Aquatic organisms are densely colonized by a wide variety of microorganisms, such as bacteria, fungi, algae, and protozoans. For example, a rough estimate based on literature data suggests that the abundance of zooplankton-associated bacteria alone can rival or exceed that of free-living bacteria. With the exception of a few pathogens, little is known about the ecology of these microbial symbionts, such as their life cycle, their interactions with the hosts and adjacent microbes, and the evolution of this symbiotic relationship. Higher organisms present specific microhabitats with very different environmental conditions than the surrounding water, and they may therefore support the proliferation and activities of distinct microbial communities, with important biogeochemical consequences. For example, earlier research has suggested that the guts and feces of zooplankton and fish may support anaerobic microbial processes that otherwise cannot occur in the oxygen-rich water columns.
Recent advances in methodology such as microprofiling allow researchers to characterize microhabitats within the higher organisms in unprecedented details. Rapid development of single-cell and molecular techniques for phylogenetic and physiological analyses also offers enormous opportunities to study these symbionts at different scales, from a single gene to the whole community, and even their evolutionary changes in near real time. New experimental approaches using genetically accessible model systems and individual-based modeling can also provide a mechanistic and systematic understanding of host-symbiont relationships.
This Research Topic aims to highlight new findings on the molecular and functional ecology of microbial symbionts in all aquatic environments. The goal is to promote exchange among experts from various fields to advance a conceptual framework for future studies on the interactions between microbial symbionts and higher organisms in aquatic systems.

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.