{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T06:18:25Z","timestamp":1783491505527,"version":"3.55.0"},"reference-count":55,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T00:00:00Z","timestamp":1783468800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100019957","name":"Shaanxi Academy of Sciences","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100019957","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:p>\n                    Leaf variegation in\n                    <jats:italic>Aspidistra elatior<\/jats:italic>\n                    provides a useful system for exploring localized plant\u2013microbiome associations, yet the biological factors linked to sector-specific chlorosis remain unclear. To investigate potential relationships among endophytic microbial communities, host transcriptomic responses, and metabolic variation, we integrated 16S\/ITS amplicon sequencing, transcriptomics, and widely targeted LC\u2013MS\/MS-based metabolomics across normal green (GG), adjacent green (SG), and chlorotic spot (SS) sectors. SS sectors showed sector-associated bacterial community patterns characterized by lower Shannon diversity relative to SG, enrichment of unclassified\n                    <jats:italic>Rickettsiales<\/jats:italic>\n                    ,\n                    <jats:italic>Stenotrophomonas<\/jats:italic>\n                    , and\n                    <jats:italic>Salinivibrio<\/jats:italic>\n                    , and reduced abundance of several\n                    <jats:italic>Actinobacteriota<\/jats:italic>\n                    -associated taxa. By contrast, fungal community structure remained comparatively stable across sectors. Transcriptomic analysis identified sector-associated expression differences involving stress- and defense-related genes, including heat shock protein 70 (HSP70) and the F-box regulator SKIP23. Metabolomic profiling identified 52 core differentially accumulated metabolites (DEMs) between SS and SG, of which 37 showed higher abundance in SS. These metabolites included alkaloids, flavonoids, phenolic acids, and amino acids and derivatives. Integrated multi-omics correlation analyses linked host gene-expression modules to metabolite classes and revealed a significant correspondence between bacterial community dissimilarity and metabolic variation across sectors. Together, these findings identify SS sectors as spatially distinct leaf microenvironments in which bacterial community structure, host transcriptional state, and metabolite accumulation vary in parallel, placing localized variegation in a broader microbiome\u2013host\u2013metabolite context.\n                  <\/jats:p>","DOI":"10.3389\/fpls.2026.1860906","type":"journal-article","created":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:55:19Z","timestamp":1783490119000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":0,"title":["Multi-omics analysis reveals associations among endophytic microbiome shifts, host transcriptional responses, and metabolic variation across variegated leaf sectors of Aspidistra elatior"],"prefix":"10.3389","volume":"17","author":[{"given":"Yan","family":"Wang","sequence":"first","affiliation":[{"name":"Shaanxi Institute of Microbiology, Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Academy of Sciences","place":["Xi\u2019an, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fu","family":"Wang","sequence":"additional","affiliation":[{"name":"Xi\u2019an Angel Biotechnology Co., Ltd.","place":["Xi\u2019an, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yan","family":"Li","sequence":"additional","affiliation":[{"name":"Shaanxi Institute of Microbiology, Shaanxi Key Laboratory of Qinling Ecological Security, Shaanxi Academy of Sciences","place":["Xi\u2019an, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shanshan","family":"Han","sequence":"additional","affiliation":[{"name":"Bio-Agriculture Institute of Shaanxi Province, Shaanxi Academy of