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

Volume 74, Issue 11

gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral No Access

Abstract

The photosynthetic microorganisms within the coral holobiont produce energy and organic compounds through photosynthesis, which are vital for the biocalcification and heat tolerance of coral hosts. However, aerobic anoxygenic phototrophic bacteria (AAPB), which are one of the most important photosynthetic microorganisms, have not been thoroughly investigated in this environment. In this study, a novel AAPB, SCSIO 66989, was isolated from the reef-building coral sp. and considered a beneficial microorganism for corals (BMC). The polyphasic taxonomic analysis showed that it had the highest similarities with DSM 22379 (95.9%) and ATCC BAA-2084 (95.7%). Phylogenetic analysis showed that it formed an independent clade, distinguishing it from other genera within the family . The predominant fatty acids were C c and/or C c and C. The major respiratory quinone was ubiquinone-10 (Q-10). Sphingolipid, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylcholine were the diagnostic polar lipids. The average nucleotide identity, average amino acid identity and digital DNA–DNA hybridization values between SCSIO 66989 and the type strains of DSM 22379 and ATCC BAA-2084 were 69.2–70.0%, 58.6–61.2% and 19.2–19.7%, respectively. These results indicate that strain SCSIO 66989 represents a new species of a novel genus in the family , for which the name gen. nov. sp. nov. is proposed.

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  • Accepted:
  • Published Online:
Keyword(s): aerobic anoxygenic phototrophic bacteria , Alterisphingorhabdus coralli sp. nov. , beneficial microorganisms for corals and Sphingomonadaceae
Funding
This study was supported by the:
  • Northern Borders University (Award NBU-FFR-2024–2046-05)
    • Principal Award Recipient: SyedRaziuddin Quadri
  • China Postdoctoral Science Foundation (Award 2023M733591)
    • Principal Award Recipient: SongbiaoShi
  • Key Research and Development Project of Hainan Province (Award 321CXTD447)
    • Principal Award Recipient: Xin-PengTian
© 2024 The Authors
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2024-11-21
2025-11-16

