1887

Abstract

Members within the family are morphologically and genetically highly diverse, and originate mostly from coastal marine environments. In this study, a novel species of this family, designated M0103, was isolated from the surface of a sea snail . Strain M0103 is Gram-stain-negative, halophilic, non-motile and non-Bacteriochlorophyll -producing bacterium. Several phenotypic characteristics of the isolate were similar to other species within this family, such as the sole respiratory quinone Q-10 and major fatty acid components C 7c, C and C. Strain M0103 contains a diphosphatidylglycerol, a phosphatidylglycerol, a phosphatidylcholine, a phosphatidy ethanolamine, a phosphatidylinositol, five unidentified phospholipids and four unidentified polar lipids. Based on the 16S rRNA gene sequence analysis, this isolate showed the closest phylogenetic relationship with ‘’ GH1-23 (95.1 %). Values of average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) of genome sequences were of 70.1–76.4 % and 18.3–20.9 % between the isolate and 24 closely related type strains. Analysis the 4.0 Mb genome of strain M0103 revealed several putative genes associated with cellular stress resistance, which may play protective roles for the isolate in the adaptation to a marine environment. Phylogenetic, phenotypic and chemotaxonomic analyses suggested that strain M0103 represents a novel genus and novel species of the family , for which the name gen. nov., sp. nov. is proposed. The type strain is M0103 (=MCCC 1K03619=KCTC 62358).

Funding
This study was supported by the:
  • The Special Project for the Base of Guangxi Science and Technology and Talents (Award AD17129019)
    • Principle Award Recipient: ShushiHuang
  • Guangxi Key Laboratory of Marine Natural Products and Combinatorial Biosynthesis Chemistry (Award 17-259-74)
    • Principle Award Recipient: ShushiHuang
  • The Fundamental Research Funds for Guangxi Academy of Sciences (Award 2018YBJ303)
    • Principle Award Recipient: WenjinHu
  • The Fundamental Research Funds for Guangxi Academy of Sciences (Award 2019YBJ101)
    • Principle Award Recipient: XinliPan
  • National Natural Science Foundation of China (Award 31560017)
    • Principle Award Recipient: ShushiHuang
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.004821
2021-06-28
2021-07-29
Loading full text...

Full text loading...

