{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T18:32:20Z","timestamp":1792089140357,"version":"4.4.0"},"reference-count":46,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T00:00:00Z","timestamp":1775001600000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100018531","name":"Major Science and Technology Projects in Yunnan Province","doi-asserted-by":"publisher","award":["202102AE090005, 202205AF150017, 202101BD070001-106, 202202AE090034-04, YNWR-QNBJ-2020-180"],"award-info":[{"award-number":["202102AE090005, 202205AF150017, 202101BD070001-106, 202202AE090034-04, YNWR-QNBJ-2020-180"]}],"id":[{"id":"10.13039\/501100018531","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Plant Sci."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>The rhizosphere metabolome is a crucial mediator of plant-substrate interactions, yet how different cultivation substrates reprogram this metabolic interface and influence crop performance remains poorly understood.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Using tomato as a model, we employed non-targeted metabolomics based on solvent extraction followed by gas chromatography-mass spectrometry (GC-MS) to compare rhizosphere metabolic profiles under three substrates: conventional facility soil (SL), pinecone residue (PR), and peat substrate (PS).<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>We identified and annotated 276 metabolites, with lipids and lipid-like molecules being the most abundant class (24.28%). Substrate type fundamentally reshaped the metabolome, with PR inducing the most distinct profile and PS triggering the most extensive metabolic reprogramming (277 differential metabolites). Notably, over 91% of differential metabolites were up-regulated upon tomato cultivation. The superior physicochemical properties (e.g., lower bulk density, higher nutrient availability) of organic substrates (PR and PS) were linked to both the distinct metabolic signatures and significant enhancements in tomato growth and fruit quality, particularly in PS which showed an 80.08% yield increase and a 50.19% boost in fruit vitamin C content.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Our findings demonstrate that organic substrates, especially peat, enhance plant performance by activating a more diverse and functionally specialized rhizosphere metabolome, providing a mechanistic basis for optimizing substrate selection in facility agriculture.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fpls.2026.1783719","type":"journal-article","created":{"date-parts":[[2026,4,1]],"date-time":"2026-04-01T05:42:39Z","timestamp":1775022159000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Substrate-driven reprogramming of the rhizosphere metabolome underlies enhanced tomato growth and quality in soilless cultivation"],"prefix":"10.3389","volume":"17","author":[{"given":"Yu","family":"Chen","sequence":"first","affiliation":[{"name":"College of Resources and Environment, Yunnan Agricultural University","place":["Kunming, China"]},{"name":"Key Laboratory for Improving Quality and Productivity of Arable Land of Yunnan Province, College of Resources and Environment, Yunnan Agricultural University","place":["Kunming, Yunnan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuyuan","family":"Chai","sequence":"additional","affiliation":[{"name":"College of Resources and Environment, Yunnan Agricultural University","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Chen","sequence":"additional","affiliation":[{"name":"Kunming Changshui International Airport Power Energy Department","place":["Kunming, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jing","family":"Shi","sequence":"additional","affiliation":[{"name":"College of Resources and Environment, Yunnan Agricultural University","place":["Kunming, China"]},{"name":"Key Laboratory for Improving Quality and Productivity of Arable Land of Yunnan Province, College of Resources and Environment, Yunnan Agricultural University","place":["Kunming, Yunnan, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,4,1]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","DOI":"10.3390\/plants11223153","article-title":"Changes in soil characteristics, microbial metabolic pathways, TCA cycle metabolites and crop productivity following frequent application of municipal solid waste compost","volume":"11","author":"Abbey","year":"2022","journal-title":"Plants"},{"key":"B2","doi-asserted-by":"publisher","DOI":"10.1016\/j.envexpbot.2020.104119","article-title":"Metabolic responses of Vaccinium corymbosum L. cultivars to Al3+ toxicity and gypsum amendment","volume":"176","author":"Alarc\u00f3n-Poblete","year":"2020","journal-title":"Environ. 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