Marine microbiome
All animals on Earth form associations with microorganisms, including protists, bacteria, archaea, fungi, and viruses. In the ocean, animal–microbial relationships were historically explored in single host–symbiont systems. However, new explorations into the diversity of marine microorganisms associating with diverse marine animal hosts is moving the field into studies that address interactions between the animal host and a more multi-member microbiome. The potential for microbiomes to influence the health, physiology, behavior, and ecology of marine animals could alter current understandings of how marine animals adapt to change, and especially the growing climate-related and anthropogenic-induced changes already impacting the ocean environment.
In the oceans, it is challenging to find eukaryotic organisms that do not live in close relationship with a microbial partner. Host-associated microbiomes also influence biogeochemical cycling within ecosystems with cascading effects on biodiversity and ecosystem processes. The microbiomes of diverse marine animals are currently under study, from simplistic organisms including sponges and ctenophores to more complex organisms such as sea squirts and sharks.
Background
Within the vast biological diversity that inhabits the world's oceans, it would be challenging to find a eukaryotic organism that does not live in close relationship with a microbial partner. Such symbioses, i.e., persistent interactions between host and microbe in which none of the partners gets harmed and at least one of them benefits, are ubiquitous from shallow reefs to deep-sea hydrothermal vents. Studies on corals, sponges, and mollusks have revealed some of the profoundly important symbiotic roles microbes play in the lives of their hosts. These studies, however, have tended to focus on a small number of specific microbial taxa. In contrast, most hosts retain groups of many hundreds of different microbes pervasively influences the functioning of Earth's ecosystems, including ecosystem productivity. However, this research has focused almost exclusively on macroorganisms. Because microbial symbionts are integral parts of most living organisms, the understanding of how microbial symbionts contribute to host performance and adaptability needs broadening.Foundations of productive ecosystems
s, such as many types of corals, deep-sea mussels, and hydrothermal vent tubeworms, contribute to primary productivity and create the structural habitats and nutrient resources that are the foundation of their respective ecosystems. All of these taxa engage in mutualistic nutritional symbioses with microbes. There are many examples of marine nutritional mutualisms in which microbes enable hosts to utilize resources or substrates otherwise unavailable to the host alone. Such symbioses have been described in detail in reduced and anoxic sediments and hydrothermal vents. Moreover, many foundational species of marine macroalgae are vitamin auxotrophs, and their productivity depends on provisioning from their epiphytic bacteria. Reefs often consist of stony corals, one of the most well-known examples of a mutualistic symbiosis, in which the dinoflagellate alga Symbiodiniaceae supplies the coral with glucose, glycerol, and amino acids, while the coral provides the algae with a protected environment and limiting compounds needed for photosynthesis. However, this is a classic example of a mutualistic symbiosis that is sensitive to environmental disturbances, which can disrupt the fragile interactions between host and microbe. When reefs become warm and eutrophic, mutualistic Symbiodiniaceae may induce cellular damage to the host and/or sequester more resources for their own growth, thereby injuring and parasitizing their hosts. Reef fishes, which seek homes on coral reefs, are important in fostering coral recovery in the wake of disturbance. Epulopiscium bacteria in the guts of surgeonfishes produce enzymes that allow their hosts to digest complex polysaccharides, enabling the host fish to feed on tough, leathery red and brown macroalgae. This trophic innovation has facilitated niche diversification among coral reef herbivores. Surgeonfishes are critical to the functioning of Indo-Pacific coral reefs, as they are among the only fishes capable of consuming large macroalgae that bloom in the wake of ecosystem disturbance and suppress coral recovery.Along with more standard examples of nutritional symbioses in animals, recent advances in genome sequencing technology have led to the discovery of many endosymbiotic associations in marine protists These illustrate the incorporation of various new biochemical functions, such as photosynthesis, nitrogen fixation and recycling, and methanogenesis, into protist hosts by endosymbionts. Endosymbiosis in protists is widespread and represents an important source of innovation. Previously unrecognized metabolic innovations of marine microbial symbioses that are ecologically important are discovered regularly. For example, Candidatus Kentron nourish their ciliate hosts in the genus Kentrophoros and recycle acetate and propionate, which are low-value cellular waste products from their hosts, into biomass. Another example is the anaerobic marine ciliate Strombidium purpureum. The ciliate lives under anaerobic conditions and harbors endosymbiotic purple nonsulfur bacteria that contain both bacteriochlorophyll a and spirilloxanthin. The endosymbionts are photosynthetically active; hence, this symbiosis represents an evolutionary transition of an aerobic organism to an anaerobic one while incorporating organelles.
