Genome Analysis of a New Rhodothermaceae Strain Isolated from a Hot Spring

Abstract

A bacterial strain, designated RA, was isolated from water sample of a hot spring on Langkawi Island of Malaysia using marine agar. Strain RA is an aerophilic and thermophilic microorganism that grows optimally at 50–60°C and is capable of growing in marine broth containing 1–10% (w/v) NaCl. 16S rRNA gene sequence analysis demonstrated that this strain is most closely related (<90% sequence identity) to Rhodothermaceae, which currently comprises of six genera: Rhodothermus (two species), Salinibacter (three species), Salisaeta (one species), Rubricoccus (one species), Rubrivirga (one species), and Longimonas (one species). Notably, analysis of average nucleotide identity (ANI) values indicated that strain RA may represent the first member of a novel genus of Rhodothermaceae. The draft genome of strain RA is 4,616,094 bp with 3630 protein-coding gene sequences. Its GC content is 68.3%, which is higher than that of most other genomes of Rhodothermaceae. Strain RA has genes for sulfate permease and arylsulfatase to withstand the high sulfur and sulfate contents of the hot spring. Putative genes encoding proteins involved in adaptation to osmotic stress were identified which encode proteins namely Na+/H+ antiporters, a sodium/solute symporter, a sodium/glutamate symporter, trehalose synthase, malto-oligosyltrehalose synthase, choline-sulfatase, potassium uptake proteins (TrkA and TrkH), osmotically inducible protein C, and the K+ channel histidine kinase KdpD. Furthermore, genome description of strain RA and comparative genome studies in relation to other related genera provide an overview of the uniqueness of this bacterium.

Complete genome sequence of Rhodothermaceae bacterium RA with cellulolytic and xylanolytic activities

“…Strain RA (KCTC 62031) was originally isolated from a hot spring located in Langkawi, a Malaysian island (Goh et al 2016 ). The cells were resuscitated from 20% ( v / v ) glycerol stock, grown on marine agar plates (pH 7.5), and incubated at 50 °C for 48 h. Colonies on the agar plates were scraped and DNA extraction using a Quick-DNA™ Miniprep Plus kit (Zymo Research, Irvine, USA).…”

“…Currently members of family Rhodothermaceae consists of six genera: Rhodothermus (Alfredsson et al 1988 ; Marteinsson et al 2010 ), Salinibacter (Antón et al 2002 ; Makhdoumi-Kakhki et al 2012 ), Salisaeta (Vaisman and Oren 2009 ), Longimonas (Xia et al 2015 ), Longibacter (Xia et al 2016 ), and Natronotalea (Sorokin et al 2017 ). Members of the genera Rubricoccus and Rubrivirga were previously affiliated to family Rhodothermaceae (Park et al 2011 , 2013 ; Goh et al 2016 ), but have recently been reassigned and classified as members of a new family, family Rubricoccaceae (Munoz et al 2016 ). Genome sequences are available from representatives of hall genera of family Rhodothermaceae except for any representative of genus Natronotalea .…”

“…To date, complete genome sequences of two representatives of this family, namely, Rhodothermus marinus and Salinibacter ruber , are available. Strain RA is a halo-thermophile (optimum growth at 2% w/v NaCl, 50 °C) which was isolated from a saline hot spring located on Langkawi Island, Malaysia (6°25′22″N, 99°48′49″E) (Goh et al 2016 ; Chan et al 2017 ). Due to the low DNA–DNA similarity as measured by Genome-to-Genome Distance Calculator (GGDC), 16S rRNA gene similarity, and the housekeeping genes to the other members of the family Rhodothermaceae , strain RA has been assigned as an unclassified taxon of the family Rhodothermaecae , order Bacteroidetes Order II.…”

“…suggests that it should be included as a new species in a newly created genus status. The genome of strain RA was initially sequenced in 2015 using a HiSeq 2500 platform and assembled into 91 contigs (Goh et al 2016 ). Here, we report on the full genome using a PacBio single-molecule sequencing platform and in the presence of lignocellulose biomass-degrading enzymes.…”

Microbial diversity of thermophiles with biomass deconstruction potential in a foliage‐rich hot spring

“…(Currie et al., ) are known for decomposing biomass at high temperatures (Bhalla, Bansal, Kumar, Bischoff, & Sani, ). Furthermore, members of the genera Thermotoga (Yu et al., ), Rhodothermus (Keshk, ), Anoxybacillus (Chan et al., ), Rhodothermaceae strain RA (Goh et al., ), and Caldicellulosiruptor (Peng et al., ) were found to produce thermostable enzymes for biomass saccharification.…”