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Abstract

Five strains representing a novel family within the were isolated from the estuarine grasses and . All strains were facultatively anaerobic, Gram-negative, short, motile, polar monotrichous rods that were mesophilic, oxidase-negative, catalase-positive, had DNA G+C contents of 41.5–44.4 mol% and required seawater salts or NaCl. Growth was observed at pH 3.5–8.0. Polar lipids diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, phosphatidylmonomethylethanolamine, aminophospholipid, phospholipids and unidentified aminolipids were found in the representative strain S-G2-2. The major menaquinone and ubiquinone were MK-8 (100 %) and Q-8 (93 %), respectively. Predominant fatty acids present were C aldehyde and/or unknown fatty acid 10.9525 (MIDI designation) and/or iso-C I/C 3-OH, Cω7/Cω6, C, C cyclo and Cω7and/or Cω6. The nearly full-length 16S rRNA gene sequences of the strains were very similar (99–100 % similarity), and the strains were identified as members of the same species by DNA–DNA relatedness measurements. 16S rRNA gene sequence analysis revealed that the strains formed a monophyletic lineage within the order . All five strains fixed N. Analysis of partial gene sequences also revealed a monophyletic lineage within the , and the sequences were dissimilar to those of any previously described diazotroph. Differences between the novel strains and other members of the include the inability to produce cytochrome oxidase. The novel strains were metabolically versatile. On the basis of the information described above, the new genus and species gen. nov., sp. nov. are proposed to accommodate the five strains within a new family, fam. nov. The type strain of is S-G2-2 ( = ATCC BAA-1368  = DSM 18577).

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2011-05-01
2020-01-24
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References

  1. Altschul S. F. , Madden T. L. , Schäffer A. A. , Zhang J. , Zhang Z. , Miller W. , Lipman D. J. . ( 1997; ). Gapped blast and psi-blast: a new generation of protein database search programs. . Nucleic Acids Res 25:, 3389–3402 [CrossRef] [PubMed].
    [Google Scholar]
  2. Atlas R. M. . ( 1993; ). Handbook of Microbiological Media. Boca Raton, FL:: CRC Press;.
    [Google Scholar]
  3. Bagwell C. E. , Piceno Y. M. , Ashburne-Lucas A. , Lovell C. R. . ( 1998; ). Physiological diversity of the rhizosphere diazotroph assemblages of selected salt marsh grasses. . Appl Environ Microbiol 64:, 4276–4282.[PubMed]
    [Google Scholar]
  4. Benson D. A. , Boguski M. S. , Lipman D. J. , Ostell J. , Ouellette B. F. . ( 1998; ). GenBank. . Nucleic Acids Res 26:, 1–7. [CrossRef] [PubMed]
    [Google Scholar]
  5. Bowman J. P. , McMeekin T. A. . ( 2005; ). Order X. Alteromonadales ord. nov.. In Bergey’s Manual of Systematic Bacteriology, , 2nd edn., vol. 2B, p. 443. Edited by Brenner D. J. , Krieg N. R. , Staley J. T. , Garrity G. M. . . New York:: Springer;. [CrossRef]
    [Google Scholar]
  6. Boyle C. D. , Patriquin D. G. . ( 1981; ). Carbon metabolism of Spartina alterniflora Loisel in relation to that of associated nitrogen-fixing bacteria. . New Phytol 89:, 275–288. [CrossRef]
    [Google Scholar]
  7. Brown M. M. , Friez M. J. , Lovell C. R. . ( 2003; ). Expression of nifH genes by diazotrophic bacteria in the rhizosphere of short form Spartina alterniflora . . FEMS Microbiol Ecol 43:, 411–417 [CrossRef] [PubMed].
    [Google Scholar]
  8. Busse H.-J. , Denner E. B. M. , Lubitz W. . ( 1996; ). Classification and identification of bacteria: current approaches to an old problem. Overview of methods used in bacterial systematics. . J Biotechnol 47:, 3–38 [CrossRef] [PubMed].
    [Google Scholar]
  9. Chenna R. , Sugawara H. , Koike T. , Lopez R. , Gibson T. J. , Higgins D. G. , Thompson J. D. . ( 2003; ). Multiple sequence alignment with the clustal series of programs. . Nucleic Acids Res 31:, 3497–3500. [CrossRef] [PubMed].
    [Google Scholar]
  10. Clark W. A. . ( 1976; ). A simplified Leifson flagella stain. . J Clin Microbiol 3:, 632–634.[PubMed]
    [Google Scholar]
  11. Dame R. F. , Kenny P. D. . ( 1986; ). Variability of Spartina alterniflora primary production in the euhaline North Inlet Estuary. . Mar Ecol Prog Ser 32:, 71–80. [CrossRef]
    [Google Scholar]
  12. Elliott J. I. , Brewer J. M. . ( 1978; ). The inactivation of yeast enolase by 2,3-butanedione. . Arch Biochem Biophys 190:, 351–357 [CrossRef] [PubMed].
