Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis

Applied Microbiology and Biotechnology

Volumn 97, Issue 15, 2013, Pages 6991-7003

  Chandna, Piyush ^a   Mallik, Sarita ^b   Kuhad, Ramesh Chander ^a  

^a UNIVERSITY OF DELHI   (India)

^b INDIANA UNIVERSITY   (United States)

Author keywords

Amplified rDNA restriction analysis; Bacterial diversity; Phylogeny; Ribosomal DNA

Indexed keywords

AGRICULTURAL BY-PRODUCTS; AMPLIFIED RDNA RESTRICTION ANALYSIS; BACTERIAL DIVERSITY; PATTERN RECOGNITION SOFTWARES; PHYLOGENETIC INFORMATION; PHYLOGENETIC RELATIONSHIPS; PHYLOGENY; RIBOSOMAL DNA;

AGRICULTURAL WASTES; BACILLI; BACTERIOLOGY; BIOLOGY; COMPOSTING; PATTERN RECOGNITION; RNA;

GENES;

ALLYL ISOTHIOCYANATE; MOLASSES; RNA 16S; TYPE II SITE SPECIFIC DEOXYRIBONUCLEASE;

BACTERIUM; COMPOST; CULTIVATION; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; NUMERICAL MODEL; PHYLOGENETICS; PHYLOGENY; SOFTWARE; SPECIES DIVERSITY;

ACIDOVORAX; ACTINOBACTERIA; AMPLIFIED RIBOSOMAL DNA RESTRICTION ANALYSIS; ARTICLE; ASH; BACILLI; BACTERIUM ISOLATE; BETAPROTEOBACTERIA; COMAMONAS; COMPOST; CULTIVATED SPECIES; ENTEROBACTER; GAMMAPROTEOBACTERIA; GENE SEQUENCE; KLEBSIELLA; KOCURIA; LYSINIBACILLUS; MICROBACTERIUM BARKERI; MICROBIAL COMMUNITY; MICROBIAL DIVERSITY; NONHUMAN; NUCLEOTIDE SEQUENCE; PATTERN RECOGNITION; PHYLOGENY; PHYLUM; RICE; RICE BRAN; SERRATIA; STAPHYLOCOCCUS; TERRIBACILLUS; URINE; WHEAT BRAN;

AGRICULTURE; BACTERIA; BASE SEQUENCE; BIODIVERSITY; DNA PRIMERS; DNA, BACTERIAL; PHYLOGENY; POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; SOIL;

ACIDOVORAX; ACTINOBACTERIA; BACILLI (CLASS); BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); BETAPROTEOBACTERIA; COMAMONAS; ENTEROBACTER; GAMMAPROTEOBACTERIA; KLEBSIELLA; KOCURIA; MICROBACTERIUM BARKERI; SERRATIA; STAPHYLOCOCCUS;

EID: 84880515023     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-012-4434-0     Document Type: Article

References (42)

