Assessment of bacterial diversity during composting of agricultural byproducts

BMC Microbiology

Volumn 13, Issue 1, 2013, Pages

  Chandna, Piyush ^a   Nain, Lata ^b   Singh, Surender ^b   Kuhad, Ramesh Chander ^a  

^a UNIVERSITY OF DELHI   (India)

^b INDIAN AGRICULTURAL RESEARCH INSTITUTE   (India)

Author keywords

Agricultural by products; Bacterial diversity; Compost; Culturable; Phylogeny

Indexed keywords

NITROGEN; RNA 16S;

ACIDOVORAX; ACTINOBACTERIA; AGRICULTURAL BYPRODUCT; AGRICULTURE; ARTICLE; BACILLALES; BACILLUS; BACTERIUM DIVERSITY; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; BIOCHEMICAL COMPOSITION; BURKHOLDERIALES; COMAMONAS; COMPOSTING; COOLING; ENTEROBACTER; ENTEROBACTERIALES; GENE SEQUENCE; GRAM NEGATIVE BACTERIUM; GRAM POSITIVE BACTERIUM; KLEBSIELLA; KOCURIA; LYSINIBACILLUS KOCURIA; MESOPHILIC BACTERIUM; MICROBACTERIUM; MICROBIOLOGICAL PARAMETERS; NONHUMAN; PHYSICAL CHEMISTRY; QUALITATIVE ANALYSIS; SERRATIA; STAPHYLOCOCCUS; TERRIBACILLUS; THERMOPHILIC BACTERIUM;

BACTERIA; BACTERIAL LOAD; BACTERIAL TYPING TECHNIQUES; BIODIVERSITY; CLUSTER ANALYSIS; DNA, BACTERIAL; DNA, RIBOSOMAL; MOLECULAR SEQUENCE DATA; ORYZA SATIVA; PHYLOGENY; POACEAE; RNA, RIBOSOMAL, 16S; SEQUENCE ANALYSIS, DNA; SOIL; SOIL MICROBIOLOGY; TRITICUM;

ACIDOVORAX; ACTINOBACTERIA (CLASS); BACILLALES; BACILLUS (BACTERIUM); BACTERIA (MICROORGANISMS); BURKHOLDERIALES; COMAMONAS; ENTEROBACTER; ENTEROBACTERIALES; FUNGI; KLEBSIELLA; KOCURIA; MICROBACTERIUM; NEGIBACTERIA; POSIBACTERIA; SERRATIA; STAPHYLOCOCCUS; TRITICUM AESTIVUM;

EID: 84877071200     PISSN: None     EISSN: 14712180     Source Type: Journal    
DOI: 10.1186/1471-2180-13-99     Document Type: Article

References (74)

