{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T11:04:35Z","timestamp":1789988675584,"version":"4.0.1"},"reference-count":88,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,18]],"date-time":"2026-09-18T00:00:00Z","timestamp":1789689600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100008871","name":"Major Science and Technology Projects in Yunnan Province","doi-asserted-by":"publisher","award":["202202AG050013"],"award-info":[{"award-number":["202202AG050013"]}],"id":[{"id":"10.13039\/501100008871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008871","name":"Yunnan Fundamental Research Projects","doi-asserted-by":"publisher","award":["202601AT070119"],"award-info":[{"award-number":["202601AT070119"]}],"id":[{"id":"10.13039\/501100008871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008871","name":"Yunnan Fundamental Research Projects","doi-asserted-by":"publisher","award":["202501CF070177"],"award-info":[{"award-number":["202501CF070177"]}],"id":[{"id":"10.13039\/501100008871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008871","name":"Yunnan Fundamental Research Projects","doi-asserted-by":"publisher","award":["202403AP140003"],"award-info":[{"award-number":["202403AP140003"]}],"id":[{"id":"10.13039\/501100008871","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100008871","name":"Yunnan Fundamental Research Projects","doi-asserted-by":"publisher","award":["YNWR-QNBJ-2019-142"],"award-info":[{"award-number":["YNWR-QNBJ-2019-142"]}],"id":[{"id":"10.13039\/501100008871","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Crown gall remains difficult to manage because pathogenic agrobacteria can persist in soil, rhizosphere niches, infected roots, plant residues, and propagative materials, while repeated wounding creates new infection sites. This review examines how these reservoirs interact with soil and plant-associated microbiota to shape disease recurrence. Crown gall-specific studies show that gall and graft-union communities are spatially structured and identify pathogen competition, opine use, and virulence-related functions as processes that may shape disease-associated microbial assemblages. Evidence from better-characterized suppressive soils further identifies niche occupation, resource competition, bacterial\u2013fungal interactions, and community stability as mechanisms worth testing in crown gall systems. Sanitation, wound protection, and single-strain biocontrol remain central to preventive management in nurseries and perennial production systems, whereas microbiome-based approaches remain complementary and experimental. Evaluation of locally adapted microbial consortia should consider pathogen rebound in infection-relevant niches, persistence of protective microorganisms, functional activity, new gall incidence, soil conditions, and non-target effects. Distinguishing crown gall-specific evidence from cross-pathosystem inference will help define testable mechanisms and appropriate criteria for field evaluation.<\/jats:p>","DOI":"10.3390\/microorganisms14092089","type":"journal-article","created":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T10:25:43Z","timestamp":1789986343000},"page":"2089","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Ecological\u00a0Management of Crown Gall-Affected Soils: Pathogen Reservoirs, Disease-Suppressive Microbiomes, and Helper Consortia"],"prefix":"10.3390","volume":"14","author":[{"given":"Yaojie","family":"Shi","sequence":"first","affiliation":[{"name":"Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuewei","family":"Wu","sequence":"additional","affiliation":[{"name":"Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-4240-1382","authenticated-orcid":false,"given":"Chao","family":"Li","sequence":"additional","affiliation":[{"name":"Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9836-0252","authenticated-orcid":false,"given":"Yuzhu","family":"Song","sequence":"additional","affiliation":[{"name":"Research Center of Molecular Medicine of Yunnan Province, Faculty of Life Science and Technology, Kunming University of Science and Technology, Kunming 650500, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,18]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1038\/s41579-020-0412-1","article-title":"Plant\u2013microbiome