Abstract
A yellow-orange, rod-shaped (0.3–0.4 × 2.2–3.8 µm), Gram-stain-negative, non-motile, atrichous bacterium, designated strain 1062T, was isolated from tidal zone sediment collected from Xiaoshi Island, Weihai, Shandong Province, China. Growth of strain 1062T occurred at 15–43 °C (optimum, 37 °C), pH 6.0–9.5 (optimum, pH 7.5) and with 0.5–7.0% (w/v) NaCl (optimum, 2.0–3.0%). Nitrate was not reduced to nitrite or nitrogen. Positive for catalase and oxidase activity, as well as the hydrolysis of casein, DNA, starch and Tweens 20, 40, 60, but negative for hydrolysis of alginate, CM-cellulose, agar and Tweens 80. The 16S rRNA gene sequence comparisons indicated that strain 1062T had a sequence similarity of 96.2% with Fulvivirga lutimaris KCTC 42720T and 94.3% with Fulvivirga kasyanovii KCTC 12832T. Phylogenetic analysis showed that strain 1062T belonged to the genus Fulvivirga. The genomic DNA G + C content was 45.1 mol%. The ANI values of strain 1062T in comparison to F. kasyanovii KCTC 12832T and F. lutimaris KCTC 42720T were all lower than 70%. The dDDH values of strain 1062T in comparison to F. kasyanovii KCTC 12832T and F. lutimaris KCTC 42720T were all lower than 20%. The average amino acid identity values of strain 1062T in comparison to F. kasyanovii KCTC 12832T and F. lutimaris KCTC 42720T were all lower than 60%. The major fatty acids (> 5%) of strain 1062T were iso-C15:0, iso-C15:0 G, iso-C15:0 3OH, iso-C17:0 3-OH and summed feature 3 (C16:1ω7c/C16:1ω6c). The polar lipids consist of an aminolipid, phosphatidylethanolamine, phosphatidyglycerol and diphosphatidylglycerol. The major respiratory quinone was MK-7. Based on the results of physiological, biochemical and chemotaxonomic characteristics, the strain 1062T (= KCTC 72868T = MCCC 1H00499T) was identified as a new species of the genus Fulvivirga and the name Fulvivirga sedimenti sp. nov, is proposed.
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Abbreviations
- KCTC:
-
Korean Collection for Type Culture
- MCCC:
-
Marine Culture Collection of China
- MA:
-
Marine agar 2216
- MB:
-
Marine broth 2216
- dDDH:
-
Digital DNA–DNA hybridization
- AAI:
-
Average amino acid identity
- ANI:
-
Average nucleotide identity
- MEGA:
-
Molecular Evolutionary Genetics Analysis
References
Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ (1990) Basic local alignment search tool. J Mol Biol 215(3):403–410. https://doi.org/10.1016/S0022-2836(05)80360-2
Athalye M, Noble WC, Minnikin DE (1985) Analysis of cellular fatty acids by gas chromatography as a tool in the identification of medically important coryneform bacteria. J Appl Bacteriol 58(5):507–512. https://doi.org/10.1111/j.1365-2672.1985.tb01491.x
Bae SS, Jung YH, Kwon YM et al (2022) Fulvivirga lutea sp. nov., a marine bacterium isolated from seawater. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.005188
Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50(5):1861–1868. https://doi.org/10.1099/00207713-50-5-1861
Dong XZ, Cai MY (2001) Determination of biochemical characteristics. In: Dong XZCM (ed) Manual for the systematic identification of general bacteria. Science Press, Beijing, pp 370–398
Du ZJ, Wang Y, Dunlap C, Rooney AP, Chen GJ (2014) Draconibacterium orientale gen. nov., sp. nov., isolated from two distinct marine environments, and proposal of Draconibacteriaceae fam. nov. Int J Syst Evol Microbiol 64(Pt 5):1690–1696. https://doi.org/10.1099/ijs.0.056812-0
Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17(6):368–376. https://doi.org/10.1007/BF01734359
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39(4):783–791. https://doi.org/10.1111/j.1558-5646.1985.tb00420.x
Goldberg SR, Correa H, Haltli BA, Kerr RG (2020) Fulvivirga aurantia sp. nov. and Xanthovirga aplysinae gen. nov., sp. nov., marine bacteria isolated from the sponge Aplysina fistularis, and emended description of the genus Fulvivirga. Int J Syst Evol Microbiol 70(4):2766–2781. https://doi.org/10.1099/ijsem.0.004108
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(Pt 1):81–91. https://doi.org/10.1099/ijs.0.64483-0
Jung YT, Ha MJ, Park S, Lee JS, Yoon JH (2016) Fulvivirga lutimaris sp. nov, isolated from a tidal flat sediment. Int J Syst Evol Microbiol 66(7):2604–2609. https://doi.org/10.1099/ijsem.0.001085
