Acknowledgement
We thank Professor Aharon Oren for his expert advice concerning the genus and species epithet and Latin etymology. This study was supported by National Research Foundation of Korea (2019R1A2C2007038 and 2021R1A2C1005151) and the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program.
References
- Ryu SH, Lee DS, Park M, Wang Q, Jang HH, Park W, et al. 2008. Caenimonas koreensis gen. nov., sp. nov., isolated from activated sludge. Int. J. Syst. Evol. Microbiol. 58: 1064-1068. https://doi.org/10.1099/ijs.0.65416-0
- Kim SJ, Weon HY, Kim YS, Moon JY, Seok SJ, Hong SB, et al. 2012. Caenimonas terrae sp. nov., isolated from a soil sample in Korea, and emended description of the genus Caenimonas Ryu et al. 2008. J. Microbiol. 50: 864-868. https://doi.org/10.1007/s12275-012-1587-6
- Parte AC. 2018. LPSN - List of prokaryotic names with standing in nomenclature (Bacterio.net), 20 years on. Int. J. Syst. Evol. Microbiol. 68: 1825-1829. https://doi.org/10.1099/ijsem.0.002786
- Dahal RH, Lee H, Chaudhary DK, Kim DY, Son J, Kim J, et al. 2021. Caenimonas soli sp. nov., isolated from soil. Arch. Microbiol. 203: 1123-1129. https://doi.org/10.1007/s00203-020-02110-8
- Xu J, Sheng M, Yang Z, Qiu J, Zhang J, Zhang L, He J. 2020. Caenimonas sedimenti sp. nov., isolated from sediment of the wastewater outlet of an agricultural chemical plant. Curr. Microbiol. 77: 3767-3772. https://doi.org/10.1007/s00284-020-02145-6
- Xu L, Han Y, Yi M, Yi H, Guo E, Zhang A. 2019. Shift of millet rhizosphere bacterial community during the maturation of parent soil revealed by 16S rDNA high-throughput sequencing. Appl. Soil Ecol. 135: 157-165. https://doi.org/10.1016/j.apsoil.2018.12.004
- Tindall BJ, Rossello-Mora R, Busse HJ, Ludwig W, Kampfer P. 2010. Notes on the characterization of prokaryote strains for taxonomic purposes. Int. J. Syst. Evol. Microbiol. 60: 249-266. https://doi.org/10.1099/ijs.0.016949-0
- Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 1991. 16S ribosomal DNA amplification for phylogenetic study. J. Bacteriol. 173: 697-703. https://doi.org/10.1128/jb.173.2.697-703.1991
- Yoon SH, Ha SM, 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. Int. J. Syst. Evol. Microbiol. 67: 1613-1617. https://doi.org/10.1099/ijsem.0.001755
- Saitou N, Nei M. 1987. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol. Biol. Evol. 4: 406-425.
- Felsenstein J. 1981. Evolutionary trees from DNA sequences: a maximum likelihood approach. J. Mol. Evol. 17: 368-376. https://doi.org/10.1007/BF01734359
- Nei M, Kumar S, Takahashi K. 1998. The optimization principle in phylogenetic analysis tends to give incorrect topologies when the number of nucleotides or amino acids used is small. Proc. Natl. Acad. Sci. USA 95: 12390-12397. https://doi.org/10.1073/pnas.95.21.12390
- Kumar S, Stecher G, Li M, Knyaz C, Tamura K. 2018. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35: 1547-1549. https://doi.org/10.1093/molbev/msy096
- Kimura M. 1983. The neutral theory of molecular evolution, Cambridge: Cambridge University Press.
- Bolger AM, Lohse M, Usadel B. 2014. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30: 2114-2120. https://doi.org/10.1093/bioinformatics/btu170
- Simao FA, Waterhouse RM, Ioannidis P, Kriventseva EV, Zdobnov EM. 2015. BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs. Bioinformatics 31: 3210-3212. https://doi.org/10.1093/bioinformatics/btv351
- Aziz RK, Bartels D, Best A, DeJongh M, Disz T, Edwards RA, et al. 2008. The RAST server: rapid annotations using subsystems technology. BMC Genomics 9: 75. https://doi.org/10.1186/1471-2164-9-75
- Blin K, Shaw S, Steinke K, Villebro R, Ziemert N, Lee SY, et al. 2019. AntiSMASH 5.0: updates to the secondary metabolite genome mining pipeline. Nucleic Acids Res. 47: W81-W87. https://doi.org/10.1093/nar/gkz310
- Davis JJ, Wattam AR, Aziz RK, Brettin T, Butler R, Butler RM, et al. 2020. The PATRIC bioinformatics resource center: expanding data and analysis capabilities. Nucleic Acids Res. 48: D606-D612.
