Environmental Microbiome最新文献

{"title":"Effects of marine sediment as agricultural substrate on soil microbial diversity: an amplicon sequencing study.","authors":"Dámaris Núñez-Gómez, Pablo Melgarejo, Juan José Martínez-Nicolás, Francisca Hernández, Rafael Martínez-Font, Vicente Lidón, Pilar Legua","doi":"10.1186/s40793-023-00519-4","DOIUrl":"10.1186/s40793-023-00519-4","url":null,"abstract":"<p><strong>Background: </strong>The soil microbiota has a direct impact on plant development and other metabolic systems, such as the degradation of organic matter and the availability of microelements and metabolites. In the context of agricultural soils, microbial activity is crucial for maintaining soil health and productivity. Thus, the present study aimed to identify, characterize, and quantify the microbial communities of four types of substrates with varying proportions of marine port sediment used for cultivating lemons. By investigating microbial diversity and relative abundance, the work aimed to highlight the importance of soil microbial communities in agriculture when alternative culture media was used.</p><p><strong>Results: </strong>The composition and structure of the sampled microbial communities were assessed through the amplification and sequencing of the V3-V4 variable regions of the 16 S rRNA gene The results revealed a diverse microbial community composition in all substrate samples, with a total of 41 phyla, 113 classes, 266 orders, 405 families, 715 genera, and 1513 species identified. Among these, Proteobacteria, Bacteroidota, Planctomycetota, Patescibacteria, Chloroflexi, Actinobacteriota, Acidobacteriota, Verrucomicrobiota, and Gemmatimonadota accounted for over 90% of the bacterial reads, indicating their dominance in the substrates.</p><p><strong>Conclusions: </strong>The impact of the substrate origin on the diversity and relative abundace of the microbiota was confirmed. The higher content of beneficial bacterial communities for plant development identified in peat could explain why is considered an ideal agricultural substrate. Development of \"beneficial for plants\" bacterial communities in alternative agricultural substrates, regardless of the edaphic characteristics, opens the possibility of studying the forced and specific inoculation of these culture media aiming to be agriculturally ideals.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-08-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10408225/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9956191","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Impact of the fungal pathogen Fusarium oxysporum on the taxonomic and functional diversity of the common bean root microbiome.","authors":"Lucas William Mendes, Jos M Raaijmakers, Mattias de Hollander, Edis Sepo, Ruth Gómez Expósito, Alisson Fernando Chiorato, Rodrigo Mendes, Siu Mui Tsai, Victor J Carrión","doi":"10.1186/s40793-023-00524-7","DOIUrl":"10.1186/s40793-023-00524-7","url":null,"abstract":"<p><strong>Background: </strong>Plants rely on their root microbiome as the first line of defense against soil-borne fungal pathogens. The abundance and activities of beneficial root microbial taxa at the time prior to and during fungal infection are key to their protective success. If and how invading fungal root pathogens can disrupt microbiome assembly and gene expression is still largely unknown. Here, we investigated the impact of the fungal pathogen Fusarium oxysporum (fox) on the assembly of rhizosphere and endosphere microbiomes of a fox-susceptible and fox-resistant common bean cultivar.</p><p><strong>Results: </strong>Integration of 16S-amplicon, shotgun metagenome as well as metatranscriptome sequencing with community ecology analysis showed that fox infections significantly changed the composition and gene expression of the root microbiome in a cultivar-dependent manner. More specifically, fox infection led to increased microbial diversity, network complexity, and a higher proportion of the genera Flavobacterium, Bacillus, and Dyadobacter in the rhizosphere of the fox-resistant cultivar compared to the fox-susceptible cultivar. In the endosphere, root infection also led to changes in community assembly, with a higher abundance of the genera Sinorhizobium and Ensifer in the fox-resistant cultivar. Metagenome and metatranscriptome analyses further revealed the enrichment of terpene biosynthesis genes with a potential role in pathogen suppression in the fox-resistant cultivar upon fungal pathogen invasion.</p><p><strong>Conclusion: </strong>Collectively, these results revealed a cultivar-dependent enrichment of specific bacterial genera and the activation of putative disease-suppressive functions in the rhizosphere and endosphere microbiome of common bean under siege.