{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T07:32:57Z","timestamp":1790753577270,"version":"4.1.0"},"reference-count":70,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2020,1,9]],"date-time":"2020-01-09T00:00:00Z","timestamp":1578528000000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Mol. Biosci."],"DOI":"10.3389\/fmolb.2019.00151","type":"journal-article","created":{"date-parts":[[2020,1,9]],"date-time":"2020-01-09T10:23:01Z","timestamp":1578565381000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":19,"title":["Carbon Amendments Influence Composition and Functional Capacities of Indigenous Soil Microbiomes"],"prefix":"10.3389","volume":"6","author":[{"given":"Jos\u00e9 Pablo","family":"Dundore-Arias","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sarah C.","family":"Castle","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura","family":"Felice","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruth","family":"Dill-Macky","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Linda L.","family":"Kinkel","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2020,1,9]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1046\/j.1442-9993.2001.01070.x","article-title":"A new method for non-parametric multivariate analysis of variance","volume":"26","author":"Anderson","year":"2001","journal-title":"Austral. Ecol"},{"key":"B2","first-page":"349","article-title":"Strategies for quantitative isolation of Streptomyces from soil for studies of pathogen ecology and disease biocontrol","author":"Becker","year":"1999","journal-title":"Recent Research Developments in Microbiology, Research Signpost, Vol. 3 (Trivandrum)"},{"key":"B3","doi-asserted-by":"publisher","first-page":"136","DOI":"10.1016\/j.soilbio.2009.10.012","article-title":"Identifying the characteristics of organic soil amendments that suppress soilborne plant diseases","volume":"42","author":"Bonanomi","year":"2010","journal-title":"Soil Biol. Biochem."},{"key":"B4","doi-asserted-by":"publisher","first-page":"964","DOI":"10.1111\/j.1365-2435.2008.01404.x","article-title":"Soil carbon stocks in experimental mesocosms are dependent on the rate of labile carbon, nitrogen and phosphorous input to soil","volume":"22","author":"Bradford","year":"2008","journal-title":"Funct. Ecol"},{"key":"B5","doi-asserted-by":"publisher","first-page":"1243","DOI":"10.1038\/ismej.2009.68","article-title":"Exogenous glucosinolate produced by Arabidopsis thaliana has an impact on microbes in the rhizosphere and plant roots","volume":"3","author":"Bressan","year":"2009","journal-title":"ISME J."},{"key":"B6","doi-asserted-by":"publisher","first-page":"335","DOI":"10.1038\/nmeth.f.303","article-title":"QIIME allows analysis of high-throughput community sequencing data","volume":"7","author":"Caporaso","year":"2010","journal-title":"Nat. Methods"},{"key":"B7","doi-asserted-by":"publisher","first-page":"3073","DOI":"10.1073\/pnas.71.8.3073","article-title":"Interference competition and niche theory","volume":"71","author":"Case","year":"1974","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B8","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1023\/A:1020809400075","article-title":"Root exudates as mediators of mineral acquisition in low-nutrient environments","volume":"245","author":"Dakora","year":"2002","journal-title":"Plant Soil"},{"key":"B9","doi-asserted-by":"publisher","first-page":"5069","DOI":"10.1128\/AEM.03006-05","article-title":"Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB","volume":"72","author":"DeSantis","year":"2006","journal-title":"Appl. Environ. Microbiol."},{"key":"B10","doi-asserted-by":"publisher","first-page":"498","DOI":"10.3389\/fmicb.2019.00498","article-title":"Carbon amendments induce shifts in nutrient use, inhibitory,and resistance phenotypes among soilborne Streptomyces","volume":"10","author":"Dundore-Arias","year":"2019","journal-title":"Front. Microbiol"},{"key":"B11","doi-asserted-by":"publisher","first-page":"329","DOI":"10.1007\/s11104-016-2968-0","article-title":"Nutrient use preferences among soil Streptomyces suggest greater resource competition in monoculture than polyculture plant communities","volume":"409","author":"Essarioui","year":"2016","journal-title":"Plant