The draft genome of Andean Rhodopseudomonas sp. strain AZUL predicts genome plasticity and adaptation to chemical homeostasis

Abstract

The genus Rhodopseudomonas comprises purple non-sulfur bacteria with extremely versatile metabolisms. Characterization of several strains revealed that each is a distinct ecotype highly adapted to its specific micro-habitat. Here we present the sequencing, genomic comparison and functional annotation of AZUL, a Rhodopseudomonas strain isolated from a high altitude Andean lagoon dominated by extreme conditions and fluctuating levels of chemicals. Average nucleotide identity (ANI) analysis of 39 strains of this genus showed that the genome of AZUL is 96.2% identical to that of strain AAP120, which suggests that they belong to the same species. ANI values also show clear separation at the species level with the rest of the strains, being more closely related to R. palustris. Pangenomic analyses revealed that the genus Rhodopseudomonas has an open pangenome and that its core genome represents roughly 5 to 12% of the total gene repertoire of the genus. Functional annotation showed that AZUL has genes that participate in conferring genome plasticity and that, in addition to sharing the basal metabolic complexity of the genus, it is also specialized in metal and multidrug resistance and in responding to nutrient limitation. Our results also indicate that AZUL might have evolved to use some of the mechanisms involved in resistance as redox reactions for bioenergetic purposes. Most of those features are shared with strain AAP120, and mainly involve the presence of additional orthologs responsible for the mentioned processes. Altogether, our results suggest that AZUL, one of the few bacteria from its habitat with a sequenced genome, is highly adapted to the extreme and changing conditions that constitute its niche.

Keywords: Chemical resistance; High-altitude Andean lakes; Pangenomic analysis; Purple non-sulfur bacteria; Rhodopseudomonas.

Fig. 1

Average Nucleotide Identity (ANI) values of strains within the Rhodopseudomonas genus. Thirty-nine strains were analyzed using the OAU software. The percentages of identity are highlighted as a color scale shown to the right of the image. A similarity tree is shown on top of the identity matrix. The name of each strain follows the taxonomy proposed in Imhoff et al. [60]

Fig. 2

Unrooted tree of Rhodopseudomonas strains based on the core genome. Core genes obtained with Roary were concatenated, aligned and used to infer phylogenetic relationships with the neighbour joining method using FastTree, all part of the Roary pipeline. The tree scale in number of nucleotide substitutions per site is shown

Fig. 3

Pangenomic analysis of 31 Rhodopseudomonas strains using the exponential model. The number of gene clusters were plotted as a function of the number n of strains added sequentially. Black circles are the values obtained with the different orders in the addition of strains. The continuous red curves represent the least-squares fit of the data to an exponential function [33]. A Core genome plot. The core genome size with the addition of the 31st strain is 1,397. B Pangenome size trend. The equations are shown at the top of each plot

Fig. 4

Gene count of main process classes in Rhodopseudomonas according to PATRIC. Comparisons between the 31 strains used for pangenomic analyses was done using PATRIC Comparative Pathways tool. AZUL is highlighted in gray. A similarity tree built using ANI values is shown

Fig. 5

Schematic view of the main operons involved in metal resistance in the AZUL genome. A Genes of the czc system for resistance to cadmium, cobalt and zinc (yellow boxes). B Copper resistance cop (blue boxes) and cus (purple boxes), cupredoxin genes (cdx₁ and cdx-2, dark gray boxes), silP and tolC (green). C Chr chromate efflux genes chrA, chrB, chrC, srpC and chrp (pink boxes). D Mercury resistance genes merP, merF, merT and merR1 genes, located in the vicinity of tniQ, tniB and tnsB genes, which participate in transposition (all orange boxes). E The main regulatory units of the AZUL arsenic resistance system (blue boxes) contain arsC, acr3, arsH and regulatory arsR and hlyU genes. In all the operons, box arrowheads show the orientation of each coding region. Light gray boxes represent unrelated or hypothetical coding regions and green boxes represent genes for resistance to other stressors. The numbered black lines indicate the size of each operon in base pairs. The scale is maintained for each resistance system, but different systems have different scales, in bp. For details about the function of each gene, please refer to Table 4