- Meier-Kolthoff JP, Goker M. 2019. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat. Commun. 10: 2182. https://doi.org/10.1038/s41467-019-10210-3
- Yoon SH, Ha SM, Lim J, Kwon S, Chun J. 2017. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110: 1281-1286. https://doi.org/10.1007/s10482-017-0844-4
- Meier-Kolthoff JP, Auch AF, Klenk HP, Goker M. 2013. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 14: 60. https://doi.org/10.1186/1471-2105-14-60
- Smibert R, Krieg NR. 1994. Phenotypic characterization, pp. 607-654. In Gerhardt P, Murray R, Wood W, Krieg N (eds.), Methods for General and Molecular Bacteriology. American Society for Microbiology, Washington DC, USA
- Bauer AW, Kirby WM, Sherris JC, Turck M. 1966. Antibiotic susceptibility testing by a standardized single disk method. Am. J. Clin. Pathol. 45: 493-496. https://doi.org/10.1093/ajcp/45.4_ts.493
- Sasser M. 2001. Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101.
- Minnikin DE, O'Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, et al. 1984. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J. Microbiol. Methods 2: 233-241. https://doi.org/10.1016/0167-7012(84)90018-6
- Tindall BJ, Sikorski J, Smibert RA, Krieg NR. 2007. Phenotypic characterization and the principles of comparative systematics. pp. 330-393. In Reddy CA, Beveridge TJ, Breznak JA, Marzluf G, Schmidt TM, Snyder LR (eds), Methods for General and Molecular Microbiology, 3rd Ed. American Society for Microbiology, Washington DC, USA.
- Kates M. 1972. Techniques of lipidology, Elsevier, New York, USA.
- Oren A, Duker S, Ritter S. 1996. The polar lipid composition of Walsby's square bacterium. FEMS Microbiol. Lett. 138: 135-140. https://doi.org/10.1111/j.1574-6968.1996.tb08146.x
- Tamaoka J. 1986. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol. 123: 251-256. https://doi.org/10.1016/S0076-6879(86)23028-1
- Busse J, Auling G. 1988. Polyamine pattern as a chemotaxonomic marker within the Proteobacteria. Syst. Appl. Microbiol. 11: 1-8. https://doi.org/10.1016/S0723-2020(88)80040-7
- Sharrar AM, Crits-Christoph A, Meheust R, Diamond S, Starr EP, Banfield JF. 2020. Bacterial secondary metabolite biosynthetic potential in soil varies with phylum, depth, and vegetation type. mBio 11: e00416-20.
- Hibbing ME, Fuqua C, Parsek MR, Peterson SB. 2010. Bacterial competition: surviving and thriving in the microbial jungle. Nat. Rev. Microbiol. 8: 15-25. https://doi.org/10.1038/nrmicro2259
- Helfrich EJN, Lin GM, Voigt CA, Clardy J. 2019. Bacterial terpene biosynthesis: challenges and opportunities for pathway engineering. Beilstein J. Org. Chem. 15: 2889-2906. https://doi.org/10.3762/bjoc.15.283
- Agrawal S, Acharya D, Adholeya A, Barrow CJ, Deshmukh SK. 2017. Nonribosomal peptides from marine microbes and their antimicrobial and anticancer potential. Front. Pharmacol. 8: 828. https://doi.org/10.3389/fphar.2017.00828
- Zhang J, Du L, Liu F, Xu F, Hu B, Venturi V, et al. 2014. Involvement of both PKS and NRPS in antibacterial activity in Lysobacter enzymogenes OH11. FEMS Microbiol. Lett. 355: 170-176. https://doi.org/10.1111/1574-6968.12457
- Schoner TA, Gassel S, Osawa A, Tobias NJ, Okuno Y, Sakakibara Y, et al. 2016. Aryl polyenes, a highly abundant class of bacterial natural products, are functionally related to antioxidative carotenoids. Chembiochem 17: 247-253. https://doi.org/10.1002/cbic.201500474
- Hegemann JD, Zimmermann M, Xie X, Marahiel MA. 2015. Lasso peptides: an intriguing class of bacterial natural products. Acc. Chem. Res. 48: 1909-1919. https://doi.org/10.1021/acs.accounts.5b00156
- Ding YP, Khan IU, Li MM, Xian WD, Liu L, Zhou EM, et al. 2019. Calidifontimicrobium sediminis gen. nov., sp. nov., a new member of the family Comamonadaceae. Int. J. Syst. Evol. Microbiol. 69: 434-440. https://doi.org/10.1099/ijsem.0.003167
- Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, et al. 2018. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int. J. Syst. Evol. Microbiol. 68: 461-466. https://doi.org/10.1099/ijsem.0.002516
- Kim M, Oh HS, Park SC, Chun J. 2014. Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int. J. Syst. Evol. Microbiol. 64: 346-351. https://doi.org/10.1099/ijs.0.059774-0
- Auch AF, von Jan M, Klenk HP, Goker M. 2010. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand. Genomic Sci. 2: 117-134. https://doi.org/10.4056/sigs.531120
- Richter M, Rossello-Mora R. 2009. Shifting the genomic gold standard for the prokaryotic species definition. Proc. Natl. Acad. Sci. USA 106: 19126-19131. https://doi.org/10.1073/pnas.0906412106
- Busse HJ. 2011. Polyamines, pp. 239-259. In Rainey F, Oren A, (eds.), Academic Press, Methods in Microbiology.