Soil"},{"key":"B12","doi-asserted-by":"publisher","first-page":"157","DOI":"10.1007\/s00248-016-0907-5","article-title":"Plant community richness mediates inhibitory interactions and resource competition between Streptomyces and Fusarium populations in the rhizosphere","volume":"74","author":"Essarioui","year":"2017","journal-title":"Microb. Ecol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"89","DOI":"10.1007\/s11104-014-2243-1","article-title":"Soil Streptomyces communities in a prairie establishment reflect interactions between soil edaphic characteristics and plant host","volume":"386","author":"Felice","year":"2014","journal-title":"Plant Soil"},{"key":"B14","doi-asserted-by":"publisher","first-page":"1354","DOI":"10.1890\/05-1839","article-title":"Toward an ecological classification of soil bacteria","volume":"88","author":"Fierer","year":"2007","journal-title":"Ecology"},{"key":"B15","doi-asserted-by":"publisher","first-page":"626","DOI":"10.1073\/pnas.0507535103","article-title":"The diversity and biogeography of soil bacterial communities","volume":"103","author":"Fierer","year":"2006","journal-title":"Proc. Natl. Acad. Sci. U.S.A."},{"key":"B16","doi-asserted-by":"publisher","first-page":"1446","DOI":"10.3389\/fmicb.2016.01446","article-title":"Mineral vs. organic amendments: microbial community structure, activity and abundance of agriculturally relevant microbes are driven by long-term fertilization strategies","volume":"7","author":"Francioli","year":"2016","journal-title":"Front. Microbiol"},{"key":"B17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1038\/protex.2016.030","article-title":"An optimized protocol for high-throughput amplicon-based microbiome profiling","author":"Gohl","year":"","journal-title":"Nat. Protoc. Exchange"},{"key":"B18","doi-asserted-by":"publisher","first-page":"942","DOI":"10.1038\/nbt.3601","article-title":"Systematic improvement of amplicon marker gene methods for increased accuracy in microbiome studies","volume":"34","author":"Gohl","year":"","journal-title":"Nat. Biotechnol."},{"key":"B19","doi-asserted-by":"publisher","first-page":"2529","DOI":"10.3389\/fmicb.2017.02529","article-title":"Current insights into the role of rhizosphere bacteria in disease suppressive soils","volume":"8","author":"G\u00f3mez Exp\u00f3sito","year":"2017","journal-title":"Front. Microbiol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"68","DOI":"10.3389\/fsufs.2018.00068","article-title":"How valuable are organic amendments as tools for the phytomanagement of degraded soils? The knowns, known unknowns, and unknowns","volume":"2","author":"G\u00f3mez-Sagasti","year":"2018","journal-title":"Front. Sustain. Food Syst"},{"key":"B21","doi-asserted-by":"publisher","first-page":"494","DOI":"10.1101\/gr.112730.110","article-title":"Chimeric 16S rRNA sequence formation and detection in Sanger and 454-pyrosequenced PCR amplicons","volume":"21","author":"Haas","year":"2011","journal-title":"Genome Res"},{"key":"B22","doi-asserted-by":"crossref","first-page":"368","DOI":"10.1128\/AEM.32.3.368-375.1976","article-title":"Influences of soil acidity on Streptomyces populations inhabiting forest soils","volume":"32","author":"Hagedorn","year":"1976","journal-title":"Appl. Environ. Microbiol"},{"key":"B23","doi-asserted-by":"publisher","first-page":"1177","DOI":"10.1038\/ismej.2014.210","article-title":"Distinct soil microbial diversity under long-term organic and conventional farming","volume":"9","author":"Hartmann","year":"2015","journal-title":"ISME J."},{"key":"B24","doi-asserted-by":"publisher","first-page":"517","DOI":"10.2136\/sssaj1964.03615995002800040020x","article-title":"Contribution of organic matter and clay to soil cation-exchange capacity as affected by the pH of the saturating solution1","volume":"28","author":"Helling","year":"1964","journal-title":"Soil Sci. Soc. Am. J."