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.Falkowski, P. G., Barber, R. T., & Smetacek, V. (1998). Biogeochemical Controls and Feedbacks on Ocean Primary Production. Science, 281(5374), 200–206. https://doi.org/10.1126/science.281.5374.200 Diazotrophic cyanobacteria, for example, fix atmospheric nitrogen, boosting productivity in nutrient-poor waters.Zehr, J. P., & Kudela, R. M. (2011). Nitrogen cycle of the open ocean: From genes to ecosystems. Annual Review of Marine Science, 3(1), 197-225. https://doi.org/10.1146/annurev-marine-120709-142819 As primary producers, phytoplankton absorb CO2 through photosynthesis, contributing to the biological carbon pump and long-term carbon sequestration.Legendre, L., & and Rassoulzadegan, F. (1995). Plankton and nutrient dynamics in marine waters. Ophelia, 41(1), 153–172. https://doi.org/10.1080/00785236.1995.10422042Turner, J. T. (2015). Zooplankton fecal pellets, marine snow, phytodetritus and the ocean's biological pump. Progress in Oceanography, 130, 205–248. https://doi.org/10.1016/j.pocean.2014.08.005
Phytoplankton–microbiome interactions are central to the global 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.Dickey, J. R., Mercer, N. M., Kuijpers, M. C. M., Props, R., & Jackrel, S. L. (2025). Biodiversity within phytoplankton-associated microbiomes regulates host physiology, host community ecology, and nutrient cycling. mSystems, 10(2), e0146224. https://doi.org/10.1128/msystems.01462-24Ahern, O. M., Whittaker, K. A., Williams, T. C., Hunt, D. E., & Rynearson, T. A. (2021). Host genotype structures the microbiome of a globally dispersed marine phytoplankton. Proceedings of the National Academy of Sciences of the United States of America, 118(48), e2105207118. https://doi.org/10.1073/pnas.2105207118Duncan, A., Barry, K., Daum, C., Eloe-Fadrosh, E., Roux, S., Schmidt, K., Tringe, S. G., Valentin, K. U., Varghese, N., Salamov, A., Grigoriev, I. V., Leggett, R. M., Moulton, V., & Mock, T. (2022). Metagenome-assembled genomes of phytoplankton microbiomes from the Arctic and Atlantic Oceans. Microbiome, 10(1). https://doi.org/10.1186/s40168-022-01254-7 Chemical signaling—through Quorum sensing and Infochemicals—regulate microbial behavior, impacting bloom dynamics, symbiosis, and defense mechanisms.Zhou, J., Lyu, Y., Richlen, M., Anderson, D. M., & Cai, Z. (2016). Quorum sensing is a language of chemical signals and plays an ecological role in algal-bacterial interactions. Critical Reviews in Plant Sciences, 35(2), 81–105. https://doi.org/10.1080/07352689.2016.1172461Kuhlisch, C., Shemi, A., Barak-Gavish, N., Schatz, D., & Vardi, A. (2024). Algal blooms in the ocean: Hot spots for chemically mediated microbial interactions. Nature Reviews. Microbiology, 22(3), 138–154. https://doi.org/10.1038/s41579-023-00975-2 Viruses also affect phytoplankton populations by driving nutrient turnover and mediating carbon flow.Flynn, K. J., Mitra, A., Wilson, W. H., Kimmance, S. A., Clark, D. R., Pelusi, A., & Polimene, L. (2022). "Boom-and-busted" dynamics of phytoplankton-virus interactions explain the paradox of the plankton. The New Phytologist, 234(3), 990–1002. https://doi.org/10.1111/nph.18042Rhodes, C. J., Truscott, J. E., & Martin, A. P. (2008). Viral infection as a regulator of oceanic phytoplankton populations. Journal of Marine Systems, 74(1), 216–226. https://doi.org/10.1016/j.jmarsys.2008.01.005
Current research focuses on microbial diversity, environmental drivers, and chemical communication, all of which are crucial to understanding the phytoplankton microbiome's ecological functions. These microbial interactions shape marine ecosystem stability, food web dynamics, and global climate processes.
Ecological role and function Symbiotic relationships between phytoplankton and their microbiomes are crucial for promoting phytoplankton growth, resilience to stress, and overall ecological stability. Microorganisms, including bacteria and archaea, provide essential nutrients like nitrogen and phosphorus through nitrogen fixation and nutrient recycling. In return, phytoplankton offer a stable habitat, supplying organic compounds and surface areas where microbes can attach.
