Skip to content
1887

Abstract

The is one of the dominant bacterial phyla in corals. However, the exact taxa of those coral bacteria under the are still unclear. Two aerobic, Gram-stain-negative, non-motile rods, designated strains BMA10 and BMA12, were isolated from stony coral collected from Weizhou Island, PR China. Global alignment of 16S rRNA gene sequences indicated that both strains are closest to species of with the highest identities being lower than 93 %, and the similarity value between these two strains was 92.3 %. Phylogenetic analysis based on 16S rRNA gene and genome sequences indicated that these two strains form an monophylogenetic lineage alongside the families , , , , , and in the order , phylum . The genomic DNA G+C contents of BMA10 and BMA12 were 38.4 and 41.9 mol%, respectively. The major polar lipids of BMA10 were phosphatidylethanolamine, unidentified aminophospholipid, four unidentified aminolipids, and five unidentified lipids. While those of BMA12 were phosphatidylethanolamine, two unidentified aminolipids, and five unidentified lipids. The major cellular fatty acids detected in both isolates were iso-C and C 5. Carbohydrate-active enzyme analysis indicated these two strains may utilize coral mucus or chitin. Based on above characteristics, these two strains are suggested to represent two new species in two new genera of a new family in the order , for which the name gen. nov., sp. nov., gen. nov., sp. nov. and fam. nov. are proposed. The type strain of is BMA10 (=MCCC 1K08300=KCTC 102045), and that for is BMA12 (=MCCC 1K08309=KCTC 102046).

Funding
This study was supported by the:
  • National Natural Sciences Foundation of China (Award 41866004)
    • Principle Award Recipient: WangGuanghua
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.006376
2024-05-13
2025-05-15
Loading full text...

Full text loading...