interactions: From community assembly to plant health","volume":"18","author":"Trivedi","year":"2020","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1284","DOI":"10.1094\/PHYTO-03-17-0111-RVW","article-title":"Disease Suppressive Soils: New Insights from the Soil Microbiome","volume":"107","author":"Schlatter","year":"2017","journal-title":"Phytopathology"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1111\/1462-2920.13976","article-title":"Ecological and evolutionary dynamics of a model facultative pathogen: Agrobacterium and crown gall disease of plants","volume":"20","author":"Barton","year":"2018","journal-title":"Environ. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"380","DOI":"10.1016\/S1360-1385(03)00162-6","article-title":"Agrobacterium tumefaciens as an agent of disease","volume":"8","author":"Escobar","year":"2003","journal-title":"Trends Plant Sci."},{"key":"ref_5","doi-asserted-by":"crossref","unstructured":"Gordon, J.E., and Christie, P.J. (2014). The Agrobacterium Ti Plasmids. Microbiol. Spectr., 2.","DOI":"10.1128\/microbiolspec.PLAS-0010-2013"},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"16","DOI":"10.1128\/MMBR.67.1.16-37.2003","article-title":"Agrobacterium-mediated plant transformation: The biology behind the \u201cgene-jockeying\u201d tool","volume":"67","author":"Gelvin","year":"2003","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1007\/s00425-022-03951-x","article-title":"Agrobacterium-mediated gene transfer: Recent advancements and layered immunity in plants","volume":"256","author":"Tiwari","year":"2022","journal-title":"Planta"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"5660","DOI":"10.1128\/JB.180.21.5660-5667.1998","article-title":"Wound-released chemical signals may elicit multiple responses from an Agrobacterium tumefaciens strain containing an octopine-type Ti plasmid","volume":"180","author":"Kalogeraki","year":"1998","journal-title":"J. Bacteriol."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"e0000523","DOI":"10.1128\/jb.00005-23","article-title":"Agrobacterium tumefaciens: A Transformative Agent for Fundamental Insights into Host-Microbe Interactions, Genome Biology, Chemical Signaling, and Cell Biology","volume":"205","author":"Brown","year":"2023","journal-title":"J. Bacteriol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1104\/pp.92.2.281","article-title":"Crown gall disease and hairy root disease: A sledgehammer and a tackhammer","volume":"92","author":"Gelvin","year":"1990","journal-title":"Plant Physiol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"201","DOI":"10.1128\/aem.63.1.201-207.1997","article-title":"Diversity of opines and opine-catabolizing bacteria isolated from naturally occurring crown gall tumors","volume":"63","author":"Moore","year":"1997","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"3358","DOI":"10.1128\/AEM.68.7.3358-3365.2002","article-title":"Seasonal fluctuations and long-term persistence of pathogenic populations of Agrobacterium spp. in soils","volume":"68","author":"Krimi","year":"2002","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_13","first-page":"15","article-title":"The Ecology of Agrobacterium vitis and Management of Crown Gall Disease in Vineyards","volume":"418","author":"Hao","year":"2018","journal-title":"Curr. Top. Microbiol. Immunol."},{"key":"ref_14","doi-asserted-by":"crossref","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":"ref_15","first-page":"007131","article-title":"Updated taxonomy of the family Rhizobiaceae with proposals for 8 novel genera and 32 novel combinations","volume":"76","author":"Harrison","year":"2026","journal-title":"Int. J. Syst. Evol. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"5542","DOI":"10.1128\/AEM.01131-16","article-title":"Grapevine (Vitis vinifera) Crown Galls Host Distinct Microbiota","volume":"82","author":"Faist","year":"2016","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Gan, H.M., Szegedi, E., Fersi, R., Chebil, S., Kov\u00e1cs, L., Kawaguchi, A., Hudson, A.O., Burr, T.J., and Savka, M.A. (2019). Insight into the Microbial Co-occurrence and Diversity of 73 Grapevine (Vitis vinifera) Crown Galls Collected Across the Northern Hemisphere. Front. Microbiol., 10.","DOI":"10.3389\/fmicb.2019.01896"},{"key":"ref_18","doi-asserted-by":"crossref","unstructured":"Oksel, C., Liyanapathiranage, P., Parajuli, M., Avin, F.A., Jennings, C., Simmons, T., and Baysal-Gurel, F. (2024). Evaluation of Chemical and Biological Products for Control of Crown Gall on Rose. Pathogens, 13.","DOI":"10.3390\/pathogens13080708"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"8846","DOI":"10.1073\/pnas.0602965103","article-title":"Bases of biocontrol: Sequence predicts synthesis and mode of action of agrocin 84, the Trojan horse antibiotic that controls crown gall","volume":"103","author":"Kim","year":"2006","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"741","DOI":"10.1128\/aem.55.3.741-746.1989","article-title":"Evidence of Biological Control of Agrobacterium tumefaciens Strains Sensitive and Resistant to Agrocin 84 by Different Agrobacterium radiobacter Strains on Stone Fruit Trees","volume":"55","author":"Gorris","year":"1989","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1128\/aem.59.1.309-315.1993","article-title":"Biological Control of Agrobacterium tumefaciens, Colonization, and pAgK84 Transfer with Agrobacterium radiobacter K84 and the Tra Mutant Strain K1026","volume":"59","author":"Vicedo","year":"1993","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"3977","DOI":"10.1128\/AEM.64.10.3977-3982.1998","article-title":"Construction of a range of derivatives of the biological control strain Agrobacterium rhizogenes K84: A study of factors involved in biological control of crown gall disease","volume":"64","author":"McClure","year":"1998","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1936","DOI":"10.1128\/AEM.65.5.1936-1940.1999","article-title":"Cocolonization of the rhizosphere by pathogenic Agrobacterium strains and nonpathogenic strains K84 and K1026, used for crown gall biocontrol","volume":"65","author":"Penyalver","year":"1999","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"28429","DOI":"10.1007\/s11356-020-09124-1","article-title":"Agrobacterium tumefaciens C58 presence affects Bacillus velezensis 32a ecological fitness in the tomato rhizosphere","volume":"27","author":"Abdallah","year":"2020","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/s41579-021-00604-w","article-title":"Priority effects in microbiome assembly","volume":"20","author":"Debray","year":"2022","journal-title":"Nat. Rev. Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"wrad003","DOI":"10.1093\/ismejo\/wrad003","article-title":"Rhizoviticin is an alphaproteobacterial tailocin that mediates biocontrol of grapevine crown gall disease","volume":"18","author":"Ishii","year":"2024","journal-title":"ISME J."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"547","DOI":"10.2183\/pjab.93.035","article-title":"Biological control for grapevine crown gall using nonpathogenic Rhizobium vitis strain ARK-1","volume":"93","author":"Kawaguchi","year":"2017","journal-title":"Proc. Jpn. Acad. Ser. B Phys. Biol. Sci."},{"key":"ref_28","doi-asserted-by":"crossref","unstructured":"Kawaguchi, A., Nita, M., Ishii, T., Watanabe, M., and Noutoshi, Y. (2019). Biological control agent Rhizobium (=Agrobacterium) vitis strain ARK-1 suppresses expression of the essential and non-essential vir genes of tumorigenic R. vitis. BMC Res. Notes, 12.","DOI":"10.1186\/s13104-018-4038-6"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"1760","DOI":"10.1094\/PDIS-10-24-2085-RE","article-title":"Four Antimicrobial Compounds and ISR Induction are Involved in Biocontrol of Crown Gall Disease by the Plant Beneficial Rhizobacterium Bacillus velezensis FZB42","volume":"109","author":"Qin","year":"2025","journal-title":"Plant Dis."},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Li, Y., Gao, Z., Kong, W., Xiao, Y., Adjei, M.O., and Fan, B. (2025). Biocontrol of Crown Gall Disease of Cherry Trees by Bacillus velezensis. Plants, 14.","DOI":"10.3390\/plants14030475"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Chen, L., Wang, X., Ma, Q., Bian, L., Liu, X., Xu, Y., Zhang, H., Shao, J., and Liu, Y. (2020). Bacillus velezensis CLA178-Induced Systemic Resistance of Rosa multiflora Against Crown Gall Disease. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.587667"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"347","DOI":"10.1146\/annurev-phyto-082712-102340","article-title":"Induced systemic resistance by beneficial microbes","volume":"52","author":"Pieterse","year":"2014","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Ben Gharsa, H., Bouri, M., Hamdane, A.M., Schuster, C., Leclerque, A., and Rhouma, A. (2021). Bacillus velezensis strain MBY2, a potential agent for the management of crown gall disease. PLoS ONE, 16.","DOI":"10.1371\/journal.pone.0252823"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"uhae049","DOI":"10.1093\/hr\/uhae049","article-title":"Defensive alteration of root exudate composition by grafting Prunus sp. onto resistant rootstock contributes to reducing crown gall disease","volume":"11","author":"Chen","year":"2024","journal-title":"Hortic. Res."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"599","DOI":"10.1094\/PDIS-06-20-1179-RE","article-title":"Reduced Root Secretion of Valine in Rosa-Microbe Interaction Contributes to the Decreased Colonization of Pathogenic Agrobacterium tumefaciens","volume":"105","author":"Chen","year":"2021","journal-title":"Plant Dis."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"127569","DOI":"10.1016\/j.micres.2023.127569","article-title":"Characterization of Bacillus velezensis 32a metabolites and their synergistic bioactivity against crown gall disease","volume":"280","author":"Yousfi","year":"2024","journal-title":"Microbiol. Res."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1743","DOI":"10.1007\/s00203-020-02141-1","article-title":"Contribution of macrolactin in Bacillus velezensis CLA178 to the antagonistic activities against Agrobacterium tumefaciens C58","volume":"203","author":"Chen","year":"2021","journal-title":"Arch. Microbiol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"128327","DOI":"10.1016\/j.micres.2025.128327","article-title":"Long-term compost fertilization enhanced soil disease suppressiveness by fostering interactions between root exudates and the rhizosphere microbiome","volume":"302","author":"Wang","year":"2026","journal-title":"Microbiol. Res."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"137","DOI":"10.1186\/s40168-020-00892-z","article-title":"Bio-organic fertilizers stimulate indigenous soil Pseudomonas populations to enhance plant disease suppression","volume":"8","author":"Tao","year":"2020","journal-title":"Microbiome"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"8126","DOI":"10.1038\/s41467-023-43926-4","article-title":"Crop rotation and native microbiome inoculation restore soil capacity to suppress a root disease","volume":"14","author":"Zhou","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_41","doi-asserted-by":"crossref","unstructured":"Priyadarshini, C., Lal, R., Yuan, P., Liu, W., Adhikari, A., Bhandari, S., and Xia, Y. (2025). Plant Disease Suppressiveness Enhancement via Soil Health Management. Biology, 14.","DOI":"10.3390\/biology14080924"},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"277","DOI":"10.1146\/annurev-phyto-080516-035608","article-title":"Organic Amendments for Pathogen and Nematode Control","volume":"58","author":"Rosskopf","year":"2020","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"583","DOI":"10.1016\/j.tplants.2017.04.008","article-title":"Let the Core Microbiota Be Functional","volume":"22","author":"Lemanceau","year":"2017","journal-title":"Trends Plant Sci."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"247","DOI":"10.1038\/s41477-018-0139-4","article-title":"Core microbiomes for sustainable agroecosystems","volume":"4","author":"Toju","year":"2018","journal-title":"Nat. Plants"},{"key":"ref_45","doi-asserted-by":"crossref","unstructured":"de Souza, R.S.C., Armanhi, J.S.L., and Arruda, P. (2020). From Microbiome to Traits: Designing Synthetic Microbial Communities for Improved Crop Resiliency. Front. Plant Sci., 11, Erratum in Front. Plant Sci.\u00a02020, 11, 614083.","DOI":"10.3389\/fpls.2020.01179"},{"key":"ref_46","doi-asserted-by":"crossref","unstructured":"Panchal, K., Sudhir, A., and Prajapati, A.S. (2025). Engineering the plant microbiome: Synthetic community approaches to enhance crop protection. