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Using amplicon sequencing and genome\u2010resolved metagenomics, we examined how cross\u2010domain microbial networks and functional gene potential respond to long\u2010term phosphorus and nitrogen limitation along the well\u2010characterized Ecological Staircase chronosequence in Mendocino, California, USA. Microbial diversity and abundance declined sharply with terrace age for prokaryotes, predatory protists, and bacteriophages, whereas fungi and phototrophic protists increased in nutrient\u2010depleted, acidic soils. These compositional shifts were accompanied by major changes in reconstructed microbial networks: relative modularity increased alongside robustness, indicating adaptive reorganization that may sustain ecosystem function under resource scarcity. Fungi emerged as central stabilizers in these restructured networks, carrying enriched genetic potential to degrade plant polymers and mobilize phosphorus and nitrogen. Despite a decline in overall phage diversity, the relative abundance of phages encoding phosphorus\u2010mobilizing auxiliary metabolic genes increased, suggesting that viral contributions to host phosphorus metabolism may be enhanced under nutrient limitation. Together, these results demonstrate that ecosystem retrogression drives cross\u2010domain microbial reorganization toward fewer but more interconnected lineages, characterized by greater integration of functional genetic potential. This reorganization enhances the potential for functional resilience under extreme nutrient limitation, revealing how microbial networks adapt to maintain the capacity for nutrient cycling and stability as soils age and fertility declines.<\/jats:p>","DOI":"10.1002\/mlf2.70087","type":"journal-article","created":{"date-parts":[[2026,7,20]],"date-time":"2026-07-20T06:40:28Z","timestamp":1784529628000},"page":"486-506","update-policy":"https:\/\/doi.org\/10.1002\/crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Ecosystem retrogression enhances cross\u2010domain microbial stability and increases the genetic potential for nutrient cycling"],"prefix":"10.1002","volume":"5","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-2954-3477","authenticated-orcid":false,"given":"Javier A.","family":"Ceja\u2010Navarro","sequence":"first","affiliation":[{"name":"Center for Ecosystem Science and Society Northern Arizona University Flagstaff Arizona USA"},{"name":"Department of 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