{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T20:25:21Z","timestamp":1790108721238,"version":"4.0.1"},"reference-count":86,"publisher":"Public Library of Science (PLoS)","issue":"11","license":[{"start":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T00:00:00Z","timestamp":1668556800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"Colorado State University Agricultural Experiment Station"},{"name":"USDA Cooperative Agreement"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>Soil microbiome disruption methods are regularly used to reduce populations of microbial pathogens, often resulting in increased crop growth. However, little is known about the effect of soil microbiome disruption on non-pathogenic members of the soil microbiome. Here, we applied soil microbiome disruption in the form of moist-heat sterilization (autoclaving) to reduce populations of naturally occurring soil microbiota. The disruption was applied to analyze bacterial community rearrangement mediated by four crops (corn, beet, lettuce, and tomato) grown in three historically distinct agroecosystem soils (conventional, organic, and diseased). Applying the soil disruption enhanced plant influence on rhizosphere bacterial colonization, and significantly different bacterial communities were detected between the tested crops. Furthermore, bacterial genera showed significant abundance increases in ways both unique-to and shared-by each tested crop. As an example, corn uniquely promoted abundances of <jats:italic>Pseudomonas<\/jats:italic> and <jats:italic>Sporocytophaga<\/jats:italic>, regardless of the disrupted soil in which it was grown. Whereas the promotion of <jats:italic>Bosea<\/jats:italic>, <jats:italic>Dyadobacter<\/jats:italic> and <jats:italic>Luteoliobacter<\/jats:italic> was shared by all four crops when grown in disrupted soils. In summary, soil disruption followed by crop introduction amplified the plant colonization of potential beneficial bacterial genera in the rhizosphere.<\/jats:p>","DOI":"10.1371\/journal.pone.0277529","type":"journal-article","created":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T18:29:42Z","timestamp":1668623382000},"page":"e0277529","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":30,"title":["Soil microbiome disruption reveals specific and general plant-bacterial relationships in three agroecosystem soils"],"prefix":"10.1371","volume":"17","author":[{"given":"Michael J.","family":"DiLegge","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Daniel K.","family":"Manter","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-6046-4948","authenticated-orcid":true,"given":"Jorge M.","family":"Vivanco","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2022,11,16]]},"reference":[{"issue":"5","key":"pone.0277529.ref001","doi-asserted-by":"crossref","first-page":"999","DOI":"10.1111\/1751-7915.12804","article-title":"Microbes, Big Yields: enhancing food crop production with biological solutions","volume":"10","author":"P Trivedi","year":"2017","journal-title":"Microb Biotechnol"},{"issue":"9","key":"pone.0277529.ref002","doi-asserted-by":"crossref","first-page":"e02738","DOI":"10.1128\/AEM.02738-17","article-title":"High microbial diversity promotes soil ecosystem functioning","volume":"84","author":"PA Maron","year":"2018","journal-title":"Appl. Environ. Microbiol"},{"issue":"1","key":"pone.0277529.ref003","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1111\/jam.14273","article-title":"Co-Inoculation of Bacillus Sp. and Pseudomonas Putida at Different Development Stages Acts as a Biostimulant to Promote Growth, Yield and Nutrient Uptake of Tomato\u201d","volume":"127","author":"Y He","year":"2019","journal-title":"Jol Appl