Sciences","place":["Xi\u2019an, Shaanxi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,8]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.1016\/j.heliyon.2024.e31573","article-title":"A review on mechanisms and prospects of endophytic bacteria in biocontrol of plant pathogenic fungi and their plant growth-promoting activities","volume":"10","author":"Ali","year":"2024","journal-title":"Heliyon"},{"key":"B2","doi-asserted-by":"publisher","first-page":"949","DOI":"10.1111\/ppa.12639","article-title":"Association between genetic variability and titre of Grapevine Pinot gris virus with disease symptoms","volume":"66","author":"Bertazzon","year":"2017","journal-title":"Plant Pathol."},{"key":"B3","doi-asserted-by":"publisher","DOI":"10.1016\/j.flora.2025.152815","article-title":"The secrets of variegated leaves: molecular to physiological and ecological insights","volume":"331","author":"Bhardwaj","year":"2025","journal-title":"Flora"},{"key":"B4","doi-asserted-by":"publisher","DOI":"10.3390\/microorganisms13030524","article-title":"Exserohilum turcicum alters phyllosphere microbiome diversity and functions\u2014implications for plant health management","volume":"13","author":"Chao","year":"2025","journal-title":"Microorganisms"},{"key":"B5","doi-asserted-by":"publisher","first-page":"36","DOI":"10.1093\/jxb\/eraa417","article-title":"Shaping the leaf microbiota: plant\u2013microbe\u2013microbe interactions","volume":"72","author":"Chaudhry","year":"2021","journal-title":"J. Exp. Bot."},{"key":"B6","doi-asserted-by":"publisher","first-page":"653","DOI":"10.1038\/s41586-020-2185-0","article-title":"A plant genetic network for preventing dysbiosis in the phyllosphere","volume":"580","author":"Chen","year":"2020","journal-title":"Nature"},{"key":"B7","doi-asserted-by":"publisher","DOI":"10.1016\/j.scitotenv.2024.175334","article-title":"Growth period and variety together drive the succession of phyllosphere microbial communities of grapevine","volume":"950","author":"Cui","year":"2024","journal-title":"Sci. Total Environ."},{"key":"B8","doi-asserted-by":"publisher","DOI":"10.1016\/j.bioflm.2024.100203","article-title":"Oxidative stress responses in biofilms","volume":"7","author":"da Cruz Nizer","year":"2024","journal-title":"Biofilm"},{"key":"B9","doi-asserted-by":"publisher","first-page":"265","DOI":"10.1186\/s12870-024-04973-1","article-title":"Mutation mapping of a variegated EMS tomato reveals an FtsH-like protein precursor potentially causing patches of four phenotype classes in the leaves with distinctive internal morphology","volume":"24","author":"Dechkrong","year":"2024","journal-title":"BMC Plant Biol."},{"key":"B10","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2019.02888","article-title":"Beneficial endophytic bacteria\u2013Serendipita indica interaction for crop enhancement and resistance to phytopathogens","volume":"10","author":"del Barrio-Duque","year":"2019","journal-title":"Front. Microbiol."},{"key":"B11","doi-asserted-by":"publisher","first-page":"277","DOI":"10.1007\/s11104-020-04512-5","article-title":"Interaction between endophytic Proteobacteria strains and Serendipita indica enhances biocontrol activity against fungal pathogens","volume":"451","author":"del Barrio-Duque","year":"2020","journal-title":"Plant Soil"},{"key":"B12","doi-asserted-by":"publisher","first-page":"77","DOI":"10.1186\/s40793-025-00734-1","article-title":"Rapid and sustained differentiation of disease-suppressive phyllosphere microbiomes in tomato following experimental microbiome selection","volume":"20","author":"Ehau-Taumaunu","year":"2025","journal-title":"Environ. Microbiome"},{"key":"B13","doi-asserted-by":"publisher","DOI":"10.1093\/ismejo\/wraf155","article-title":"Metabolic interactions underlying phyllosphere microbiota assembly","volume":"19","author":"Feng","year":"2025","journal-title":"ISME J."},{"key":"B14","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1429166","article-title":"Leaf age structures phyllosphere microbial communities in the field and greenhouse","volume":"15","author":"Geyer","year":"2024","journal-title":"Front. Microbiol."