Abstract
A Gram-staining-negative, aerobic and pear-shaped bacterial strain, designated WL0036T, was isolated from coastal sediment sample collected in Nantong city, Jiangsu province of China (120° 51′ 13″ E, 32° 6′ 26″ N) in October 2020. Strain WL0036T was found to grow at 20–37 °C (optimum, 28 °C) with 0–9.0% NaCl (optimum, 2.5–4.0%) and displayed alkaliphilic growth with the pH range of pH 6.0–10.0 (optimum, pH 7.0–8.0). The polar lipids profile of strain WL0036T included phosphatidylcholine, phosphatidylethanolamine, glycolipid and an unidentified lipid. The major isoprenoid quinone was determined to be Q-11 and the major fatty acids were C16:0, 11-methyl-C18:1ω7c, and summed features 8 (C18:1ω6c and/or C18:1ω7c). The G + C content of genomic DNA was 61.8%. Phylogenetic trees constructed based on 16S rRNA gene sequence and bac120 gene set (a collection of 120 single-copy protein sequences prevalent in bacteria) indicted that strain WL0036T clustered with strains Hyphomonas neptunium ATCC 15444T and H. polymorpha PS728T. The average nucleotide identities between strain WL0036T and strains H. neptunium ATCC 15444T and H. polymorpha PS728T were 80.7% and 81.2%, respectively. Strain WL0036T showed 22.8% and 23.2% of digital DNA-DNA hybridization identities with H. neptunium ATCC 15444T and H. polymorpha PS728T, respectively. As inferred from the phenotypic and genotypic characteristics and the phylogenetic trees, strain WL0036T ought to be recognized as a novel species in genus Hyphomonas, for which the name Hyphomonas sediminis sp. nov. is proposed. The type strain is WL0036T (= MCCC 1K05843T = JCM 34658T = GDMCC 1.2413T).
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Data availability
All of the data supporting the conclusions of this article are included within the article and its additional files. The genome datasets and the 16S rRNA gene sequence of Hyphomonas sediminis WL0036T generated during the current study are available in the GenBank/EMBL/DDBJ repository under accession number JAIEZP000000000 and OL605964. Other datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request. Other genome sequence data detailed information was listed in Suppl. Table S1.
References
Alcock BP et al (2020) CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database. Nucleic Acids Res 48:517–525. https://doi.org/10.1093/nar/gkz935
Collins MD, Jones D (1980) Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Bacteriol 48:459–470. https://doi.org/10.1111/j.1365-2672.1980.tb01036.x
Collins MD et al (1977) Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Appl Microbiol 100:221–230. https://doi.org/10.1099/00221287-100-2-221
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 20:406–416. https://doi.org/10.2307/2412116
Goris J, Konstantinidis KT, Klappenbach JAJM et al (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
Huerta-Cepas J, Forslund K, Coelho LP et al (2017) Fast genome-wide functional annotation through orthology assignment by eggNOG-Mapper. Mol Biol Evol 34:2115–2122. https://doi.org/10.1093/molbev/msx148
Kanehisa M, Sato Y, Kawashima M et al (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44:457–462. https://doi.org/10.1093/nar/gkv1070
Kimura M (1980) A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120. https://doi.org/10.1007/BF01731581
Kumar S et al (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35:1547–1549. https://doi.org/10.1093/molbev/msy096
Lai Q et al (2015) 2000. request for an opinion. Int J Syst Evol Microbiol 65:321–321. https://doi.org/10.1099/ijs.0.066118-0
Li C, Lai Q, Li G et al (2014a) Hyphomonas beringensis sp. nov. and Hyphomonas chukchiensis sp. nov., isolated from surface seawater of the bering sea and chukchi sea. Antonie Van Leeuwenhoek 106:657–665. https://doi.org/10.1007/s10482-014-0236-y
Li C, Lai Q, Li G et al (2014b) Multilocus sequence analysis for the assessment of phylogenetic diversity and biogeography in hyphomonas bacteria from diverse marine environments. PLoS ONE 9:101394–101394. https://doi.org/10.1371/journal.pone.0101394