Microbiol"},{"key":"pone.0277529.ref004","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/ismej.2013.196","article-title":"Rhizosphere Microbiome Assemblage Is Affected by Plant Development\u201d","volume":"8","author":"JM Chaparro","year":"2014","journal-title":"The ISME journal"},{"key":"pone.0277529.ref005","doi-asserted-by":"crossref","first-page":"17677","DOI":"10.1038\/s41598-019-53623-2","article-title":"Plant Growth-Promoting Microbial Soil Amendment Dynamically Alters the Strawberry Root Bacterial Microbiome","volume":"9","author":"S Deng","year":"2019","journal-title":"Sci Rep"},{"key":"pone.0277529.ref006","doi-asserted-by":"crossref","first-page":"6116","DOI":"10.1038\/s41598-018-24537-2","article-title":"Long-Term Coffee Monoculture Alters Soil Chemical Properties and Microbial Communities","volume":"8","author":"Q Zhao","year":"2018","journal-title":"Sci Rep"},{"key":"pone.0277529.ref007","doi-asserted-by":"crossref","first-page":"20160026","DOI":"10.1098\/rstb.2016.0026","article-title":"Rapid Emergence of Pathogens in Agro-Ecosystems: Global Threats to Agricultural Sustainability and Food Security","volume":"371","author":"BA McDonald","year":"2016","journal-title":"Phil. Trans. R. Soc. B"},{"issue":"1","key":"pone.0277529.ref008","doi-asserted-by":"crossref","first-page":"e0211163","DOI":"10.1371\/journal.pone.0211163","article-title":"Effects of long-term fertilization on soil organic carbon mineralization and microbial community structure","volume":"14","author":"Z Guo","year":"2019","journal-title":"PLoS ONE"},{"issue":"5","key":"pone.0277529.ref009","doi-asserted-by":"crossref","first-page":"e0217018","DOI":"10.1371\/journal.pone.0217018","article-title":"The Effects of Chemical and Organic Fertilizer Usage on Rhizosphere Soil in Tea Orchards\u201d","volume":"14","author":"W Lin","year":"2019","journal-title":"PloS one"},{"issue":"4","key":"pone.0277529.ref010","doi-asserted-by":"crossref","first-page":"1718","DOI":"10.20546\/ijcmas.2017.604.206","article-title":"Impact of Fertigation and Target Yield Levels on Soil Microbial Biomass and Cane Yield of Ratoon Sugarcane","volume":"6","author":"B Patil","year":"2017","journal-title":"Int. J. Curr. Microbiol. App. Sci"},{"issue":"12","key":"pone.0277529.ref011","first-page":"4649","article-title":"\u201cEnvironmental Impacts from Pesticide Use: a Case Study of Soil Fumigation in Florida Tomato Production.\u201d International journal of environmental research and public health","volume":"8","author":"D Sande","year":"2011","journal-title":"MDPI"},{"issue":"27","key":"pone.0277529.ref012","doi-asserted-by":"crossref","first-page":"15","DOI":"10.1016\/j.copbio.2013.09.003","article-title":"Agricultural Soils, Pesticides and Microbial Diversity","author":"CS Jacobsen","year":"2014","journal-title":"Curr. Opin. Biotechnol"},{"key":"pone.0277529.ref013","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1007\/s11104-012-1361-x","article-title":"Harnessing the rhizosphere microbiome through plant breeding and agricultural management","volume":"360","author":"MG Bakker","year":"2012","journal-title":"Plant and Soil"},{"key":"pone.0277529.ref014","article-title":"Root Exudates Regulate Soil Fungal Community Composition and Diversity","author":"CD Broeckling","year":"2008","journal-title":"Appl. Environ. Microbiol"},{"issue":"263","key":"pone.0277529.ref015","doi-asserted-by":"crossref","first-page":"7","DOI":"10.1016\/j.agee.2018.04.018","article-title":"Organic Management and Cover Crop Species Steer Soil Microbial Community Structure and Functionality along with Soil Organic Matter Properties","author":"LB Mart\u00ednez-Garc\u00eda","year":"2018","journal-title":"Agriculture, Ecosystems & Environment"},{"key":"pone.0277529.ref016","doi-asserted-by":"crossref","first-page":"1329","DOI":"10.1094\/PDIS-02-10-0090","article-title":"Pyrosequencing assessment of soil microbial communities in organic and conventional potato farms","volume":"94","author":"A Sugiyama","year":"2010","journal-title":"Plant Disease"},{"issue":"12","key":"pone.0277529.ref017","doi-asserted-by":"crossref","first-page":"100176","DOI":"10.1016\/j.rhisph.2019.100176","article-title":"Soil Sterilization Leads to Re-Colonization of a Healthier Rhizosphere Microbiome","author":"K Li","year":"2019","journal-title":"Rhizosphere"},{"key":"pone.0277529.ref018","article-title":"Crop Rotational Diversity Increases Disease Suppressive Capacity of Soil Microbiomes","author":"AL Peralta","year":"2018","journal-title":"Ecological Society of America"},{"key":"pone.0277529.ref019","unstructured":"Wolf DC, Skipper HD. Soil Sterilization. Methods of Soil Analysis: Part 2-Microbiological and Biochemical Properties. Soil Science Society of America, 1994."},{"key":"pone.0277529.ref020","first-page":"863240","article-title":"Microbial Inoculants and Their Impact on Soil Microbial Communities: a Review","author":"D Trabelsi","year":"2013","journal-title":"BioMed Res Int"},{"issue":"50","key":"pone.0277529.ref021","first-page":"217","article-title":"De-coupling of root-microbiome associations followed by antagonist inoculation improves rhizosphere soil suppressiveness","author":"M Qiu","year":"2013","journal-title":"Biol. and Fert. of Soils"},{"issue":"4","key":"pone.0277529.ref022","doi-asserted-by":"crossref","first-page":"1159","DOI":"10.1073\/pnas.1109326109","article-title":"Microbial Diversity Determines the Invasion of Soil by a Bacterial Pathogen","volume":"109","author":"JD van Elsas","year":"2012","journal-title":"Proc Natl Acad Sci U S A"},{"key":"pone.0277529.ref023","doi-asserted-by":"crossref","first-page":"145","DOI":"10.1201\/9780203738535-5","volume-title":"Statistical models in S. Routledge","author":"JM Chambers","year":"2017"},{"issue":"1","key":"pone.0277529.ref024","doi-asserted-by":"crossref","first-page":"e1","DOI":"10.1093\/nar\/gks808","article-title":"Evaluation of general 16S ribosomal RNA gene PCR primers for classical and next-generation sequencing-based diversity studies","volume":"41","author":"A Klindworth","year":"2013","journal-title":"Nucleic Acids Res"},{"issue":"22","key":"pone.0277529.ref025","doi-asserted-by":"crossref","first-page":"939","DOI":"10.1101\/gr.128124.111","article-title":"Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture","author":"N Rohland","year":"2012","journal-title":"Genome Res"},{"key":"pone.0277529.ref026","unstructured":"Faircloth B, Glenn T. Ecol. And Evol Biology, UCLA. (2011) Serapure_v2.2."},{"issue":"7","key":"pone.0277529.ref027","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"BJ Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"pone.0277529.ref028","doi-asserted-by":"crossref","first-page":"10","DOI":"10.14806\/ej.17.1.200","article-title":"(cutadept): Cutadapt removes adapter sequences from high-throughput sequencing reads","volume":"17","author":"M. Martin","year":"2011","journal-title":"EMBnet.journal"},{"key":"pone.0277529.ref029","unstructured":"Oksanen JF, Blanchet G, Friendly M, Kindt R, Legendre P, McGlinn D, et al. vegan: Community Ecology Package. R package version 2.5\u20136. 