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References

  1. Peixoto RS, Rosado PM, Leite DC de A, Rosado AS, Bourne DG. Beneficial Microorganisms for Corals (BMC): proposed mechanisms for coral health and resilience. Front Microbiol 2017; 8:341 [View Article] [PubMed]
     [Google Scholar]
  2. Rädecker N, Pogoreutz C, Voolstra CR, Wiedenmann J, Wild C. Nitrogen cycling in corals: the key to understanding holobiont functioning?. Trends Microbiol 2015; 23:490–497 [View Article] [PubMed]
     [Google Scholar]
  3. Wang W, Tang K, Wang P, Zeng Z, Xu T et al. The coral pathogen Vibrio coralliilyticus kills non-pathogenic holobiont competitors by triggering prophage induction. Nat Ecol Evol 2022; 6:1132–1144 [View Article] [PubMed]
     [Google Scholar]
  4. Cao X, Wang L, Lin J, Wu G, Tang K et al. Differential bioaccumulation and tolerances of massive and branching scleractinian corals to polycyclic aromatic hydrocarbons in situ. Sci Total Environ 2024; 931:172920 [View Article]
     [Google Scholar]
  5. Burriesci MS, Raab TK, Pringle JR. Evidence that glucose is the major transferred metabolite in dinoflagellate-cnidarian symbiosis. J Exp Biol 2012; 215:3467–3477 [View Article] [PubMed]
     [Google Scholar]
  6. Davy SK, Allemand D, Weis VM. Cell biology of cnidarian-dinoflagellate symbiosis. Microbiol Mol Biol Rev 2012; 76:229–261 [View Article] [PubMed]
     [Google Scholar]
  7. Koblížek M. Ecology of aerobic anoxygenic phototrophs in aquatic environments. FEMS Microbiol Rev 2015; 39:854–870 [View Article] [PubMed]
     [Google Scholar]
  8. Soora M, Cypionka H. Light enhances survival of Dinoroseobacter shibae during long-term starvation. PLoS One 2014; 8:e83960 [View Article]
     [Google Scholar]
  9. Shiba T, Simidu U. Erythrobacter longus gen. nov., sp. nov., an aerobic bacterium which contains bacteriochlorophyll a. Int J Syst Evol Microbiol 1982; 32:211–217 [View Article]
     [Google Scholar]
  10. Kosako Y, Yabuuchi E, Naka T, Fujiwara N, Kobayashi K. Proposal of Sphingomonadaceae Fam. Nov., consisting of Sphingomonas Yabuuchi et al. 1990, Erythrobacter Shiba and Shimidu 1982, Erythromicrobium Yurkov et al. 1994, Porphyrobacter Fuerst et al. 1993, Zymomonas Kluyver and van Niel 1936, and Sandaracinobacter Yurkov et al. 1997, with the type genus Sphingomonas Yabuuchi et al. 1990. Microbiol Immunol 1990; 44:563–575
     [Google Scholar]
  11. Lee K-B, Liu C-T, Anzai Y, Kim H, Aono T et al. The hierarchical system of the “Alphaproteobacteria”: description of Hyphomonadaceae fam. nov., Xanthobacteraceae fam. nov. and Erythrobacteraceae fam. nov. Int J Syst Evol Microbiol 2005; 55:1907–1919 [View Article] [PubMed]
     [Google Scholar]
  12. 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]
  13. Sly LI, Cahill MM. Transfer of Blastobacter natatorius (Sly 1985) to the genus Blastomonas gen. nov. as Blastomonas natatoria comb. nov. Int J Syst Bacteriol 1997; 47:566–568 [View Article]
     [Google Scholar]
  14. Feng G-D, Zhang X-J, Yang S-Z, Li A-Z, Yao Q et al. Transfer of Sphingorhabdus marina, Sphingorhabdus litoris, Sphingorhabdus flavimaris and Sphingorhabdus pacifica corrig. into the novel genus Parasphingorhabdus gen. nov. and Sphingopyxis baekryungensis into the novel genus Novosphingopyxis gen. nov. within the family Sphingomonadaceae. Int J Syst Evol Microbiol 2020; 70:2147–2154 [View Article]
     [Google Scholar]
  15. Jogler M, Chen H, Simon J, Rohde M, Busse HJ et al. Description of Sphingorhabdus planktonica gen. nov., sp. nov. and reclassification of three related members of the genus Sphingopyxis in the genus Sphingorhabdus gen. nov.. Int J Syst Evol Microbiol 2013; 63:1342–1349 [View Article]
     [Google Scholar]
  16. Cui XL, Mao PH, Zeng M, Li WJ, Zhang LP et al. Streptimonospora salina gen. nov., sp. nov., a new member of the family Nocardiopsaceae. Int J Syst Evol Microbiol 2001; 51:357–363 [View Article] [PubMed]
