Genomic and Transcriptomic Evidence for Carbohydrate Consumption among Microorganisms in a Cold Seep Brine Pool

Abstract

The detailed lifestyle of microorganisms in deep-sea brine environments remains largely unexplored. Using a carefully calibrated genome binning approach, we reconstructed partial to nearly-complete genomes of 51 microorganisms in biofilms from the Thuwal cold seep brine pool of the Red Sea. The recovered metagenome-assembled genomes (MAGs) belong to six different phyla: Actinobacteria, Proteobacteria, Candidatus Cloacimonetes, Candidatus Marinimicrobia, Bathyarchaeota, and Thaumarchaeota. By comparison with close relatives of these microorganisms, we identified a number of unique genes associated with organic carbon metabolism and energy generation. These genes included various glycoside hydrolases, nitrate and sulfate reductases, putative bacterial microcompartment biosynthetic clusters (BMC), and F420H2 dehydrogenases. Phylogenetic analysis suggested that the acquisition of these genes probably occurred through horizontal gene transfer (HGT). Metatranscriptomics illustrated that glycoside hydrolases are among the most highly expressed genes. Our results suggest that the microbial inhabitants are well adapted to this brine environment, and anaerobic carbohydrate consumption mediated by glycoside hydrolases and electron transport systems (ETSs) is a dominant process performed by microorganisms from various phyla within this ecosystem.

Genomic and transcriptomic evidence of light-sensing, porphyrin biosynthesis, Calvin-Benson-Bassham cycle, and urea production in Bathyarchaeota

“…Sulfate or sulfite was previously reported as the important environmental factors to shape the distribution of bathyarchaeotal subgroups [18,30,57], and genomic evidence for dissimilatory sulfate and sulfite reduction via genes sat-aprAB (sulfate adenylyltransferaseadenylylsulfate reductase) were also reported [17,58]. They both suggested that Bathyarchaeota could participate the global sulfur cycle.…”

Parallel Evolution of Genome Streamlining and Cellular Bioenergetics across the Marine Radiation of a Bacterial Phylum

“…More-recent work has shown that members of this phylum can use a broad diversity of alternative electron acceptors in the ocean and likely play a central role in shaping biogeochemical cycles along environmental gradients ( 20 ). Moreover, other studies have shown that Marinimicrobia are present and active in a broad array of marine environments, including coastal and pelagic surface waters, cold seep brine pools, coastal “dead zones,” and oxygen minimum zones (OMZs), and likely mediate key transformations of nitrogen and sulfur throughout the global ocean ( 21 – 27 ). In contrast to the broad environmental distributions typical of other bacterial phyla, Marinimicrobia are unusual in that the vast majority of known diversity in this group has been observed in marine environments, thereby providing a unique opportunity for comparative genomic analyses to assess the factors shaping their genome evolution throughout their radiation into the contemporary ocean.…”

Anti-biofilm effect of a butenolide/polymer coating and metatranscriptomic analyses

“…Metatranscriptomic analysis was performed using the method described in a previous study (Zhang et al 2016). The quality of the cDNA sequences was controlled using the next-generation sequencing QC toolkit (Patel and Jain 2012) before being assembled by SPAdes Genome Assembler 3.6.1 (Bankevich et al 2012) on a local server.…”