1887

Abstract

Two bacterial strains were isolated from coal mine water in China. Isolates were facultatively anaerobic, Gram-stain-negative, rod-shaped, motile by means of a single polar flagellum, and they did not produce bacteriochlorophyll α. Cells grew in tryptic soy broth with 0–5.5 % (w/v) NaCl, at 4–55 °C and pH 3.5–10.5. Isolates were positive for catalase, oxidase, urease, Voges–Proskauer test, gelatin hydrolysis and H2S production. Analysis of 16S rRNA gene sequences indicated that the closest relatives of strains Q4.6 and Q2.11 were the type strains Labrenzia suaedae DSM 22153 (97.4 %), Pannonibacter phragmitetus DSM 14782 (96.9 and 97.0 %) and Pannonibacter indicus DSM 23407 (96.8 %). The genomic average nucleotide identity (ANI) value for Q4.6 and Q2.11 was 100 %; however, this value was less than 77.7 % for the type strains P. phragmitetus and P. indicus , and less than 74.0 % for the type strain L. suaedae . The cellular fatty acid profile of strains Q4.6 and Q2.11 consisted primarily of C18 : 1ω7c. The principal quinone of the isolates was Q-10. The polar lipid profile consisted of diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine and phosphatidyl choline. On the basis of phylogenetic analysis, genomic ANI analysis, DNA–DNA hybridization results, as well as phenotypic and chemotaxonomic data, strains Q4.6 and Q2.11 are assigned as a novel species within the genus Pannonibacter . The type strain is Pannonibacter carbonis Q4.6 (=CGMCC 1.15703=KCTC 52466).

Loading

Article metrics loading...

/content/journal/ijsem/10.1099/ijsem.0.002794
2018-04-25
2019-10-23
Loading full text...

Full text loading...

/deliver/fulltext/ijsem/68/6/2042.html?itemId=/content/journal/ijsem/10.1099/ijsem.0.002794&mimeType=html&fmt=ahah