Li C, Lai Q, Li G et al (2014c) Hyphomonas atlanticus sp. nov., isolated from the atlantic ocean and emended description of the genus Hyphomonas. Syst Appl Microbiol 37:423–428. https://doi.org/10.1016/j.syapm.2014.05.013
Li X, Li C, Lai Q et al (2016) Hyphomonas pacifica sp. nov., isolated from deep sea of the pacific ocean. Antonie Van Leeuwenhoek 109:1111–1119. https://doi.org/10.1007/s10482-016-0712-7
Meier-Kolthoff JP, Auch AF, Klenk H-P et al (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
Minnikin DE, O’Donnell AG, Goodfellow M 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
Moore RL, Weiner RM, Gebers R (1984) Notes: Genus Hyphomonas Pongratz 1957 nom. rev. emend., Hyphomonas polymorpha Pongratz 1957 nom. rev. emend., and Hyphomonas neptunium (Leifson 1964) comb. nov. emend. (Hyphomicrobium neptunium). Int J Syst Bacteriol 34:71–73. https://doi.org/10.1099/00207713-34-1-71
Nurk S et al (2013) Assembling single-cell genomes and mini-metagenomes from chimeric MDA products. J Comput Biol 20:714–737. https://doi.org/10.1089/cmb.2013.0084
Okonechnikov K, Golosova O, Fursov M et al (2012) Unipro UGENE: a unified bioinformatics toolkit. Bioinformatics 28:1166–1167. https://doi.org/10.1093/bioinformatics/bts091
Pardi F, Guillemot S, Gascuel O (2010) Robustness of phylogenetic inference based on minimum evolution. Bull Math Biol 72:1820–1839. https://doi.org/10.1007/s11538-010-9510-y
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
Pongratz E (1957) D’une bactérie pédiculée isolée d’un pus de sinus. Pathobiology 20:593–608. https://doi.org/10.1159/000160167
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
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
Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI technical note 101. Microbial ID Inc, Newark
Tamaoka J (1986) Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Meth Enzymol 123:251–256. https://doi.org/10.1016/s0076-6879(86)23028-1
Tatusova T et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
Weiner RM, Devine RA, Powell DM et al (1985) Hyphomonas oceanitis sp.nov., Hyphomonas hirschiana sp. nov., and Hyphomonas jannaschiana sp. nov. Int J Syst Bacteriol 35:237–243. https://doi.org/10.1099/00207713-35-3-237
Weiner RM et al (2000) Hyphomonas adhaerens sp. nov., Hyphomonas johnsonii sp. nov. and Hyphomonas rosenbergii sp. nov., marine budding and prosthecate bacteria. Int J Syst Evol Microbiol 50:459–469. https://doi.org/10.1099/00207713-50-2-459
Weisburg WG, Barns SM, Pelletier DA et al (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 S-H, Ha S-M, Kwon S et al (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
Zhang D-F, Cui X-W, Zhao Z et al (2020) Sphingomonas hominis sp. nov., isolated from hair of a 21-year-old girl. Antonie Van Leeuwenhoek 113:1523–1530. https://doi.org/10.1007/s10482-020-01460-z
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This research was supported by the National Natural Science Foundation of China (No. 31900001), the China Postdoctoral Science Foundation (2020M671312) and the Fundamental Research Funds for the Central Universities (B210202140).
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DFZ and WJL designed research and project outline. LW and DFZ performed isolation, deposition and polyphasic taxonomy. DFZ, LW and WH performed genome analysis. LW, WJL AHZ and DFZ drafted the manuscript. AHZ, WH, ZYG, JKH and CL revised the manuscript. All authors read and approved the final manuscript.
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Wang, L., He, W., Gao, ZY. et al. Hyphomonas sediminis sp. nov., isolated from marine sediment. Antonie van Leeuwenhoek 115, 1177–1185 (2022). https://doi.org/10.1007/s10482-022-01765-1
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DOI: https://doi.org/10.1007/s10482-022-01765-1