These interactions bolster the phytoplankton's ability to cope with environmental challenges, such as oxidative stress, pathogens, and harmful algal blooms, through the protective functions of specific microbial communities.Ashraf, N., Ahmad, F., & Lu, Y. (2023). Synergy between microalgae and microbiome in polluted waters. Trends in Microbiology, 31(1), 9–21. https://doi.org/10.1016/j.tim.2022.06.004Jackrel, S. L., Yang, J. W., Schmidt, K. C., & Denef, V. J. (2021). Host specificity of microbiome assembly and its fitness effects in phytoplankton. The ISME Journal, 15(3), 774–788. https://doi.org/10.1038/s41396-020-00812-x Additionally, microbiomes influence marine primary production by enhancing nutrient uptake and stimulating phytoplankton growth, which in turn supports higher trophic levels in marine food webs.Choi, C. J., Jauzein, C., & Erdner, D. L. (2023). High-resolution phylogenetic analysis reveals long-term microbial dynamics and microdiversity in phytoplankton microbiome. Journal of Eukaryotic Microbiology, 70(3), e12966. https://doi.org/10.1111/jeu.12966
Moreover, the microbes associated with phytoplankton are key players in biogeochemical cycles. They facilitate nitrogen fixation and break down organic matter, releasing usable nitrogen and carbon that fuel phytoplankton growth and help close crucial nutrient loops.Jiao, N., Robinson, C., Azam, F., Thomas, H., Baltar, F., Dang, H., Hardman-Mountford, N. J., Johnson, M., Kirchman, D. L., Koch, B. P., Legendre, L., Li, C., Liu, J., Luo, T., Luo, Y.-W., Mitra, A., Romanou, A., Tang, K., Wang, X., ... Zhang, R. (2014). Mechanisms of microbial carbon sequestration in the ocean – future research directions. Biogeosciences, 11(19), 5285–5306. https://doi.org/10.5194/bg-11-5285-2014 These dynamic interactions between phytoplankton and their microbiomes are instrumental in maintaining ocean productivity and the functioning of marine ecosystems.
Microbial diversity and environmental influences
Role of microbiomes in phytoplankton physiology and ecological interactions
Microbial diversity within eukaryotes influences host physiology, nutrient cycling, and community dynamics in marine ecosystems. Higher microbiome diversity correlates with increased bacterial phenotypic and taxonomic diversity, while lower diversity leads to reduced bacterial diversity. The microbiome of phytoplankton also affects phytoplankton growth and survival rates, which affect oceanic cycles. Additionally, microbial diversity affects phytoplankton biomass, with low diversity linked to higher biomass and higher diversity to lower biomass. Under stressful conditions, such as rising water temperatures, the impact of microbiome diversity on phytoplankton community structure is amplified, decreasing community diversity and abundance. Increased microbial diversity also elevates the levels of dissolved nitrogen and phosphorus in the water.
Phytoplankton are genetically diverse, spanning 12 taxonomic divisions, yet maintain conserved metabolic functions vital for biogeochemical stability, such as photosynthesis and nutrient cycling. Cyanobacteria, an ancient group, dominate modern phytoplankton populations and contributed to the evolution of eukaryotic algae and plants through endosymbiosis. This functional redundancy has ensured phytoplankton's resilience despite environmental changes. Environmental stresses, including chemical alterations in ocean chemistry by phytoplankton, drive phylogenetic diversity and reinforce ecosystem stability.
Phytoplankton release dissolved organic matter (DOM), which sustains their microbiome and part of the bacterioplankton community.Yang, J. W., & Denef, V. J. (2024). Dissecting host-microbiome interaction effects on phytoplankton microbiome composition and diversity. Environmental Microbiology, 26(2), e16585. https://doi.org/10.1111/1462-2920.16585 Microbial communities in these systems are shaped by deterministic processes, enhancing host function, while free-living communities are more flexible and less diverse. Microevolution through host-microbe interactions supports ecological adaptation and niche differentiation.
Influence of host genotype on phytoplankton-associated microbiomes The phycosphere refers to the region surrounding individual phytoplankton, where algae, bacteria, archaea, and viruses interact. Among these organisms, bacteria have the most significant influence on the phycosphere. The specific conditions of the phycosphere help select particular bacterial populations, which in turn shape the microbial community. Over time, as these communities evolve, they can also enhance the fitness of the host.
The interactions between bacteria and phytoplankton are complex. In marine ecosystems, it remains unclear whether the genetic makeup of the host influences the bacterial community composition. However, it is known that phytoplankton species are categorized into populations based on their genetic traits, often linked to their ability to survive in specific environmental conditions. For instance, a study on T. rotula showed that the genotype of the host phytoplankton influences the microbial community surrounding it.
Influence of chemical signaling on phytoplankton-associated microbiomes and algal blooms
Phytoplankton interact with surrounding microbial communities through chemical signaling, exchanging compounds that influence growth, metabolism, and community composition. Microbes provide essential nutrients such as vitamins and nitrogen, while phytoplankton release organic molecules that help structure microbial populations.
These interactions are often concentrated in the phycosphere, however, during large blooms, chemical signals can operate over broader scales due to increased cell density and compound concentration.
Throughout the bloom cycle—ranging from dormancy to demise—chemical signals mediate different ecological roles. In early stages, signals like DMSP attract beneficial bacteria. During peak growth, microbes exchange growth-promoting compounds, while in later stages, stress-related signals may trigger defense or cell death, contributing to bloom decline and nutrient recycling.
These microscale chemical exchanges shape microbial succession and impact broader ecosystem functions, including carbon and nutrient cycling.
Composition and diversity of phytoplankton-associated microbial communities