Abstract
A Gram-stain-negative, aerobic, chemoheterotrophic, rod-shaped bacterium motile by a polar flagellum, designated IMCC34675T, was isolated from Chungju Lake, an artificial freshwater reservoir in Republic of Korea. The 16S rRNA gene sequence analysis indicated that strain IMCC34675T belongs to the genus Uliginosibacterium, sharing ≤ 97.1% sequence similarities with the type strains of the genus. Whole genome sequencing of strain IMCC34675T revealed a 4.1 Mbp of genome size with 62.4% of the DNA G + C content. The IMCC34675T genome shared 73.3% of average nucleotide identity and 19.9% of digital DNA-DNA hybridization values to the genome of Uliginosibacterium gangwonense DSM 18521T, the type species of the genus. The major fatty acids of strain IMCC34675T were summed feature 3 (comprising C16:1ω6c and/or C16:1ω7c) and C16:0. The respiratory quinone detected in the strains was ubiquinone-8 (Q-8). The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol, diphosphatidylglycerol, one unidentified aminophospholipid, one aminolipid, and five unidentified lipids. Based on the phylogenetic and phenotypic characterization, strain IMCC34675T was considered to represent a novel species within the genus Uliginosibacterium, for which the name Uliginosibacterium aquaticum sp. nov. is proposed with IMCC34675T (= KACC 21758T = NBRC 114418T) as the type strain.
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References
Weon HY, Kim BY, Yoo SH, Kwon SW, Go SJ, Stackebrandt E (2008) Uliginosibacterium gangwonense gen. nov., sp. nov., isolated from a wetland, Yongneup, in Korea. Int J Syst Evol Microbiol 58:131–135. https://doi.org/10.1099/ijs.0.64567-0
Chen WM, Li YS, Chen ZH, Young CC, Sheu SY (2016) Uliginosibacterium paludis sp. nov., isolated from a marsh. Int J Syst Evol Microbiol 66:5118–5123. https://doi.org/10.1099/ijsem.0.001481
Kang JY, Chun J, Jahng KY (2017) Uliginosibacterium flavum sp. nov. isolated from an artificial lake. J Microbiol 55:595–599. https://doi.org/10.1007/s12275-017-7002-6
Han JH, Baek K, Ahn YH, Lee WJ, Lee MH (2018) Uliginosibacterium sangjuense sp. nov., isolated from sediment of the Nakdong River. Antonie Van Leeuwenhoek 111:259–264. https://doi.org/10.1007/s10482-017-0946-z
Hwang WM, Kim SM, Kang K, Ahn TY (2018) Uliginosibacterium sediminicola sp. nov., isolated from freshwater sediment. Int J Syst Evol Microbiol 68:924–929. https://doi.org/10.1099/ijsem.0.002611
Ferrando L, Fernandez Scavino A (2015) Strong shift in the diazotrophic endophytic bacterial community inhabiting rice (Oryza sativa) plants after flooding. FEMS Microbiol Ecol 91:fiv104. https://doi.org/10.1093/femsec/fiv104
Aggarwal S, Gomez-Smith CK, Jeon Y, LaPara TM, Waak MB, Hozalski RM (2018) Effects of chloramine and coupon material on biofilm abundance and community composition in bench-scale simulated water distribution systems and comparison with full-scale water mains. Environ Sci Technol 52:13077–13088. https://doi.org/10.1021/acs.est.8b02607
Wang J, Rong H, Zhang C (2018) Evaluation of the impact of dissolved oxygen concentration on biofilm microbial community in sequencing batch biofilm reactor. J Biosci Bioeng 125:532–542. https://doi.org/10.1016/j.jbiosc.2017.11.007
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
Jeon HT, Joung Y, Kim S, Lim Y, Cho J-C (2017) A report on 17 unrecorded bacterial species in Korea isolated from Lakes Soyang and Chungju in 2016. J Species Res 6:163–170. https://doi.org/10.12651/JSR.2017.6.2.163
Kim J-H, Kim Y-H, Lee I-K (1998) Dynamics of phytoplankton community in Lake Chungju. Algae 13:339–354
Kim J-B, Moon M-S, Lee D-H, Lee S-T, Bazzicalupo M, Kim C-K (2004) Comparative analysis of cyanobacterial communities from polluted reservoirs in Korea. J Microbiol 42:181–187
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
Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876–4882. https://doi.org/10.1093/nar/25.24.4876
