Natalia Timanikova, Kyle Fletcher, Jon-Wong Han, Pieter van West, Steve Woodward, Gwang-Hoon Kim, Frithjof C. Küpper, Marius Wenzel
{"title":"Macroalgal eukaryotic microbiome composition indicates novel phylogenetic diversity and broad host spectrum of oomycete pathogens","authors":"Natalia Timanikova, Kyle Fletcher, Jon-Wong Han, Pieter van West, Steve Woodward, Gwang-Hoon Kim, Frithjof C. Küpper, Marius Wenzel","doi":"10.1111/1462-2920.16656","DOIUrl":"10.1111/1462-2920.16656","url":null,"abstract":"<p>Seaweeds are important components of marine ecosystems with emerging potential in aquaculture and as sources of biofuel, food products and pharmacological compounds. However, an increasingly recognised threat to natural and industrial seaweed populations is infection with parasitic single-celled eukaryotes from the relatively understudied oomycete lineage. Here we examine the eukaryomes of diverse brown, red and green marine macroalgae collected from polar (Baffin Island), cold-temperate (Falkland Islands) and tropical (Ascension Island) locations, with a focus on oomycete and closely related diatom taxa. Using 18S rRNA gene amplicon sequencing, we show unexpected genetic and taxonomic diversity of the eukaryomes, a strong broad-brush association between eukaryome composition and geographic location, and some evidence of association between eukaryome structure and macroalgal phylogenetic relationships (phylosymbiosis). However, the oomycete fraction of the eukaryome showed disparate patterns of diversity and structure, highlighting much weaker association with geography and no evidence of phylosymbiosis. We present several novel haplotypes of the most common oomycete <i>Eurychasma dicksonii</i> and report for the first time a cosmopolitan distribution and absence of host specificity of this important pathogen. This indicates rich diversity in macroalgal oomycete pathogens and highlights that these pathogens may be generalist and highly adaptable to diverse environmental conditions.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"26 6","pages":""},"PeriodicalIF":5.1,"publicationDate":"2024-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16656","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179103","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}
Phuong N. Nguyen, Farida Samad-zada, Katherine D. Chau, Sandra M. Rehan
{"title":"Microbiome and floral associations of a wild bee using biodiversity survey collections","authors":"Phuong N. Nguyen, Farida Samad-zada, Katherine D. Chau, Sandra M. Rehan","doi":"10.1111/1462-2920.16657","DOIUrl":"10.1111/1462-2920.16657","url":null,"abstract":"<p>The health of bees can be assessed through their microbiome, which serves as a biomarker indicating the presence of both beneficial and harmful microorganisms within a bee community. This study presents the characterisation of the bacterial, fungal, and plant composition on the cuticle of adult bicoloured sweat bees (<i>Agapostemon virescens</i>). These bees were collected using various methods such as pan traps, blue vane traps and sweep netting across the northern extent of their habitat range. Non-destructive methods were employed to extract DNA from the whole pinned specimens of these wild bees. Metabarcoding of the 16S rRNA, ITS and rbcL regions was then performed. The study found that the method of collection influenced the detection of certain microbial and plant taxa. Among the collection methods, sweep net samples showed the lowest fungal alpha diversity. However, minor differences in bacterial or fungal beta diversity suggest that no single method is significantly superior to others. Therefore, a combination of techniques can cater to a broader spectrum of microbial detection. The study also revealed regional variations in bacterial, fungal and plant diversity. The core microbiome of <i>A. virescens</i> comprises two bacteria, three fungi and a plant association, all of which are commonly detected in other wild bees. These core microbes remained consistent across different collection methods and locations. Further extensive studies of wild bee microbiomes across various species and landscapes will help uncover crucial relationships between pollinator health and their environment.</p>","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":"26 6","pages":""},"PeriodicalIF":5.1,"publicationDate":"2024-05-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16657","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141179041","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}
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, Luis Pérez-Vicente, David E. Torres, Anouk van Westerhoven, Harold J. G. Meijer, Michael F. Seidl, 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":"26 5","pages":""},"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}
{"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":"26 5","pages":""},"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}
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, Melissa Alegría, Felipe Sepúlveda, Katherine García, Gastón Higuera, Daniel Castillo, Francisco E. Fontúrbel, 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":"26 5","pages":""},"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}
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, Minna K. Männistö, Lee J. Kerkhof, 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":"26 5","pages":""},"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}
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, Christian Berg, Louis-Félix Bersier, Sarah M. Gray, 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":"26 5","pages":""},"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}
Daniel J. Nebauer, Leanne A. Pearson, Brett A. Neilan
{"title":"Critical steps in an environmental metaproteomics workflow","authors":"Daniel J. Nebauer, Leanne A. Pearson, 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":"26 5","pages":""},"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}
{"title":"Biogeography and impact of nitrous oxide reducers in rivers across a broad environmental gradient on emission rates","authors":"Sibo Zhang, Xinghui Xia, Leilei Yu, Shaoda Liu, Xiaokang Li, Junfeng Wang, Yue Zheng, Lanfang Han, Qian Tan, 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":"26 5","pages":""},"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}
{"title":"Examining the impacts of salt specificity on freshwater microbial community and functional potential following salinization","authors":"Jonathon B. Van Gray, 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":"26 5","pages":""},"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}