},{"key":"B15","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2026.1748715","article-title":"Integrated metabolomic and transcriptomic analysis of the mechanism underlying leaf variegation in Miscanthus sinensis \u2018Zebrinus\u2019","volume":"17","author":"Han","year":"2026","journal-title":"Front. Plant Sci."},{"key":"B16","doi-asserted-by":"publisher","DOI":"10.1016\/j.biortech.2025.132890","article-title":"Bacterial soluble secondary metabolites enhance algal tolerance to pyridine in an indirect-contact symbiotic system","volume":"435","author":"Hou","year":"2025","journal-title":"Bioresour. Technol."},{"key":"B17","doi-asserted-by":"publisher","first-page":"90","DOI":"10.1109\/MCSE.2007.55","article-title":"Matplotlib: A 2D graphics environment","volume":"9","author":"Hunter","year":"2007","journal-title":"Comput. Sci. Eng."},{"key":"B18","doi-asserted-by":"publisher","DOI":"10.1016\/j.postharvbio.2021.111693","article-title":"Postharvest-induced microbiota remodeling increases fungal diversity in the phyllosphere mycobiota of broccoli florets","volume":"181","author":"Kim","year":"2021","journal-title":"Postharvest Biol. Technol."},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1016\/j.envres.2023.115304","article-title":"Multiomics provides insights into the succession of microbiota and metabolite during plant leaf fermentation","volume":"221","author":"Lei","year":"2023","journal-title":"Environ. Res."},{"key":"B20","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2026.1740520","article-title":"Disease-induced changes in Panax ginseng phyllosphere fungal community assembly and functional adaptation","volume":"17","author":"Liu","year":"2026","journal-title":"Front. Microbiol."},{"key":"B21","doi-asserted-by":"publisher","first-page":"246","DOI":"10.1111\/plb.13495","article-title":"EChinacea purpurea microbiota: bacterial\u2013fungal interactions and the interplay with host and non-host plant species in vitro dual culture","volume":"25","author":"Maggini","year":"2023","journal-title":"Plant Biol."},{"key":"B22","first-page":"56","article-title":"Data structures for statistical computing in Python","author":"McKinney","year":"2010"},{"key":"B23","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2024.1489900","article-title":"Microbial communities in the phyllosphere and endosphere of Norway spruce under attack by Heterobasidion","volume":"15","author":"Meng","year":"2025","journal-title":"Front. Microbiol."},{"key":"B24","doi-asserted-by":"publisher","DOI":"10.3390\/antiox13080985","article-title":"Gut microbiota dysbiosis, oxidative stress, inflammation, and epigenetic alterations in metabolic diseases","volume":"13","author":"Mostafavi Abdolmaleky","year":"2024","journal-title":"Antioxidants"},{"key":"B25","doi-asserted-by":"publisher","first-page":"301","DOI":"10.1007\/s00035-021-00273-8","article-title":"Manipulation of phyllosphere bacterial communities reversibly alters the plant microbiome and leaf traits in the field","volume":"132","author":"Ohler","year":"2022","journal-title":"Alp. Bot."},{"key":"B26","doi-asserted-by":"publisher","DOI":"10.32614\/cran.package.vegan","article-title":"vegan: Community Ecology Package. R package version 2.7-5","author":"Oksanen","year":"2025"},{"key":"B27","doi-asserted-by":"publisher","first-page":"1251","DOI":"10.21273\/hortsci15929-21","article-title":"Characterization of anatomical and physiological effects of variegation mutation on grapevine","volume":"56","author":"Olson","year":"2021","journal-title":"HortScience"},{"key":"B28","doi-asserted-by":"publisher","first-page":"100708","DOI":"10.1016\/j.microb.2026.100708","article-title":"Phyllosphere epiphytic fungi: diversity, environmental interactions, and selection factors","volume":"11","author":"Oubohssaine","year":"2026","journal-title":"Microbe"},{"key":"B29","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2011.00100","article-title":"The microbe-free plant: fact or artifact","volume":"2","author":"Partida-Mart\u00ednez","year":"2011","journal-title":"Front. Plant Sci."