The genomic sequence of Exiguobacterium chiriqhucha str. N139 reveals a species that thrives in cold waters and extreme environmental conditions

Abstract

We report the genome sequence of Exiguobacterium chiriqhucha str. N139, isolated from a high-altitude Andean lake. Comparative genomic analyses of the Exiguobacterium genomes available suggest that our strain belongs to the same species as the previously reported E. pavilionensis str. RW-2 and Exiguobacterium str. GIC 31. We describe this species and propose the chiriqhucha name to group them. 'Chiri qhucha' in Quechua means 'cold lake', which is a common origin of these three cosmopolitan Exiguobacteria. The 2,952,588-bp E. chiriqhucha str. N139 genome contains one chromosome and three megaplasmids. The genome analysis of the Andean strain suggests the presence of enzymes that confer E. chiriqhucha str. N139 the ability to grow under multiple environmental extreme conditions, including high concentrations of different metals, high ultraviolet B radiation, scavenging for phosphorous and coping with high salinity. Moreover, the regulation of its tryptophan biosynthesis suggests that novel pathways remain to be discovered, and that these pathways might be fundamental in the amino acid metabolism of the microbial community from Laguna Negra, Argentina.

Keywords: Arsenic resistance; Bacterial metabolism; Exiguobacterium; Extremophiles; High altitude Andean lakes; Metals or metalloids; Tryptophan biosynthesis; UV resistance.

Figure 1. Evolutionary history of the genus Exiguobacterium.

(A) Phylogenetic reconstruction using complete genomic sequences of 17 representative Exiguobacterium strains. The tree was built with PhyloPhlAn (Segata et al., 2013). (B) Synteny among Exiguobacterium strains. Nucleotide syntenic blocks are represented by colored bars. Red links denote no rearrangements between the blocks compared. Blue links denote rearrangements between the blocks compared. Blue numbers in the phylogeny denote the minimum number of rearrangements obtained with MGR. Plasmids from E. sibiricum are displayed at the right (separated from the chromosome by backslashes). Black numbers indicate bootstrap values different from 100%.

Figure 2. Differential interference contrast image of E. chiriqhucha str. N139.

Figure 3. Circular genome map of E. chiriqhucha str. N139.

Circle tracks from out towards inside are as follows: (1) Length in nucleotides for each contig; (2) Coding Sequences (CDS) in the Forward Strand (light blue); (3) CDS in the reverse strand (dark blue); (4) Strain Specific Genes (SSGs) in the forward strand (light purple); (5) SSGs in the reverse strand (dark purple); (6) GC Skew (gray). Skew and gene distribution follow that of a typical Firmicute genome. The Strain Specific Genes in the contigs that belong to the chromosome appear to be randomly distributed, whilst they seem to be concentrated in the contigs 12 and 13, which are probably the ones belonging to megaplasmids. The circular plot was done with Circos software (Krzywinski et al., 2009).

Figure 4. Effect of ultraviolet B (UV-B) radiation on Exiguobacterium strains.

Percentage survival to UV-B radiation of str. N139 (dark circle), str. S17 (light circle) and str. DSMZ 6208 (dark triangle). The influence of UV-B radiation was studied by exposing liquid cultures to increasing doses, varying exposure times between 0 and 240 min.