1. Bioremediation of Agricultural Wastes through Vermicomposting. Suthar S, Biorem. J 2009 13 1 21 28 10.1080/10889860802690513
2. Biogas generation potential by anaerobic digestion for sustainable energy development in India. Rao PV, Baral SS, Dey R, Mutnuri S, Renew Sustain Energy Rev 2010 14 7 2086 2094 10.1016/j.rser.2010.03.031
3. Organic matter evolution index (OMEI) as a measure of composting efficiency. Adani F, Genevini PL, Gasperi F, Zorzi G, Comp Sci & Utiliz 1997 5 2 53 62 23456860
4. Biocontrol of foliar fungal diseases with compost extracts. Weltzien HC, Microbial Ecology of Leaves New York, NY, USA: Springer-Verlag, Andrews JH, Hirano S, 1991 430 450
5. Effects of windrow turning and seasonal temperatures on composting hog manure from hoop structures. Tiquia SM, Richard TL, Honeyman MS, Environ Technol 2000 21 9 1037 1046 10.1080/09593332108618048
6. Bacterial diversity in finished compost and vermicompost: differences revealed by cultivation-independent analyses of PCR-amplified 16S rRNA genes. Fracchia L, Dohrmann AB, Martinotti MG, Tebbe CC, Appl Microbiol Biotechnol 2006 71 6 942 952 10.1007/s00253-005-0228-y 16395545
7. Microbiological Aspects of biowaste during composting in a monitored compost bin. Ryckeboer J, Mergaert J, Coosemans J, Deprins K, Swings J, J Appl Microbiol 2003 94 1 127 137 10.1046/j.1365-2672.2003.01800.x 12492933
8. Characterisation of source-separated household waste intended for composting. Sundberg C, Franke-Whittle IH, Kauppi S, Yu D, Romantschuk M, Insam H, Håkan J, Bioresour Technol 2011 102 3 2859 2867 10.1016/j.biortech. 2010.10.075 21075618
9. Characterization of microbial diversity by determining terminal restriction fragment length polymorphisms of genes encoding 16S rRNA. Liu WT, Marsh TL, Cheng H, Forney LJ, Appl Environ Microbiol 1997 63 11 4516 4522 9361437
10. Bacterial community fingerprinting of amplified 16S and 16-23S ribosomal DNA gene sequences and restriction endonuclease analysis (ARDRA). Massol-Deya AA, Odelson DA, Hickey RF, Tiedje JM, Molecular microbial ecology manual Dordrecht: Kluwer, Akkermans ADL, van Elsas JD, deBruijn FJ, 1995 1 8
11. A molecular view of microbial diversity and the biosphere. Pace NR, Sci 1997 276 5313 734 740 10.1126/science.276.5313.734
12. Succession of microbial communities during hot composting as detected by PCR-single-strand-conformation polymorphism-based genetic profiles of small-subunit rRNA genes. Peters S, Koschinsky S, Schwieger F, Tebbe CC, Appl Environ Microbiol 2000 66 3 930 936 10.1128/AEM.66.3.930-936.2000 10698754
13. Microbial diversity in hot synthetic compost as revealed by PCR-amplified rRNA sequences from cultivated isolates and extracted DNA. Dees PM, Ghiorse WC, FEMS Microbiol Ecol 2001 35 2 207 216 10.1111/j.1574-6941.2001.tb00805.x 11295460
14. Phylogeny Based on 16S rRNA/DNA. Stackebrandt E, eLS Chichester: John Wiley & Sons Ltd 2009 http://onlinelibrary.wiley.com/doi/10.1002/ 9780470015902.a0000462.pub2/abstract. (http://onlinelibrary.wiley.com/book/10. 1002/047001590X)
15. Genetic fingerprinting of microbial communities: present status and future perspective. Muyzer G, Proceedings of the 8th International Symposium on Microbial Ecology Halifax, Nova Scotia: Atlantic Canada Society for Microbial Ecology, Bell CR, Brylinsky M, Johnson-Green P, 1999 1 10
16. Biornass and metabolic activity of heterotrophic marine bacteria. Van Es FB, Meyer Reil LA, Advances in microbial ecology New York, USA: Plenum Publishing Corp, Marshall KC, 6 1982 ll 170
