Pearl in the mud: Genome assembly and binning of a cold seep Thiomargarita nelsonii cell and associated epibionts from an environmental metagenome

Abstract

As the study of microbes and their impact on the environment grows, so too does the desire to understand the genetic basis of the physiologies that make possible interactions between microbial cells and their environment. Since it is now much more cost-effective to sequence bacterial genomes, environmental metagenomic assembly is a very attractive option for obtaining the genetic blueprints of bacterial physiologies. Bacteria of the genus Thiomargarita (Greek; theio-: sulfur; margarites: pearl), pose a particularly interesting quandary. The genus includes the world's largest bacteria, but as uncultured organisms, their physiologies and basis for their gigantism are not well understood. In order to investigate the genetic basis for these modes, a single cell MDA amplification approach was used on T. nelsonii cells collected at the Hydrate Ridge methane seep off of the coast of Oregon. These particular cells were derived from a gastropod-attached epibiont community. Next-generation sequencing produced a metagenomic product representing both T. nelsonii and attached bacteria (epibionts). These reads were assembled into contigs, binned using the tetranucleotide frequency of the resultant contigs, and finalized using a more stringent secondary assembly. The resulting draft genome shows evidence in Thiomargarita nelsonii for a complete denitrification pathway not previously known in large, vacuolated, sulfur-oxidizing bacteria. Additionally, the genes necessary for polyphosphate metabolism were observed. Polyphosphate metabolism is thought to play a role in the formation of phosphatic minerals that serve as important reservoirs in the marine phosphorous cycle.