{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T16:06:43Z","timestamp":1779466003090,"version":"3.53.1"},"reference-count":46,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2026,4,23]],"date-time":"2026-04-23T00:00:00Z","timestamp":1776902400000},"content-version":"vor","delay-in-days":112,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"General Program of the Chongqing Natural Science Foundation","award":["2024NSCQ-MSX2167"],"award-info":[{"award-number":["2024NSCQ-MSX2167"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,1,14]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Understanding how plant\u2013microbe\u2013soil interactions vary across spatial scales is essential for elucidating belowground ecological dynamics, particularly in rare and ecologically sensitive species. Here, we investigated the diversity, function, and assembly of root-associated bacterial communities in Thuja sutchuenensis Franch. along continuous vertical gradients. Through an integrative multi-omics approach, morphological assessment, and soil physicochemical profiling, we uncovered a compartmentalized and spatially structured rhizosphere system. We observed a marked enrichment of soil nutrients, particularly carbon, nitrogen, and available phosphorus, in the rhizosphere compared with bulk soil. Bacterial diversity declined in the endosphere, accompanied by taxonomic and functional shifts, including enrichment of Proteobacteria and Actinobacteriota and metabolic pathways related to host interaction and xenobiotic degradation. Root and soil metabolomes also showed depth-specific signatures, with surface compartments enriched in flavonoids and defense compounds, and deeper layers characterized by core metabolic functions. Co-occurrence network and correlation analyses highlighted key bacterial hubs and revealed strong links between nutrient levels and bacterial diversity. Together, this study provides new insight into the organization of plant\u2013soil ecosystems and offers a framework for conservation and ecological restoration strategies for endangered cliffside species.<\/jats:p>","DOI":"10.1093\/ismeco\/ycag115","type":"journal-article","created":{"date-parts":[[2026,4,21]],"date-time":"2026-04-21T11:30:42Z","timestamp":1776771042000},"source":"Crossref","is-referenced-by-count":0,"title":["Spatial structuring of root-associated bacteria and metabolic landscapes in an endangered cliffside conifer\n                    <i>Thuja sutchuenensis<\/i>\n                    Franch"],"prefix":"10.1093","volume":"6","author":[{"given":"Youwei","family":"Zuo","sequence":"first","affiliation":[{"name":"Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Peng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Wenqiao","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhijang","family":"Yang","sequence":"additional","affiliation":[{"name":"Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongping","family":"Deng","sequence":"additional","affiliation":[{"name":"Key Laboratory of Eco-Environment in the Three Gorges Reservoir Region, Ministry of Education, School of Life Sciences, Southwest University , Beibei, Chongqing 400715 ,","place":["China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,4,23]]},"reference":[{"key":"2026052211372428200_ref1","doi-asserted-by":"publisher","first-page":"14860","DOI":"10.3390\/ijms140714860","article-title":"Genetic diversity of the critically endangered thuja sutchuenensis revealed by issr markers and the implications for conservation","volume":"14","author":"Liu","year":"2013","journal-title":"Int J Mol Sci"},{"key":"2026052211372428200_ref2","doi-asserted-by":"publisher","first-page":"100","DOI":"10.21608\/japs.2024.249826.1000","article-title":"Genus thuja: a comprehensive review on botany, traditional uses, pharmacological activities and phytochemistry","volume":"1","author":"Darwish","year":"2024","journal-title":"J Adv Pharm Sci"},{"key":"2026052211372428200_ref3","doi-asserted-by":"publisher","first-page":"78","DOI":"10.1016\/j.pld.2023.06.005","article-title":"Conservation genomic investigation of an endangered conifer, thuja sutchuenensis, reveals low genetic diversity but also low genetic load","volume":"46","author":"Tao","year":"2024","journal-title":"Plant Divers"},{"key":"2026052211372428200_ref4","first-page":"28","article-title":"Community structure and population regeneration of an endangered plant, thuja sutchuenensis","volume":"38","author":"Xin","year":"2016","journal-title":"J Beijing For