Isolation, identification and characterization of Paenibacillus polymyxa CR1 with potentials for biopesticide, biofertilization, biomass degradation and biofuel production

BMC Microbiology

Volumn 16, Issue 1, 2016, Pages

  Weselowski, Brian ^a   Nathoo, Naeem ^a,b   Eastman, Alexander William ^a,b   MacDonald, Jacqueline ^b   Yuan, Ze Chun ^a,b  

^a LONDON RESEARCH AND DEVELOPMENT CENTRE   (Canada)

^b UNIVERSITY OF WESTERN ONTARIO   (Canada)

Author keywords

antagonism; biocontrol; biofertilizer; biological nitrogen fixation; biomass degradation; biopesticide; diazotroph; Paenibacillus polymyxa; PGPR; plant growth promotion

Indexed keywords

CELLULOSE; HEMICELLULOSE; INDOLEACETIC ACID; LIGNIN; NITROGEN; PESTICIDE; PHOSPHORUS; BIOFUEL; BIOLOGICAL CONTROL AGENT; FERTILIZER; INDOLEACETIC ACID DERIVATIVE; LIGNOCELLULOSE; PHYTOHORMONE; RNA 16S;

ANTIBACTERIAL ACTIVITY; ANTIFUNGAL ACTIVITY; ARABIDOPSIS; ARTICLE; BACILLUS CEREUS; BACTERIUM ISOLATION; BIODEGRADATION; BIOFUEL PRODUCTION; BIOLOGICAL PEST CONTROL; BIOMASS; CANADA; CONTROLLED STUDY; CUCUMBER; CYLINDROCARPON; HARVEST; IN VITRO STUDY; MAIZE; NONHUMAN; NUCLEOTIDE SEQUENCE; PAENIBACILLUS POLYMYXA; PHYTOPHTHORA SOJAE; PLANT GROWTH; PLANT RESIDUE; PLANT ROOT; POTATO; PSEUDOMONAS SYRINGAE; RHIZOCTONIA SOLANI; SUSTAINABLE AGRICULTURE; TOMATO; XANTHOMONAS CAMPESTRIS; AGRICULTURE; ANTIBIOSIS; ASCOMYCETES; BIOLOGICAL CONTROL AGENT; GENETICS; GROWTH, DEVELOPMENT AND AGING; ISOLATION AND PURIFICATION; METABOLISM; MICROBIOLOGY; NITROGEN FIXATION; PATHOGENICITY; PHYLOGENY; PHYSIOLOGY; PHYTOPHTHORA; PLANT DISEASE; PREVENTION AND CONTROL; RHIZOCTONIA;

AGRICULTURE; ANTIBIOSIS; ARABIDOPSIS; ASCOMYCOTA; BACILLUS CEREUS; BIOFUELS; BIOLOGICAL CONTROL AGENTS; BIOMASS; CANADA; CUCUMIS SATIVUS; FERTILIZERS; INDOLEACETIC ACIDS; LIGNIN; LYCOPERSICON ESCULENTUM; NITROGEN FIXATION; PAENIBACILLUS POLYMYXA; PEST CONTROL, BIOLOGICAL; PHOSPHORUS; PHYLOGENY; PHYTOPHTHORA; PLANT DISEASES; PLANT GROWTH REGULATORS; PLANT ROOTS; PSEUDOMONAS SYRINGAE; RHIZOCTONIA; RNA, RIBOSOMAL, 16S; SOIL MICROBIOLOGY; SOLANUM TUBEROSUM; XANTHOMONAS CAMPESTRIS; ZEA MAYS;

EID: 84992223452     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/s12866-016-0860-y     Document Type: Article

References (54)