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1705289"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"828","DOI":"10.1016\/j.tim.2026.04.008","article-title":"Dynamical model-guided SynCom design for sustainable agriculture","volume":"34","author":"Miao","year":"2026","journal-title":"Trends Microbiol."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"uhaf286","DOI":"10.1093\/hr\/uhaf286","article-title":"Decoding endophytic microbiome dynamics: Engineering antagonistic synthetic consortia for targeted fusarium suppression in monoculture regimes","volume":"13","author":"Qin","year":"2026","journal-title":"Hortic. Res."},{"key":"ref_49","doi-asserted-by":"crossref","unstructured":"Bashizi, T.F., Kim, M.-J., Lim, K., Lee, G., Tagele, S.B., and Shin, J.-H. (2025). Application of a Synthetic Microbial Community to Enhance Pepper Resistance Against Phytophthora capsici. Plants, 14.","DOI":"10.3390\/plants14111625"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"3878","DOI":"10.1093\/jxb\/eraa111","article-title":"Tailoring plant-associated microbial inoculants in agriculture: A roadmap for successful application","volume":"71","author":"Saad","year":"2020","journal-title":"J. Exp. Bot."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e2509303123","DOI":"10.1073\/pnas.2509303123","article-title":"High bacterial diversity drives the suppression of a soilborne plant disease","volume":"123","author":"Bai","year":"2026","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"5005","DOI":"10.1111\/1462-2920.15097","article-title":"Rhizosphere microbiome functional diversity and pathogen invasion resistance build up during plant development","volume":"22","author":"Hu","year":"2020","journal-title":"Environ. Microbiol."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1002","DOI":"10.1038\/s41564-020-0719-8","article-title":"Competition for iron drives phytopathogen control by natural rhizosphere microbiomes","volume":"5","author":"Gu","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_54","doi-asserted-by":"crossref","unstructured":"G\u00f3mez Exp\u00f3sito, R., de Bruijn, I., Postma, J., and Raaijmakers, J.M. (2017). Current Insights into the Role of Rhizosphere Bacteria in Disease Suppressive Soils. Front. Microbiol., 8.","DOI":"10.3389\/fmicb.2017.02529"},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"309","DOI":"10.1146\/annurev.phyto.40.030402.110010","article-title":"Microbial populations responsible for specific soil suppressiveness to plant pathogens","volume":"40","author":"Weller","year":"2002","journal-title":"Annu. Rev. Phytopathol."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1097","DOI":"10.1126\/science.1203980","article-title":"Deciphering the rhizosphere microbiome for disease-suppressive bacteria","volume":"332","author":"Mendes","year":"2011","journal-title":"Science"},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"58","DOI":"10.1186\/s40168-018-0445-0","article-title":"Microbial interactions within the plant holobiont","volume":"6","author":"Hassani","year":"2018","journal-title":"Microbiome"},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"106615","DOI":"10.1016\/j.pestbp.2025.106615","article-title":"Mortierella alpina bioinoculant potentiates native microbiota for soil borne disease suppression in Panax notoginseng cultivation","volume":"214","author":"Liu","year":"2025","journal-title":"Pestic. Biochem. Physiol."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Zhou, Q., Wang, Y., Zhou, T., Yusupu, K., Gao, D., Zhao, H., and Ma, L. (2026). A minimal cross-kingdom SynCom promotes plant growth and suppresses wheat crown rot via coordinated rhizosphere microbiome remodeling. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1758273"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"128528","DOI":"10.1016\/j.micres.2026.128528","article-title":"Cross-kingdom synthetic microbial consortium controls citrus Huanglongbing and root rot by modulating the rhizosphere microbiome and plant defense","volume":"309","author":"Liu","year":"2026","journal-title":"Microbiol. Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"7890","DOI":"10.1038\/s41467-022-35452-6","article-title":"Cross-kingdom synthetic microbiota supports tomato suppression of Fusarium wilt disease","volume":"13","author":"Zhou","year":"2022","journal-title":"Nat. Commun."