1887

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY logo

Volume 69, Issue 2

Phycocomes zhengii gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae isolated from the phycosphere of Chlorella vulgaris Free

Abstract

A Gram-stain-negative, motile with flagellum, ovoid- or rod-shaped, aerobic bacterium, was isolated from the phycosphere of the microalga Chlorellavulgaris and designated as strain LMIT002. The bacterium formed white, circular and smooth colonies on marine agar 2216 after 48 h incubation at 25 °C. On the basis of 16S rRNA gene sequence analysis, strain LMIT002 was found to be affiliated with the family Rhodobacteraceae of the order Rhodobacterales, and formed a distinct group. The 16S rRNA gene sequence similarities between strain LMIT002 and type strains in the family including Poseidonocella pacifica DSM 29316, Roseobacter litoralis and Rhodovulum sulfidophilum were 95.1, 95.0 and 95.0 %, respectively. Strain LMIT002grew optimally at 25 °C, pH 6.0 and in the presence of 2.0 % (w/v) NaCl. The genomic DNA G+C content was 67.0 mol% (the thermal denaturation method) or 66.9 % (genome sequencing). The sole respiratory quinone was ubiquinone-8, while the major fatty acids were summed feature 8 (C18 : 1 ω7с/C18 : 1 ω6с). The draft genome of strain LMIT002 was sequenced and annotated, with the results showing that it had a total size of 4 607 780 bp and comprised 4557 genes. Functional genes encoding the production of vitamin B12, indole-3-acetic acid and transform dimethylsulphoniopropionate were detected. Given its distinct genomic, morphological and physiological differences from previously described type strains, strain LMIT002 is proposed as a representative of a novel genus of the family Rhodobacteraceae , with the name Phycocomes zhengii gen. nov., sp. nov. The type strain is LMIT002 (=KCTC 62390=CICC 24357).

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): dimethylsulphoniopropionate , genome , indole-3-acetic acid , nitrate reduction and vitamin
© 2019 IUMS
Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.003194
2018-12-21
2024-04-20
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/69/2/535.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.003194&mimeType=html&fmt=ahah