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-08-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10401788/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9936845","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Meeting report of the sixth annual tri-service microbiome consortium symposium.","authors":"Ida G Pantoja-Feliciano De Goodfellow, Richard Agans, Robyn Barbato, Sophie Colston, Michael S Goodson, Rasha Hammamieh, Kristy Hentchel, Robert Jones, J Philip Karl, Robert Kokoska, Dagmar H Leary, Camilla Mauzy, Kenneth Racicot, Blake W Stamps, Vanessa Varaljay, Jason W Soares","doi":"10.1186/s40793-023-00523-8","DOIUrl":"10.1186/s40793-023-00523-8","url":null,"abstract":"<p><p>The Tri-Service Microbiome Consortium (TSMC) was founded to enhance collaboration, coordination, and communication of microbiome research among DoD organizations and to facilitate resource, material and information sharing amongst consortium members, which includes collaborators in academia and industry. The 6th Annual TSMC Symposium was a hybrid meeting held in Fairlee, Vermont on 27-28 September 2022 with presentations and discussions centered on microbiome-related topics within seven broad thematic areas: (1) Human Microbiomes: Stress Response; (2) Microbiome Analysis & Surveillance; (3) Human Microbiomes Enablers & Engineering; (4) Human Microbiomes: Countermeasures; (5) Human Microbiomes Discovery - Earth & Space; (6) Environmental Micro & Myco-biome; and (7) Environmental Microbiome Analysis & Engineering. Collectively, the symposium provided an update on the scope of current DoD microbiome research efforts, highlighted innovative research being done in academia and industry that can be leveraged by the DoD, and fostered collaborative opportunities. This report summarizes the activities and outcomes from the 6th annual TSMC symposium.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":6.2,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10399065/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10314062","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Insights into the prokaryotic communities of the abyssal-hadal benthic-boundary layer of the Kuril Kamchatka Trench.","authors":"Susanna Gorrasi,&nbsp;Andrea Franzetti,&nbsp;Angelika Brandt,&nbsp;Ulrike Minzlaff,&nbsp;Marcella Pasqualetti,&nbsp;Massimiliano Fenice","doi":"10.1186/s40793-023-00522-9","DOIUrl":"https://doi.org/10.1186/s40793-023-00522-9","url":null,"abstract":"<p><strong>Background: </strong>The Kuril-Kamchatka Trench (maximum depth 9604 m), located in the NW Pacific Ocean, is among the top seven deepest hadal trenches. The work aimed to investigate the unexplored abyssal-hadal prokaryotic communities of this fascinating, but underrated environment.</p><p><strong>Results: </strong>As for the bacterial communities, we found that Proteobacteria (56.1-74.5%), Bacteroidetes (6.5-19.1%), and Actinobacteria (0.9-16.1%) were the most represented bacterial phyla over all samples. Thaumarchaeota (52.9-91.1%) was the most abundant phylum in the archaeal communities. The archaeal diversity was highly represented by the ammonia-oxidizing Nitrosopumilus, and the potential hydrocarbon-degrading bacteria Acinetobacter, Zhongshania, and Colwellia were the main bacterial genera. The α-diversity analysis evidenced that both prokaryotic communities were characterized by low evenness, as indicated by the high Gini index values (> 0.9). The β-diversity analysis (Redundancy Analysis) indicated that, as expected, the depth significantly affected the structure of the prokaryotic communities. The co-occurrence network revealed seven prokaryotic groups that covaried across the abyssal-hadal zone of the Kuril-Kamchatka Trench. Among them, the main group included the most abundant archaeal and bacterial OTUs (Nitrosopumilus OTU A2 and OTU A1; Acinetobacter OTU B1), which were ubiquitous across the trench.</p><p><strong>Conclusions: </strong>This manuscript represents the first attempt to characterize the prokaryotic communities of the KKT abyssal-hadal zone. Our results reveal that the most abundant prokaryotes harbored by the abyssal-hadal zone of Kuril-Kamchatka Trench were chemolithotrophic archaea and heterotrophic bacteria, which did not show a distinctive pattern distribution according to depth. In particular, Acinetobacter, Zhongshania, and Colwellia (potential hydrocarbon degraders) were the main bacterial genera, and Nitrosopumilus (ammonia oxidizer) was the dominant representative of the archaeal diversity.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-08-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10398949/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10314058","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"A symbiotic footprint in the plant root microbiome.","authors":"Kyle Hartman,&nbsp;Marc W Schmid,&nbsp;Natacha Bodenhausen,&nbsp;S Franz Bender,&nbsp;Alain Y Valzano-Held,&nbsp;Klaus Schlaeppi,&nbsp;Marcel G A van der Heijden","doi":"10.1186/s40793-023-00521-w","DOIUrl":"https://doi.org/10.1186/s40793-023-00521-w","url":null,"abstract":"<p><strong>Background: </strong>A major aim in plant microbiome research is determining the drivers of plant-associated microbial communities. While soil characteristics and host plant identity present key drivers of root microbiome composition, it is still unresolved whether the presence or absence of important plant root symbionts also determines overall microbiome composition. Arbuscular mycorrhizal fungi (AMF) and N-fixing rhizobia bacteria are widespread, beneficial root symbionts that significantly enhance plant nutrition, plant health, and root structure. Thus, we hypothesized that symbiont types define the root microbiome structure.