Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones

Abstract

Metagenome of a versatile chemolithoautotroph from expanding oceanic dead zones Summary: Time-resolved metagenomic approaches are used to describe carbon and energy metabolism of an ecologically relevant microbe from expanding oceanic dead zones mediating carbon sequestration, sulfur-detoxification and biological nitrogen loss.

Isolation of an aerobic sulfur oxidizer from the SUP05/Arctic96BD-19 clade

“…The potential for sulfur oxidation was confirmed by identifying sulfur (S1) in the extracellular globules using scanning transmission electron microscopy ( Figure 1a) combined with energy-dispersive X-ray spectroscopy (Figures 1b and c). These data support the genomic findings of Walsh et al (2009), which suggested that members of this clade have the capacity to oxidize and store S1 due to an incomplete Sox pathway. Suspected roles in marine carbon and sulfur cycles were further evaluated using previously published PCR primers or new primers targeting genes involved in carbon fixation and sulfur oxidation (Blazejak et al, 2006;Swan et al, 2011).…”

“…Of the primer pairs tried, only the dissimilatory aprA gene was identified (Hipp et al, 1997;Kelly et al, 1997;Friedrich et al, 2005;Blazejak et al, 2006). The inability to amplify carbon fixation genes using degenerate primers suggests that cultured GSOs are significantly diverged from known GSOs that occupy anoxic zones and the deep ocean (Walsh et al, 2009;Swan et al, 2011) or that they get all of their carbon from organic compounds.…”

The metatranscriptome of a deep-sea hydrothermal plume is dominated by water column methanotrophs and lithotrophs

“…The increased abundance of SUP05 sox gene transcripts in the Guaymas Basin plume-among the most plume-enriched genes in the metatranscriptome-provides evidence that SUP05 responds to reduced sulfur compounds commonly found within the plume environment (Figure 2). The prevalence and activity of this group in the deep sea deserves further attention, especially in light of its potential impact on the global cycling of carbon, sulfur, nitrogen and important greenhouse gases (Walsh et al, 2009;Canfield et al, 2010).…”

“…SUP05 is abundant in oxic/anoxic interfacial environments such as deep-sea hydrothermal plumes (Sunamura et al, 2004;Dick and Tebo, 2010;German et al, 2010), oxygen minimum zones (Stevens and Ulloa, 2008;Lavik et al, 2009;Walsh et al, 2009;Canfield et al, 2010) and symbioses with deep-sea bivalves (Newton et al, 2007). Our data set supports previous genomic studies that showed that members of this group are chemolithoautotrophic, obtaining energy by coupling sulfur oxidation to reduction of nitrate and/or oxygen (Newton et al, 2007;Walsh et al, 2009). The increased abundance of SUP05 sox gene transcripts in the Guaymas Basin plume-among the most plume-enriched genes in the metatranscriptome-provides evidence that SUP05 responds to reduced sulfur compounds commonly found within the plume environment (Figure 2).…”

Genome Sequence of Strain IMCC2047, a Novel Marine Member of the Gammaproteobacteria

“…Phylogenetic analysis based on 16S rRNA gene sequences showed that strain IMCC2047 formed a distinct phyletic clade and was most closely related to species of the genus Microbulbifer (90.1 to 92.3%) of the Gammaproteobacteria among the validly published species. Environmental clone sequences showing higher sequence similarity have been also reported from various marine habitats, including a mangrove ecosystem (DQ234156; 99.9%) (8), the Arctic surface sediment (EU287390; 99.0%) (7), an oxygen minimum zone (GQ350234; 98.0%) (12), and ocean crust (EU491487; 97.6%) (11). Taking into consideration the unique phylogenetic position of IMCC2047 and wide distribution of highly similar 16S rRNA gene sequences, we performed genome sequencing of strain IMCC2047.…”