References

  1. Garrity GM, Bell JA, Libum TG. Family i. Rhodobacteraceae fam. Nov. In. Garrity G, Brenner D, Krieg N, Staley J. eds In Bergey’s Manual of systematic Bacteriology, 2 ed, part C. edn Vol 2 New York: Springer; 2005 p 161
    [Google Scholar]
  2. Giovannoni S, Rappé MS. Evolution, diversity and molecular ecology of marine prokaryote. Kirchman D. eds In Microbial Ecology of the Oceans New York: Wiley; 2000 pp 47–84
    [Google Scholar]
  3. Parte AC. LPSN — List of Prokaryotic names with Standing in Nomenclature ( https://lpsn.dsmz.de/family/rhodobacteraceae), 20 years on. Int J Syst Evol Microbiol 2018; 68:1825–1829 [View Article] [PubMed]
    [Google Scholar]
  4. Choi Y-S, Oh J-S, Roh D-H. Pelagicola marinus sp. nov. isolated from deep-sea water. Int J Syst Evol Microbiol 2019; 69:3961–3966
    [Google Scholar]
  5. Li S, Tang K, Liu K, Jiao N. Thiobacimonas profunda gen. nov., sp. nov., a member of the family Rhodobacteraceae isolated from deep-sea water. Int J Syst Evol Microbiol 2015; 65:359–364 [View Article] [PubMed]
    [Google Scholar]
  6. Lai Q, Liu X, Yuan J, Xie S, Shao Z. Pararhodobacter marinus sp. nov., isolated from deep-sea water of the Indian Ocean. Int J Syst Evol Microbiol 2019; 69:932–936 [View Article] [PubMed]
    [Google Scholar]
  7. Barnier C, Clerissi C, Lami R, Intertaglia L, Lebaron P et al. Description of Palleronia rufa sp. nov., a biofilm-forming and ahl-producing Rhodobacteraceae, reclassification of Hwanghaeicola aestuarii as Palleronia aestuarii comb. nov., Maribius pontilimi as Palleronia pontilimi comb. nov., Maribius salinus as Palleronia salina comb. nov., Maribius pelagius as Palleronia pelagia comb. nov. and emended description of the genus Palleronia. Syst Appl Microbiol 2020; 43:126018 [View Article] [PubMed]
    [Google Scholar]
  8. Jung HS, Jeong SE, Chun BH, Quan ZX, Jeon CO. Rhodophyticola porphyridii gen. nov., sp. nov., isolated from a red alga, Porphyridium marinum. Int J Syst Evol Microbiol 2019; 69:1656–1661 [View Article] [PubMed]
    [Google Scholar]
  9. Kumari P, Bhattacharjee S, Poddar A, Das SK. Sulfitobacter faviae sp. nov., isolated from the coral Faviaveroni. Int J Syst Evol Microbiol 2016; 66:3786–3792 [View Article] [PubMed]
    [Google Scholar]
  10. Chang YQ, Meng X, ZZ D, Du ZJ. Oceanibium sediminis gen. nov., sp. nov., isolated from marine sediment. Int J Syst Evol Microbiol 2019; 69:249
    [Google Scholar]
  11. Zhang R, Wang C, Wang XT, Mu DS, Du ZJ. Jannaschia formosa sp. nov., isolated from marine saltern sediment. Int J Syst Evol Microbiol 2019; 69:2037–2042
    [Google Scholar]
  12. Töpel M, Pinder MIM, Johansson ON, Kourtchenko O, Godhe A et al. Whole-genome sequence of the novel Antarctobacter heliothermus strain SMS3, found in association with the marine diatom Skeletonema marinoi. J Genomics 2018; 6:113–116 [View Article] [PubMed]
    [Google Scholar]
  13. Jami M, Lai Q, Ghanbari M, Moghadam MS, Kneifel W et al. Celeribacter persicus sp. nov., a polycyclic-aromatic-hydrocarbon-degrading bacterium isolated from mangrove soil. Int J Syst Evol Microbiol 2016; 66:1875–1880 [View Article] [PubMed]
    [Google Scholar]
  14. Schaefer JK, Goodwin KD, McDonald IR, Murrell JC, Oremland RS. Leisingera methylohalidivorans gen. nov., sp. nov., a marine methylotroph that grows on methyl bromide. Int J Syst Evol Microbiol 2002; 52:851–859 [View Article] [PubMed]
    [Google Scholar]
  15. Breider S, Freese HM, Spröer C, Simon M, Overmann J et al. Phaeobacter porticola sp. nov., an antibiotic-producing bacterium isolated from a sea harbour. Int J Syst Evol Microbiol 2017; 67:2153–2159 [View Article] [PubMed]
    [Google Scholar]
  16. Phippen CBW, Jørgensen CM, Bentzon-Tilia M, Gotfredsen CH, Larsen TO et al. Isolation of methyl Troposulfenin from phaeobacter inhibens. J Nat Prod 2019; 82:1387–1390 [View Article] [PubMed]
    [Google Scholar]
  17. Novak HR, Sayer C, Isupov MN, Paszkiewicz K, Gotz D et al. Marine Rhodobacteraceae l-haloacid dehalogenase contains a novel HIS/GLU dyad that could activate the catalytic water. FEBS J 2013; 280:1664–1680 [View Article] [PubMed]
    [Google Scholar]
  18. Li F, Tuo L, Su Z-W, Wei X-Q, Zhang X-Y et al. Nocardioides sonneratiae sp. nov., an endophytic actinomycete isolated from a branch of Sonneratia apetala. Int J Syst Evol Microbiol 2017; 67:2592–2597 [View Article] [PubMed]
    [Google Scholar]
  19. Skerman VBD. A Guide to the Identification of the Genera of Bacteria, 2nd edn. Baltimore, MD: Williams, Wilkins; 1967
