{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,19]],"date-time":"2026-08-19T19:48:54Z","timestamp":1787168934756,"version":"build-2736575974"},"reference-count":61,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T00:00:00Z","timestamp":1777593600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100019196","name":"Sustainable Agriculture Research and Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100019196","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100005825","name":"National Institute of Food and Agriculture","doi-asserted-by":"publisher","award":["GSC2023039, CDFA 10.170, Hatch #9647-1"],"award-info":[{"award-number":["GSC2023039, CDFA 10.170, Hatch #9647-1"]}],"id":[{"id":"10.13039\/100005825","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Legume cover crops are increasingly incorporated into sustainable production systems, yet their influence on rhizosphere microbial communities remains poorly characterized, particularly for underutilized warm-season species. In this study, we investigated rhizosphere bacterial communities associated with cowpea (\n                    <jats:italic>Vigna unguiculata<\/jats:italic>\n                    ), tepary bean (\n                    <jats:italic>Phaseolus acutifolius<\/jats:italic>\n                    ), and sunn hemp (\n                    <jats:italic>Crotalaria juncea<\/jats:italic>\n                    ) in an organic production system using 16S rRNA amplicon sequencing and compared them with fallow soils. All legume species were associated with shifts in bacterial community composition relative to fallow soil, with increased relative abundance of copiotrophic taxa such as\n                    <jats:italic>Proteobacteria<\/jats:italic>\n                    , while fallow soils were dominated by oligotrophic groups within\n                    <jats:italic>Actinobacteriota<\/jats:italic>\n                    . Distinct species-specific recruitment patterns were observed: tepary bean rhizospheres showed higher relative abundance of\n                    <jats:italic>Rhizobiales<\/jats:italic>\n                    , associated with taxa involved in biological nitrogen fixation, whereas cowpea and sunn hemp supported bacterial groups linked to organic matter turnover and plant growth. Weighted UniFrac analyses indicated clear separation between cover-cropped and fallow soils, accounting for approximately 54% of community variation. Functional predictions using PICRUSt2 suggested representation of pathways related to central carbon metabolism, amino acid biosynthesis, and siderophore production under legume rhizospheres. Predicted pathways associated with nitrogen metabolism also tended to be more represented under cover crops, although no pathways remained significant after false discovery rate correction. Overall, these findings indicate that summer legume cover crops are associated with shifts in rhizosphere bacterial communities and predicted functional potential relative to fallow soils. These findings highlight the potential of species selection in shaping rhizosphere microbial communities in organic production systems and provide a foundation for future studies investigating microbial processes associated with cover cropping.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1790810","type":"journal-article","created":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T15:50:45Z","timestamp":1777650645000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Functional and taxonomic shifts in rhizosphere microbiomes of summer legume cover crops"],"prefix":"10.3389","volume":"17","author":[{"given":"Sri Kiran","family":"Reddy Alla","sequence":"first","affiliation":[{"name":"Department of Horticultural Sciences, Texas A&M University","place":["College Station, TX, United States"]},{"name":"Texas A&M AgriLife Research and Extension","place":["Uvalde, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Vijay","family":"Joshi","sequence":"additional","affiliation":[{"name":"Department of Horticultural Sciences, Texas A&M University","place":["College Station, TX, United States"]},{"name":"Texas A&M AgriLife Research and Extension","place":["Uvalde, TX, United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,5,1]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1130969","article-title":"Diversity and function of soybean rhizosphere microbiome under nature farming","volume":"14","author":"Agyekum","year":"2023","journal-title":"Front. Microbiol."