1. Acinas SG, Rodríguez-Valera F, Pedrós-Alió C (1997) Spatial and temporal variation in marine bacterioplankton diversity as shown by RFLP fingerprinting of PCR amplified 16S rDNA. FEMS Microbiol Ecol 24(1):27-40
2. Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Streehl K (1999) Short protocols in molecular biology (4th Edn). Wiley, New York, 1512
3. Blanc M, Marilley L, Beffa T, Aragno M (1999) Thermophilic bacterial communities in hot composts as revealed by most probable number counts and molecular (16S rDNA) methods. FEMS Microbiol Ecol 28(2):141-149
4. Cihan Arzu C, Tekin N, Ozcan B, Cokmus C (2012) The genetic diversity of genus Bacillus and the related genera revealed by 16S rRNA gene sequences and ARDRA analyses isolated from geothermal regions of turkey. Braz J Microbiol 43(1):309-324
5. Dees PM, Ghiorse WC (2001) Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. FEMS Microbiol Ecol 35(2):207-216
6. DeLong EF (1992) Archaea in costal marine sediments. Proc Natl Acad Sci 89:5685-5689
7. Deng S, Hiruki C, Robertson JA, Stemke GW (1992) Detection by PCR and differentiation by restriction fragment length polymorphism of Acholeplasma, Spiroplasma, Mycoplasma and Ureaplasma based upon 16S rRNA genes. Genome Res 1:202-204
8. Frederic B, Gich EA, Figueras Jordi B, Abella Charles A, Dolors BM, Manel P (2000) Assessment of microbial community structure changes by amplified ribosomal DNA restriction analysis (ARDRA). Int Microbiol 3:103-106
9. Funke G, Carlotti A (1994) Differentiation of Brevibacterium spp. encountered in clinical specimens. J Clin Microbiol 32(7):1729-1732
10. Han SZ, Wang ET, Chen WX (2005) Diverse bacteria isolated from root nodules of Phaseolus vulgaris and species within the genera Campylotropis and Cassia grown in China. Syst Appl Microbiol 28(3):265-276
11. Hughes MS, Skuce RA, Beck LA, Neill SD (1993) Identification of mycobacteria from animals by restriction enzyme analysis and direct DNA cycle sequencing of polymerase chain reaction-amplified 16S rRNA gene sequences. J Clin Microbiol 31(12):3216-3222
12. Hunter PR, Gaston MA (1988) Numerical index of the discriminatory ability of typing systems: an application of Simpson's index of diversity. J Clin Microbiol 26(11):2465
13. Jannes G, Vaneechoutte M, Lannoo M, Gillis M, Vancanneyt M, Vandamme P, Verschraegen G, Van Heuverswyn H, Rossau R (1993) Polyphasic taxonomy leading to the proposal of Moraxella canis sp. nov. for Moraxella catarrhalis-like strains. Int J Syst Bacteriol 43(3):438-449
14. Laguerre G, Allard MR, Revoy F, Amarger N (1994) Rapid identification of rhizobia by restriction fragment length polymorphism analysis of PCR-amplified 16S rRNA genes. Appl Environ Microbiol 60(1):56-63
15. Maidack BL, Olsen GJ, Larsen N, Overbeek R, McCaughey MJ, Woese CR (1996) The ribosomal database project (RDP). Nucl Acid Res 24:82-85
16. Malik S, Beer M, Megharaj M, Naidu R (2008) The use of molecular techniques to characterize the microbial communities in contaminated soil and water. Environ Int 34(2):265-276
17. Martinez-Murcia AJ, Acinas SG, Rodriguez Valera F (1995) Evaluation of prokaryotic diversity by restrictase digestion of 16S rDNA directly amplified from hypersaline environments. FEMS Microbiol Ecol 17(4):247-256
18. Massana R, Murray AE, Preston CM, Delong EF (1997) Vertical distribution and phylogenetic characterization of marine planktonic Archaea in the Santa Barbara channel. Appl Environ Microbiol 63(1):50-56
19. Massol-Deya AA, Whallon J, Hickey RF, Tiedje JM (1995) Channel structures in aerobic biofilms of fixed-film reactors treating contaminated groundwater. Appl Environ Microbiol 61(2):769-777
20. Moreira JL, Mota RM, Horta MF, Teixeira SMR, Neumann E, Nicoli JR, Nunes AC (2005) Identification to the species level of Lactobacillus isolated in probiotic prospecting studies of human, animal or food origin by 16S-23S rRNA restriction profiling. BMC Microbiol 23:5-15
21. Moyer CL, Dobbs FC, Karl DM (1994) Estimation of diversity and community structure through restriction fragment length polymorphism distribution analysis of bacterial 16S rRNA genes from a microbial mat at an active, hydrothermal vent system, Loihi Seamount, Hawaii. Appl Environ Microbiol 60(3):871-879
