Comparative genomics of vesicomyid clam (Bivalvia: Mollusca) chemosynthetic symbionts

Irene LG Newton 0 1 Peter R Girguis 1 Colleen M Cavanaugh 1 0 Department of Microbiology, Tufts University , 136 Harrison Avenue, Boston, MA 02111 , USA 1 Harvard University, Organismic and Evolutionary Biology , 16 Divinity Avenue, Cambridge, MA 02138 , USA Background: The Vesicomyidae (Bivalvia: Mollusca) are a family of clams that form symbioses with chemosynthetic gamma-proteobacteria. They exist in environments such as hydrothermal vents and cold seeps and have a reduced gut and feeding groove, indicating a large dependence on their endosymbionts for nutrition. Recently, two vesicomyid symbiont genomes were sequenced, illuminating the possible nutritional contributions of the symbiont to the host and making genomewide evolutionary analyses possible. Results: To examine the genomic evolution of the vesicomyid symbionts, a comparative genomics framework, including the existing genomic data combined with heterologous microarray hybridization results, was used to analyze conserved gene content in four vesicomyid symbiont genomes. These four symbionts were chosen to include a broad phylogenetic sampling of the vesicomyid symbionts and represent distinct chemosynthetic environments: cold seeps and hydrothermal vents. Conclusion: The results of this comparative genomics analysis emphasize the importance of the symbionts' chemoautotrophic metabolism within their hosts. The fact that these symbionts appear to be metabolically capable autotrophs underscores the extent to which the host depends on them for nutrition and reveals the key to invertebrate colonization of these challenging environments. - Background Symbiosis between prokaryotic and eukaryotic cells is a globally important phenomenon that influences the physiology, ecology, and evolution of virtually every organism on this planet [1-3]. Eukaryotic hosts expand their ecological niches through symbiosis with these metabolically diverse bacteria and archaea. An illustrative case is that of the chemosynthetic endosymbionts, which enable their hosts to populate and thrive in challenging environments such as deep-sea hydrothermal vents and cold seeps [4]. In these environments, reduced inorganic compounds are generated either biotically (e.g. microbial sulfate reduction) or abiotically (e.g. hydrothermal alteration). Chemosynthetic symbionts use the energy derived from the oxidation of these molecules to fix inorganic carbon [5]. Benefits for both partners in chemosynthetic symbioses are evident. The bacteria gain further access to the energy substrates they require from both oxic and anoxic habitats while the animals are provided with much, if not all, of their nutritional requirements [6-8]. The intimate structural and metabolic coupling often found in chemosynthetic symbioses underscores the importance of these relationships to host survival. The vesicomyid clams are one of the better studied chemosynthetic symbioses and exist at hydrothermal vents, hydrocarbon seeps, and other chemically reduced environments. They are also relatively young as a group, as vesicomyid fossils date the formation of the symbiosis to the Cretaceous, between 50100 Ma ago [9]. These clams have a greatly reduced gut and feeding groove [10] and, based on isotopic evidence, are thought to depend almost entirely on their endosymbionts for their carbon [11-13]. With respect to the animal host, the association is essential no living vesicomyids have been found devoid of symbionts. Furthermore, these symbionts have not yet been found outside the host, have never been cultured in the laboratory, and are thought to be predominantly maternally transmitted each generation via the egg [1416]. Previous studies of other bacterial symbionts suggest that symbiont transmission strategy is a predominant factor governing nutritional symbiont genome evolution. Bacterial symbionts transferred to the next host generation via the egg (vertical transmission) experience population bottlenecks upon transmission and few opportunities for recombination [17]. Because of the underlying deletion bias in bacterial genome evolution, and the limited amount of gene flow available to these symbionts, their genomes are minimized. For example, the genomes of the vertically transmitted, mutualistic insect endosymbionts Buchnera, Baumannia, Blochmannia, and Wigglesworthia are all reduced in size and content [18-21], exhibiting few chromosomal rearrangements, or horizontal gene transfer events [22-25]. However, these insect nutritional symbionts retain the genomic repetoire needed to provide key metabolic intermediates, vitamins, and amino acids often missing from their hosts' specialized diets [26], suggesting that host nutritional needs might select for retention of specific biosynthetic pathways. Conversely, those pathways redundant with host capabilities or nutrition are often lost completely [26]. In contrast to the strictly vertically transmitted symbionts, those that undergo occasional environmental or horizontal transmission (lateral acquisition) tend to have slightly larger genomes that exhibit evidence of recombination. For example, Wolbachia pipientis, the ubiquitous insect reproductive parasite, may be laterally transmitted [27,28], and their genomes are littered with mobile genetic elements, prophages and harbor clear evidence of past recombination events [29,30]. It must be noted, however, that transmission strategy for many symbionts cannot be distinctly or clearly demarcated; depending on the association, symbionts are perpetuated via a spectrum from strict vertical transmission to lateral acquisition. The insect reproductive parasites (such as Wolbachia and CFBs) are vertically transmitted but occasionally laterally acquired. Indeed, there is also some phylogenetic evidence, in the form of incongruent host and symbiont trees, against strict vertical transmission of the vesicomyid symbionts [31]. More recently, two different strains of the vesicomyid symbionts have been found within the same host, corroborating the lateral acquisition hypothesis suggested by the phylogenetic evidence above [32]. However, the vesicomyid symbionts are found in host primary oocytes [15,16] and their genomes are reduced, and exhibit a high A+T content [33,34], suggesting that although occasional lateral transmission may occur, the predominant transmission strategy used by the vesicomyids is vertical. This mixed transmission strategy suggested for the vesicomyid symbionts has the potential to influence the genomic evolution of these bacteria. Research on the comparative evolutionary genomics of insect symbionts [18,19,21,35,36] suggests that symbionts with strictly vertical transmission strategies would lose genetic material redundant with host capabilities and retain metabolic pathways necessary for host survival. Occasional lateral transmission might offer the opportunity for recombination and horizontal gene transfer, possibly mitigating the negative effects associated wi (...truncated)