Environmental microbiology最新文献

Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning 利用机器学习识别濒危加勒比鹿角珊瑚中的假定珊瑚病原体

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-09-17 DOI: 10.1111/1462-2920.16700

Jason D. Selwyn, Brecia A. Despard, Miles V. Vollmer, Emily C. Trytten, Steven V. Vollmer

{"title":"Identification of putative coral pathogens in endangered Caribbean staghorn coral using machine learning","authors":"Jason D. Selwyn, Brecia A. Despard, Miles V. Vollmer, Emily C. Trytten, Steven V. Vollmer","doi":"10.1111/1462-2920.16700","DOIUrl":"10.1111/1462-2920.16700","url":null,"abstract":"Coral diseases contribute to the rapid decline in coral reefs worldwide, and yet coral bacterial pathogens have proved difficult to identify because 16S rRNA gene surveys typically identify tens to hundreds of disease-associate bacteria as putative pathogens. An example is white band disease (WBD), which has killed up to 95% of the now-endangered Caribbean Acropora corals since 1979, yet the pathogen is still unknown. The 16S rRNA gene surveys have identified hundreds of WBD-associated bacterial amplicon sequencing variants (ASVs) from at least nine bacterial families with little consensus across studies. We conducted a multi-year, multi-site 16S rRNA gene sequencing comparison of 269 healthy and 143 WBD-infected Acropora cervicornis and used machine learning modelling to accurately predict disease outcomes and identify the top ASVs contributing to disease. Our ensemble ML models accurately predicted disease with greater than 97% accuracy and identified 19 disease-associated ASVs and five healthy-associated ASVs that were consistently differentially abundant across sampling periods. Using a tank-based transmission experiment, we tested whether the 19 disease-associated ASVs met the assumption of a pathogen and identified two pathogenic candidate ASVs—ASV25 Cysteiniphilum litorale and ASV8 Vibrio sp. to target for future isolation, cultivation, and confirmation of Henle-Koch's postulate via transmission assays.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-09-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16700","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142237019","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

Warm temperature inhibits cytoplasmic incompatibility induced by endosymbiotic Rickettsiella in spider hosts 暖温抑制蜘蛛宿主体内共生立克次体诱导的细胞质不相容性

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-09-10 DOI: 10.1111/1462-2920.16697

Jordyn D. Proctor, Virginija Mackevicius-Dubickaja, Yuval Gottlieb, Jennifer A. White

{"title":"Warm temperature inhibits cytoplasmic incompatibility induced by endosymbiotic Rickettsiella in spider hosts","authors":"Jordyn D. Proctor, Virginija Mackevicius-Dubickaja, Yuval Gottlieb, Jennifer A. White","doi":"10.1111/1462-2920.16697","DOIUrl":"10.1111/1462-2920.16697","url":null,"abstract":"Bacterial endosymbionts manipulate reproduction in arthropods to increase their prevalence in the host population. One such manipulation is cytoplasmic incompatibility (CI), wherein the bacteria sabotage sperm in infected males to reduce the hatch rate when mated with uninfected females, but zygotes are ‘rescued’ when that male mates with an infected female. In the spider Mermessus fradeorum (Linyphiidae), Rickettsiella symbionts cause variable levels of CI. We hypothesised that temperature affects the strength of CI and its rescue in M. fradeorum, potentially mediated by bacterial titre. We reared Rickettsiella-infected spiders in two temperature conditions (26°C vs. 20°C) and tested CI induction in males and rescue in females. In incompatible crosses between infected males and uninfected females, the hatch rate from warm males was doubled (mean ± standard error = 0.687 ± 0.052) relative to cool males (0.348 ± 0.046), indicating that CI induction is weaker in warm males. In rescue crosses between infected females and infected males, female rearing temperature had a marginal effect on CI rescue, but the hatch rate remained high for both warm (0.960 ± 0.023) and cool females (0.994 ± 0.004). Bacterial titre, as measured by quantitative polymerase chain reaction, was lower in warm than cool spiders, particularly in females, suggesting that bacterial titre may play a role in causing the temperature-mediated changes in CI.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-09-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142160998","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

