Whole Genome Comparison of Thermus sp. NMX2.A1 Reveals Principal Carbon Metabolism Differences with Closest Relation Thermus scotoductus SA-01

Abstract

Genome sequencing of the yellow-pigmented, thermophilic bacterium Thermus sp. NMX2.A1 resulted in a 2.29 Mb draft genome that encodes for 2312 proteins. The genetic relationship between various strains from the genus Thermus was assessed based on phylogenomic analyses using a concatenated set of conserved proteins. The resulting phylogenetic tree illustrated that Thermus sp. NMX2 A.1 clusters together with Thermus scotoductus SA-01, despite being isolated from vastly different geographical locations. The close evolutionary relationship and metabolic parallels between the two strains has previously been recognized; however, neither strain’s genome data were available at that point in time. Genomic comparison of the Thermus sp. NMX2.A1 and T. scotoductus SA-01, as well as other closely related Thermus strains, revealed a high degree of synteny at both the genomic and proteomic level, with processes such as denitrification and natural cell competence appearing to be conserved. However, despite this high level of similarity, analysis revealed a complete, putative Calvin–Benson–Bassham (CBB) cycle in NMX2.A1 that is absent in SA-01. Analysis of horizontally transferred gene islands provide evidence that NMX2 selected these genes due to pressure from its HCO3- rich environment, which is in stark contrast to that of the deep subsurface isolated SA-01.

High‐quality draft genome sequence of Gaiella occulta isolated from a 150 meter deep mineral water borehole and comparison with the genome sequences of other deep‐branching lineages of the phylum Actinobacteria

“…A complete CBB cycle has also been identified in the genome of Thermus sp. NMX2.A1 although CO 2 fixation through this pathway has not been confirmed in this organism (Müller et al, ).…”

Insights into ecological roles of uncultivated bacteria in Katase hot spring sediment from long-read metagenomics

“…Meiothermus MAGs of Deinococcota also encoded a key gene, ribulose 1,5-bisphosphate carboxylase/oxygenase (form I) of the CBB pathway ( Supplementary Table S5 ), as previously reported in other Meiothermus spp. ( Muller et al, 2016 ; Raposo et al, 2019 ). As described above, a Meiothermus MAG (mg070) was highly abundant among the MAGs.…”

“…Meiothermus MAGs of Deinococcota also encoded a key gene, ribulose 1,5-bisphosphate carboxylase/oxygenase (form I) of the CBB pathway (Supplementary Table S5), as previously reported in other Meiothermus spp. (Muller et al, 2016;Raposo et al, 2019) Nanoarchaeota Nanoarchaeia mg001 sp 1 0 .54 4 0 4 5 1 0 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 mg004 gen 1 4 .44 3 6 4 9 9 8 3 49 5 0 0 0 0 0 0 0 0 0 0 1 1 0 1 0 1 0 0 0 1 0 0 0 1 1 1 0 1 15 3 3 0 mg005 gen 1 4 .86 1 7 4 3 1 17 2 50 7 0 0 1 0 0 0 0 0 0 1 1 1 0 1 0 1 0 0 0 1 0 1 0 1 1 1 0 1 18 4 4 0 Blastocatellia mg006 -1 2 .69 1 50 46 21 1 37 2 0 0 0 1 0 0 0 0 0 0 0 0 0 1 0 0 1 0 0 0 0 0 0 1 1 0 0 0 1 0 0 0 Thermoanaerobaculia mg007* -1 2 .76 1 4 5 8 1 5 0 31 1 0 0 0 0 0 0 0 0 0 0 1 1 1 1 0 0 0 0 0 1 0 0 0 1 0 1 1 1 9 7 7 1 mg008 gen 2 2 .44 8 42 8 1 27 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 2 0 0 0 mg009 gen 4 3 .45 7 34 14 0 45 3 0 1 0 1 0 0 0 0 0 0 0 1 0 0 0 1 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 Thermoleophilia mg012 gen 1 2 .62 4 3 5 1 1 1 0 31 1 0 1 1 1 0 0 0 0 0 1 0 0 0 0 0 0 0 1 0 0 0 0 0 1 1 0 0 0 1 0 0 0 UBA4738 mg013 sp 4 2 .20 7 47 5 0 26 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 1 0 0 0 mg015 -41 3.34 28 47 23 1 25 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 3 0 0 0 mg018* sp 1 2 .99 8 64 50 44 1 25 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 8 0 0 0 mg021 -5 2 .98 7 56 48 1 26 4 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 1 0 0 0 0 6 0 0 0 mg022 sp 7 4 .11 1 0 5 6 1 39 3 32 1 0 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 0 0 0 0 1 0 1 0 1 1 0 3 6 2 0 mg023 sp 30 4.58 21 54 153 6 32 9 0 0 0 0 0 0 0 0 0 0 0 1 1 1 0 1 1 0 0 0 0 1 1 1 0 1 0 0 2 6 2 0 UBA5829 mg024* sp 1 3 .29 2 3 4 3 1 03 5 21 6 0 0 1 0 0 0 0 0 0 0 0 1 0 1 0 0 0 0 1 0 0 0 0 1 0 1 1 0 4 2 2 1 mg025 sp 1 2 .27 1 0 4 9 8 0 14 2 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 2 0 0 mg031 gen 24 3.91 22 37 18 0 29 3 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 0 0 0 0 0 0 0 0 0 0 9 2 0 0 mg032 sp 15 2.76 7 4 2 4 2 1 56 6 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 1 0 0 0 0 0 0 0 0 0 0 0 0 2 1 0 0 mg033 -4 2 .85 9 2 4 9 4 0 38 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 1 0 0 mg034 gen 36 2.54 217 43 9 0 30 1 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 1 0 0 0 2 1 0 0…”

Relationships between fluid mixing, biodiversity, and chemosynthetic primary productivity in Yellowstone hot springs

“…While Sulfurihydrogenibium is known for its autotrophic capabilities and encodes key proteins involved in the rTCA cycle (Huber & Eder, 2006), Thermus are traditionally considered to be heterotrophs (Williams & Da Costa, 1992). The RSW planktonic Thermus MAG encodes form I RuBisCO (RbcSL) homologues and these have been previously identified in the genomes of Thermus strains isolated from high temperature environments that also have high concentrations of bicarbonate (Müller et al, 2016). However, to our knowledge, no isolated Thermus strain has been shown to fix CO 2 in laboratory settings.…”