Physiological and genomic features of a novel sulfur-oxidizing gammaproteobacterium belonging to a previously uncultivated symbiotic lineage isolated from a hydrothermal vent

Abstract

Strain Hiromi 1, a sulfur-oxidizing gammaproteobacterium was isolated from a hydrothermal vent chimney in the Okinawa Trough and represents a novel genus that may include a phylogenetic group found as endosymbionts of deep-sea gastropods. The SSU rRNA gene sequence similarity between strain Hiromi 1 and the gastropod endosymbionts was approximately 97%. The strain was shown to grow both chemolithoautotrophically and chemolithoheterotrophically with an energy metabolism of sulfur oxidation and O2 or nitrate reduction. Under chemolithoheterotrophic growth conditions, the strain utilized organic acids and proteinaceous compounds as the carbon and/or nitrogen sources but not the energy source. Various sugars did not support growth as a sole carbon source. The observation of chemolithoheterotrophy in this strain is in line with metagenomic analyses of endosymbionts suggesting the occurrence of chemolithoheterotrophy in gammaproteobacterial symbionts. Chemolithoheterotrophy and the presence of homologous genes for virulence- and quorum sensing-related functions suggest that the sulfur-oxidizing chomolithotrophic microbes seek animal bodies and microbial biofilm formation to obtain supplemental organic carbons in hydrothermal ecosystems.

Figure 1. Electron micrographs of the new isolate strain Hiromi 1.

A transmission electron micrograph of a negatively stained cell (A) and a thin section cell (B) grown under the chemolithoautotrophic condition. White and black arrows indicate intracellular particle and outer membrane, respectively. Scanning micrographs of cells adhering on elemental sulfur by pilus to biofilm (C, D). Cells attached on biofilm formation and pili structures were shown by large and small black arrows. Other cells grew under the polysaccharide-like substances. Bars, 0.2 µm (A), 0.5 µm (B) and 1 µm (C, D).

Figure 2. A SSU rRNA gene phylogenetic tree of chemolithoautotrophic and methanotrophic Gammaproteobacteria including strain Hiromi 1 constructed by the neighbor-joining method using 1253 identical positions.

Bootstrap values higher than 50% are presented. GenBank/EMBL/DDBJ accession numbers are given in parentheses. Bar indicates 1 substitutions per 100 nucleotides.

Figure 3. Predicted central metabolism of strain Hiromi 1.

Red lines indicate conserved pathways in most of the publically accessible genomes of the chemolithoautotrophic Gammaproteobacteria. EC numbers are given on each enzymatic reaction. Light blue font indicates concentrations (per pmol 10¹⁰ cells) of metabolites. Metabolites that were not targets of the metabolomic analysis were given neither concentrations nor N.D. N.D.; not detected. Pi, phosphate; PPi, pyrophosphate; Glc, α-D-glucose; αG6P, α-D-glucose-6-phosphate; G1P, α-D-glucose-1-phosphate; βG6P, β-D-glucose-1-phosphate; F6P, β-D-fructose-6-phophate; FBP, β-D-fructose-1,6-bisphosphate; GAP, glyceraldehyde-3-phosphate; GBP, glycerate-1,3-bisphosphate; G3P, glycerate-3-phosphate; G2P, glycerate-2-phosphate; PEP, phosphoenolpyruvate; E4P, erythrose-4-phosphate; acetyl-P, acetyl phosphate; DHAP, dihydroxyacetone phosphate; X5P, D-xylulose-5-phosphate; SBP, D-sedoheptulose-1,7-bisphosphate; S7P, D-sedoheptulose-7-phosphate; RuBP, ribulose-1,5-bisphosphate; Ru5P, ribulose-5-phophate; R5P, D-ribose-5-phosphate.

Figure 4. Predicted sulfur oxidation pathways of strain Hiromi 1 inferred from the previously published literatures , –, , .

TCEP; tris(2-carboxyethyl)phosphine.