Two novel bacterial species CJ51T and CJ63T belonging to the genus Chryseobacterium were isolated from the Upo wetland and the Han River, South Korea, respectively. Cells of these strains were Gram-stain-negative, aerobic, non-motile, rod-shaped, and catalase- and oxidase-positive. Both strains were shown to grow optimally at 30 °C and pH 7 in the absence of NaCl on tryptic soy agar. Phylogenetic analysis based on 16S rRNA gene sequences showed that strains CJ51T and CJ63T belonged to the genus Chryseobacterium and were most closely related to Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT with 98.47% and 98.46% 16S rRNA sequence similarities, respectively. The average nucleotide identity values of strains CJ51T and CJ63T with its closely related type strains Chryseobacterium piperi CTMT and Chryseobacterium piscicola VQ-6316sT were 81.9% and 82.1%, respectively. The major fatty acids of strains CJ51T and CJ63T were iso-C15:0, iso-C17:0 3-OH and summed feature 9 (C16:0 10-methyl and/or iso-C17:1ω9c). Menaquinone 6 (MK-6) was identified as the primary respiratory quinone in both strains. The major polar lipids of strains CJ51T and CJ63T were phosphatidylethanolamine and several unidentified amino lipids and lipids. Based on polyphasic taxonomy data, strains CJ51T and CJ63T represent novel species of the genus Chryseobacterium, for which names Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. are proposed respectively. The type strains are CJ51T (= KACC 22749T = JCM 35632T) and CJ63T (= KACC 22750T = JCM 35633T).
This is a preview of subscription content, access via your institution.
Buy single article
Instant access to the full article PDF.
Price excludes VAT (USA)
Tax calculation will be finalised during checkout.
The GenBank data were already described in the Materials and Methods and is not necessarily to be mentioned in description.
Alcock, B. P., Raphenya, A. R., Lau, T. T. Y., Tsang, K. K., Bouchard, M., Edalatmand, A., Huynh, W., Nguyen, A. V., Cheng, A. A., Liu, S., et al. (2020). CARD 2020: Antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Research, 48, 517–525.
Baker, G. C., Smith, J. J., & Cowan, D. A. (2003). Review and re-analysis of domain-specific 16S primers. Journal of Microbiological Methods, 55, 541–555.
Bayliss, S. C., Thorpe, H. A., Coyle, N. M., Sheppard, S. K., & Feil, E. J. (2019). PIRATE: A fast and scalable pangenomics toolbox for clustering diverged orthologues in bacteria. GigaScience, 8, giz119.
Chen, X. Y., Zhao, R., Chen, Z. L., Liu, L., Li, X. D., & Li, Y. H. (2015). Chryseobacterium polytrichastri sp. nov. isolated from a moss (Polytrichastrum formosum) and emended description of the genus Chryseobacterium. Antonie van Leeuwenhoek, 107(2), 403–410.
Chin, C.-S., Alexander, D. H., Marks, P., Klammer, A. A., Drake, J., Heiner, C., Clum, A., Copeland, A., Huddleston, J., Eichler, E. E., et al. (2013). Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nature Methods, 10, 563–569.
Chun, J., Oren, A., Ventosa, A., Christensen, H., Arahal, D. R., da Costa, M. S., Rooney, A. P., Yi, H., Xu, X.-W., De Meyer, S., et al. (2018). Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 68, 461–466.
Collins, M. D. (1985). 11 Analysis of isoprenoid quinones. Methods in Microbiology, 18, 329–366.
Dusa, A. (2021) venn: Draw venn diagrams
Edgar, R. C. (2004). MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Research, 32, 1792–1797.
Felsenstein, J. (1985). Confidence limits on phylogenies: An approach using the bootstrap. Evolution, 39, 783–791.
Hahnke, R. L., Meier-Kolthoff, J. P., Garcia-Lopez, M., Mukherjee, S., Huntemann, M., Ivanova, N. N., et al. (2016). Genome-Based Taxonomic Classification of Bacteroidetes. Frontiers in Microbiology, 7, 2003.
Holmes, B., Owen, R. J., Steigerwalt, A. G., & Brenner, D. J. (1984). Flavobacterium gleum, a new species found in human clinical specimens. International Journal of Systematic Bacteriology, 34, 21–25.
Hyatt, D., Chen, G. L., Locascio, P. F., Land, M. L., Larimer, F. W., & Hauser, L. J. (2010). Prodigal: Prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics, 11, 119.
