Frank Stewart Home

Bacteria and Archaea constitute the overwhelming majority of genetic and metabolic diversity on this planet. To understand these organisms in their native habitats, environmental microbiologists are tasked with two fundamental questions. First, how do ecological and evolutionary processes (e.g., symbiosis, competition, recombination, natural selection) create and structure genetic diversity? Second, how is this genetic diversity linked to the diverse biogeochemical functions of microorganisms in nature?

Our research explores these questions for marine microorganisms, using the tools of genomics and molecular biology. We are particularly interested in how microbial genome evolution and physiology are affected by symbiotic interactions with higher taxa. In tandem with this work, we study free-living microorganisms, as they provide important reference points for understanding symbiont biology and mediate key global biogeochemical cycles in the ocean’s water column and sediments. Our research integrates the broad fields of microbiology, molecular evolution, and marine biology. This work has both descriptive and experimental components, and involves a blend of field, molecular, and bioinformatic techniques, the latter focused (primarily) on the analysis of high-throughput sequencing datasets. We welcome inquiries from potential students, post-docs, and collaborators who share these interests.

A holistic understanding of microbial diversity and function requires studies targeting varying levels of biological complexity, from individual cells to entire communities and ecosystems. Advances in DNA sequencing have transformed our capacity to study microorganisms across complexity gradients. Entire genomes can now be sequenced within hours, facilitating comparative studies of genome architecture and content. Additionally, high-throughput shotgun sequencing can characterize the diverse pool of genes (DNA) and expressed transcripts (RNA) of an entire microbial community (the metagenome and metatranscriptome, respectively).

In combination with single-gene or genome analyses, we use massively parallel sequencing (e.g., 454 technology) to analyze the metatranscriptome of microbial communities [for examples of these methods, see Frias-Lopez et al. 2008, PNAS, 105:3805-3810; Stewart et al. 2010, ISME J, 4:896-907]. The resulting datasets contain hundreds of thousands of sequence fragments (reads) from both the transcriptionally active gene pool and the pool of non-coding RNA molecules (e.g., ribosomal RNA, smRNA). When coupled to metagenomic (DNA) data, metatranscriptomic analyses help clarify the link between the genetic potential of a community and its actual functional state (inferred from the transcript pool), reveal novel molecular and ecological adaptations to the geochemical environment, and inform theory about the molecular evolution of highly expressed genes. This work has focused primarily on bacterioplankton communities, sampled either directly from the marine environment or manipulated within an experimental framework (e.g., via mesocosm or bioreactor treatments). However, we are also applying these methods to other systems, including microbial symbioses.

Symbiosis, defined broadly as a long-term interaction between species, is among the most pervasive evolutionary and ecological strategies in marine ecosystems, impacting fundamental processes such as speciation, ecosystem structuring, primary production, nutrient cycling, and disease. Marine microbial symbioses span a striking diversity of hosts and symbionts from all three Domains of life. These associations vary widely in key biological factors, including the extent to which symbionts affect host fitness (e.g., mutualism vs. commensalism vs. parasitism), integrate into host tissue, and exchange genetic material with free-living microorganisms. Though such factors have been explored for several well-studied associations, such as coral-algae mutualisms, most marine symbioses remain understudied.

In particular, our research explores the evolution and physiology of symbioses between chemoautotrophic bacteria and marine invertebrates. These symbioses, in which bacteria use the energy of reduced chemicals (e.g., sulfide, methane) to fix carbon for their host, have been observed in seven host phyla, play vital ecological roles as primary producers and ecosystem engineers in reducing habitats (e.g., anoxic sediments, hydrothermal vents), and are potential models for the ancient prokaryote-eukaryote associations that gave rise to the eukaryotic cell. In addition, several of these symbionts are closely related to free-living bacteria that mediate carbon fixation and sulfur cycling in the water column (e.g., the sulfur-oxidizing SUP05 lineage found in oxygen minimum zones).

High-throughput methods can provide exciting insight into the molecular basis of these associations. We are currently optimizing transcriptomic techniques for studying gene expression in intracellular chemoautotrophic symbionts, enabling a community-level analysis of how symbiont metabolism and cell function vary in response to environmental conditions, geography, or the developmental or physiological state of the host. Coupled with these studies, we use genomic and multi-locus approaches to study the evolution of these associations, asking questions such as: How does symbiont genome evolution vary in response to symbiont transmission mode and the level of symbiont-host specificity? How are symbiont and host genome diversity structured within and across populations and in response to factors external to the symbiosis, such as the genetic composition of a free-living symbiont community? Answering these questions for functionally diverse associations sheds important light on the role of microbial symbiosis as a driver of biological innovation.

