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INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo International Journal of Systematic and Evolutionary Microbiology

Volume 71, Issue 7

gen. nov., sp. nov., a marine bacterium isolated from the sea sponge Free

Abstract

A Gram-stain-negative, strictly aerobic, motile bacterium, designated strain RKSG073, was isolated from the sea sponge , collected off the west coast of San Salvador, The Bahamas. Cells were curved-to-spiral rods with single, bipolar (amphitrichous) flagella, oxidase- and catalase-positive, non-nitrate-reducing and required salt for growth. RKSG073 grew optimally at 30–37 °C, pH 6–7, and with 2–3 % (w/v) NaCl. The predominant fatty acids of RKSG073 were summed feature 8 (Cω6 and/or Cω7) and C. Major isoprenoid quinones were identified as Q-10 and Q-9. Phylogenetic analyses of nearly complete 16S rRNA genes and genome sequences positioned strain RKSG073 in a clade with its closest relative AH-MY2 (92.1 % 16S rRNA gene sequence similarity), which subsequently clustered with Gri0909, ZC80 and type species of the genera , and . The DNA G+C content calculated from the genome of RKSG073 was 42.2 mol%. On the basis of phylogenetic distinctiveness and polyphasic analysis, here we propose that RKSG073 (culture deposit numbers: ATCC collection = TSD-74, BCCM collection = LMG 29869) represents the type strain of a novel genus and species within the family , order and class , for which the name gen. nov., sp. nov. is proposed.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): Alphaproteobacteria , Curvivirga aplysinae , Kiloniellaceae , marine , novel bacterium , Rhodospirillales and sea sponge
Funding
This study was supported by the:
  • Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (Award 462303)
    • Principal Award Recipient: StaceyR Goldberg
© 2021 The Authors
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2021-07-06
2025-11-10

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References

  1. Hentschel U, Usher KM, Taylor MW. Marine sponges as microbial fermenters. FEMS Microbiol Ecol 2006; 55:167–177 [View Article] [PubMed]
     [Google Scholar]
  2. Schmitt S, Tsai P, Bell J, Fromont J, Ilan M et al. Assessing the complex sponge microbiota: core, variable and species-specific bacterial communities in marine sponges. ISME J 2012; 6:564–576 [View Article] [PubMed]
     [Google Scholar]
  3. Hentschel U, Piel J, Degnan SM, Taylor MW. Genomic insights into the marine sponge microbiome. Nat Rev Microbiol 2012; 10:641–654 [View Article] [PubMed]
     [Google Scholar]
  4. Easson CG, Thacker RW. Phylogenetic signal in the community structure of host-specific microbiomes of tropical marine sponges. Front Microbiol 2014; 5:532 [View Article] [PubMed]
     [Google Scholar]
  5. Pita L, Rix L, Slaby BM, Franke A, Hentschel U. The sponge holobiont in a changing ocean: from microbes to ecosystems. Microbiome 2018; 6:46 [View Article] [PubMed]
     [Google Scholar]
  6. Rappé MS, Giovannoni SJ. The uncultured microbial majority. Annu Rev Microbiol 2003; 57:369–394 [View Article] [PubMed]
     [Google Scholar]
  7. Fieseler L, Horn M, Wagner M, Hentschel U. Discovery of the novel candidate phylum “Poribacteria” in marine sponges. Appl Environ Microbiol 2004; 70:3724–3732 [View Article] [PubMed]
     [Google Scholar]
  8. Versluis D, McPherson K, van Passel MWJ, Smidt H, Sipkema D. Recovery of previously uncultured bacterial genera from three Mediterranean sponges. Mar Biotechnol 2017; 19:454–468 [View Article]
     [Google Scholar]
  9. Sipkema D, Schippers K, Maalcke WJ, Yang Y, Salim S et al. Multiple approaches to enhance the cultivability of bacteria associated with the marine sponge Haliclona (gellius) sp. Appl Environ Microbiol 2011; 77:2130–2140 [View Article] [PubMed]
     [Google Scholar]