},{"key":"B25","doi-asserted-by":"publisher","first-page":"397","DOI":"10.1007\/s11104-010-0428-9","article-title":"The effects of substrate composition, quantity, and diversity on microbial activity","volume":"335","author":"Hern\u00e1ndez","year":"2010","journal-title":"Plant Soil"},{"key":"B26","first-page":"270","article-title":"A method of assaying soils for numbers of actinomycetes antagonistic to fungal pathogens","volume":"49","author":"Herr","year":"1959","journal-title":"Phytopathology"},{"key":"B27","doi-asserted-by":"publisher","first-page":"6","DOI":"10.1093\/femsec\/fix006","article-title":"Revisiting life strategy concepts in environmental microbial ecology, FEMS Microbiol","volume":"93","author":"Ho","year":"2017","journal-title":"Ecol"},{"key":"B28","doi-asserted-by":"publisher","first-page":"27","DOI":"10.3389\/fpls.2014.00027","article-title":"Root traits and microbial community interactions in relation to phosphorus availability and acquisition, with particular reference to brassica","volume":"5","author":"Hunter","year":"2014","journal-title":"Front. Plant Sci."},{"key":"B29","doi-asserted-by":"publisher","first-page":"44382","DOI":"10.1038\/srep44382","article-title":"Linking the belowground microbial composition, diversity and activity to soilborne disease suppression and growth promotion of tomato amended with biochar","volume":"7","author":"Jaiswal","year":"2017","journal-title":"Sci. Rep."},{"key":"B30","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1038\/ismej.2013.175","article-title":"Sympatric inhibition and niche differentiation suggest alternative coevolutionary trajectories among Streptomycetes","volume":"8","author":"Kinkel","year":"2014","journal-title":"ISME J."},{"key":"B31","doi-asserted-by":"publisher","first-page":"731","DOI":"10.1007\/s10342-016-0968-5","article-title":"Functional diversity of soil microbial communities in boreal and temperate Scots pine forests","volume":"35","author":"Klimek","year":"2016","journal-title":"Eur. J. Forest Res."},{"key":"B32","doi-asserted-by":"publisher","first-page":"32","DOI":"10.1111\/j.1472-765X.2005.01727.x","article-title":"pH effects on 10 Streptomyces spp. growth and sporulation depend on nutrients","volume":"41","author":"Kontro","year":"2005","journal-title":"Lett. Appl. Microbiol."},{"key":"B33","doi-asserted-by":"publisher","first-page":"199","DOI":"10.1146\/annurev-phyto-080614-120357","article-title":"Soil health paradigms and implications for disease management","volume":"53","author":"Larkin","year":"2015","journal-title":"Annu. Rev. Phytopathol."},{"key":"B34","doi-asserted-by":"publisher","first-page":"2407","DOI":"10.1016\/j.soilbio.2008.05.021","article-title":"The influence of soil properties on the structure of bacterial and fungal communities across land-use types","volume":"40","author":"Lauber","year":"2008","journal-title":"Soil Biol. Biochem"},{"key":"B35","doi-asserted-by":"publisher","first-page":"3","DOI":"10.3389\/fmicb.2017.00003","article-title":"The potential of Streptomyces as biocontrol agents against the rice blast fungus, Magnaporthe oryzae (Pyricularia oryzae)","volume":"8","author":"Law","year":"2017","journal-title":"Front. Microbiol"},{"key":"B36","doi-asserted-by":"publisher","first-page":"1685","DOI":"10.1002\/clen.201600229","article-title":"Can soil pH be used to help explain soil organic carbon stocks?","volume":"44","author":"Liao","year":"2016","journal-title":"Clean\u2013Soil Air Water"},{"key":"B37","doi-asserted-by":"publisher","first-page":"e0121304","DOI":"10.1371\/journal.pone.0121304","article-title":"Bioorganic fertilizer enhances soil suppressive capacity against bacterial wilt of tomato","volume":"10","author":"Liu","year":"2015","journal-title":"PLoS ONE"},{"key":"B38","doi-asserted-by":"publisher","first-page":"7","DOI":"10.1016\/j.apsoil.2016.10.002","article-title":"Labile carbon input determines the direction and magnitude of the priming effect","volume":"109","author":"Liu","year":"2017","journal-title":"Appl. Soil Ecol."},{"key":"B39","doi-asserted-by":"publisher","first-page":"31","DOI":"10.1186\/1471-2105-13-31","article-title":"PANDAseq: paired-end assembler for illumina sequences","volume":"13","author":"Masella","year":"2012","journal-title":"BMC Bioinformatics"},{"key":"B40","doi-asserted-by":"publisher","first-page":"610","DOI":"10.1038\/ismej.2011.139","article-title":"An improved greengenes taxonomy with explicit ranks for ecological and evolutionary analyses of bacteria and archaea","volume":"6","author":"McDonald","year":"2012","journal-title":"ISME J"},{"key":"B41","doi-asserted-by":"publisher","first-page":"754","DOI":"10.1097\/01.ss.0000228366.17459.19","article-title":"Effect of organic amendments on soil pH and Al solubility and use of laboratory indices to predict their liming effect","volume":"171","author":"Naramabuye","year":"2006","journal-title":"Soil Sci."