{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,30]],"date-time":"2026-07-30T14:01:47Z","timestamp":1785420107419,"version":"3.56.0"},"reference-count":65,"publisher":"MDPI AG","issue":"11","license":[{"start":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T00:00:00Z","timestamp":1779667200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001809","name":"National Natural Science Foundation of China","doi-asserted-by":"publisher","award":["32160063"],"award-info":[{"award-number":["32160063"]}],"id":[{"id":"10.13039\/501100001809","id-type":"DOI","asserted-by":"publisher"}]},{"award":["32160063"],"award-info":[{"award-number":["32160063"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Yunnan Provincial Undergraduate Universities\u2019 Association","award":["202401BA070001-121"],"award-info":[{"award-number":["202401BA070001-121"]}]},{"name":"Yunnan Provincial Undergraduate Universities\u2019 Association","award":["202501BA070001-100"],"award-info":[{"award-number":["202501BA070001-100"]}]},{"DOI":"10.13039\/501100007846","name":"Yunnan Provincial Department of Education","doi-asserted-by":"crossref","award":["2026J1148"],"award-info":[{"award-number":["2026J1148"]}],"id":[{"id":"10.13039\/501100007846","id-type":"DOI","asserted-by":"crossref"}]},{"award":["2026J1148"],"award-info":[{"award-number":["2026J1148"]}],"id":[{"id":"https:\/\/ror.org\/02yrxdp92","id-type":"ROR","asserted-by":"publisher"}]},{"name":"Zhaotong \u201cXingzhao Talent Support Program\u201d Team Project","award":["2023-3"],"award-info":[{"award-number":["2023-3"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Biology"],"abstract":"<jats:p>The Gastrodia elata Blume (GE) life cycle is unique, since its successful germination and growth rely on symbiosis with specific fungi (e.g., Armillaria mellea). However, the community succession, tissue specificity and functional potential of endophytic and rhizosphere bacterial communities during the seed formation stage of GE remain unclear. Here, we used high-throughput 16S rRNA gene sequencing to systematically explore the composition, diversity, and dynamic succession of bacterial communities across different stages of seed formation and among various tissues. Our results revealed that the endophytic community remained relatively stable across most developmental stages and tissue types (ANOSIM R = 0.4568, p = 0.001), with significant compositional shifts only occurring at the fruiting stage in specific tissues (stems and seeds). In contrast, the rhizosphere soil bacterial community showed stronger developmental succession (ANOSIM R = 0.7037, p = 0.001), with progressive divergence and the strongest segregation observed between the initial planting and fruiting stages. Alpha diversity peaked at the flowering stage for endophytic bacteria (Shannon index) and at the bud formation stage for rhizosphere soil bacteria, with persistent core taxa (Bacteroides in endophytic bacteria, Pseudarthrobacter in rhizosphere soil bacteria) dominating across stages. Functional predictions revealed stable core metabolic pathways, with stage-specific enrichments of glycolysis or gluconeogenesis at late developmental stages. These results provide novel ecological insights into the spatiotemporal dynamics of bacterial communities across different stages of GE seed formation, highlighting the distinct ecological strategies of endophytic and rhizosphere soil bacteria during the reproductive development of the plant.<\/jats:p>","DOI":"10.3390\/biology15110829","type":"journal-article","created":{"date-parts":[[2026,5,25]],"date-time":"2026-05-25T15:05:08Z","timestamp":1779721508000},"page":"829","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Community Succession and Diversity Variation of Endophytic and Rhizosphere Soil Bacteria Across Gastrodia elata Seed Formation Stages"],"prefix":"10.3390","volume":"15","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0441-4257","authenticated-orcid":false,"given":"Kaize","family":"Shen","sequence":"first","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Key Laboratory of Smart Villages and Agri-Cultural-Tourism Integration, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Mingjian","family":"Xu","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-3321-6687","authenticated-orcid":false,"given":"Wei","family":"Zhou","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Hongyin","family":"Zhou","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6503-2164","authenticated-orcid":false,"given":"Weihua","family":"Wang","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yani","family":"Su","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Haiyan","family":"He","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shunqiang","family":"Yang","sequence":"additional","affiliation":[{"name":"Yunnan Key Laboratory of Gastrodia and Fungi Symbiotic