Genomic Analysis of Pseudomonas sp. Strain SCT, an Iodate-Reducing Bacterium Isolated from Marine Sediment, Reveals a Possible Use for Bioremediation

Abstract

Strain SCT is an iodate-reducing bacterium isolated from marine sediment in Kanagawa Prefecture, Japan. In this study, we determined the draft genome sequence of strain SCT and compared it to complete genome sequences of other closely related bacteria, including Pseudomonas stutzeri . A phylogeny inferred from concatenation of core genes revealed that strain SCT was closely related to marine isolates of P. stutzeri . Genes present in the SCT genome but absent from the other analyzed P. stutzeri genomes comprised clusters corresponding to putative prophage regions and possible operons. They included pil genes, which encode type IV pili for natural transformation; the mer operon, which encodes resistance systems for mercury; and the pst operon, which encodes a Pi-specific transport system for phosphate uptake. We found that strain SCT had more prophage-like genes than the other P. stutzeri strains and that the majority (70%) of them were SCT strain-specific. These genes, encoded on distinct prophage regions, may have been acquired after branching from a common ancestor following independent phage transfer events. Thus, the genome sequence of Pseudomonas sp. strain SCT can provide detailed insights into its metabolic potential and the evolution of genetic elements associated with its unique phenotype.

Comparative Genomics of Pseudomonas stutzeri Complex: Taxonomic Assignments and Genetic Diversity

“…Although rarely causing infections, over the past two decades, P. stutzeri complex members have been increasingly recognized as a cause of infection in humans ( Scotta et al, 2012 ; Hequette-Ruz et al, 2018 ; Halabi et al, 2019 ). The P. stutzeri complex has received particular attention because of specific physiological properties, such as denitrification ( Pena et al, 2012 ), nitrogen fixation ( Lalucat et al, 2006 ; Yan et al, 2008 ; Busquets et al, 2013 ; Paerl et al, 2018 ), degradation of aromatic compounds ( Brunet-Galmes et al, 2012 ; Busquets et al, 2013 ; Gomila et al, 2015a ; Hirose et al, 2015 ; Brown et al, 2017 ), and metal resistance and potential application in bioremediation ( Li et al, 2012 ; Chakraborty et al, 2017 ; Zheng et al, 2018 ; Harada et al, 2019 ). It was shown that one third of P. stutzeri complex members are naturally transformable ( Sikorski et al, 2002b ; Busquets et al, 2012 ; Smith et al, 2014 ), which may be one of the major driving forces causing its high level of intraspecific heterogeneity.…”

A novel dimethylsulfoxide reductase family of molybdenum enzyme, Idr, is involved in iodate respiration by Pseudomonas sp. SCT

“…strain SCT from marine sediment (Amachi et al, 2007). Phylogenetic analyses based on 16S rRNA gene and concatenation of its core genes revealed that strain SCT was closely related to Pseudomonas stutzeri (Harada et al, 2019). Strain SCT was originally isolated as a bacterium that was able to reduce 200 μM iodate when grown anaerobically with 10 mM nitrate as the electron acceptor (denitrifying condition).…”

Prevalence of heterotrophic methylmercury detoxifying bacteria across oceanic regions

“…In addition, the operon mer can be either codified in the chromosome ( 69 ) or in plasmids ( 28 , 70 ), and usually, mer genes are components of transposons ( 71 ), and integrons ( 72 , 73 ). Thus, different copies of the mer genes including maybe different sequence variants ( 29 , 74 ), could be found within a same strain providing to the strains different tolerances to mercury compounds. This specificity is further supported by the fact that no correlation was observed between the ability to reduce Hg and the taxonomic groups observed in the phylogenetic trees, although negative results should be interpreted with caution.…”