1. Dobermann A. Nutrient use efficiency - measurement and management. In Krauss A, Association internationale de l'industrie des engrais, Isherwood K (Eds) Fertilizer Best Management Practice: General Principles, Strategy for their Adoption and Voluntary Initiatives vs Regulations. IFA International Workshop On Fertilizer Best Management Practices. Brussels, Belgium. 2007.
2. Sarathchandra SU, Ghani AA, Yeates GW, Burch G, Cox NR. Effect of nitrogen and phosphate fertilizers on microbial and nematode diversity in pasture soils. J Biol Biochem. 2001;33:953-64.
3. Arias-Estévez M, López-Periago E, Martínez-Carballo E, Simal-Gándara J, Mejuto JC, García-Río L. The mobility and degradation of pesticides in soils and the pollution of groundwater resources. Agr Ecosyst Environ. 2008;123:247-60.
4. Bloemberg GV, Lugtenberg BJJ. Molecular basis of plant growth promotion and biocontrol by Rhizobacteria. Curr Opin Plant Biol. 2001;4:343-50.
5. Bohlool BB, Ladka JK, Garrity DP, George T. Biological nitrogen fixation for sustainable agriculture: A perspective. Plant Soil. 1992;141:1-11.
6. Jakobsen J, Leggett ME, Richardson AE. Rhizosphere microorganisms and plant phosphorous uptake. In: Sims JT, Sharpley AN, editors. Phosphorous: agriculture and the environment. Madison, WI, USA.: American Society for Agronomy; 2005. p. 439-94.
7. Rodriguez H, Fraga R. Phosphate solubilizing bacteria and their role in plant growth promotion. Biotechnol Adv. 1999;17:319-39.
8. Glick B, Cheng Z, Czarny J, Duan J. Promotion of plant growth by ACC deaminase producing soil bacteria. Eur J Plant Pathol. 2007;119:329-39.
9. Glickmann E, Dessaux Y. A critical examination of the specificity of the Salkowski reagent for indolic compounds produced by phytopathogenic bacteria. Appl Env Microbiol. 1995;61:793-6.
10. Patten CL, Glick BR. Role of Pseudomonas putida indoleacetic acid in development of the host plant root system. Appl Env Microbiol. 2002;68:3795-801.
11. Spaepen S, Vanderleyden J, Remans R. Indole-3-acetic acid in microbial and microorganism-plant signaling. FEMS Microbiol Rev. 2007;31:425-48.
12. Bhattacharyya PN, Jha DK. Plant growth-promoting rhizobacteria (PGPR): emergence in agriculture. World J Mcrobiol Biotechnol. 2012;28:1327-50.
13. Lal S, Tabacchioni S. Ecology and biotechnological potential of Paenibacillus polymyxa: a minireview. Indian J Microbiol. 2009;49:2-10.
14. Udeigwe TK, Teboh JM, Eze PN, Stietiya MH, Kumar V, Hendrix J, Mascagni Jr HJ, Ying T, Kandakji T. Implications of leading crop production practices on environmental quality and human health. J Environ Manage. 2015;151:267-79.
15. Ling N, Xue C, Huang Q, Yang X, Xu Y, Shen Q. Development of a mode of application of bioorganic fertilizer for improving the biocontrol efficacy to Fusarium wilt. BioControl. 2010;55:673-83.
16. Ryu CM, Kim J, Choi O, Kim SH, Park CS. Improvement of biological control capacity of Paenibacillus polymyxa E681 by seed pelleting on sesame. Biol Control. 2006;39:282-9.
17. Anand R, Grayston S, Chanway C. N2-fixation and seedling growth promotion of lodgepole pine by endophytic Paenibacillus polymyxa. Microb Ecol. 2013;66:369-74.
18. Puri A, Padda KP, Chanway CP. Evidence of nitrogen fixation and growth promotion in canola (Brassica napus L.) by an endophytic diazotroph Paenibacillus polymyxa P2b-2R. Biol Fert Soils. 2016;52:119-25.
19. Xie J, Shi H, Du Z, Wang T, Liu X, Chen S. Comparative genomic and functional analysis reveal conservation of plant growth promoting traits in Paenibacillus polymyxa and its closely related species. Sci Rep. 2016;6:21329.
20. Eastman AW, Heinrichs DE, Yuan ZC. Comparative and genetic analysis of the four sequenced Paenibacillus polymyxa genomes reveals a diverse metabolism and conservation of genes relevant to plant-growth promotion and competitiveness. BMC Genomics. 2014;15:851.
21. Eastman AW, Weselowski B, Nathoo N, Yuan ZC. Complete genome sequence of Paenibacillus polymyxa CR1, a plant growth-promoting bacterium isolated from the corn rhizosphere exhibiting potential for biocontrol, biomass degradation, and biofuel production. Genome Announc. 2014;2:e01218-13.
22. Eastman AW, Yuan ZC. Development and validation of an rDNA operon based primer walking strategy applicable to de novo bacterial genome finishing. Front Microbiol. 2015;5:769.
23. Timmusk S, van West P, Gow NAR, Huffstutler RP. Paenibacillus polymyxa antagonizes oomycete plant pathogens Phytophthora palmivora and Pythium aphanidermatum. J Appl Microbiol. 2009;106:1473-81.
24. Kim SG, Khan Z, Jeon YH, Kim YH. Inhibitory effect of Paenibacillus polymyxa GBR-462 on Phytophthora capsici causing phytophthora blight in chili pepper. J Phytopathol. 2009;157:229-37.
25. Kavitha S, Senthilkumar S, Gnanamanickam A, Inayathullah M, Jayakumar R. Isolation and partial characterization of antifungal protein from Bacillus polymyxa strain VLB16. Process Biochem. 2005;40:3236-43.