</p><p><strong>Results: </strong>We grew 17 plant species from five families differing in their symbiotic associations (no symbioses, AMF only, rhizobia only, or AMF and rhizobia) in a greenhouse and used bacterial and fungal amplicon sequencing to characterize their root microbiomes. Although plant phylogeny and species identity were the most important factors determining root microbiome composition, we discovered that the type of symbioses also presented a significant driver of diversity and community composition. We found consistent responses of bacterial phyla, including members of the Acidobacteria, Chlamydiae, Firmicutes, and Verrucomicrobia, to the presence or absence of AMF and rhizobia and identified communities of OTUs specifically enriched in the different symbiotic groups. A total of 80, 75 and 57 bacterial OTUs were specific for plant species without symbiosis, plant species forming associations with AMF or plant species associating with both AMF and rhizobia, respectively. Similarly, 9, 14 and 4 fungal OTUs were specific for these plant symbiont groups. Importantly, these generic symbiosis footprints in microbial community composition were also apparent in absence of the primary symbionts.</p><p><strong>Conclusion: </strong>Our results reveal that symbiotic associations of the host plant leaves an imprint on the wider root microbiome - which we term the symbiotype. These findings suggest the existence of a fundamental assembly principle of root microbiomes, dependent on the symbiotic associations of the host plant.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-07-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10391997/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9928234","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Microbiome specificity and fluxes between two distant plant taxa in Iberian forests.","authors":"Zaki Saati-Santamaría,&nbsp;Rocío Vicentefranqueira,&nbsp;Miroslav Kolařik,&nbsp;Raúl Rivas,&nbsp;Paula García-Fraile","doi":"10.1186/s40793-023-00520-x","DOIUrl":"https://doi.org/10.1186/s40793-023-00520-x","url":null,"abstract":"<p><strong>Background: </strong>Plant-associated microbial communities play important roles in host nutrition, development and defence. In particular, the microbes living within internal plant tissues can affect plant metabolism in a more intimate way. Understanding the factors that shape plant microbial composition and discovering enriched microbes within endophytic compartments would thus be valuable to gain knowledge on potential plant-microbial coevolutions. However, these interactions are usually studied through reductionist approaches (in vitro models or crop controlled systems). Here, we investigate these ecological factors in wild forest niches using proximally located plants from two distant taxa (blueberry and blackberry) as a model.</p><p><strong>Results: </strong>Although the microbial communities were quite similar in both plants, we found that sampling site had a high influence on them; specifically, its impact on the rhizosphere communities was higher than that on the roots. Plant species and sample type (root vs. rhizosphere) affected the bacterial communities more than the fungal communities. For instance, Xanthobacteraceae and Helotiales taxa were more enriched in roots, while the abundance of Gemmatimonadetes was higher in rhizospheres. Acidobacteria abundance within the endosphere of blueberry was similar to that in soil. Several taxa were significantly associated with either blackberry or blueberry samples regardless of the sampling site. For instance, we found a significant endospheric enrichment of Nevskia in blueberry and of Sphingobium, Novosphingobium and Steroidobacter in blackberry.</p><p><strong>Conclusions: </strong>There are selective enrichment and exclusion processes in the roots of plants that shapes a differential composition between plant species and sample types (root endosphere-rhizosphere). The special enrichment of some microbial taxa in each plant species might suggest the presence of ancient selection and/or speciation processes and might imply specific symbiosis. The selection of fungi by the host is more pronounced when considering the fungal trait rather than the taxonomy. This work helps to understand plant-microbial interactions in natural ecosystems and the microbiome features of plants.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-07-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10363313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9854048","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reciprocal influence of soil, phyllosphere, and aphid microbiomes.","authors":"Adrian Wolfgang,&nbsp;Ayco J M Tack,&nbsp;Gabriele Berg,&nbsp;Ahmed Abdelfattah","doi":"10.1186/s40793-023-00515-8","DOIUrl":"10.1186/s40793-023-00515-8","url":null,"abstract":"<p><strong>Background: </strong>The effect of soil on the plant microbiome is well-studied. However, less is known about the impact of the soil microbiome in multitrophic systems. Here we examined the effect of soil on plant and aphid microbiomes, and the reciprocal effect of aphid herbivory on the plant and soil microbiomes. We designed microcosms, which separate below and aboveground compartments, to grow oak seedlings with and without aphid herbivory in soils with three different microbiomes. We used amplicon sequencing and qPCR to characterize the bacterial and fungal communities in soils, phyllospheres, and aphids.