17. Bacillus marmarensis sp. nov., an alkaliphilic, protease-producing bacterium isolated from mushroom compost. Denizci AA, Kazan D, Erarslan A, Int J Sys Evol Microbiol 2010 60 7 1590 1594 10.1099/ijs.0.012369-0
18. Isolation and characterization of novel bacterial strains exhibiting ligninolytic potential. Bandounas L, Wierckx NJP, de Winde JH, Ruijssenaars HJ, BMC Biotechnology 2011 11 94 10.1186/1472-6750-11-94 21995752
19. Composting. Biddlestone AJ, Gray KR, Comprehensive Biotechnology: The Principles, Applications, and Regulations of Biotechnology in Industry, Agriculture, and Medicine Oxford: Pergamon Press, Moo-Young M, 1985 1059 1070
20. Nutrient content in rice husk ash of some Malaysian rice varieties. Hashim AB, Aminuddin H, Siva KB, Pert J Trop Agric Sci 1996 19 1 77 80
21. Composting certain agricultural residues to potting soils. Saber M, Mohammed Z, Badr-el-Din S, Awad N, J Ecol Nat Environ 2011 3 3 78 84
22. Methods to improve the composting process of the solid fraction of dairy cattle slurry. Brito LM, Coutinho J, Smith SR, Bioresour Technol 2008 99 18 8955 8960 10.1016/j.biortech.2008.05.005 18556195
23. Maturity and stability parameters of composts prepared with a, wide range of organic wastes. Bernal MP, Paredes C, Sanchez-Monedero MA, Cegarra J, Biores Technol 1998 63 1 91 99 10.1016/S0960-8524(97)00084-9
24. City refuse compost as a phosphorus source to overcome the P-fixation capacity of sesquioxide-rich soils. Iglesias-Jimenez E, Garcia PV, Espino M, Hernadez JM, Plant and Soil 1993 148 115 127 10.1007/BF02185391
25. Microbial succession during a composting process as evaluated by denaturing gradient gel electrophoresis analysis. Ishii K, Fukui M, Takii S, J Appl Microbiol 2000 89 5 768 777 10.1046/j.1365-2672.2000.01177.x 11119150
26. Microbial analysis of compost using cowdung as booster. Adegunloye DV, Adetuyi FC, Akinosoye FA, Doyeni MO, Pak J Nut 2007 6 5 506 510 10.3923/pjn.2007.506.510
27. Composting of food wastes using cow and pig dung as booster. Adegunloye DV, Adetuyi FC, Afr J Bas & Appl Sci 2009 1 3-4 70 75
28. Conversion of Waste into Wealth: A Study in Solid Waste Management. Janakiram T, Sridevi K, E-Journal of Chemistry 2010 7 4 1340 1345 (http://www.e-journals.net/) 10.1155/2010/549185
29. Nitrogen and phosphorous dynamics in cocomposted yard trimmings and broiler litter. Felton GK, Carr LE, Prigge CE, Bouwkamp JC, Comp Sci Utiliz 2004 12 4 349 355
30. Effect of composting on characterization and leaching of copper, manganese and zinc from swine manure. Jenn-Hung H, Shang-Lien L, Environ Poll 2011 114 1 119 127
31. Organic Waste Processing loa Q: Combining raw materials for composting. Willson GB, Biocycl 1989 30 5 82 85
32. Paulin B, O'Malley P, Compost production and use in horticulture Department of Agriculture and Food, Government of Western Australia 2008 Bulletin 4746 ISSN 1833 7236 (http://www.agric.wa.gov.au/objtwr/imported-assets/ content/hort/compost-bulletin08.pdf)
33. Viability and activity in readily culturable bacteria: a review and discussion of the practical issues. Kell DB, Kaprelyants AS, Weichart DH, Harwood CR, Barer MR, Ant von Leeuwen 1998 73 2 169 187 10.1023/A:1000664013047
34. Viable counts and viability. Postgate JR, Meth Microbiol 1969 1 611 628
35. Hargerty DJ, Pavoni JL, Heer JE, Solid Waste Management New York: Van Nostrand Reinhold 1999 12 13
36. Bacteriology of composting. Golueke CG, Biocycl 1992 33 55 57
37. Ribosomal DNA sequencing as a tool for identification of bacterial pathogens. Kolbert CP, Persing DH, Curr Opin Microbiol 1999 2 3 299 305 10.1016/S1369-5274(99)80052-6 10383862
