Microbial Networks Within the Extended Phycosphere: Bridging Cells, Communities, and Biogeochemical Function in Aquatic Systems

The phycosphere represents one of the most dynamic ecological boundaries in aquatic environments. Within this narrow chemical and biological gradient, bacteria, archaea, and protists exchange metabolites, signalling molecules, and genetic material that influence nutrient cycling, algal physiology, and ecosystem productivity. Recent advances in single cell genomics, metabolomics, and microsensor technologies have revolutionized our ability to study these interactions, yet current knowledge remains fragmented and often species specific, lacking integration across taxa and spatial scales.
Emerging evidence indicates that microscale microbial interactions extend far beyond the classical definition of the phycosphere, underpinning community assembly, stress adaptation, and biogeochemical coupling throughout aquatic food webs. These associations influence harmful bloom formation, primary production efficiency, and the resilience of planktonic communities under stressors such as eutrophication, warming, and deoxygenation. Bridging the gap between cell level processes and ecosystem level outcomes therefore represents a frontier challenge for aquatic microbiology.
This Research Topic aims to examine the diversity, mechanisms, and ecological relevance of microbial interactions surrounding aquatic primary producers at multiple spatial and temporal scales. We encourage studies that broaden the phycosphere concept to encompass interactions among microalgae, cyanobacteria, heterotrophic microbes, fungi, protists, and viruses in both marine and freshwater systems. Multidisciplinary contributions integrating molecular, biochemical, metabolomic, physiological, imaging, computational, and modelling approaches are highly welcome. We particularly encourage studies investigating the discovery, identification, production, secretion, transport, exchange, and ecological functions of metabolites that mediate interactions among aquatic microorganisms. Emerging technologies such as spatial metabolomics, mass spectrometry imaging, NanoSIMS, Raman microspectroscopy, Imaging Flow cytometry (IFC), Atomic force microscopy (ATM) and other single-cell analytical approaches are especially encouraged to resolve microbial interactions at unprecedented spatial resolution. We also welcome studies applying artificial intelligence, machine learning, network analysis, and multi-omics integration to predict microbial interactions and uncover ecological mechanisms. Together, these approaches will help illuminate how chemical communication and microscale processes shape community assembly, ecosystem functioning, and biogeochemical cycling, while fostering the discovery of novel bioactive natural products and metabolites from aquatic microbial communities.To gather further insights within these boundaries, we welcome articles addressing, but not limited to, the following themes:
- Microbial diversity and functional dynamics within and beyond the phycosphere
- Cross domain interactions among algae, bacteria, archaea, and viruses
- Chemical signalling and metabolite exchange at the algae–microbe interface
- Discovery, identification, and functional characterization of metabolites mediating microbial interactions
- Production, transport, delivery, and uptake of metabolites in aquatic microbial ecosystems
- Natural product discovery and chemical ecology of phycosphere-associated microorganisms
- Spatial metabolomics, mass spectrometry imaging (e.g., MALDI-MSI), NanoSIMS, Raman microspectroscopy, ATM, IFC and other technologies for resolving microbial interactions
- Effects of environmental perturbations on microscale microbial associations
- Evolutionary drivers and ecological consequences of symbiosis and antagonism
- Technological advances enabling in situ or single cell observation of microbial interactions
- Artificial intelligence, machine learning, network analysis, and multi-omics integration for understanding and predicting microbial interactions
- Multi-omics approaches integrating genomics, transcriptomics, proteomics, metabolomics, and environmental metadata
- Scaling up microscale observations to ecosystem and biogeochemical models

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

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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: Phycosphere, Algae-bacteria interactions, Chemical signalling, Metabolomics, Microbial community assembly, Biogeochemical cycling, Multi-omics, Harmful algal blooms

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.