},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2013.00165","article-title":"The rhizosphere revisited: Root microbiomics","volume":"4","author":"Bakker","year":"2013","journal-title":"Front. Plant Sci."},{"key":"B3","doi-asserted-by":"publisher","first-page":"489","DOI":"10.1007\/s11104-021-04963-4","article-title":"Hot or not? Connecting rhizosphere hotspots to total soil respiration","volume":"464","author":"Becker","year":"2021","journal-title":"Plant Soil"},{"key":"B4","doi-asserted-by":"publisher","first-page":"478","DOI":"10.1016\/j.tplants.2012.04.001","article-title":"The rhizosphere microbiome and plant health","volume":"17","author":"Berendsen","year":"2012","journal-title":"Trends Plant Sci."},{"key":"B5","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1017\/S1742170517000278","article-title":"A review of economic considerations for cover crops as a conservation practice","volume":"34","author":"Bergtold","year":"2017","journal-title":"Renewable Agric. Food Syst."},{"key":"B6","doi-asserted-by":"publisher","first-page":"2449","DOI":"10.2134\/agronj15.0086","article-title":"Cover crops and ecosystem services: Insights from studies in temperate soils","volume":"107","author":"Blanco-Canqui","year":"2015","journal-title":"Agron. J."},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.3389\/fcimb.2025.1517208","article-title":"Standardization of 16S rRNA gene sequencing using nanopore long-read technology","author":"Butler","year":"2025","journal-title":"Front. Cell. Infect. Microbiol"},{"key":"B8","doi-asserted-by":"publisher","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: High-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat. Methods"},{"key":"B9","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":"B10","doi-asserted-by":"publisher","DOI":"10.1016\/j.apsoil.2023.105012","article-title":"Pinpointing the distinctive impacts of ten cover crop species on the resident and active fractions of the soil microbiome","volume":"190","author":"Cazzaniga","year":"2023","journal-title":"Appl. Soil Ecol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"e55731","DOI":"10.1371\/journal.pone.0055731","article-title":"Root exudation of phytochemicals in arabidopsis follows specific patterns that are developmentally programmed and correlate with soil microbial functions","volume":"8","author":"Chaparro","year":"2013","journal-title":"PloS One"},{"key":"B12","article-title":"Managing cover crops profitably","volume-title":"Sustainable Agriculture Research and Education (SARE) Program Handbook Series, Book 9","author":"Clark","year":"2007"},{"key":"B13","doi-asserted-by":"publisher","first-page":"9","DOI":"10.1038\/s41579-024-01079-1","article-title":"Harnessing the plant microbiome for sustainable crop production","volume":"23","author":"Compant","year":"2024","journal-title":"Nat. Rev. Microbiol"},{"key":"B14","doi-asserted-by":"publisher","first-page":"3472","DOI":"10.1038\/s41598-022-06860-x","article-title":"Genetically related cowpea genotypes exhibit similar bacterial communities in the rhizosphere","volume":"12","author":"de Albuquerque","year":"2022","journal-title":"Sci. Rep."},{"key":"B15","doi-asserted-by":"publisher","first-page":"672295","DOI":"10.1101\/672295","article-title":"PICRUSt2: An improved and extensible approach for metagenome inference","author":"Douglas","year":"2019","journal-title":"bioRxiv"},{"key":"B16","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1016\/j.agee.2015.07.025","article-title":"Plant-specific effects of sunn hemp (crotalaria juncea) and sudex (sorghum bicolor\u00d7Sorghum bicolor var. Sudanense) on the abundance and composition of soil microbial community","volume":"213","author":"Eo","year":"2015","journal-title":"Agric. Ecosyst. Environ."