Biology, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Engineering Research Center of Green Planting and Processing of Gastrodia, Zhaotong University, Zhaotong 657000, China"},{"name":"School of Agronomy and Life Sciences, Zhaotong University, Zhaotong 657000, China"},{"name":"Yunnan Key Laboratory of Smart Villages and Agri-Cultural-Tourism Integration, Zhaotong University, Zhaotong 657000, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,5,25]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2554","DOI":"10.1093\/plphys\/kiad198","article-title":"Symbiosis between Dendrobium catenatum protocorms and Serendipita indica involves the plant hypoxia response pathway","volume":"192","author":"Xu","year":"2023","journal-title":"Plant Physiol."},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"e0218524","DOI":"10.1128\/spectrum.02185-24","article-title":"Shifts in bacterial community composition during symbiotic seed germination of a terrestrial orchid and effects on protocorm development","volume":"12","author":"Zhao","year":"2024","journal-title":"Microbiol. Spectr."},{"key":"ref_3","doi-asserted-by":"crossref","first-page":"604964","DOI":"10.3389\/fmicb.2020.604964","article-title":"Diversity and structure of the endophytic bacterial communities associated with three terrestrial Orchid species as Revealed by 16S rRNA Gene Metabarcoding","volume":"11","author":"Alibrandi","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_4","doi-asserted-by":"crossref","unstructured":"Novak, S.D., Aguirre, K.A., Neher, W.R., and Torres, A.M. (2026). Bacterial endophytes journey from the seed to the seedling: An analysis of community structural shifts and bacterial localization during colonization. BMC Plant Biol., 26.","DOI":"10.1186\/s12870-026-08113-9"},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"1697953","DOI":"10.3389\/fmicb.2026.1697953","article-title":"Unveiling the diversity and mechanisms of plant growth-promoting bacteria in orchids: A comprehensive review","volume":"17","author":"Ramzan","year":"2026","journal-title":"Front. Microbiol."},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"Sun, Y., Jin, J., Wang, X., Zhu, W., Gao, J., Li, J., Xie, Q., Wei, Y., Lu, C., and Zhu, G. (2025). Isolation of endophytic phosphate-solubilizing bacteria from Chinese Cymbidium (Cymbidium spp.) Orchid Roots. Microorganisms, 13.","DOI":"10.3390\/microorganisms13102229"},{"key":"ref_7","doi-asserted-by":"crossref","unstructured":"Mametja, N.M., Ramadwa, T.E., Managa, M., and Masebe, T.M. (2025). Recent advances and developments in bacterial endophyte identification and application: A 20-year yandscape review. Plants, 14.","DOI":"10.20944\/preprints202506.1466.v1"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"775665","DOI":"10.3389\/fmicb.2021.775665","article-title":"Analysis of endophytic bacterial diversity from different Dendrobium stems and discovery of an endophyte produced dendrobine-type sesquiterpenoid alkaloids","volume":"12","author":"Wang","year":"2021","journal-title":"Front. Microbiol."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Mahadeo, K., Ta\u00efbi, A., Meile, J.-C., C\u00f4me, B., Gauvin-Bialecki, A., Boubakri, H., Herrera-Belaroussi, A., and Kodja, H.J.B. (2024). Exploring endophytic bacteria communities of Vanilla planifolia. BMC Microbiol., 24.","DOI":"10.1186\/s12866-024-03362-w"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Liu, J., Zeng, D., Huang, Y., Zhong, L., Liao, J., Shi, Y., Jiang, H., Luo, Y., Liang, Y., and Chai, S. (2024). The structure and diversity of bacteria and fungi in the roots and rhizosphere soil of three different species of Geodorum. BMC Genom., 25.","DOI":"10.1186\/s12864-024-10143-2"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"1309038","DOI":"10.3389\/fpls.2023.1309038","article-title":"The role of symbiotic fungi in the life cycle of Gastrodia elata Blume (Orchidaceae): A comprehensive review","volume":"14","author":"Liu","year":"2023","journal-title":"Front. Plant Sci."},{"key":"ref_12","first-page":"686","article-title":"Retrospect on the research of the cultivation of Gastrodia elata Bl, a rare traditional Chinese medicine","volume":"113","author":"Xu","year":"2000","journal-title":"Chin. Med. J."},{"key":"ref_13","first-page":"237","article-title":"Studies on the life cycle of Gastrodia elata","volume":"11","author":"Xu","year":"1989","journal-title":"Zhongguo Yi Xue Ke Xue Yuan Xue Bao"},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"1092552","DOI":"10.3389\/fmicb.2022.1092552","article-title":"High-throughput sequencing-based analysis of the composition and diversity of endophytic bacteria community in tubers of Gastrodia elata f.glauca","volume":"13","author":"Zheng","year":"2022","journal-title":"Front. Microbiol."