Genomic features of Bacillus altitudinis RDK4 attributed with Pb-tolerant phenotype

Abstract

Group of Bacillus have high resilience capacity in harsh conditions, including in a heavy metal contamination environment. We isolated Bacillus altitudinis RDK4 from soil around an ex-mining area which showed lead-tolerant phenotype. In this study, the genomics of RDK4 was analyzed to identify genes or pathways potentially involved in lead-tolerant activity and was employed for evolutionary relationships analysis of this isolate towards other Bacillus species. Whole genome sequence of RDK4 was obtained by using Oxford Nanopore Technology platform. The genome size of RDK4 was 3,704,351 bp (3700 coding sequences), in circular form, with average GC% of 41.44%. Functional categories of RDK4 annotated genes resulted in four dominant categories included genetic information processing (13.6%), signalling and cellular process (11.0%), environmental information processing (9.6%) and carbohydrate metabolism (9.6%). Some pathways (complete modules) that are potentially involved in the lead-tolerant phenotype were identified, including the biosynthesis of biosurfactants (fengycin, lychensin), antioxidants (terpenes, polyketides), and siderophores (schizokinen). In addition, genetic properties of metal-efflux system (cadA, FieF) and exopolysaccharide-mediated metal sequestration (eps operon) and antioxidative response genes (katA, ahpC, TrxA, SodA/C) were also present in the RDK4 genome. Thus, the lead-tolerant phenotype is potentially the result of a combination of these modes of action. Comparative genome analysis revealed that as many as 1523 protein clusters were shared between RDK4 and other Bacillus species. Interestingly, RDK4 was found to be in a close evolutionary relationship with B. subtilis and B. megaterium, sharing 215 and 85 specific protein clusters, respectively. These findings highlight the genetic properties and lead-tolerance mechanisms of RDK4, which support its application as a bioremediation agent.