},{"key":"B17","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/s11427-024-2876-0","article-title":"Root exudates and microbial metabolites: Signals and nutrients in plantmicrobe interactions","volume":"68","author":"Fan","year":"2025","journal-title":"Sci. China Life Sci"},{"key":"B18","doi-asserted-by":"publisher","first-page":"1915","DOI":"10.1038\/s41396-020-0648-9","article-title":"Variation in rhizosphere microbial communities and its association with the symbiotic efficiency of rhizobia in soybean","volume":"14","author":"Han","year":"2020","journal-title":"ISME. J."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-025-65829-2","article-title":"Rhizosheath-inhabiting Massilia are linked to heterosis in roots of maize","volume":"16","author":"He","year":"2025","journal-title":"Nat. Commun"},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.3389\/fsufs.2020.619676","article-title":"Rhizobia as a source of plant growth-promoting molecules: Potential applications and possible operational mechanisms","volume":"4","author":"Jaiswal","year":"2021","journal-title":"Front. Sustain. Food Syst."},{"key":"B21","doi-asserted-by":"publisher","DOI":"10.1016\/j.soilbio.2019.107701","article-title":"Do cover crops benefit soil microbiome? A meta-analysis of current research","volume":"142","author":"Kim","year":"2020","journal-title":"Soil Biol. Biochem."},{"key":"B22","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1016\/j.soilbio.2019.05.011","article-title":"Rhizosphere size and shape: temporal dynamics and spatial stationarity","volume":"135","author":"Kuzyakov","year":"2019","journal-title":"Soil Biology and Biochemistry"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.1016\/j.apsoil.2021.104166","article-title":"Cover crops shape the soil bacterial community in a tropical soil under no-till","volume":"168","author":"Leite","year":"2021","journal-title":"Appl. Soil Ecol."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2016.02064","article-title":"Cowpea nodules harbor non-rhizobial bacterial communities that are shaped by soil type rather than plant genotype","volume":"7","author":"Leite","year":"2017","journal-title":"Front. Plant Sci."},{"key":"B25","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2021.772420","article-title":"Rhizosphere microbiome: The emerging barrier in plant-pathogen interactions","volume":"12","author":"Li","year":"2021","journal-title":"Front. Microbiol."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.1128\/spectrum.01673-25","article-title":"QIIME2 enhances multi-amplicon sequencing data analysis: A standardized pipeline for 16S rRNA profiling","volume":"13","author":"Licata","year":"2025","journal-title":"Microbiol. Spectr"},{"key":"B27","doi-asserted-by":"publisher","first-page":"836","DOI":"10.1038\/s41467-022-28448-9","article-title":"Rhizosphere bacteriome structure and functions","volume":"13","author":"Ling","year":"2022","journal-title":"Nat. Commun."},{"key":"B28","doi-asserted-by":"publisher","first-page":"33","DOI":"10.3390\/plants5030033","article-title":"The role of flavonoids in nodulation host-range specificity: An update","volume":"5","author":"Liu","year":"2016","journal-title":"Plants"},{"key":"B29","doi-asserted-by":"publisher","first-page":"342","DOI":"10.1038\/s41467-022-28034-z","article-title":"Microbiome differential abundance methods produce different results across 38 datasets","volume":"13","author":"Nearing","year":"2022","journal-title":"Nat. Commun."},{"key":"B30","doi-asserted-by":"crossref","first-page":"193","DOI":"10.1007\/978-981-95-2294-1_10","article-title":"Microbiomes: Exploring their potentials and developing strategies for sustainable legume production","volume-title":"Meta-omics in crop improvement: Volume I: Methods and approaches","author":"Nysanth","year":"2025"},{"key":"B31","first-page":"1","article-title":"Package \u2018vegan.\u2019","author":"Oksanen","year":"2013"},{"key":"B32","doi-asserted-by":"publisher","first-page":"10.1099\/ijsem.0.005056","DOI":"10.1099\/ijsem.0.005056","article-title":"Valid publication of the names of forty-two phyla of prokaryotes","volume":"71","author":"Oren","year":"2021","journal-title":"International Journal of Systematic and Evolutionary Microbiology"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1093\/ismejo\/wrae223","article-title":"Probiotic model for studying rhizosphere interactions of root exudates and the functional microbiome","volume":"18","author":"Pang","year":"2024","journal-title":"ISME. J."