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1389907","DOI":"10.3389\/fmicb.2024.1389907","article-title":"Features of bacterial and fungal communities in the rhizosphere of Gastrodia elata cultivated in greenhouse for early harvest","volume":"15","author":"Khanh","year":"2024","journal-title":"Front. Microbiol."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"128489","DOI":"10.1016\/j.micres.2026.128489","article-title":"Rhizomorph endophytic bacterial community of Armillaria and growth promotion of Armillaria gallica and Gastrodia elata","volume":"307","author":"Jin","year":"2026","journal-title":"Microbiol. Res."},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Fan, Y., Tian, M., Hu, D., and Xiong, Y. (2025). Exploring the biocultural nexus of Gastrodia elata in Zhaotong: A pathway to ecological conservation and economic growth. Biology, 14.","DOI":"10.3390\/biology14070846"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"18457","DOI":"10.1038\/s41598-025-99706-1","article-title":"Comprehensive quantitative evaluation and mechanism analysis of influencing factors on yield and quality of cultivated Gastrodia elata Blume","volume":"15","author":"Jiang","year":"2025","journal-title":"Sci. Rep."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"e16168","DOI":"10.1002\/ajb2.16168","article-title":"Congeneric temperate orchids recruit similar-yet differentially abundant-endophytic bacterial communities that are uncoupled from soil, but linked to host phenology and population size","volume":"110","author":"Kaur","year":"2023","journal-title":"Am. J. Bot."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1002\/jobm.202100462","article-title":"Surface sterilization for isolation of endophytes: Ensuring what (not) to grow","volume":"62","author":"Sahu","year":"2022","journal-title":"J. Basic Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"382","DOI":"10.1094\/PDIS-01-22-0001-RE","article-title":"Analyses of multilocus sequences and morphological features reveal Ilyonectria Species associated with black rot disease of Gastrodia elata","volume":"108","author":"Qiao","year":"2024","journal-title":"Plant Dis."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"7769","DOI":"10.1128\/AEM.02144-12","article-title":"Residual viral and bacterial contamination of surfaces after cleaning and disinfection","volume":"78","author":"Tuladhar","year":"2012","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"1233555","DOI":"10.3389\/fmicb.2023.1233555","article-title":"Effect of symbiotic fungi-Armillaria gallica on the yield of Gastrodia elata Bl. and insight into the response of soil microbial community","volume":"14","author":"Wang","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"1421","DOI":"10.1007\/s00253-015-7039-6","article-title":"Denitrifying sulfide removal process on high-salinity wastewaters in the presence of Halomonas sp.","volume":"100","author":"Liu","year":"2016","journal-title":"Appl. Microbiol. Biotechnol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"2345942","DOI":"10.1080\/20002297.2024.2345942","article-title":"Impact of HbA1c control and type 2 diabetes mellitus exposure on the oral microbiome profile in the elderly population","volume":"16","author":"Zeng","year":"2024","journal-title":"J. Oral Microbiol."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"85","DOI":"10.1007\/978-1-0716-3072-3_5","article-title":"A practical guide to 16S rRNA microbiome analysis in musculoskeletal disorders","volume":"2649","author":"Rooney","year":"2023","journal-title":"Methods Mol. Biol."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Maki, K.A., Wolff, B., Varuzza, L., Green, S.J., and Barb, J.J. (2023). Multi-amplicon microbiome data analysis pipelines for mixed orientation sequences using QIIME2: Assessing reference database, variable region and pre-processing bias in classification of mock bacterial community samples. PLoS ONE, 18.","DOI":"10.1371\/journal.pone.0280293"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"i884","DOI":"10.1093\/bioinformatics\/bty560","article-title":"fastp: An ultra-fast all-in-one FASTQ preprocessor","volume":"34","author":"Chen","year":"2018","journal-title":"Bioinformatics"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"2957","DOI":"10.1093\/bioinformatics\/btr507","article-title":"FLASH: Fast length adjustment of short reads to improve genome assemblies","volume":"27","author":"Salzberg","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"2194","DOI":"10.1093\/bioinformatics\/btr381","article-title":"UCHIME improves sensitivity and speed of chimera detection","volume":"27","author":"Edgar","year":"2011","journal-title":"Bioinformatics"},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"996","DOI":"10.1038\/nmeth.2604","article-title":"UPARSE: Highly accurate OTU sequences from microbial amplicon reads","volume":"10","author":"Edgar","year":"2013","journal-title":"Nat. Methods"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"5261","DOI":"10.1128\/AEM.00062-07","article-title":"Naive Bayesian classifier for rapid assignment of rRNA sequences into the new bacterial taxonomy","volume":"73","author":"Wang","year":"2007","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"7537","DOI":"10.1128\/AEM.01541-09","article-title":"Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities","volume":"75","author":"Schloss","year":"2009","journal-title":"Appl. Environ. Microbiol."