Comparative genomic analysis of two Arctic Pseudomonas strains reveals insights into the aerobic denitrification in cold environments

Abstract

Background: Biological denitrification has been commonly adopted for the removal of nitrogen from sewage effluents. However, due to the low temperature during winter, microorganisms in the wastewater biological treatment unit usually encounter problems such as slow cell growth and low enzymatic efficiency. Hence, the isolation and screening of cold-tolerant aerobic denitrifying bacteria (ADB) have recently drawn attention. In our previous study, two Pseudomonas strains PMCC200344 and PMCC200367 isolated from Arctic soil demonstrated strong denitrification ability at low temperatures. The two Arctic strains show potential for biological nitrogen removal from sewage in cold environments. However, the genome sequences of these two organisms have not been reported thus far.

Results: Here, the basic characteristics and genetic diversity of strains PMCC200344 and PMCC200367 were described, together with the complete genomes and comparative genomic results. The genome of Pseudomonas sp. PMCC200344 was composed of a circular chromosome of 6,478,166 bp with a G + C content of 58.60% and contained a total of 5,853 genes. The genome of Pseudomonas sp. PMCC200367 was composed of a circular chromosome of 6,360,061 bp with a G + C content of 58.68% and contained 5,801 genes. Not only prophages but also genomic islands were identified in the two Pseudomonas strains. No plasmids were observed. All genes of a complete set of denitrification pathways as well as various putative cold adaptation and heavy metal resistance genes in the genomes were identified and analyzed. These genes were usually detected on genomic islands in bacterial genomes.

Conclusions: These analytical results provide insights into the genomic basis of microbial denitrification in cold environments, indicating the potential of Arctic Pseudomonas strains in nitrogen removal from sewage effluents at low temperatures.

Keywords: Aerobic denitrification; Arctic; Cold adaptation; Heavy metal resistance; Pseudomonas.

Fig. 1

Transmission electron micrographs of the cellular morphology of Pseudomonas strains PMCC200344 (a) and PMCC200367 (b)

Fig. 2

Genome BLAST Distance Phylogeny method (GBDP) for phylogenetic placement analysis using FastME 2.1.6.1 with 100 bootstrap values. a 16S rRNA gene sequence-based phylogeny of strains PMCC200344 and PMCC200367 with the closely related type strains and whole genomes with 77.3% average branch support. b Whole-genome sequence-based phylogeny of strains PMCC200344 and PMCC200367 with the closely related type strains and whole genomes with 92.0% average branch support. The numbers above branches represent the GBDP pseudobootstrap value greater than 60%

Fig. 3

Circular maps of Pseudomonas sp. PMCC200344 (a) and PMCC200367 (b). From outside to center, rings 1 and 4 show protein-coding genes colored by COG categories on the forward/reverse strand; rings 2 and 3 denote genes on the forward/reverse strand; ring 5 shows the G + C % content plot; ring 6 shows the GC skew; the innermost ring shows the marker of genome size

Fig. 4

Number of genes associated with the 22 general COG functional categories in the genome of Pseudomonas sp. PMCC200344 (a) and PMCC200367 (b)

Fig. 5

Putative nitrate reduction pathways and related genes in Pseudomonas strains PMCC200344 and PMCC200367 after KEGG annotation [–17]

Fig. 6

Heavy metal resistance genes distributed in PMCC200344 and PMCC200367. a Zinc ABC transporter permease, b arsenical resistance protein, c copper resistance system, d iron (III) transport system, e zinc/cadmium/lead-transporting ATPase, f chromate transporter, g copper resistance gene

Fig. 7

Comparison of the gene content of strains PMCC200344 and PMCC200367 with other Pseudomonas reference species. a The Pseudomonas core and pan genome plotted for 30 genome sequences of Pseudomonas-related species. b Venn diagram depicting the core and unique genes among PMCC200344 and PMCC200367 and 28 other relevant reference species. c Number of genes associated with the 23 general COG functional categories. The gene number of category B is zero

Fig. 8

Genome collinearity analysis of Pseudomonas sp. PMCC200367 and PMCC200344. The different color blocks represent different conservative regions between PMCC200344 and PMCC200367, which are connected by lines of corresponding colors. The color block below the horizontal line indicates that the gene region of the same color block on the genome for comparison is inverted