</p><p><strong>Results: </strong>Soil microbiomes significantly affected the microbial communities of phyllospheres and, to a lesser extent, aphid microbiomes, indicating plant-mediated assembly processes from soil to aphids. While aphid herbivory significantly decreased microbial diversity in phyllospheres independent of soil microbiomes, the effect of aphid herbivory on the community composition in soil varied among the three soils.</p><p><strong>Conclusions: </strong>This study provides experimental evidence for the reciprocal influence of soil, plant, and aphid microbiomes, with the potential for the development of new microbiome-based pest management strategies.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-07-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10362670/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9857478","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Pioneer Arabidopsis thaliana spans the succession gradient revealing a diverse root-associated microbiome.","authors":"Vera Hesen,&nbsp;Yvet Boele,&nbsp;Tanja Bakx-Schotman,&nbsp;Femke van Beersum,&nbsp;Ciska Raaijmakers,&nbsp;Ben Scheres,&nbsp;Viola Willemsen,&nbsp;Wim H van der Putten","doi":"10.1186/s40793-023-00511-y","DOIUrl":"https://doi.org/10.1186/s40793-023-00511-y","url":null,"abstract":"<p><strong>Background: </strong>Soil microbiomes are increasingly acknowledged to affect plant functioning. Research in molecular model species Arabidopsis thaliana has given detailed insights of such plant-microbiome interactions. However, the circumstances under which natural A. thaliana plants have been studied so far might represent only a subset of A. thaliana's full ecological context and potential biotic diversity of its root-associated microbiome.</p><p><strong>Results: </strong>We collected A. thaliana root-associated soils from a secondary succession gradient covering 40 years of land abandonment. All field sites were situated on the same parent soil material and in the same climatic region. By sequencing the bacterial and fungal communities and soil abiotic analysis we discovered differences in both the biotic and abiotic composition of the root-associated soil of A. thaliana and these differences are in accordance with the successional class of the field sites. As the studied sites all have been under (former) agricultural use, and a climatic cline is absent, we were able to reveal a more complete variety of ecological contexts A. thaliana can appear and sustain in.</p><p><strong>Conclusions: </strong>Our findings lead to the conclusion that although A. thaliana is considered a pioneer plant species and previously almost exclusively studied in early succession and disturbed sites, plants can successfully establish in soils which have experienced years of ecological development. Thereby, A. thaliana can be exposed to a much wider variation in soil ecological context than is currently presumed. This knowledge opens up new opportunities to enhance our understanding of causal plant-microbiome interactions as A. thaliana cannot only grow in contrasting soil biotic and abiotic conditions along a latitudinal gradient, but also when those conditions vary along a secondary succession gradient. Future research could give insights in important plant factors to grow in more ecologically complex later-secondary succession soils, which is an impending direction of our current agricultural systems.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-07-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10357733/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9840235","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Evolutionary patterns of archaea predominant in acidic environment.","authors":"Rafael Bargiela,&nbsp;Aleksei A Korzhenkov,&nbsp;Owen A McIntosh,&nbsp;Stepan V Toshchakov,&nbsp;Mikhail M Yakimov,&nbsp;Peter N Golyshin,&nbsp;Olga V Golyshina","doi":"10.1186/s40793-023-00518-5","DOIUrl":"https://doi.org/10.1186/s40793-023-00518-5","url":null,"abstract":"<p><strong>Background: </strong>Archaea of the order Thermoplasmatales are widely distributed in natural acidic areas and are amongst the most acidophilic prokaryotic organisms known so far. These organisms are difficult to culture, with currently only six genera validly published since the discovery of Thermoplasma acidophilum in 1970. Moreover, known great diversity of uncultured Thermoplasmatales represents microbial dark matter and underlines the necessity of efforts in cultivation and study of these archaea. Organisms from the order Thermoplasmatales affiliated with the so-called \"alphabet-plasmas\", and collectively dubbed \"E-plasma\", were the focus of this study. These archaea were found predominantly in the hyperacidic site PM4 of Parys Mountain, Wales, UK, making up to 58% of total metagenomic reads. However, these archaea escaped all cultivation attempts.