{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T10:22:21Z","timestamp":1788430941658,"version":"build-2803163510"},"reference-count":56,"publisher":"Wiley","license":[{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T00:00:00Z","timestamp":1788393600000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/doi.wiley.com\/10.1002\/tdm_license_1.1"}],"content-domain":{"domain":["onlinelibrary.wiley.com"],"crossmark-restriction":true},"short-container-title":["Plant Cell &amp;amp; Environment"],"abstract":"<jats:title>ABSTRACT<\/jats:title>\n                  <jats:p>Harnessing plant microbiomes for sustainable agriculture requires understanding not only whether they can boost crop performance, but also how ecological processes govern their assembly, stability, and functional contributions across environments. While we previously showed that seed tuber microbiomes can predict potato vigour using machine learning, it remained unclear how ecological processes shape tuber microbiome stability and functionality across host genotypes, tuber compartments, soil types, and years. Here, we analyzed the national\u2010scale dataset of 240 field\u2010collected potato seedlots, spanning six genotypes, two soil types, and two growing years, with a focus on the spatially distinct heel and eye compartments of the potato tuber. By profiling over 1200 bacterial and fungal communities and linking microbiome composition to plant performance, we show that plant genotype and tuber compartment are the strongest determinants of microbial diversity and composition. Compartment\u2010specific enrichment of functional traits revealed spatial partitioning of microbial functions, with organic compound conversion and nitrogen cycling dominant in the heel, and energy metabolism enriched in the eye. Applying a macroecological abundance\u2013occupancy framework, we identified a stable core microbiome of bacterial and fungal taxa that persisted across all environments and years. These core members were more strongly associated with plant growth\u2010related traits than non\u2010core taxa, and core taxa in different tuber compartments showed distinct correlations with taxa of potential pathogenic relevance. Together, our findings demonstrate that tuber compartments act as ecological filters that structure persistent, functionally specialised microbiomes linked to plant growth\u2010related traits across environments. By providing an ecological and functional framework for compartment\u2010resolved, stable core microbiomes, this study advances mechanistic understanding of plant\u2013microbe interactions and identifies stable microbial partners as promising targets for improving potato resilience and productivity.<\/jats:p>","DOI":"10.1111\/pce.70843","type":"journal-article","created":{"date-parts":[[2026,9,3]],"date-time":"2026-09-03T10:09:38Z","timestamp":1788430178000},"update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Ecological Filtering by Tuber Compartments Shapes Stable Core Microbiomes That Underpin Potato Plant Growth Across Environments"],"prefix":"10.1111","author":[{"given":"Yizhu","family":"Qiao","sequence":"first","affiliation":[{"name":"Plant\u2010Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life Utrecht University Utrecht The Netherlands"},{"name":"Jiangsu Provincial Key Lab for Organic\u2010based Fertilizer Creation and Soil Health Manipulation Nanjing Agricultural University Nanjing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Junqing","family":"Qiao","sequence":"additional","affiliation":[{"name":"Plant\u2010Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life Utrecht University Utrecht The Netherlands"},{"name":"Institute of Plant Protection Jiangsu Academy of Agricultural Science Nanjing China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Roeland L.","family":"Berendsen","sequence":"additional","affiliation":[{"name":"Plant\u2010Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life Utrecht University Utrecht The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0003-2230-7126","authenticated-orcid":false,"given":"Xu","family":"Cheng","sequence":"additional","affiliation":[{"name":"Shenzhen Branch, Guangdong Laboratory of Lingnan Modern Agriculture, Key Laboratory of Synthetic Biology Ministry of Agriculture and Rural Affairs, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences Shenzhen China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-5473-4646","authenticated-orcid":false,"given":"Corn\u00e9 M.J.","family":"Pieterse","sequence":"additional","affiliation":[{"name":"Plant\u2010Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life Utrecht University Utrecht The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-4710-7978","authenticated-orcid":false,"given":"Yang","family":"Song","sequence":"additional","affiliation":[{"name":"Plant\u2010Microbe Interactions, Institute of Environmental Biology, Department of Biology, Science4Life Utrecht University Utrecht The Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"311","published-online":{"date-parts":[[2026,9,3]]},"reference":[{"key":"e_1_2_8_2_1","doi-asserted-by":"crossref","first-page":"281","DOI":"10.1111\/j.1469-8137.2009.03160.x","article-title":"The UNITE Database for Molecular Identification of Fungi \u2013 Recent Updates and Future Perspectives","volume":"186","author":"Abarenkov K.","year":"2010","journal-title":"New Phytologist"},{"key":"e_1_2_8_3_1","doi-asserted-by":"crossref","DOI":"10.1371\/journal.pbio.1002352","article-title":"Microbial Hub Taxa Link Host and Abiotic Factors to Plant Microbiome Variation","volume":"14","author":"Agler M. 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