},{"key":"B30","article-title":"patchwork: The Composer of Plots. R package version 1.3.1","author":"Pedersen","year":"2025"},{"key":"B31","doi-asserted-by":"publisher","DOI":"10.3390\/ijms232314853","article-title":"Fine mapping of BoVl conferring the variegated leaf in ornamental kale (Brassica oleracea var. acephala)","volume":"23","author":"Ren","year":"2022","journal-title":"Int. J. Mol. Sci."},{"key":"B32","doi-asserted-by":"publisher","DOI":"10.1016\/j.stress.2025.100807","article-title":"Metabolomic insights on the response of winter wheat cultivars to Fusarium head blight infection and inoculation with a biocontrol strain in open field","volume":"16","author":"Risoli","year":"2025","journal-title":"Plant Stress"},{"key":"B33","doi-asserted-by":"publisher","DOI":"10.1016\/j.plaphy.2025.110214","article-title":"Stable-isotope-assisted metabolomics enables the study of (a)biotic stress-related metabolism of tyrosine compared to phenylalanine in wheat","volume":"228","author":"Rypar","year":"2025","journal-title":"Plant Physiol. Biochem."},{"key":"B34","doi-asserted-by":"publisher","first-page":"3889","DOI":"10.1111\/pce.15429","article-title":"A multi-omics meta-analysis of rhizosphere microbiome reveals growth-promoting marker bacteria at different stages of legume development","volume":"49","author":"Sahil","year":"2026","journal-title":"Plant Cell Environ"},{"key":"B35","doi-asserted-by":"publisher","DOI":"10.1126\/science.adf5121","article-title":"Metabolic interaction models recapitulate leaf microbiota ecology","volume":"381","author":"Sch\u00e4fer","year":"2023","journal-title":"Science"},{"key":"B36","doi-asserted-by":"publisher","first-page":"122","DOI":"10.1016\/j.molp.2022.12.005","article-title":"Specialized metabolites as versatile tools in shaping plant\u2013microbe associations","volume":"16","author":"Singh","year":"2022","journal-title":"Mol. Plant"},{"key":"B37","doi-asserted-by":"publisher","DOI":"10.1002\/ndr2.12206","article-title":"First report of Cocksfoot mottle virus infecting wheat in Estonia","volume":"48","author":"S\u00f5mera","year":"2023","journal-title":"New Dis. Rep."},{"key":"B38","doi-asserted-by":"publisher","DOI":"10.64898\/2026.03.27.714703","article-title":"Infection of maize by Ustilago maydis remodels the phyllosphere microbiome and requires the activity of antimicrobial effectors","author":"Sorger","year":"2026","journal-title":"bioRxiv"},{"key":"B39","doi-asserted-by":"publisher","DOI":"10.48130\/bpr-0025-0002","article-title":"Leaf metabolites drive the functional composition of the phyllosphere microbiome in tea plants","volume":"5","author":"Tan","year":"2025","journal-title":"Beverage Plant Res."},{"key":"B40","doi-asserted-by":"publisher","first-page":"139","DOI":"10.1007\/s11274-020-02908-0","article-title":"Plant resistance and leaf chemical characteristic jointly shape phyllosphere bacterial community","volume":"36","author":"Tian","year":"2020","journal-title":"World J. Microbiol. Biotechnol."},{"key":"B41","doi-asserted-by":"publisher","first-page":"1469","DOI":"10.2307\/3558455","article-title":"Heterophylly in the yellow waterlily, Nuphar variegata (Nymphaeaceae): effects of [CO2], natural sediment type, and water depth","volume":"88","author":"Titus","year":"2001","journal-title":"Am. J. Bot."},{"key":"B42","doi-asserted-by":"publisher","first-page":"86","DOI":"10.1007\/s10126-025-10458-5","article-title":"Unveiling the characteristics of microbiota in different mucosal layers of leopard coral grouper (Plectropomus leopardus)","volume":"27","author":"Wang","year":"2025","journal-title":"Mar. Biotechnol."