     [Google Scholar]
  17. 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]
  18. 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]
  19. Fitch WM. Toward defining the course of evolution: minimum change for a specific tree topology. Syst Biol 1971; 20:406–416 [View Article]
     [Google Scholar]
  20. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17:368–376 [View Article] [PubMed]
     [Google Scholar]
  21. Chaumeil PA, Mussig AJ, Hugenholtz P, Parks DH. GTDB-Tk: a toolkit to classify genomes with the genome taxonomy database. Bioinformatics 2019; 36:1925–1927 [View Article] [PubMed]
     [Google Scholar]
  22. 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] [PubMed]
     [Google Scholar]
  23. 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]
  24. Sun J, Lu F, Luo Y, Bie L, Xu L et al. OrthoVenn3: an integrated platform for exploring and visualizing orthologous data across genomes. Nucleic Acids Res 2023; 51:W397–W403 [View Article]
     [Google Scholar]
  25. Chen C, Wu Y, Li J, Wang X, Zeng Z et al. TBtools-II: a “one for all, all for one” bioinformatics platform for biological big-data mining. Mol Plant 2023; 16:1733–1742 [View Article] [PubMed]
     [Google Scholar]
  26. 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]
  27. Xu L, Yue X-L, Li H-Z, Jian S-L, Shu W-S et al. Aerobic anoxygenic phototrophic bacteria in the marine environments revealed by Raman/fluorescence-guided single-cell sorting and targeted metagenomics. Environ Sci Technol 2024; 58:7087–7098 [View Article] [PubMed]
     [Google Scholar]
  28. Tindall BJ, Sikorski J, Smibert RA, Krieg NR. Phenotypic characterization and the principles of comparative systematics. Methods Gen Mol Microbiol 2007330–393 [View Article]
     [Google Scholar]
  29. Gonzalez C, Gutierrez C, Ramirez C. Halobacterium vallismortis sp. nov. an amylolytic and carbohydrate-metabolizing, extremely halophilic bacterium. Can J Microbiol 1978; 24:710–715 [View Article] [PubMed]
     [Google Scholar]
  30. Hirose S, Matsuura K, Haruta S. Phylogenetically diverse aerobic anoxygenic phototrophic bacteria isolated from epilithic biofilms in Tama River, Japan. Microbes Environ 2016; 31:299–306 [View Article] [PubMed]
     [Google Scholar]
  31. Hirose S, Tank M, Hara E, Tamaki H, Mori K et al. Aquabacterium pictum sp. nov., the first aerobic bacteriochlorophyll a-containing fresh water bacterium in the genus Aquabacterium of the class Betaproteobacteria. Int J Syst Evol Microbiol 2020; 70:596–603 [View Article]
     [Google Scholar]
  32. Hirose S, Asano T, Hamada M, Morohoshi S, Kunihiro T et al. Roseomonas fluvialis sp. nov., an aerobic bacteriochlorophyll a-containing freshwater bacterium isolated from river epilithic biofilm. Int J Syst Evol Microbiol 2023; 73:005810 [View Article] [PubMed]
     [Google Scholar]
  33. Yabuuchi E, Yano I, Oyaizu H, Hashimoto Y, Ezaki T et al. Proposals of Sphingomonas paucimobilis gen. nov. and comb. nov., Sphingomonas parapaucimobilis sp. nov., Sphingomonas yanoikuyae sp. nov., Sphingomonas adhaesiva sp. nov., Sphingomonas capsulata comb. nov., and two genospecies of the genus Sphingomonas. Microbiol Immunol 1990; 34:99–119 [View Article] [PubMed]
     [Google Scholar]
  34. Baik KS, Choe HN, Park SC, Hwang YM, Kim EM et al. Sphingopyxis rigui sp. nov. and Sphingopyxis wooponensis sp. nov., isolated from wetland freshwater, and emended description of the genus Sphingopyxis. Int J Syst Evol Microbiol 2013; 63:1297–1303 [View Article] [PubMed]
     [Google Scholar]
  35. Holmes B, Owen RJ, Evans A, Malnick H, Willcox WR. Pseudomonas paucimobilis, a new species isolated from human clinical specimens, the hospital environment, and other sources. Int J Syst Evol Microbiol 1977; 27:133–146 [View Article]
     [Google Scholar]
