Phylogenomic analyses and comparative genomic studies of Thermus strains isolated from Tengchong and Tibet hot springs, China

Abstract

Genus Thermus is the main focus of researcher among the thermophiles. Members of this genus are the inhabitants of both natural and artificial thermal environments. We performed phylogenomic analyses and comparative genomic studies to unravel the genomic diversity among the strains belonging to the genus Thermus as well their strategiesto adapt in geographically different thermal springs. Sixteen Thermus strains were isolated and sequenced from two geographically different hot springs, Qucai hot springs in Tibet and Tengchong hot springs in Yunnan, China. 16S rRNA gene based phylogeny and phylogenomic analyses based on concatenated set of conserved proteins 971 (supermatrix and gene content methods) revealed a mixed distribution of the Thermus strains. The phylogenomic analyses results suggest fundamentally similar trends of adaptabilityof genus Thermus at high-temperature environments. Whole genome based phylogenetic analysis showed, all 16 Thermus strains belong to five species; T. oshimai (YIM QC-2-109, YIM 1640, YIM 1627, 77359, 77923, 77838), T.antranikianii (YIM 73052, 77412, 77311, 71206), T. brokianus (YIM 73518, 71318, 72351), T. hydrothermalis (YIM 730264 and 77927) and T. thalpophilus (77420). Although the genomes of different strains of Thermus of same species were highly similar, but subtle differences were found.CRISPR loci were detected through genome-widescreening, which showed that Thermus isolates from two different thermal locations had well developed defense system against viruses and adopt similar strategy for survival. Additionally, comparative genome analysis screened competence loci across all the Thermus genomes which reveal that they acquire DNA from environment very efficiently. In the present study it was found that Thermusstrains from two different geothermal springs use two mechanism of incomplete denitrification pathway, some Thermusstrains produces nitric oxide while others nitrious oxide (dinitrogen oxide), which show the heterotrophic lifestyle of Thermus genus. All isolated organisms encoded complete pathways for glycolysis, tricarboxylic acid (TCA) and pentose phosphate. Calvin Benson Bassham cycle genes were identified in genomes of T. oshimai and T. antranikianii strains, while genomes of all T. brokianus strains and organism 77420 were lacking. Arsenic, cadmium and cobalt-zinc-cadmium resistant genes were detected in genomes of all sequenced Thermusstrains. Strains 77420, 77311, 73518, 77412 and 72351 genomes were found harboring genes for siderophores production. Sox gene clusters were identified in all sequenced genomes, except strain YIM 730264, suggesting a mode of chemolithotrophy.