Univ"},{"key":"2026052211372428200_ref5","doi-asserted-by":"publisher","first-page":"931","DOI":"10.1080\/0972060X.2014.884774","article-title":"Essential oil and important activities of thuja orientalis and thuja occidentalis","volume":"18","author":"Jasuja","year":"2015","journal-title":"J Essent Oil Bear Plants"},{"key":"2026052211372428200_ref6","doi-asserted-by":"publisher","first-page":"e0125307","DOI":"10.1371\/journal.pone.0125307","article-title":"Community structure and survival of tertiary relict thuja sutchuenensis (cupressaceae) in the subtropical daba mountains, southwestern China","volume":"10","author":"Tang","year":"2015","journal-title":"PLoS One"},{"key":"2026052211372428200_ref7","doi-asserted-by":"publisher","first-page":"113821","DOI":"10.1016\/j.envres.2022.113821","article-title":"Plant-soil-microbes: a tripartite interaction for nutrient acquisition and better plant growth for sustainable agricultural practices","volume":"214","author":"Das","year":"2022","journal-title":"Environ Res"},{"key":"2026052211372428200_ref8","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s40168-018-0526-0","article-title":"Soil microbiomes with distinct assemblies through vertical soil profiles drive the cycling of multiple nutrients in reforested ecosystems","volume":"6","author":"Jiao","year":"2018","journal-title":"Microbiome"},{"key":"2026052211372428200_ref9","doi-asserted-by":"publisher","first-page":"4199","DOI":"10.3390\/ijms20174199","article-title":"Mechanistic insights into arbuscular mycorrhizal fungi-mediated drought stress tolerance in plants","volume":"20","author":"Bahadur","year":"2019","journal-title":"Int J Mol Sci"},{"key":"2026052211372428200_ref10","first-page":"319","volume-title":"Mycorrhizal Mediation of Soil","author":"Pickles"},{"key":"2026052211372428200_ref11","doi-asserted-by":"publisher","first-page":"123","DOI":"10.1111\/j.1469-8137.1996.tb01152.x","article-title":"Decomposition, nitrogen and phosphorus mineralization from beech leaf litter colonized by ectomycorrhizal or litter-decomposing basidiomycetes","volume":"134","author":"Colpaert","year":"1996","journal-title":"New Phytol"},{"key":"2026052211372428200_ref12","doi-asserted-by":"publisher","first-page":"960","DOI":"10.1111\/1365-2745.12888","article-title":"Poor plant performance under simulated climate change is linked to mycorrhizal responses in a semi-arid shrubland","volume":"106","author":"Le\u00f3n-S\u00e1nchez","year":"2018","journal-title":"J Ecol"},{"key":"2026052211372428200_ref13","doi-asserted-by":"publisher","first-page":"105","DOI":"10.1007\/s40858-022-00544-7","article-title":"Biocontrol of soil borne diseases by plant growth promoting rhizobacteria","volume":"48","author":"Abdelaziz","year":"2023","journal-title":"Trop Plant Pathol"},{"key":"2026052211372428200_ref14","doi-asserted-by":"publisher","first-page":"1145715","DOI":"10.3389\/fpls.2023.1145715","article-title":"Molecular interaction between plants and trichoderma species against soil-borne plant pathogens","volume":"14","author":"Dutta","year":"2023","journal-title":"Front Plant Sci"},{"key":"2026052211372428200_ref15","first-page":"111","volume-title":"The Rhizosphere","author":"Brimecombe"},{"key":"2026052211372428200_ref16","first-page":"471","volume-title":"Sustainable Agriculture under Drought Stress","author":"Etesami"},{"key":"2026052211372428200_ref17","doi-asserted-by":"publisher","first-page":"gkaf042","DOI":"10.1093\/nar\/gkaf042","article-title":"G-quadruplex structures in 16s rrna regions correlate with thermal adaptation in prokaryotes","volume":"53","author":"Lyu","year":"2025","journal-title":"Nucleic Acids Res"},{"key":"2026052211372428200_ref18","doi-asserted-by":"publisher","first-page":"1833","DOI":"10.1016\/j.soilbio.2009.06.003","article-title":"Importance of spatially structured environmental heterogeneity in controlling microbial community composition at small spatial scales in an agricultural field","volume":"41","author":"Franklin","year":"2009","journal-title":"Soil Biol Biochem"},{"key":"2026052211372428200_ref19","first-page":"167","article-title":"The effects of fine scale environmental variation on microbial community structure and functioning in aquatic environments","volume":"5","author":"Smart","year":"2008","journal-title":"Environ Microbiol Res Trends"},{"key":"2026052211372428200_ref20","doi-asserted-by":"publisher","first-page":"e00260","DOI":"10.1128\/spectrum.00260-22","article-title":"Contrasting responses of multispatial soil fungal communities of thuja sutchuenensis franch., an extremely