{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T18:55:49Z","timestamp":1790016949545,"version":"4.0.1"},"reference-count":53,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2025,2,10]],"date-time":"2025-02-10T00:00:00Z","timestamp":1739145600000},"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. Microbiol."],"abstract":"<jats:p>The alternating planting of corn and soybeans is regarded as an effective strategy in addressing the challenges faced in soybean cultivation. However, the precise mechanisms that control the bacterial microbiome in soybean roots in the soil, particularly in continuous cropping and rotational corn\u2013soybean farming rotations, are remain unclear. This study employed both field and pot positioning experiments, using high-throughput and generic metabolomics sequencing techniques to explore the dynamics between soybean plants, root microflora, and soil metabolites, especially in the context of continuous cropping and fluctuating corn\u2013soybean crop rotation. The process that included rotating corn soybeans significantly enhanced their grain yield, dry weight, soil nitrogen concentration, urease activity, as well as the accumulation of nitrogen, phosphorus, and potassium in various plant organs, compared to the traditional practice of continuous soybean cultivation. There is a significant reduction in the transit of bacterial operational taxonomic units (OTUs) from the rhizosphere to the endosphere through rhizoplane. The number of bacterial OTUs that are consumed and enriched on rhizoplane is greater than those that are enriched and absorbed in the endosphere. Continuous cropping practices significantly boost Burkholderiales, whereas chloroplast microorganisms significantly improve crop rotation techniques. Soil environmental factors, such as urease and accessible phosphorus, are crucial in establishing the relative prevalence of Rhodanobacter and other bacterial groups. Soil metabolites, such as benzyl alcohol, show a positive correlation with Cyanobacteria, while acidic compounds, such as D-arabinitol, are positively linked with Burkholderiales. This study indicates that the rotation of corn and soybean crops facilitates the growth of soybeans, increases nutrient accumulation in both plants and soil, enhances the presence of beneficial bacteria, and improves soybean yields.<\/jats:p>","DOI":"10.3389\/fmicb.2025.1534809","type":"journal-article","created":{"date-parts":[[2025,2,10]],"date-time":"2025-02-10T06:49:59Z","timestamp":1739170199000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":4,"title":["Effects of continuous cropping on bacterial community diversity and soil metabolites in soybean roots"],"prefix":"10.3389","volume":"16","author":[{"given":"Liwei","family":"An","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xinnan","family":"Lu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pengyu","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jiayao","family":"Sun","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baiming","family":"Cong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Rula","family":"Sa","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dexin","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2025,2,10]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1290","DOI":"10.3390\/microorganisms9061290","article-title":"Genome-wide metabolic reconstruction of the synthesis of Polyhydroxyalkanoates from sugars and fatty acids by Burkholderia Sensu Lato species","volume":"9","author":"Alvarez-Santullano","year":"2021","journal-title":"Microorganisms"},{"key":"ref2","doi-asserted-by":"publisher","first-page":"26","DOI":"10.11829\/j.issn.1001-0629.2023-0199","article-title":"Analysis of soil-specific metabolites in uncultivated cherry orchard based on metabolomics","volume":"41","author":"Baixia","year":"2024","journal-title":"Grassl. Sci."},{"key":"ref3","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-017-0241-2","article-title":"Structural variability and niche differentiation in the rhizosphere and endosphere bacterial microbiome of field-grown poplar trees","volume":"5","author":"Beckers","year":"2017","journal-title":"Microbiome"},{"key":"ref4","doi-asserted-by":"publisher","first-page":"591","DOI":"10.2136\/sssaj1974.03615995003800040021x","article-title":"Microbial growth rate in glucose-amended soil","volume":"38","author":"Behera","year":"1974","journal-title":"Soil Sci. Soc. Am. J."