Genome-based comparative analyses of Antarctic and temperate species of Paenibacillus

• Published in: PloS one 2014-10, Vol.9 (10), p.e108009
• Main Authors: Dsouza, Melissa, Taylor, Michael W, Turner, Susan J, Aislabie, Jackie
• Format: Article
• Language: English
• Subjects: Amino Acids - genetics; Antarctic Regions; Bacteria; Biology and Life Sciences; Cold shock; Cold Temperature; Deinococcus; Deoxyribonucleic acid; DNA; Ecology and Environmental Sciences; Firmicutes; Gene sequencing; Genes; Genes, Bacterial; Genome, Bacterial - genetics; Genomes; Metabolism; Microbial Viability - genetics; Moisture content; Molecular biology; Molecular Sequence Data; Nutrient content; Osmotic Pressure; Oxidative Stress; Paenibacillus; Paenibacillus - genetics; Physiology; Polar environments; Proteins; Radiation; Scaling; Signal transduction; Soil analysis; Soil Microbiology; Soils; Species Specificity; Sporulation; Strains (organisms); Stress, Physiological - genetics; Survival; Temperature extremes; Trends; U.V. radiation; Ultraviolet radiation; Water content
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0108009

Antarctic soils represent a unique environment characterised by extremes of temperature, salinity, elevated UV radiation, low nutrient and low water content. Despite the harshness of this environment, members of 15 bacterial phyla have been identified in soils of the Ross Sea Region (RSR). However, the survival mechanisms and ecological roles of these phyla are largely unknown. The aim of this study was to investigate whether strains of Paenibacillus darwinianus owe their resilience to substantial genomic changes. For this, genome-based comparative analyses were performed on three P. darwinianus strains, isolated from gamma-irradiated RSR soils, together with nine temperate, soil-dwelling Paenibacillus spp. The genome of each strain was sequenced to over 1,000-fold coverage, then assembled into contigs totalling approximately 3 Mbp per genome. Based on the occurrence of essential, single-copy genes, genome completeness was estimated at approximately 88%. Genome analysis revealed between 3,043-3,091 protein-coding sequences (CDSs), primarily associated with two-component systems, sigma factors, transporters, sporulation and genes induced by cold-shock, oxidative and osmotic stresses. These comparative analyses provide an insight into the metabolic potential of P. darwinianus, revealing potential adaptive mechanisms for survival in Antarctic soils. However, a large proportion of these mechanisms were also identified in temperate Paenibacillus spp., suggesting that these mechanisms are beneficial for growth and survival in a range of soil environments. These analyses have also revealed that the P. darwinianus genomes contain significantly fewer CDSs and have a lower paralogous content. Notwithstanding the incompleteness of the assemblies, the large differences in genome sizes, determined by the number of genes in paralogous clusters and the CDS content, are indicative of genome content scaling. Finally, these sequences are a resource for further investigations into the expression of physiological attributes that enable survival under extreme conditions and selection processes that affect prokaryotic genome evolution.