My lab focuses on mechanisms and controls of microbial population dynamics. Our research has an emphasis on carbon cycling in marine ecosystems - processes which regulate carbon fixation and energy transfer to higher trophic levels. These processes are critical to sustainability of oceanic food webs, global climate and human health.
Much of our work has focused on growth and grazing mortality rates of microbial photoautotrophs, including picophytoeukaryotes (cells < 2 microm in diameter). This research highlights the need to understand interactions between unicellular algae, heterotrophic microbes and the protists that consume them in order to more fully comprehend and model carbon cycling. See YouTube video on genomic approaches to this work.
We are pursuing three interlinked research areas in order to develop a mechanistic understanding of microbial contributions to global carbon cycling: molecular underpinnings of physiological growth controls; microbe-microbe interactions, including competition processes/trophic linkages (food web dynamics); and quantitative, mechanistically-based models of functional diversity, primary production and trophic transfer in marine environments – or, at the moment, working to provide data that can improve such models. Fundamental to these studies is the recognition that:
- microbes cannot be treated as bulk communities because their individual adaptive strategies and real time behavior are critical to food web dynamics, and
- microbes must be studied at habitat scales relevant to their adaptive strategies to determine how their metabolism influences larger-scale ecosystem dynamics.
This type of research is essential to the development of mechanistic models of ocean biogeochemistry and efforts to conserve marine ecosystems.
Specific Research Directions:
Neither top-down (e.g. grazing mortality) nor bottom-up (e.g. nutrient stress) approaches provide the necessary basis for understanding population dynamics and biotic transport of carbon in marine systems. Detailed identification and characterization of specific forces acting on important microbial populations as well as the interaction between these forces will allow better understanding of ecosystem dynamics. This requires going beyond measurements of community based properties (e.g. bulk bacterial activity) or even population specific rates. Instead, we must develop a mechanistic view of autotroph/heterotroph as well as heterotroph/heterotroph interactions.
We are addressing mechanisms and controls of trophic transfer using a multi-faceted approach employing molecular and biochemical techniques, genomics, proteomics and in situ studies. We also use flow cytometry quite extensively, and have in house both a standard clinical instrument (EPICS XL, Coulter Corp., ACCURI, BD) as well as a high speed cell sorter (InFlux, BD) which we use for discrimination and separation of natural microbial populations. Most recently we have used this instrument to sort natural populations at sea and sequence their genomes – an approach we term Targeted Metagenomics – because we don’t go through the process of culturing, nor do we deal with the bulk community. Four major research objectives are being combined to aid development of high resolution, population specific field approaches:
1. Competition processes and population dynamics of phytoplankton. Elucidating the underpinnings of niche differentiation and competition is essential to understanding food webs. We published genome sequences from two pico algae isolates (Micromonas sp. RCC299 and Micromonas pusilla CCMP1545) sequenced in collaboration with the JGI, U.S. Department of Energy in Worden et al. Science 2009. These two isolates were once considered a single species (Micromonas pusilla), but are very clearly not the same species. They show massive genome divergence, share only ~90% of their protein-encoding genes and show other fundamental differences. The genome of RCC299 represents one of the few fully sequenced eukaryotic genomes (closed). These organisms also fall at the base of the green lineage and hence shed light on the evolution of higher plants, in addition to being important marine primary producers. We have been team members in the 2006 analysis of the genome of Ostreococcus tauri, a tiny, marine photosynthetic eukaryote discovered in 1994, and in the analyses of other important marine algae, including Emiliania huxleyi, Fragilariopsis cylindrus and Bigelowiella natans. Lab field research has led to a better understanding of the distributions of various picoeukaryotes including ecotypes of Ostreococcus (see Demir et al. ISME J 2010) and Bathycoccus (see Monier et al. ISME J 2013). Much of this research highlights the overlap in resource utilization capabilities of heterotrophic and autotrophic microorganisms. We are now testing genome derived hypotheses on niche differentiation through large scale transcriptomics and proteomics. If you are interested in working with us on the ongoing Micromonas systems biology project please contact Alex.
An example of comparative physiology research in the lab is a project aimed to understand the photobiology of Micromonas and Ostreococcus. Specifically, their relative success in high-light/high-ultraviolet radiation environments is being investigated by a combination of genomic (in silico), micro-array, quantitative-PCR and biochemical approaches. Using gene and protein expression to detect real-time cell response to environmental changes (e.g. mitigating negative effects and capitalizing on favorable conditions) will help identify conditions of immediate relevance to survival or success. We are currently focusing on photoautotrophs but plan to apply similar approaches to predator populations. By avoiding the use of heavy-handed field manipulations that may be of little ecological relevance, this approach will help researchers define conditions contributing to the relative success of individual microbial populations. Click here to learn more about prasinophyte genomes.
