{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,28]],"date-time":"2026-10-28T22:13:25Z","timestamp":1793225605691,"version":"4.5.0"},"reference-count":140,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T00:00:00Z","timestamp":1782950400000},"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:p>Extreme environmental stressors, including freezing temperatures, strong ultraviolet radiation, and nutrient scarcity, pose a serious threat to global food security in high-altitude cold-arid agroecosystems. Ecological stability depends on the phytobiome, which is made up of plant hosts, their microbiomes, and the edaphic environment. Although plant-associated microbiomes are important in providing stress tolerance, existing management strategies predominantly employ descriptive single-strain inoculants, which often fail under open field conditions due to competitive exclusion and environmental drift. The review summarizes recent mechanistic insights into how psychrotolerant microorganisms modify host physiology to alleviate low-temperature stress. We examine the biophysical and biochemical processes involved, with a particular emphasis on the microbial impact on the host plant\u2019s internal ICE1-CBF-COR transcriptional cascade and redox homeostasis, the role of biofilm-mediated extracellular polymeric substances (EPS) in root-zone thermal buffering, and the kinetic inhibition of ice crystallization by antifreeze proteins. Furthermore, we evaluate how genome-scale metabolic modeling can be combined with sophisticated integrated multi-omics approaches, particularly metagenomics, metatranscriptomics, and metabolomics, to create structurally stable synthetic microbial communities (SynComs), going beyond traditional isolation methods. Lastly, we discuss how regional microbial biobanks and ecological network modeling can maximize consortia persistence, addressing the translational obstacles that prevent laboratory-scale efficacy from reproducing in the field. This synthesis presents a methodical approach for creating robust phytobiomes in vulnerable mountain agroecosystems by moving the emphasis from descriptive cataloging to predictable, function-driven synthetic ecology.<\/jats:p>","DOI":"10.3389\/fmicb.2026.1876810","type":"journal-article","created":{"date-parts":[[2026,7,2]],"date-time":"2026-07-02T17:13:50Z","timestamp":1783012430000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":2,"title":["Multi-omics and synthetic microbial ecology for engineering climate-resilient phytobiomes in cold-arid agroecosystems: current advances and future perspectives"],"prefix":"10.3389","volume":"17","author":[{"given":"Vikash","family":"Kumar","sequence":"first","affiliation":[{"name":"School of Horticulture Science and Technology, Kargil Campus University of Ladakh","place":["Kargil, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Faizan","family":"Ahmad","sequence":"additional","affiliation":[{"name":"School of Horticulture Science and Technology, Kargil Campus University of Ladakh","place":["Kargil, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alok","family":"Rai","sequence":"additional","affiliation":[{"name":"Faculty of Agricultural Sciences, GLA University","place":["Mathura, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Akhilesh","family":"Kushwaha","sequence":"additional","affiliation":[{"name":"School of Horticulture Science and Technology, Kargil Campus University of Ladakh","place":["Kargil, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kshitij","family":"Parmar","sequence":"additional","affiliation":[{"name":"Amity Institute of Organic Agriculture, Amity University Uttar Pradesh","place":["Noida, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ramji","family":"Singh","sequence":"additional","affiliation":[{"name":"Sardar Vallabhbhai Patel University of Agriculture and Technology","place":["Meerut, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ajay","family":"Tomar","sequence":"additional","affiliation":[{"name":"Amity Institute of Organic Agriculture, Amity University Uttar Pradesh","place":["Noida, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Chitranjan","family":"Kumar","sequence":"additional","affiliation":[{"name":"Amity Institute of Organic Agriculture, Amity University Uttar Pradesh","place":["Noida, India"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1965","published-online":{"date-parts":[[2026,7,2]]},"reference":[{"key":"B1","doi-asserted-by":"crossref","first-page":"301","DOI":"10.1016\/B978-0-323-91595-3.00006-9","article-title":"Cold-tolerant and cold-loving microorganisms and their applications","volume-title":"Trends of Applied Microbiology for Sustainable Economy","author":"Abeysinghe","year":"2022"},{"key":"B2","doi-asserted-by":"publisher","first-page":"1782","DOI":"10.3390\/biology11121782","article-title":"Plant microbiome engineering: hopes or hypes.","volume":"11","author":"Afridi","year":"","journal-title":"Biology"},{"key":"B3","doi-asserted-by":"publisher","first-page":"899464","DOI":"10.3389\/fpls.2022.899464","article-title":"New opportunities in plant microbiome engineering for increasing agricultural sustainability under stressful conditions.","volume":"13","author":"Afridi","year":"","journal-title":"Front. 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