The role of endospore appendages in spore–spore interactions in the pathogenic Bacillus cereus group 致病性蜡样芽孢杆菌中内生孢子附属物在孢子-孢子相互作用中的作用。

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-09-03 DOI: 10.1111/1462-2920.16678

Unni Lise Jonsmoen, Dmitry Malyshev, Mike Sleutel, Elise Egeli Kristensen, Ephrem Debebe Zegeye, Han Remaut, Magnus Andersson, Marina Elisabeth Aspholm

{"title":"The role of endospore appendages in spore–spore interactions in the pathogenic Bacillus cereus group","authors":"Unni Lise Jonsmoen, Dmitry Malyshev, Mike Sleutel, Elise Egeli Kristensen, Ephrem Debebe Zegeye, Han Remaut, Magnus Andersson, Marina Elisabeth Aspholm","doi":"10.1111/1462-2920.16678","DOIUrl":"10.1111/1462-2920.16678","url":null,"abstract":"Species within the Bacillus cereus sensu lato group, known for their spore-forming ability, are recognized for their significant role in food spoilage and food poisoning. The spores of B. cereus are adorned with numerous pilus-like appendages, referred to as S-ENAs and L-ENAs. These appendages are thought to play vital roles in self-aggregation, adhesion, and biofilm formation. Our study investigates the role of S-ENAs and L-ENAs, as well as the impact of various environmental factors on spore-to-spore contacts and the interaction between spores and vegetative cells, using both bulk and single-cell approaches. Our findings indicate that ENAs, especially their tip fibrillae, play a crucial role in spore self-aggregation, but not in the adhesion of spores to vegetative cells. The absence of L-BclA, which forms the L-ENA tip fibrillum, reduced spore aggregation mediated by both S-ENAs and L-ENAs, highlighting the interconnected roles of S-ENAs and L-ENAs. We also found that increased salt concentrations in the liquid environment significantly reduced spore aggregation, suggesting a charge dependency of spore-spore interactions. By shedding light on these complex interactions, our study offers valuable insights into spore dynamics. This knowledge can inform future studies on spore behaviour in environmental settings and assist in developing strategies to manage bacterial aggregation for beneficial purposes, such as controlling biofilms in food production equipment.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16678","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125094","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

Comparative genomics identifies key adaptive traits of sponge-associated microbial symbionts 比较基因组学确定了海绵相关微生物共生体的关键适应性状。

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-09-03 DOI: 10.1111/1462-2920.16690

Paul A. O'Brien, Steven J. Robbins, Shangjin Tan, Laura Rix, David J. Miller, Nicole S. Webster, Guojie Zhang, David G. Bourne

{"title":"Comparative genomics identifies key adaptive traits of sponge-associated microbial symbionts","authors":"Paul A. O'Brien, Steven J. Robbins, Shangjin Tan, Laura Rix, David J. Miller, Nicole S. Webster, Guojie Zhang, David G. Bourne","doi":"10.1111/1462-2920.16690","DOIUrl":"10.1111/1462-2920.16690","url":null,"abstract":"Sponge microbiomes are often highly diverse making it difficult to determine which lineages are important for maintaining host health and homeostasis. Characterising genomic traits associated with symbiosis can improve our knowledge of which lineages have adapted to their host and what functions they might provide. Here we examined five microbial families associated with sponges that have previously shown evidence of cophylogeny, including Endozoicomonadaceae, Nitrosopumilaceae, Spirochaetaceae, Microtrichaceae and Thermoanaerobaculaceae, to better understand the mechanisms behind their symbiosis. We compared sponge-associated genomes to genomes found in other environments and found that sponge-specific clades were enriched in genes encoding many known mechanisms for symbiont survival, such as avoiding phagocytosis and defence against foreign genetic elements. We expand on previous knowledge to show that glycosyl hydrolases with sulfatases and sulfotransferases likely form multienzyme degradation pathways to break and remodel sulfated polysaccharides and reveal an enrichment in superoxide dismutase that may prevent damage from free oxygen radicals produced by the host. Finally, we identified novel traits in sponge-associated symbionts, such as urea metabolism in Spirochaetaceae which was previously shown to be rare in the phylum Spirochaetota. These results identify putative mechanisms by which symbionts have adapted to living in association with sponges.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16690","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142125093","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

