Aquincola amnicola sp. nov., isolated from a freshwater river

Archives of Microbiology

Volumn 200, Issue 5, 2018, Pages 811-817

  Chen, Wen Ming ^a   Chen, Yi Ling ^a   Li, Yi Shu ^a   Sheu, Shih Yi ^a  

^a NATIONAL KAOHSIUNG UNIVERSITY OF APPLIED SCIENCES   (Taiwan)

Author keywords

Aquincola amnicola sp. nov; Betaproteobacteria; Polyphasic taxonomy; Rubrivivax Roseateles Leptothrix Ideonella Aquabacterium

Indexed keywords

CARDIOLIPIN; FATTY ACID; FRESH WATER; GENOMIC DNA; LIPID; PHOSPHATIDYLETHANOLAMINE; PHOSPHATIDYLGLYCEROL; QUINONE DERIVATIVE; BACTERIAL DNA; RNA 16S;

AQUINCOLA AMNICOLA; ARTICLE; BACTERIAL STRAIN; BETAPROTEOBACTERIA; FLAGELLUM; LEPTOTHRIX; NONHUMAN; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; RIVER; SEQUENCE ANALYSIS; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; MICROBIOLOGY; MOLECULAR TYPING; TAIWAN;

BASE COMPOSITION; BETAPROTEOBACTERIA; DNA, BACTERIAL; MOLECULAR TYPING; PHYLOGENY; RIVERS; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; TAIWAN; WATER MICROBIOLOGY;

EID: 85041913671     PISSN: 03028933     EISSN: 1432072X     Source Type: Journal    
DOI: 10.1007/s00203-018-1492-4     Document Type: Article

References (33)

1. Anzai Y, Kudo Y, Oyaizu H (1997) The phylogeny of genera Chryseomonas, Flavimonas, and Pseudomonas supports synonymy of these three genera. Int J Syst Bacteriol 47:249–251
2. Beveridge TJ, Lawrence JR, Murray RGE (2007) Sampling and staining for light microscopy. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology, Washington, DC, pp 19–33
3. Bowman JP (2000) Description of Cellulophaga algicola sp. nov., isolated from the surfaces of Antarctic algae, and reclassification of Cytophaga uliginosa (ZoBell and Upham 1944) Reichenbach 1989 as Cellulophaga uliginosa comb. nov. Int J Syst Evol Microbiol 50:1861–1868
4. Breznak JA, Costilow RN (2007) Physicochemical factors in growth. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology. Washington, DC, pp 309–329
5. Chen WM, Laevens S, Lee TM, Coenye T, de Vos P, Mergeay M, Vandamme P (2001) Ralstonia taiwanensis sp. nov., isolated from root nodules of Mimosa species and sputum of a cystic fibrosis patient. Int J Syst Evol Microbiol 51:1729–1735
6. Cole JR, Wang Q, Cardenas E, Fish J, Chai B, Farris RJ, Kulam-Syed-Mohideen AS, McGarrell DM, Marsh T, Garrity GM, Tiedje JM (2009) The Ribosomal Database Project: improved alignments and new tools for rRNA analysis. Nucleic Acids Res 37(Database issue):D141–D145
7. Collins MD (1994) Isoprenoid quinones. In: Goodfellow M, O’Donnell G (eds) A chemical methods in prokaryotic systematics. Wiley, Chichester, pp 265–309
8. Embley TM, Wait R (1994) Structural lipids of eubacteria. In: Goodfellow M, O’Donnell AG (eds) Chemical methods in prokaryotic systematics. Wiley, Chichester, pp 121–161
9. Ezaki T, Hashimoto Y, Yabuuchi E (1989) Fluorometric DNA–DNA 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 Bacteriol 39:224–229
10. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
11. Felsenstein J (1993) PHYLIP (phylogeny inference package), version 3.5c. Distributed by the author. Department of Genome Sciences, University of Washington, Seattle
12. Hall TA (1999) BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 41:95–98
13. Kim M, Oh HS, Park SC, Chun J (2014) Towards a taxonomic coherence between average nucleotide identity and 16S rRNA gene sequence similarity for species demarcation of prokaryotes. Int J Syst Evol Microbiol 64:346–351
14. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
15. Kluge AG, Farris FS (1969) Quantitative phyletics and the evolution of anurans. Syst Zool 18:1–32
16. Kumar S, Stecher G, Tamura K (2016) MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol 33:1870–1874
17. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, other authors (2007) Clustal W and clustal X version 2.0. Bioinformatics 23:2947–2948
18. Lechner U, Brodkorb D, Geyer R, Hause G, Hartig C, Auling G, Fayolle-Guichard F, Piveteau P, Muller RH, Rohwerder T (2007) Aquincola tertiaricarbonis gen. nov., sp. nov., a tertiary butyl moiety-degrading bacterium. Int J Syst Evol Microbiol 57:1295–1303
19. Mesbah M, Premachandran U, Whitman WB (1989) Precise measurement of the G + C content of deoxyribonucleic acid by high-performance liquid chromatography. Int J Syst Bacteriol 39:159–167
20. Nokhal TH, Schlegel HG (1983) Taxonomic study of Paracoccus denitrificans. Int J Syst Bacteriol 33:26–37
21. Piveteau P, Fayolle F, Vandecasteele JP, Monot F (2001) Biodegradation of tert-butyl alcohol and related xenobiotics by a methylotrophic bacterial isolate. Appl Microbiol Biotechnol 55:369–373
22. Powers EM (1995) Efficacy of the Ryu nonstaining KOH technique for rapidly determining gram reactions of food-borne and waterborne bacteria and yeasts. Appl Environ Microbiol 61:3756–3758
23. Rzhetsky A, Nei M (1993) Theoretical foundation of the minimum-evolution method of phylogenetic inference. Mol Biol Evol 10:1073–1095
24. Saitou N, Nei M (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425
25. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. MIDI Inc, Newark
26. Schlegel HG, Lafferty R, Krauss I (1970) The isolation of mutants not accumulating poly-β-hydroxybutyric acid. Arch Mikrobiol 71:283–294
27. Spiekermann P, Rehm BHA, Kalscheuer R, Baumeister D, Steinbüchel A (1999) A sensitive, viable-colony staining method using nile red for direct screening of bacteria that accumulate polyhydroxyalkanoic acids and other lipid storage compounds. Arch Microbiol 171:73–80
28. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152–155
29. Tindall BJ, Sikorski J, Smibert RA, Krieg NR (2007) Phenotypic characterization and the principles of comparative systematics. In: Reddy CA, Beveridge TJ, Breznak JA, Marzluf GA, Schmidt TM, Snyder LR (eds) Methods for general and molecular bacteriology, 3rd edn. American Society for Microbiology. Washington, DC, pp 330–393
30. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O (1987) Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37:463–464
31. Weisburg WG, Burns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
32. Wen CM, Tseng CS, Cheng CY, Li YK (2002) Purification, characterization and cloning of a chitinase from Bacillus sp. NCTU2. Biotechnol Appl Biochem 35:213–219
33. Yoon SH, Ha SM, Kwon S, Lim J, Kim Y, Seo H, Chun J (2017) Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies. Int J Syst Evol Microbiol 67:1613–1617