},{"key":"B42","unstructured":"OksanenJ.\n            BlanchetF. G.\n            FriendlyM.\n            KindtR.\n            LegendreP.\n            McGlinnD.\n          Vegan: Community Ecology Package. R package version 2.4\u201332017"},{"key":"B43","unstructured":"OksanenJ.\n            Guillaume BlanchetF.\n            KindtR.\n            LegendreP.\n            MinchinP. R.\n            O'HaraR. B.\n          Vegan: Community Ecology Package. R package version 2.3-02015"},{"key":"B44","doi-asserted-by":"publisher","first-page":"580","DOI":"10.1890\/05-0383","article-title":"Ecological consequences of carbon substrate identity and diversity in a laboratory study","volume":"87","author":"Orwin","year":"2006","journal-title":"Ecology"},{"key":"B45","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1094\/PHYTO-06-12-0129-R","article-title":"Pathogen variation and urea influence selection and success of Streptomyces mixtures in biological control","volume":"103","author":"Otto-Hanson","year":"2013","journal-title":"Phytopathology"},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1007\/s00248-019-01443-2","article-title":"Densities and inhibitory phenotypes among indigenous Streptomyces spp. vary across native and agricultural habitats","author":"Otto-Hanson","year":"2019","journal-title":"Microb. Ecol"},{"key":"B47","unstructured":"ViennaR Foundation for Statistical Computing.R: A Language and Environment for Statistical Computing.2014"},{"key":"B48","doi-asserted-by":"publisher","first-page":"3463","DOI":"10.1890\/10-0426.1","article-title":"Consistent effects of nitrogen fertilization on soil bacterial communities in contrasting systems","volume":"91","author":"Ramirez","year":"2010","journal-title":"Ecology"},{"key":"B49","doi-asserted-by":"publisher","first-page":"e2004248","DOI":"10.1371\/journal.pbio.2004248","article-title":"Modifying and reacting to the environmental pH can drive bacterial interactions","volume":"16","author":"Ratzke","year":"2018","journal-title":"PLoS Biol."},{"key":"B50","doi-asserted-by":"publisher","first-page":"1589","DOI":"10.1128\/AEM.02775-08","article-title":"Contrasting soil pH effects on fungal and bacterial growth suggest functional redundancy in carbon mineralization","volume":"75","author":"Rousk","year":"2009","journal-title":"Appl. Environ. Microbiol"},{"key":"B51","doi-asserted-by":"publisher","first-page":"1547","DOI":"10.1104\/pp.108.127613","article-title":"Root-secreted malic acid recruits beneficial soil bacteria","volume":"148","author":"Rudrappa","year":"2008","journal-title":"Plant Physiol."},{"key":"B52","doi-asserted-by":"publisher","first-page":"35","DOI":"10.1023\/A:1011820002779","article-title":"Suppression of the root-lesion nematode (Pratylenchus penetrans) in alfalfa by Streptomyces spp","volume":"235","author":"Samac","year":"2001","journal-title":"Plant Soil"},{"key":"B53","doi-asserted-by":"publisher","first-page":"442","DOI":"10.1038\/ja.2010.78","article-title":"Carbon source regulation of antibiotic production","volume":"63","author":"S\u00e1nchez","year":"2010","journal-title":"J. Antibiot."},{"key":"B54","doi-asserted-by":"publisher","first-page":"413","DOI":"10.1007\/s00248-008-9433-4","article-title":"Resource amendments influence density and competitive phenotypes of Streptomyces in soil","volume":"57","author":"Schlatter","year":"2009","journal-title":"Microb. Ecol."},{"key":"B55","doi-asserted-by":"publisher","first-page":"186","DOI":"10.1186\/s12862-015-0470-6","article-title":"Do tradeoffs structure antibiotic inhibition, resistance, and resource use among soil-borne Streptomyces?","volume":"15","author":"Schlatter","year":"2015","journal-title":"BMC Evol. Biol"},{"key":"B56","doi-asserted-by":"publisher","first-page":"1481","DOI":"10.1016\/S0038-0717(01)00057-800057-8","article-title":"Shifts in substrate utilization potential and structure of soil microbial communities in response to carbon substrates","volume":"33","author":"Schutter","year":"2001","journal-title":"Soil Biol. Biochem"},{"key":"B57","doi-asserted-by":"publisher","first-page":"862","DOI":"10.1111\/j.1574-6976.2011.00313.x","article-title":"Streptomyces as symbionts: an emerging and widespread theme?","volume":"36","author":"Seipke","year":"2012","journal-title":"FEMS Microbiol. Rev."