In this review, we have attempted specifically to include those studies that use molecular or biochemical data to describe the physiology and evolution of the
Riftia pachyptila symbiosis. While this unique chemosynthetic association has been a primary focus of hydrothermal vent research (for additional reviews see Fisher 1995; Nelson and Fisher 1995; van Dover 2000; Cavanaugh et al. 2005; Minic and Herve 2004; van Dover and Lutz 2004), studies of the molecular biology of the Riftia endosymbiont have been hindered greatly by the inability to grow the bacterium in pure culture. However, with the Riftia symbiont genome sequence in process (R. Feldman and H. Felbeck, pers. comm.), we will soon have detailed knowledge of the genes that mediate symbiont growth, metabolism, and behavior both prior to and following invasion of the tubeworm host. Several important questions remain unanswered. For instance, through what mechanisms does symbiont sulfide oxidation proceed? How are biologically important elements (e.g., nitrogen, phosphorus, sulfur, iron) obtained by and cycled within the symbiont? Do these bacterial pathways provide important intermediates required for host metabolism? What transport processes and signal pathways are responsible for host-symbiont specificity and symbiont invasion of host cells? What factors (e.g., substrate gradients, cell cycle controls) regulate symbiont growth and division, and how are these factors coordinated with the regulation of the host cell cycle? How is the genetic structure of symbiont populations affected by environmental symbiont transmission, and how does population-level genetic diversity vary over spatial, habitat, and temporal gradients and between symbiotic and free-living populations? To answer these questions it will be particularly prudent to use genomic data not only to understand symbiont evolution but also to design in situ expression studies that can accurately assess the dynamics of both genegene and symbiont-host interactions. Doing so presents a challenge, but one for which researchers will be rewarded with even more fascinating details about this remarkable symbiosis.
Acknowledgements. We thank Monika Bright and Andrea Nussbaumer for stimulating discussions, the captains and crews of the R/V Atlantis and the R/V Atlantis II, the pilots and crews of the DSV Alvin, Chuck Fisher and all of the Chief Scientists and scientific teams of the deep-sea expeditions enabling research on the vent organisms. We gratefully acknowledge support from the Ocean Sciences Division of the National Science Foundation (NSF-OCE 9504257 and OCE 0002460), the NOAA Undersea Research Program through the West Coast and Polar Regions National Undersea Research Center at the University of Alaska at Fairbanks (UAF-WA # 98-06), the National Institutes of Health Genetics and Genomics Training Grant (to FJS) and a Hansewissenschaftkolleg Fellowship (to CMC).
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