</p><p><strong>Results: </strong>Their genome-based metabolism revealed its peptidolytic potential, in line with the physiology of the previously studied Thermoplasmatales isolates. Analyses of the genome and evolutionary history reconstruction have shown both the gain and loss of genes, that may have contributed to the success of the \"E-plasma\" in hyperacidic environment compared to their community neighbours. Notable genes among them are involved in the following molecular processes: signal transduction, stress response and glyoxylate shunt, as well as multiple copies of genes associated with various cellular functions; from energy production and conversion, replication, recombination, and repair, to cell wall/membrane/envelope biogenesis and archaella production. History events reconstruction shows that these genes, acquired by putative common ancestors, may determine the evolutionary and functional divergences of \"E-plasma\", which is much more developed than other representatives of the order Thermoplasmatales. In addition, the ancestral hereditary reconstruction strongly indicates the placement of Thermogymnomonas acidicola close to the root of the Thermoplasmatales.</p><p><strong>Conclusions: </strong>This study has analysed the metagenome-assembled genome of \"E-plasma\", which denotes the basis of their predominance in Parys Mountain environmental microbiome, their global ubiquity, and points into the right direction of further cultivation attempts. The results suggest distinct evolutionary trajectories of organisms comprising the order Thermoplasmatales, which is important for the understanding of their evolution and lifestyle.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10354927/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"10220408","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Elucidating the effects of organic vs. conventional cropping practice and rhizobia inoculation on rhizosphere microbial diversity and yield of peanut.","authors":"Dev Paudel,&nbsp;Liping Wang,&nbsp;Ravin Poudel,&nbsp;Janam P Acharya,&nbsp;Samantha Victores,&nbsp;Cleber Henrique Lopes de Souza,&nbsp;Esteban Rios,&nbsp;Jianping Wang","doi":"10.1186/s40793-023-00517-6","DOIUrl":"https://doi.org/10.1186/s40793-023-00517-6","url":null,"abstract":"<p><p>Legumes such as peanut (Arachis hypogea) can fulfill most of their nitrogen requirement by symbiotic association with nitrogen-fixing bacteria, rhizobia. Nutrient availability is largely determined by microbial diversity and activity in the rhizosphere that influences plant health, nutrition, and crop yield, as well as soil quality and soil fertility. However, our understanding of the complex effects of microbial diversity and rhizobia inoculation on crop yields of different peanut cultivars under organic versus conventional farming systems is extremely limited. In this research, we studied the impacts of conventional vs. organic cultivation practices and inoculation with commercial vs. single strain inoculum on peanut yield and soil microbial diversity of five peanut cultivars. The experiment was set up in the field following a split-split-plot design. Our results from the 16 S microbiome sequencing showed considerable variations of microbial composition between the cultivation types and inoculum, indicating a preferential association of microbes to peanut roots with various inoculum and cropping system. Alpha diversity indices (chao1, Shannon diversity, and Simpson index) of soil microbiome were generally higher in plots with organic than conventional inorganic practices. The cultivation type and inoculum explained significant differences among bacterial communities. Taxonomic classification revealed two phyla, TM6 and Firmicutes were significantly represented in inorganic as compared to organic soil, where significant phyla were Armatimonadetes, Gemmatimonadetes, Nitrospirae, Proteobacteria, Verrucomicrobia, and WS3. Yields in the organic cultivation system decreased by 10-93% of the yields in the inorganic cultivation system. Cultivar G06 and T511 consistently showed relative high yields in both organic and inorganic trials. Our results show significant two-way interactions between cultivation type and genotype for most of the trait data collected. Therefore, it is critical for farmers to choose varieties based on their cultivation practices. Our results showed that bacterial structure was more uniform in organic fields and microbial diversity in legumes was reduced in inorganic fields. This research provided guides for farmers and scientists to improve peanut yield while promoting microbial diversity and increasing sustainability.</p>","PeriodicalId":48553,"journal":{"name":"Environmental Microbiome","volume":null,"pages":null},"PeriodicalIF":7.9,"publicationDate":"2023-07-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10355010/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"9844777","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"环境科学与生态学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}