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Paludibacterium denitrificans sp. nov., a Novel Denitrifying Bacterium Isolated from Activated Sludge

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Abstract

A Gram-reaction-negative, facultatively aerobic, motile, non-spore-forming, rod-shaped, and denitrifying bacterium, designated dN18-1T, was isolated from activated sludge, Republic of Korea. This bacterium was investigated via a polyphasic approach to reveal its taxonomic position. Phylogenetic analysis based on 16S rRNA gene sequence indicated that strain dN18-1T belongs to the genus Paludibacterium and is most closely related to P. purpuratum KCTC 42852T (96.2% sequence similarity), P. yongneupense KACC 11601T (96.1%), and P. paludis BCRC 80514T (95.2%). The average nucleotide identity values and digital DNA-DNA hybridization values calculated between strain dN18-1T and the closely related strains were 72.5–73.1% and 19.0–19.6%. The genome comprises of 3,347,996 bp with a G + C content of 57.3 mol%. Strain dN18-1T possesses ubiquinone Q-8 as a predominant respiratory quinone, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c), summed feature 8 (C18:1 ω6c/C18:1 ω7c), C16:0 and C12:0, as its major fatty acids (>5%). The polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids and four unidentified aminophospholipids. The results of ANI calculation, digital DNA-DNA hybridization, physiological and biochemical tests allowed phenotypic differentiation of strain dN18-1T from rephrase other genus Paludibacterium species with validly published names. Therefore, this isolate represents a novel species, for which the name Paludibacterium denitrificans sp. nov. (type strain dN18-1T = KACC 19537T = CGMCC 1.16961T) is proposed.

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Funding

This research was supported by the project on survey and excavation of Korean indigenous species of the National Institute of Biological Resources (NIBR) and by a grant from the Korea Research Institute of Bioscience & Biotechnology (KRIBB) Research Initiative Program (KGM5232113).

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Authors and Affiliations

  1. Major in Applied Biotechnology, Hankyong National University, 327 Chungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea

    Ji Eun Lee, Gyu-Min Choi, Soon Youl Lee & Wan-Taek Im

  2. AceEMzyme Co., Ltd., Academic Industry Cooperation, 327 Chungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea

    Gyu-Min Choi & Wan-Taek Im

  3. Korean Collection for Type Cultures, Korea Research Institute of Bioscience and Biotechnology, 181 Ipsin-gil, Jeongeup-si, Jeollabuk-do, 56212, Republic of Korea

    Yong-Jae Lee & Sang-Mi Lee

  4. HK Ginseng Research Center, 327 Chungang-no, Anseong-si, Gyeonggi-do, 17579, Republic of Korea

    Wan-Taek Im

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Contributions

Conceived and designed the experiments: JEL, GMC (2nd author), YJL (3rd author), WTI. Performed the experiments: JEL GMC. Analyzed the data: JEL GMC YJL SML WTI. Wrote the paper: JEL WTI.

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Correspondence to Wan-Taek Im.

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This article does not contain any studies with human participants or animals performed by any of the authors. Moreover, all authors read and approved the final manuscript. All the authors declare that they have no direct or indirect conflict of interest.

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It is the original work of the author. The work described has not been submitted elsewhere for publication, in whole or in part, and all authors listed carry out the data analysis and manuscript writing.

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Supplementary Information

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Supplementary file1 (DOCX 26 kb)

284_2022_2855_MOESM2_ESM.pptx

Supplementary file2 (PPTX 52 kb) Fig. S1 Phylogenetic tree (constructed with maximum-likelihood method) showing the relationships of strain dN18-1T with other related species of the genus Paludibacterium. Bootstrap values (expressed as percentages of 1000 replications) greater than 50% are shown at the branch points

284_2022_2855_MOESM3_ESM.pptx

Supplementary file3 (PPTX 53 kb) Fig. S2 The phylogenetic tree was constructed from a comparative analysis of whole-genome sequences showing the relationships of strain dN18-1T with related species of the family Chromobacteriaceae. This tree was constructed via Automated Multi-Locus Species Tree online web server. Bar represents 0.02 substitutions per nucleotide position

Supplementary file4 (PPTX 63 kb) Fig. S3 The genome annotation of strain dN18-1T

284_2022_2855_MOESM5_ESM.pptx

Supplementary file5 (PPTX 747 kb) Fig. S4 Transmission electron microscopy micrograph showing morphology of strain dN18-1T. Cells were grown on R2A agar at 30 °C for 3 days. Bar, 1 μm

284_2022_2855_MOESM6_ESM.pptx

Supplementary file6 (PPTX 267 kb) Fig. S5 Two-dimensional thin-layer chromatography of the total polar lipids of strain dN18-1T. Chloroform-methanol-water (65:25:4, by vol.) was used in the first direction, followed by chloroform-acetic acid-methanol-water (40:7.5:6:2, by vol.) in the second direction. The following spray reagents were used for detection: (a) 5% ethanoic molybdophosphoric acid (for total lipids); (b) molybdenum blue (Sigma) (for phosphorus-containing polar lipids); (c) 2% ninhydrin (for amino lipids). PE, phosphatidylethanolamine; PG, phosphatidylglycerol; DPG, diphosphatidylglycerol; PL, unidentified phospholipid; APL, aminophospholipid

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Lee, J.E., Choi, GM., Lee, YJ. et al. Paludibacterium denitrificans sp. nov., a Novel Denitrifying Bacterium Isolated from Activated Sludge. Curr Microbiol 79, 158 (2022). https://doi.org/10.1007/s00284-022-02855-z

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