Paenibacillus yonginensis sp. nov., a potential plant growth promoting bacterium isolated from humus soil of Yongin forest

Antonie van Leeuwenhoek, International Journal of General and Molecular Microbiology

Volumn 106, Issue 5, 2014, Pages 935-945

  Sukweenadhi, Johan ^a,c   Kim, Yeon Ju ^a   Lee, Kwang Je ^a   Koh, Sung Cheol ^b   Hoang, Van An ^a   Nguyen, Ngoc Lan ^a   Yang, Deok Chun ^a  

^a Kyung Hee University   (South Korea)

^b Korea Maritime University   (South Korea)

^c UNIVERSITY OF SURABAYA   (Indonesia)

Author keywords

Gram staining positive; Paenibacillus yonginensis; Plant growth promoting

Indexed keywords

ALANINE; AMINOPHOSPHOLIPID; DIAMINOPIMELIC ACID; FATTY ACID; GALACTOSE; GLUTAMIC ACID; INDOLEACETIC ACID; MENAQUINONE; PEPTIDOGLYCAN; PHOSPHATE; PHOSPHATIDYLETHANOLAMINE; RIBOSE; SIDEROPHORE; SODIUM CHLORIDE; SPERMIDINE; TRYPTOPHAN; XYLOSE; BACTERIAL DNA; CARBOHYDRATE; FARNOQUINONE; PHOSPHOLIPID; POLYAMINE; RIBOSOME DNA; RNA 16S;

ARTICLE; BACTERIAL CELL WALL; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM ISOLATE; CHEMOTAXONOMY; CONTROLLED STUDY; DNA CONTENT; FOREST; NONHUMAN; NUCLEOTIDE SEQUENCE; PAENIBACILLUS; PAENIBACILLUS BARENGOLTZII; PAENIBACILLUS PHOENICIS; PAENIBACILLUS TIMONENSIS; PAENIBACILLUS YONGINENSIS; PHYLOGENETIC TREE; SOIL; SOUTH KOREA; AEROBIC METABOLISM; BACTERIUM IDENTIFICATION; CHEMISTRY; CLASSIFICATION; CLUSTER ANALYSIS; DNA BASE COMPOSITION; DNA SEQUENCE; GENETICS; ISOLATION AND PURIFICATION; KOREA; LOCOMOTION; METABOLISM; MICROBIOLOGY; MOLECULAR GENETICS; PH; PHYLOGENY; PHYSIOLOGY; TEMPERATURE;

BACTERIA (MICROORGANISMS); PAENIBACILLUS;

AEROBIOSIS; BACTERIAL TYPING TECHNIQUES; BASE COMPOSITION; CARBOHYDRATES; CLUSTER ANALYSIS; DIAMINOPIMELIC ACID; DNA, BACTERIAL; DNA, RIBOSOMAL; FATTY ACIDS; FORESTS; HYDROGEN-ION CONCENTRATION; KOREA; LOCOMOTION; MOLECULAR SEQUENCE DATA; PAENIBACILLUS; PEPTIDOGLYCAN; PHOSPHOLIPIDS; PHYLOGENY; POLYAMINES; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SODIUM CHLORIDE; SOIL MICROBIOLOGY; TEMPERATURE; VITAMIN K 2;

EID: 84909990347     PISSN: 00036072     EISSN: 15729699     Source Type: Journal    
DOI: 10.1007/s10482-014-0263-8     Document Type: Article

References (51)