Acquisition of elemental sulfur by sulfur-oxidising Sulfolobales 硫氧化硫杆菌对元素硫的获取

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-08-29 DOI: 10.1111/1462-2920.16691

Maria C. Fernandes-Martins, Carli Springer, Daniel R. Colman, Eric S. Boyd

{"title":"Acquisition of elemental sulfur by sulfur-oxidising Sulfolobales","authors":"Maria C. Fernandes-Martins, Carli Springer, Daniel R. Colman, Eric S. Boyd","doi":"10.1111/1462-2920.16691","DOIUrl":"10.1111/1462-2920.16691","url":null,"abstract":"Elemental sulfur (S80)-oxidising Sulfolobales (Archaea) dominate high-temperature acidic hot springs (>80°C, pH <4). However, genomic analyses of S80-oxidising members of the Sulfolobales reveal a patchy distribution of genes encoding sulfur oxygenase reductase (SOR), an S80 disproportionating enzyme attributed to S80 oxidation. Here, we report the S80-dependent growth of two Sulfolobales strains previously isolated from acidic hot springs in Yellowstone National Park, one of which associated with bulk S80 during growth and one that did not. The genomes of each strain encoded different sulfur metabolism enzymes, with only one encoding SOR. Dialysis membrane experiments showed that direct contact is not required for S80 oxidation in the SOR-encoding strain. This is attributed to the generation of hydrogen sulfide (H2S) from S80 disproportionation that can diffuse out of the cell to solubilise bulk S80 to form soluble polysulfides (Sx2−) and/or S80 nanoparticles that readily diffuse across dialysis membranes. The Sulfolobales strain lacking SOR required direct contact to oxidise S80, which could be overcome by the addition of H2S. High concentrations of S80 inhibited the growth of both strains. These results implicate alternative strategies to acquire and metabolise sulfur in Sulfolobales and have implications for their distribution and ecology in their hot spring habitats.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16691","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142090515","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

3-Hydroxypropionate production from myo-inositol by the gut acetogen Blautia schinkii 肠道乙酰菌 Blautia schinkii 从肌醇中产生 3-羟基丙酸盐

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-08-29 DOI: 10.1111/1462-2920.16692

Raphael Trischler, Stefanie M. Rustler, Anja Poehlein, Rolf Daniel, Milena Breitenbach, Eric J. N. Helfrich, Volker Müller

{"title":"3-Hydroxypropionate production from myo-inositol by the gut acetogen Blautia schinkii","authors":"Raphael Trischler, Stefanie M. Rustler, Anja Poehlein, Rolf Daniel, Milena Breitenbach, Eric J. N. Helfrich, Volker Müller","doi":"10.1111/1462-2920.16692","DOIUrl":"https://doi.org/10.1111/1462-2920.16692","url":null,"abstract":"Species of the genus Blautia are not only abundant in the human gut but also contribute to human well-being. Our study demonstrates that the gut acetogen Blautia schinkii can grow on myo-inositol. We identified the pathway of myo-inositol degradation through a combination of physiological and biochemical studies, genome-wide expression profiling and homology searches. Initially, myo-inositol is oxidized to 2-keto-myo-inositol. This compound is then metabolized by a series of enzymes – a dehydratase, hydrolase, isomerase and kinase – to form 2-deoxy-5-keto-d-gluconic acid 6-phosphate. This intermediate is split by an aldolase into malonate semialdehyde and dihydroxyacetone phosphate, which is an intermediate of the Embden–Meyerhof–Parnas pathway. This pathway leads to the production of pyruvate and, subsequently, acetate. Concurrently, malonate semialdehyde is reduced to 3-hydroxypropionate (3-HP). The genes responsible for myo-inositol degradation are clustered on the genome, except for the gene encoding the aldolase. We identified the putative aldolase Fba_3 and 3-HP dehydrogenase Adh1 encoding genes bioinformatically and verified them biochemically using enzyme assays with heterologously produced and purified protein. The major fermentation end products were 3-HP and acetate, produced in similar amounts. The production of the unusual fermentation end product 3-HP is significant not only for human health but also for the potential bioindustrial production of this highly desired compound.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-08-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16692","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100016","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