References

  1. Krieg NR, Ludwig W, Euzeby J. Phylum XIV. Bacteroidetes phyl. nov. In Whitman WB, Krieg NR, Staley JT, Brown DR, Hedlund BP et al. eds Bergey’s Manual of Systematic Bacteriology New York: Springer; 2010 pp 25–469
    [Google Scholar]
  2. Ludwig W, Euzéby J, Whitman WB. Road map of the phyla Bacteroidetes, Spirochaetes, Tenericutes (Mollicutes), Acidobacteria, Fibrobacteres, Fusobacteria, Dictyoglomi, Gemmatimonadetes, Lentisphaerae, Verrucomicrobia, Chlamydiae and Planctomycetes. In Krieg NR, Staley JT, Brown DR, Hedlund BP, Paster BJ et al. eds Bergey’s Manual of Systematic Bacteriology New York: Springer; 2010 pp 1–24
    [Google Scholar]
  3. Munoz R, Rosselló-Móra R, Amann R. Revised phylogeny of Bacteroidetes and proposal of sixteen new taxa and two new combinations including Rhodothermaeota phyl. nov. Syst Appl Microbiol 2016; 39:281–296 [View Article] [PubMed]
    [Google Scholar]
  4. Hahnke RL, Meier-Kolthoff JP, García-López M, Mukherjee S, Huntemann M et al. Genome-based taxonomic classification of Bacteroidetes. Front Microbiol 2016; 7:2003 [View Article] [PubMed]
    [Google Scholar]
  5. Parks DH, Chuvochina M, Waite DW, Rinke C, Skarshewski A et al. A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life. Nat Biotechnol 2018; 36:996–1004 [View Article]
    [Google Scholar]
  6. Whitman WB, Oren A, Chuvochina M, da Costa MS, Garrity GM et al. Proposal of the suffix –ota to denote phyla. Addendum to ‘Proposal to include the rank of phylum in the International Code of Nomenclature of Prokaryotes. Int J Syst Evol Microbiol 2018; 68:967–969 [View Article]
    [Google Scholar]
  7. Stanier L. Family I. Cytophagaceae Stanier 1940, 630, emend. mut. char. In Buchanan RE, Gibbons NE. eds Bergey’s Manual of Determinative Bacteriology, 8th. edn vol 630 Baltimore: The Williams and Wilkins Co; 1940 pp 99–127
    [Google Scholar]
  8. Sefrji FO, Michoud G, Marasco R, Merlino G, Daffonchio D. Mangrovivirga cuniculi gen. nov., sp. nov., a moderately halophilic bacterium isolated from bioturbated Red Sea mangrove sediment, and proposal of the novel family Mangrovivirgaceae fam. nov. Int J Syst Evol Microbiol 2021; 71:004866 [View Article]
    [Google Scholar]
  9. Choi EJ, Beatty DS, Paul LA, Fenical W, Jensen PR. Mooreia alkaloidigena gen. nov., sp. nov. and Catalinimonas alkaloidigena gen. nov., sp. nov., alkaloid-producing marine bacteria in the proposed families Mooreiaceae fam. nov. and Catalimonadaceae fam. nov. in the phylum Bacteroidetes. Int J Syst Evol Microbiol 2013; 63:1219–1228 [View Article] [PubMed]
    [Google Scholar]
  10. García-López M, Meier-Kolthoff JP, Tindall BJ, Gronow S, Woyke T et al. Analysis of 1,000 type-strain genomes improves taxonomic classification of Bacteroidetes. Front Microbiol 2019; 10:2083 [View Article] [PubMed]
    [Google Scholar]
  11. Wexler HM. Bacteroides: the good, the bad, and the nitty-gritty. Clin Microbiol Rev 2007; 20:593–621 [View Article] [PubMed]
    [Google Scholar]
  12. Pan X, Raaijmakers JM, Carrión VJ. Importance of Bacteroidetes in host-microbe interactions and ecosystem functioning. Trends Microbiol 2023; 31:959–971 [View Article] [PubMed]
    [Google Scholar]
  13. Fisher R, O’Leary RA, Low-Choy S, Mengersen K, Knowlton N et al. Species richness on coral reefs and the pursuit of convergent global estimates. Curr Biol 2015; 25:500–505 [View Article] [PubMed]
    [Google Scholar]
  14. Knowlton N, Brainard RE, Fisher R, Moews M, Plaisance L et al. Coral reef biodiversity. In AD McIntyre. ed Life in the World’s Oceans: Diversity Distribution and Abundance Oxford: Blackwell Publishing Ltd; 2010 pp 65–74
    [Google Scholar]
  15. De’ath G, Fabricius KE, Sweatman H, Puotinen M. The 27-year decline of coral cover on the Great Barrier Reef and its causes. Proc Natl Acad Sci USA 2012; 109:17995–17999 [View Article] [PubMed]
    [Google Scholar]
  16. van Oppen MJH, Blackall LL. Coral microbiome dynamics, functions and design in a changing world. Nat Rev Microbiol 2019; 17:557–567 [View Article]
    [Google Scholar]
  17. Rohwer F, Seguritan V, Azam F, Knowlton N. Diversity and distribution of coral-associated bacteria. Mar Ecol Prog Ser 2002; 243:1–10 [View Article]
    [Google Scholar]
  18. Lim HJ, Lee EH, Yoon Y, Chua B, Son A. Portable lysis apparatus for rapid single-step DNA extraction of Bacillus subtilis. J Appl Microbiol 2016; 120:379–387 [View Article] [PubMed]
    [Google Scholar]
  19. Li R, Zhu H, Ruan J, Qian W, Fang X et al. De novo assembly of human genomes with massively parallel short read sequencing. Genome Res 2010; 20:265–272 [View Article]
    [Google Scholar]
  20. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, and Goodfellow M. eds Nucleic Acid Techniques in Bacterial Systematics Chichester: John Wiley & Sons; 1991
    [Google Scholar]
  21. Yoon S-H, Ha S-M, Kwon S, Lim J, Kim Y et al. Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 2017; 67:1613–1617 [View Article]