2019"},{"issue":"4","key":"pone.0277529.ref030","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data","volume":"8","author":"PJ McMurdie","year":"2013","journal-title":"PLoS ONE"},{"key":"pone.0277529.ref031","doi-asserted-by":"crossref","unstructured":"Manter DK, Korsa M, Tebbe C, Delgado JA. myPhyloDB: a local web server for the storage and analysis of metagenomic data. Database (Oxford) J. Biol. Databases Curation, 2016. https:\/\/doi.org\/10.1093\/database\/baw037","DOI":"10.1093\/database\/baw037"},{"key":"pone.0277529.ref032","doi-asserted-by":"crossref","first-page":"293.","DOI":"10.1186\/1471-2105-15-293","article-title":"jvenn: an interactive Venn diagram viewer","volume":"15","author":"P Bardou","year":"2014","journal-title":"BMC Bioinformatics"},{"key":"pone.0277529.ref033","doi-asserted-by":"crossref","first-page":"1958","DOI":"10.2134\/jeq2005.0024","article-title":"Autoclaving soil samples affects algal-available phosphorus","volume":"34","author":"BH Anderson","year":"2005","journal-title":"J. Environ. Qual"},{"key":"pone.0277529.ref034","doi-asserted-by":"crossref","first-page":"116446","DOI":"10.1016\/j.envpol.2021.116446","article-title":"Effect of sterilization on cadmium immobilization and bacterial community in alkaline soil remediated by mercapto-palygorskite","volume":"273","author":"Y Wang","year":"2021","journal-title":"Environ. Pollution"},{"issue":"48","key":"pone.0277529.ref035","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1007\/s00374-012-0691-4","article-title":"Manipulating the soil microbiome to increase soil health and plant fertility","author":"JM Chaparro","year":"2012","journal-title":"Biol Fertil Soils"},{"key":"pone.0277529.ref036","doi-asserted-by":"crossref","first-page":"e19502","DOI":"10.1371\/journal.pone.0019502","article-title":"Decreased functional diversity and biological pest control in conventional compared to organic crop fields","volume":"6","author":"J Krauss","year":"2011","journal-title":"PLoS One"},{"issue":"3","key":"pone.0277529.ref037","doi-asserted-by":"crossref","first-page":"548","DOI":"10.1128\/MMBR.64.3.548-572.2000","article-title":"Resistance of Bacillus Endospores to Extreme Terrestrial and Extraterrestrial Environments","volume":"64","author":"WL Nicholson","year":"2000","journal-title":"Micro. and Mol. Biol. Revs"},{"issue":"6","key":"pone.0277529.ref038","doi-asserted-by":"crossref","first-page":"683","DOI":"10.1016\/j.jbiosc.2014.11.006","article-title":"Prospecting cold deserts of north western Himalayas for microbial diversity and plant growth promoting attributes","volume":"119","author":"AN Yadav","year":"2015","journal-title":"J. Biosci. Bioeng"},{"issue":"50","key":"pone.0277529.ref039","doi-asserted-by":"crossref","first-page":"28","DOI":"10.1016\/j.ejsobi.2011.11.012","article-title":"Nematodes and protozoa affect plants differently, depending on soil nutrient status","author":"L Bj\u00f8rnlund","year":"2012","journal-title":"Eu Jol of Soil Biol"},{"issue":"8","key":"pone.0277529.ref040","doi-asserted-by":"crossref","first-page":"1035","DOI":"10.1080\/01904167.2018.1433211","article-title":"Plant growth promoting potential of psychrotolerant Dyadobacter sp. for pulses and finger millet and impact of inoculation on soil chemical properties and diazotrophic abundance","volume":"41","author":"S Kumar","year":"2018","journal-title":"Journal of Plant Nutrition"},{"issue":"125","key":"pone.0277529.ref041","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1016\/j.ecoenv.2015.11.020","article-title":"Brevundimonas diminuta mediated alleviation of arsenic toxicity and plant growth promotion in Oryza sativa L","author":"N Singh","year":"2016","journal-title":"Ecotoxicol. and Environ. Safety"},{"issue":"1","key":"pone.0277529.ref042","article-title":"Plant growth promotion by endophytic bacteria isolated from rice (Oryza sativa)","volume":"21","author":"W Raweekul","year":"2016","journal-title":"Thammasat Int Jol of Sci and Tech"},{"issue":"12","key":"pone.0277529.ref043","doi-asserted-by":"crossref","first-page":"e82443","DOI":"10.1371\/journal.pone.0082443","article-title":"The Rhizosphere Selects for Particular