},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"486","DOI":"10.5812\/ijem.3505","article-title":"Normality tests for statistical analysis: A guide for non-statisticians","volume":"10","author":"Ghasemi","year":"2012","journal-title":"Int. J. Endocrinol. Metab."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"872","DOI":"10.1111\/iej.13911","article-title":"The root canal microbiome diversity and function. A whole-metagenome shotgun analysis","volume":"57","author":"Costalonga","year":"2024","journal-title":"Int. Endod. J."},{"key":"ref_36","doi-asserted-by":"crossref","first-page":"149","DOI":"10.1016\/j.neuroscience.2025.04.050","article-title":"Association between the relative abundance of butyrate-producing and mucin-degrading taxa and Parkinson\u2019s disease","volume":"576","author":"Rust","year":"2025","journal-title":"Neuroscience"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"e11004","DOI":"10.1002\/ece3.11004","article-title":"Fungal communities associated with early immature tubers of wild Gastrodia elata","volume":"14","author":"Li","year":"2024","journal-title":"Ecol. Evol."},{"key":"ref_38","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1186\/s40793-020-00358-7","article-title":"Tax4Fun2: Prediction of habitat-specific functional profiles and functional redundancy based on 16S rRNA gene sequences","volume":"15","author":"Wemheuer","year":"2020","journal-title":"Environ. Microbiome"},{"key":"ref_39","doi-asserted-by":"crossref","unstructured":"Chen, H., and Boutros, P.C. (2011). VennDiagram: A package for the generation of highly-customizable Venn and Euler diagrams in R. BMC Bioinform., 12.","DOI":"10.1186\/1471-2105-12-35"},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"713","DOI":"10.1093\/procel\/pwad024","article-title":"The best practice for microbiome analysis using R","volume":"14","author":"Wen","year":"2023","journal-title":"Protein Cell"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"111445","DOI":"10.1016\/j.foodcont.2025.111445","article-title":"A Gastrodia elata green tea pulsed light sterilization model based on cost-benefit and GA-SVR algorithm","volume":"177","author":"Li","year":"2025","journal-title":"Food Control."},{"key":"ref_42","doi-asserted-by":"crossref","first-page":"129886","DOI":"10.1016\/j.talanta.2026.129886","article-title":"Differential analysis of Gastrodia elata f. glauca and Gastrodia elata f. viridis based on metabolomics, and origin traceability of Yunnan Gastrodia elata f. glauca using near-infrared spectroscopy combined with DD-SIMCA","volume":"308","author":"Rong","year":"2026","journal-title":"Talanta"},{"key":"ref_43","first-page":"28","article-title":"Development situations and countermeasures of Gastrodia elata Industry in Zhaotong City","volume":"12","author":"Zhu","year":"2021","journal-title":"AgEcon Search"},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"1734174","DOI":"10.3389\/fpls.2026.1734174","article-title":"Altitude modulates growth and bioactive compounds in two Gastrodia elata forms through the microenvironment and soil microbes","volume":"17","author":"Diao","year":"2026","journal-title":"Front. Plant Sci."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1007\/s12223-021-00939-0","article-title":"Endophytic fungal communities and their biotechnological implications for agro-environmental sustainability","volume":"67","author":"Yadav","year":"2022","journal-title":"Folia. Microbiol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"70","DOI":"10.1007\/s00425-024-04501-3","article-title":"A review on endophytic bacteria of orchids: Functional roles toward synthesis of bioactive metabolites for plant growth promotion and disease biocontrol","volume":"260","author":"Saikia","year":"2024","journal-title":"Planta"},{"key":"ref_47","doi-asserted-by":"crossref","unstructured":"Yao, N., Wang, T., Jiang, J., Yang, Y., and Cao, X. (2024). Coriolopsis strumosa as an Orchid endophytic fungus and Its spatial distribution in Epidendrum sp. (Orchidaceae). Microorganisms, 12.","DOI":"10.3390\/microorganisms12061054"},{"key":"ref_48","doi-asserted-by":"crossref","first-page":"733","DOI":"10.1016\/j.tplants.2024.02.001","article-title":"Orchids acquire fungal carbon for seed germination: Pathways and players","volume":"29","author":"Zhao","year":"2024","journal-title":"Trends Plant Sci."