| Microorganisms are fundamental to ecosystem functioning, driving essential biogeochemical cycles and sustaining ecosystem services across marine, terrestrial, freshwater, and host-associated environments. Rapid environmental change driven by climate variability, pollution, and anthropogenic disturbance had increasingly altered microbial communities in ways that were not adequately explained by taxonomic composition alone. This limitation prompted a shift in microbial ecology toward function-centered analyses enabled by advances in functional meta-omics. This review examined how metagenomics, metatranscriptomics, metaproteomics, and integrated multi-omics approaches advanced understanding of microbial functional potential, activity, and metabolic output under environmental perturbation. Conceptual frameworks linking genetic potential to realized function were synthesized, highlighting the roles of functional diversity, redundancy, and network organization in community resistance and resilience. Case studies across diverse ecosystems illustrated how environmental stressors reshaped microbial metabolic pathways and ecosystem services, often without corresponding changes in taxonomic structure. The review also evaluated bioinformatic tools and analytical pipelines used for functional annotation, pathway reconstruction, and cross-omics data integration. Key challenges associated with multi-omics research were identified, including high computational demands, lack of methodological standardization, and difficulties in integrating heterogeneous datasets for predictive modeling. Despite these constraints, functional microbiome characterization was shown to provide critical insights for forecasting ecosystem responses to environmental change and for informing applications in environmental management, bioremediation, and sustainable resource use. Overall, the transition from taxonomic inventories to function-based frameworks seems to be essential for advancing predictive microbial ecology and for understanding the role of microbiomes in maintaining planetary health.
Keywords: Functional meta-omics, Microbial ecology, Metagenomics, Environmental perturbations, Functional diversity, Ecosystem resilience.
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