Groups of Acidobacteria and Verrucomicrobia","volume":"8","author":"U Nunes da Rocha","year":"2013","journal-title":"PLoS ONE"},{"issue":"4","key":"pone.0277529.ref044","doi-asserted-by":"crossref","first-page":"1008","DOI":"10.1007\/s00248-012-0071-5","article-title":"Plant Growth-Promoting Rhizobacteria Associated with Ancient Clones of Creosote Bush (Larrea tridentata)","volume":"64","author":"MA Jorquera","year":"2012","journal-title":"Microb. Ecol"},{"issue":"5","key":"pone.0277529.ref045","doi-asserted-by":"crossref","first-page":"864","DOI":"10.1007\/s12275-012-1587-6","article-title":"Caenimonas terrae sp nov, isolated from a soil sample in Korea, and emended description of the genus Caenimonas Ryu et al. 2008","volume":"50","author":"SJ Kim","year":"2012","journal-title":"Jol. Microbiol"},{"issue":"12","key":"pone.0277529.ref046","doi-asserted-by":"crossref","first-page":"4930","DOI":"10.1099\/ijsem.0.001447","article-title":"Sphingoaurantiacus capsulatus sp nov, isolated from mountain soil, and emended description of the genus Sphingoaurantiacus","volume":"66","author":"Y Tan","year":"2016","journal-title":"Int. J. System. Evol. Microbiol"},{"issue":"1","key":"pone.0277529.ref047","doi-asserted-by":"crossref","first-page":"308","DOI":"10.1099\/ijsem.0.000714","article-title":"Rhabdobacter roseus gen nov, sp nov, isolated from soil","volume":"66","author":"RH Dahal","year":"2016","journal-title":"Int. J. System. Evol. Microbiol"},{"issue":"4","key":"pone.0277529.ref048","doi-asserted-by":"crossref","first-page":"279","DOI":"10.1007\/s40093-015-0107-1","article-title":"Cultivable bacterial diversity and early plant growth promotion by the traditional organic formulations prepared using organic waste materials","volume":"4","author":"R Anandham","year":"2015","journal-title":"Int. J. Recucl. Org. Waste Agric."},{"key":"pone.0277529.ref049","doi-asserted-by":"crossref","unstructured":"Subrahmanyam G, Kumar A, Sandilya SP, Chutia M, Yadav AN. Diversity, Plant Growth Promoting Attributes, and Agricultural Applications of Rhizospheric Microbes. In book: Yadav A, Singh J, Rastegari A, Yadav N (eds) Plant Microbiomes for Sustainable Agriculture Sustainable Development and Biodiversity, vol 25 Springer, Cham 2020. http:\/\/dx.doi.org\/10.1007\/978-3-030-38453-1_1","DOI":"10.1007\/978-3-030-38453-1_1"},{"issue":"1","key":"pone.0277529.ref050","doi-asserted-by":"crossref","first-page":"14","DOI":"10.3390\/microorganisms6010014","article-title":"Bacterial microbiota of rice roots: 16S-based taxonomic profiling of endophytic and rhizospheric diversity, endophytes isolation and simplified endophytic community","volume":"6","author":"F Moronta-Barrios","year":"2018","journal-title":"Microorganisms"},{"issue":"4","key":"pone.0277529.ref051","doi-asserted-by":"crossref","first-page":"851","DOI":"10.1099\/ijsem.0.001683","article-title":"Devosia elaeis sp nov, isolated from oil palm rhizospheric soil","volume":"67","author":"MNM Nor","year":"2017","journal-title":"Int. J. System. Evol. Microbiol."},{"issue":"61","key":"pone.0277529.ref052","first-page":"217","article-title":"Isolation and Characterization of New Plant Growth-Promoting Bacterial Endophytes\u201d","author":"S Rashid","year":"2011","journal-title":"App. Soil Ecol"},{"issue":"84","key":"pone.0277529.ref053","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.apsoil.2014.06.011","article-title":"Plant defence inducers rapidly influence the diversity of bacterial communities in a potting mix","author":"LC Carvalhais","year":"2014","journal-title":"App. Soil Ecol."