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<p>Microbial communities maintain biogeochemical function despite environmental stress, yet whether functional redundancy, metabolic complementarity, and temporal partitioning operate in coordination across environmental transitions remains unclear. We integrated genome-resolved metatranscriptomics with metabolomics collected from Saguaro National Park, Arizona in 2021, to link taxon-specific gene expression to metabolite shifts during monsoon-driven transitions. Multi-omics analyses supported three coordinated stability mechanisms. Overlapping carbon and nitrogen pathways indicated functional redundancy, while nitrification and cross-taxon cooperation suggested metabolic complementarity. Distinct transcriptional signatures revealed temporal partitioning: dry-adapted taxa expressed stress tolerance, carbon storage turnover, and NADPH-generating pathways, whereas wet-adapted taxa activated glycolysis, tricarboxylic acid cycle, and carbohydrate-processing enzymes after rainfall. Metabolite profiles mirrored these shifts, with osmoprotectants accumulating during drought and amino acids and oxidative stress metabolites increasing after rewetting. Multi-omics integration explained transcriptional (69%) and metabolite variance (14%). These findings improve predictions of ecosystem responses to altered precipitation and inform the design of stress-resilient microbial consortia.</p>

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Multi-omics integration reveals how coordinated microbial mechanisms maintain biogeochemical stability in water-limited soils

  • 期刊论文

  • 出版模式：

    开放获取

  • 发表日期：

    2026年5月22日

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  • Viviana Freire-Zapata,
  • Christian Ayala-Ortiz,
  • Lawrence R. Walker,
  • Malak M. Tfaily

摘要

Microbial communities maintain biogeochemical function despite environmental stress, yet whether functional redundancy, metabolic complementarity, and temporal partitioning operate in coordination across environmental transitions remains unclear. We integrated genome-resolved metatranscriptomics with metabolomics collected from Saguaro National Park, Arizona in 2021, to link taxon-specific gene expression to metabolite shifts during monsoon-driven transitions. Multi-omics analyses supported three coordinated stability mechanisms. Overlapping carbon and nitrogen pathways indicated functional redundancy, while nitrification and cross-taxon cooperation suggested metabolic complementarity. Distinct transcriptional signatures revealed temporal partitioning: dry-adapted taxa expressed stress tolerance, carbon storage turnover, and NADPH-generating pathways, whereas wet-adapted taxa activated glycolysis, tricarboxylic acid cycle, and carbohydrate-processing enzymes after rainfall. Metabolite profiles mirrored these shifts, with osmoprotectants accumulating during drought and amino acids and oxidative stress metabolites increasing after rewetting. Multi-omics integration explained transcriptional (69%) and metabolite variance (14%). These findings improve predictions of ecosystem responses to altered precipitation and inform the design of stress-resilient microbial consortia.