{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T08:47:24Z","timestamp":1785833244817,"version":"3.56.0"},"reference-count":190,"publisher":"MDPI AG","issue":"8","license":[{"start":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T00:00:00Z","timestamp":1785196800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Ministry of Science and Higher Education of the Republic of Kazakhstan","award":["BR28713215"],"award-info":[{"award-number":["BR28713215"]}]},{"award":["BR28713215"],"award-info":[{"award-number":["BR28713215"]}],"id":[{"id":"https:\/\/ror.org\/05tyne317","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Microorganisms"],"abstract":"<jats:p>Soil microbiomes are essential for nutrient cycling, plant health, stress resilience, and sustainable agriculture. Recent advances in high-throughput sequencing, multi-omics technologies, systems biology, and artificial intelligence (AI) have transformed our understanding of plant\u2013microbiome interactions and enabled the development of innovative microbiome engineering strategies. This review provides a comprehensive overview of the mechanisms governing plant-associated soil microbiome assembly, microbial community functions, plant\u2013microbe communication, and microbiome-mediated stress resistance in agricultural ecosystems. Current approaches to plant-associated soil microbiome manipulation and engineering, including microbial inoculants, synthetic microbial communities (SynComs), microbiome transplantation, rhizosphere steering, and synthetic biology-based interventions, are critically examined. The review further discusses the growing role of metagenomics, metabolomics, metatranscriptomics, machine learning (ML), and precision agriculture technologies in improving microbiome characterization, prediction, and management. Particular attention is given to the application of microbiome-based solutions for sustainable crop production, nutrient management, biological control, climate-smart agriculture, and ecosystem restoration. Despite significant progress, challenges related to field-scale variability, colonization stability, biosafety, regulatory frameworks, and data integration continue to limit large-scale implementation. Future advances in precision microbiome engineering are expected to combine ecological principles, multi-omics technologies, AI, and synthetic biology to develop predictive and resilient microbiome-based solutions for sustainable and climate-resilient agriculture.<\/jats:p>","DOI":"10.3390\/microorganisms14081648","type":"journal-article","created":{"date-parts":[[2026,7,28]],"date-time":"2026-07-28T13:07:33Z","timestamp":1785244053000},"page":"1648","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Engineering Plant-Associated Soil Microbiomes for Sustainable and Climate-Resilient Agriculture: Mechanisms, Technologies, and Applications"],"prefix":"10.3390","volume":"14","author":[{"given":"Amankeldi K.","family":"Sadanov","sequence":"first","affiliation":[{"name":"LLP \u201cResearch and Production Center for Microbiology and Virology\u201d, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5416-3209","authenticated-orcid":false,"given":"Gul","family":"Baimakhanova","sequence":"additional","affiliation":[{"name":"LLP \u201cResearch and Production Center for Microbiology and Virology\u201d, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7119-950X","authenticated-orcid":false,"given":"Baiken B.","family":"Baimakhanova","sequence":"additional","affiliation":[{"name":"LLP \u201cResearch and Production Center for Microbiology and Virology\u201d, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Saltanat","family":"Orazymbet","sequence":"additional","affiliation":[{"name":"LLP \u201cResearch and Production Center for Microbiology and Virology\u201d, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7045-1865","authenticated-orcid":false,"given":"Irina","family":"Ratnikova","sequence":"additional","affiliation":[{"name":"LLP \u201cResearch and Production Center for Microbiology and Virology\u201d, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irina","family":"Smirnova","sequence":"additional","affiliation":[{"name":"LLP \u201cResearch and Production Center for Microbiology and Virology\u201d, Almaty 050010, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nurgul","family":"Mamytova","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7924-4977","authenticated-orcid":false,"given":"Raikhan","family":"Sydykbekova","sequence":"additional","affiliation":[{"name":"Department of Biotechnology, Faculty of Biology and Biotechnology, Al-Farabi Kazakh National University, Almaty 050040, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3892-7920","authenticated-orcid":false,"given":"Bekzhan D.","family":"Kossalbayev","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan"},{"name":"Ecology Research Institute, Khoja Akhmet Yassawi International Kazakh Turkish University, Turkistan 161200, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Gulzat S.","family":"Aitkaliyeva","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-7429-4994","authenticated-orcid":false,"given":"Ayaz M.","family":"Belkozhayev","sequence":"additional","affiliation":[{"name":"Department of Chemical and Biochemical Engineering, Geology and Oil-Gas Business Institute Named After K. Turyssov, Satbayev University, Almaty 050043, Kazakhstan"},{"name":"M.A. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty 050012, Kazakhstan"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,7,28]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1186\/s12245-025-00901-8","article-title":"Climate change and the global food chain: A catalyst for emerging infectious diseases?","volume":"18","author":"Chandipwisa","year":"2025","journal-title":"Int. J. Emerg. Med."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Ullah, A., Bano, A., and Khan, N. (2021). Climate change and salinity effects on crops and chemical communication between plants and plant growth-promoting microorganisms under stress. Front. Sustain. Food Syst., 5.","DOI":"10.3389\/fsufs.2021.618092"},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"e02345-20","DOI":"10.1128\/AEM.02345-20","article-title":"Agricultural soil management practices differentially shape the bacterial and fungal microbiome of Sorghum bicolor","volume":"87","author":"Wipf","year":"2021","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Delitte, M., Caulier, S., Bragard, C., and Desoignies, N. (2021). Plant Microbiota Beyond Farming Practices: A Review. Front. Sustain. Food Syst., 5.","DOI":"10.3389\/fsufs.2021.624203"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"236","DOI":"10.1007\/s00284-026-04811-7","article-title":"Soil microbiome for climate-smart agriculture in legumes: A review","volume":"83","author":"Tamang","year":"2026","journal-title":"Curr. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"100636","DOI":"10.1016\/j.cpb.2026.100636","article-title":"Bacterial endophytes at the interface of plant physiology, stress adaptation, and microbiome engineering","volume":"48","author":"Alizadeh","year":"2026","journal-title":"Curr. Plant Biol."},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Bertola, M., Ferrarini, A., and Visioli, G. (2021). Improvement of soil microbial diversity through sustainable agricultural practices and its evaluation by -omics approaches: A perspective for the environment, food quality and human safety. Microorganisms, 9.","DOI":"10.3390\/microorganisms9071400"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Li, S., Chiodi, C., Maucieri, C., Della Lucia, M.C., Zardinoni, G., Ravi, S., Squartini, A., Concheri, G., Geng, G., and Wang, Y. (2026). Profiling soil\u2013plant\u2013microbial communities: DNA and multi-omics techniques. Genes, 17.","DOI":"10.3390\/genes17030303"},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"evag029","DOI":"10.1093\/gbe\/evag029","article-title":"Recent microbial evolutionary insights from metagenomics","volume":"18","author":"Moguel","year":"2026","journal-title":"Genome Biol. Evol."