohio [OH], USA). Community responses depended on the site of origin, with NE and OH exhibiting more pronounced decreases in community diversity in response to Na<sub>2</sub>SO<sub>4</sub> and MgCl<sub>2</sub> than other salt amendments. A closer examination of taxonomic and functional diversity metrics suggests that core features of communities are more resistant to induced salt stress and that marginal features at both a population and functional level are more likely to exhibit significant structural shifts based on salt specificity. The lack of uniformity in community response highlights the need to consider the compositional complexities of salinization to accurately identify the ecological consequences of instances of salt pollution.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16628","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140952961","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms 揭示新型碳水化合物结合模块在浮游植物大量繁殖期间海洋类杆菌多模块蛋白与层叠蛋白相互作用中的作用
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-16 DOI: 10.1111/1462-2920.16624
Marie-Katherin Zühlke, Elizabeth Ficko-Blean, Daniel Bartosik, Nicolas Terrapon, Alexandra Jeudy, Murielle Jam, Fengqing Wang, Norma Welsch, Alexandra Dürwald, Laura Torres Martin, Robert Larocque, Diane Jouanneau, Tom Eisenack, François Thomas, Anke Trautwein-Schult, Hanno Teeling, Dörte Becher, Thomas Schweder, Mirjam Czjzek
{"title":"Unveiling the role of novel carbohydrate-binding modules in laminarin interaction of multimodular proteins from marine Bacteroidota during phytoplankton blooms","authors":"Marie-Katherin Zühlke,&nbsp;Elizabeth Ficko-Blean,&nbsp;Daniel Bartosik,&nbsp;Nicolas Terrapon,&nbsp;Alexandra Jeudy,&nbsp;Murielle Jam,&nbsp;Fengqing Wang,&nbsp;Norma Welsch,&nbsp;Alexandra Dürwald,&nbsp;Laura Torres Martin,&nbsp;Robert Larocque,&nbsp;Diane Jouanneau,&nbsp;Tom Eisenack,&nbsp;François Thomas,&nbsp;Anke Trautwein-Schult,&nbsp;Hanno Teeling,&nbsp;Dörte Becher,&nbsp;Thomas Schweder,&nbsp;Mirjam Czjzek","doi":"10.1111/1462-2920.16624","DOIUrl":"https://doi.org/10.1111/1462-2920.16624","url":null,"abstract":"<p>Laminarin, a β(1,3)-glucan, serves as a storage polysaccharide in marine microalgae such as diatoms. Its abundance, water solubility and simple structure make it an appealing substrate for marine bacteria. Consequently, many marine bacteria have evolved strategies to scavenge and decompose laminarin, employing carbohydrate-binding modules (CBMs) as crucial components. In this study, we characterized two previously unassigned domains as laminarin-binding CBMs in multimodular proteins from the marine bacterium <i>Christiangramia forsetii</i> KT0803<sup>T</sup>, thereby introducing the new laminarin-binding CBM families CBM102 and CBM103. We identified four CBM102s in a surface glycan-binding protein (SGBP) and a single CBM103 linked to a glycoside hydrolase module from family 16 (GH16_3). Our analysis revealed that both modular proteins have an elongated shape, with GH16_3 exhibiting greater flexibility than SGBP. This flexibility may aid in the recognition and/or degradation of laminarin, while the constraints in SGBP could facilitate the docking of laminarin onto the bacterial surface. Exploration of bacterial metagenome-assembled genomes (MAGs) from phytoplankton blooms in the North Sea showed that both laminarin-binding CBM families are widespread among marine <i>Bacteroidota</i>. The high protein abundance of CBM102- and CBM103-containing proteins during phytoplankton blooms further emphasizes their significance in marine laminarin utilization.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16624","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140952960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
Specificities and commonalities of the Planctomycetes plasmidome Planctomycetes 质粒体的特异性和共性
IF 5.1 2区 生物学
Environmental microbiology Pub Date : 2024-05-10 DOI: 10.1111/1462-2920.16638
María del Mar Quiñonero-Coronel, Damien Paul Devos, M. Pilar Garcillán-Barcia
{"title":"Specificities and commonalities of the Planctomycetes plasmidome","authors":"María del Mar Quiñonero-Coronel,&nbsp;Damien Paul Devos,&nbsp;M. Pilar Garcillán-Barcia","doi":"10.1111/1462-2920.16638","DOIUrl":"https://doi.org/10.1111/1462-2920.16638","url":null,"abstract":"<p>Plasmids, despite their critical role in antibiotic resistance and modern biotechnology, are understood in only a few bacterial groups in terms of their natural ecological dynamics. The bacterial phylum Planctomycetes, known for its unique molecular and cellular biology, has a largely unexplored plasmidome. This study offers a thorough exploration of the diversity of natural plasmids within Planctomycetes, which could serve as a foundation for developing various genetic research tools for this phylum. Planctomycetes plasmids encode a broad range of biological functions and appear to have coevolved significantly with their host chromosomes, sharing many homologues. Recent transfer events of insertion sequences between cohabiting chromosomes and plasmids were also observed. Interestingly, 64% of plasmid genes are distantly related to either chromosomally encoded genes or have homologues in plasmids from other bacterial groups. The planctomycetal plasmidome is composed of 36% exclusive proteins. Most planctomycetal plasmids encode a replication initiation protein from the Replication Protein A family near a putative iteron-containing replication origin, as well as active type I partition systems. The identification of one conjugative and three mobilizable plasmids suggests the occurrence of horizontal gene transfer via conjugation within this phylum. This comprehensive description enhances our understanding of the plasmidome of Planctomycetes and its potential implications in antibiotic resistance and biotechnology.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":5.1,"publicationDate":"2024-05-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16638","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140907049","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"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
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