Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov

Chun-Zhi Jin; Ye Zhuo; Xuewen Wu; So-Ra Ko; Taihua Li; Feng-Jie Jin; Chi-Yong Ahn; Hee-Mock Oh; Hyung-Gwan Lee; Long Jin

doi:10.3390/microorganisms8020262

Genomic and Metabolic Insights into Denitrification, Sulfur Oxidation, and Multidrug Efflux Pump Mechanisms in the Bacterium Rhodoferax sediminis sp. nov

Microorganisms. 2020 Feb 15;8(2):262. doi: 10.3390/microorganisms8020262.

Authors

Chun-Zhi Jin^{1

2}, Ye Zhuo¹, Xuewen Wu¹, So-Ra Ko³, Taihua Li¹, Feng-Jie Jin¹, Chi-Yong Ahn³, Hee-Mock Oh³, Hyung-Gwan Lee³, Long Jin¹

Affiliations

¹ Co-Innovation Centre for Sustainable Forestry in Southern China, College of Biology and the Environment, Nanjing Forestry University, Nanjing 210-037, China.
² Industrial Biomaterial Research Center, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea.
³ Cell Factory Research Centre, Korea Research Institute of Bioscience & Biotechnology (KRIBB), Daejeon 34141, Korea.

Abstract

This genus contains both phototrophs and nonphototrophic members. Here, we present a high-quality complete genome of the strain CHu59-6-5^T, isolated from a freshwater sediment. The circular chromosome (4.39 Mbp) of the strain CHu59-6-5^T has 64.4% G+C content and contains 4240 genes, of which a total of 3918 genes (92.4%) were functionally assigned to the COG (clusters of orthologous groups) database. Functional genes for denitrification (narGHJI, nirK and qnor) were identified on the genomes of the strain CHu59-6-5^T, except for N₂O reductase (nos) genes for the final step of denitrification. Genes (soxBXAZY) for encoding sulfur oxidation proteins were identified, and the FSD and soxF genes encoding the monomeric flavoproteins which have sulfide dehydrogenase activities were also detected. Lastly, genes for the assembly of two different RND (resistance-nodulation division) type efflux systems and one ABC (ATP-binding cassette) type efflux system were identified in the Rhodoferax sediminis CHu59-6-5^T. Phylogenetic analysis based on 16S rRNA sequences and Average Nucleotide Identities (ANI) support the idea that the strain CHu59-6-5^T has a close relationship to the genus Rhodoferax. A polyphasic study was done to establish the taxonomic status of the strain CHu59-6-5^T. Based on these data, we proposed that the isolate be classified to the genus Rhodoferax as Rhodoferax sediminis sp. nov. with isolate CHu59-6-5^T.

Keywords: RND efflux systems; Rhodoferax; Rhodoferax sediminis; denitrification; sulfur oxidation.