},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"20200179","DOI":"10.1098\/rstb.2020.0179","article-title":"Role of soil in the regulation of human and plant pathogens: Soils\u2019 contributions to people","volume":"376","author":"Samaddar","year":"2021","journal-title":"Philos. Trans. R. Soc. B Biol. Sci."},{"key":"ref_11","doi-asserted-by":"crossref","unstructured":"Gupta, A., Singh, U.B., Sahu, P.K., Paul, S., Kumar, A., Malviya, D., Singh, S., Kuppusamy, P., Singh, P., and Paul, D. (2022). Linking soil microbial diversity to modern agriculture practices: A review. Int. J. Environ. Res. Public Health, 19.","DOI":"10.3390\/ijerph19053141"},{"key":"ref_12","doi-asserted-by":"crossref","unstructured":"Dastogeer, K.M.G., Kao-Kniffin, J., and Okazaki, S. (2022). Editorial: Plant microbiome: Diversity, functions, and applications. Front. Microbiol., 13.","DOI":"10.3389\/fmicb.2022.1039212"},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Ray, P., Lakshmanan, V., Labb\u00e9, J.L., and Craven, K.D. (2020). Microbe to microbiome: A paradigm shift in the application of microorganisms for sustainable agriculture. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.622926"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e14750","DOI":"10.1002\/advs.202514750","article-title":"Principles for rigorous design and application of synthetic microbial communities","volume":"13","author":"Zhang","year":"2026","journal-title":"Adv. Sci."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"487","DOI":"10.1053\/j.gastro.2025.02.035","article-title":"Machine learning and artificial intelligence in the multi-omics approach to gut microbiota","volume":"169","author":"Rozera","year":"2025","journal-title":"Gastroenterology"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"100812","DOI":"10.1016\/j.xplc.2024.100812","article-title":"Rational management of the plant microbiome for the second green revolution","volume":"5","author":"Li","year":"2024","journal-title":"Plant Commun."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1186\/s13213-025-01831-9","article-title":"Sustainable bioremediation through microbial community design and smart ecological monitoring","volume":"76","author":"Pegu","year":"2026","journal-title":"Ann. Microbiol."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"koaf185","DOI":"10.1093\/plcell\/koaf185","article-title":"Potential and challenges for application of microbiomes in agriculture","volume":"37","author":"Copeland","year":"2025","journal-title":"Plant Cell"},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1002\/mlf2.12043","article-title":"Guided by the principles of microbiome engineering: Accomplishments and perspectives for environmental use","volume":"1","author":"Hu","year":"2022","journal-title":"mLife"},{"key":"ref_20","doi-asserted-by":"crossref","unstructured":"Hanif, M.S., Tayyab, M., Baillo, E.H., Islam, M.M., Islam, W., and Li, X. (2024). Plant microbiome technology for sustainable agriculture. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1500260"},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"705","DOI":"10.1038\/s41467-025-67353-9","article-title":"The soil microbiome as an indicator of ecosystem multifunctionality in European soils","volume":"17","author":"Romero","year":"2025","journal-title":"Nat. Commun."},{"key":"ref_22","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_23","doi-asserted-by":"crossref","unstructured":"Fu, X., Huang, Y., Fu, Q., Qiu, Y., Zhao, J., Li, J., Wu, X., Yang, Y., Liu, H., and Yang, X. (2023). Critical transition of soil microbial diversity and composition triggered by plant rhizosphere effects. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1252821"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"e71312","DOI":"10.1002\/fsn3.71312","article-title":"Integrating microbiomes for regenerative food systems: Recent insights, implementations, and emerging trends","volume":"13","author":"Arshad","year":"2025","journal-title":"Food Sci. Nutr."},{"key":"ref_25","doi-asserted-by":"crossref","unstructured":"Zholdasbek, A., Tekebayeva, Z., Kulzhanova, K., Abzhalelov, A., Bekshin, Z., Yevneyeva, D., Saylau, M., Li, X., Tan, Z., and Wang, Z. (2026). Microbiome and plant relationship: A symbiosis against phytopathogens. Front. Plant Sci., 17.","DOI":"10.3389\/fpls.2026.1722279"},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"607","DOI":"10.1039\/D3MO00089C","article-title":"Integrated multi-omics analyses of microbial communities: A review of the current state and future directions","volume":"19","author":"Muth","year":"2023","journal-title":"Mol. Omics"},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Duan, D., Wang, M., Han, J., Li, M., Wang, Z., Zhou, S., Xin, W., and Li, X. (2025). Advances in multi-omics integrated analysis methods based on the gut microbiome and their applications. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1509117"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"103887","DOI":"10.1016\/j.isci.2022.103887","article-title":"A framework for integrating microbial dispersal modes into soil ecosystem ecology","volume":"25","author":"Choudoir","year":"2022","journal-title":"iScience"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"21","DOI":"10.1002\/mlf2.12116","article-title":"Ranking environmental and edaphic attributes driving soil microbial community structure and activity with special attention to spatial and temporal scales","volume":"3","author":"Gupta","year":"2024","journal-title":"mLife"},{"key":"ref_30","doi-asserted-by":"crossref","unstructured":"Ding, J., and Yu, S. (2025). Integrating soil physicochemical properties and microbial functional prediction to assess land-use impacts in a cold-region wetland ecosystem. Life, 15.","DOI":"10.3390\/life15060972"},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Hu, F., Chen, P., Zhang, J., Guo, Y., Li, K., Liu, S., Li, L., Chen, X., Cui, J., and Long, X.E. (2026). Root-driven filtering overrides biochar and microbial inoculants in structuring bacterial assemblages of seawater rice cultivation ecosystem in a saline\u2013alkali soil. Microorganisms, 14.","DOI":"10.3390\/microorganisms14020480"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Dadi, F.A., Muthusamy, S., Ghosh, S., Muleta, D., Tesfaye, K., Assefa, F., Xu, J., Ghadamgahi, F., Ortiz, R., and Vetukuri, R.R. (2025). Plant development influences dynamic shifts in the root compartment microbiomes of wild and domesticated finger millet cultivars. BMC Microbiol., 25.","DOI":"10.1186\/s12866-025-03976-8"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"2705","DOI":"10.1042\/BCJ20180615","article-title":"Interactions between plants and soil shaping the root microbiome under abiotic stress","volume":"476","author":"Hartman","year":"2019","journal-title":"Biochem. J."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"115039","DOI":"10.1016\/j.ecolind.2026.115039","article-title":"Mixed plantations regulate soil microbial-mediated ecological processes along the root\u2013soil continuum in sandy ecosystems","volume":"188","author":"Ren","year":"2026","journal-title":"Ecol. Indic."