Reproduction and host development
Extending beyond nutritional symbioses, microbial symbionts can alter the reproduction, development, and growth of their hosts. Specific bacterial strains in marine biofilms often directly control the recruitment of planktonic larvae and propagules, either by inhibiting settlement or by serving as a settlement cue. For example, the settlement of zoospores from the green alga Ulva intestinalis onto the biofilms of specific bacteria is mediated by their attraction to the quorum-sensing molecule, acyl-homoserine lactone, secreted by the bacteria. Classic examples of marine host–microbe developmental dependence include the observation that algal cultures grown in isolation exhibited abnormal morphologies and the subsequent discovery of morphogenesis-inducing compounds, such as thallusin, secreted by epiphytic bacterial symbionts. Bacteria are also known to influence the growth of marine plants, macroalgae, and phytoplankton by secreting phytohormones such as indole acetic acid and cytokinin-type hormones. In the marine choanoflagellate Salpingoeca rosetta, both multicellularity and reproduction are triggered by specific bacterial cues, offering a view into the origins of bacterial control over animal development signaling in biofilms.Biogeochemical cycling
Host-associated microbiomes also influence biogeochemical cycling within ecosystems with cascading effects on biodiversity and ecosystem processes. For example, microbial symbionts comprise up to 40% of the biomass of their sponge hosts. Through a process termed the "sponge-loop," they convert dissolved organic carbon released by reef organisms into particulate organic carbon that can be consumed by heterotrophic organisms. Along with the coral–Symbiodiniaceae mutualism, this sponge-bacterial symbiosis helps explain Darwin's paradox, i.e., how highly productive coral reef ecosystems exist within otherwise oligotrophic tropical seas. Some sponge symbionts play a significant role in the marine phosphorus cycle by sequestering nutrients in the form of polyphosphate granules in the tissue of their host and nitrogen cycling, e.g., through nitrification, denitrification, and ammonia oxidation.]. Many macroalgal-associated bacteria are specifically adapted to degrade complex algal polysaccharides and modify both the quality and quantity of organic carbon supplied to the ecosystem. The sulfur-oxidizing gill endosymbionts of lucinid clams contribute to primary productivity through chemosynthesis and facilitate the growth of seagrasses by lowering sulfide concentrations in tropical sediments. Gammaproteobacterial symbionts of lucinid clams and stilbonematid nematodes were also recently shown to be capable of nitrogen fixation remains ripe for exploration and, indeed, requires a more integrated framework from the fields of microbiology, evolutionary biology, community ecology, and oceanography. Individual taxa within the microbiome may help hosts withstand a wide range of environmental conditions, including those predicted under scenarios of climate change. Next, we explore two different avenues of how interdisciplinary collaborations could advance this line of research.Examples
Phytoplankton
A phytoplankton microbiome is the community of microorganisms—mainly bacteria, but also including fungi and viruses—that live in association with phytoplankton. These microbiomes play a critical role in marine ecosystems by supporting phytoplankton health, facilitating nutrient cycling, sustaining food webs, and contributing to climate regulation.Microbial partners help decompose organic matter and recycle key nutrients like nitrogen and carbon, sustaining primary production and supporting ocean productivity and phytoplankton community structure. Diazotrophic cyanobacteria, for example, fix atmospheric nitrogen, boosting productivity in nutrient-poor waters. As primary producers, phytoplankton absorb CO2 through photosynthesis, contributing to the biological carbon pump and long term carbon sequestration.
Phytoplankton–microbiome interactions are central to marine biogeochemical cycles. Microbial diversity influences host physiology and ecosystem functions, while environmental factors such as temperature, nutrient levels, and ocean chemistry shape microbiome composition and function. Chemical signaling—through quorum sensing and infochemicals—regulate microbial behavior, impacting bloom dynamics, symbiosis, and defense mechanisms. Viruses also affect phytoplankton populations by driving nutrient turnover and mediating carbon flow.