endangered conifer in southwestern China. Microbiology","volume":"10","author":"Zuo","year":"2022","journal-title":"Spectrum"},{"key":"2026052211372428200_ref21","doi-asserted-by":"publisher","first-page":"881921","DOI":"10.3389\/fmicb.2022.881921","article-title":"Comparative analyses of rhizosphere bacteria along an elevational gradient of thuja sutchuenensis","volume":"13","author":"Zuo","year":"2022","journal-title":"Front Microbiol"},{"key":"2026052211372428200_ref22","doi-asserted-by":"publisher","first-page":"559","DOI":"10.1111\/1755-0998.12109","article-title":"Principles of transcriptome analysis and gene expression quantification: an rna-seq tutorial","volume":"13","author":"Wolf","year":"2013","journal-title":"Mol Ecol Resour"},{"key":"2026052211372428200_ref23","doi-asserted-by":"publisher","first-page":"tpae120","DOI":"10.1093\/treephys\/tpae120","article-title":"How is tree growth rate linked to root functional traits in phylogenetically related poplar hybrids?","volume":"44","author":"Rabearison","year":"2024","journal-title":"Tree Physiol"},{"key":"2026052211372428200_ref24","doi-asserted-by":"publisher","first-page":"eaba3756","DOI":"10.1126\/sciadv.aba3756","article-title":"The fungal collaboration gradient dominates the root economics space in plants","volume":"6","author":"Bergmann","year":"2020","journal-title":"Sci Adv"},{"key":"2026052211372428200_ref25","doi-asserted-by":"publisher","first-page":"1123","DOI":"10.1111\/nph.17072","article-title":"Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs","volume":"232","author":"Freschet","year":"2021","journal-title":"New Phytol"},{"key":"2026052211372428200_ref26","doi-asserted-by":"publisher","first-page":"695","DOI":"10.1146\/annurev.arplant.50.1.695","article-title":"Roots in soil: unearthing the complexities of roots and their rhizospheres","volume":"50","author":"McCully","year":"1999","journal-title":"Annu Rev Plant Biol"},{"key":"2026052211372428200_ref27","doi-asserted-by":"publisher","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":"2026052211372428200_ref28","doi-asserted-by":"publisher","first-page":"145","DOI":"10.56557\/upjoz\/2024\/v45i134143","article-title":"Symbiotic relationships between nitrogen-fixing bacteria and leguminous plants ecological and evolutionary perspectives: a review","volume":"45","author":"Chellem","year":"2024","journal-title":"Uttar Pradesh J Zool"},{"key":"2026052211372428200_ref29","first-page":"325","volume-title":"Biotechnology for Biofuel Production and Optimization","author":"Lu"},{"key":"2026052211372428200_ref30","doi-asserted-by":"publisher","first-page":"1259853","DOI":"10.3389\/fpls.2023.1259853","article-title":"Enhancing plant growth in biofertilizer-amended soil through nitrogen-transforming microbial communities","volume":"14","author":"Li","year":"2023","journal-title":"Front Plant Sci"},{"key":"2026052211372428200_ref31","doi-asserted-by":"publisher","first-page":"e70009","DOI":"10.1111\/1462-2920.70009","article-title":"Microbial community of a sandy beach subterranean estuary is spatially heterogeneous and impacted by winter waves","volume":"26","author":"Bullington","year":"2024","journal-title":"Environ Microbiol"},{"key":"2026052211372428200_ref32","doi-asserted-by":"publisher","first-page":"1115","DOI":"10.1890\/11-1030.1","article-title":"Compositional divergence and convergence in arbuscular mycorrhizal fungal communities","volume":"93","author":"Caruso","year":"2012","journal-title":"Ecology"},{"key":"2026052211372428200_ref33","doi-asserted-by":"publisher","first-page":"297","DOI":"10.1007\/978-81-322-1620-9_17","article-title":"Mapk signaling cascades and transcriptional reprogramming in plant\u2013pathogen interactions","volume":"1","author":"Taj","year":"2014","journal-title":"Approaches to plant stress and their management"},{"key":"2026052211372428200_ref34","doi-asserted-by":"crossref","first-page":"489","DOI":"10.1007\/978-3-319-31305-4_30","article-title":"The photobiology of symbiodinium spp.: linking physiological diversity to the implications of stress and resilience","volume":"11","author":"Warner","year":"2016","journal-title":"The Cnidaria, past, present and future: The world of Medusa and her sisters"},{"key":"2026052211372428200_ref35","doi-asserted-by":"publisher","first-page":"619499","DOI":"10.3389\/fmicb.2021.619499","article-title":"Spatiotemporal dynamics of maize (zea mays l.) root growth and its potential consequences for the assembly of the rhizosphere microbiota","volume":"12","author":"Bonkowski","year":"2021","journal-title":"Front