Erratum to: Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China (Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology (2014) 105, (501-510) DOI: 10.1007/s10482-013-0102-3);Bacillus bingmayongensis sp. nov., isolated from the pit soil of Emperor Qin's Terra-cotta warriors in China

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 105, Issue 3, 2014, Pages 501-510

  Liu, Bo ^a   Liu, Guo Hong ^a   Hu, Gui Ping ^a,b   Cetin, Sengonca ^c   Lin, Nai Quan ^b   Tang, Jian Yang ^a   Tang, Wei Qi ^b   Lin, Ying Zhi ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b FUJIAN AGRICULTURE AND FORESTRY UNIVERSITY   (China)

^c UNIVERSITY OF BONN   (Germany)

Author keywords

Average nucleotide identity; Bacillus bingmayongensis; Emperor Qin's Terra cotta Warriors; Polyphasic taxonomy

Indexed keywords

11 METHYLDODECANOIC ACID; 13 METHYLTRIDECANOIC ACID; 15 METHYLHEXACANOIC ACID; CATALASE; DIAMINOPIMELIC ACID; FATTY ACID; HOMARYLAMINE; MENAQUINONE; METHYL 12 METHYLTETRADECANOATE; METHYL HEPTADECANOATE; METHYL PENTADECANOATE; METHYL TRIDECANOATE; MK 4; MK 5; OXIDOREDUCTASE; PALMITIC ACID; PALMITIC ACID METHYL ESTER; PEPTIDOGLYCAN; UNCLASSIFIED DRUG; UNSATURATED FATTY ACID;

AEROBIC BACTERIUM; ARTICLE; BACILLUS; BACILLUS BINGMAYONGENSIS; BACILLUS BINGMAYONGENSIS STRAIN FJAT 13831; BACILLUS PSEUDOMYCOIDES STRAIN DSM 12442; BACTERIAL CELL WALL; BACTERIAL STRAIN; BACTERIUM DETECTION; BACTERIUM ISOLATE; BACTERIUM ISOLATION; CHINA; COMPARATIVE GENOMIC HYBRIDIZATION; COMPARATIVE STUDY; CORRELATION ANALYSIS; DNA DNA HYBRIDIZATION; EMPEROR QIN TERA COTTA WARRIOR; ENDOSPORE-FORMING RODS AND COCCI; FATTY ACID ANALYSIS; GENE SEQUENCE; GENETIC SIMILARITY; GRAVEYARD SOIL; HISTORY; MICROBIAL ACTIVITY; MORPHOLOGICAL TRAIT; NONHUMAN; NUCLEIC ACID ANALYSIS; NUCLEOTIDE SEQUENCE; PHENOTYPE; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SOIL; TAXONOMIC IDENTIFICATION;

BACILLUS PSEUDOMYCOIDES;

BACILLUS; BACTERIAL TYPING TECHNIQUES; FATTY ACIDS; GENES, BACTERIAL; PHENOTYPE; PHYLOGENY; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY;

EID: 84894237927     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-014-0150-3     Document Type: Erratum

References (55)