26. Chen X, Wang G, Xu M, Jin J, Liu X. Antifungal peptide produced by Paenibacillus polymyxa BRF-1 isolated from soybean rhizosphere. Afr J Microbiol Res. 2010;4:2692-8.
27. Hong CE, Kwon SY, Park JM. Biocontrol activity of Paenibacillus polymyxa AC-1 against Pseudomonas syringae and its interaction with Arabidopsis thaliana. Microbiol Res. 2016;185:13-21.
28. Pichard B, Larue JP, Thouvenot D. Gavaserin and saltavalin, new peptide antibiotics produced by Bacillus polymyxa. FEMS Microbiol Lett. 1995;133:215-8.
29. Lee SH, Cho YE, Park SH, Balaraju K, Park JW, Lee SW, Park K. An antibiotic fusaricidin: a cyclic depsipeptide from Paenibacillus polymyxa E681 induces systemic resistance against Phytophthora blight of red-pepper. Phytoparasitica. 2013;41:49-58.
30. Mehnaz S, Weselowski B, Lazarovits G. Isolation and identification of Gluconacetobacter azotocaptans from corn rhizosphere. Syst Appl Microbiol. 2006;29:496-501.
31. Galloway JN, Cowling EB. Reactive nitrogen and the world: 200 years of change. AMBIO. 2002;31:64-71.
32. Rodriguez H, Fraga R, Gonzalez T, Bashan Y. Genetics of phosphate solubilization and its potential applications for improving plant growth-promoting bacteria. Plant Soil. 2006;287:15-21.
33. Wakelin SA, Warren RA, Harvey PR, Ryder MH. Phosphate solubilization by Penicillium spp. closely associated with wheat roots. Biol Fertil Soils. 2004;40:36-43.
34. Yadav KS, Dadarwal KR. Phosphate solubilization and mobilization through soil microorganisms. In: Dadarwal KR, editor. Biotechnological Approaches in Soil Microorganisms for Sustainable Crop Production. Jodhpur, India.: Scientific Publishers; 1997. p. 293-308.
35. Bashan Y. Inoculants of plant growth-promoting bacteria for use in agriculture. Biotechnol Adv. 1998;16:729-70.
36. Hardoim PR, van Overbeek LS, Elsas JD. Properties of bacterial endophytes and their proposed role in plant growth. Trends Microbiol. 2008;16:463-71.
37. Kim YC, Leveau J, McSpadden Gardner BB, Pierson EA, Pierson LS, Ryu C. The multifactorial basis for plant health promotion by plant-associated bacteria. Appl Environ Microbiol. 2011;77:1548-55.
38. Kuklinsky-Sobral J, Araujo WL, Mendes R, Geraldi IO, Pizzirani-Kleiner AA, Azevedo JL. Isolation and characterization of soybean-associated bacteria and their potential for plant growth promotion. Environ Microbiol. 2004;6:1244-51.
39. Li L, Hou X, Tsuge T, Ding M, Aoyama T, Oka A, Gu H, Zhao Y, Qu LK. The possible action mechanisms of indole-3-acetic acid methyl ester in Arabidopsis. Plant Cell Rep. 2008;27:575-84.
40. Magalhães DB, De Carvalho MEA, Bon E, Neto JSA, Kling SH. Colorimetric assay for lignin peroxidase activity determination using methylene blue as substrate. Biotechnol Tech. 1996;10:273-6.
41. Carder JH. Detection and quantitation of cellulase by Congo red staining of substrates in a cup-plate diffusion assay. Anal Biochem. 1986;153:75-9.
42. Bugg TDH, Ahmad M, Hardiman EM, Singh R. The emerging role for bacteria in lignin degradation and bio-product formation. Curr Opin Biotechnol. 2011;22:394-400.
43. Galkiewicz JP, Kellogg CA. Cross-kingdom amplification using bacterial-specific primers: complications for coral microbial ecology. Appl Enviro Microbiol. 2008;74:7828-31.
44. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F. The CLUSTAL-X Windows interface: Flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876-82.
45. Saitou N, Nei M. The neighbor-joining method: A new method for reconstructing phylogenetic trees. Mol Biol Evol. 1987;4:406-25.
46. Kluge AG, Farris JS. Quantitative phyletics and the evolution of anurans. Syst Zool. 1969;18:1-32.
47. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 2007;24:1596-9.
48. Kimura M. A simple method for estimating evolutionary rate of base substitutions through comparative studies of nucleotide sequences. J Mol Evol. 1980;16:111-20.
49. Swofford DL. Phylogenetic analysis using parisomy (∗and other methods). Version 3. Sunderland: Sinauer Associates; 1998.
50. Abraham EP, Gardner AD, Chain E, Heatley NG, Fletcher CM, Jennings MA, Florey HW. Further observations on penicillin. The Lancet. 1941;238:177-89.
51. Doebereiner J. Isolation and identification of aerobic nitrogen fixing bacteria. In: Alef K, Nannipieri P, editors. Methods in applied soil microbiology and biochemistry. Cambridge, MA, USA.: Academic; 1994. p. 134-41.
52. Bashan Y, Holguin G, Lifshitz R. Isolation and characterization of plant growth-promoting rhizobacteria. In: Glick BR, Thompson JE, editors. Methods in plant molecular biology and biotechnology. BocaRaton, FL, USA.: CRC Press; 1993. p. 331-45.
53. Mehta S, Nautiyal CS. An efficient method for qualitative screening of phosphate-solubilizing bacteria. Curr Microbiol. 2001;43:51-6.
54. Gordon SA, Weber RP. Colorimetric estimates of indoleacteic acid. Plant Physiol. 1951;26:192-5.