},{"issue":"101","key":"pone.0277529.ref054","doi-asserted-by":"crossref","first-page":"8485","DOI":"10.1007\/s00253-017-8550-8","article-title":"Interactions of plant growth-promoting rhizobacteria and soil factors in two leguminous plants","author":"X Xiao","year":"2017","journal-title":"Appl Microbiol Biotechnol"},{"key":"pone.0277529.ref055","unstructured":"Alkhnajari A.Microbial diversity of buckwheat rhizosphere in wirework-infested and non-infested soils using metagenomics [Island Scholar Master\u2019s thesis] 2019; University of Prince Edward Islands"},{"issue":"8","key":"pone.0277529.ref056","doi-asserted-by":"crossref","first-page":"931","DOI":"10.1002\/jobm.201400898","article-title":"Nitrogen fixing bacteria in the family Acetobacteraceaeand their role in agriculture","volume":"55","author":"VM Reis","year":"2015","journal-title":"Jol Basic Microbol"},{"issue":"5","key":"pone.0277529.ref057","doi-asserted-by":"crossref","first-page":"1439","DOI":"10.1099\/ijs.0.02978-0","article-title":"Diversity and evolution of Bdellovibrio-and-like organisms (BALOs), reclassification of Bacteriovorax starrii as Peredibacter starrii gen nov, comb nov, and description of the Bacteriovorax\u2013Peredibacter clade as Bacteriovoracaceae fam nov","volume":"54","author":"Y Davidov","year":"2004","journal-title":"Int. J. System. Evol. Microbiol"},{"issue":"9","key":"pone.0277529.ref058","article-title":"Enhanced tomato plant growth in soil under reduced P supply through microbial inoculants and microbiome shifts FEMS","volume":"95","author":"N Eltlbany","year":"2019","journal-title":"Microbiol. Ecol."},{"issue":"9","key":"pone.0277529.ref059","doi-asserted-by":"crossref","first-page":"663","DOI":"10.1111\/jph.12729","article-title":"Conventional farming impairs Rhizoctonia solani disease suppression by disrupting soil food web","volume":"166","author":"G Bonanomi","year":"2018","journal-title":"J. Phytopathol."},{"issue":"Pt 2","key":"pone.0277529.ref060","first-page":"578","article-title":"Arachidicoccus rhizosphaerae gen nov, sp nov, a plant-growth-promoting bacterium in the family Chitinophagaceae isolated from rhizosphere soil","volume":"65","author":"M Madhaiyan","year":"2014","journal-title":"Int. J. System. Evol. Microbiol."},{"issue":"3","key":"pone.0277529.ref061","doi-asserted-by":"crossref","first-page":"518","DOI":"10.1099\/ijs.0.023002-0","article-title":"Hydrotalea flava gen nov, sp nov, a new member of the phylum Bacteroidetes and allocation of the genera Chitinophaga, Sediminibacterium, Lacibacter, Flavihumibacter, Flavisolibacter, Niabella, Niastella, Segetibacter, Parasegetibacter, Terrimonas, Ferruginibacter, Filimonas and Hydrotalea to the family Chitinophagaceae fam nov","volume":"61","author":"P K\u00e4mpfer","year":"2011","journal-title":"Int. J. System. Evol. Microbiol"},{"issue":"11","key":"pone.0277529.ref062","doi-asserted-by":"crossref","first-page":"2591","DOI":"10.1099\/ijs.0.64938-0","article-title":"Solimonas soli gen nov, sp nov, isolated from soil of a ginseng field","volume":"57","author":"MK Kim","year":"2007","journal-title":"Int. J. System. Evol. Microbiol."},{"key":"pone.0277529.ref063","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1016\/j.bcab.2017.11.007","article-title":"Pseudomonas stutzeri E25 and Stenotrophomonas maltophilia CR71 endophytes produce antifungal volatile organic compounds and exhibit additive plant growth-promoting effects","volume":"13","author":"D Rojas-Sol\u00eds","year":"2018","journal-title":"Biocatalysis and Agri. Biotechnol."