},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"136","DOI":"10.1186\/s40168-019-0750-2","article-title":"Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization","volume":"7","author":"Chen","year":"2019","journal-title":"Microbiome"},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"e0223822","DOI":"10.1128\/spectrum.02238-22","article-title":"Improved cultivation and isolation of diverse endophytic bacteria inhabiting Dendrobium Roots by Using Simply Modified Agar Media","volume":"10","author":"Nishioka","year":"2022","journal-title":"Microbiol. Spectr."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"e0014023","DOI":"10.1128\/mra.00140-23","article-title":"Survey of the endophytic bacteria inhabiting wild Daucus seed using 16S rRNA Gene amplicon sequencing","volume":"12","author":"Kumar","year":"2023","journal-title":"Microbiol. Resour. Announc."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"500","DOI":"10.1002\/sae2.12075","article-title":"Evaluation of 16S rRNA gene primer pairs for bacterial community profiling in an across soil and ryegrass plant study","volume":"2","author":"Shi","year":"2023","journal-title":"J. Sustain. Agric. Environ."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"e31573","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":"ref_54","doi-asserted-by":"crossref","first-page":"1164","DOI":"10.1016\/j.tplants.2025.05.001","article-title":"Coexistence ecology of pathogen-inhibiting microbes in the phytobiome","volume":"30","author":"Elhady","year":"2025","journal-title":"Trends Plant Sci."},{"key":"ref_55","doi-asserted-by":"crossref","unstructured":"Xu, Y., Li, J., Qiao, C., Yang, J., Li, J., Zheng, X., Wang, C., Cao, P., Li, Y., and Chen, Q. (2024). Rhizosphere bacterial community is mainly determined by soil environmental factors, but the active bacterial diversity is mainly shaped by plant selection. BMC Microbiol., 24.","DOI":"10.1186\/s12866-024-03611-y"},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"1103550","DOI":"10.3389\/fmicb.2023.1103550","article-title":"Revealing the relative importance among plant species, slope positions, and soil types on rhizosphere microbial communities in northern tropical karst and non-karst seasonal rainforests of China","volume":"14","author":"Zhang","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref_57","doi-asserted-by":"crossref","first-page":"120248","DOI":"10.1016\/j.indcrop.2024.120248","article-title":"Insight into the Gastrodia elata microbiome and its relationship with secondary metabolites","volume":"223","author":"Chen","year":"2025","journal-title":"Ind. Crops Prod."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"110915","DOI":"10.1016\/j.dib.2024.110915","article-title":"Whole genome sequence data of a lignocellulose-degrading bacterium, Arthrobacter koreensis BSB isolated from the soils of Santiniketan, India","volume":"57","author":"Show","year":"2024","journal-title":"Data Brief"},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"e0100323","DOI":"10.1128\/spectrum.01003-23","article-title":"Pangenome analysis provides insights into the genetic diversity, metabolic versatility, and evolution of the genus Flavobacterium","volume":"11","author":"Kim","year":"2023","journal-title":"Microbiol. Spectr."},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"143776","DOI":"10.1016\/j.chemosphere.2024.143776","article-title":"Isolation of Massilia species capable of degrading Poly(3-hydroxybutyrate) isolated from eggplant (Solanum melongena L.) field","volume":"368","author":"Chhetri","year":"2024","journal-title":"Chemosphere"},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1211649","DOI":"10.3389\/fmicb.2023.1211649","article-title":"Dynamic distribution of Massilia spp. in sewage, substrate, plant rhizosphere\/phyllosphere and air of constructed wetland ecosystem","volume":"14","author":"Xu","year":"2023","journal-title":"Front. Microbiol."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"1257","DOI":"10.3389\/fmicb.2020.01257","article-title":"The effect of plant geographical location and developmental stage on root-associated microbiomes of Gymnadenia conopsea","volume":"11","author":"Lin","year":"2020","journal-title":"Front. Microbiol."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"1690","DOI":"10.1111\/nph.17291","article-title":"Temporal turnover in mycorrhizal interactions: A proof of concept with orchids","volume":"230","author":"Jacquemyn","year":"2021","journal-title":"New Phytol."},{"key":"ref_64","doi-asserted-by":"crossref","first-page":"790","DOI":"10.1038\/ismej.2013.196","article-title":"Rhizosphere microbiome assemblage is affected by plant development","volume":"8","author":"Chaparro","year":"2014","journal-title":"ISME J."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Chen, L., Wang, Y.C., Qin, L.Y., He, H.Y., Yu, X.L., Yang, M.Z., and Zhang, H.B. (2019). Dynamics of fungal communities during Gastrodia elata growth. 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