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"139","DOI":"10.1186\/s40168-020-00915-9","article-title":"Soil origin and plant genotype structure distinct microbiome compartments in the model legume Medicago truncatula","volume":"8","author":"Brown","year":"2020","journal-title":"Microbiome"},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"1452","DOI":"10.1038\/s41598-020-58402-y","article-title":"Wheat dwarfing influences selection of the rhizosphere microbiome","volume":"10","author":"Kavamura","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"12234","DOI":"10.1038\/s41598-020-69175-9","article-title":"Domestication-driven changes in plant traits associated with changes in the assembly of the rhizosphere microbiota in tetraploid wheat","volume":"10","author":"Spor","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"171","DOI":"10.1186\/s40168-021-01118-6","article-title":"Plant developmental stage drives the differentiation in ecological role of the maize microbiome","volume":"9","author":"Xiong","year":"2021","journal-title":"Microbiome"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"1130","DOI":"10.1038\/s41564-025-01973-1","article-title":"Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation","volume":"10","author":"Keel","year":"2025","journal-title":"Nat. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"113915","DOI":"10.1016\/j.envres.2022.113915","article-title":"Soil microbial community structures are shaped by agricultural systems revealing little temporal variation","volume":"214","author":"Fox","year":"2022","journal-title":"Environ. Res."},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"7101060","DOI":"10.1155\/tswj\/7101060","article-title":"Advancing nutrient management strategies for sustainable crop productivity in a changing climate: A systematic review","volume":"2025","author":"Yimer","year":"2025","journal-title":"Sci. World J."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1186\/s40168-020-00875-0","article-title":"Microbiome definition re-visited: Old concepts and new challenges","volume":"8","author":"Berg","year":"2020","journal-title":"Microbiome"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"1668","DOI":"10.1038\/s41467-024-45925-5","article-title":"Dynamic root microbiome sustains soybean productivity under unbalanced fertilization","volume":"15","author":"Wang","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_44","doi-asserted-by":"crossref","unstructured":"Li, Y., Wang, C., Chang, H., Zhang, Y., Liu, S., and He, W. (2023). Metagenomics reveals the effect of long-term fertilization on carbon cycle in the maize rhizosphere. Front. Microbiol., 14.","DOI":"10.3389\/fmicb.2023.1170214"},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"1349","DOI":"10.1038\/s42003-024-07059-8","article-title":"Agricultural practices influence soil microbiome assembly and interactions at different depths identified by machine learning","volume":"7","author":"Mo","year":"2024","journal-title":"Commun. Biol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"5090","DOI":"10.1038\/s41467-023-40810-z","article-title":"Acidification suppresses the natural capacity of soil microbiome to fight pathogenic Fusarium infections","volume":"14","author":"Li","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"67","DOI":"10.1038\/s44264-025-00109-6","article-title":"Sustainable soil management practices are associated with increases in crop defense through soil microbiome changes","volume":"3","author":"Bloom","year":"2025","journal-title":"npj Sustain. Agric."},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"1547","DOI":"10.1038\/s42003-025-08910-2","article-title":"Metabolome-driven microbiome assembly in ginger (Zingiber officinale) enhances nutrient cycling and crop yield through keystone taxa","volume":"8","author":"Wang","year":"2025","journal-title":"Commun. Biol."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1038\/s41522-025-00897-2","article-title":"Biofertilizer induces soil disease suppression by activating pathogen suppressive protist taxa","volume":"12","author":"Pei","year":"2026","journal-title":"npj Biofilms Microbiomes"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"wraf249","DOI":"10.1093\/ismejo\/wraf249","article-title":"Epigenetic landscape underlying plant\u2013microbiome chemical communication","volume":"19","author":"Gui","year":"2025","journal-title":"ISME J."},{"key":"ref_51","doi-asserted-by":"crossref","unstructured":"Stirnemann, E.M., and Sasse, J. (2025). How to harness the effects of exudates and microbes that support beneficial plant\u2013plant interactions for sustainable agriculture. PLoS Biol., 23.","DOI":"10.1371\/journal.pbio.3003416"},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1016\/j.jare.2021.11.020","article-title":"How plants recruit their microbiome? New insights into beneficial interactions","volume":"40","author":"Santoyo","year":"2022","journal-title":"J. Adv. Res."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"481","DOI":"10.1038\/s41477-021-00897-y","article-title":"Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation","volume":"7","author":"Yu","year":"2021","journal-title":"Nat. Plants"},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"3436","DOI":"10.1038\/s41467-024-47752-0","article-title":"Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly","volume":"15","author":"Tao","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"207","DOI":"10.1186\/s40168-024-01914-w","article-title":"Volatile-mediated interspecific plant interaction promotes root colonization by beneficial bacteria via induced shifts in root exudation","volume":"12","author":"Zhou","year":"2024","journal-title":"Microbiome"},{"key":"ref_56","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_57","doi-asserted-by":"crossref","first-page":"6535","DOI":"10.1038\/s41467-024-49643-w","article-title":"The lactonase BxdA mediates metabolic specialisation of maize root bacteria to benzoxazinoids","volume":"15","author":"Thoenen","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"4398","DOI":"10.1038\/s41467-026-71037-3","article-title":"Rhizobacteria opportunistically boost colonization and impair plant fitness by degrading plant-derived coumarins under iron deficiency","volume":"17","author":"Gu","year":"2026","journal-title":"Nat. Commun."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"118","DOI":"10.1007\/s10482-026-02330-w","article-title":"Harnessing the plant microbiome: Innovation towards sustainable agriculture and ecological resilience","volume":"119","author":"Kumar","year":"2026","journal-title":"Antonie Leeuwenhoek"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"93","DOI":"10.1111\/nph.70644","article-title":"Unraveling complexity in climate change effects on beneficial plant\u2013microbe interactions: Mechanisms, resilience, and future directions","volume":"249","author":"Afkhami","year":"2026","journal-title":"New Phytol."},{"key":"ref_61","doi-asserted-by":"crossref","unstructured":"Shams, S.-N.-U., Khan, M.A.R., Islam, S.S., Jarin, A., Islam, M.N., Anik, T.R., Abdelrahman, M., Ha, C.V., Montague, T., and Tran, L.-S.P. (2026). Harnessing plant microbiomes to modulate molecular signaling and regulatory networks in drought stress adaptation. Int. J. Mol. Sci., 27.","DOI":"10.3390\/ijms27031139"},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"31","DOI":"10.1021\/acs.chemrev.2c00431","article-title":"Microbiome and human health: Current understanding, engineering, and enabling technologies","volume":"123","author":"Aggarwal","year":"2023","journal-title":"Chem. Rev."