Whole genome sequence analysis of Cupriavidus campinensis S14E4C, a heavy metal resistant bacterium

Abstract

Cupriavidus sp. are model organisms for heavy metal(loid) resistance and aromatic compound's degradation studies and these characteristics make them a perfect candidate for biotechnological purposes. Bacterial strain S14E4C (identified as Cupriavidus campinensis) was isolated from a playground by enrichment method in a 0.25 mM containing medium. The analysis revealed that this bacterium is able to tolerate high concentrations of heavy metal(loid)s: Cd up to 19.5 mM, Pb to 9 mM, Hg to 5.5 mM and As to 2 mM in heavy metal(loid) salt containing nutrient medium. The whole genome data and analysis of the type strain of C. campinensis CCUG:44526^T have not been available so far, thus here we present the genome sequencing results of strain S14E4C of the same species. Analysis was carried out to identify possible mechanisms for the heavy metal resistance and to map the genetic data of C. campinensis. The annotation pipelines revealed that the total genome of strain S14E4C is 6,375,175 bp length with a GC content of 66.3% and contains 2 plasmids with 295,460 bp (GC content 59.9%) and 50,483 bp (GC content 63%). In total 4460 coding sequences were assigned to known functions and 1508 to hypothetical proteins. Analysis proved that strain S14E4C is having gene clusters such as czc, mer, cus, chr, ars to encode various heavy metal resistance mechanisms that play an important role to survive in extreme environments.

Keywords: Cupriavidus campinensis; Heavy metal resistance; Whole genome sequence.

Fig. 1

A circular graphical display of the genome (contains chromosome and plasmid contigs) and applicable genes. This includes CDS on the forward strand, CDS on the reverse strand, RNA genes, Transposase, pseudogene, GC content and GC skew. The figure was prepared by CGView circular genome visualization tool [62]. (Color figure online)

Fig. 2

Subsystem coverage and category distribution of whole genome. The pie chart demonstrates the counts for each subsystem feature and the subsystem coverage. Genes for each Subsystem Category were shown in brackets. (Color figure online)

Fig. 3

Mercury resistance gene cluster: The chromosomal region of the focus gene (top) is compared with three similar organisms. The graphic depicts the focus gene, which is red and numbered 1. Sets of genes with similar sequence are grouped with the same number and colour (1- mercuric ion reductase merA; 2- TnpA transposase (left), Transposase Tn3 (right); 3- periplasmic mercury (2 +) binding protein merP; 4- mercuric transport protein merT; 5- transcriptional regulator merR family; 6- mercuric resistance operon coregulator merD; 7- mercuric transport protein merC; 8- mercuric transport protein merE; 9- DNA-invertase). Genes whose relative position is conserved in at least three other species are functionally coupled and share grey background boxes

Fig. 4

Phylogenetic relationship of Cupriavidus campinensis S14E4C strain and the species of Cupriavidus based on 16S rRNA gene sequence. Cluster analysis was based upon the neighbour-joining method with Polynucleobacter cosmopolitanus CIP 109840^T (AJ550672) as the outgroup root. The MrBayes method were used to generate the tree and its support values (only values above 50% are presented). Bar, 0.02 substitutions per nucleotide position. Tree was visualised by FigTree v1.4.4

Fig. 5

Phylogenomic tree of the Cupriavidus campinensis S14E4C based on concatenation of 16S rRNA gene with core genes (e.g. gyrB, rpoD, recA, etc.). Tree was built on PATRIC online pipeline

Fig. 6

Phylogenomic tree predicted on TYGS database. Genomic G + C content (63.53–68.47%), δ values (0.08–0.2), overall genome sequence length (5,783,696–9,185,558 bp), number of proteins (5142–7932). Values increase based on the colour range (from white to black) [59]