Abstract
BackgroundNext-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured. Here, we provide a metagenomic description of chemoautotrophic gammaproteobacterial symbionts associated with Thyasira cf. gouldi, a sediment-dwelling bivalve from the family Thyasiridae. Thyasirid symbionts differ from those of other bivalves by being extracellular, and recent work suggests that they are capable of living freely in the environment.ResultsThyasira cf. gouldi symbionts appear to form mixed, non-clonal populations in the host, show no signs of genomic reduction and contain many genes that would only be useful outside the host, including flagellar and chemotaxis genes. The thyasirid symbionts may be capable of sulfur oxidation via both the sulfur oxidation and reverse dissimilatory sulfate reduction pathways, as observed in other bivalve symbionts. In addition, genes for hydrogen oxidation and dissimilatory nitrate reduction were found, suggesting varied metabolic capabilities under a range of redox conditions. The genes of the tricarboxylic acid cycle are also present, along with membrane bound sugar importer channels, suggesting that the bacteria may be mixotrophic.ConclusionsIn this study, we have generated the first thyasirid symbiont genomic resources. In Thyasira cf. gouldi, symbiont populations appear non-clonal and encode genes for a plethora of metabolic capabilities; future work should examine whether symbiont heterogeneity and metabolic breadth, which have been shown in some intracellular chemosymbionts, are signatures of extracellular chemosymbionts in bivalves.
Highlights
Next-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured
Overview of metagenome Our analysis recovered a large number of contigs (12, 504, with an N50 of 1870) that we consider to represent the symbiont population’s metagenome; these contigs could not be assembled into a single genome
The contigs from our metagenome show highly similar trinucleotide and tetranucleotide frequency distributions, supporting our interpretations that: 1) the sequences we retained as belonging to symbionts come from highly similar bacteria; and 2) the metagenome contained few contaminants, as expected given the very high abundance of morphologically similar symbionts observed on Thyasira cf. gouldi gills using transmission electron microscopy [20]
Summary
Next-generation sequencing has opened new avenues for studying metabolic capabilities of bacteria that cannot be cultured. Many species of marine bivalves living near oxic-anoxic boundaries form nutritional symbioses with chemoautotrophic bacteria, which are maintained in or on the host’s gills [1,2,3,4]. In such associations, called chemosynthetic symbioses or chemosymbioses, the bacteria provide the host with nutrients and protection from chemical stress, while the host constitutes a protective and suitable environment for the bacterial symbionts [2, 5, 6]. Acquired symbionts could potentially form diverse or heterogeneous populations within host individuals if multiple symbionts are acquired from a genetically diverse founding population
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