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"824","DOI":"10.1016\/j.immuni.2014.05.015","article-title":"Finding the missing links among metabolites, microbes, and the host","volume":"40","author":"Dorrestein","year":"2014","journal-title":"Immunity"},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"2622","DOI":"10.1038\/s41396-022-01288-7","article-title":"Flavonoid-attracted Aeromonas sp. from the Arabidopsis root microbiome enhances plant dehydration resistance","volume":"16","author":"He","year":"2022","journal-title":"ISME J."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"3520","DOI":"10.1038\/s41467-024-47773-9","article-title":"Purines enrich root-associated Pseudomonas and improve wild soybean growth under salt stress","volume":"15","author":"Zheng","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"10068","DOI":"10.1038\/s41467-024-54417-5","article-title":"Root hair developmental regulators orchestrate drought-triggered microbiome changes and the interaction with beneficial Rhizobiaceae","volume":"15","author":"Wang","year":"2024","journal-title":"Nat. Commun."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"22473","DOI":"10.1038\/s41598-022-26551-x","article-title":"Coumarin biosynthesis genes are required after foliar pathogen infection for the creation of a microbial soil-borne legacy that primes plants for SA-dependent defenses","volume":"12","author":"Vismans","year":"2022","journal-title":"Sci. Rep."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"111","DOI":"10.1186\/s40168-025-02103-z","article-title":"Microbe-mediated stress resistance in plants: The roles played by core and stress-specific microbiota","volume":"13","author":"Liu","year":"2025","journal-title":"Microbiome"},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"2823","DOI":"10.1038\/s41564-025-02148-8","article-title":"Precipitation legacy effects on soil microbiota facilitate adaptive drought responses in plants","volume":"10","author":"Ginnan","year":"2025","journal-title":"Nat. Microbiol."},{"key":"ref_70","doi-asserted-by":"crossref","unstructured":"Suman, A., Govindasamy, V., Ramakrishnan, B., Aswini, K., SaiPrasad, J., Sharma, P., Pathak, D., and Annapurna, K. (2022). Microbial community- and function-based synthetic bioinoculants: A perspective for sustainable agriculture. Front. Microbiol., 12.","DOI":"10.3389\/fmicb.2021.805498"},{"key":"ref_71","doi-asserted-by":"crossref","first-page":"2765","DOI":"10.1038\/s41564-024-01827-2","article-title":"A cross-systems primer for synthetic microbial communities","volume":"9","author":"Mehlferber","year":"2024","journal-title":"Nat. Microbiol."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"863240","DOI":"10.1155\/2013\/863240","article-title":"Microbial inoculants and their impact on soil microbial communities: A review","volume":"2013","author":"Trabelsi","year":"2013","journal-title":"BioMed Res. Int."},{"key":"ref_73","doi-asserted-by":"crossref","first-page":"197","DOI":"10.1007\/s11274-017-2364-9","article-title":"Mechanisms of Action of Plant Growth-Promoting Bacteria","volume":"33","author":"Olanrewaju","year":"2017","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_74","doi-asserted-by":"crossref","first-page":"963401","DOI":"10.6064\/2012\/963401","article-title":"Plant Growth-Promoting Bacteria: Mechanisms and Applications","volume":"2012","author":"Glick","year":"2012","journal-title":"Scientifica"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"126439","DOI":"10.1016\/j.micres.2020.126439","article-title":"ACC Deaminase in Plant Growth-Promoting Bacteria (PGPB): An Efficient Mechanism to Counter Salt Stress in Crops","volume":"235","author":"Glick","year":"2020","journal-title":"Microbiol. Res."},{"key":"ref_76","doi-asserted-by":"crossref","first-page":"228","DOI":"10.1186\/s40168-025-02225-4","article-title":"Emerging crops and plant growth-promoting bacteria (PGPB): A synergistic approach to climate-resilient agriculture","volume":"13","author":"Aparicio","year":"2025","journal-title":"Microbiome"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"225","DOI":"10.1016\/j.ecoenv.2018.03.013","article-title":"Use of Plant Growth-Promoting Rhizobacteria (PGPRs) with Multiple Plant Growth-Promoting Traits in Stress Agriculture: Action Mechanisms and Future Prospects","volume":"156","author":"Etesami","year":"2018","journal-title":"Ecotoxicol. Environ. Saf."},{"key":"ref_78","doi-asserted-by":"crossref","first-page":"22835","DOI":"10.1038\/s41598-021-02018-3","article-title":"Assemblage of indigenous arbuscular mycorrhizal fungi and green waste compost enhance drought stress tolerance in carob (Ceratonia siliqua L.) trees","volume":"11","author":"Boutasknit","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_79","doi-asserted-by":"crossref","unstructured":"Brescia, F., Vlassi, A., Bejarano, A., Seidl, B., Marchetti-Deschmann, M., Schuhmacher, R., and Puopolo, G. (2021). Characterisation of the antibiotic profile of Lysobacter capsici AZ78, an effective biological control agent of plant pathogenic microorganisms. Microorganisms, 9.","DOI":"10.3390\/microorganisms9061320"},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"119559","DOI":"10.1016\/j.envpol.2022.119559","article-title":"Claroideoglomus etunicatum affects the structural and functional genes of the rhizosphere microbial community to help maize resist Cd and La stresses","volume":"307","author":"Hao","year":"2022","journal-title":"Environ. Pollut."},{"key":"ref_81","doi-asserted-by":"crossref","first-page":"100791","DOI":"10.1016\/j.rhisph.2023.100791","article-title":"Entrophospora etunicata: A mycorrhizal biostimulant with the potential to enhance the production of bioactive health-promoting compounds in leaves of Capsicum chinense seedlings","volume":"28","author":"Luz","year":"2023","journal-title":"Rhizosphere"},{"key":"ref_82","doi-asserted-by":"crossref","unstructured":"Zarei, M., Abdar, N., Shahriari, A.G., Mirmazloum, I., and Ge\u00f6sel, A. (2024). Effects of Claroideoglomus etunicatum fungus on the growth parameters of maize (Zea mays L.) plants under boron toxicity and salt stress. Agronomy, 14.","DOI":"10.3390\/agronomy14051013"},{"key":"ref_83","doi-asserted-by":"crossref","unstructured":"Lee, S.-M., Yang, H., Kong, H.G., Riu, M., and Ryu, C.-M. (2025). Better than One: A Synthetic Community of Gram-Positive Bacteria Protects Pepper Plants from Aphid Infestation through De Novo Volatile Production. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1589266"},{"key":"ref_84","doi-asserted-by":"crossref","unstructured":"Yadav, J., Gehlot, P., Soni, P., and Jain, T. (2026). Plant microbiome engineering: From inoculation to genome editing. Front. Microbiol., 17.","DOI":"10.3389\/fmicb.2026.1781381"},{"key":"ref_85","doi-asserted-by":"crossref","unstructured":"Rakhmatova, M., Khusanov, T., Kushiev, K., Tekebayeva, Z., Wang, Z., Temirbekova, A., Amantayeva, A., Abzhalelov, A., Bekshin, Z., and Dubey, A.K. (2026). Harnessing nitrogen-fixing and phosphate-mobilizing bacteria for sustainable agriculture. Microorganisms, 14.","DOI":"10.3390\/microorganisms14040803"},{"key":"ref_86","doi-asserted-by":"crossref","unstructured":"Gupta, A., Rai, S., Bano, A., Sharma, S., Kumar, M., Binsuwaidan, R., Khan, M.S., Upadhyay, T.K., Alshammari, N., and Saeed, M. (2022). ACC deaminase produced by PGPR mitigates the adverse effect of osmotic and salinity stresses in Pisum sativum through modulating the antioxidants activities. Plants, 11.","DOI":"10.3390\/plants11243419"},{"key":"ref_87","doi-asserted-by":"crossref","first-page":"1327","DOI":"10.1007\/s11274-011-0979-9","article-title":"Plant Growth-Promoting Rhizobacteria (PGPR): Emergence in Agriculture","volume":"28","author":"Bhattacharyya","year":"2012","journal-title":"World J. Microbiol. Biotechnol."