1. Ash C, Farrow JAE, Wallbanks S, Collins MD (1991) Phylogenetic heterogeneity of the genus Bacillus as revealed by comparative analysis of small-subunit-ribosomal RNA sequences. Lett Appl Microbiol 13:202–206
2. Bauer AW, Kirby WMM, Sherris JC, Turck M (1966) Antibiotic susceptibility testing by a standardized single disk method. Am J Clin Pathol 45:493–496
3. Benardini JN, Vaishampayan PA, Schwendner P, Swanner E, Fukui Y, Osman S, Satomi M, Venkateswaran K (2011) Paenibacillus phoenicis sp. nov., isolated from the Phoenix Lander assembly facility and a subsurface molybdenum mine. Int J Syst Evol Microbiol 61:1338–1343
4. Beneduzi A, Costa PB, Parma M, Melo IS, Bodanese-Zanettini MH, Passaglia LM (2010) Paenibacillus riograndensis sp. nov., a nitrogen-fixing species isolated from the rhizosphere of Triticum aestivum. Int J Syst Evol Microbiol 60:128–133
5. Carro L, Flores-Félix JD, Cerda-Castillo E, Ramírez-Bahena MH, Igual JM, Tejedor C, Velázquez E, Peix A (2013) Paenibacillus endophyticus sp. nov., isolated from nodules of Cicer arietinum. Int J Syst Evol Microbiol 63:4433–4438
6. Collins MD (1985) Isoprenoid quinone analyses in bacterial classification and identification. In: Goodfellow M, Minnikin DE (eds) Chemical methods in bacterial systematics. Academic Press, London, pp 267–287
7. Cowan ST, Steel KJ (1974) Manual for the identification of medical bacteria, 3rd edn. Cambridge University Press, Cambridge
8. Dsouza M, Taylor MW, Ryan J, MacKenzie A, Lagutin K, Anderson RF, Turner SJ, Aislabie J (2014) Paenibacillus darwinianus sp. nov., isolated from gamma-irradiated Antarctic soil. Int J Syst Evol Microbiol 64:1406–1411
9. Felsenstein J (1981) Evolutionary trees from DNA sequences: a maximum likelihood approach. J Mol Evol 17:368–376
10. Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
11. Fitch WM (1971) Toward defining the course of evolution: minimum change for a specific tree topology. Syst Zool 20:406–416
12. Glickmann E, Dessaux Y (1995) A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Environ Microbiol 61:793–796
13. Gomori G (1955) Preparation of buffers for use in enzyme studies. In: Colowick SP, Kaplan NO (eds) Methods in enzymology. Academic Press, New York, pp 138–146
14. 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
15. Hayat R, Ali S, Amara U, Khalid R, Ahmed I (2010) Soil beneficial bacteria and their role in plant growth promotion: a review. Ann Microbiol 60:579–598
16. Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 1:36 (Web Server issue):W5-9. doi: 10.1093/nar/gkn201
17. Kim MK, Im WT, Ohta H, Lee M, Lee ST (2005) Sphingopyxisgranuli sp. nov., a ß-glucosidase-producing bacterium in the family Sphingomonadaceae in α-4 subclass of the Proteobacteria. J Microbiol 43:152–157
18. Kim OS, Cho YJ, Lee K, Yoon SH, Kim M, Na H, 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. Kimura M (1983) The neutral theory of molecular evolution. Cambridge University Press, Cambridge
20. Lane DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt E, Goodfellow M (eds) Nucleic acid techniques in bacterial systematics. Wiley, Chichester, pp 115–176
21. Logan NA, Berge O, Bishop AH, Busse HJ, De Vos P, Fritze D, Heyndrickx M, Kämpfer P, Rabinovitch L, Salkinoja-Salonen MS, Seldin L, Ventosa A (2009) Proposed minimal standards for describing new taxa of aerobic, endospore-forming bacteria. Int J Syst Evol Microbiol 59:2114–2121
22. 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
23. Minnikin DE, ODonnell AG, Goodfellow M, Alderson G, Athalye M, Schaal A, Parlett JH (1984) An integrated procedure for the extraction of bacterial isoprenoid quinones and polar lipids. J Microbiol Methods 2:233–241
24. Montes MJ, Mercade E, Bozal N, Guinea J (2004) Paenibacillus antarcticus sp. nov., a novel psychrotolerant organism from the Antarctic environment. Int J Syst Evol Microbiol 54:1521–1526
25. Osman S, Satomi M, Venkateswaran K (2006) Paenibacillus pasadenensis sp. nov. and Paenibacillus barengoltzii sp. nov., isolated from a spacecraft assembly facility. Int J Syst Evol Microbiol 56:1509–1514