},{"key":"pone.0277529.ref064","doi-asserted-by":"crossref","first-page":"513","DOI":"10.1007\/s00203-016-1332-3","article-title":"The plant growth-promoting effect of the nitrogen-fixing endophyte Pseudomonas stutzeri A15","volume":"199","author":"VTK Pham","year":"2017","journal-title":"Arch Microbiol"},{"key":"pone.0277529.ref065","doi-asserted-by":"crossref","unstructured":"Preston GM. Plant perceptions of plant growth-promoting Pseudomonas Phil Trans R Soc Lond, 2004; B359907\u2013918. https:\/\/doi.org\/10.1098\/rstb.2003.1384","DOI":"10.1098\/rstb.2003.1384"},{"issue":"2","key":"pone.0277529.ref066","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1111\/j.1365-2672.1972.tb03692.x","article-title":"Electronmicroscopic Observations on the Degradation of Cellulose Fibres by Cellvibrio fulvus and Sporocytophaga myxococcoides","volume":"35","author":"B Berg","year":"1972","journal-title":"J. Applied Bacteriol"},{"issue":"8","key":"pone.0277529.ref067","doi-asserted-by":"crossref","first-page":"376","DOI":"10.1007\/s13205-018-1391-z","article-title":"Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities","author":"KJ Liew","year":"2018","journal-title":"3 Biotech"},{"issue":"2","key":"pone.0277529.ref068","doi-asserted-by":"crossref","first-page":"300","DOI":"10.1128\/am.15.2.300-303.1967","article-title":"Effect of herbicides on cellulose decomposition by Sporocytophaga myxococcoides","volume":"15","author":"WJ Lembeck","year":"1967","journal-title":"Appl Microbiol"},{"issue":"4","key":"pone.0277529.ref069","doi-asserted-by":"crossref","first-page":"351","DOI":"10.1002\/abio.370170411","article-title":"Isolation of phenoxy herbicide-degrading Rhodoferax species from contaminated building material","volume":"17","author":"A Ehrig","year":"1997","journal-title":"Acta Biotechnologica"},{"issue":"3","key":"pone.0277529.ref070","doi-asserted-by":"crossref","first-page":"298","DOI":"10.1007\/s00248-002-2006-z","article-title":"Contribution of Cytophaga-like Bacteria to the Potential of Turnover of Carbon, Nitrogen, and Phosphorus by Bacteria in the Rhizosphere of Barley (Hordeum vulgare L)","volume":"43","author":"J Johansen","year":"2002","journal-title":"Microbial Ecology"},{"key":"pone.0277529.ref071","doi-asserted-by":"crossref","unstructured":"Barman D, Dkhar MS. Plant Growth-Promoting Potential of Endophytic Bacteria Isolated from Costus speciosus in Tropical Deciduous Forest of Eastern Himalaya. Proc. Natl. Acad. Sci., 2018; India, Sect. B. Biol Sci. https:\/\/doi.org\/10.1007\/s40011-018-0998-5","DOI":"10.1007\/s40011-018-0998-5"},{"issue":"25","key":"pone.0277529.ref072","doi-asserted-by":"crossref","first-page":"1066","DOI":"10.1016\/j.sjbs.2018.03.003","article-title":"Effect of Plant Growth Promoting Bacillus Spp. on Nutritional Properties of Amaranthus Hypochondriacus Grains","volume":"6","author":"C Pandey","year":"2018","journal-title":"Saudi Journal of Biological Sciences"},{"key":"pone.0277529.ref073","volume-title":"Secondary Metabolites of Plant Growth Promoting Rhizomicroorganisms","author":"E. Sansinenea","year":"2019"},{"issue":"3","key":"pone.0277529.ref074","first-page":"5686874","article-title":"Evaluation of Bacillus Strains for Plant Growth Promotion and Predictability of Efficacy by In Vitro Physiological Traits","author":"RJ Akinrinlola","year":"2018","journal-title":"Intl J Microbiol"},{"key":"pone.0277529.ref075","unstructured":"Nieuwesteeg N. Biological control of fungal plant pathogens by tomato endosphere bacteria [Unpublished Master\u2019s Thesis] 2015; Wageningen University and Research Center"},{"issue":"10","key":"pone.0277529.ref076","doi-asserted-by":"crossref","first-page":"2451","DOI":"10.1099\/ijs.0.018713-0","article-title":"Mucilaginibacter gossypii sp nov and Mucilaginibacter gossypiicola sp nov, plant-growth-promoting bacteria isolated from cotton rhizosphere soils","volume":"60","author":"M Madhaiyan","year":"2009","journal-title":"Int. J. System. Evol. Microbiol."