References

  1. Borsodi AK, Micsinai A, Kovács G, Tóth E, Schumann P et al. Pannonibacter phragmitetus gen. nov., sp. nov., a novel alkalitolerant bacterium isolated from decomposing reed rhizomes in a Hungarian soda lake. Int J Syst Evol Microbiol 2003; 53: 555– 561 [CrossRef] [PubMed]
    [Google Scholar]
  2. Bandyopadhyay S, Schumann P, Das SK. Pannonibacter indica sp. nov., a highly arsenate-tolerant bacterium isolated from a hot spring in India. Arch Microbiol 2013; 195: 1– 8 [CrossRef] [PubMed]
    [Google Scholar]
  3. Holmes B, Segers P, Coenye T, Vancanneyt M, Vandamme P. Pannonibacter phragmitetus, described from a Hungarian soda lake in 2003, had been recognized several decades earlier from human blood cultures as Achromobacter groups B and E. Int J Syst Evol Microbiol 2006; 56: 2945– 2948 [CrossRef] [PubMed]
    [Google Scholar]
  4. Bandyopadhyay S, Das SK. Functional analysis of ars gene cluster of Pannonibacter indicus strain HT23T (DSM 23407T) and identification of a proline residue essential for arsenate reductase activity. Appl Microbiol Biotechnol 2016; 100: 3235– 3244 [CrossRef]
    [Google Scholar]
  5. Chai LY, Huang SH, Yang ZH, Peng B, Huang Y et al. Hexavalent chromium reduction by Pannonibacter phragmitetus BB isolated from soil under chromium-containing slag heap. J Environ Sci Health A Tox Hazard Subst Environ Eng 2009; 44: 615– 622 [CrossRef] [PubMed]
    [Google Scholar]
  6. Shi Y, Chai L, Yang Z, Jing Q, Chen R et al. Identification and hexavalent chromium reduction characteristics of Pannonibacter phragmitetus. Bioprocess Biosyst Eng 2012; 35: 843– 850 [CrossRef] [PubMed]
    [Google Scholar]
  7. Wang Y, Peng B, Yang Z, Tang C, Chen Y et al. Treatment of Cr(VI) contaminated water with Pannonibacter phragmitetus BB. Environ Earth Sci 2014; 71: 4333– 4339 [CrossRef]
    [Google Scholar]
  8. Wang Y, Yang Z, Peng B, Chai L, Wu B et al. Biotreatment of chromite ore processing residue by Pannonibacter phragmitetus BB. Environ Sci Pollut Res Int 2013; 20: 5593– 5602 [CrossRef]
    [Google Scholar]
  9. Zhang J, Wang Y, Zhou JT, Wang R, Goh S et al. Enhanced biodegradation of 4-aminobenzenesulfonate in membrane bioreactor by Pannonibacter sp. W1. Water Sci Technol 2011; 63: 2752– 2758 [CrossRef] [PubMed]
    [Google Scholar]
  10. Ray S, Prajapati V, Patel K, Trivedi U. Optimization and characterization of PHA from isolate Pannonibacter phragmitetus ERC8 using glycerol waste. Int J Biol Macromol 2016; 86: 741– 749 [CrossRef] [PubMed]
    [Google Scholar]
  11. Biebl H, Pukall R, Lünsdorf H, Schulz S, Allgaier M et al. Description of Labrenzia alexandrii gen. nov., sp. nov., a novel alphaproteobacterium containing bacteriochlorophyll a, and a proposal for reclassification of Stappia aggregata as Labrenzia aggregata comb. nov., of Stappia marina as Labrenzia marina comb. nov. and of Stappia alba as Labrenzia alba comb. nov., and emended descriptions of the genera Pannonibacter, Stappia and Roseibium, and of the species Roseibium denhamense and Roseibium hamelinense. Int J Syst Evol Microbiol 2007; 57: 1095– 1107 [CrossRef] [PubMed]
    [Google Scholar]
  12. Camacho M, Redondo-Gómez S, Rodríguez-Llorente I, Rohde M, Spröer C et al. Labrenzia salina sp. nov., isolated from the rhizosphere of the halophyte Arthrocnemum macrostachyum. Int J Syst Evol Microbiol 2016; 66: 5173– 5180 [CrossRef] [PubMed]
    [Google Scholar]
  13. Bibi F, Jeong JH, Chung EJ, Jeon CO, Chung YR. Labrenzia suaedae sp. nov., a marine bacterium isolated from a halophyte, and emended description of the genus Labrenzia. Int J Syst Evol Microbiol 2014; 64: 1116– 1122 [CrossRef] [PubMed]
    [Google Scholar]
  14. Tang Y-Q, Ji P, Lai G-L, Chi C-Q, Liu Z-S et al. Diverse microbial community from the coalbeds of the Ordos Basin, China. Int J Coal Geol 2012; 90-91: 21– 33 [CrossRef]
    [Google Scholar]
  15. Barnhart EP, de León KB, Ramsay BD, Cunningham AB, Fields MW. Investigation of coal-associated bacterial and archaeal populations from a diffusive microbial sampler (DMS). Int J Coal Geol 2013; 115: 64– 70 [CrossRef]
    [Google Scholar]
  16. Susilawati R, Esterle JS, Golding SD, Mares TE. Microbial methane potential for the south Sumatra basin coal: formation water screening and coal substrate bioavailability. Energy Procedia 2015; 65: 282– 291 [CrossRef]
    [Google Scholar]
  17. Küster E. Outline of a comparative study of criteria used in characterization of the Actinomycetes. Int Bull Bacteriol Nomencl Taxon 1959; 9: 97– 104 [CrossRef]
    [Google Scholar]
  18. Xi L, Qiao N, Zhang Z, Yan L, Li F et al. Sinorhodobacter hungdaonensis sp. nov. isolated from activated sludge collected from a municipal wastewater treatment plant. Antonie van Leeuwenhoek 2017; 110: 27– 32 [CrossRef] [PubMed]
    [Google Scholar]
  19. West M, Burdash NM, Freimuth F. Simplified silver-plating stain for flagella. J Clin Microbiol 1977; 6: 414– 419 [PubMed]
    [Google Scholar]
  20. Smibert RM, Krieg NR. Shenotypic characterization. In Gerhardt P, Murray RGE, Wood WA, Krieg NR. (editors) Methods for General and Molecular Bacteriology Washington, DC: American Society for Microbiology; 1994; pp. 607– 654