Ilardi, P., Fernandez, J., & Avendano-Herrera, R. (2009). Chryseobacterium piscicola sp. nov., isolated from diseased salmonid fish. International Journal of Systematic and Evolutionary Microbiology, 59, 3001–3005.
Im, W. T., Yang, J. E., Kim, S. Y., & Yi, T. H. (2011). Chryseobacterium ginsenosidimutans sp. nov., a bacterium with ginsenoside-converting activity isolated from soil of a Rhus vernicifera-cultivated field. International Journal of Systematic and Evolutionary Microbiology, 61, 1430–1435.
Jukes, T., & Cantor, C. (1969). Evolution of protein molecules. Mammalian Protein Metabolism, 3, 21–132.
Kämpfer, P., Vaneechoutte, M., Lodders, N., De Baere, T., Avesani, V., Janssens, M., Busse, H. J., & Wauters, G. (2009). Description of Chryseobacterium anthropi sp. nov. to accommodate clinical isolates biochemically similar to Kaistella koreensis and Chryseobacterium haifense proposal to reclassify Kaistella koreensis as Chryseobacterium koreense comb. nov. and emended description of the genus Chryseobacterium. International Journal of Systematic and Evolutionary Microbiology, 59, 2421–2428.
Kangale, L. J., Raoult, D., Ghigo, E., & Fournier, P.-E. (2021). Chryseobacterium schmidteae sp. nov. a novel bacterial species isolated from planarian Schmidtea mediterranea. Scientific Reports, 11, 11002.
Kim, K. K., Lee, K. C., Oh, H. M., & Lee, J. S. (2008). Chryseobacterium aquaticum sp. nov., isolated from a water reservoir. International Journal of Systematic and Evolutionary Microbiology, 58, 533–537.
Kim, J., Na, S.-I., Kim, D., & Chun, J. (2021). UBCG2: Up-to-date bacterial core genes and pipeline for phylogenomic analysis. Journal of Microbiology, 59, 609–615.
Kim, M., Oh, H.-S., Park, S.-C., & Chun, J. (2014). Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. International Journal of Systematic and Evolutionary Microbiology, 64, 346–351.
Kumar, S., Stecher, G., Li, M., Knyaz, C., & Tamura, K. (2018). MEGA X: Molecular evolutionary genetics analysis across computing platforms. Molecular Biology and Evolution, 35, 1547–1549.
Lee, I., Ouk Kim, Y., Park, S. C., & Chun, J. (2016). OrthoANI: An improved algorithm and software for calculating average nucleotide identity. International Journal of Systematic and Evolutionary Microbiology, 66, 1100–1103.
Lucena, T., Ruvira, M. A., Macián, M. C., Arahal, D. R., Aznar, R., & Pujalte, M. J. (2021). Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems. International Journal of Systematic and Evolutionary Microbiology, 71, 005020.
Manni, M., Berkeley, M. R., Seppey, M., & Zdobnov, E. M. (2021). BUSCO: Assessing genomic data quality and beyond. Current Protocols, 1, e323.
Meier-Kolthoff, J. P., Carbasse, J. S., Peinado-Olarte, R. L., & Göker, M. (2022). TYGS and LPSN: A database tandem for fast and reliable genome-based classification and nomenclature of prokaryotes. Nucleic Acids Research, 50, 801–807.
Minnikin, D. E., O’Donnell, A. G., Goodfellow, M., Alderson, G., Athalye, M., Schaal, A., & Parlett, J. H. (1984). An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. Journal of Microbiological Methods, 2, 233–241.
Montero-Calasanz, M. C., Goker, M., Rohde, M., Sproer, C., Schumann, P., Busse, H. J., Schmid, M., Klenk, H. P., Tindall, B. J., & Camacho, M. (2014). Chryseobacterium oleae sp. nov. an efficient plant growth promoting bacterium in the rooting induction of olive tree (Olea europaea L.) cuttings and emended descriptions of the genus Chryseobacterium, C. daecheongense, C. gambrini, C. gleum, C. joostei, C. jejuense, C. luteum, C. shigense, C. taiwanense, C. ureilyticum, and, C. vrystaatense. Systematic and Applied Microbiology, 37(5), 342–350.
Nei, M., & Kumar, S. (2000). Molecular evolution and phylogenetics. Oxford University Press.