26. Park MJ, Kim HB, An DS, Yang HC, Oh ST, Chung HJ, Yang DC (2007) Paenibacillus soli sp. nov., a xylanolytic bacterium isolated from soil. Int J Syst Evol Microbiol 57:146–150
27. Park DS, Jeong WJ, Lee KH, Oh HW, Kim BC, Bae KS, Park HY (2009) Paenibacillus pectinilyticus sp. nov., isolated from the gut of Diestrammena apicalis. Int J Syst Evol Microbiol 59:1342–1347
28. Pikovskaya RI (1948) Mobilization of phosphorus in soil in connection with vital activity of some microbial species. Mikrobiologya 17:362–370
29. Priest FG (2009) Genus I. Paenibacillus. In: DeVos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds) Bergey’s manual of systematic bacteriology, vol 2, 2nd edn. Springer, New York, pp 269–296
30. Saha P, Mondal AK, Mayilraj S, Krishnamurthi S, Bhattacharya A, Chakrabarti T (2005) Paenibacillus assamensis sp. nov., a novel bacterium isolated from a warm spring in Assam, India. Int J Syst Evol Microbiol 55:2577–2581
31. Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
32. Sánchez MM, Fritze D, Blanco A, Spröer C, Tindall BJ, Schumann P, Kroppenstedt RM, Diaz P, Pastor FI (2005) Paenibacillus barcinonensis sp. nov., a xylanase-producing bacterium isolated from a rice field in the Ebro River delta. Int J Syst Evol Microbiol 55:935–939
33. Sasser M (1990) Identification of bacteria by gas chromatography of cellular fatty acids, MIDI Technical Note 101. DE: MIDI Inc, Newark
34. Scherer PA, Kneifel H (1983) Distribution of polyamines in methanogenic bacteria. J Bacteriol 154:1315–1322
35. Schleifer KH (1985) Analysis of the chemical composition and primary structure of murein. Methods Microbiol 18:123–156
36. Schumann P (2011) Peptidoglycan structure. Methods Microbiol 38:101–129
37. Schwyn B, Neilands JB (1987) Universal chemical assay for the detection and determination of siderophores. Anal Biochem 160:47–56
38. Shida O, Takagi H, Kadowaki K, Nakamura LK, Komagata K (1997) Transfer of Bacillus alginolyticus, Bacillus chondroitinus, Bacillus curdlanolyticus, Bacillus glucanolyticus, Bacillus kobensis, and Bacillus thiaminolyticus to the genus Paenibacillus and emended description of the genus Paenibacillus. Int J Syst Bacteriol 47:289–298
39. Shokri D, Emtiazi G (2010) Indole-3-acetic acid (IAA) production in symbiotic and non-symbiotic nitrogen-fixing bacteria and its optimization by Taguchi design. Curr Microbiol 61:217–225
40. Skerman VBD (1967) A guide to the identification of the genera of bacteria, 2nd edn. Williams and Wilkins, Baltimore
41. Staneck JL, Roberts GD (1974) Simplified approach to identification of aerobic actinomycetes by thin-layer chromatography. Appl Microbiol 28:226–231
42. Taibi G, Schiavo MR, Gueli MC, Calanni Rindina P, Muratore R, Nicotra CMA (2000) Rapid and simultaneous high-performance liquid chromatography assay of polyamines and monoacetylpolyamines in biological specimens. J Chromatogr B 745:431–437
43. Tamura K, Stecher G, Peterson D, Filipski A, Kumar S (2013) MEGA6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol 30:2725–2729
44. 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
45. Valverde A, Peix A, Rivas R, Velázquez E, Salazar S, Santa-Regina I, Rodríguez-Barrueco C, Igual JM (2008) Paenibacillus castaneae sp. nov., isolated from the phyllosphere of Castanea sativa Miller. Int J Syst Evol Microbiol 58:2560–2564
46. Vaz-Moreira I, Faria C, Nobre MF, Schumann P, Nunes OC, Manaia CM (2007) Paenibacillus humicus sp. nov., isolated from poultry litter compost. Int J Syst Evol Microbiol 57:2267–2271
47. Verma N, Singh NA, Kumar N, Raghu HV (2013) Screening of different media for sporulation of Bacillus megaterium. Int J Micro Res Rev 1(4):068–073
48. Wang L, Baek SH, Cui Y, Lee HG, Lee ST (2012) Paenibacillus sediminis sp. nov., a xylanolytic bacterium isolated from a tidal flat. Int J Syst Evol Microbiol 62:1284–1288
49. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173:697–703
50. Weller DM (2007) Pseudomonas biocontrol agents of soilborne pathogens: looking back over 30 years. Phytopathology 97:250–256
51. Yoon JH, Kang SJ, Yeo SH, Oh TK (2005) Paenibacillus alkaliterrae sp. nov., isolated from an alkaline soil in Korea. Int J Syst Evol Microbiol 55:2339–2344