1. Ahmed I, Yokota A, Yamazoe A, Fujiwara T (2007) Proposal of Lysinibacillus boronitolerans gen. nov. sp. nov., and transfer of B. fusiformis to L. fusiformis comb. nov. and Bacillus sphaericus to L. sphaericus comb. nov. Int J Syst Evol Microbiol 57:1117-1125
2. Atlas RM (1993) Handbook of microbiological media, 2nd edn. In: Parks LC (ed). CRC Press, Boca Raton
3. Baik KS, Lim CH, Park SC, Kim EM, Rhee MS, Seong CN (2010) Bacillus rigui sp. nov., isolated from wetland fresh water. Int J Syst Evol Microbiol 60:2204-2209
4. Bhandari V, Ahmod NZ, Shah HN, Gupta RS (2013) Molecular signatures for Bacillus species: demarcation of the B. subtilis and B. cereus clades in molecular terms and proposal to limit the placement of new species into the genus Bacillus. Int J Syst Evol Microbiol 63:2712-2726
5. Chen YG, Hao DF, Chen QH, Zhang YQ, Liu JB, He JW, Tang SK, Li WJ (2011) Bacillus hunanensis sp. nov., a slightly halophilic bacterium isolated from non-saline forest soil. Antonie Van Leeuwenhoek 99:481-488
6. Cohn F (1872) Untersuchungen über Bacterien. Beitrage zur Biologie der Pflanzen 1:127-244
7. De Ley J, Cattoir H, Cattoir R, Reynaert A (1970) The quantitative measurement of DNA hybridization from renaturation rates. Eur J Biochem 12:133-142
8. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evol 40:783-791
9. Gatson JW, Benz BF, Chandrasekaran C, Satomi M, Venkateswaran K, Hart ME (2006) Bacillus tequilensis sp. nov., isolated from a 2000-year-old Mexican shaft-tomb, is closely related to B. subtilis. Int J Syst Evol Microbiol 56:1475-1484
10. Gonzalez JM, 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
11. Goris J, Konstantinidis KT, Klappenbach JA, Coenye T, Vandamme P, Tiedje JM (2007) DNA-DNA hybridization values and their relationship to whole-genome sequence similarities. Int J Syst Evol Microbiol 57:81-91
12. Gregersen T (1978) Rapid method for distinction of Gram-negative from Gram-positive bacteria. Eur J Appl Microbiol Biotechnol 5:123-127
13. Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comp Appl Biosci 3:8275-8282
14. Jukes TH, Cantor CR (1969) Evolution of protein molecules. In: Munro HN (ed) Mammalian protein metabolism, vol 3. Academic Press, New York, pp 21-132
15. Jung MY, Kim JS, Paek WK, Lim J, Lee H, Kim PI, Ma JY, Kim W, Chang YH (2011) Bacillus manliponensis sp. nov., a new member of the B. cereus group isolated from foreshore tidal flat sediment. J Microbiol 49:1027-1032
16. Kämpfer P, Blasczyk K, Auling G (1994) Characterization of Aeromonas genomic species by using quinone, polyamine, and fatty acid patterns. Can J Microbiol 40:844-850
17. Kaneda T (1977) Fatty acids of the genus Bacillus: an example of branched-chain preference. Bacteriol Rev 41:391-418
18. Kim OS, Cho YJ, Lee K, Yoon SH, Na H, Kim M, Park SC, Jeon YS, Lee JH, Yi H, Won S, Chun J (2012) Introducing EzTaxon-e: a prokaryotic 16S rRNA gene sequence database with phylotypes that represent uncultured species. Int J Syst Evol Microbiol 62:716-721
19. Konstantinidis KT, Tiedje JM (2005a) Genomic insights that advance the species definition for prokaryotes. Proc Natl Acad Sci USA 102:2567-2572
20. Konstantinidis KT, Tiedje JM (2005b) Towards a genome based taxonomy for prokaryotes. J Bacteriol 187:6258-6264
21. La Duc MT, Satomi M, Agata N, Venkateswaran K (2004a) gyrB as a phylogenetic discriminator for members of the Bacillus anthracis-cereus- thuringiensis group. J Microbiol Methods 56:383-394
22. La Duc MT, Satomi M, Venkateswaran K (2004b) Bacillus odysseyi sp. nov., a round-spore-forming Bacillus isolated from the Mars Odyssey spacecraft. Int J Syst Evol Microbiol 54:195-201
23. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, Thompson JD, Gibson TJ, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23(21):2947-2948
24. Liu B, Liu GH, Lin NQ, Tang JY (2012a) Bacillus identification and phylogenetic analysis, isolated from the 1st pit soil of Emperor Qin's Terracotta Warrior. Fujian J Agric Sci 27:563-573
25. Liu GH, Liu B, Lin NQ, Tang WQ, Tang JY, Lin YZ (2012b) Genome sequence of the aerobic bacterium Bacillus sp. strain FJAT-13831. J Bacteriol 194:6633
26. Logan NA, Berkeley RCW (1984) Identification of Bacillus strains using the API system. J Gen Microbiol 130:1871-1882
27. Nazina TN, Lebedeva EV, Poltaraus AB, Tourova TP, Grigoryan AA, Sokolova DSH, Lysenko AM, Osipov GA (2004) Geobacillus gargensis sp. nov., a novel thermophile from a hot spring, and the reclassification of Bacillus vulcani as Geobacillus vulcani comb. nov. Int J Syst Evol Microbiol 54:2019-2024
28. Owen RJ, Hill LR (1979) The estimation of base compositions, base pairing and genome size of bacterial deoxyribonucleic acids. In: Skinner FA, Lovelock DW (eds) Identification methods for microbiologists (Society for Applied Bacteriology Technical Series no. 14), 2nd edn. Academic Press, London, pp 277-296
29. Priest FG (1993) Systematics and ecology of Bacillus. In: Sonenshein AL, Hoch JA, Losick R (eds) Bacillus subtilis and other Gram-positive bacteria - Biochemistry, physiology, and molecular genetics. ASM press, American Society for Microbiology, Washington. ISBN 1-55581-053-5