    [Google Scholar]
  22. Pruesse E, Peplies J, Glöckner FO. SINA: accurate high-throughput multiple sequence alignment of ribosomal RNA genes. Bioinformatics 2012; 28:1823–1829 [View Article]
    [Google Scholar]
  23. Kozlov AM, Darriba D, Flouri T, Morel B, Stamatakis A. RAxML-NG: a fast, scalable and user-friendly tool for maximum likelihood phylogenetic inference. Bioinformatics 2019; 35:4453–4455 [View Article]
    [Google Scholar]
  24. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406–425 [View Article] [PubMed]
    [Google Scholar]
  25. Swofford DL. PAUP, phylogenetic analysis using parsimony. version 3.1. Computer program distributed by the Illinois Natural History Survey. In Mccarthy 1993
    [Google Scholar]
  26. Kumar S, Stecher G, Li M, Knyaz C, Tamura K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol 2018; 35:1547–1549 [View Article]
    [Google Scholar]
  27. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the Genome Taxonomy Database. Bioinformatics 2020; 36:1925–1927 [View Article]
    [Google Scholar]
  28. Price MN, Dehal PS, Arkin AP. FastTree 2 – approximately maximum-likelihood trees for large alignments. PLoS One 2010; 5:e9490 [View Article]
    [Google Scholar]
  29. Xie J, Chen Y, Cai G, Cai R, Hu Z et al. Tree Visualization By One Table (tvBOT): a web application for visualizing, modifying and annotating phylogenetic trees. Nucleic Acids Res 2023; 51:W587–W592 [View Article]
    [Google Scholar]
  30. Yarza P, Yilmaz P, Pruesse E, Glöckner FO, Ludwig W et al. Uniting the classification of cultured and uncultured bacteria and archaea using 16S rRNA gene sequences. Nat Rev Microbiol 2014; 12:635–645 [View Article] [PubMed]
    [Google Scholar]
  31. Auch AF, von Jan M, Klenk H-P, Göker M. Digital DNA-DNA hybridization for microbial species delineation by means of genome-to-genome sequence comparison. Stand Genomic Sci 2010; 2:117–134 [View Article] [PubMed]
    [Google Scholar]
  32. Meier-Kolthoff JP, Auch AF, Klenk H-P, Göker M. Genome sequence-based species delimitation with confidence intervals and improved distance functions. BMC Bioinformatics 2013; 14:60 [View Article] [PubMed]
    [Google Scholar]
  33. Yoon S-H, Ha S, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Antonie van Leeuwenhoek 2017; 110:1281–1286 [View Article]
    [Google Scholar]
  34. Kim D, Park S, Chun J. Introducing EzAAI: a pipeline for high throughput calculations of prokaryotic average amino acid identity. J Microbiol 2021; 59:476–480 [View Article]
    [Google Scholar]
  35. Barco RA, Garrity GM, Scott JJ, Amend JP, Nealson KH et al. A genus definition for bacteria and archaea based on a standard genome relatedness index. MBio 2020; 11:10–1128
    [Google Scholar]
  36. Konstantinidis KT, Rosselló-Móra R, Amann R. Uncultivated microbes in need of their own taxonomy. ISME J 2017; 11:2399–2406 [View Article] [PubMed]
    [Google Scholar]
  37. Johnson EA, Schroeder WA. Microbial carotenoids. In Fiechter A. ed Downstream Processing Biosurfactants Carotenoids Berlin: Springer-Verlag; 2006 pp 119–178 [View Article]
    [Google Scholar]
  38. Zheng J, Ge Q, Yan Y, Zhang X, Huang L et al. dbCAN3: automated carbohydrate-active enzyme and substrate annotation. Nucleic Acids Res 2023; 51:W115–W121 [View Article] [PubMed]
    [Google Scholar]
  39. Busk PK. Accurate, automatic annotation of peptidases with hotpep-protease. Green Chemical Engineering 2020; 1:124–130 [View Article]
    [Google Scholar]
  40. Bernardet J-F, Nakagawa Y, Holmes B. Proposed minimal standards for describing new taxa of the family Flavobacteriaceae and emended description of the family. Int J Syst Evol Microbiol 2002; 52:1049–1070 [View Article] [PubMed]
    [Google Scholar]
  41. Zhao L-H, Wang Z-J, Song C, Xing X, Liu Y-Y et al. Fulvivirga marina sp. nov. and Fulvivirga sediminis sp. nov., two novel Bacteroidetes isolated from the marine sediment. Int J Syst Evol Microbiol 2022; 72:005308 [View Article]
    [Google Scholar]
  42. Jung YT, Ha MJ, Park S, Lee JS, Yoon JH. Fulvivirga lutimaris sp. nov., isolated from a tidal flat sediment. Int J Syst Evol Microbiol 2016; 66:2604–2609 [View Article]
    [Google Scholar]
  43. Kamekura M. Lipids of extreme halophiles. In Vreeland RH, Hochstein LI. eds The Biology of Halophilic Bacteria Boca Raton: CRC Press; p 1993 [View Article]
    [Google Scholar]
  44. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
    [Google Scholar]
  45. Collins M. Isoprenoid quinones. In Goodfellow M, O’Donnell AG. eds Chemical Methods in Prokaryotic Systematics Chichester: Wiley; 1994 pp 345–401
    [Google Scholar]
  46. Komagata K, Suzuki K-I. 4 Lipid and cell-wall analysis in bacterial systematics. In Colwell RR, Grigorova R. eds Methods in Microbiology vol 19 Academic Press; 1988 pp 161–207
    [Google Scholar]
