Phytoplankton are the major photosynthetic organisms in aquatic environments that play a critical role in the global carbon cycle as well as the biogeochemical cycling of many other elements. They are the base of the marine food web, and thus are intricately linked to marine fisheries and ocean productivity. Despite being classified as autotrophic, most phytoplankton depend on closely associated bacteria that provide them with essential metabolites and cofactors required for their survival and adaptation to the changing environment. In exchange, phytoplankton provide these bacterial microbiomes with dissolved organic matter (DOM) that attracts and nurtures these algal microbiomes. Exchanges between phytoplankton cells and their microbiome occur in a small region that surrounds algal cells called the phycosphere. Exchanges of metabolites in the phycosphere is believed to influence major phenomena in the oceans, including primary productivity, harmful algal blooms, carbon export, and cloud formation. These exchanges occur on the pico- to nanoliter scale, which renders these relationships within the phycosphere challenging to examine at relevant scales. Additionally, the high microbial diversity in the ocean hinders our ability to study these relationships by simply sampling the ocean using traditional techniques.
To address these challenges, our lab:
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Uses model systems to study symbiosis between major phytoplankton lineages (namely diatoms and dinoflagellates) and their microbiome
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Develops cutting-edge techniques to sample the phycosphere using novel microfluidic approaches
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Innovates methods in single-cell genomics and ultra-high resolution mass spectrometry to characterize and quantify new symbiotic relations in the phycosphere.
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Microbiome Assembly
Our lab investigates the mechanisms that govern phytoplankton microbiome assembly.
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Central to our research is the idea that microbiome assembly is a multifaceted process that must be studied across biological scales. We unravel these mechanisms by integrating environmental sampling, in vitro experiments, and advanced genomic, transcriptomic, and metabolomic analyses. A major focus of our work is the phytoplankton phycosphere, the microscale environment surrounding phytoplankton cells that is analogous to the plant rhizosphere and serves as a hotspot for microbial activity. Interactions within the phycosphere shape bacterial colonization, attachment, and community assembly.
We seek to understand the interplay between bacteria and phytoplankton which drive selection, modulation, and maintenance of phytoplankton microbiomes.We combine field sampling with laboratory-based approaches to characterize these interactions. Field sampling involves the collection of phytoplankton cells (single cells and high-density bloom samples) from natural environments and analyzing their associated microbiomes using 16S rRNA amplicon sequencing and shotgun metagenomics. Single-cell analyses reveal host-specific microbiome filtering in situ, demonstrating how individual diatoms maintain distinct microbial communities. Using microbiome-manipulation experiments in which phytoplankton are cured of their native microbiomes and re-inoculated with defined bacterial communities, we track community dynamics and identify key members involved in assembly. These approaches allow us to investigate how early colonization events, including initial encounter, chemotaxis, attachment, and interspecies interactions set the trajectory for microbiome development.
Through comparative genomics and transcriptomics, we identify genetic determinants that enable bacteria to transition between lifestyles and promote stable attachment to host cells. From the host perspective, we examine how phytoplankton shape their microbiomes through chemical cross-talk. We identify host-derived secondary metabolites as molecular regulators of bacterial motility and attachment that selectively promote symbiotic taxa while constraining opportunistic bacteria. Together, these metabolites act as chemical filters that restructure microbial interaction networks and reinforce functional and competitive dynamics within the phycosphere.
Chemical Signaling
Diatoms and bacteria engage in a sophisticated chemical dialogue within the phycosphere, which is a nutrient-rich microscale hub surrounding phytoplankton cells where exuded metabolites attract motile bacteria and trigger tightly regulated lifestyle switches. This interaction is fundamentally anchored by the reciprocal exchange of metabolites, with diatoms providing organic carbon and specialized organosulfur compounds, such as taurine, DMSP, and DHPS, in return for bacterially-derived growth factors including B vitamins, iron-sequestering siderophores, and remineralized ammonium. Our lab focuses on investigating these exchanges using an integrated multi-omics toolkit that combines functional metagenomics, comparative transcriptomics, and high-resolution mass spectrometry to track nutrient transfers, as well as the reconstruction of metagenome-assembled genomes (MAGs) to map these interactions across global ocean datasets.
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Bacterial populations coordinate these physical associations through quorum sensing (QS), which regulates a "swim-or-stick" lifestyle switch that enhances surface attachment and biofilm formation on the diatom host. Beyond basic nutrition, the partners employ inter-kingdom signaling to modulate their environment. For instance, specific bacteria convert diatom-secreted tryptophan into the hormone indole-3-acetic acid (IAA) to promote host cell division, while diatoms utilize unique secondary metabolites like rosmarinic and azelaic acids to selectively recruit beneficial symbionts and suppress opportunistic or algicidal competitors. Recent discoveries by the lab have expanded this framework to include the vitamin B6 catabolites 4-pyridoxolactone, pyridoxal, pyridoxamine, and 4-pyridoxate, which act as potent, bidirectional cues that trigger combinatorial transcriptional reprogramming, priming both organisms to enter a symbiotic state. These complex exchanges, ranging from mutualistic cross-feeding to antagonistic chemical warfare, ultimately govern phytoplankton bloom dynamics and marine biogeochemical cycles.