    [Google Scholar]
  21. Sorokin DY. Is there a limit for high-pH life?. Int J Syst Evol Microbiol 2005; 55: 1405– 1406 [CrossRef] [PubMed]
    [Google Scholar]
  22. Dong X, Cai M. Manual of Systematic and Determinative Bacteriology Beijing: Academic Press; 2001
    [Google Scholar]
  23. Tamaoka J. Analysis of bacterial menaquinone mixtures by reverse-phase high-performance liquid chromatography. Methods Enzymol 1986; 123: 251– 256 [PubMed] [Crossref]
    [Google Scholar]
  24. Collins MD, Goodfellow M, Minnikin DE, Alderson G. Menaquinone composition of mycolic acid-containing actinomycetes and some sporoactinomycetes. J Appl Bacteriol 1985; 58: 77– 86 [CrossRef] [PubMed]
    [Google Scholar]
  25. Collins MD, Pirouz T, Goodfellow M, Minnikin DE. Distribution of menaquinones in actinomycetes and corynebacteria. J Gen Microbiol 1977; 100: 221– 230 [CrossRef] [PubMed]
    [Google Scholar]
  26. Collins MD, Jones D. Lipids in the classification and identification of coryneform bacteria containing peptidoglycans based on 2, 4-diaminobutyric acid. J Appl Microbiol 1980; 48: 459– 470 [CrossRef]
    [Google Scholar]
  27. Minnikin DE, Collins MD, Goodfellow M. Fatty acid and polar lipid composition in the classification of Cellulomonas, Oerskovia and related taxa. J Appl Microbiol 1979; 47: 87– 95
    [Google Scholar]
  28. Sasser M. Identification of bacteria by gaschromatography of cellular fatty acids. Midi Technical Note Midi 1990
    [Google Scholar]
  29. Chun J, Goodfellow M. A phylogenetic analysis of the genus Nocardia with 16S rRNA gene sequences. Int J Syst Bacteriol 1995; 45: 240– 245 [CrossRef] [PubMed]
    [Google Scholar]
  30. Lane DJ. 16S/23S rRNA sequencing. In Stackebrandt E, Goodfellow M. (editors) Nucleic Acid Techniques in Bacterial Systematics New York, NY, USA: Wiley; 1991; pp. 115– 175
    [Google Scholar]
  31. Nagashima KV, Hiraishi A, Shimada K, Matsuura K. Horizontal transfer of genes coding for the photosynthetic reaction centers of purple bacteria. J Mol Evol 1997; 45: 131– 136 [CrossRef] [PubMed]
    [Google Scholar]
  32. Yoon SH, Ha SM, 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 [CrossRef] [PubMed]
    [Google Scholar]
  33. Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol 2016; 33: 1870 [CrossRef] [PubMed]
    [Google Scholar]
  34. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4: 406– 425 [CrossRef] [PubMed]
    [Google Scholar]
  35. Liu C, Han K, Lee DJ, Wang Q. Simultaneous biological removal of phenol, sulfide, and nitrate using expanded granular sludge bed reactor. Appl Microbiol Biotechnol 2016; 100: 4211– 4217 [CrossRef] [PubMed]
    [Google Scholar]
  36. Felsenstein J. Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 1981; 17: 368– 376 [CrossRef] [PubMed]
    [Google Scholar]
  37. Felsenstein J. Confidence limits on phylogenies: an approach using the bootstrap. Evolution 1985; 39: 783– 791 [CrossRef] [PubMed]
    [Google Scholar]
  38. Ezaki T, Hashimoto Y, Yabuuchi E. Fluorometric deoxyribonucleic acid-deoxyribonucleic acid hybridization in microdilution wells as an alternative to membrane filter hybridization in which radioisotopes are used to determine genetic relatedness among bacterial strains. Int J Syst Evol Microbiol 1989; 39: 224– 229 [CrossRef]
    [Google Scholar]
  39. Rong X, Huang Y. Taxonomic evaluation of the Streptomyces griseus clade using multilocus sequence analysis and DNA-DNA hybridization, with proposal to combine 29 species and three subspecies as 11 genomic species. Int J Syst Evol Microbiol 2010; 60: 696– 703 [CrossRef] [PubMed]
    [Google Scholar]
  40. Xi L, Zhang Z, Qiao N, Zhang Y, Li J et al. Complete genome sequence of the novel thermophilic polyhydroxyalkanoates producer Aneurinibacillus sp. XH2 isolated from Gudao oilfield in China. J Biotechnol 2016; 227: 54– 55 [CrossRef] [PubMed]
    [Google Scholar]
  41. Yoon SH, Sm H, Lim J, Kwon S, Chun J. A large-scale evaluation of algorithms to calculate average nucleotide identity. Anton Leeuw Int J G 2017; 1– 6
    [Google Scholar]
  42. 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 [CrossRef] [PubMed]
    [Google Scholar]
  43. Chun J, Rainey FA. Integrating genomics into the taxonomy and systematics of the Bacteria and Archaea. Int J Syst Evol Microbiol 2014; 64: 316– 324 [CrossRef] [PubMed]
    [Google Scholar]
  44. Wayne LG, Moore WEC, Stackebrandt E, Kandler O, Colwell RR et al. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Evol Microbiol 1987; 37: 463– 464 [CrossRef]
    [Google Scholar]
  45. Stackebrandt E, Goebel BM. Taxonomic note: A Place for DNA-DNA Reassociation and 16S rRNA sequence snalysis in the present species definition in bacteriology. Inte J Syst Evol Microbiol 1994; 44: 846– 849 [CrossRef]
    [Google Scholar]
http://instance.metastore.ingenta.com/content/journal/ijsem/10.1099/ijsem.0.002794
Loading
/content/journal/ijsem/10.1099/ijsem.0.002794
Loading

Data & Media loading...

Supplements

Supplementary File 1

PDF

Most Cited This Month

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