  10. Montalvo NF, Davis J, Vicente J, Pittiglio R, Ravel J et al. Integration of culture-based and molecular analysis of a complex sponge-associated bacterial community. PLoS ONE 2014; 9:1–8
     [Google Scholar]
  11. Laport MS. Isolating bacteria from sponges: Why and how. Current Pharma Biotech 2018; 18:1224–1236
     [Google Scholar]
  12. Brenner D, Krieg N, Staley J, Garrity G. Class I. Alphaproteobacteria class. nov. In Bergey’s Manual of Systematic Bacteriology, 2nd ed, vol. 2 (The Proteobacteria), part C (The Alpha-, Beta-, Delta-, and Epsilonproteobacteria) New York: Springer; 2005
     [Google Scholar]
  13. Trujillo M, Dedysh S, DeVos P, Hedlund B, Kämpfer P. Rhodospirillales. In Bergey’s Manual of Systematics of archaea and bacteria UK: John Wiley & Sons, Inc; 2015
     [Google Scholar]
  14. Hördt A, López MG, Meier-Kolthoff JP, Schleuning M, Weinhold L-M et al. Analysis of 1,000+ type-strain genomes substantially improves taxonomic classification of Alphaproteobacteria. Front Microbiol 2020; 11:468 [View Article] [PubMed]
     [Google Scholar]
  15. Brinkhoff T, Giebel HA, Simon M. Diversity, ecology, and genomics of the Roseobacter clade: A short overview. Arch Microbiol 2008; 189:531–539 [View Article] [PubMed]
     [Google Scholar]
  16. Yilmaz P, Yarza P, Rapp JZ, Glöckner FO. Expanding the world of marine bacterial and archaeal clades. Front Microbiol 2015; 6:1524 [View Article] [PubMed]
     [Google Scholar]
  17. Muñoz-Gómez SA, Hess S, Burger G, Lang BF, Susko E et al. An updated phylogeny of the Alphaproteobacteria reveals that the parasitic Rickettsiales and Holosporales have independent origins. Elife 2019; 8:455
     [Google Scholar]
  18. Williams KP, Sobral BW, Dickerman AW. A robust species tree for the Alphaproteobacteria. J Bacteriol 2007; 189:4578–4586 [View Article] [PubMed]
     [Google Scholar]
  19. Wiese J, Thiel V, Gärtner A, Schmaljohann R, Imhoff JF. Kiloniella laminariae gen. nov., sp. nov., an alphaproteobacterium from the marine macroalga Laminaria saccharina. Int J Syst Evol Microbiol 2009; 59:350–356 [View Article] [PubMed]
     [Google Scholar]
  20. Pfennig N, Truper H. Higher taxa of the phototrophic bacteria. Int J Syst Bacter 1971; 21:17–18
     [Google Scholar]
  21. Park S, Park JM, Kang CH, Yoon JH. Aestuariispira insulae gen. nov., sp. nov., a lipolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 2014; 64:1841–1846 [View Article] [PubMed]
     [Google Scholar]
  22. Marmur J. A procedure for the isolation of deoxyribonucleic acid from micro-organisms. J Mol Biol 1961; 3:208–IN1
     [Google Scholar]
  23. Correa H, Haltli B, Duque C, Kerr R. Bacterial communities of the gorgonian octocoral Pseudopterogorgia elisabethae. Microb Ecol 2013; 66:972–985 [View Article] [PubMed]
     [Google Scholar]
  24. Pike RE, Haltli B, Kerr RG. Description of Endozoicomonas euniceicola sp. nov. and Endozoicomonas gorgoniicola sp. nov., bacteria isolated from the octocorals Eunicea fusca and Plexaura sp., and an emended description of the genus Endozoicomonas. Int J Syst Evol Microbiol 2013; 63:4294–4302 [View Article] [PubMed]
     [Google Scholar]
  25. Manefield M, Whiteley AS, Griffiths RI, Bailey MJ. RNA stable isotope probing, a novel means of linking microbial community function to phylogeny. Appl Environ Microbiol 2002; 68:5367–5373 [View Article] [PubMed]
     [Google Scholar]
  26. Gontang EA, Fenical W, Jensen PR. Phylogenetic diversity of gram-positive bacteria cultured from marine sediments. Appl Environ Microbiol 2007; 73:3272–3282 [View Article] [PubMed]
     [Google Scholar]
  27. Lane DJ. 16S/23S rRNA sequencing. Stackebrandt E, Goodfellow M. eds In Nucleic Acid Techniques in Bacterial Systematics New York, NY: John Wiley & Sons, Inc; 1991 pp 115–175
     [Google Scholar]
  28. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403–410 [View Article] [PubMed]