2. Food quality issues and functional responses of microbial predators. Within the last 7 years tremendous diversity of marine protists has been revealed based on environmental SSU rDNA gene sequencing. Many of these protists are novel, not yet cultured and of unknown functional roles. Some are likely to be predators, while others are photosynthetic or mixotrophic. We are characterizing both novel and ubiquitous protists. Furthermore, we are studying interactions between predator and prey populations. In combination with other studies our research shows that protistan grazers can exhibit prey specificity, as well as functional responses, and that assimilation efficiencies differ dramatically between prey groups (e.g. Prochlorococcus is assimilated more efficiently than Synechococcus). Thus, different prey can be consumed at different rates and a greater proportion of carbon from some prey groups is transferred to higher trophic levels than from others. This impacts not only the complexity of trophic linkages amongst the smaller size fractions but also the diversity and distribution of microbial populations (via selective protistan grazing). To accurately model food webs, protistan grazing strategies and prey digestibility (some are of better food quality than others) must be accounted for. We are developing biochemical and proteomic approaches as well as ‘species’-specific probes to target and study specific interactions in natural systems, including analysis of protistan food vacuoles and food particle processing. Cues employed in prey selectivity, prey switching and the influence of food quality on these interactions are under study. These studies also address parasitism by novel protists, one group of which has already been found to parasitize dinoflagellates (which can cause red tides and toxic blooms). The regulatory role of parasitism in marine systems is largely unknown.
We have several ongoing DOE funded Community Sequencing Projects or Technology Development Projects in this area. These include sequencing chrysomonad species, one of which is purely heterotrophic and the other of which is mixotrophic, as well as sorted cells from the natural environment.
3. Biochemical and molecular mechanisms of microbe-algae interactions and conditions specifically influencing interaction type. Although we know that bacteria attach to algae (even to picophytoplankton), the relationship between these organisms has not yet been characterized despite its potential influence on population dynamics and biogeochemical cycles. The relationship could be mutualistic, or range from mutualistic to parasitic or pathogenic as environmental conditions or colonizing bacterial populations change.
Mechanisms of interactions amongst microorganisms are key to modeling system dynamics accurately. Our goal is to conduct a series of innovative field studies with a suite of new, sensitive tools to probe the strength and direction of these linkages/interactions and quantify carbon flow to other trophic compartments. Our work will allow development of mechanistically based ecosystem models for prediction of primary production, carbon cycling and marine food web dynamics. This is the least developed research area in the lab and an area we expect to make a 'push' in over the next two years.
4. Targeted Metagenomics. There are still many uncultured marine protists – including within the pico-size fraction. An approach developed in the lab that has generated new discoveries on their evolution and ecology has been sequence partial genomes from cells taken directly from the environment. Because these pico algae have quite large genomes (especially as compared to bacteria), pursuing metagenomic information using “bulk samples” (i.e. collecting cells by filtration of many liters of seawater) has been challenging, and complex to tease apart bioinformatically. Starting in 2005 we combined flow sorting with multiple displacement amplification (developed in Roger Lasken’s lab) in order to specifically target and sequence picophytoeukaryote populations. Our interest has been in sequencing population metagenomes as opposed to single cells. Using this approach we published the first genome sequence (partial genome) for a haptophyte - in this case a pico-prymnesiophyte (Cuvelier et al. PNAS 2010), and a partial Bathycoccus genome (Monier et al. EM 2012, epubl Sept 2011) as well as the complete chloroplast genome of a wild pelagophyte (Worden et al. Current Biology 2012).
Some of these targeted metagenomes have now been used to analyze traditional Bulk Metagenomes from a well characterized transect from the Pacific coast to open ocean waters (Line 67) and other locations. High resolution contextual environmental data has been analyzed by a number of MBARI scientists — including Ken Johnson and Francisco Chavez. Melding Targeted Metagenomics with Bulk Metagenomics (using the Targeted Metagenomes as reference genomes for uncultureds) revealed the global distribution of a wild Pelagomonas, using a reference plastid genome sequenced directly from the environment (Worden et al. Current Biology 2012), as well as interesting HGT patterns between Ostreococcus and Bathycoccus with marine prasinoviruses (Monier et al. EM 2012, epubl Sept 2011).