Research Projects

If you are interested in joining the Dyhrman Microbial Oceanography Group please email Dr. Sonya Dyhrman.

Emiliania huxleyi Pan Genome

Emiliania huxleyi is a numerically and ecologically important phytoplankton species in the ocean known for its cosmopolitan distribution and ability to form large blooms in coastal and open ocean regions. Studies of E. huxleyi variants in culture have found differences in growth, function and activity potential among them. The E. huxleyi variants also differ in some of the genes they carry. It has been hypothesized that this genomic variability may underlie the global success of this phytoplankton species by allowing adaptation of variants to diverse environments. Yet, the direct connection between genomic content and ecological success remains unclear.  The overarching goal of this project is to define the role of the pan genome (set of variable genes) in E. huxleyi ecology and biogeography through a series of genomic analyses, computational field surveys, and laboratory-based experiments. This project is sequencing the genomes of several E. huxleyi isolates from across the global ocean and combining them with existing genome sequences to constrain the core and variable portions of the pan genome. Using this new pan genome reference database and leveraging global scale metagenomics and metatranscriptomic surveys, this project is estimating ecotype diversity of E. huxleyi across ocean regions to identify patterns of environmental selection. This project additionally focuses on identifying the physiological and transcriptional responses of a selection of sequenced strains and their responses to shifts in their nutrient environments in controlled laboratory studies where one isolate can be competed against the other. As E. huxleyi plays such a significant role in marine ecosystems and the global carbon cycle it is important that its pan genome and its impact on the biogeography and ecology of E. huxleyi is taken into consideration. It is likely that these dynamics are acutely important to predicting how this genus, and perhaps others, respond to changing environmental conditions in the future ocean.

Drivers of Ecosystem Function (PERI-SCOPE)

How do resource supply ratios drive phytoplankton succession, competition, niche partitioning and the concomitant ecosystem functions like primary production, and nitrogen fixation?  We are using a novel dual sequencing approach to reconstruct both the expressed taxonomic diversity of the phytoplankton as well as the metabolism of phytoplankton and their symbionts over time in two month-long mesocosm studies with 8 different treatments in triplicate at large volume.  This mesocosm study is part of the Simons Collaboration on Ocean Ecosystem Processes (SCOPE), where multi-omic measurements, activities, and geochemistry can be collectively brought together to yield ecosystem-level insight on the processes that underpin the dynamics of oligotrophic systems like the North Pacific Subtropical Gyre.

Station ALOHA Time-Series

Cyanobacteria and eukaryotic phytoplankton play a critical role in the fixation of C, driving the biological pump in the global ocean. Predictive ocean biogeochemical and primary production models suffer from the lack of resolution of both community composition and metabolic activities. For example, nutrient availability is known to play a critical role in driving the distribution and activities of phytoplankton, yet there are surprisingly fundamental gaps in our understanding of how key species metabolize nutrients like N and P, and, in particular, how this metabolic potential is expressed and modulated in field populations. It is also increasingly recognized that cell-cell interactions within associations or consortia, for instance between diazotrophs and a diatom host (DDA) (Harke et al. 2019), may influence phytoplankton activities and the concomitant fate of resources like C and N. Our focus has been to resolve the dynamics and activities of microbes such as Trichodesmium, DDAs and phytoplankton groups like diatoms, haptophytes and dinoflagellates, the co-called keystone microbiome. We have over two years of samples from the Hawaiian Ocean Time (HOT) series.  Collected in the context of other HOT measurements, we are leveraging these samples to identify the traits that underpin phytoplankton taxonomic and functional diversity, and how this functional capacity is expressed.  With these data we are able to ask and answer questions about how resources drive community dynamics in the North Pacific Subtropical Gyre, and the role of epibionts and symbionts in shaping host metabolic potential, and ecosystem function,  among other research.

Mesoscale eddy influences on the taxonomic diversity and expressed functional profiles of large eukaryotic phytoplankton in the North Pacific Subtropical Gyre.

Physical and biological forces influence primary production in the oligotrophic ocean and change across broad temporal and spatial scales. Large eukaryotic phytoplankton, such as diatoms and haptophytes, despite relatively rare occurrence in oligotrophic waters, are responsible for the majority of organic matter flux to the ocean interior and higher trophic levels. Mesoscale eddies are known to have a dramatic impact on phytoplankton community structure and function, enhancing primary productivity and potential carbon export. For this work, we are looking at mesoscale eddy influences on the taxonomic diversity and expressed functional profiles of surface communities of large eukaryotic phytoplankton and their associated heterotrophic bacteria (microbiome) from the North Pacific Subtropical Gyre across annual time-scales.

Resolving the effects of resource availability, predation and competition on brown tide dynamics using metatranscriptomics.