},{"key":"ref_88","doi-asserted-by":"crossref","unstructured":"Ajijah, N., Fiodor, A., Pandey, A.K., Rana, A., and Pranaw, K. (2023). Plant Growth-Promoting Bacteria with Biofilm-Forming Ability: A Multifaceted Agent for Sustainable Agriculture. Diversity, 15.","DOI":"10.3390\/d15010112"},{"key":"ref_89","doi-asserted-by":"crossref","unstructured":"Shayanthan, A., Ordo\u00f1ez, P.A.C., and Oresnik, I.J. (2022). The Role of Synthetic Microbial Communities (SynCom) in Sustainable Agriculture. Front. Agron., 4.","DOI":"10.3389\/fagro.2022.896307"},{"key":"ref_90","doi-asserted-by":"crossref","first-page":"10","DOI":"10.1038\/s43705-022-00094-8","article-title":"Exploring rhizo-microbiome transplants as a tool for protective plant\u2013microbiome manipulation","volume":"2","author":"Jiang","year":"2022","journal-title":"ISME Commun."},{"key":"ref_91","doi-asserted-by":"crossref","unstructured":"Orozco-Mosqueda, M.D.C., Kumar, A., Babalola, O.O., and Santoyo, G. (2023). Rhizobiome transplantation: A novel strategy beyond single-strain\/consortium inoculation for crop improvement. Plants, 12.","DOI":"10.3390\/plants12183226"},{"key":"ref_92","doi-asserted-by":"crossref","first-page":"150136","DOI":"10.1016\/j.scitotenv.2021.150136","article-title":"Squash root microbiome transplants and metagenomic inspection for in situ arid adaptations","volume":"805","author":"Romero","year":"2022","journal-title":"Sci. Total Environ."},{"key":"ref_93","doi-asserted-by":"crossref","first-page":"107933","DOI":"10.1016\/j.soilbio.2020.107933","article-title":"Mycorrhizal association of common European tree species shapes biomass and metabolic activity of bacterial and fungal communities in soil","volume":"149","author":"Nilsson","year":"2020","journal-title":"Soil Biol. Biochem."},{"key":"ref_94","doi-asserted-by":"crossref","first-page":"449","DOI":"10.1002\/ppp3.10365","article-title":"Linking soil health to human health: Arbuscular mycorrhizae play a key role in plant uptake of the antioxidant ergothioneine from soils","volume":"5","author":"Carrara","year":"2023","journal-title":"Plants People Planet"},{"key":"ref_95","doi-asserted-by":"crossref","first-page":"109702","DOI":"10.1016\/j.soilbio.2024.109702","article-title":"Arbuscular mycorrhizal fungal highways\u2014What, how and why?","volume":"202","author":"Vieira","year":"2025","journal-title":"Soil Biol. Biochem."},{"key":"ref_96","doi-asserted-by":"crossref","unstructured":"Dantas, L.V.A., Silva, R.L.O., Sim\u00f5es, W.L., Yano-Melo, A.M., and Melo, N.F. (2025). Mycorrhizal symbiosis and water deficit: Morphophysiological and gene expression responses in Caatinga passion fruit. Stresses, 5.","DOI":"10.3390\/stresses5010018"},{"key":"ref_97","doi-asserted-by":"crossref","first-page":"169","DOI":"10.1146\/annurev-bioeng-082120-022836","article-title":"Integrating systems and synthetic biology to understand and engineer microbiomes","volume":"23","author":"Leggieri","year":"2021","journal-title":"Annu. Rev. Biomed. Eng."},{"key":"ref_98","doi-asserted-by":"crossref","first-page":"2683","DOI":"10.1111\/nph.70951","article-title":"Engineering next-generation crops through CRISPR-mediated horizontal gene transfer","volume":"249","author":"Sen","year":"2026","journal-title":"New Phytol."},{"key":"ref_99","doi-asserted-by":"crossref","first-page":"314","DOI":"10.1038\/s41564-019-0631-2","article-title":"Control of nitrogen fixation in bacteria that associate with cereals","volume":"5","author":"Ryu","year":"2020","journal-title":"Nat. Microbiol."},{"key":"ref_100","doi-asserted-by":"crossref","first-page":"349","DOI":"10.1186\/s12934-024-02634-4","article-title":"A single-plasmid-based, easily curable CRISPR\/Cas9 system for rapid, iterative genome editing in Pseudomonas putida KT2440","volume":"23","author":"Wen","year":"2024","journal-title":"Microb. Cell Fact."},{"key":"ref_101","doi-asserted-by":"crossref","first-page":"845","DOI":"10.1111\/1751-7915.13443","article-title":"Pseudomonas putida KT2440 is HV1 certified, not GRAS","volume":"12","author":"Kampers","year":"2019","journal-title":"Microb. Biotechnol."},{"key":"ref_102","doi-asserted-by":"crossref","unstructured":"Rodr\u00edguez-Romero, N., Clavijo-Salinas, J.C., Wist, J., Gutierrez, C.F., Uribe-Velez, D., Holmes, E., and Sanabria, J. (2025). Engineering nitrogen-fixing microbiomes with waste-derived carbon sources: Toward circular and resilient biofertilizer solution. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1676616"},{"key":"ref_103","doi-asserted-by":"crossref","unstructured":"Veres, S., Elhawat, N., Rengel, Z., and Alshaal, T. (2026). Nitrogen management in crop\u2013soil\u2013environment systems: Pathways toward sustainable and climate-resilient agriculture. Int. J. Mol. Sci., 27.","DOI":"10.3390\/ijms27052477"},{"key":"ref_104","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1186\/s12263-018-0594-6","article-title":"Studying microbial functionality within the gut ecosystem by systems biology","volume":"13","author":"Hornung","year":"2018","journal-title":"Genes Nutr."},{"key":"ref_105","doi-asserted-by":"crossref","first-page":"e00026-20","DOI":"10.1128\/MMBR.00026-20","article-title":"Microbial community resilience across ecosystems and multiple disturbances","volume":"85","author":"Philippot","year":"2021","journal-title":"Microbiol. Mol. Biol. Rev."},{"key":"ref_106","doi-asserted-by":"crossref","unstructured":"McClure, R., Naylor, D., Farris, Y., Davison, M., Fansler, S.J., Hofmockel, K.S., and Jansson, J.K. (2020). Development and analysis of a stable, reduced-complexity model soil microbiome. Front. Microbiol., 11.","DOI":"10.3389\/fmicb.2020.01987"},{"key":"ref_107","doi-asserted-by":"crossref","first-page":"e01349-20","DOI":"10.1128\/mBio.01349-20","article-title":"Deconstructing the soil microbiome into reduced-complexity functional modules","volume":"11","author":"Naylor","year":"2020","journal-title":"mBio"},{"key":"ref_108","doi-asserted-by":"crossref","first-page":"992","DOI":"10.1038\/s42003-021-02514-2","article-title":"Moisture modulates soil reservoirs of active DNA and RNA viruses","volume":"4","author":"Wu","year":"2021","journal-title":"Commun. Biol."},{"key":"ref_109","doi-asserted-by":"crossref","first-page":"e02595-21","DOI":"10.1128\/mBio.02595-21","article-title":"DNA viral diversity, abundance, and functional potential vary across grassland soils with a range of historical moisture regimes","volume":"12","author":"Wu","year":"2021","journal-title":"mBio"},{"key":"ref_110","doi-asserted-by":"crossref","first-page":"34","DOI":"10.1186\/s40168-022-01427-4","article-title":"Rapid remodeling of the soil lipidome in response to a drying\u2013rewetting event","volume":"11","author":"Couvillion","year":"2023","journal-title":"Microbiome"},{"key":"ref_111","doi-asserted-by":"crossref","unstructured":"Delgado-Baquerizo, M., Eldridge, D.J., Liu, Y.R., Liu, Z.W., Coleine, C., and Trivedi, P. (2025). Soil biodiversity and function under global change. PLoS Biol., 23.","DOI":"10.1371\/journal.pbio.3003093"},{"key":"ref_112","doi-asserted-by":"crossref","first-page":"184","DOI":"10.1186\/s40168-024-01868-z","article-title":"Networks as tools for defining emergent properties of microbiomes and their stability","volume":"12","author":"Kajihara","year":"2024","journal-title":"Microbiome"},{"key":"ref_113","doi-asserted-by":"crossref","first-page":"e00055-19","DOI":"10.1128\/mSystems.00055-19","article-title":"Selection, succession, and stabilization of soil microbial consortia","volume":"4","author":"Zegeye","year":"2019","journal-title":"mSystems"},{"key":"ref_114","doi-asserted-by":"crossref","first-page":"e00372-22","DOI":"10.1128\/msystems.00372-22","article-title":"Interaction networks are driven by community-responsive phenotypes in a chitin-degrading consortium of soil microbes","volume":"7","author":"McClure","year":"2022","journal-title":"mSystems"},{"key":"ref_115","doi-asserted-by":"crossref","first-page":"7666","DOI":"10.1038\/s41467-023-42967-z","article-title":"Hi-C metagenome sequencing reveals soil phage\u2013host interactions","volume":"14","author":"Wu","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_116","doi-asserted-by":"crossref","first-page":"e70719","DOI":"10.1111\/ppl.70719","article-title":"Machine learning approaches to assess soil microbiome dynamics and bio-sustainability","volume":"178","author":"Pace","year":"2026","journal-title":"Physiol. Plant."