Trophic strategies of picoeukaryotic phytoplankton vary over time and with depth in the North Pacific Subtropical Gyre 北太平洋亚热带环流中浮游植物的营养策略随时间和深度的变化而变化。

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-08-21 DOI: 10.1111/1462-2920.16689

Kyle F. Edwards, Yoshimi M. Rii, Qian Li, Logan M. Peoples, Matthew J. Church, Grieg F. Steward

{"title":"Trophic strategies of picoeukaryotic phytoplankton vary over time and with depth in the North Pacific Subtropical Gyre","authors":"Kyle F. Edwards, Yoshimi M. Rii, Qian Li, Logan M. Peoples, Matthew J. Church, Grieg F. Steward","doi":"10.1111/1462-2920.16689","DOIUrl":"10.1111/1462-2920.16689","url":null,"abstract":"In oligotrophic oceans, the smallest eukaryotic phytoplankton are both significant primary producers and predators of abundant bacteria such as Prochlorococcus. However, the drivers and consequences of community dynamics among these diverse protists are not well understood. Here, we investigated how trophic strategies along the autotrophy-mixotrophy spectrum vary in importance over time and across depths at Station ALOHA in the North Pacific Subtropical Gyre. We combined picoeukaryote community composition from a 28-month time-series with traits of diverse phytoplankton isolates from the same location, to examine trophic strategies across 13 operational taxonomic units and 8 taxonomic classes. We found that autotrophs and slower-grazing mixotrophs tended to prevail deeper in the photic zone, while the most voracious mixotrophs were relatively abundant near the surface. Within the mixed layer, there was greater phagotrophy when conditions were most stratified and when Chl a concentrations were lowest, although the greatest temporal variation in trophic strategy occurred at intermediate depths (45–100 m). Dynamics at this site are consistent with previously described spatial patterns of trophic strategies. The success of relatively phagotrophic phytoplankton at shallower depths in the most stratified waters suggests that phagotrophy is a competitive strategy for acquiring nutrients when energy from light is plentiful.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016709","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

Distinct actors drive different mechanisms of biopolymer processing in polar marine coastal sediments 极地海洋沿岸沉积物中生物聚合物加工的不同驱动机制。

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-08-21 DOI: 10.1111/1462-2920.16687

Katrin Knittel, Sebastian Miksch, Chyrene Moncada, Sebastian Silva-Solar, Jannika Moye, Rudolf Amann, Carol Arnosti

{"title":"Distinct actors drive different mechanisms of biopolymer processing in polar marine coastal sediments","authors":"Katrin Knittel, Sebastian Miksch, Chyrene Moncada, Sebastian Silva-Solar, Jannika Moye, Rudolf Amann, Carol Arnosti","doi":"10.1111/1462-2920.16687","DOIUrl":"10.1111/1462-2920.16687","url":null,"abstract":"Heterotrophic bacteria in the ocean initiate biopolymer degradation using extracellular enzymes that yield low molecular weight hydrolysis products in the environment, or by using a selfish uptake mechanism that retains the hydrolysate for the enzyme-producing cell. The mechanism used affects the availability of hydrolysis products to other bacteria, and thus also potentially the composition and activity of the community. In marine systems, these two mechanisms of substrate processing have been studied in the water column, but to date, have not been investigated in sediments. In surface sediments from an Arctic fjord of Svalbard, we investigated mechanisms of biopolymer hydrolysis using four polysaccharides and mucin, a glycoprotein. Extracellular hydrolysis of all biopolymers was rapid. Moreover, rapid degradation of mucin suggests that it may be a key substrate for benthic microbes. Although selfish uptake is common in ocean waters, only a small fraction (0.5%–2%) of microbes adhering to sediments used this mechanism. Selfish uptake was carried out primarily by Planctomycetota and Verrucomicrobiota. The overall dominance of extracellular hydrolysis in sediments, however, suggests that the bulk of biopolymer processing is carried out by a benthic community relying on the sharing of enzymatic capabilities and scavenging of public goods.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-08-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16687","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142016708","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

