Genome Variation in the Model Halophilic Bacterium Salinibacter ruber

Abstract

The halophilic bacterium Salinibacter ruber is an abundant and ecologically important member of halophilic communities worldwide. Given its broad distribution and high intraspecific genetic diversity, S. ruber is considered one of the main models for ecological and evolutionary studies of bacterial adaptation to hypersaline environments. However, current insights on the genomic diversity of this species is limited to the comparison of the genomes of two co-isolated strains. Here, we present a comparative genomic analysis of eight S. ruber strains isolated at two different time points in each of two different Mediterranean solar salterns. Our results show an open pangenome with contrasting evolutionary patterns in the core and accessory genomes. We found that the core genome is shaped by extensive homologous recombination (HR), which results in limited sequence variation within population clusters. In contrast, the accessory genome is modulated by horizontal gene transfer (HGT), with genomic islands and plasmids acting as gateways to the rest of the genome. In addition, both types of genetic exchange are modulated by restriction and modification (RM) or CRISPR-Cas systems. Finally, genes differentially impacted by such processes reveal functional processes potentially relevant for environmental interactions and adaptation to extremophilic conditions. Altogether, our results support scenarios that conciliate “Neutral” and “Constant Diversity” models of bacterial evolution.

Mining for Perchlorate Resistance Genes in Microorganisms From Sediments of a Hypersaline Pond in Atacama Desert, Chile

“…The fact that these genes would belong to unidentified microorganisms together with the low sequence identities of the gene products remark the novelty of the encoded proteins. The high G + C content of this perchlorateresistance genes may indicate that most of these genes may have been retrieved from halophilic microorganisms (Jones and Baxter, 2016;González-Torres and Gabaldón, 2018). In fact, closest similar proteins of some of the identified gene products belonged to halophilic bacteria, as H. ochraceum (pJR12-orf2 and pJR35-orf2) and R. ekhonensis (pJR56-orf2).…”

“…The G + C content varied from 51 to 75%, indicating a diverse phylogenetic affiliation. Most of inserts showed a G + C content higher than 60%, which could be explained by their halophilic origin (Jones and Baxter, 2016;González-Torres and Gabaldón, 2018). The inserts of the nine plasmids harbored a total of 17 predicted ORFs, twelve of them truncated.…”

Intermediate-Salinity Systems at High Altitudes in the Peruvian Andes Unveil a High Diversity and Abundance of Bacteria and Viruses

“…Other halophilic bacteria, such as Pseudomonas (2.15%) and Halomonas (0.94%), were identified in lower proportions than previously reported [1,44,47]. Even the main bacteria described in hypersaline systems, such as Salinibacter ruber [52,53] and Rhodovibrio salinarum [1], were found in low abundance (~0.07%, each species) in our study, probably because the altitudes of these sites affect bacterial structures, as we have shown.…”

Population Genomics of Microbial Biostalactites: Non-recombinogenic Genome Islands and Microdiversification by Transposons

“…A genome island similar to F. myxofaciens scrapyards has been described in phylogenetically distinct bacteria including Roseococcus , Salinibacter , and Myxococcus ( Wielgoss et al, 2016 ; González-Torres and Gabaldon, 2018 ; Wang et al, 2020 ). The authors propose several functions of this region, including gates for gene exchange with unrelated microbial lineages, initial genetic divergence of populations, self/non-self discrimination and accumulation of mobilome.…”