},{"key":"ref_117","doi-asserted-by":"crossref","unstructured":"Przymus, P., Rykaczewski, K., Mart\u00edn-Segura, A., Truu, J., Carrillo De Santa Pau, E., Kolev, M., Naskinova, I., Gruca, A., Sampri, A., and Frohme, M. (2025). Deep learning in microbiome analysis: A comprehensive review of neural network models. Front. Microbiol., 15.","DOI":"10.3389\/fmicb.2024.1516667"},{"key":"ref_118","doi-asserted-by":"crossref","unstructured":"Fan, B.L., Chen, L.H., Chen, L.L., and Guo, H. (2025). Integrative multi-omics approaches for identifying and characterizing biological elements in crop traits: Current progress and future prospects. Int. J. Mol. Sci., 26.","DOI":"10.3390\/ijms26041466"},{"key":"ref_119","doi-asserted-by":"crossref","first-page":"101531","DOI":"10.1016\/j.cels.2026.101531","article-title":"Artificial intelligence for microbiology and microbiome research","volume":"17","author":"Wang","year":"2026","journal-title":"Cell Syst."},{"key":"ref_120","doi-asserted-by":"crossref","unstructured":"Aghdam, R., Tang, X., Shan, S., Lankau, R., and Sol\u00eds-Lemus, C. (2024). Human limits in machine learning: Prediction of potato yield and disease using soil microbiome data. BMC Bioinform., 25.","DOI":"10.1186\/s12859-024-05977-2"},{"key":"ref_121","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1186\/s40793-024-00578-1","article-title":"Interpretable machine learning decodes soil microbiome\u2019s response to drought stress","volume":"19","author":"Hagen","year":"2024","journal-title":"Environ. Microbiome"},{"key":"ref_122","doi-asserted-by":"crossref","first-page":"e00053-19","DOI":"10.1128\/CMR.00053-19","article-title":"Performance and application of 16S rRNA gene cycle sequencing for routine identification of bacteria in the clinical microbiology laboratory","volume":"33","author":"Church","year":"2020","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_123","doi-asserted-by":"crossref","first-page":"355","DOI":"10.1038\/s43247-025-02330-0","article-title":"Exploring crop health and its associations with fungal soil microbiome composition using machine learning applied to remote sensing data","volume":"6","author":"Faurdal","year":"2025","journal-title":"Commun. Earth Environ."},{"key":"ref_124","doi-asserted-by":"crossref","unstructured":"Liang, X., Yu, S., Ju, Y., Wang, Y., and Yin, D. (2025). Integrated management practices foster soil health, productivity, and agroecosystem resilience. Agronomy, 15.","DOI":"10.20944\/preprints202506.2355.v1"},{"key":"ref_125","doi-asserted-by":"crossref","first-page":"11069","DOI":"10.1038\/s41598-026-39537-w","article-title":"Soil microbiome prediction using traditional machine learning and deep learning models","volume":"16","author":"Aouabed","year":"2026","journal-title":"Sci. Rep."},{"key":"ref_126","doi-asserted-by":"crossref","first-page":"D387","DOI":"10.1093\/nar\/gkab1053","article-title":"The Sequence Read Archive: A Decade More of Explosive Growth","volume":"50","author":"Katz","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_127","doi-asserted-by":"crossref","first-page":"D753","DOI":"10.1093\/nar\/gkac1080","article-title":"MGnify: The Microbiome Sequence Data Analysis Resource in 2023","volume":"51","author":"Richardson","year":"2023","journal-title":"Nucleic Acids Res."},{"key":"ref_128","doi-asserted-by":"crossref","first-page":"796","DOI":"10.1038\/s41592-018-0141-9","article-title":"Qiita: Rapid, Web-Enabled Microbiome Meta-Analysis","volume":"15","author":"Gonzalez","year":"2018","journal-title":"Nat. Methods"},{"key":"ref_129","doi-asserted-by":"crossref","unstructured":"Manono, B.O., Mwami, B., Mutavi, S., and Nzilu, F. (2026). Precision farming with smart sensors: Current state, challenges and future outlook. Sensors, 26.","DOI":"10.3390\/s26030882"},{"key":"ref_130","doi-asserted-by":"crossref","unstructured":"Mansoor, S., Iqbal, S., Popescu, S.M., Kim, S.L., Chung, Y.S., and Baek, J.H. (2025). Integration of smart sensors and IoT in precision agriculture: Trends, challenges and future prospectives. Front. Plant Sci., 16.","DOI":"10.3389\/fpls.2025.1587869"},{"key":"ref_131","doi-asserted-by":"crossref","unstructured":"Naylor, D., Naasko, K., Smith, M., Couvillion, S., Nicora, C., Trejo, J., Fransen, S., Danczak, R., McClure, R., and Hofmockel, K.S. (2023). Interactive effects of depth and differential irrigation on soil microbiome composition and functioning. Front. Microbiomes, 2.","DOI":"10.3389\/frmbi.2023.1078024"},{"key":"ref_132","doi-asserted-by":"crossref","first-page":"e01758-23","DOI":"10.1128\/mbio.01758-23","article-title":"Influence of soil depth, irrigation, and plant genotype on the soil microbiome, metaphenome, and carbon chemistry","volume":"14","author":"Naasko","year":"2023","journal-title":"mBio"},{"key":"ref_133","doi-asserted-by":"crossref","unstructured":"Smith, M.L., Weitz, K.K., Thompson, A.M., Jansson, J.K., Hofmockel, K.S., and Lipton, M.S. (2023). Real-time and rapid respiratory response of the soil microbiome to moisture shifts. Microorganisms, 11.","DOI":"10.3390\/microorganisms11112630"},{"key":"ref_134","doi-asserted-by":"crossref","first-page":"e00956-23","DOI":"10.1128\/mbio.00956-23","article-title":"Fungal organic acid uptake of mineral-derived K is dependent on distance from carbon hotspot","volume":"14","author":"Bhattacharjee","year":"2023","journal-title":"mBio"},{"key":"ref_135","doi-asserted-by":"crossref","unstructured":"Tang, L. (2024). Soil fertility, plant nutrition and nutrient management. Plants, 14.","DOI":"10.3390\/plants14010034"},{"key":"ref_136","doi-asserted-by":"crossref","unstructured":"Chen, Q., Song, Y., An, Y., Lu, Y., and Zhong, G. (2024). Soil microorganisms: Their role in enhancing crop nutrition and health. Diversity, 16.","DOI":"10.3390\/d16120734"},{"key":"ref_137","first-page":"100322","article-title":"Rhizosphere microbiome regulation: Unlocking the potential for plant growth","volume":"8","author":"Luo","year":"2024","journal-title":"Curr. Res. Microb. Sci."},{"key":"ref_138","doi-asserted-by":"crossref","unstructured":"Arafat, Y., Din, I.U., Tayyab, M., Jiang, Y., Chen, T., Cai, Z., Zhao, H., Lin, X., Lin, W., and Lin, S. (2020). Soil sickness in aged tea plantation is associated with a shift in microbial communities as a result of plant polyphenol accumulation in the tea gardens. Front. Plant Sci., 11.","DOI":"10.3389\/fpls.2020.00601"},{"key":"ref_139","doi-asserted-by":"crossref","first-page":"48080","DOI":"10.1007\/s11356-021-14033-y","article-title":"Sugarcane monoculture drives microbial community composition, activity and abundance of agricultural-related microorganisms","volume":"28","author":"Tayyab","year":"2021","journal-title":"Environ. Sci. Pollut. Res."