Abstract
A bacterial strain, designated J12C1-MA-4T, was isolated from liquid culture of the dinoflagellate Ceratoperidinium margalefii. The bacterium was Gram-negative, aerobic, and rod-shaped. Oxidase and catalase were positive. Optimal growth was observed at 30 °C, pH 7.0, in the presence of 1% (w/v) NaCl. Phylogenetic analyses based on 16S rRNA gene and a 92 core gene set suggested that the strain J12C1-MA-4T belongs to the family Rhodobacteraceae in the class Alphaproteobacteria and represents a taxon separated from other genera. 16S rRNA gene sequence of the strain J12C1-MA-4T showed high similarities to Loktanella ponticola KCTC 42133T (95.7%), Pseudooctadecabacter jejudonensis KCTC 32525T (95.5%) and Jannaschia helgolandensis KCTC 12191T (95.3%). The genome length of strain J12C1-MA-4T was 3,621,968 bp with a DNA G + C content of 64.48 mol%. The major cellular fatty acids of strain J12C1-MA-4T were summed feature 8 (comprising C18:1ω7c and/or C18:1ω6c) (> 10%). Phosphatidylglycerol (PG), phosphatidylcholine (PC), phospholipids (PL), lipids 1 (L1) and aminolipid (AL) were shown to be the major polar lipids. The sole predominant isoprenoid quinone was Q-10. Based on phylogenetic, phenotypic, chemotaxonomic and genomic features, we propose that strain J12C1-MA-4T represent a novel species in the novel genus of the family Rhodobacteraceae, with the proposed name Gymnodinialimonas ceratoperidinii gen. nov., sp. nov.. The type strain is J12C1-MA-4T (=KCTC 82770T =GDMCC 1.2729T).
This is a preview of subscription content, log in via an institution to check access.
Similar content being viewed by others
Data availability
The GenBank accession numbers of the 16S rRNA gene and the whole-genome sequences of the strain J12C1-MA-4T are MZ457320 and CP079194, respectively.
Abbreviations
- ANI:
-
Average nucleotide identity
- dDDH:
-
Digital DNA–DNA hybridization
- GGDC:
-
Genome-to-genome distance calculation
- LBA:
-
Luria–Bertani agar
- R2A:
-
Reasoner’s 2A agar
- MA:
-
Marine agar 2216
- TSA:
-
Tryptic soy agar
- PDA:
-
Potato dextrose agar
- NA:
-
Nutrient agar
References
Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH, Emerson D (2020) A genus definition for bacteria and archaea based on a standard genome relatedness index. Mbio. https://doi.org/10.1128/mBio.02475-19
Billerbeck S, Orchard J, Tindall BJ, Giebel HA, Brinkhoff T, Simon M (2015) Description of Octadecabacter temperatus sp. nov., isolated from the southern North Sea, emended descriptions of the genus Octadecabacter and its species and reclassification of Octadecabacter jejudonensis Park and Yoon 2014 as Pseudooctadecabacter jejudonensis gen. nov., comb. nov. Int J Syst Evol Microbiol 65:1967–1974. https://doi.org/10.1099/ijs.0.000205
Collins M, Shah H, Minnikin D (1980) A note on the separation of natural mixtures of bacterial menaquinones using reverse phase thin-layer chromatography. J Appl Microbiol 48:277–282. https://doi.org/10.1111/j.1365-2672.1980.tb01227.x
Jiang L, Lim CJ, Kim SG, Jeong JC, Kim CY, Kim DH, Kim SW, Lee J (2020) Saccharibacillus brassicae sp. nov., an endophytic bacterium isolated from kimchi cabbage (Brassica rapa subsp. pekinensis) seeds. J Microbiol 58:24–29. https://doi.org/10.1007/s12275-020-9346-6
Jiang Y, Jiang L, Peng Y, Kim KH, Shin HH, Kim YM, Lee J, Li Z (2021) Flagellatimonas centrodinii gen. nov., sp. nov, a novel member of the family Nevskiaceae isolated from toxin-producing dinoflagellate Centrodinium punctatum. Int J Syst Evol Microbiol. https://doi.org/10.1099/ijsem.0.005084
Jung Y-T, Park S, Park J-M, Yoon J-H (2014) Loktanella ponticola sp. nov. isolated from seawater. Int J Syst Evol Microbiol 64(Pt_11):3717–3723. https://doi.org/10.1099/ijs.0.068361-0
Kong YH, Sun C, Guo LL, Xu L, Wu YH, Xu XW (2021) Alterinioella nitratireducens gen. nov., sp. nov., isolated from seawater in the West Pacific Ocean. Curr Microbiol 78:2455–2463. https://doi.org/10.1007/s00284-021-02475-z
