Abstract
Niche adaptation has long been recognized to drive intra-species differentiation and speciation, yet knowledge about its relatedness with hereditary variation of microbial genomes is relatively limited. Using Leptospirillum ferriphilum species as a case study, we present a detailed analysis of genomic features of five recognized strains. Genome-to-genome distance calculation preliminarily determined the roles of spatial distance and environmental heterogeneity that potentially contribute to intra-species variation within L. ferriphilum species at the genome level. Mathematical models were further constructed to extrapolate the expansion of L. ferriphilum genomes (an ‘open’ pan-genome), indicating the emergence of novel genes with new sequenced genomes. The identification of diverse mobile genetic elements (MGEs) (such as transposases, integrases, and phage-associated genes) revealed the prevalence of horizontal gene transfer events, which is an important evolutionary mechanism that provides avenues for the recruitment of novel functionalities and further for the genetic divergence of microbial genomes. Comprehensive analysis also demonstrated that the genome reduction by gene loss in a broad sense might contribute to the observed diversification. We thus inferred a plausible explanation to address this observation: the community-dependent adaptation that potentially economizes the limiting resources of the entire community. Now that the introduction of new genes is accompanied by a parallel abandonment of some other ones, our results provide snapshots on the biological fitness cost of environmental adaptation within the L. ferriphilum genomes. In short, our genome-wide analyses bridge the relation between genetic variation of L. ferriphilum with its evolutionary adaptation.
Highlights
The emergence of generation sequencing technologies accompanied with developing methodological and computational approaches has yielded valuable insights into the genetic traits of microorganisms in various habitats worldwide, such as their metabolic capabilities and evolutionary adaptation (Cordero and Polz, 2014; Ji et al, 2014; Zhang and Sievert, 2014; Youssef et al, 2015; Zhang et al, 2016a,b,e, 2017a)
We present the comprehensive study of L. ferriphilum pan-genome and the elucidation of genetic diversity among L. ferriphilum strains
Five L. ferriphilum genomes available in NCBI repository were collected for this study, including the draft genomes of strains DX and ZJ isolated from two different copper mine tailings in China, the complete genome (NCBI ID: CP002919) of strain ML-04 obtained from an acidic water near a hot spring in China (Mi et al, 2011), the complete genome (NCBI ID: CP007243) of strain YSK isolated from an acid mine drainage in China (Jiang et al, 2015), and the draft genomes of strain Sp-Cl obtained from a bioleaching solutions draining in Chile (Issotta et al, 2016)
Summary
The emergence of generation sequencing technologies accompanied with developing methodological and computational approaches has yielded valuable insights into the genetic traits of microorganisms in various habitats worldwide, such as their metabolic capabilities and evolutionary adaptation (Cordero and Polz, 2014; Ji et al, 2014; Zhang and Sievert, 2014; Youssef et al, 2015; Zhang et al, 2016a,b,e, 2017a). Evolutionary Adaptation of Leptospirillum ferriphilum databases have fueled the field of comparative genomics. Studies on bacterial genomes significantly expanded the scope of interspecies divergence (Ullrich et al, 2016; Zhang et al, 2016e). Spatial distance and environmental heterogeneity are recognized to be two major factors that contribute to genetic variation of microbial genomes and populations (Ramette and Tiedje, 2007). The contribution of environmental factors to microbial biogeography is relatively more than that of geographic distributions (Lin et al, 2013). It is of value to determine the potential relevance between hereditary variation of bacterial strains and adaptation to different ecological niches, probably reflecting the responsive mechanisms to local environmental perturbations
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