     [Google Scholar]
  29. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA et al. Clustal W and Clustal X version 2.0. Bioinformatics 2007; 23:2947–2948 [View Article] [PubMed]
     [Google Scholar]
  30. Hall T. BioEdit: an important software for molecular biology. GERF Bull Biosci 2011; 2:60–61
     [Google Scholar]
  31. Felsenstein J. Evolutionary trees from DNA sequences: A maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  32. 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]
  33. Eck RV, Dayhoff MO. eds Atlas of Protein Sequence and Structure Silver Spring, MD: National Biomedical Research Foundation; 1965
     [Google Scholar]
  34. 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] [PubMed]
     [Google Scholar]
  35. Tavaré S. Some probabilistic and statistical problems in the analysis of DNA sequences. Lectures Math Life Sci 1986; 17:57–86
     [Google Scholar]
  36. Shoemaker JS, Fitch WM. Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated. Mol Biol Evol 1989; 6:270–289 [View Article] [PubMed]
     [Google Scholar]
  37. Yang Z. Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: approximate methods. J Mol Evol 1994; 39:306–314 [View Article] [PubMed]
     [Google Scholar]
  38. Gu X, Fu YX, Li WH. Maximum likelihood estimation of the heterogeneity of substitution rate among nucleotide sites. Mol Biol Evol 1995; 12:546–557
     [Google Scholar]
  39. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution 1985; 39:783–791 [View Article] [PubMed]
     [Google Scholar]
  40. Kim J, Jeong SE, Khan SA, Jeon CO. Hwanghaeella grinnelliae gen. nov., sp. nov., isolated from a marine red alga. Int J Syst Evol Microbiol 2019; 67:21–3550
     [Google Scholar]
  41. Illumina Nextera Xt Dna Library Prep Kit Reference Guide (15031942) 2019
     [Google Scholar]
  42. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821–829 [View Article] [PubMed]
     [Google Scholar]
  43. Yoon SH, 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
     [Google Scholar]
  44. Lee I, Chalita M, Ha S-M, Na S-I, Yoon SH et al. ContEst16S: an algorithm that identifies contaminated prokaryotic genomes using 16S RNA gene sequences. Int J Syst Evol Microbiol 2017; 67:2053–2057
     [Google Scholar]
  45. Lee I, Ouk Kim Y, Park SC, 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]
  46. Jain C, Rodriguez-R LM, Phillippy AM, Konstantinidis KT, Aluru S. High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries. Nat Commun 20189
     [Google Scholar]
  47. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T et al. The RAST Server: rapid annotations using subsystems technology. BMC Genomics 2008; 9:75–89 [View Article] [PubMed]
     [Google Scholar]
  48. Alanjary M, Steinke K, Ziemert N. AutoMLST: an automated web server for generating multi-locus species trees highlighting natural product potential. Nucleic Acids Res 2019; 47:W276–W282 [View Article] [PubMed]
     [Google Scholar]
  49. Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res 2011; 39:W29–37 [View Article] [PubMed]
     [Google Scholar]
  50. Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J et al. The Pfam protein families database: towards a more sustainable future. Nucleic Acids Res 2016; 44:D279–85 [View Article] [PubMed]
     [Google Scholar]
  51. Haft DH, Selengut JD, White O. The TIGRFAMs database of protein families. Nucleic Acids Res 2003; 31:371–373 [View Article] [PubMed]
     [Google Scholar]
  52. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772–780 [View Article] [PubMed]
     [Google Scholar]
  53. Capella-Gutiérrez S, Silla-Martínez JM, Gabaldon T. trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses. Bioinformatics 2009; 25:1972–1973 [View Article] [PubMed]
     [Google Scholar]