References

  1. Field CB, Behrenfeld MJ, Randerson JT, Falkowski P. Primary production of the biosphere: integrating terrestrial and oceanic components. Science 1998; 281:237–240 [View Article][PubMed]
     [Google Scholar]
  2. Seymour JR, Amin SA, Raina JB, Stocker R. Zooming in on the phycosphere: the ecological interface for phytoplankton-bacteria relationships. Nat Microbiol 2017; 2:17065 [View Article][PubMed]
     [Google Scholar]
  3. Ramanan R, Kim B-H, Cho D-H, Oh H-M, Kim H-S et al. Algae-bacteria interactions: evolution, ecology and emerging applications. Biotechnol Adv 2016; 34:14–29
     [Google Scholar]
  4. Pujalte MJ, Lucena T, Ruvira MA, Arahal DR, Macián MC et al. The family Rhodobacteraceae. The Prokaryotes Springer; 2014 pp. 439–512
     [Google Scholar]
  5. Buchan A, González JM, Moran MA. Overview of the marine roseobacter lineage. Appl Environ Microbiol 2005; 71:5665–5677 [View Article][PubMed]
     [Google Scholar]
  6. Buchan A, Lecleir GR, Gulvik CA, González JM. Master recyclers: features and functions of bacteria associated with phytoplankton blooms. Nat Rev Microbiol 2014; 12:686–698 [View Article][PubMed]
     [Google Scholar]
  7. Wagner-Döbler I, Biebl H. Environmental biology of the marine Roseobacter lineage. Annu Rev Microbiol 2006; 60:255–280 [View Article][PubMed]
     [Google Scholar]
  8. Archer SD, Tarran GA, Stephens JA, Butcher LJ, Kimmance SA. Combining cell sorting with gas chromatography to determine phytoplankton group-specific intracellular dimethylsulphoniopropionate. Aquatic Microbial Ecology 2011; 62:109–121 [View Article]
     [Google Scholar]
  9. Moran MA, Reisch CR, Kiene RP, Whitman WB. Genomic insights into bacterial DMSP transformations. Ann Rev Mar Sci 2012; 4:523–542 [View Article][PubMed]
     [Google Scholar]
  10. Newton RJ, Griffin LE, Bowles KM, Meile C, Gifford S et al. Genome characteristics of a generalist marine bacterial lineage. ISME J 2010; 4:784–798 [View Article][PubMed]
     [Google Scholar]
  11. Wagner-Döbler I, Ballhausen B, Berger M, Brinkhoff T, Buchholz I et al. The complete genome sequence of the algal symbiont Dinoroseobacter shibae: a hitchhiker's guide to life in the sea. ISME J 2010; 4:61–77 [View Article][PubMed]
     [Google Scholar]
  12. Guillard RR, Ryther JH. Studies of marine planktonic diatoms. I. Cyclotella nana Hustedt, and Detonula confervacea (cleve) Gran. Can J Microbiol 1962; 8:229–239 [View Article][PubMed]
     [Google Scholar]
  13. Smibert RM, Krieg NR. Phenotypic characterization. Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994 pp. 611–651
     [Google Scholar]
  14. Collee JG, Miles R, Watt B. Tests for identification of bacteria. Mackie and McCartney Practical Medical Microbiology vol. 14 1996 pp. 131–149
     [Google Scholar]
  15. Wang H, Laughinghouse HD, Anderson MA, Chen F, Willliams E et al. Novel bacterial isolate from Permian groundwater, capable of aggregating potential biofuel-producing microalga Nannochloropsis oceanica IMET1. Appl Environ Microbiol 2012; 78:1445–1453 [View Article][PubMed]
     [Google Scholar]
  16. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M et al. Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 2012; 62:716–721 [View Article][PubMed]
     [Google Scholar]
  17. Li R, Li Y, Kristiansen K, Wang J. SOAP: short oligonucleotide alignment program. Bioinformatics 2008; 24:713–714 [View Article][PubMed]
     [Google Scholar]
  18. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 2013; 30:2725–2729 [View Article][PubMed]
     [Google Scholar]
  19. Zuo G, Hao B. CVTree3 web server for whole-genome-based and alignment-free prokaryotic phylogeny and taxonomy. Genomics Proteomics Bioinformatics 2015; 13:321–331 [View Article][PubMed]
     [Google Scholar]
  20. Qin QL, Xie BB, Zhang XY, Chen XL, Zhou BC et al. A proposed genus boundary for the prokaryotes based on genomic insights. J Bacteriol 2014; 196:2210–2215 [View Article][PubMed]
     [Google Scholar]
  21. Nedashkovskaya OI, Kim SB, Han SK, Rhee MS, Lysenko AM et al. Ulvibacter litoralis gen. nov., sp. nov., a novel member of the family Flavobacteriaceae isolated from the green alga Ulva fenestrata. Int J Syst Evol Microbiol 2004; 54:119–123 [View Article][PubMed]