    [Google Scholar]
  20. Weisburg WG, Barns SM, Pelletier DA, Lane DJ. 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 1991; 173:697–703 [View Article] [PubMed]
    [Google Scholar]
  21. Kumar S, Stecher G, Tamura K. MEGA7: Molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33:1870–1874 [View Article] [PubMed]
    [Google Scholar]
  22. 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]
  23. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
    [Google Scholar]
  24. Takahashi K, Nei M. Efficiencies of fast algorithms of phylogenetic inference under the criteria of maximum parsimony, minimum evolution, and maximum likelihood when a large number of sequences are used. Mol Biol Evol 2000; 17:1251–1258 [View Article] [PubMed]
    [Google Scholar]
  25. Lee I, Kim YO, Park S-C, Chun J. Orthoani: An improved algorithm and software for calculating average nucleotide identity. Int J Syst Evol Microbiol 2016; 66:1100–1103 [View Article] [PubMed]
    [Google Scholar]
  26. Rodriguez-R LM, Konstantinidis KT. The enveomics collection: a toolbox for specialized analyses of microbial genomes and metagenomes. PeerJ Preprints 2016; 4:e1900v1901
    [Google Scholar]
  27. Qin Q-L, Xie B-B, Zhang X-Y, Chen X-L, Zhou B-C et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article] [PubMed]
    [Google Scholar]
  28. 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]
  29. Meier-Kolthoff JP, Göker M. TYGS is an automated high-throughput platform for state-of-the-art genome-based taxonomy. Nat Commun 2019; 10:2182 [View Article] [PubMed]
    [Google Scholar]
  30. Wirth JS, Whitman WB. Phylogenomic analyses of a clade within the roseobacter group suggest taxonomic reassignments of species of the genera Aestuariivita, Citreicella, Loktanella, Nautella, Pelagibaca, Ruegeria, Thalassobius, Thiobacimonas and Tropicibacter, and the proposal of six novel genera. Int J Sys Evol Microbiol 2018; 68:2393–2411 [View Article]
    [Google Scholar]
  31. Chun J, Oren A, Ventosa A, Christensen H, Arahal DR et al. Proposed minimal standards for the use of genome data for the taxonomy of prokaryotes. Int J Syst Evol Microbiol 2018; 68:461–466 [View Article] [PubMed]
    [Google Scholar]
  32. Cappuccino JG, Sherman N. Microbiology: a Laboratory Manual, 6th edn. San Francisco, CA: Benjamin Cummings Pearson Education; 2002
    [Google Scholar]
  33. Sasser M. Bacterial Identification by Gas Chromatographic Analysis of Fatty Acid Methyl Esters GC-FAME MIDI Technical Note; 2006
    [Google Scholar]
  34. Brown NL, Lloyd JR, Jakeman K, Hobman JL, Bontidean I et al. Heavy metal resistance genes and proteins in bacteria and their application. Biochem Soc Trans 1998; 26:662–665 [View Article] [PubMed]
    [Google Scholar]
  35. Sprocati AR, Alisi C, Segre L, Tasso F, Galletti M et al. Investigating heavy metal resistance, bioaccumulation and metabolic profile of a metallophile microbial consortium native to an abandoned mine. Sci Total Environ 2006; 366:649–658 [View Article] [PubMed]
    [Google Scholar]
  36. Lim S, Jung J-H, Blanchard L, de Groot A. Conservation and diversity of radiation and oxidative stress resistance mechanisms in Deinococcus species. FEMS Microbiology Reviews 2018; 43:19–52
    [Google Scholar]
  37. Wang N-N, Zhou L-Y, Wang X-P, Li Y-X, Du Z-J. Oceaniglobus ichthyenteri sp. nov., isolated from the gut microflora of sea bass (Dicentrarchus labrax L.) and emended description of the genus Oceaniglobus. Int J Syst Evol Microbiol 2019; 69:2892–2898
    [Google Scholar]
  38. Lee SD. Maribius pontilimi sp. nov., isolated from a tidal mudflat. Int J Syst Evol Microbiol 2018; 68:353–357 [View Article] [PubMed]
    [Google Scholar]
  39. Cho JC, Giovannoni SJ. Oceanicola granulosus gen. nov., sp. nov. and Oceanicola batsensis sp. nov., poly-beta-hydroxybutyrate-producing marine bacteria in the order “Rhodobacterales”. Int J Syst Evol Microbiol 2004; 54:1129–1136 [View Article] [PubMed]
    [Google Scholar]
  40. Park S, Choi SJ, Won S-M, Yoon J-H. Jannaschia confluentis sp. nov., isolated from the junction between the ocean and a freshwater spring. Int J Syst Evol Microbiol 2018; 68:669–674 [View Article] [PubMed]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.004821
Loading
/content/journal/ijsem/10.1099/ijsem.0.004821
Loading

Data & Media loading...

Supplements

Supplementary material 1

PDF

Most cited this month Most Cited RSS feed

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