Decoding Soil and Aquatic Microbiomes through Integrated Multi-Omics Approaches: From Structure to Function

Soil and aquatic microbiomes are critical regulators of ecosystem health, nutrient cycling, and climate resilience. However, their immense diversity and complex interactions remain insufficiently understood. Traditional molecular techniques—though valuable—often provide limited insights into the functional relationships within these microbial communities. Recent advances in multi-omics technologies, including genomics, transcriptomics, proteomics, and metabolomics, have revolutionized microbial research by enabling system-level analyses. Integrating these approaches offers unprecedented opportunities to map microbial structure, infer metabolic pathways, and predict functional responses to environmental changes. Understanding these dynamics is particularly vital under increasing anthropogenic pressures such as pollution, land use alteration, and climate change. Decoding soil and aquatic microbiomes through multi-omics integration thus holds great promise for advancing sustainable agriculture, water quality management, and ecosystem restoration.The primary goal of this research topic is to develop and apply integrated multi-omics frameworks to unravel the structural and functional complexities of soil and aquatic microbiomes. Specifically, the project aims to:- Characterize microbial diversity, abundance, and community composition across varying environmental conditions using high-resolution metagenomics.- Link gene expression, protein profiles, and metabolite networks to ecological processes through transcriptomic, proteomic, and metabolomic analyses.- Employ computational modeling and machine learning for data integration, enabling prediction of microbial functions and ecosystem-level responses.- Identify key microbial taxa and biomarkers responsible for nutrient cycling/transformation leading to better plant growth, pollutant degradation, and climate-regulating biochemical cycles.By merging structural and functional datasets, this research topic will provide a comprehensive microbial interaction maps that span soil and water systems. These findings will provide mechanistic insights into microbial ecosystem services, improve environmental monitoring strategies, and support the design of data-driven conservation and remediation measures under changing global conditions.This proposed research topic welcomes contributions from interdisciplinary fields encompassing microbiology, bioinformatics, aquaculture and aquatic sciences, soil sciences, plant biology, environmental science, and systems biology. Authors are invited to submit original research articles, reviews, and case studies focusing on multi-omics analyses of soil and aquatic microbiomes. Topics may include microbial network modeling, integrative data pipelines, novel bioinformatics tools and workflows, functional analysis, and microbial ecosystem responses to stressors. Emphasis will be placed on studies that demonstrate quantitative integration across genomic, proteomic, and metabolomic layers, translating structural data into functional and ecological interpretations. Submissions should be methodologically rigorous, highlighting reproducibility and open data practices. Collaborative works that combine experimental and computational perspectives are particularly encouraged, aiming to establish unified insights bridging molecular mechanisms and ecosystem functioning. Manuscript submissions should follow the journal’s formatting guidelines, ensuring clarity, reproducibility, and relevance to advancing microbiome science through innovative multi-omics integration. Topic editors: Swarna Kanchan, Frederic ANDRES, Minu Kesheri Source: https://www.frontiersin.org/research-topics/78109/decoding-soil-and-aquatic-microbiomes-through-integrated-multi-omics-approaches-from-structure-to-function