    [Google Scholar]
  13. Felsenstein J. . ( 1985; ). Confidence limits on phylogenies: an approach using the bootstrap. . Evolution 39:, 783–791. [CrossRef]
    [Google Scholar]
  14. Gandy E. L. , Yoch D. C. . ( 1988; ). Relationship between nitrogen-fixing sulfate reducers and fermenters in salt marsh sediments and roots of Spartina alterniflora . . Appl Environ Microbiol 54:, 2031–2036.[PubMed]
    [Google Scholar]
  15. Garland J. L. , Mills A. L. . ( 1991; ). Classification and characterization of heterotrophic microbial communities on the basis of patterns of community-level sole-carbon-source utilization. . Appl Environ Microbiol 57:, 2351–2359.[PubMed]
    [Google Scholar]
  16. Gerhardt P. , Murray R. G. E. , Costilow T. N. , Nester E. W. , Wood W. A. , Krieg N. R. , Phillips G. B. . ( 1981; ). Manual of Methods for General Bacteriology. Washington, DC:: American Society for Microbiology;.
    [Google Scholar]
  17. Golyshin P. N. , Chernikova T. N. , Abraham W. R. , Lünsdorf H. , Timmis K. N. , Yakimov M. M. . ( 2002; ). Oleiphilaceae fam. nov., to include Oleiphilus messinensis gen. nov., sp. nov., a novel marine bacterium that obligately utilizes hydrocarbons. . Int J Syst Evol Microbiol 52:, 901–911 [CrossRef] [PubMed].
    [Google Scholar]
  18. Gonzalez J. M. , Saiz-Jimenez C. . ( 2005; ). A simple fluorimetric method for the estimation of DNA-DNA relatedness between closely related microorganisms by thermal denaturation temperatures. . Extremophiles 9:, 75–79 [CrossRef] [PubMed].
    [Google Scholar]
  19. Hale M. G. , Moore L. D. , Griffin G. J. . ( 1978; ). Root exudates and exudation. . In Interactions between Non-pathogenic Soil Microorganisms and Plants, pp. 163–203. Edited by Dommergues Y. R. , Krupa S. V. . . New York:: Elsevier;.[CrossRef]
    [Google Scholar]
  20. Hanson R. B. . ( 1983; ). Nitrogen fixation activity (acetylene reduction) in the rhizosphere of salt marsh angiosperms, Georgia, USA. . Bot Mar 26:, 49–60. [CrossRef]
    [Google Scholar]
  21. Ivanova E. P. , Flavier S. , Christen R. . ( 2004; ). Phylogenetic relationships among marine Alteromonas-like proteobacteria: emended description of the family Alteromonadaceae and proposal of Pseudoalteromonadaceae fam. nov., Colwelliaceae fam. nov., Shewanellaceae fam. nov., Moritellaceae fam. nov., Ferrimonadaceae fam. nov., Idiomarinaceae fam. nov. and Psychromonadaceae fam. nov.. Int J Syst Evol Microbiol 54:, 1773–1788 [CrossRef] [PubMed].
    [Google Scholar]
  22. Kumar Y. , Goodfellow M. . ( 2008; ). Five new members of the Streptomyces violaceusniger 16S rRNA gene clade: Streptomyces castelarensis sp. nov., comb. nov., Streptomyces himastatinicus sp. nov., Streptomyces mordarskii sp. nov., Streptomyces rapamycinicus sp. nov. and Streptomyces ruanii sp. nov.. Int J Syst Evol Microbiol 58:, 1369–1378.[CrossRef]
    [Google Scholar]
  23. Lane D. J. . ( 1991; ). 16S/23S rRNA sequencing. . In Nucleic Acid Techniques in Bacterial Systematics, pp. 115–175. Edited by Stackebrandt E. , Goodfellow M. . . Chichester:: Wiley;.
    [Google Scholar]
  24. Lovell C. R. . ( 2002; ). Plant-microbe interactions in the marine environment. . In The Encyclopedia of Environmental Microbiology, vol. 5, pp. 2539–3544. Edited by Bitton G. . . New York:: Wiley;.
    [Google Scholar]
  25. Lovell C. R. , Piceno Y. M. , Quattro J. M. , Bagwell C. E. . ( 2000; ). Molecular analysis of diazotroph diversity in the rhizosphere of the smooth cordgrass, Spartina alterniflora . . Appl Environ Microbiol 66:, 3814–3822 [CrossRef] [PubMed].
    [Google Scholar]
  26. Lovell C. R. , Decker P. V. , Bagwell C. E. , Thompson S. , Matsui G. Y. . ( 2008; ). Analysis of a diverse assemblage of diazotrophic bacteria from Spartina alterniflora using DGGE and clone library screening. . J Microbiol Methods 73:, 160–171 [CrossRef] [PubMed].
    [Google Scholar]
  27. Ludwig W. , Schleifer K. H. . ( 1994; ). Bacterial phylogeny based on 16S and 23S rRNA sequence analysis. . FEMS Microbiol Rev 15:, 155–173 [CrossRef] [PubMed].