},{"key":"B34","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2023.1163832","article-title":"Recruitment of the rhizo-microbiome army: Assembly determinants and engineering of the rhizosphere microbiome as a key to unlocking plant potential","volume":"14","author":"Park","year":"2023","journal-title":"Front. Microbiol."},{"key":"B35","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1007\/bf03179980","article-title":"The contributions of nitrogen-fixing crop legumes to the productivity of agricultural systems","volume":"48","author":"Peoples","year":"2009","journal-title":"Symbiosis"},{"key":"B36","doi-asserted-by":"publisher","first-page":"2244","DOI":"10.1038\/ismej.2017.85","article-title":"Linking rhizosphere microbiome composition of wild and domesticated phaseolus vulgaris to genotypic and root phenotypic traits","volume":"11","author":"P\u00e9rez-Jaramillo","year":"2017","journal-title":"ISME. J."},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1128\/msystems.00973-21","article-title":"Whole-genome duplication and host genotype affect rhizosphere microbial communities","volume":"7","author":"Ponsford","year":"2022","journal-title":"mSystems"},{"key":"B38","doi-asserted-by":"crossref","DOI":"10.1002\/plr2.20322","article-title":"Release of tepary bean cultivar \u2018USDA Fortuna \u2019with improved disease and insect resistance, seed size, and culinary quality.","volume":"18","author":"Porch","year":"2024","journal-title":"Journal of Plant Registrations"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-47159-xnysanth","article-title":"Microbiomes: Exploring their potentials and developing strategies for sustainable legume production","author":"Qiao","year":"2024","journal-title":"Nat. Commun"},{"key":"B40","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-47159-x","article-title":"Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification","volume":"15","author":"Qiao","year":"20224","journal-title":"Nat. Commun"},{"key":"B41","doi-asserted-by":"publisher","first-page":"347","DOI":"10.1111\/omi.12434","article-title":"Critical review of 16S rRNA gene sequencing workflow in microbiome studies: From primer selection to advanced data analysis","volume":"38","author":"Regueira-Iglesias","year":"2023","journal-title":"Mol. Oral. Microbiol."},{"key":"B42","doi-asserted-by":"publisher","DOI":"10.3389\/fsufs.2021.668195","article-title":"From microns to meters: Exploring advances in legume microbiome diversity for agroecosystem benefits","volume":"5","author":"Schaedel","year":"2021","journal-title":"Front. Sustain. Food Syst."},{"key":"B43","doi-asserted-by":"crossref","first-page":"R60","DOI":"10.1186\/gb-2011-12-6-r60","article-title":"Metagenomic biomarker discovery and explanation","volume":"12","author":"Segata","year":"2011","journal-title":"Genome Biology"},{"key":"B44","doi-asserted-by":"publisher","first-page":"183","DOI":"10.1186\/s40168-024-01886-x","article-title":"Cover crop root exudates impact soil microbiome functional trajectories in agricultural soils","volume":"12","author":"Seitz","year":"2024","journal-title":"Microbiome"},{"key":"B45","doi-asserted-by":"publisher","first-page":"76","DOI":"10.1046\/j.1365-3180.2002.00264.x","article-title":"Effect of tillage, cover crop and crop rotation on the composition of weed flora in a sandy soil","volume":"42","author":"Shrestha","year":"2002","journal-title":"Weed. Res."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.1016\/j.jafr.2023.100938","article-title":"Moth bean and tepary bean as green nitrogen sources in intensive winter wheat cropping systems","volume":"15","author":"Singh","year":"2024","journal-title":"J. Agric. Food Res."},{"key":"B47","doi-asserted-by":"publisher","first-page":"46","DOI":"10.1186\/s40168-020-00815-y","article-title":"Inference-based accuracy of metagenome prediction tools varies across sample types and functional categories","volume":"8","author":"Sun","year":"2020","journal-title":"Microbiome"},{"key":"B48","doi-asserted-by":"publisher","DOI":"10.1093\/jpe\/rtae092","article-title":"Depth-dependent effects of leguminous crops on soil nitrogen-fixing microbial communities","volume":"17","author":"Tao","year":"2024","journal-title":"J. Plant Ecol."