22. Nesme X, Vaneechoutte M, Orso S, Hoste B, Swings J (1995) Diversity and genetic relatedness within genera Xanthomonas and Stenotrophomonas using restriction endonuclease site differences of PCR amplified 16S rRNA gene. Syst Appl Microbiol 18:127-135
23. Ntougias S, Zervakis GI, Kavroulakis N, Ehaliotis C, Papadopoulou KK (2004) Bacterial diversity in spent mushroom compost assessed by amplified rDNA restriction analysis and sequencing of cultivated isolates. Syst Appl Microbiol 27(6):746-754
24. Ralph D, McClelland M, Welsh J, Baranton G, Perolat P (1993) Leptospira species categorized by arbitrarily primed polymerase chain reaction (PCR) and by mapped restriction polymorphisms in PCR-amplified rRNA genes. J Bacteriol l75(4):973-981
25. Rastogi Gurdeep, Rajesh K. Sani (2011) Molecular techniques to assess microbial community structure, function, and dynamics in the environment. Ahmad et al. (eds.) Microbes and microbial technology: 29 agricultural and environmental applications, DOI 10.1007/978-1-4419-7931-5-2,© Springer Science+Business Media, LLC 2011.
26. Rodas AM, Ferrer S, Pardo I (2003) 16S-ARDRA, a tool for identification of lactic acid bacteria isolated from grape must and wine. Syst Appl Microbiol 26(3):412-422
27. Soto LP, Frizzo LS, Bertozzi E, Avataneo E, Sequeira GJ, Rosmini MR (2010) Molecular microbial analysis of Lactobacillus strains isolated from the gut of calves for potential probiotic use. Vet Med Intern. doi: 10.4061/2010/274987, Article ID 274987, 7 pages
28. 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(4):846-849
29. Stakenborg T, Vicca J, Butaye P, Maes D, De Baere T, Verhelst R, Peeters J, de Kruif A, Haesebrouck F, Vaneechoutte M (2005) Evaluation of amplified rDNA restriction analysis (ARDRA) for the identification of Mycoplasma species. BMC Infect Disea 5:46-56
30. Susilowati A, Wahyudi Aris T, Lestari Y, Wiyono S, Suwanto A (2010) Genetic diversity of antifung-producing rhizobacteria of Pseudomonas sp. isolated from rhizosphere of soybean plant. Microbiol 4(1):33-38
31. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA 5: molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Mol Biol Evol 28(10):2731-2739
32. 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. Nucl Acid Res 25(24):4876-4882
33. Van de Peer Y, Nicoläi S, De Rijk P, De Wachter R (1996) Database on the structure of small subunit RNA. Nucl Acid Res 22(17):3488-3494
34. Vaneechoutte M, De Beenhouwer H, Claeys G, Verschraegen G, De Rouck A, Paepe N, Elaichouni A, Portaels F (1993) Identification of Mycobacterium species by using amplified ribosomal DNA restriction analysis. J Clin Microbiol 31(8):2061-2065
35. Vaneechoutte ML, Dijkshoorn I, Tjernberg A, Elaichouni P, de Vos CG, Verschraegen G (1995) Identification of Acinetobacter genomic species by amplified ribosomal DNA restriction analysis. J Clin Microbiol 33(1):11-15
36. Vila J, Marcos MA, Jimenez de Anta MT (1996) A comparative study of different PCR-based DNA fingerprinting techniques for typing of the Acinetobacter calcoaceticus-A. baumannii complex. J Med Microbiol 44(6):482-489
37. Watabe M, Rao JR, Xu J, Millar BC, Ward RF, Moore JE (2004) Identification of novel eubacteria from spent mushroom compost (SMC) waste by DNA sequence typing: ecological considerations of disposal on agricultural land. Wast Manag 24(1):81-86
38. Weisburg WG, Barns SM, Pelletier DA, Lane DJ (1991) 16S ribosomal DNA amplification for phylogenetic study. J Bacteriol 173(2):697-703
39. Wilmotte A, van der Auwera G, de Wachter R (1993) Structure of the 16S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenetic analysis. FEBS Lett 317:96-100
40. Wilson MJ, Wade WG, Weightman AJ (1995) Restriction fragment length polymorphism analysis of PCR-amplified 16S rDNA of human Capnocytophaga. J Appl Bacteriol 78:394-401
41. Woese CR (1987) Bacterial evolution. Microbiol Rev 51(2):221-271
42. Xiang S, Yao T, An L, Xu LP, Guo JH (2005) 16S rRNA sequences and differences in bacteria isolated from the Muztag Ata Glacier at increasing depths. Appl Environ Microbiol 71(8):4619-4627