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"972","DOI":"10.15212\/ZOONOSES-2024-0067","article-title":"Roles of Tick Symbiotic Microorganisms in Pathogen Transmission","volume":"5","author":"Chang","year":"2025","journal-title":"Zoonoses"},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3033","DOI":"10.1038\/s41467-018-05516-7","article-title":"Soil bacterial networks are less stable under drought than fungal networks","volume":"9","author":"Griffiths","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"20230118","DOI":"10.1002\/VIW.20230118","article-title":"Succession of the oral microbiome with the increasing severity of periodontitis","volume":"5","author":"Mi","year":"2024","journal-title":"View"},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"e0017723","DOI":"10.1128\/mbio.00177-23","article-title":"Soil Inoculation and Blocker-Mediated Sequencing Show Effects of the Antibacterial T6SS on Agrobacterial Tumorigenesis and Gallobiome","volume":"14","author":"Wang","year":"2023","journal-title":"mBio"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"evad228","DOI":"10.1093\/gbe\/evad228","article-title":"Opportunistic Bacteria of Grapevine Crown Galls Are Equipped with the Genomic Repertoire for Opine Utilization","volume":"15","author":"Faist","year":"2023","journal-title":"Genome Biol. Evol."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"36518","DOI":"10.1007\/s11356-018-3570-1","article-title":"Lipopeptides from Bacillus amyloliquefaciens strain 32a as promising biocontrol compounds against the plant pathogen Agrobacterium tumefaciens","volume":"25","author":"Abdallah","year":"2018","journal-title":"Environ. Sci. Pollut. Res. Int."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"196","DOI":"10.1111\/jam.12797","article-title":"Bacillus amyloliquefaciens strain 32a as a source of lipopeptides for biocontrol of Agrobacterium tumefaciens strains","volume":"119","author":"Tounsi","year":"2015","journal-title":"J. Appl. Microbiol."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"606","DOI":"10.1126\/science.aaw9285","article-title":"Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome","volume":"366","author":"Cordovez","year":"2019","journal-title":"Science"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"100045","DOI":"10.1016\/j.lmd.2025.100045","article-title":"Review of metabolomics and microbiomics in esophageal cancer: From pathogenesis to prognosis","volume":"2","author":"Cao","year":"2025","journal-title":"LabMed Discov."},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"127880","DOI":"10.1016\/j.micres.2024.127880","article-title":"Delineating the soil physicochemical and microbiological factors conferring disease suppression in organic farms","volume":"289","author":"Chaudhary","year":"2024","journal-title":"Microbiol. Res."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"172","DOI":"10.1186\/s40168-026-02416-7","article-title":"MdUGT88F1 enhances plant resistance to Fusarium proliferatum f.sp. malus domestica MR5 via root exudate-mediated assembly of disease-suppressive rhizosphere microbiota","volume":"14","author":"Duan","year":"2026","journal-title":"Microbiome"},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"5125","DOI":"10.1038\/s41467-024-49218-9","article-title":"Fusaric acid mediates the assembly of disease-suppressive rhizosphere microbiota via induced shifts in plant root exudates","volume":"15","author":"Jin","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"1245","DOI":"10.1038\/s44318-025-00685-w","article-title":"Reactive oxygen species in the rhizosphere orchestrate the recruitment of beneficial bacteria","volume":"45","author":"Guo","year":"2026","journal-title":"EMBO J."},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"2738","DOI":"10.1038\/s41467-018-05122-7","article-title":"Root exudate metabolites drive plant-soil feedbacks on growth and defense by shaping the rhizosphere microbiota","volume":"9","author":"Hu","year":"2018","journal-title":"Nat. Commun."