},{"key":"B49","doi-asserted-by":"publisher","first-page":"1670","DOI":"10.2135\/cropsci2016.09.0746","article-title":"Early metabolic and photosynthetic responses to drought stress in common and tepary bean","volume":"57","author":"Traub","year":"2017","journal-title":"Crop Sci."},{"key":"B50","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pbio.3002604","article-title":"Identifying causes and consequences of rhizosphere microbiome heritability","volume":"22","author":"Wagner","year":"2024","journal-title":"PloS Biol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"124","DOI":"10.1186\/s40168-024-01839-4","article-title":"Lateral root-enriched Massilia associated with plant flowering in maize","volume":"12","author":"Wang","year":"2024","journal-title":"Microbiome"},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.3390\/app15137127","article-title":"A review of plant-microbe interactions in the rhizosphere and the role of root exudates in microbiome engineering","volume":"15","author":"Wankhade","year":"2025","journal-title":"Appl. Sci"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1664417","article-title":"Microbial communities and their association with soil health indicators under cover crop diversification","author":"Wooliver","year":"2025","journal-title":"Front. Microbiol"},{"key":"B54","doi-asserted-by":"publisher","DOI":"10.1093\/bioinformatics\/btaf269","article-title":"PICRUSt2-SC: an update to the reference database used for functional prediction within PICRUSt2","volume":"41","author":"Wright","year":"2025","journal-title":"Bioinformatics"},{"key":"B55","doi-asserted-by":"publisher","first-page":"1641","DOI":"10.1111\/mec.14027","article-title":"Two cultivated legume plants reveal the enrichment process of the microbiome in the rhizocompartments","volume":"26","author":"Xiao","year":"2017","journal-title":"Mol. Ecol."},{"key":"B56","doi-asserted-by":"publisher","DOI":"10.1093\/femsre\/fuaf008","article-title":"Plant exudates-driven microbiome recruitment and assembly facilitates plant health management","volume":"49","author":"Yang","year":"2025","journal-title":"FEMS Microbiol. Rev"},{"key":"B57","doi-asserted-by":"publisher","first-page":"5659","DOI":"10.1021\/acs.jafc.3c09160","article-title":"Deciphering microbial community and nitrogen fixation in the legume rhizosphere","volume":"72","author":"Yang","year":"2024","journal-title":"J. Agric. Food. Chem."},{"key":"B58","doi-asserted-by":"publisher","first-page":"143","DOI":"10.1016\/s0168-1656<(>01<)>00342-x","article-title":"Rhizobia from wild legumes: Diversity, taxonomy, ecology, and biotechnology","volume":"91","author":"Zahran","year":"2001","journal-title":"J. Biotechnol."},{"key":"B59","doi-asserted-by":"publisher","DOI":"10.3390\/agronomy15122691","article-title":"Cover-crop types and soil depths shape soil microbial diversity and enhance network complexity","author":"Zhang","year":"2025","journal-title":"Agronomy"},{"key":"B60","doi-asserted-by":"publisher","first-page":"606","DOI":"10.1111\/nph.18409","article-title":"The spatial distribution of rhizosphere microbial activities under drought: water availability is more important than root-hair-controlled exudation","volume":"236","author":"Zhang","year":"2022","journal-title":"New Phytol."},{"key":"B61","doi-asserted-by":"crossref","DOI":"10.3389\/fmicb.2021.766364","article-title":"Advances in metagenomics and its application in environmental microorganisms","volume":"12","author":"Zhang","year":"2021","journal-title":"Front. Microbiol."}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1790810\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,1]],"date-time":"2026-05-01T15:50:49Z","timestamp":1777650649000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1790810\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,5,1]]},"references-count":61,"alternative-id":["10.3389\/fpls.2026.1790810"],"URL":"https:\/\/doi.org\/10.3389\/fpls.2026.1790810","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,5,1]]},"article-number":"1790810"}}