Micro Niche Ecosystems in Aquatic Environments

Aquatic microbiology increasingly recognizes the critical influence of microscale habitats - such as marine snow, suspended particles, biofilms, and sharp redox interfaces - on the structuring and functioning of microbial life. Recent studies demonstrate that these discrete niches offer unique microenvironments that shape biodiversity, dictate chemical transformations, and mediate interactions across bacteria, archaea, and microbial eukaryotes. While macroscale gradients and processes are well studied, the relevance of localized conditions and their emergent properties remain at the frontier of aquatic microbial ecology. A key challenge persists in linking phenomena observable at the microscale, like community assembly and metabolic exchange, to broader biogeochemical cycles, carbon sequestration, and ecosystem health.

This Research Topic invites studies that examine how microscale habitat structure and heterogeneity influence microbial interactions and aquatic ecosystem functioning. We particularly welcome work that connects small-scale processes to larger-scale ecological and biogeochemical outcomes across marine, freshwater, and transitional environments. Experimental, observational, and modelling studies are all encouraged, especially those that provide mechanistic insight or help bridge spatial scales. This Research Topic welcomes submissions across aquatic environments and microbial groups, provided they clearly address the relationship between microscale habitat heterogeneity and microbial-driven processes in aquatic systems.

We welcome articles addressing, but not limited to, the following themes:

• Structure and formation of micro-niche habitats (e.g., marine snow, biofilms, particle-associated aggregates)

• Microbial interactions and competition within micro-niches

• Consequences of micro-niche conditions for community assembly and diversity

• Coupling of microscale gradients to biogeochemical fluxes (carbon, nitrogen, other elements)

• Methodological innovations for studying aquatic micro-niches (e.g., imaging, modelling, molecular approaches)

• Ecological and evolutionary implications of micro-niche specialization

Article types and fees

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

• Editorial
• FAIR² Data
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• ... 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:

• Editorial
• FAIR² Data
• Hypothesis and Theory
• Methods
• Mini Review
• Opinion
• Original Research
• Perspective
• Review
• Systematic Review
• Technology and Code

Keywords: Microscale, Particle-associated microbes, Biofilms, Community assembly, Biogeochemical fluxes

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.