  36. Kämpfer P, Witzenberger R, Denner EBM, Busse HJ, Neef A. Sphingopyxis witflariensis sp. nov., isolated from activated sludge. Int J Syst Evol Microbiol 2002; 52:2029–2034 [View Article] [PubMed]
     [Google Scholar]
  37. Jeong SE, Kim KH, Baek K, Jeon CO. Parasphingopyxis algicola sp. nov., isolated from a marine red alga Asparagopsis taxiformis and emended description of the genus Parasphingopyxis Uchida et al. 2012. Int J Syst Evol Microbiol 2017; 67:3877–3881 [View Article]
     [Google Scholar]
  38. Sly LI. Emendation of the genus Blastobacter Zavarzin 1961 and description of Blastobacter natatorius sp. nov. Int J Syst Evol Microbiol 1985; 35:40–45 [View Article]
     [Google Scholar]
  39. Fujii K, Satomi M, Morita N, Motomura T, Tanaka T et al. Novosphingobium tardaugens sp. nov., an oestradiol-degrading bacterium isolated from activated sludge of a sewage treatment plant in Tokyo. Int J Syst Evol Microbiol 2003; 53:47–52 [View Article] [PubMed]
     [Google Scholar]
  40. Kim BS, Lim YW, Chun J. Sphingopyxis marina sp. nov. and Sphingopyxis litoris sp. nov., isolated from seawater. Int J Syst Evol Microbiol 2008; 58:2415–2419 [View Article] [PubMed]
     [Google Scholar]
  41. Sasser M. Identification of bacteria by gas chromatography of cellular fatty acids. USFCC Newsl 1990; 20:1–6
     [Google Scholar]
  42. Kämpfer P, Kroppenstedt RM. Numerical analysis of fatty acid patterns of coryneform bacteria and related taxa. Can J Microbiol 1996; 42:989–1005 [View Article]
     [Google Scholar]
  43. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100:221–230 [View Article] [PubMed]
     [Google Scholar]
  44. 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]
  45. Castro DJ, Llamas I, Béjar V, Martínez-Checa F. Blastomonas quesadae sp. nov., isolated from a saline soil by dilution-to-extinction cultivation. Int J Syst Evol Microbiol 2017; 67:2001–2007 [View Article] [PubMed]
     [Google Scholar]
  46. Shan Y, Liu G, Cai R, Liu R, Zheng R et al. A deep-sea bacterium senses blue light via a BLUF-dependent pathway. mSystems 2022; 7:e0127921 [View Article]
     [Google Scholar]
  47. Cai R, He W, Zhang J, Liu R, Yin Z et al. Blue light promotes zero-valent sulfur production in a deep-sea bacterium. EMBO J 2023; 42:e112514 [View Article] [PubMed]
     [Google Scholar]
  48. Park S-Y, Tame JRH. Seeing the light with BLUF proteins. Biophys Rev 2017; 9:169–176 [View Article] [PubMed]
     [Google Scholar]
  49. Price MN, Deutschbauer AM, Arkin AP. GapMind: automated annotation of amino acid biosynthesis. mSystems 2020; 5:e00291-20 [View Article] [PubMed]
     [Google Scholar]
  50. Shinzato C, Shoguchi E, Kawashima T, Hamada M, Hisata K et al. Using the Acropora digitifera genome to understand coral responses to environmental change. Nature 2011; 476:320–323 [View Article] [PubMed]
     [Google Scholar]
  51. Robbins SJ, Singleton CM, Chan CX, Messer LF, Geers AU et al. A genomic view of the reef-building coral Porites lutea and its microbial symbionts. Nat Microbiol 2019; 4:2090–2100 [View Article] [PubMed]
     [Google Scholar]
  52. Reynolds D, Thomas T. Evolution and function of eukaryotic-like proteins from sponge symbionts. Mol Ecol 2016; 25:5242–5253 [View Article] [PubMed]
     [Google Scholar]
  53. Díez-Vives C, Moitinho-Silva L, Nielsen S, Reynolds D, Thomas T. Expression of eukaryotic-like protein in the microbiome of sponges. Mol Ecol 2017; 26:1432–1451 [View Article] [PubMed]
     [Google Scholar]
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Alterisphingorhabdus coralli gen. nov. sp. nov., a novel aerobic anoxygenic phototrophic bacteria isolated from reef-building coral
Int J Syst Evol Microbiol 74, 006577 (2024); https://doi.org/10.1099/ijsem.0.006577
/content/journal/ijsem/10.1099/ijsem.0.006577
/content/journal/ijsem/10.1099/ijsem.0.006577
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