Genomic stasis over millions of years in subseafloor sediment 海底沉积物中数百万年的基因组停滞。

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-08-15 DOI: 10.1111/1462-2920.16674

Arkadiy I. Garber, Gustavo A. Ramírez, Steven D'Hondt

{"title":"Genomic stasis over millions of years in subseafloor sediment","authors":"Arkadiy I. Garber, Gustavo A. Ramírez, Steven D'Hondt","doi":"10.1111/1462-2920.16674","DOIUrl":"10.1111/1462-2920.16674","url":null,"abstract":"One of the significant challenges in microbiology is to understand the extent and mechanisms of evolution within life beneath the surface of the Earth. The population bottleneck that microbes in deep marine sediment experience implies that mutational and population genetic forces could lead to higher levels of relaxed selection and an increase in pseudogenes. To investigate this hypothesis, a group of Thalassospira strains were isolated from subseafloor sediment that is 3 to 6 million years old, as reported by Orsi and colleagues in 2021. These isolates, representing lineages that have been buried for millions of years, offer an excellent opportunity to study the evolution of life beneath the seafloor over a long period. The existence of closely related strains from environments on the surface of the Earth enabled us to examine the impact of selection within each group. We discovered that isolates from beneath the seafloor show lineage-specific similarities to Thalassospira from the surface world, both in the overall intensity of selection on the genome and in the specific genes affected by mutation. We found no signs of increased relaxed selection or other notable genomic changes in the genomes of the Thalassospira isolates from beneath the seafloor, suggesting that these subseafloor isolates were awakened from a million-year near-stasis. The unique genomic characteristics of each Thalassospira lineage from beneath the seafloor must then reflect genetic changes that surface-inhabiting decendants acquired in the past 3–6 million years. Remarkably, Thalassospira lineages beneath the surface appear to have stably maintained their genomes in the midst of metabolic dormancy and extremely long generation times.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16674","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987674","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

Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter 揭示无处不在的 Solirubrobacter 的基因组和环境多样性。

IF 4.3 2区生物学

Environmental microbiology Pub Date : 2024-08-15 DOI: 10.1111/1462-2920.16685

Angélica Jara-Servin, Gerardo Mejia, Miguel F. Romero, Mariana Peimbert, Luis David Alcaraz

{"title":"Unravelling the genomic and environmental diversity of the ubiquitous Solirubrobacter","authors":"Angélica Jara-Servin, Gerardo Mejia, Miguel F. Romero, Mariana Peimbert, Luis David Alcaraz","doi":"10.1111/1462-2920.16685","DOIUrl":"10.1111/1462-2920.16685","url":null,"abstract":"Solirubrobacter, though widespread in soils and rhizospheres, has been relatively unexplored despite its ubiquity. Previously acknowledged as a common soil bacterium, our research explores its phylogenomics, pangenomics, environmental diversity, and interactions within bacterial communities. By analysing seven genomic sequences, we have identified a pangenome consisting of 19,645 protein families, of which 2644 are shared across all studied genomes, forming the core genome. Interestingly, despite the non-motility of reported isolates, we discovered genes for flagellin and a partial flagellum assembly pathway. Examining the 16S ribosomal RNA genes of Solirubrobacter revealed substantial diversity, with 3166 operational taxonomic units identified in Mexican soils. Co-occurrence network analysis further demonstrated its significant integration within bacterial communities. Through phylogenomic scrutiny, we conclusively excluded the NCBI's GCA_009993245.1 genome from being classified as a Solirubrobacter. Our research into the metagenomic diversity of Solirubrobacter across various environments confirmed its presence in rhizospheres and certain soils, underscoring its adaptability. The geographical ubiquity of Solirubrobacter in rhizospheres raises intriguing questions regarding its potential interactions with plant hosts and the biotic and abiotic factors influencing its presence in soil. Given its ecological significance and genetic diversity, Solirubrobacter warrants further investigation as a potentially crucial yet underappreciated keystone species.","PeriodicalId":11898,"journal":{"name":"Environmental microbiology","volume":null,"pages":null},"PeriodicalIF":4.3,"publicationDate":"2024-08-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://onlinelibrary.wiley.com/doi/epdf/10.1111/1462-2920.16685","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141987675","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