},{"key":"B58","doi-asserted-by":"publisher","first-page":"2751","DOI":"10.1128\/AEM.00247-16","article-title":"Regional similarities and consistent patterns of local variation in beach sand bacterial communities throughout the Northern Hemisphere","volume":"82","author":"Staley","year":"2016","journal-title":"Appl. Environ. Microbiol"},{"key":"B59","doi-asserted-by":"publisher","first-page":"253","DOI":"10.3389\/fmicb.2013.00253","article-title":"Plant soil interactions alter carbon cycling in an upland grassland soil","volume":"4","author":"Thomson","year":"2013","journal-title":"Front. Microbiol"},{"key":"B60","doi-asserted-by":"publisher","first-page":"14","DOI":"10.1094\/PBIOMES-05-17-0024-R","article-title":"Cropping history effects on pathogen suppressive and signaling dynamics in Streptomyces communities Phytobiomes J","volume":"2","author":"Vaz Jauri","year":"2018"},{"key":"B61","doi-asserted-by":"publisher","first-page":"119","DOI":"10.1093\/femsec\/fiw119","article-title":"Streptomyces as a plant's best friend?","volume":"92","author":"Viaene","year":"2016","journal-title":"FEMS Microbiol. Ecol."},{"key":"B62","first-page":"13","article-title":"pH and lime requirement","volume-title":"Recommended Chemical Soil Test Procedures for the North Central Region.","author":"Watson","year":"1988"},{"key":"B63","unstructured":"WeiT.\n            SimkoV.\n          ViennaR Foundation for Statistical Computingcorrplot: Visualization of a Correlation Matrix. R package version 0.77.2016"},{"key":"B64","doi-asserted-by":"publisher","first-page":"271","DOI":"10.1007\/s11104-004-0300-x","article-title":"Green manures and crop sequences influence alfalfa root rot and pathogen inhibitory activity among soil-borne Streptomycetes","volume":"268","author":"Wiggins","year":"","journal-title":"Plant Soil"},{"key":"B65","doi-asserted-by":"publisher","first-page":"178","DOI":"10.1094\/PHYTO-95-0178","article-title":"Green manures and crop sequences influence potato diseases and pathogen inhibitory activity of indigenous Streptomycetes","volume":"95","author":"Wiggins","year":"","journal-title":"Phytopathology"},{"key":"B66","doi-asserted-by":"publisher","first-page":"40093","DOI":"10.1038\/srep40093","article-title":"pH is the primary determinant of the bacterial community structure in agricultural soils impacted by polycyclic aromatic hydrocarbon pollution","volume":"7","author":"Wu","year":"2017","journal-title":"Sci. Rep."},{"key":"B67","doi-asserted-by":"publisher","first-page":"285","DOI":"10.1006\/bcon.2001.1015","article-title":"Biological control of Phytophthora root rots on alfalfa and soybean with Streptomyces","volume":"23","author":"Xiao","year":"2002","journal-title":"Biol. Control"},{"key":"B68","doi-asserted-by":"publisher","first-page":"395","DOI":"10.1007\/s00248-014-0530-2","article-title":"Soil pH determines microbial diversity and composition in the park grass experiment","volume":"69","author":"Zhalnina","year":"2015","journal-title":"Microb. Ecol"},{"key":"B69","doi-asserted-by":"publisher","first-page":"450","DOI":"10.1094\/PHYTO.1998.88.5.450","article-title":"Compost and compost water extract-induced systemic acquired resistance in cucumber and Arabidopsis","volume":"88","author":"Zhang","year":"1998","journal-title":"Phytopathology"},{"key":"B70","doi-asserted-by":"publisher","first-page":"1325","DOI":"10.3389\/fmicb.2017.01325","article-title":"Fertilization shapes bacterial community structure by alteration of soil pH","volume":"8","author":"Zhang","year":"2017","journal-title":"Front. Microbiol"}],"container-title":["Frontiers in Molecular Biosciences"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmolb.2019.00151\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,1,9]],"date-time":"2020-01-09T10:23:06Z","timestamp":1578565386000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/article\/10.3389\/fmolb.2019.00151\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020,1,9]]},"references-count":70,"alternative-id":["10.3389\/fmolb.2019.00151"],"URL":"https:\/\/doi.org\/10.3389\/fmolb.2019.00151","relation":{},"ISSN":["2296-889X"],"issn-type":[{"value":"2296-889X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2020,1,9]]},"article-number":"151"}}