},{"issue":"1","key":"pone.0277529.ref077","first-page":"1","article-title":"Diversity of Endophytic Actinomycetes Isolated from Roots and Root Nodules of Pueraria candollei Grah ex Benth and the Analyses of Their Secondary Metabolites","volume":"44","author":"P Boonsnongcheep","year":"2017","journal-title":"Chiang Mai J Sci"},{"issue":"323","key":"pone.0277529.ref078","doi-asserted-by":"crossref","first-page":"350","DOI":"10.1016\/j.jhazmat.2016.05.034","article-title":"Bisphenol-A removal by the halophyte Juncus acutus in a phytoremediation pilot: Characterization and potential role of the endophytic community","author":"E Syranidou","year":"2017","journal-title":"Journal of Hazardous Materials"},{"issue":"42","key":"pone.0277529.ref079","doi-asserted-by":"crossref","first-page":"117","DOI":"10.1134\/S0003683806020013","article-title":"Microbial producers of plant growth stimulators and their practical use: A review","author":"EA Tsavkelova","year":"2006","journal-title":"Appl Biochem Microbiol"},{"issue":"202","key":"pone.0277529.ref080","doi-asserted-by":"crossref","first-page":"153","DOI":"10.1007\/s00203-019-01728-7","article-title":"Characterization and biotechnological application of protease from thermophilic Thermomonas haemolytica","author":"E Gulmus","year":"2020","journal-title":"Arch Microbiol"},{"issue":"9","key":"pone.0277529.ref081","article-title":"Initial soil microbiome composition and functioning predetermine future plant health","volume":"5","author":"Z Wei","year":"2019","journal-title":"Sci Adv"},{"issue":"6","key":"pone.0277529.ref082","doi-asserted-by":"crossref","first-page":"2274","DOI":"10.1111\/1365-2745.12967","article-title":"A heritable symbiont and host-associated factors shape fungal endophyte communities across spatial scales","volume":"106","author":"JG Harrison","year":"2018","journal-title":"Journal of Ecology"},{"key":"pone.0277529.ref083","doi-asserted-by":"crossref","first-page":"862","DOI":"10.3389\/fpls.2019.00862","article-title":"Plant Host-Associated Mechanisms for Microbial Selection","volume":"10","author":"P Jones","year":"2019","journal-title":"Front Plant Sci"},{"issue":"12","key":"pone.0277529.ref084","doi-asserted-by":"crossref","first-page":"e0208852","DOI":"10.1371\/journal.pone.0208852","article-title":"Enrichment of Verrucomicrobia, Actinobacteria and Burkholderiales drives selection of bacterial community from soil by maize roots in a traditional milpa agroecosystem","volume":"13","author":"E Aguirre-von-Wobeser","year":"2018","journal-title":"PLoS ONE"},{"issue":"2","key":"pone.0277529.ref085","doi-asserted-by":"crossref","first-page":"297","DOI":"10.1111\/j.1574-6941.2011.01156.x","article-title":"Verrucomicrobia subdivision 1 strains display a difference in the colonization of the leek (Allium porrum) rhizosphere","volume":"78","author":"UN Nunes da Rocha","year":"2011","journal-title":"FEMS Microbiol. Ecol."},{"issue":"2","key":"pone.0277529.ref086","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1016\/j.mimet.2010.08.003","article-title":"Real-Time PCR Detection of Holophagae (Acidobacteria) and Verrucomicrobia Subdivision 1 Groups in Bulk and Leek (Allium Porrum) Rhizosphere Soils","volume":"83","author":"UN Nunes da Rocha","year":"2010","journal-title":"Jol. Microbiol. Methods"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0277529","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,16]],"date-time":"2022-11-16T18:30:34Z","timestamp":1668623434000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0277529"}},"subtitle":[],"editor":[{"given":"Ying","family":"Ma","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2022,11,16]]},"references-count":86,"journal-issue":{"issue":"11","published-online":{"date-parts":[[2022,11,16]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0277529","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,11,16]]}}}