| Home | Research | People | Publications | JointheLab | |
Research in my lab is focused on mechanisms and controls of microbial population dynamics with an emphasis on carbon cycling in marine ecosystems. These processes, which regulate carbon fixation and energy transfer to higher trophic levels, are critical to sustainability of oceanic food webs, global climate and human health. For more information view Collaborators and Funding Sources.
To date, much of our work has focused on growth and grazing mortality rates of microbial photoautotrophs, including picophytoeukaryotes (less than two micrometers 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. Follow this link for a YouTube 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.
(AZ Worden)
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 (the EPICS XL, Coulter Corp.) as well as a high speed cell sorter (the InFlux, Cytopeia Inc.) 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. It is now recognized that resource utilization capabilities of heterotrophic and autotrophic microorganisms overlap. We recently released the genome sequences of two strains (RCC299 and CCMP1545) of the “species” Micromonas pusilla, sequenced in collaboration with the Joint Genome Institute of the U.S. Department of Energy and significant participation by our collaborators at Ghent University. The genome of RCC299 represents one of the few fully sequenced eukaryotic genomes (closed). These organisms 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. The divergence between these strains is much greater than expected based on their high 18S rRNA gene identity. These differences extend not just to their respective gene complements, but also much more fundamental levels. We are also members of a team of collaborators from Ghent University, the Station Biologique de Roscoff, and Laboratoire Arago at Banyuls sur Mer who sequenced and annotated the genome of Ostreococcus tauri, a tiny, but important marine photosynthetic eukaryote discovered in 1994. A second Ostreococcus genome from a strain isolated from waters off the Scripps Institution of Oceanography's Pier (coastal Pacific Ocean USA) has just been released. This strain, Ostreococcus CCE9901 was the focus of my NSF Postdoctoral fellowship research, for which I identified and characterized CCE9901 in addition to exploring its ecology, after which we (successfully) proposed it as a genome sequencing candidate relevant to the DOE mission. Taken together, these genomes are being used to develop hypothesis driven studies on niche differentiation. If you are interested in working on the Micromonas genomes please contact Alex Worden.
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 on the following words to learn more 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 protozoan 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.
Our most recent work in this area is a DOE funded Community Sequencing Project entitled: “Mechanisms of marine protistan predation: genomics and transcriptomics of predatory nanoflagellates” which was approved in June 2008. This involves collaboration with Emily Roberts at Swansea University and Jens Boenigk at the Austrian Academy of Sciences as well as investigators at the J. Craig Venter Institute and University of Southern California. Transcripts from three chrysomonad species will be sequenced, as well as the complete genomes of two of these, one of which is purely heterotrophic and the other of which is mixotrophic.
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. These organisms likely have quite large genomes (especially as compared to bacteria) and therefore pursuing metagenomic information for these organisms using “bulk samples” (i.e. collecting cells by filtration of many liters of seawater) is challenging, and complex to tease apart bioinformatically. We have combined flow sorting with the multiple displacement amplification approach developed in Roger Lasken’s lab in order to more specifically target and sequence different picophytoeukaryotes populations. Our interest has been in sequencing population metagenomes as opposed to single cells. This approach has worked very well – and we are now working on methods to perform Targeted Metatranscriptomic sequencing. An exciting project underway now uses traditional Bulk Metagenomics to analyze samples collected along a well characterized transect from the coast near MBARI to open ocean waters. This collaboration with Ginger Armbrust’s Lab (University of Washington; experts on the larger phytoplankton) involves shotgun cloning and sequencing of nucleics from Bulk Metagenomic samples. In addition, on the side, testing of next generation sequencing, as well as small subunit sequencing is all being done in collaboration with George Weinstock who directs the Genome Sequencing Center at Washington University St. Louis. 454-FLX sequencing of Bulk Metagenomic samples was performed at Pennsylvania State University. High resolution contextual environmental data has been analyzed by a number of MBARI scientists of different expertise - these include Ken Johnson, Francisco Chavez and Zbigniew Kolber. In parallel we are working to meld Targeted Metagenomics with the Bulk Metagenomic approach – using the Targeted Metagenomes as a form of reference genomes for the uncultureds.
|
Andy
Allen, Scientist J. Craig Venter Institute Jonathan
Eisen, Professor Stephen Giovannoni,
Professor Ursula
Goodenough, Professor Yves
Van de Peer, Professor George Weinstock, Professor |
|
| Photo: Research cruise on the R/V Seward Johnson, from Bardados to Cape Verde and back, Summer 2006 |
| |
|
|
|
|