  54. Trifinopoulos J, Nguyen LT, Haeseler von A, Minh BQ. W-IQ-TREE: A fast online phylogenetic tool for maximum likelihood analysis. Nucleic Acids Res 2016; 44:W232–5 [View Article]
     [Google Scholar]
  55. Letunic I, Bork P. Interactive Tree Of Life (iTOL): an online tool for phylogenetic tree display and annotation. Bioinformatics 2007; 23:127–128 [View Article] [PubMed]
     [Google Scholar]
  56. Gee AH, Hunt GA. Single cell technic a presentation of the pipette method as a routine laboratory procedure. J Bacteriol 1928; 16:327–353 [View Article] [PubMed]
     [Google Scholar]
  57. Haber M, Shefer S, Giordano A, Orlando P, Gambacorta A et al. Luteivirga sdotyamensis gen. Nov., sp. Nov., a novel bacterium of the phylum bacteroidetes isolated from the mediterranean sponge Axinella polypoides. Int J Syst Evol Microbiol 2013; 63:939–945 [View Article] [PubMed]
     [Google Scholar]
  58. Bauer AW, Perry DM, Kirby WM. Single-disk antibiotic-sensitivity testing of staphylococci; An analysis of technique and results. AMA Arch Intern Med 1959; 104:208–216 [View Article] [PubMed]
     [Google Scholar]
  59. Wang L, Li X, Lai Q, Shao Z. Kiloniella litopenaei sp. nov., isolated from the gut microflora of Pacific white shrimp, Litopenaeus vannamei. Antonie van Leeuwenhoek 2015; 108:1293–1299 [View Article] [PubMed]
     [Google Scholar]
  60. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids Microbial ID: Inc; 1989
     [Google Scholar]
  61. Tindall BJ. Lipid composition of Halobacterium lacusprofundi. FEMS Microbiol Lett 1990; 66:199–202 [View Article]
     [Google Scholar]
  62. Lohman DC, Forouhar F, Beebe ET, Stefely MS, Minogue CE et al. Mitochondrial COQ9 is a lipid-binding protein that associates with COQ7 to enable coenzyme Q biosynthesis. Proc Natl Acad Sci USA 2014; 111:E4697–E4705
     [Google Scholar]
  63. Ventosa A, Marquez MC, Kocur M, Tindall BJ. Comparative study of ‘Micrococcus sp.’ strains CCM 168 and CCM 1405 and members of the genus Salinicoccus. Int J Syst Bacteriol 1993; 43:245–248 [View Article] [PubMed]
     [Google Scholar]
  64. Worliczek HL, Kämpfer P, Rosengarten R, Tindall BJ, Busse HJ. Polar lipid and fatty acid profiles--re-vitalizing old approaches as a modern tool for the classification of mycoplasmas?. Syst Appl Microbiol 2007; 30:355–370 [View Article] [PubMed]
     [Google Scholar]
  65. Minnikin DE, O’Donnell AG, Goodfellow M, Alderson G, Athalye M et al. An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 1984; 2:233–241 [View Article]
     [Google Scholar]
  66. Wang Z, Benning C. Arabidopsis thaliana polar glycerolipid profiling by thin layer chromatography (TLC) coupled with gas-liquid chromatography (GLC. J Vis Exp 2011; 49:2518
     [Google Scholar]
  67. Chen S, Xu Y, Zheng C, Ke L-X. Marivibrio halodurans gen. nov., sp. nov., a marine bacterium in the family Rhodospirillaceae isolated from underground rock salt. Int J Syst Evol Microbiol 2017; 67:4266–4271
     [Google Scholar]
  68. López-López A, Pujalte MJ, Benlloch S, Mata-Roig M, Rosselló-Móra R et al. Thalassospira lucentensis gen. nov., sp. nov., a new marine member of the α-Proteobacteria. Int J Syst Evol Microbiol 2002; 52:1277–1283 [View Article] [PubMed]
     [Google Scholar]
  69. Tsubouchi T, Ohta Y, Haga T, Usui K, Shimane Y et al. Thalassospira alkalitolerans sp. nov. and Thalassospira mesophila sp. nov., isolated from a decaying bamboo sunken in the marine environment, and emended description of the genus Thalassospira. Int J Syst Evol Microbiol 2014; 64:107–115 [View Article] [PubMed]
     [Google Scholar]
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Curvivirga aplysinae gen. nov., sp. nov., a marine bacterium isolated from the sea sponge Aplysina fistularis
Int J Syst Evol Microbiol 71, 004873 (2021); https://doi.org/10.1099/ijsem.0.004873
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