Genome-Based Comparative Analyses of Antarctic and Temperate Species of Paenibacillus

Abstract

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.

Genomic and phenotypic insights into the ecology of Arthrobacter from Antarctic soils

“…The fewer CDSs, the lowered metabolic versatility, and the significant reduction in CDSs associated with transcription and carbohydrate transport and metabolism, suggest the occurrence of genome content scaling in four of the seven Antarctic Arthrobacter isolates. This occurrence was also reported in three strains of Paenibacillus darwinianus that were isolated from gamma-irradiated soils of the RSR [ 73 , 74 ]. In bacteria, an increase in genome size is often linked with an increase in metabolic versatility, allowing bacteria to produce new enzymes that exploit a wide range of environmental conditions [ 75 ].…”

Current knowledge and perspectives of Paenibacillus: a review

“…Genome size ranges from 3.02 Mbp (for P. darwinianus Br, isolated from Antarctic soil [10]) to 8.82 Mbp (for P. mucilaginosus K02, implicated in silicate mineral weathering [11]) and genes number from 3064 ( P. darwinianus Br) to 8478 ( P. sophorae S27, a rhizobacterium). Like P. darwinianus , the insect pathogens P. larvae and P. popilliae have genomes on the smaller side (4.51 and 3.83 Mbp, respectively), perhaps reflecting their niche specialization.…”

Isolation and Identification of Streptomyces ramulosus from Soil and Determination of Antimicrobial Property of its Pigment

“…In most actinomycete species, DNA base composition is comprised of 63-78% guanine+cytosine (G+C), which is more than other bacteria (2). These bacteria are heterotrophic, filamentous, rod-shaped, aerobic, immotile, and asexual spore-forming (3).…”