Li Z, Mertens KN, Nézan E, Chomérat N, Bilien G, Iwataki M, Shin HH (2019) Discovery of a new clade nested within the genus Alexandrium (Dinophyceae): morpho-molecular characterization of Centrodinium punctatum (Cleve) F.J.R. Taylor Protist 170:168–186. https://doi.org/10.1016/j.protis.2019.02.003
Liang KYH, Orata FD, Boucher YF, Case RJ (2021) Roseobacters in a sea of poly- and paraphyly: whole genome-based taxonomy of the family Rhodobacteraceae and the proposal for the split of the “Roseobacter Clade” into a novel family, Roseobacteraceae. Fam Nov Front Microbiol 12:683109. https://doi.org/10.3389/fmicb.2021.683109
Luo C, Rodriguez RL, Konstantinidis KT (2014) MyTaxa: an advanced taxonomic classifier for genomic and metagenomic sequences. Nucleic Acids Res 42:e73. https://doi.org/10.1093/nar/gku169
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
Minnikin D 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
Moustafa A et al (2010) Transcriptome profiling of a toxic dinoflagellate reveals a gene-rich protist and a potential impact on gene expression due to bacterial presence. PLoS ONE 5:e9688. https://doi.org/10.1371/journal.pone.0009688
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
Palmer M, Steenkamp ET, Blom J, Hedlund BP, Venter SN (2020) All ANIs are not created equal: implications for prokaryotic species boundaries and integration of ANIs into polyphasic taxonomy. Int J Syst Evol Microbiol 70:2937–2948. https://doi.org/10.1099/ijsem.0.004124
Park S, Choi SJ, Won S-M, Yoon J-H (2017) Loktanella acticola sp. nov. isolated from seawater. Int J Syst Evol Microbiol 67(10):4175–4180. https://doi.org/10.1099/ijsem.0.002274
Sanudo-Wilhelmy SA, Gomez-Consarnau L, Suffridge C, Webb EA (2014) The role of B vitamins in marine biogeochemistry. Ann Rev Mar Sci 6:339–367. https://doi.org/10.1146/annurev-marine-120710-100912
Sasser M (2006) Bacterial identification by gas chromatographic analysis of fatty acids methyl esters (GC-FAME). MIDI Technical MIDI Technical Note #101 MIDI Inc, Newark, DE, USA.
Tang YZ, Koch F, Gobler CJ (2010) Most harmful algal bloom species are vitamin B1 and B12 auxotrophs. Proc Natl Acad Sci USA 107:20756–20761. https://doi.org/10.1073/pnas.1009566107
Tatusova T et al (2016) NCBI prokaryotic genome annotation pipeline. Nucleic Acids Res 44:6614–6624. https://doi.org/10.1093/nar/gkw569
Van Trappen S, Mergaert J, Swings J (2004) Loktanella salsilacus gen. nov., sp. nov., Loktanella fryxellensis sp. nov. and Loktanella vestfoldensis sp. nov., new members of the Rhodobacter group, isolated from microbial mats in Antarctic lakes. Int J Syst Evol Microbiol 54:1263–1269. https://doi.org/10.1099/ijs.0.03006-0
Wagner-Döbler I, Rheims H, Felske A, Pukall R, Tindall BJ (2003) Jannaschia helgolandensis gen. nov., sp. nov., a novel abundant member of the marine Roseobacter clade from the North Sea. Int J Syst Evol Microbiol 53:731–738. https://doi.org/10.1099/ijs.0.02377-0
Yoon SH et al (2017a) 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
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 110:1281–1286. https://doi.org/10.1007/s10482-017-0844-4
Funding
This work was supported by grant from the Korea Research Institute of Bioscience and Biotechnology (KRIBB) Research Initiative Program (KGM5232221), MarineBiotics project (20210469) funded by the Ministry of the Oceans and Fisheries, and the National Research Foundation of Korea (NRF) grant funded by the Korea government (MSIT) (No. NRF-2021R1C1C1008377).
Author information
Authors and Affiliations
Corresponding author
Ethics declarations
Conflict of interest
The authors declare that there are no conflicts 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.
Supplementary Information
Below is the link to the electronic supplementary material.
Rights and permissions
About this article
Cite this article
Jiang, Y., Peng, Y., Shin, H.H. et al. Gymnodinialimonas ceratoperidinii gen. nov., sp. nov., isolated from rare marine dinoflagellate Ceratoperidinium margalefii. Arch Microbiol 204, 185 (2022). https://doi.org/10.1007/s00203-022-02797-x
Received:
Revised:
Accepted:
Published:
DOI: https://doi.org/10.1007/s00203-022-02797-x