Kroppenstedt RM (1982) Separation of bacterial menaquinones by HPLC using reverse phase (RP18) and a silver loaded ion exchanger as stationary phases. J Liq Chromatogr 5(12):2359–2367. https://doi.org/10.1080/01483918208067640
Kumar S, Stecher G, Li M, Knyaz C, Tamura K (2018) MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol Biol Evol 35(6):1547–1549. https://doi.org/10.1093/molbev/msy096
Lane DJ (1991) 16S/23S rRNA Sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematic. Wiley, New York, pp 115–175
Li R, Zhu H, Ruan J et al (2010) De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 20(2):265–272. https://doi.org/10.1101/gr.097261.109
Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M (2013) Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinform 14(1):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(5):233–241. https://doi.org/10.1016/0167-7012(84)90018-6
Mu DS, Liang QY, Wang XM et al (2018) Metatranscriptomic and comparative genomic insights into resuscitation mechanisms during enrichment culturing. Microbiome 6(1):230. https://doi.org/10.1186/s40168-018-0613-2
Nedashkovskaya OI, Kim SB, Shin DS, Beleneva IA, Mikhailov VV (2007) Fulvivirga kasyanovii gen. nov., sp. nov., a novel member of the phylum Bacteroidetes isolated from seawater in a mussel farm. Int J Syst Evol Microbiol 57(Pt 5):1046–1049. https://doi.org/10.1099/ijs.0.64641-0
Nupur SS, Kumar Singh P, Suresh K, Anil Kumar P (2012) Fulvivirga imtechensis sp. nov., a member of the phylum Bacteroidetes. Int J Syst Evol Microbiol 62(9):2213–2217. https://doi.org/10.1099/ijs.0.036608-0
Rodriguez-R LM, Konstantinidis KTJMM (2014) Bypassing cultivation to identify bacterial species: culture-independent genomic approaches identify credibly distinct clusters, avoid cultivation bias, and provide true insights into microbial species. Microbe Mag 9:111–118
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4(4):406–425. https://doi.org/10.1093/oxfordjournals.molbev.a040454
Yoon SH, Ha SM, Kwon S et al (2017a) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67(5):1613–1617. https://doi.org/10.1099/ijsem.0.001755
Yoon SH, Ha SM, Lim J, Kwon S, Chun J (2017b) A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie Van Leeuwenhoek 110(10):1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Zhao LH, Wang ZJ, Song C et al (2022) Fulvivirga marina sp. nov. and Fulvivirga sediminis sp. nov., two novel Bacteroidetes isolated from the marine sediment. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.005308
Acknowledgements
The implementation of scanning electron microscope was supported by the Physical-Chemical Materials Analytical and Testing Center of Shandong University at Weihai.
Funding
This work was supported by Science & Technology Fundamental Resources Investigation Program (Grant No. 2019FY100700), National Natural Science Foundation of China (32200003) and Shandong University (Weihai) interdisciplinary cultivation project “Research on resources & environment and high-quality development of marine economy”.
Author information
Authors and Affiliations
Contributions
XL and HY isolated the strain 1062T. Shao-Juan Du helped process cell samples and photograph cell morphology. XL and HY finished the experiment and manuscript. ZD and MY offered experiment guidance and critical revision of manuscripts. All authors contributed to the article and approved the submitted version.
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
Additional information
Communicated by Erko Stackebrandt.
Publisher's Note
Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.
The GenBank accession number for the 16S rRNA gene sequence of strain 1062T is MW391774. The whole-genome shotgun project of strain 1062T has been deposited into DDBJ/EMBL/GenBank under the accession number JAIXNE000000000.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
Springer Nature or its licensor (e.g. a society or other partner) holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.
About this article
Cite this article
Liu, Xj., Yu, H., Du, SJ. et al. Fulvivirga sedimenti sp.nov, isolated from the sediment of oceanic tidal zone. Arch Microbiol 204, 727 (2022). https://doi.org/10.1007/s00203-022-03344-4
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-03344-4