},{"key":"B43","doi-asserted-by":"publisher","DOI":"10.3390\/agronomy15081944","article-title":"Root-exudate-mediated modulation of the rhizosphere microbiome in Brassica juncea var. tumida during Plasmodiophora brassicae infection","volume":"15","author":"Wang","year":"2025","journal-title":"Agronomy"},{"key":"B44","doi-asserted-by":"publisher","first-page":"19","DOI":"10.1016\/j.cbpc.2018.11.010","article-title":"Chlorpyrifos disturbs hepatic metabolism associated with oxidative stress and gut microbiota dysbiosis in adult zebrafish","volume":"216","author":"Wang","year":"2019","journal-title":"Comp. Biochem. Physiol. C. Toxicol. Pharmacol."},{"key":"B45","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2025.1551476","article-title":"Temporal dynamics of walnut phyllosphere microbiota under synergistic pathogen exposure and environmental perturbation","volume":"16","author":"Wang","year":"2025","journal-title":"Front. Microbiol."},{"key":"B46","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2024.1459533","article-title":"Unraveling the specialized metabolic pathways in medicinal plant genomes: a review","volume":"15","author":"Wang","year":"2024","journal-title":"Front. Plant Sci."},{"key":"B47","doi-asserted-by":"publisher","DOI":"10.21105\/joss.03021","article-title":"seaborn: statistical data visualization","volume":"6","author":"Waskom","year":"2021","journal-title":"J. Open Source Software"},{"key":"B48","doi-asserted-by":"crossref","DOI":"10.1007\/978-3-319-24277-4","volume-title":"Ggplot2: Elegant Graphics for Data Analysis","author":"Wickham","year":"2016"},{"key":"B49","doi-asserted-by":"publisher","first-page":"943","DOI":"10.1111\/tpj.12344","article-title":"Proteomic evidence for genetic epistasis: ClpR4 mutations switch leaf variegation to virescence in Arabidopsis","volume":"76","author":"Wu","year":"2013","journal-title":"Plant J."},{"key":"B50","doi-asserted-by":"publisher","first-page":"1","DOI":"10.7324\/JABB.2025.239716ed","article-title":"Phyllospheric microbiomes for agricultural sustainability","volume":"13","author":"Yadav","year":"2025","journal-title":"J. Appl. Biol. Biotechnol."},{"key":"B51","doi-asserted-by":"publisher","first-page":"766","DOI":"10.1038\/s42003-025-08196-4","article-title":"Changes in the assembly and functional adaptation of endophytic microbial communities in Amorphophallus species with different levels of resistance to necrotrophic bacterial pathogen stress","volume":"8","author":"Yang","year":"2025","journal-title":"Commun. Biol."},{"key":"B52","doi-asserted-by":"publisher","DOI":"10.21273\/hortsci.33.3.446d","article-title":"Effect of irradiance level and paclobutrazol on reduction of leaf damage in Begonia \u00d7 cheimantha","volume":"33","author":"Yoon","year":"1998","journal-title":"HortScience"},{"key":"B53","doi-asserted-by":"publisher","DOI":"10.3389\/fpls.2024.1363063","article-title":"Integrated microbiome and metabolomics analysis reveal the relationship between plant-specialized metabolites and microbial community in Phellodendron amurense","volume":"15","author":"Zhang","year":"2024","journal-title":"Front. Plant Sci."},{"key":"B54","doi-asserted-by":"publisher","first-page":"307","DOI":"10.1002\/9781119312994.apr0701","article-title":"F-box proteins in plants","volume":"2","author":"Zhang","year":"2019","journal-title":"Annu. Plant Rev. Online"},{"key":"B55","doi-asserted-by":"publisher","DOI":"10.1111\/mpp.13459","article-title":"The F-box protein OsFBX156 positively regulates rice defence against the blast fungus Magnaporthe oryzae by mediating ubiquitination-dependent degradation of OsHSP71.1","volume":"25","author":"Zhao","year":"2024","journal-title":"Mol. Plant Pathol."}],"container-title":["Frontiers in Plant Science"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1860906\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,7,8]],"date-time":"2026-07-08T05:55:22Z","timestamp":1783490122000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fpls.2026.1860906\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,7,8]]},"references-count":55,"alternative-id":["10.3389\/fpls.2026.1860906"],"URL":"https:\/\/doi.org\/10.3389\/fpls.2026.1860906","relation":{},"ISSN":["1664-462X"],"issn-type":[{"value":"1664-462X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,7,8]]},"article-number":"1860906"}}