    [Google Scholar]
  28. Ludwig W. , Strunk O. , Klugbauer S. , Klugbauer N. , Weizenegger M. , Neumaier J. , Bachleitner M. , Schleifer K. H. . ( 1998; ). Bacterial phylogeny based on comparative sequence analysis. . Electrophoresis 19:, 554–568 [CrossRef] [PubMed].
    [Google Scholar]
  29. Marello T. A. , Bochner B. R. . ( 1989; ). BIOLOG References Manual: Metabolic Reactions of Gram-negative Species. Haywood, CA:: Biolog and Science Tech Publishers;.
    [Google Scholar]
  30. Mesbah M. , Whitman W. B. . ( 1989; ). Measurement of deoxyguanosine/thymidine ratios in complex mixtures by high-performance liquid chromatography for determination of the mole percentage guanine+cytosine of DNA. . J Chromatogr A 479:, 297–306 [CrossRef] [PubMed].
    [Google Scholar]
  31. Mesbah M. , Premachandran U. , Whitman W. B. . ( 1989; ). Precise measurement of the G+C content of deoxyribonucleic acid by high-performance liquid chromatography. . Int J Syst Bacteriol 39:, 159–167. [CrossRef]
    [Google Scholar]
  32. Morris J. T. , Haskin B. . ( 1990; ). A 5-year record of aerial primary production and stand characteristics of Spartina alterniflora . . Ecology 71:, 2209–2217. [CrossRef]
    [Google Scholar]
  33. Patriquin D. G. , McClung C. R. . ( 1978; ). Nitrogen accretion, and nature and possible significance of N2 fixation (acetylene reduction) in a Nova Scotian Spartina alterniflora stand. . Mar Biol 47:, 227–242. [CrossRef]
    [Google Scholar]
  34. Piceno Y. M. , Noble P. A. , Lovell C. R. . ( 1999; ). Spatial and temporal assessment of diazotroph assemblage composition in vegetated salt marsh sediments using denaturing gradient gel electrophoresis analysis. . Microb Ecol 38:, 157–167 [CrossRef] [PubMed].
    [Google Scholar]
  35. Steppe T. F. , Olson J. B. , Paerl H. W. , Litaker R. W. , Belnap J. . ( 1996; ). Consortial N2 fixation: a strategy for meeting nitrogen requirements of marine and terrestrial cyanobacterial mats. . FEMS Microbiol Ecol 21:, 149–156. [CrossRef]
    [Google Scholar]
  36. Tamura K. , Dudley J. , Nei M. , Kumar S. . ( 2007; ). mega4: molecular evolutionary genetics analysis (mega) software version 4.0. . Mol Biol Evol 24:, 1596–1599 [CrossRef] [PubMed].
    [Google Scholar]
  37. Thompson J. D. , Gibson T. J. , Plewniak F. , Jeanmougin F. , Higgins D. G. . ( 1997; ). The clustal_x windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. . Nucleic Acids Res 25:, 4876–4882 [CrossRef] [PubMed].
    [Google Scholar]
  38. Whiting G. J. , Morris J. T. . ( 1986; ). Nitrogen fixation (C2H2 reduction) in a salt marsh: its relationship to temperature and an evaluation of an in situ chamber technique. . Soil Biol Biochem 18:, 515–521. [CrossRef]
    [Google Scholar]
  39. Whiting G. J. , Gandy E. L. , Yoch D. C. . ( 1986; ). Tight coupling of root-associated nitrogen fixation and plant photosynthesis in the salt marsh grass Spartina alterniflora and carbon dioxide enhancement of nitrogenase activity. . Appl Environ Microbiol 52:, 108–113.[PubMed]
    [Google Scholar]
  40. Zehr J. P. , Capone D. G. . ( 1996; ). Problems and promises of assaying the genetic potential for nitrogen fixation in the marine environment. . Microb Ecol 32:, 263–281 [CrossRef] [PubMed].
    [Google Scholar]
  41. Zehr J. P. , Jenkins B. D. , Short S. M. , Steward G. F. . ( 2003; ). Nitrogenase gene diversity and microbial community structure: a cross-system comparison. . Environ Microbiol 5:, 539–554 [CrossRef] [PubMed].
    [Google Scholar]
  42. Zhou J.-Z. , Fries M. R. , Chee-Sanford J. C. , Tiedje J. M. . ( 1995; ). Phylogenetic analyses of a new group of denitrifiers capable of anaerobic growth of toluene and description of Azoarcus tolulyticus sp. nov.. Int J Syst Bacteriol 45:, 500–506 [CrossRef] [PubMed].
    [Google Scholar]
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Polar lipid analysis from strain S-G2-2 by TLC. DPG, Diphosphatidylglycerol; PE, phosphatidylethanolamine; PG, phosphatidylglycerol; PMME, phosphatidylmonomethylethanolamine; P1–P2, unidentified phospholipids; PN, unidentified aminophospholipid; AL1–AL2, unidentified aminolipids; L1, unidentified lipid.

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