38. Use of 16S ribosomal RNA gene analyses to characterize the bacterial signature associated with poor oral health in West Virginia. Olson JC, Cuff CF, Lukomski S, Lukomska E, Canizales Y, Wu B, Crout RJ, Thomas JG, McNeil DW, Weyant RJ, Marazita ML, Paster BJ, Elliott T, BMC Oral Health 2011 11 1 7 10.1186/1472-6831-11-1 21208407
39. Application of COMPOCHIP microarray to investigate the bacterial communities of different composts. Franke-Whittle IH, Knapp BA, Fuchs J, Kaufmann R, Insam H, Microb Ecol 2009 57 3 510 521 10.1007/s00248-008-9435-2 18818861
40. Bacterial diversity in spent mushroom compost assessed by amplified rDNA restriction analysis and sequencing of cultivated isolates. Ntougias S, Zervakis GI, Kavroulakis N, Ehaliotis C, Papadopoulou KK, Syst Appl Microbiol 2004 27 6 746 754 10.1078/0723202042369857 15612633
41. Assessment of bacterial diversity in agricultural by-product compost by sequencing of cultivated isolates and amplified rDNA restriction analysis. Chandna P, Mallik S, Kuhad RC, Appl Microbiol Biotechnol 2012 10.1007/s00253-012-4434-0
42. Microbial diversity in a baggase-based compost prepared for the production of Agaricus brasiliensis. Silva CF, Azevedo RS, Braga C, Silva R, Dias ES, Schwan RF, Braz J Microbiol 2009 40 3 590 600 10.1590/S1517- 83822009000300023
43. Bacteria associated with compost used for cultivation of Nigerian edible mushrooms Pleurotus tuber-regium (Fr.) Singer, and Lentinus squarrosulus (Berk.). Gbolagade JS, Afr J of Biotech 2006 5 4 338 342
44. Murray PR, Drew WL, Kobayashi GS, Thompson JH, Medical Microbiology PA: Mosby Publ Philadelphia 1990
45. Occurrence of microorganisms pathogenic for man and animals in source separated biowaste and compost-importance, controls, limits, epidemiology. Strauch D, "The Science of Composting" London: CEC, Blackie Academic and Professional, de Bertoldi M, Sequi P, Lemmes B, Tizano P, 1996 224 232
46. Potential of thermophilic bacteria as microbial inoculant for commercial scale white button mushroom (Agaricus bisporus) compost production. Ahlawat OP, Vijay B, J Sci & Ind Res 2010 69 12 948 955 20665010
47. Molecular analysis of bacterial community succession during prolonged compost curing. Danon M, Franke-Whittle IH, Insam H, Chen Y, Hadar Y, FEMS Microbiol. Ecol 2008 65 1 133 144 10.1111/j.1574-6941.2008.00506.x 18537836
48. Compost: a study of the development process and end-product potential for suppression of turfgrass disease. Boulter JI, Boland GJ, Trevors JT, W J Microbio Biotech 2000 16 2 115 134 10.1023/A:1008901420646
49. Bacillus as PGPR in Crop Ecosystem. Kumar A, Prakash A, Johri BN, Bacteria in Agrobiology: Crop Ecosystems Berlin Heidelberg: Springer-Verlag, Maheshwari DK, 2011 10.1007/978-3-642-18357-7-2, #
50. A survey of bacteria and fungi occurring during composting and self-heating processes. Ryckeboer J, Mergaert J, Vaes K, Klammer S, De Clercq D, Coosemans J, Insam H, Swings J, Ann Microbiol 2003 53 4 349 410
51. Diversity of Bacterial Isolates from Commercial and Homemade Composts. Vaz-Moreira I, Silva ME, Manaia CM, Nunes OC, Microbial Ecol 2008 55 4 714 722 10.1007/s00248-007-9314-2
52. Comamonas composti sp. nov., isolated from food waste compost. Young CC, Chou JH, Arun AB, Yen WS, Sheu SY, Shen FT, Lai WA, Rekha PD, Chen WM, Int J Syst Bacteriol 2008 58 1 251 256
53. Extracellular degradation of medium chain length poly (β-hydroxyalkanoates) by Comamonas sp. Quinteros R, Goodwin S, Lenz RW, Park WH, Int J Biolog Macromol 1999 25 1-3 135 143
