The focus of the research in my laboratory is the marine microorganism, Prochlorococcus. This organism is the dominant primary producer in the oceans, the smallest known phototroph, and the most abundant photosynthetic cell on the planet. Over the past ten years we have set as our goal to develop Prochlorococcus as a model system for cross-scale systems biology. We seek to understand the biology of this single organism from the genome level to the global scale. To this end I have built a sizable group of students and post-docs spanning the fields of biochemistry, genomics, virology, microbial ecology, and oceanography, all united around this tiny cell, Prochlorococcus. It is our conviction that we must break down the barriers between disciplines to fully understand Life, in all of its dimensions.
Our work is shaped in large part by the following set of questions:
The origins and nature of genomic diversity in closely related Prochlorococcus strains. How different are the genome sequences of closely related Prochlorococcus strains? What are the patterns of gene loss and gain among the strains and what do they tell us about the evolutionary drivers? Does the core genome - those genes shared by all strains - supply all of the metabolic functions necessary for life? Can we interpret the strain to strain differences in gene content in the context of the distributions of 'ecotypes' along environmental gradients in the field? What are the features of Prochlorococcus genomic diversity in the growing meta-genomic data base in the oceans, and what can it tell us about the forces that shape the assembly of these communities?
Phage/Host interactions. What is the diversity of phage that infect Prochlorococcus in the oceans, and what are the characteristics of their lytic cycle? What are the host ranges of different phage, and how do these relate to the properties of host and phage? What role do phage play in horizontal gene transfer in this system?…in overall mortality? What is the gene flow between host and phage over evolutionary time, and how has this shaped the ecology of both?
Ecotype dynamics in the oceans: How does the abundance of Prochlorococcus ecotypes change with time and space in the oceans, and what selective and neutral forces shape these patterns? How well can we predict these patterns using realistic coupled physical/chemical/biological models?
Role of Prochlorococcus in ocean food webs and biogeochemistry: What types of carbon compounds are produced and excreted by Prochlorococcus in the ocean habitat? What types of microbes assimilate these metabolites, and is this a mutualistic relationship? What organisms eat Prochlorococcus? What 'sensing' mechanisms have evolved between mutualistic partners and predator and prey?
Obviously this is a very broad set of questions, but they are all united by a single, 'minimal' organism that can be readily studied in the laboratory and over its entire habitat - which can be well-characterized - in the wild.
We have developed a battery of tools and capabilities to help us address these questions, including:
- An extensive culture collection of 40 Prochlorococcus strains isolated from the world's oceans
- A culture collection of hundreds of phage strains that infect them
- The complete genome sequences of 13 Prochlorococcus strains, 11 Synechococcus strains, and of 28 cyanophage that infect them
- A computational infrastructure for genome analysis
- Affymetrix micro-arrays for two hosts and phage enable functional genomic analyses
- High speed cell sorting, proteomic capabilities
- Access to regular sampling at time series stations in the Atlantic and Pacific Oceans where Prochlorococcus is numerically dominant
- Q-PCR techniques for measuring ecotype abundances in the field
It is our hope that through our studies of Prochlorococcus we will better appreciate the full complexity of Life's properties and processes; Not only those that are encoded in an organism's DNA, but also those emerging at higher levels of biospheric organization.