     [Google Scholar]
  22. Yi H, Chun J. Hongiella mannitolivorans gen. nov., sp. nov., Hongiella halophila sp. nov. and Hongiella ornithinivorans sp. nov., isolated from tidal flat sediment. Int J Syst Evol Microbiol 2004; 54:157–162 [View Article][PubMed]
     [Google Scholar]
  23. Shieh WY, Chen YW, Chaw SM, Chiu HH. Vibrio ruber sp. nov., a red, facultatively anaerobic, marine bacterium isolated from sea water. Int J Syst Evol Microbiol 2003; 53:479–484 [View Article][PubMed]
     [Google Scholar]
  24. Romanenko LA, Tanaka N, Svetashev VI, Kalinovskaya NI. Poseidonocella pacifica gen. nov., sp. nov. and Poseidonocella sedimentorum sp. nov., novel alphaproteobacteria from the shallow sandy sediments of the Sea of Japan. Arch Microbiol 2012; 194:113–121 [View Article][PubMed]
     [Google Scholar]
  25. Mandel M, Igambi L, Bergendahl J, Dodson ML, Scheltgen E et al. Correlation of melting temperature and cesium chloride buoyant density of bacterial deoxyribonucleic acid. J Bacteriol 1970; 101:333–338[PubMed]
     [Google Scholar]
  26. Sasser M. Identification of Bacteria by Gas Chromatography of Cellular Fatty Acids, MIDI Technical Note 101. 1990
     [Google Scholar]
  27. Collins M. Isoprenoid quinone analysis in bacterial classification and identification. Chemical Methods in Bacterial Systematics London: Academic Press; 1985 pp. 267–287
     [Google Scholar]
  28. Kates M. Technique of Lipidology: Isolation, Analysis and Identification of Lipids Amsterdam: Holland Publishing Company; 1986 pp. 106241–106246
     [Google Scholar]
  29. Hiraishi A, Ueda Y. Intrageneric structure of the genus Rhodobacter: transfer of Rhodobacter sulfidophilus and related marine species to the genus Rhodovulum gen. nov. Int J Syst Bacteriol 1994; 44:15–23 [View Article]
     [Google Scholar]
  30. Seemann T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 2014; 30:2068–2069 [View Article]
     [Google Scholar]
  31. Masuda S, Hori K, Maruyama F, Ren S, Sugimoto S et al. Whole-Genome Sequence of the Purple Photosynthetic Bacterium Rhodovulum sulfidophilum Strain W4. Genome Announc 2013; 1:e0057713 [View Article][PubMed]
     [Google Scholar]
  32. Kalhoefer D, Thole S, Voget S, Lehmann R, Liesegang H et al. Comparative genome analysis and genome-guided physiological analysis of Roseobacter litoralis. BMC Genomics 2011; 12:324 [View Article][PubMed]
     [Google Scholar]
  33. Croft MT, Lawrence AD, Raux-Deery E, Warren MJ, Smith AG. Algae acquire vitamin B12 through a symbiotic relationship with bacteria. Nature 2005; 438:90–93 [View Article][PubMed]
     [Google Scholar]
  34. Kiene RP, Linn LJ, González J, Moran MA, Bruton JA. Dimethylsulfoniopropionate and methanethiol are important precursors of methionine and protein-sulfur in marine bacterioplankton. Appl Environ Microbiol 1999; 65:4549–4558[PubMed]
     [Google Scholar]
  35. Simó R. Production of atmospheric sulfur by oceanic plankton: biogeochemical, ecological and evolutionary links. Trends Ecol Evol 2001; 16:287–294 [View Article][PubMed]
     [Google Scholar]
  36. Curson AR, Todd JD, Sullivan MJ, Johnston AW. Catabolism of dimethylsulphoniopropionate: microorganisms, enzymes and genes. Nat Rev Microbiol 2011; 9:849–859 [View Article][PubMed]
     [Google Scholar]
  37. Wang H, Hill RT, Zheng T, Hu X, Wang B. Effects of bacterial communities on biofuel-producing microalgae: stimulation, inhibition and harvesting. Crit Rev Biotechnol 2016; 36:341–352 [View Article][PubMed]
     [Google Scholar]
  38. de-Bashan LE, Antoun H, Bashan Y. Involvement of indole-3-acetic acid produced by the growth-promoting bacterium Azospirillum sp. in promoting growth of Chlorella vulgaris. J Phycol 2008; 44:938–947 [View Article][PubMed]
     [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.003194
Loading
Phycocomes zhengii gen. nov., sp. nov., a marine bacterium of the family Rhodobacteraceae isolated from the phycosphere of Chlorella vulgaris
Int J Syst Evol Microbiol 69, 535 (2019); https://doi.org/10.1099/ijsem.0.003194
/content/journal/ijsem/10.1099/ijsem.0.003194
/content/journal/ijsem/10.1099/ijsem.0.003194
Loading

Data & Media loading...

Supplements

Supplementary data

PDF

Most cited 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