},{"key":"ref_140","doi-asserted-by":"crossref","unstructured":"Zhang, C., Lin, Z., Que, Y., Fallah, N., Tayyab, M., Li, S., Luo, J., Zhang, Z., Abubakar, A.Y., and Zhang, H. (2021). Straw retention efficiently improves fungal communities and functions in the fallow ecosystem. BMC Microbiol., 21.","DOI":"10.1186\/s12866-021-02115-3"},{"key":"ref_141","doi-asserted-by":"crossref","first-page":"100408","DOI":"10.1016\/j.rhisph.2021.100408","article-title":"Increased exopolysaccharide production and microbial activity affect soil water retention and field performance of tomato under water deficit","volume":"19","author":"Page","year":"2021","journal-title":"Rhizosphere"},{"key":"ref_142","doi-asserted-by":"crossref","first-page":"e14372","DOI":"10.1111\/1751-7915.14372","article-title":"Changes in root metabolites and soil microbial community structures in rhizospheres of sugarcanes under different propagation methods","volume":"17","author":"Lin","year":"2024","journal-title":"Microb. Biotechnol."},{"key":"ref_143","doi-asserted-by":"crossref","unstructured":"Prabhu, S., Poorniammal, R., and Dufoss\u00e9, L. (2025). Microbial metabolites: A sustainable approach to combat plant pests. Metabolites, 15.","DOI":"10.3390\/metabo15060418"},{"key":"ref_144","doi-asserted-by":"crossref","first-page":"127","DOI":"10.1186\/s40168-024-01841-w","article-title":"Natural plant disease suppressiveness in soils extends to insect pest control","volume":"12","author":"Harmsen","year":"2024","journal-title":"Microbiome"},{"key":"ref_145","doi-asserted-by":"crossref","unstructured":"Tziros, G.T., Samaras, A., and Karaoglanidis, G.S. (2024). Soil solarization efficiently reduces fungal soilborne pathogen populations, promotes lettuce plant growth, and affects the soil bacterial community. Biology, 13.","DOI":"10.3390\/biology13080624"},{"key":"ref_146","doi-asserted-by":"crossref","first-page":"e00802-23","DOI":"10.1128\/spectrum.00802-23","article-title":"Effects of reductive soil disinfestation combined with different types of organic materials on the microbial community and functions","volume":"12","author":"Zhan","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_147","doi-asserted-by":"crossref","first-page":"527","DOI":"10.1186\/s13071-020-04402-w","article-title":"Ketamine can be produced by Pochonia chlamydosporia: An old molecule and a new anthelmintic?","volume":"13","author":"Ferreira","year":"2020","journal-title":"Parasites Vectors"},{"key":"ref_148","doi-asserted-by":"crossref","first-page":"e16612","DOI":"10.1111\/1462-2920.16612","article-title":"Clonal genomic population structure of Beauveria brongniartii and Beauveria pseudobassiana: Pathogens of the common European cockchafer (Melolontha melolontha L.)","volume":"26","author":"Pedrazzini","year":"2024","journal-title":"Environ. Microbiol."},{"key":"ref_149","doi-asserted-by":"crossref","first-page":"340","DOI":"10.1111\/epp.12675","article-title":"Detection of Ralstonia pseudosolanacearum in drain water based on concentration, enrichment and the use of a duplex TaqMan PCR test","volume":"50","author":"Sedighian","year":"2020","journal-title":"EPPO Bull."},{"key":"ref_150","doi-asserted-by":"crossref","first-page":"3212","DOI":"10.1038\/s41598-021-82261-w","article-title":"Robotic agricultural instrument for automated extraction of nematode cysts and eggs from soil to improve integrated pest management","volume":"11","author":"Legner","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_151","doi-asserted-by":"crossref","unstructured":"Kope\u0107, P. (2024). Climate change\u2014The rise of climate-resilient crops. Plants, 13.","DOI":"10.3390\/plants13040490"},{"key":"ref_152","doi-asserted-by":"crossref","unstructured":"Feliziani, G., Bordoni, L., and Gabbianelli, R. (2025). Regenerative organic agriculture and human health: The interconnection between soil, food quality, and nutrition. Antioxidants, 14.","DOI":"10.3390\/antiox14050530"},{"key":"ref_153","doi-asserted-by":"crossref","unstructured":"Vaishnav, A., Jaiswal, D.K., and Sahu, J. (2026). Editorial: Soil biodiversity and regenerative agriculture: The path to achieve SDGs. Front. Microbiol., 16.","DOI":"10.3389\/fmicb.2025.1755391"},{"key":"ref_154","doi-asserted-by":"crossref","first-page":"1016","DOI":"10.1038\/s41467-025-67757-7","article-title":"Long-term agricultural diversification increases financial profitability, biodiversity, and ecosystem services: A second-order meta-analysis","volume":"17","author":"Raveloaritiana","year":"2026","journal-title":"Nat. Commun."},{"key":"ref_155","unstructured":"Capetz, M., Sharma, S., Padilha, R., Olsen, P., Wolk, J., Kiciman, E., and Chandra, R. (2024). Enabling adoption of regenerative agriculture through soil carbon copilots. arXiv."},{"key":"ref_156","unstructured":"Sarkar, S.K., and Ravela, S. (2026). A dynamic learning observatory reveals the rapid salinization of Satkhira, Bangladesh. arXiv."},{"key":"ref_157","doi-asserted-by":"crossref","unstructured":"Deis, L., Fort, F., Lin-Yang, Q., Balda, P., and Pou, A. (2025). Carbon sequestration, plant cover, and soil health: Strategies to mitigate climate change. Plants, 14.","DOI":"10.3390\/plants14233610"},{"key":"ref_158","doi-asserted-by":"crossref","unstructured":"Hussain, S., Hussain, S., Guo, R., Sarwar, M., Ren, X., Krstic, D., Aslam, Z., Zulifqar, U., Rauf, A., and Hano, C. (2021). Carbon sequestration to avoid soil degradation: A review on the role of conservation tillage. Plants, 10.","DOI":"10.3390\/plants10102001"},{"key":"ref_159","doi-asserted-by":"crossref","first-page":"e01129-24","DOI":"10.1128\/msystems.01129-24","article-title":"Soil microbiome interventions for carbon sequestration and climate mitigation","volume":"10","author":"Beattie","year":"2025","journal-title":"mSystems"},{"key":"ref_160","doi-asserted-by":"crossref","first-page":"1577","DOI":"10.1038\/s42003-024-07275-2","article-title":"Comprehensive tools for ecological restoration of soils foster sustainable use and resilience of agricultural land","volume":"7","author":"Neuenkamp","year":"2024","journal-title":"Commun. Biol."},{"key":"ref_161","doi-asserted-by":"crossref","unstructured":"Ka\u010dergius, A., Gegeckas, A., and Gudiukait\u0117, R. (2025). Recent advances in soil health: Influences of organic carbon and microbiota. Biology, 14.","DOI":"10.3390\/biology14050500"},{"key":"ref_162","doi-asserted-by":"crossref","unstructured":"Shu, X., Liu, W., Hu, Y., Xia, L., Fan, K., Zhang, Y., Zhang, Y., and Zhou, W. (2023). Ecosystem multifunctionality and soil microbial communities in response to ecological restoration in an alpine degraded grassland. Front. Plant Sci., 14.","DOI":"10.3389\/fpls.2023.1173962"},{"key":"ref_163","doi-asserted-by":"crossref","unstructured":"Liu, W., Yang, Z., Ye, Q., Peng, Z., Zhu, S., Chen, H., Liu, D., Li, Y., Deng, L., and Shu, X. (2023). Positive effects of organic amendments on soil microbes and their functionality in agro-ecosystems. Plants, 12.","DOI":"10.3390\/plants12223790"},{"key":"ref_164","doi-asserted-by":"crossref","first-page":"e00324-19","DOI":"10.1128\/AEM.00324-19","article-title":"Soil aggregate microbial communities: Towards understanding microbiome interactions at biologically relevant scales","volume":"85","author":"Wilpiszeski","year":"2019","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_165","doi-asserted-by":"crossref","unstructured":"Machineski, G.D.S., Menoncin, A.S., Leonardo, H.C.L., and Colozzi Filho, A. (2026). Riparian forest restoration drives the recovery of soil chemistry, microbial community structure, and enzymatic activity in the Itaipu Reservoir protection zone. Microorganisms, 14.","DOI":"10.3390\/microorganisms14020454"},{"key":"ref_166","doi-asserted-by":"crossref","first-page":"110069","DOI":"10.1016\/j.agee.2025.110069","article-title":"Artificial restoration improved the complexity of the soil microbial co-occurrence network and the resistance of microbial communities to environmental changes in degraded sandy grassland","volume":"397","author":"Mi","year":"2026","journal-title":"Agric. Ecosyst. Environ."