},{"key":"ref5","doi-asserted-by":"crossref","first-page":"17","DOI":"10.1385\/1-59259-193-0:017","article-title":"Protein stabilization by naturally occurring osmolytes","volume-title":"Protein structure, stability, and folding","author":"Bolen","year":"2001"},{"key":"ref6","doi-asserted-by":"publisher","DOI":"10.1101\/2021.09.11.459883","article-title":"Vegetation structure determines cyanobacterial communities during soil development across global biomes","author":"Cano-D\u00edaz","year":"2021","journal-title":"bioRxiv"},{"key":"ref7","doi-asserted-by":"publisher","first-page":"4516","DOI":"10.1073\/pnas.1000080107","article-title":"Global patterns of 16S rRNA diversity at a depth of millions of sequences per sample","volume":"108","author":"Caporaso","year":"2011","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref8","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/s41586-020-2185-0","article-title":"A plant genetic network for preventing dysbiosis in the phyllosphere","volume":"580","author":"Chen","year":"2020","journal-title":"Nature"},{"key":"ref9","doi-asserted-by":"publisher","first-page":"E911","DOI":"10.1073\/pnas.1414592112","article-title":"Structure, variation, and assembly of the root-associated microbiomes of rice","volume":"112","author":"Edwards","year":"2015","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref10","doi-asserted-by":"publisher","first-page":"97","DOI":"10.1007\/s11104-022-05620-0","article-title":"Composition of prokaryotic and viral community in continuously cropped field of Coptis chinensis Franch","volume":"481","author":"Fan","year":"2022","journal-title":"Plant Soil"},{"key":"ref11","doi-asserted-by":"crossref","first-page":"249","DOI":"10.5772\/61291","article-title":"Actinobacteria as plant growth promoting rhizobacteria","volume-title":"Actinobacteria-basis and biotechnological application","author":"Franco-Correa","year":"2016"},{"key":"ref12","doi-asserted-by":"publisher","first-page":"380","DOI":"10.1111\/ppl.12188","article-title":"Photosystem I shows a higher tolerance to sorbitol-induced osmotic stress than photosystem II in the intertidal macro-algae Ulva prolifera (Chlorophyta)","volume":"152","author":"Gao","year":"2014","journal-title":"Physiol. Plant."},{"key":"ref13","doi-asserted-by":"publisher","first-page":"1","DOI":"10.6064\/2012\/963401","article-title":"Plant growth-promoting bacteria: mechanisms and applications","volume":"2012","author":"Glick","year":"2012","journal-title":"Scientifica"},{"key":"ref14","doi-asserted-by":"publisher","first-page":"1039","DOI":"10.1126\/science.1153475","article-title":"Microbial biogeography: from taxonomy to traits","volume":"320","author":"Green","year":"2008","journal-title":"Science"},{"key":"ref15","doi-asserted-by":"publisher","first-page":"146140","DOI":"10.1016\/j.scitotenv.2021.146140","article-title":"Legacy effects of temporary grassland in annual crop rotation on soil ecosystem services","volume":"780","author":"Hoeffner","year":"2021","journal-title":"Sci. Total Environ."},{"key":"ref16","doi-asserted-by":"publisher","first-page":"e86269","DOI":"10.1371\/journal.pone.0086269","article-title":"Glycerol affects root development through regulation of multiple pathways in Arabidopsis","volume":"9","author":"Hu","year":"2014","journal-title":"PLoS One"},{"key":"ref17","doi-asserted-by":"publisher","first-page":"e01776","DOI":"10.1128\/spectrum.01776-22","article-title":"Biological control of melon continuous cropping obstacles: weakening the negative effects of the vicious cycle in continuous cropping soil","volume":"10","author":"Ku","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref18","doi-asserted-by":"publisher","first-page":"4837","DOI":"10.1021\/es203683v","article-title":"Bacterial production of organic acids enhances H2O2-dependent iodide oxidation","volume":"46","author":"Li","year":"2012","journal-title":"Environ. Sci. Technol."},{"key":"ref19","doi-asserted-by":"publisher","first-page":"210","DOI":"10.11829\/j.issn.1041-0679.2009-0029","article-title":"Detection of phenolic acids in corn straw decomposition liquid and their allelopathic effects on soil-borne pathogens of wheat","volume":"25","author":"Liang","year":"2009","journal-title":"Chinese Agricult. Bull."},{"key":"ref20","doi-asserted-by":"publisher","first-page":"299","DOI":"10.1016\/bs.agron.2022.02.007","article-title":"Diversifying crop rotations enhances agroecosystem services and resilience","volume":"173","author":"Liu","year":"2022","journal-title":"Adv. Agron."},{"key":"ref21","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1007\/s11104-023-06282-2","article-title":"Effects of intercropping corn with potatoes on rhizosphere soil enzyme activity and aggregate stability","volume":"30","author":"Lu","year":"2023","journal-title":"Soil Water Conserv. Res."