Aureococcus forms dense ecosystem-destructive blooms in the systems where it occurs, but understanding the drivers of these bloom dynamics is still a challenge.  Working in embayments in coastal New York, we are applying a novel dual metatranscriptome sequencing approach to profile the eco-transcriptomic responses of A. anophagefferens and co-occurring phytoplankton over the course of a bloom and in culture.  We are evaluating the expression of known nutrient stress markers to identify factors driving bloom dynamics.  By comparing the responses of Aureococcus and co-occuring phytoplankton, we hope to also describe potential competitive outcomes in a changing ocean.

Dynamics of dissolved organic phosphorus production, composition and bioavailability along a natural marine phosphate gradient.

Primary production and carbon cycling in a number of oceanic regions, including the western North Atlantic, are controlled by dissolved organic phosphorus (DOP), yet its production, composition, and bioavailability is poorly constrained. The overarching goal of this collaborative work is to use paired field and laboratory efforst to provide foundational information on the way DOP molecular characteristics translate into P-bioavailability to marine phytoplankton, and in turn how phytoplankton growing under different DIN:DIP impact the composition and bioavailability of DOP.  This work will use a unique combination of analytical and 'omics (coupled transcriptomic/metabolomic)-based approaches.

Gene expression coordination and metabolic function interactions between Trichodesmium and its microbiome over day–night cycles.

Trichodesmium is a widespread, N2 fixing marine cyanobacterium that drives inputs of newly fixed nitrogen and carbon into the oligotrophic ecosystems where it occurs. Colonies of Trichodesmium ubiquitously occur with heterotrophic bacteria that make up a diverse microbiome, and interactions within this Trichodesmium holobiont could influence the fate of fixed carbon and nitrogen.  We are using metatranscriptome sequencing to identify possible interactions between the Trichodesmium host and microbiome over day-night cycles. To date, we have shown significantly coordinated patterns of gene expression between host and microbiome, many of which had significant day-night periodicity. To fully understand and forecast future ocean dynamics, studies of Trichodesmium must consider the role of the microbiome.

Ecology and evolution of microbial interactions in a changing ocean.

The effect of ocean acidification on calcifying organisms has been well-studied, but less is known about how changing pH will affect phytoplankton. Previous work from our group showed that the mutualistic interaction between the globally abundant cyanobacterium Prochlorococcus and its "helper" bacterium Alteromonas broke down under projected future CO2 conditions, leading to a strong decrease in the fitness of Prochlorococcus. It is possible that such interspecies interactions between microbes are important for many ecological processes, but a lack of understanding of how these interactions evolve makes it difficult to predict how important they are. This project will use laboratory evolution experiments to discover how evolution shapes the interactions between bacteria and algae like Prochlorococcus, and how these co-evolutionary dynamics might influence the biogeochemical processes that shape Earth's climate.

CO2-induced responses in physiology and gene expression among eukaryotic phytoplankton.

With rising atmospheric CO2, phytoplankton face shifts in ocean chemistry including increased dissolved CO2 and acidification that will likely influence the relative competitive fitness of different phytoplankton taxa. We are working to identify the physiological and gene expression responses of different phytoplankton under different concentrations of CO2.  To date, our group has looked at the response of six species of phytoplankton including a diatom, a raphidophyte, two haptophytes, and two dinoflagellates to ambient (~400 ppm) and elevated (~800 ppm) CO2.  Eukaryotic phytoplankton have diverse gene complements and gene expression responses to CO2 perturbations and this effort highlights the value of cross-phyla comparisons for identifying gene families that respond to environmental change.  Understanding the diversity in genetic complement and gene expression response to elevated CO2 can improve predictions of the relative success of phytoplankton taxa in future ecosystems, their impacts on biogeochemical cycles, and harmful algal bloom frequency.

One-quarter of the carbon derived from photosynthesis on Earth cycles rapidly through a pool of seawater metabolites generated by the activities of microbes. These molecules help govern the global carbon cycle, provide life-supporting nutrients, and support the function of marine food webs that ensure a vital and healthy ocean.

The Center for Chemical Currencies of a Microbial Planet (C-CoMP) leverages recent advances in analytical and data sciences, incorporates new ocean sampling technologies and an open-science framework, and engages educators and policy-makers to promote a deeper understanding and appreciation of the chemicals and microbial processes that underpin ocean ecosystems and other microbiomes that affect our daily life. We are working to identify:

          (1) the chemical currencies of surface ocean carbon flux

          (2) the chemical-microbe network in the surface ocean

          (3) network sensitivity and feedbacks on climate.

The Dyhrman group is focused on phytoplankton exometabolite production, the fate of these chemical currencies, and how sensitive this economy is to a changing ocean.  See (Hennon et al. 2018, and Moran et al. 2022). Our research efforts also include capacity building in team science, open data frameworks, expanding ocean science literacy efforts, and broadening the workforce able to tackle multi-disciplinary problems. 

Check out the Center's website or @MicrobialPlanet for information on opportunities to join this effort!