Nicholson, A. C., Gulvik, C. A., Whitney, A. M., Humrighouse, B. W., Bell, M. E., Holmes, B., Steigerwalt, A. G., Villarma, A., Sheth, M., Batra, D., et al. (2020). Division of the genus Chryseobacterium: Observation of discontinuities in amino acid identity values, a possible consequence of major extinction events, guides transfer of nine species to the genus Epilithonimonas, eleven species to the genus Kaistella, and three species to the genus Halpernia gen. nov., with description of Kaistella daneshvariae sp. nov. and Epilithonimonas vandammei sp. nov. derived from clinical specimens. International Journal of Systematic and Evolutionary Microbiology, 70, 4432–4450.
Park, M. S., Jung, S. R., Lee, K. H., Lee, M. S., Do, J. O., Kim, S. B., & Bae, K. S. (2006). Chryseobacterium soldanellicola sp. nov. and Chryseobacterium taeanense sp. nov., isolated from roots of sand-dune plants. International Journal of Systematic and Evolutionary Microbiology, 56, 433–438.
Parte, A. C., SardàCarbasse, J., Meier-Kolthoff, J. P., Reimer, L. C., & Göker, M. (2020). List of prokaryotic names with standing in nomenclature (LPSN) moves to the DSMZ. International Journal of Systematic and Evolutionary Microbiology, 70, 5607–5612.
Rhoads, A., & Au, K. F. (2015). PacBio sequencing and its applications. Genomics, Proteomics and Bioinformatics, 13, 278–289.
Richter, M., & Rosselló-Móra, R. (2009). Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences, 106, 19126–19131.
Rosselló-Móra, R., & Amann, R. (2015). Past and future species definitions for Bacteria and Archaea. Systematic and Applied Microbiology, 38, 209–216.
Sasser, M. (1990). Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsletter, 20, 1–6.
Seemann, T. (2014). Prokka: Rapid prokaryotic genome annotation. Bioinformatics, 30, 2068–2069.
Strahan, B. L., Failor, K. C., Batties, A. M., Hayes, P. S., Cicconi, K. M., Mason, C. T., & Newman, J. D. (2011). Chryseobacterium piperi sp. nov., isolated from a freshwater creek. International Journal of Systematic and Evolutionary Microbiology, 61, 2162–2166.
Vandamme, P., Bernardet, J.-F., Segers, P., Kersters, K., & Holmes, B. (1994). NOTES: New perspectives in the classification of the Flavobacteria: Description of Chryseobacterium gen. nov., Bergeyella gen. nov., and Empedobacter nom. rev. International Journal of Systematic and Evolutionary Microbiology, 44, 827–831.
Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017a). Completing bacterial genome assemblies with multiplex MinION sequencing. Microb. Genom., 3, e000132.
Wick, R. R., Judd, L. M., Gorrie, C. L., & Holt, K. E. (2017b). Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads. PLoS Computational Biology, 13, e1005595.
Wu, Y. F., Wu, Q. L., & Liu, S. J. (2013). Chryseobacterium taihuense sp. nov., isolated from a eutrophic lake, and emended descriptions of the genus Chryseobacterium, Chryseobacterium taiwanense, Chryseobacterium jejuense and Chryseobacterium indoltheticum. International Journal of Systematic and Evolutionary Microbiology, 63, 913–919.
Yoon, S. H., Ha, S. M., Kwon, S., Lim, J., Kim, Y., Seo, H., & Chun, J. (2017). Introducing EzBioCloud: A taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. International Journal of Systematic and Evolutionary Microbiology, 67, 1613–1617.
This work was supported by the National Institute of Biological Resources funded by the Ministry of Environment (No. NIBR202203205) and by the Korea Ministry of Environment (MOE) as ‘the Environmental Health Action Program (2016001350004)’. This research was supported by the Chung-Ang University Graduate Research Scholarship in 2022. We thank Professor Aharon Oren for his assistance with nomenclature. We thank J. Kim for technical help at the BT research center, Chung-Ang University.
Conflict of interest
The authors declare that there are no conflicts of interest.
Below is the link to the electronic supplementary material.
About this article
Cite this article
Kim, M., Kim, YS. & Cha, CJ. Chryseobacterium paludis sp. nov. and Chryseobacterium foetidum sp. nov. Isolated from the Aquatic Environment, South Korea. J Microbiol. 61, 37–47 (2023). https://doi.org/10.1007/s12275-022-00008-2