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"167","DOI":"10.1186\/s40168-026-02409-6","article-title":"Streptomyces-induced Glycerol-3-Phosphate enriches beneficial microbiota to enhance resistance against banana Fusarium wilt","volume":"14","author":"Cai","year":"2026","journal-title":"Microbiome"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"103444","DOI":"10.1016\/j.copbio.2026.103444","article-title":"Plant microbiome regulation for sustainable agriculture","volume":"98","author":"Zhang","year":"2026","journal-title":"Curr. Opin. Biotechnol."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1007\/s00284-025-04651-x","article-title":"Unravelling the Mechanistic Role of Soil Microbial Interactions in the Suppression of Phytopathogens in Vegetable Agroecosystems of Pakistan","volume":"83","author":"Khan","year":"2025","journal-title":"Curr. Microbiol."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Zheng, Y., Han, X., Zhao, D., Wei, K., Yuan, Y., Li, Y., Liu, M., and Zhang, C.-S. (2021). Exploring Biocontrol Agents From Microbial Keystone Taxa Associated to Suppressive Soil: A New Attempt for a Biocontrol Strategy. Front. Plant Sci., 12.","DOI":"10.3389\/fpls.2021.655673"},{"key":"ref_80","doi-asserted-by":"crossref","unstructured":"Santoyo, G., Urtis-Flores, C.A., Loeza-Lara, P.D., Orozco-Mosqueda, M.D.C., and Glick, B.R. (2021). Rhizosphere Colonization Determinants by Plant Growth-Promoting Rhizobacteria (PGPR). Biology, 10.","DOI":"10.3390\/biology10060475"},{"key":"ref_81","doi-asserted-by":"crossref","unstructured":"Shi, H., Li, W., Chen, H., Meng, Y., Wu, H., Wang, J., and Shen, S. (2024). Synthetic Microbial Community Members Interact to Metabolize Caproic Acid to Inhibit Potato Dry Rot Disease. Int. J. Mol. Sci., 25.","DOI":"10.3390\/ijms25084437"},{"key":"ref_82","doi-asserted-by":"crossref","first-page":"92","DOI":"10.1007\/s00248-025-02592-3","article-title":"Cooperative Interactions Between Bacillus and Lysobacter Enhance Consortium Stability and Fusarium Wilt Suppression in Cucumber","volume":"88","author":"Sun","year":"2025","journal-title":"Microb. Ecol."},{"key":"ref_83","doi-asserted-by":"crossref","first-page":"2774","DOI":"10.1038\/s41564-024-01833-4","article-title":"Community standards and future opportunities for synthetic communities in plant-microbiota research","volume":"9","author":"Northen","year":"2024","journal-title":"Nat. Microbiol."},{"key":"ref_84","doi-asserted-by":"crossref","first-page":"ycag028","DOI":"10.1093\/ismeco\/ycag028","article-title":"Synthetic bacterial community colonizes wheat roots grown in soil and mimics the assembly pattern of a field community in a cultivar dependent manner","volume":"6","author":"Bak","year":"2026","journal-title":"ISME Commun."},{"key":"ref_85","doi-asserted-by":"crossref","first-page":"113","DOI":"10.1016\/j.jare.2025.08.040","article-title":"Synthetic microbial communities rescues strawberry from soil-borne disease by enhancing soil functional microbial abundance and multifunctionality","volume":"83","author":"Lei","year":"2026","journal-title":"J. Adv. Res."},{"key":"ref_86","doi-asserted-by":"crossref","first-page":"2448","DOI":"10.1038\/s41396-022-01290-z","article-title":"Small changes in rhizosphere microbiome composition predict disease outcomes earlier than pathogen density variations","volume":"16","author":"Gu","year":"2022","journal-title":"Isme J."},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"299","DOI":"10.1016\/j.tim.2020.11.006","article-title":"Microbial Inoculants: Silver Bullet or Microbial Jurassic Park?","volume":"29","author":"Jack","year":"2021","journal-title":"Trends Microbiol."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Panek, J., Gryta, A., Maj, W., M\u0105cik, M., Oszust, K., Pertile, G., Pylak, M., Siegieda, D., Hallama, M., and Hatano, R. (2026). Plant-soil-microbiome interactions: Mechanisms, advances, and challenges in sustainable agriculture and healthy agroecosystems. Front. Microbiol., 17.","DOI":"10.3389\/fmicb.2026.1762743"}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/9\/2089\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T10:43:57Z","timestamp":1789987437000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/9\/2089"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,18]]},"references-count":88,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["microorganisms14092089"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14092089","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,18]]}}}