},{"key":"ref22","doi-asserted-by":"publisher","first-page":"23","DOI":"10.1007\/s11104-019-04177-9","article-title":"Long-term rice-rice-rape rotation optimizes 1, 2-benzenediol concentration in rhizosphere soil and improves nitrogen-use efficiency and rice growth","volume":"445","author":"Lu","year":"2019","journal-title":"Plant Soil"},{"key":"ref23","doi-asserted-by":"publisher","first-page":"1877","DOI":"10.13287\/j.1001-9332.201607.028","article-title":"Characteristics of phosphate-solubilizing microbial community in the soil of poplar plantations under successive-planting and rotation.The","volume":"27","author":"Ma","year":"2016","journal-title":"J. Appl. Ecol."},{"key":"ref24","doi-asserted-by":"publisher","first-page":"926","DOI":"10.1016\/j.tree.2018.09.002","article-title":"Microbiomes as metacommunities: understanding host-associated microbes through metacommunity ecology","volume":"33","author":"Miller","year":"2018","journal-title":"Trends Ecol. Evol."},{"key":"ref25","doi-asserted-by":"publisher","first-page":"e00340-15","DOI":"10.1128\/mBio.00340-15","article-title":"The glycerol-dependent metabolic persistence of Pseudomonas putida KT2440 reflects the regulatory logic of the GlpR repressor","volume":"6","author":"Nikel","year":"2015","journal-title":"MBio"},{"key":"ref26","doi-asserted-by":"publisher","first-page":"128875","DOI":"10.1016\/j.jhazmat.2022.128875","article-title":"A comprehensive review of recent research concerning the role of low molecular weight organic acids on the fate of organic pollutants in soil","volume":"434","author":"Pe\u00f1a","year":"2022","journal-title":"J. Hazard. Mater."},{"key":"ref27","doi-asserted-by":"publisher","first-page":"73","DOI":"10.1139\/cjm-2013-0792","article-title":"Soybean fungal soil-borne diseases: a parameterfor measuring the effect of agricultural intensification on soil health","volume":"60","author":"P\u00e9rez-Brand\u00e1n","year":"2014","journal-title":"Can. J. Microbiol."},{"key":"ref28","doi-asserted-by":"publisher","first-page":"3940","DOI":"10.1038\/s41598-017-04213-7","article-title":"The variation in the rhizosphere microbiome of cotton with soil type, genotype and developmental stage","volume":"7","author":"Qiao","year":"2017","journal-title":"Sci. Rep."},{"key":"ref29","volume-title":"Research on the mechanism of corn\/Peanut in alleviating Peanut continuous cropping obstacles","author":"Qingkai","year":"2020"},{"key":"ref30","doi-asserted-by":"publisher","first-page":"536","DOI":"10.1007\/978-90-481-2857-0","article-title":"The rhizosphere: a playground and battlefield for soilborne pathogens and beneficial microorganisms","volume":"104","author":"Raaijmakers","year":"2010","journal-title":"Rhizosphere"},{"key":"ref31","doi-asserted-by":"publisher","first-page":"638326","DOI":"10.3389\/fmicb.2021.638326","article-title":"Changes in soil microbial activity, bacterial community composition and function in a long-term continuous soybean cropping system after maize insertion and fertilization","volume":"12","author":"Rao","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref32","doi-asserted-by":"publisher","first-page":"464","DOI":"10.1111\/2041-210X.12028","article-title":"Ecometabolomics: optimized NMR-based method","volume":"4","author":"Rivas-Ubach","year":"2013","journal-title":"Methods Ecol. Evol."},{"key":"ref33","doi-asserted-by":"publisher","first-page":"1309","DOI":"10.1016\/S0038-0717(02)00074-3","article-title":"The effects of long term nitrogen deposition on extracellular enzyme activity in an Acer saccharum forest soil","volume":"34","author":"Saiya-Cork","year":"2002","journal-title":"Soil Biol. Biochem."},{"key":"ref34","doi-asserted-by":"publisher","first-page":"1583","DOI":"10.1111\/jam.14506","article-title":"Bacillus species in soil as a natural resource for plant health and nutrition","volume":"128","author":"Saxena","year":"2020","journal-title":"J. Appl. Microbiol."},{"key":"ref35","first-page":"317","article-title":"Microbial community structure and diversity as indicators for evaluating soil quality","volume-title":"Biodiversity, biofuels, agroforestry and conservation agriculture","author":"Sharma","year":"2011"},{"key":"ref36","doi-asserted-by":"publisher","first-page":"45","DOI":"10.1104\/pp.121.1.45","article-title":"Roles of sugar alcohols in osmotic stress adaptation. Replacement of glycerol by mannitol and sorbitol in yeast","volume":"121","author":"Shen","year":"1999","journal-title":"Plant Physiol."},{"key":"ref37","doi-asserted-by":"crossref","first-page":"22","DOI":"10.1093\/ajcn\/69.1.22","article-title":"Pentadecanoic acid in serum as a marker for intake of milk fat: relations between intake of milk fat and metabolic risk factors","volume":"69","author":"Smedman","year":"1999","journal-title":"Am. J. Clin. Nutr."},{"key":"ref38","doi-asserted-by":"publisher","first-page":"253","DOI":"10.1038\/ismej.2015.73","article-title":"Molecular mechanisms underlying the close association between soil Burkholderia and fungi","volume":"10","author":"Stopnisek","year":"2016","journal-title":"ISME J."