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
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376. https://doi.org/10.1007/BF01734359
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416. https://doi.org/10.2307/2412116
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.2307/2408678
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
Bankevich A, Nurk S, Antipov D, Gurevich AA, Dvorkin M, Kulikov AS, Lesin VM, Nikolenko SI, Pham S, Prjibelski AD, Pyshkin AV, Sirotkin AV, Vyahhi N, Tesler G, Alekseyev MA, Pevzner PA (2012) SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol 19:455–477. https://doi.org/10.1089/cmb.2012.0021
Meier-Kolthoff JP, Auch AF, Klenk HP, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14:60. https://doi.org/10.1186/1471-2105-14-60
Na SI, Kim YO, Yoon SH, Ha SM, Baek I, Chun J (2018) UBCG: Up-to-date bacterial core gene set and pipeline for phylogenomic tree reconstruction. J Microbiol 56:280–285. https://doi.org/10.1007/s12275-018-8014-6
Price MN, Dehal PS, Arkin AP (2009) FastTree: computing large minimum evolution trees with profiles instead of a distance matrix. Mol Biol Evol 26:1641–1650. https://doi.org/10.1093/molbev/msp077
Kanehisa M, Sato Y, Morishima K (2016) BlastKOALA and GhostKOALA: KEGG tools for functional characterization of genome and metagenome sequences. J Mol Biol 428:726–731. https://doi.org/10.1016/j.jmb.2015.11.006
Galperin MY, Makarova KS, Wolf YI, Koonin EV (2015) Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res 43:D261-269. https://doi.org/10.1093/nar/gku1223
Marchler-Bauer A, Zheng C, Chitsaz F, Derbyshire MK, Geer LY, Geer RC, Gonzales NR, Gwadz M, Hurwitz DI, Lanczycki CJ, Lu F, Lu S, Marchler GH, Song JS, Thanki N, Yamashita RA, Zhang D, Bryant SH (2013) CDD: conserved domains and protein three-dimensional structure. Nucleic Acids Res 41:D348-352. https://doi.org/10.1093/nar/gks1243
Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
Richter M, Rosselló-Móra 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
Chun J, Oren A, Ventosa A, Christensen H, Arahal DR, da Costa MS, Rooney APM, Yi H, Xu X-W, De Meyer S, Trujillo ME (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
Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA–DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81–91. https://doi.org/10.1099/ijs.0.64483-0
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Technical Note 101. MIDI Inc., Newark
Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (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
Collins MD, Jones D (1981) A note on the separation of natural mixtures of bacterial ubiquinones using reverse-phase partition thin-layer chromatography and high performance liquid chromatography. J Appl Microbiol 51:129–134. https://doi.org/10.1111/j.1365-2672.1981.tb00916.x
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This study was supported by the research grant “Survey of freshwater organisms and specimen collection (Prokaryotes)” from Nakdonggang National Institute of Biological Resources of the Ministry of Environment in Korea and by Inha University Research Grant.
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Conceptualization, JS, MK, and J-CC; Data curation, JS, MK, and J-CC; Funding acquisition, J-CC; Investigation, JS, YJ, MK, and IK; Resources, YJ; Supervision, J-CC; Visualization, JS, MK, and IK; Writing-original draft, JS; Writing-review &editing, JS, MSP, IK, and J-CC. All authors have read and agreed to the published version of the manuscript.
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Song, J., Kim, M., Park, M.S. et al. Uliginosibacterium aquaticum sp. nov., Isolated from a Freshwater Lake. Curr Microbiol 78, 3381–3387 (2021). https://doi.org/10.1007/s00284-021-02605-7
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DOI: https://doi.org/10.1007/s00284-021-02605-7