Research * microbial genome evolution and metagenomics * prokaryote-eukaryote endosymbiosis and cospeciation * microbial ecology of marine ecosystems * deep-sea hydrothermal vents and extreme environments * population genetics and phylogeography

Black smoker on the East Pacific Rise. 2500 m depth.	TEM of symbiotic bacteria (b) in gill tissue of the hydrothermal vent clam Calyptogena magnifica. Courtesy: C. Cavanaugh, Biol. Soc. Wash. Bull. 1985.
Bacteria and Archaea constitute the overwhelming majority of genetic and metabolic diversity on this planet. To understand these organisms in their native habitats, environmental microbiologists are tasked with two fundamental questions. First, how do ecological and evolutionary processes (e.g., symbiosis, competition, recombination, natural selection) create and structure genetic diversity? Second, how is this genetic diversity linked to the diverse biogeochemical functions of microorganisms in nature? Our research explores these questions for marine microorganisms, using the tools of genomics and molecular biology. We are particularly interested in how microbial genome evolution and physiology are affected by symbiotic interactions with higher taxa. In tandem with this work, we study free-living microorganisms, as they provide important reference points for understanding symbiont biology and mediate key global biogeochemical cycles in the ocean’s water column and sediments. Our research integrates the broad fields of microbiology, molecular evolution, and marine biology. This work has both descriptive and experimental components, and involves a blend of field, molecular, and bioinformatic techniques, the latter focused (primarily) on the analysis of high-throughput sequencing datasets. We welcome inquiries from potential students, post-docs, and collaborators who share these interests. *Metagenomics and Metatranscriptomics* A holistic understanding of microbial diversity and function requires studies targeting varying levels of biological complexity, from individual cells to entire communities and ecosystems. Advances in DNA sequencing have transformed our capacity to study microorganisms across complexity gradients. Entire genomes can now be sequenced within hours, facilitating comparative studies of genome architecture and content. Additionally, high-throughput shotgun sequencing can characterize the diverse pool of genes (DNA) and expressed transcripts (RNA) of an entire microbial community (the metagenome and metatranscriptome, respectively). In combination with single-gene or genome analyses, we use massively parallel sequencing (e.g., 454 technology) to analyze the metatranscriptome of microbial communities [for examples of these methods, see Frias-Lopez et al. 2008, PNAS, 105:3805-3810; Stewart et al. 2010, ISME J, 4:896-907]. The resulting datasets contain hundreds of thousands of sequence fragments (reads) from both the transcriptionally active gene pool and the pool of non-coding RNA molecules (e.g., ribosomal RNA, smRNA). When coupled to metagenomic (DNA) data, metatranscriptomic analyses help clarify the link between the genetic potential of a community and its actual functional state (inferred from the transcript pool), reveal novel molecular and ecological adaptations to the geochemical environment, and inform theory about the molecular evolution of highly expressed genes. This work has focused primarily on bacterioplankton communities, sampled either directly from the marine environment or manipulated within an experimental framework (e.g., via mesocosm or bioreactor treatments). However, we are also applying these methods to other systems, including microbial symbioses. Symbiont Evolution and Physiology Symbiosis, defined broadly as a long-term interaction between species, is among the most pervasive evolutionary and ecological strategies in marine ecosystems, impacting fundamental processes such as speciation, ecosystem structuring, primary production, nutrient cycling, and disease. Marine microbial symbioses span a striking diversity of hosts and symbionts from all three Domains of life. These associations vary widely in key biological factors, including the extent to which symbionts affect host fitness (e.g., mutualism vs. commensalism vs. parasitism), integrate into host tissue, and exchange genetic material with free-living microorganisms. Though such factors have been explored for several well-studied associations, such as coral-algae mutualisms, most marine symbioses remain understudied. In particular, our research explores the evolution and physiology of symbioses between chemoautotrophic bacteria and marine invertebrates. These symbioses, in which bacteria use the energy of reduced chemicals (e.g., sulfide, methane) to fix carbon for their host, have been observed in seven host phyla, play vital ecological roles as primary producers and ecosystem engineers in reducing habitats (e.g., anoxic sediments, hydrothermal vents), and are potential models for the ancient prokaryote-eukaryote associations that gave rise to the eukaryotic cell. In addition, several of these symbionts are closely related to free-living bacteria that mediate carbon fixation and sulfur cycling in the water column (e.g., the sulfur-oxidizing SUP05 lineage found in oxygen minimum zones). High-throughput methods can provide exciting insight into the molecular basis of these associations. We are currently optimizing transcriptomic techniques for studying gene expression in intracellular chemoautotrophic symbionts, enabling a community-level analysis of how symbiont metabolism and cell function vary in response to environmental conditions, geography, or the developmental or physiological state of the host. Coupled with these studies, we use genomic and multi-locus approaches to study the evolution of these associations, asking questions such as: How does symbiont genome evolution vary in response to symbiont transmission mode and the level of symbiont-host specificity? How are symbiont and host genome diversity structured within and across populations and in response to factors external to the symbiosis, such as the genetic composition of a free-living symbiont community? Answering these questions for functionally diverse associations sheds important light on the role of microbial symbiosis as a driver of biological innovation.