},{"key":"ref39","doi-asserted-by":"publisher","first-page":"34","DOI":"10.1016\/j.soilbio.2015.07.022","article-title":"Competitive sorption of microbial metabolites on an iron oxide mineral","volume":"90","author":"Swenson","year":"2015","journal-title":"Soil Biol. Biochem."},{"key":"ref40","first-page":"1322","article-title":"The effects of continuous cropping on soil microbial community and yield of potato","volume":"26","author":"Tan","year":"2012","journal-title":"J. Nucl. Agricult. Sci."},{"key":"ref41","doi-asserted-by":"publisher","first-page":"1141","DOI":"10.3390\/molecules27031141","article-title":"A review of microalgae-and cyanobacteria-based biodegradation of organic pollutants","volume":"27","author":"Touliabah","year":"2022","journal-title":"Molecules"},{"key":"ref42","doi-asserted-by":"publisher","first-page":"2248","DOI":"10.1038\/ismej.2013.119","article-title":"Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants","volume":"7","author":"Turner","year":"2013","journal-title":"ISME J."},{"key":"ref43","doi-asserted-by":"publisher","first-page":"313","DOI":"10.13300\/j.cnki.hnlkxb.2012.03.008","article-title":"Marker of Bacillus amyloliquefaciens B9601-Y2 resistance gene and its colonization ability in crop roots","volume":"31","author":"Wang","year":"2012","journal-title":"J. Huazhong Agricult. Univ."},{"key":"ref44","doi-asserted-by":"publisher","first-page":"784","DOI":"10.13287\/j.1001-9332.202202.030","article-title":"Relationship between accumulation of autotoxins and soil fertility factors under long-term continuous cropping of cucumber in solar greenhouse","volume":"33","author":"Wang","year":"2022","journal-title":"J. Appl. Ecol."},{"key":"ref45","doi-asserted-by":"publisher","first-page":"212","DOI":"10.1016\/j.rhisph.2017.05.003","article-title":"The state of rhizospheric science in the era of multi-omics: a practical guide to omics technologies","volume":"3","author":"White","year":"2017","journal-title":"Rhizosphere"},{"key":"ref46","doi-asserted-by":"publisher","first-page":"70","DOI":"10.13817\/j.cnki.cyycp.2008.02.004","article-title":"Comparison of two methods for determining soil urease activity","volume":"2","author":"Xiao","year":"2008","journal-title":"Grassland Lawns"},{"key":"ref47","doi-asserted-by":"publisher","first-page":"975","DOI":"10.11766\/trxb201807020131","article-title":"Characteristics of microbial community distribution in different microhabitats of Peanut soil under continuous cropping and crop rotation patterns","volume":"56","author":"Xiaodong","year":"2019","journal-title":"Acta Pedol. Sin."},{"key":"ref48","doi-asserted-by":"publisher","first-page":"513","DOI":"10.3969\/j.issn.1000-1700.2023.05.001","article-title":"The effects of light exclusion treatments during the reproductive growth period on the photosynthetic physiology and aging of soybean leaves","volume":"54","author":"Xingdong","year":"2023","journal-title":"J. Shenyang Agricult. Univ."},{"key":"ref49","doi-asserted-by":"publisher","first-page":"833","DOI":"10.1111\/1758-2229.13126","article-title":"Microbiomes in agroecosystem: diversity, function and assembly mechanisms","volume":"14","author":"Xiong","year":"2022","journal-title":"Environ. Microbiol. Rep."},{"key":"ref50","first-page":"283","volume-title":"Environmental chemistry experiments","author":"Xueyuan","year":"2020"},{"key":"ref51","doi-asserted-by":"publisher","first-page":"402","DOI":"10.1128\/AEM.02515-15","article-title":"Pentanol and benzyl alcohol attack bacterial surface structures differently","volume":"82","author":"Yano","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"ref52","doi-asserted-by":"publisher","first-page":"488","DOI":"10.1016\/j.envint.2019.05.062","article-title":"A review of bacteriophage therapy for pathogenic bacteria inactivation in the soil environment","volume":"129","author":"Ye","year":"2019","journal-title":"Environ. Int."},{"key":"ref53","doi-asserted-by":"publisher","first-page":"1148","DOI":"10.7606\/j.issn.1004-1389.2020.08.004","article-title":"Effects of film mulching and rotation with fava beans on root exudates and allelopathic effects in continuous potato cropping fields","volume":"29","author":"Yichen","year":"2020","journal-title":"Northwest Agricult. J."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1534809\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,2,10]],"date-time":"2025-02-10T06:50:11Z","timestamp":1739170211000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2025.1534809\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,2,10]]},"references-count":53,"alternative-id":["10.3389\/fmicb.2025.1534809"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2025.1534809","relation":{},"ISSN":["1664-302X"],"issn-type":[{"value":"1664-302X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,2,10]]},"article-number":"1534809"}}