Microbiol"},{"key":"2026052211372428200_ref36","doi-asserted-by":"publisher","first-page":"8","DOI":"10.3389\/fagro.2020.00008","article-title":"Rhizosphere spatiotemporal organization\u2013a key to rhizosphere functions","volume":"2","author":"Vetterlein","year":"2020","journal-title":"Front Agron"},{"key":"2026052211372428200_ref37","doi-asserted-by":"publisher","first-page":"621","DOI":"10.3390\/ijms21020621","article-title":"Jasmonic acid signaling pathway in response to abiotic stresses in plants","volume":"21","author":"Ali","year":"2020","journal-title":"Int J Mol Sci"},{"key":"2026052211372428200_ref38","doi-asserted-by":"publisher","first-page":"122","DOI":"10.3389\/fpls.2015.00122","article-title":"Transcriptomic profiling of linolenic acid-responsive genes in ros signaling from rna-seq data in arabidopsis","volume":"6","author":"Mata-P\u00e9rez","year":"2015","journal-title":"Front Plant Sci"},{"key":"2026052211372428200_ref39","doi-asserted-by":"publisher","first-page":"eraf482","DOI":"10.1093\/jxb\/eraf482","article-title":"Lipid-mediated responses to nutrient and other stresses: roles in plant adaptation and signaling","volume":"133","author":"Pandey","year":"2025","journal-title":"J Exp Bot"},{"key":"2026052211372428200_ref40","doi-asserted-by":"publisher","first-page":"470","DOI":"10.1038\/s41564-018-0129-3","article-title":"Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly","volume":"3","author":"Zhalnina","year":"2018","journal-title":"Nat Microbiol"},{"key":"2026052211372428200_ref41","doi-asserted-by":"publisher","first-page":"102383","DOI":"10.1016\/j.pmpp.2024.102383","article-title":"Exploring phenolic compounds as natural stress alleviators in plants-a comprehensive review","volume":"133","author":"Saini","year":"2024","journal-title":"Physiol Mol Plant Pathol"},{"key":"2026052211372428200_ref42","doi-asserted-by":"publisher","first-page":"175822","DOI":"10.1016\/j.scitotenv.2024.175822","article-title":"Redundancy and resilience of microbial community under aniline stress during wastewater treatment","volume":"951","author":"Chen","year":"2024","journal-title":"Sci Total Environ"},{"key":"2026052211372428200_ref43","doi-asserted-by":"crossref","DOI":"10.2139\/ssrn.4601408","article-title":"Microbial network complexity supports the microbial structure stability and soil functionality: evidence from a natural aridity gradient in alpine ecosystem","author":"Zhang","year":"2023"},{"key":"2026052211372428200_ref44","doi-asserted-by":"publisher","first-page":"e0124456","DOI":"10.1371\/journal.pone.0124456","article-title":"Spatial heterogeneity of soil nutrients after the establishment of caragana intermedia plantation on sand dunes in alpine sandy land of the Tibet plateau","volume":"10","author":"Li","year":"2015","journal-title":"PLoS One"},{"key":"2026052211372428200_ref45","doi-asserted-by":"publisher","first-page":"159355","DOI":"10.1016\/j.scitotenv.2022.159355","article-title":"Determining the contribution of microbiome complexity to the soil nutrient heterogeneity of fertile islands in a desert ecosystem","volume":"857","author":"Li","year":"2023","journal-title":"Sci Total Environ"},{"key":"2026052211372428200_ref46","doi-asserted-by":"publisher","first-page":"670","DOI":"10.1002\/ldr.3690","article-title":"Effects of vegetation restoration on soil nutrients, plant diversity, and its spatiotemporal heterogeneity in a desert\u2013oasis ecotone","volume":"32","author":"Wu","year":"2021","journal-title":"Land Degrad Dev"}],"container-title":["ISME Communications"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/ismecommun\/advance-article-pdf\/doi\/10.1093\/ismeco\/ycag115\/68142616\/ycag115.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag115\/68142616\/ycag115.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/ismecommun\/article-pdf\/6\/1\/ycag115\/68142616\/ycag115.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,5,22]],"date-time":"2026-05-22T15:37:31Z","timestamp":1779464251000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/ismecommun\/article\/doi\/10.1093\/ismeco\/ycag115\/8661325"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,1]]},"references-count":46,"journal-issue":{"issue":"1","published-print":{"date-parts":[[2026,1,14]]}},"URL":"https:\/\/doi.org\/10.1093\/ismeco\/ycag115","relation":{},"ISSN":["2730-6151"],"issn-type":[{"value":"2730-6151","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,1]]},"published":{"date-parts":[[2026,1]]},"article-number":"ycag115"}}