Abstract
A novel bacterial strain designated CJ43T was isolated from fresh water located in Gangwon-do, South Korea, displaying multi-drug resistance. The isolate was Gram-stain-negative, aerobic, orange-pigmented, and rod-shaped. Strain CJ43T grew optimally at 30 °C and pH 7 on R2A agar in the absence of NaCl. Phylogenetic analyses based on 16S rRNA gene sequences revealed that strain CJ43T belonged to the genus Pedobacter in the family Sphingobacteriaceae and was most closely related to Pedobacter puniceum HX-22-1 T and P. glucosidilyticus 1-2 T (98.3 and 98.1% sequence similarity). The genome size of strain CJ43T was 3.9 Mb in a single contig with DNA G + C content of 34.9%. The genome included 3144 predicted protein-coding genes, as well as 55 tRNA, 9 rRNA and 3 ncRNA genes. The genome also contained 128 putative antibiotic resistance genes, reflecting its phenotypes. The average nucleotide identity values between strain CJ43T and two closely related strains P. puniceum HX-22-1 T and P. glucosidilyticus 1-2 T were 91.0 and 88.7%, respectively. In silico digital DNA-DNA hybridization results between strain CJ43T and the related strains were 42.8 and 38.6%, respectively. The major fatty acids of strain CJ43T were iso-C15:0, iso-C17:0 3-OH, and summed feature 3 (C16:1 ω6c and/or C16:1 ω7c). Strain CJ43T contained phosphatidylethanolamine as the major polar lipid and menaquinone-7 as the sole respiratory quinone. Based on the polyphasic taxonomy data, strain CJ43T represents a novel species of the genus Pedobacter, for which the name Pedobacter aquae sp. nov. is proposed with the type strain CJ43T (= KACC 21350 T = JCM 33709 T).
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Abbreviations
- ANI:
-
Average Nucleotide Identity
- dDDH:
-
Digital DNA-DNA hybridization
- ML:
-
Maximum-likelihood
- MP:
-
Maximum-parsimony
- NJ:
-
Neighbor-joining
- SMRT:
-
Single Molecule Real-Time
- UBCG:
-
Up-to-date bacterial core-gene
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Acknowledgements
Authors thank Professor Aharon Oren for assistance with nomenclature.
Funding
This work was supported by a grant from the National Institute of Biological Resources (NIBR) funded by the Ministry of Environment (MOE) of the Republic of Korea (NIBR201801204). This research was also supported by the Chung-Ang University Young Scientist Scholarship in 2019.
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Chang-Jun Cha designed the study. Material preparation, data collection and analysis were performed by Le Tran Tien Chau and Yong-Seok Kim. The first draft of the manuscript was written by Le Tran Tien Chau and all authors revised the manuscript. All authors read and approved the final manuscript.
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The 16S rRNA gene and the whole genome sequences of strain CJ43T that support the findings of this study have been deposited in the GenBank/EMBL/DDBJ database with the accession numbers MK129424 and CP043329, respectively.
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Chau, L.T.T., Kim, YS. & Cha, CJ. Pedobacter aquae sp. nov., a multi-drug resistant bacterium isolated from fresh water. Antonie van Leeuwenhoek 115, 445–457 (2022). https://doi.org/10.1007/s10482-022-01708-w
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DOI: https://doi.org/10.1007/s10482-022-01708-w