Multi-Omics Integration for Aquatic Microbial Systems Biology

Microbial communities in aquatic habitats are among the most complex and dynamic biological systems on Earth, providing essential functions in biogeochemical cycling, ecosystem resilience, and water quality regulation. These communities comprise several species interacting through complex networks of genes, metabolites, macromolecules, and environmental variables, providing highly integrated systems that maintain ecosystem function. Understanding this complexity requires comprehensive, systems-orientated approaches that transcend reductionist perspectives of discrete elements.

Integrative systems microbiology uses multi-omics technologies along with environmental and physicochemical data to identify microbial diversity and functional capacity. By combining these complementary data modalities, scientists can clarify microbe-microbe and microbe-environment interactions, uncover metabolic pathways, and discover pivotal microbial taxa influencing ecosystem processes under dynamic environmental conditions. In aquatic ecosystems, the integration of multi-omics is especially effective for analysing microbial community assemblies, adaptive responses to environmental stresses, and biogeochemical transformations at the ecosystem level. Advanced computer tools facilitate the identification of emergent ecological characteristics and offer mechanistic insights into microbial community dynamics across various spatiotemporal dimensions.

The research topic aligns with the journal's scope by highlighting multidisciplinary, data-driven frameworks that integrate genomic, metabolic, and ecological data to enhance the understanding of microbial systems biology. It promotes research that characterises microbial diversity and function while integrating these findings to simulate microbial contributions to ecosystem health, biogeochemical cycles, and environmental sustainability in aquatic environments. This research area enhances multi-omics integration in microbial systems biology, addressing essential issues regarding the organisation, adaptation, and functionality of microbial ecosystems, thereby offering critical insights for environmental management, biotechnological applications, and forecasting ecosystem responses to ongoing global change.

We invite a diverse range of submissions, including original research, reviews, novel methodologies, hypotheses and theories, and perspectives, as well as both experimental and computational studies. Topics include, but are not limited to:

· Multi-omics integration for comprehensive characterization of microbial diversity and function

· Linking microbial community structure and function through combined omics and environmental physicochemical data

· Systems-level elucidation of microbial metabolic pathways and biogeochemical cycling in freshwater, marine, and estuarine ecosystems

· Application of network inference and ecological modelling to reveal microbe-microbe and microbe-environment interactions in aquatic habitats

· Quantitative functional gene annotation using shotgun metagenomics and quantitative metaproteomics for ecosystem function prediction

· Null modelling and ecological algorithms to reveal microbial community assembly and dynamics under variable environmental conditions

· Integrating multi-omics data with environmental metadata to model microbial adaptation and resilience to stressors like pollution, temperature, and nutrient fluctuations

· Metaviromics approaches for discovery of viruses/bacteriophages and their role in the environment

· Bacteriophage evolution, phage-host interactions, and phage-based approaches for control of antimicrobial-resistant bacterial pathogens

· Investigating microbial community responses to climate change and anthropogenic disturbances using integrative omics and systems biology frameworks

· Development and application of computational tools and machine learning for integrated analysis of multi-omics aquatic microbiome data

· Identify the pollutant degradation and nutrient transformations through integrative systems microbiology

We welcome original research articles, reviews, novel methodologies, hypotheses and theories, perspectives, and both experimental and computational studies relevant to these themes.

Article types and fees

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Community Case Study
• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• ... View all formats

Articles that are accepted for publication by our external editors following rigorous peer review incur a publishing fee charged to Authors, institutions, or funders.

Article types

This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:

• Brief Research Report
• Case Report
• Clinical Trial
• Community Case Study
• Data Report
• Editorial
• FAIR² Data
• FAIR² DATA Direct Submission
• General Commentary
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Policy and Practice Reviews
• Policy Brief
• Review
• Systematic Review
• Technology and Code

Keywords: Aquatic microbiomes, multi-omics integration, systems microbiology, biogeochemical cycling, microbial community assembly, network inference, ecological modeling, metagenomics and metaproteomics, microbial adaptation and resilience

Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.