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Plain English Summary
Like plants on land, phytoplankton are the primary photosynthetic organisms in marine and fresh water. These microbes are responsible for ≥50% of all Earth's photosynthesis and oxygen production. They play a major role in removing carbon dioxide from our atmosphere and sustain fisheries throughout the oceans; however, disturbances to our oceans can cause these relations to lead to a reduction in fisheries or the development of red tides (aka harmful algal blooms). These algae do not live in isolation but are surrounded by a microbiome of bacteria that sustain their growth and survival. This relationship is based on exchanging important molecules, like sugars for energy production, amino acids for cellular growth and vitamins just to name a few, that collectively support the growth of both phytoplankton and their microbiome. These critical exchanges happen in a microscopic area surrounding algal cells, called the phycosphere. Our lab studies how these partnerships form and function, focusing on how individual phytoplankton cells assemble and maintain their own bacterial communities. Observing these phycosphere interactions directly needs highly sophisticated methods because the phycosphere is extremely tiny. To overcome this, we combine field sampling, laboratory experiments, and advanced single-cell, genomic, and chemical techniques. By analyzing both natural samples and controlled experiments, we show that individual phytoplankton cells host distinct microbiomes rather than sharing a single, uniform community. Early interactions strongly influence which bacteria become long-term partners. Phytoplankton also actively shape their microbiomes by releasing specific chemicals that attract helpful bacteria and discourage harmful ones. Diatoms and bacteria further communicate through chemical signals that coordinate their behavior. Identifying these symbiotic exchanges between phytoplankton and bacteria will enable us to understand and better predict how climate change will influence these organisms that play critical roles in sustaining life in the oceans.
Publications
Helliwell, K.E., Shibl, A.A., Amin, S.A. (2022). The diatom microbiome: New perspectives for diatom-bacteria symbioses. In: Falciatore, A., Mock, T. (eds), The Molecular Life of Diatoms. Springer Nature Switzerland.doi: 10.1007/978-3-030-92499-7_10
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​Isaac, A., Francis, B., Amann, R.I., Amin, S.A. (2021). Tight adherence (Tad) pilus genes indicate putative niche differentiation in phytoplankton bloom-associated Rhodobacterales. Frontiers in Microbiology, 12, 718297.doi: 10.3389/fmicb.2021.718297
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Shibl, A.A., Isaac, A., Ochsenkühn, M.A., Cardenas, A., Fei, C., Behringer, G., Arnoux, M., Drou, N., Santos, M.P., Gunsalus, K.C., Voolstra, C.R., Amin, S.A. (2020). Diatom modulation of select bacteria through use of two unique secondary metabolites. Proceedings of the National Academy of Sciences USA, 117, 27445–27455. doi: 10.1073/pnas.2012088117
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C. Fei, M.A. Ochsenkühn, A.A. Shibl, S.A. Amin (2020). Quorum sensing regulates ‘swim-or-stick’ lifestyle in the phycosphere. Environ. Microbiol. 22, 4761-4778.
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Behringer, G., Ochsenkühn, M.A., Fei, C., Fanning, J., Koester, J.A., and Amin, S.A. (2018). Bacterial Communities of Diatoms Display Strong Conservation Across Strains and Time. Frontiers in Microbiology, 9, 659.
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Seymour, J., Amin, S.A., Raina, J.B., Stocker, R. (2017).Zooming in on the phycosphere: The ecological interface for phytoplankton-bacteria relationships.Nature Microbiology, 2, 17065. doi: 10.1038/nmicrobiol.2017.65
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Amin, S.A., Hmelo, L.R., Van Tol, H.M., Durham, B.P., Carlson, L.T., Heal, K.R., Morales, R.L., Berthiaume, C.T., Parker, M.S., Djunaedi, B., Ingalls, A.E., Parsek, M.R., Moran, M.A., Armbrust, E.V. (2015).Interactions and signaling between a cosmopolitan phytoplankton and associated bacteria. Nature, 522, 98–101. doi: 10.1038/nature14488
Phycosphere colonization by Roseobacters
Roseobacters are among the most abundant and ecologically important group of bacteria in marine environments. They are also prominent members of the phycospheres of many phytoplankton lineages, including diatoms, dinoflagellates and coccolithophores. We aim to characterize the mechanisms that enable these bacteria to colonize diatom phycospheres and gain an advantage over other bacteria.