  47. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. In MIDI Technical Note vol 101 Newark, DE: MIDI; 1990
    [Google Scholar]
  48. Nedashkovskaya OI, Kim SB, Shin DS, Beleneva IA, Mikhailov VV. 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 2007; 57:1046–1049 [View Article] [PubMed]
    [Google Scholar]
  49. Nupur N, Sharma S, Kumar Singh P, Suresh K, Anil Kumar P. Fulvivirga imtechensis sp. nov., a member of the phylum Bacteroidetes. Int J Syst Evol Microbiol 2012; 62:2213–2217 [View Article]
    [Google Scholar]
  50. Goldberg SR, Correa H, Haltli BA, Kerr RG. 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 2020; 70:2766–2781 [View Article] [PubMed]
    [Google Scholar]
  51. Bae SS, Jung Y-H, Kwon YM, Chung D, Choi G et al. Fulvivirga lutea sp. nov., a marine bacterium isolated from seawater. Int J Syst Evol Microbiol 2022; 72:5188 [View Article]
    [Google Scholar]
  52. Nguyen TTH, Vuong TQ, Han HL, Li Z, Lee Y-J et al. Three marine species of the genus Fulvivirga, rich sources of carbohydrate-active enzymes degrading alginate, chitin, laminarin, starch, and xylan. Sci Rep 2023; 13:6301 [View Article] [PubMed]
    [Google Scholar]
  53. Cha I-T, Oh Y-S, Park S-J, Park B-J, Lee J-K et al. Reichenbachiella faecimaris sp. nov., isolated from a tidal flat, and emended descriptions of the genus Reichenbachiella and Reichenbachiella agariperforans. Int J Syst Evol Microbiol 2011; 61:1994–1999 [View Article]
    [Google Scholar]
  54. Shi M-J, Wang C, Liu Z-Y, Jiang L-X, Du Z-J. Reichenbachiella versicolor sp. nov., isolated from red alga. Int J Syst Evol Microbiol 2018; 68:3523–3527 [View Article] [PubMed]
    [Google Scholar]
  55. Nedashkovskaya OI, Kim SB, Lee DH, Lysenko AM, Shevchenko LS et al. Roseivirga ehrenbergii gen. nov., sp. nov., a novel marine bacterium of the phylum ‘Bacteroidetes’, isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 2005; 55:231–234 [View Article]
    [Google Scholar]
  56. Nedashkovskaya OI, Kim SB, Lysenko AM, Park MS, Mikhailov VV et al. Roseivirga echinicomitans sp. nov., a novel marine bacterium isolated from the sea urchin Strongylocentrotus intermedius, and emended description of the genus Roseivirga. Int J Syst Evol Microbiol 2005; 55:1797–1800 [View Article] [PubMed]
    [Google Scholar]
  57. Lau SCK, Tsoi MMY, Li X, Plakhotnikova I, Dobretsov S et al. Description of Fabibacter halotolerans gen. nov., sp. nov. and Roseivirga spongicola sp. nov., and reclassification of [Marinicola] seohaensis as Roseivirga seohaensis comb. nov. Int J Syst Evol Microbiol 2006; 56:1059–1065 [View Article] [PubMed]
    [Google Scholar]
  58. Pan J, Sun C, Wang RJ, Wu M. Roseivirga marina sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2015; 65:4239–4243 [View Article]
    [Google Scholar]
  59. Jung YT, Park S, Lee JS, Yoon JH. Roseivirga maritima sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2016; 66:2664–2670 [View Article]
    [Google Scholar]
  60. Huo Y-Y, Xu L, Wang C-S, Yang J-Y, You H et al. Fabibacter pacificus sp. nov., a moderately halophilic bacterium isolated from seawater. Int J Syst Evol Microbiol 2013; 63:3710–3714 [View Article] [PubMed]
    [Google Scholar]
  61. Wong S-K, Park S, Lee J-S, Chul Lee K, Xavier Chiura H et al. Fabibacter misakiensis sp. nov., a marine bacterium isolated from coastal surface water. Int J Syst Evol Microbiol 2015; 65:3276–3280 [View Article] [PubMed]
    [Google Scholar]
  62. Tang M, Chen C, Li J, Xiang W, Wu H et al. Fabivirga thermotolerans gen. nov., sp. nov., a novel marine bacterium isolated from culture broth of a marine cyanobacterium. Int J Syst Evol Microbiol 2016; 66:1095–1099 [View Article] [PubMed]
    [Google Scholar]
  63. Seo H-S, Kwon KK, Yang S-H, Lee H-S, Bae SS et al. Marinoscillum gen. nov., a member of the family “Flexibacteraceae”, with Marinoscillum pacificum sp. nov. from a marine sponge and Marinoscillum furvescens nom. rev., comb. nov. Int J Syst Evol Microbiol 2009; 59:1204–1208 [View Article] [PubMed]
    [Google Scholar]
  64. Cha I-T, Park S-J, Kim S-J, Kim J-G, Jung M-Y et al. Marinoscillum luteum sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2013; 63:3475–3480 [View Article] [PubMed]
    [Google Scholar]
  65. Alain K, Tindall BJ, Catala P, Intertaglia L, Lebaron P. Ekhidna lutea gen. nov., sp. nov., a member of the phylum Bacteroidetes isolated from the South East Pacific Ocean. Int J Syst Evol Microbiol 2010; 60:2972–2978 [View Article] [PubMed]
    [Google Scholar]
/content/journal/ijsem/10.1099/ijsem.0.006376
Loading
/content/journal/ijsem/10.1099/ijsem.0.006376
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Supplementary material 2

EXCEL

Supplementary material 3

EXCEL

Supplementary material 4

EXCEL
This is a required field
Please enter a valid email address
Approval was a Success
Invalid data
An Error Occurred
Approval was partially successful, following selected items could not be processed due to error