54. Comamonadaceae, a new family encompassing the acidovorans rRNA complex, including Variovorax paradoxus gen. nov., comb. nov., for Alcaligenes paradoxus (Davis 1969). Willems A, De Ley J, Gillis M, Kersters K, Int J Syst Evol Microbiol 1991 41 3 445 450
55. Verminephrobacter eiseniae gen. nov., sp. nov., a nephridial symbiont of the earthworm Eisenia foetida (Savigny). Pinel N, Davidson SK, Stahl DA, Int J Syst Evol Microbiol 2008 58 9 2147 2157 10.1099/ijs.0.65174-0 18768621
56. Interactions between microfungi and Eisenia andrei (Oligochaeta) during cattle manure vermicomposting. Pizl V, Novokova A, Pedobiologia 2003 47 5-6 895 899
57. Acidovorax-like symbionts in the nephridia of earthworms. Schramm A, Davidson S, Dodsworth J, Drake H, Stahl D, Dubilier N, Environ Microbiol 2003 5 9 804 809 10.1046/j.1462-2920.2003.00474.x 12919416
58. Combined compost and vermicomposting process in the treatment and bioconversion of sludge. Alidadi H, Parvaresh AR, Shahmansouri MR, Pourmoghadas H, Iran J Environ Heal Sci Eng 2005 2 4 251 254
59. Salinity: electrical conductivity and total dissolved solids. Rhoades JD, Methods of Soil Analysis. Part 3. Chemical Methods Madison: SSSA, Sparks DL, 1996 417 435
60. Blakemore LC, Searle PL, Daily BK, Methods for chemical analysis of soils New Zealand Soil Bureau Report IDA. D5C 1981
61. Estimation of soil organic carbon by chromic acid titration method. Walkley AJ, Black CA, Soil Sci 1934 37 29 38 10.1097/00010694-193401000-00003
62. A new method for the estimation of nitrogen in organic compounds. Kjeldahl J, Z. Anal Chem 1883 22 366
63. A method for the determination of total sulphur in soils. Steinbergs A, Analyst (London) 1955 80 457 461 10.1039/an9558000457
64. Anonymous, Guide to the interpretation of analytical data for loam less compost. Ministry of Agriculture, Fisheries and Food, No. 25. ADAS United Kingdome: Agricultural Development and Advisory Service 1988
65. Distribution and accumulation of heavy metals (Cd, Ni and Cr) in tomato plant. Moral R, Navarro-Pedreno J, Gomez I, Mataix J, Environ Bulletin 1994 3 395 399
66. Thompson M, Wood SJ, Atomic absorption methods in applied geochemistry. Atomic Absorption Spectrometry Amsterdam: Elsevier, Cantle JE, 1982 261 284
67. Trace element analysis in CRM of plant origin by inductively coupled plasma mass spectrometry. Kopĺk R, Curdova E, Suchanek M, Fresenius' J Anal Chem 1998 300 449 451 23656308
68. Study of minerals and trace elements. Fingerová H, Kopl ́k R, Fresenius J Anal Chem 1993 63 5-6 545 549
69. Sambrook J, Russell DW, Molecular Cloning New York: Cold Spring Harbor Laboratory Press 3 2001
70. Archaea in coastal marine sediments. DeLong EF, Proc Natl Acad Sci 1992 89 5685 5689 10.1073/pnas.89.12.5685 1608980
71. Structure of the 16S ribosomal RNA of the thermophilic cyanobacterium Chlorogloeopsis HTF ('Mastigocladus laminosus HTF') strain PCC7518, and phylogenetic analysis. Wilmotte A, van-der Auwera G, de Wachter R, FEBS Lett 1993 317 1-2 96 100 8428640
72. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ, Nuc Acid Res 1997 25 17 3389 3402 10.1093/nar/25.17.3389
73. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG, Nucl Acid Res 1997 25 24 4876 4882 10.1093/nar/25.24.4876
74. MEGA 5: molecular evolutionary genetic analysis using maximum likelihood, evolutionary distance and maximum parsimony methods. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S, Mol Biol Evol 2011 10.1093/molbev.msr121