{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,9]],"date-time":"2026-10-09T04:39:13Z","timestamp":1791520753999,"version":"4.3.4"},"reference-count":60,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T00:00:00Z","timestamp":1777852800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:sec>\n                    <jats:title>Introduction<\/jats:title>\n                    <jats:p>The rhizosphere microbiome serves as a critical line of defense for plant health and soil-borne disease suppression. However, the underlying mechanisms by which root-knot nematodes (RKN), a devastating soil-borne pathogen, undermine putative disease-suppressive function through destabilizing microbial interaction networks remain poorly understood.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>This study employed metagenomic sequencing coupled with microbial co-occurrence network analysis to systematically compare the community structure, interaction network topology, and functional gene profiles of the rhizosphere microbiome between healthy and RKN-infected tomato plants.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Our findings revealed that RKN infection significantly altered the community structure of bacteria, fungi, and viruses. This disturbance was associated with a systematic simplification and loss of modularity within microbial interaction networks. Specifically, intra-domain bacterial networks exhibited reduced scale and connectivity, whereas fungal networks showed strengthened internal cohesion. Cross-kingdom interactions (e.g., bacteria-fungi) were severely weakened, resulting in a topological imbalance characterized by \u201ctight within domains, loose between domains.\u201d Functional profiling further indicated a distinct metabolic reprogramming in the infected rhizosphere, with a shift in resource allocation from growth and biosynthesis toward core energy acquisition and stress response.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Collectively, our results suggest that the putative decline in disease-suppressive function following RKN infection may be mechanistically rooted in the destabilization of microbial cooperative networks and the consequent loss of functional redundancy. This study provides a novel network-level ecological framework for understanding plant-microbe-pathogen interactions and lays a theoretical foundation for microbiome-based ecological management strategies against soil-borne diseases.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.3389\/fmicb.2026.1798902","type":"journal-article","created":{"date-parts":[[2026,5,4]],"date-time":"2026-05-04T05:34:20Z","timestamp":1777872860000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Metagenomic analysis suggests that tomato root-knot nematode infestation disrupts rhizosphere microbial networks, consistent with reduced disease suppression"],"prefix":"10.3389","volume":"17","author":[{"given":"Jie","family":"Duan","sequence":"first","affiliation":[{"name":"Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region\/Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), College of Agronomy, Ministry of Agriculture and Rural Affairs, Xinjiang Agricultural University","place":["Urumqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yang","family":"Chen","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region\/Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), College of Agronomy, Ministry of Agriculture and Rural Affairs, Xinjiang Agricultural University","place":["Urumqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xiaojing","family":"Zhang","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region\/Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), College of Agronomy, Ministry of Agriculture and Rural Affairs, Xinjiang Agricultural University","place":["Urumqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chenchen","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region\/Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), College of Agronomy, Ministry of Agriculture and Rural Affairs, Xinjiang Agricultural University","place":["Urumqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianmei","family":"Gao","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region\/Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), College of Agronomy, Ministry of Agriculture and Rural Affairs, Xinjiang Agricultural University","place":["Urumqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kemei","family":"Li","sequence":"additional","affiliation":[{"name":"Key Laboratory of the Pest Monitoring and Safety Control of Crops and Forests of the Xinjiang Uygur Autonomous Region\/Key Laboratory of Prevention and Control of Invasive Alien Species in Agriculture and Forestry of the North-western Desert Oasis (Co-construction by Ministry and Province), College of Agronomy, Ministry of Agriculture and Rural Affairs, Xinjiang Agricultural University","place":["Urumqi, China"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,5,4]]},"reference":[{"key":"ref1","doi-asserted-by":"publisher","first-page":"1301698","DOI":"10.3389\/fpls.2023.1301698","article-title":"Deciphering key factors in pathogen-suppressive microbiome assembly in the rhizosphere","volume":"14","author":"Andargie","year":"2023","journal-title":"Front. 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