},{"key":"ref_167","doi-asserted-by":"crossref","first-page":"33470","DOI":"10.1038\/s41598-025-12149-6","article-title":"Differential impacts of regenerative agriculture practices on soil organic carbon: A meta-analysis of studies from India","volume":"15","author":"Patil","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_168","doi-asserted-by":"crossref","first-page":"8260","DOI":"10.1038\/s41598-026-42050-9","article-title":"Soil organic carbon stocks after ten years of reduced tillage, compost and mulch application in temperate organic agriculture","volume":"16","author":"Niether","year":"2026","journal-title":"Sci. Rep."},{"key":"ref_169","doi-asserted-by":"crossref","unstructured":"Sergaki, C., Lagunas, B., Lidbury, I., Gifford, M.L., and Sch\u00e4fer, P. (2018). Challenges and approaches in microbiome research: From fundamental to applied. Front. Plant Sci., 9.","DOI":"10.3389\/fpls.2018.01205"},{"key":"ref_170","doi-asserted-by":"crossref","first-page":"e00613-21","DOI":"10.1128\/msystems.00613-21","article-title":"The future of (soil) microbiome studies: Current limitations, integration, and perspectives","volume":"6","author":"Geisen","year":"2021","journal-title":"mSystems"},{"key":"ref_171","unstructured":"Miyamoto, H., Shigeta, K., Suda, W., Ichihashi, Y., Nihei, N., Matsuura, M., Tsuboi, A., Tominaga, N., Aono, M., and Sato, M. (2022). Agricultural quality matrix-based multiomics structural analysis of carrots in soils fertilized with thermophile-fermented compost. arXiv."},{"key":"ref_172","doi-asserted-by":"crossref","first-page":"e2319436121","DOI":"10.1073\/pnas.2319436121","article-title":"Enhanced weathering in the US Corn Belt delivers carbon removal with agronomic benefits","volume":"121","author":"Beerling","year":"2024","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"ref_173","doi-asserted-by":"crossref","first-page":"4897","DOI":"10.1038\/s41467-020-18706-z","article-title":"Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming","volume":"11","author":"Guo","year":"2020","journal-title":"Nat. Commun."},{"key":"ref_174","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\u2013soil\u2013microbiome interactions: Mechanisms, advances, and challenges in sustainable agriculture and healthy agroecosystems. Front. Microbiol., 17.","DOI":"10.3389\/fmicb.2026.1762743"},{"key":"ref_175","doi-asserted-by":"crossref","unstructured":"Adhikary, K., Selim, S., Sarkar, R., Ganguly, K., Das, J., Almuhayawi, M.S., Alruhaili, M.H., Gattan, H.S., and Karak, P. (2026). Synthetic microbiomes in bioengineered rhizospheres: New frontiers for climate-resilient agriculture. Front. Microbiol., 17.","DOI":"10.3389\/fmicb.2026.1780132"},{"key":"ref_176","doi-asserted-by":"crossref","first-page":"53","DOI":"10.1038\/s41522-025-00683-0","article-title":"The regulatory framework for microbiome-based therapies: Insights into European regulatory developments","volume":"11","author":"Rodriguez","year":"2025","journal-title":"npj Biofilms Microbiomes"},{"key":"ref_177","first-page":"100871","article-title":"Addressing challenges in microbial manufacturing: Systematic microbial biotechnology","volume":"6","author":"Liu","year":"2025","journal-title":"Innovation"},{"key":"ref_178","doi-asserted-by":"crossref","first-page":"100040","DOI":"10.1016\/j.ecz.2025.100040","article-title":"Exploring and utilizing soil microbiota: From dark to light","volume":"2","author":"Lu","year":"2025","journal-title":"Earth Crit. Zone"},{"key":"ref_179","doi-asserted-by":"crossref","unstructured":"Hemme, C.L., Atoyan, J., Cai, A., and Liu, C. (2026). Challenges and opportunities in multi-omics data acquisition and analysis: Toward integrative solutions. Biomolecules, 16.","DOI":"10.3390\/biom16020271"},{"key":"ref_180","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1016\/j.mib.2018.03.004","article-title":"Omics and multi-omics approaches to study the biosynthesis of secondary metabolites in microorganisms","volume":"45","author":"Palazzotto","year":"2018","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_181","doi-asserted-by":"crossref","first-page":"178","DOI":"10.1093\/bib\/bbz155","article-title":"Current challenges and best-practice protocols for microbiome analysis","volume":"22","author":"Bharti","year":"2021","journal-title":"Brief. Bioinform."},{"key":"ref_182","doi-asserted-by":"crossref","first-page":"108472","DOI":"10.1016\/j.soilbio.2021.108472","article-title":"Predicting measures of soil health using the microbiome and supervised machine learning","volume":"164","author":"Wilhelm","year":"2022","journal-title":"Soil Biol. Biochem."},{"key":"ref_183","doi-asserted-by":"crossref","first-page":"343","DOI":"10.1038\/s41575-025-01041-3","article-title":"A consensus statement on establishing causality, therapeutic applications and the use of preclinical models in microbiome research","volume":"22","author":"Metwaly","year":"2025","journal-title":"Nat. Rev. Gastroenterol. Hepatol."},{"key":"ref_184","doi-asserted-by":"crossref","first-page":"102172","DOI":"10.1016\/j.mib.2022.102172","article-title":"Microbiome engineering for sustainable agriculture: Using synthetic biology to enhance nitrogen metabolism in plant-associated microbes","volume":"68","author":"Han","year":"2022","journal-title":"Curr. Opin. Microbiol."},{"key":"ref_185","doi-asserted-by":"crossref","unstructured":"Sadanov, A.K., Baimakhanova, B.B., Orasymbet, S.E., Ratnikova, I.A., Turlybaeva, Z.Z., Baimakhanova, G.B., Amitova, A.A., Omirbekova, A.A., Aitkaliyeva, G.S., and Kossalbayev, B.D. (2025). Engineering useful microbial species for pharmaceutical applications. Microorganisms, 13.","DOI":"10.3390\/microorganisms13030599"},{"key":"ref_186","doi-asserted-by":"crossref","unstructured":"Tariq, A., Guo, S., Farhat, F., and Shen, X. (2025). Engineering synthetic microbial communities: Diversity and applications in soil for plant resilience. Agronomy, 15.","DOI":"10.3390\/agronomy15030513"},{"key":"ref_187","doi-asserted-by":"crossref","unstructured":"Rezaee Danesh, Y. (2025). Harnessing beneficial microbes and sensor technologies for sustainable smart agriculture. Sensors, 25.","DOI":"10.20944\/preprints202509.1849.v1"},{"key":"ref_188","doi-asserted-by":"crossref","first-page":"e00041-24","DOI":"10.1128\/msystems.00041-24","article-title":"The role of plant host genetics in shaping the composition and functionality of rhizosphere microbiomes","volume":"10","author":"Pioppi","year":"2025","journal-title":"mSystems"},{"key":"ref_189","doi-asserted-by":"crossref","first-page":"98","DOI":"10.1038\/s42003-020-0824-5","article-title":"Development of a CRISPR\/Cas9n-based tool for metabolic engineering of Pseudomonas putida for ferulic acid-to-polyhydroxyalkanoate bioconversion","volume":"3","author":"Zhou","year":"2020","journal-title":"Commun. Biol."},{"key":"ref_190","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."}],"container-title":["Microorganisms"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/8\/1648\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,4]],"date-time":"2026-08-04T08:28:52Z","timestamp":1785832132000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2607\/14\/8\/1648"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,28]]},"references-count":190,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["microorganisms14081648"],"URL":"https:\/\/doi.org\/10.3390\/microorganisms14081648","relation":{},"ISSN":["2076-2607"],"issn-type":[{"value":"2076-2607","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,28]]}}}