30. Priest FG, Goodfellow M, Todd C (1988) A numerical classification of the genus Bacillus. J Gen Microbiol 134:1847-1882
31. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406-425
32. Sambrook J, Fritschi EF, Maniatis T (1989) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory Press, New York
33. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids. In: Klement S, Rudolf K, Sands D (eds) Methods in phytobacteriology. Akademiai Kiado, Budapest, pp 199-204
34. Satomi M, Kimura B, Hamada T, Harayama S, Fujii T (2002) Phylogenetic study of the genus Oceanospirillum based on 16S rRNA and gyrB genes: emended description of the genus Oceanospirillum, description of Pseudospirillum gen. nov., Oceanobacter gen. nov. and Terasakiella gen. nov. and transfer of Oceanospirillum jannaschii and Pseudomonas stanieri to Marinobacterium as Marinobacterium jannaschii comb. nov. and Marinobacterium stanieri comb. nov. Int J Syst Evol Microbiol 52:739-747
35. Satomi M, Oikawa H, Yano Y (2003) Shewanella marinintestina sp. nov., Shewanella schlegeliana sp. nov. and Shewanella sairae sp. nov., novel eicosapentaenoic acid-producing marine bacteria isolated from sea-animal intestines. Int J Syst Evol Microbiol 53:491-499
36. Satomi M, Kimura B, Hayashi M, Okuzumi M, Fujii T (2004) Marinospirillum insulare sp. nov., a novel halophilic helical bacterium isolated from kusaya gravy. Int J Syst Evol Microbiol 54:163-167
37. Satomi M, La Duc MT, Venkateswaran K (2006) Bacillus safensis sp. nov., isolated from spacecraft and assembly facility surfaces. Int J Syst Evol Microbiol 56:1735-1740
38. Schleifer KH, Kandler O (1972) Peptidoglycan types of bacterial cell walls and their taxonomic implications. Bacteriol Rev 36:407-477
39. Smibert RM, Krieg NR (1994) Phenotypic characterization. In: Gerhardt P, Murray RGE, Wood WA, Krieg NR (eds) Methods for general and molecular bacteriology. American Society for Microbiology, Washington, pp 607-654
40. Sorokin A, Candelon B, Guilloux K, Galleron N, Wackerow-Kouzova N, Ehrlich SD, Bourguet D, Sanchis V (2006) Multiple-locus sequence typing analysis of B. cereus and B. thuringiensis reveals separate clustering and a distinct population structure of psychrotrophic strains. Appl Environ Microbiol 72:1569-1578
41. Stackebrandt E, Ebers J (2006) Taxonomic parameters revisited: tarnished gold standards. Microbiol Today 33:152-155
42. Stackebrandt E, Goebel BM (1994) Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. Int J Syst Bacteriol 44:846-849
43. Stackebrandt E, Liesack W (1993) Nucleic acids and classification. In: Goodfellow M, O'Donnell AG (eds) Handbook of new bacterial systematics. Academic Press, London, pp 152-189
44. Takami H (2007) Genomic diversity of Bacillus-related species. Nova Science Publisher, New York. ISBN 978-1 - 60456-396-2
45. Talavera G, Castresana J (2007) Improvement of phylogenies after removing divergent and ambiguously aligned blocks from protein sequence alignments. Syst Biol 56(4):564-577
46. Tamura K, Nei M, Kumar S (2004) Prospects for inferring very large phylogenies by using the neighbor-joining method. PNAS 101:11030-11035
47. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739
48. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25:4876-4882
49. Vanlaere E, Baldwin A, Gevers D, Henry D, De Brandt E, LiPuma JJ, Mahenthiralingam E, Speert DP, Dowson C, Vandamme P (2009) Taxon K, a complex within the Burkholderia cepacia complex, comprises at least two novel species, Burkholderia contaminans sp. nov. and Burkholderia lata sp. nov. Int J Syst Evol Microbiol 59:102-111
50. Venkateswaran K, Dohmoto N, Harayama S (1998) Cloning and nucleotide sequence of the gyrB gene of Vibrio parahaemolyticus and its application in detection of this pathogen in shrimp. Appl Environ Microbiol 64:681-687
51. Venkateswaran K, Moser DP, Dollhopf ME, Lies DP, Saffarini DA, MacGregor BJ, Ringelberg DB, White DC, Nishijima M (1999) Polyphasic taxonomy of the genus Shewanella and description of Shewanella oneidensis sp. nov. Int J Syst Bacteriol 49:705-724
52. Wang LT, Lee FL, Tai CJ, Kasai H (2007) Comparison of gyrB gene sequences, 16S rRNA gene sequences and DNA-DNA hybridization in the B. subtilis group. Int J Syst Bacteriol 57:1846-1850
53. Wayne LG, Brenner DJ, Colwell RR, Grimont PAD, Kandler O, Krichevsky MI, Moore LH, Moore WEC, Murray RGE (1987) International committee on systematic bacteriology. Report of the ad hoc committee on reconciliation of approaches to bacterial systematics. Int J Syst Bacteriol 37: 463-464
54. Yamamoto S, Harayama S (1995) PCR amplification and direct sequencing of gyrB gene with universal primers and their application to the detection and taxonomic analysis of Pseudomonas putida strains. Appl Environ Microbiol 61:1104-1109
55. Zhang L, Wu GL, Wang Y, Dai J, Fang CX (2011) Bacillus deserti sp. nov., a novel bacterium isolated from the desert of Xinjiang, China. Antonie Van Leeuwenhoek 99:221-229