Assessment of bacterial diversity during composting of agricultural byproducts

BMC Microbiology

Ramesh Chander Kuhad²  Surender Singh¹  Lata Nain¹  Piyush Chandna² 

[1] Division of Microbiology, Indian Agricultural Research Institute, New Delhi, 110 012, India;Lignocellulose Biotechnology Laboratory, Department of Microbiology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110 021, India

关键词: Phylogeny;    Culturable;    Bacterial diversity;    Compost;    Agricultural by-products;   

Others  :  1143761
DOI  :  10.1186/1471-2180-13-99

 received in 2013-02-05, accepted in 2013-04-18,  发布年份 2013

【 摘 要 】

Background

Composting is microbial decomposition of biodegradable materials and it is governed by physicochemical, physiological and microbiological factors. The importance of microbial communities (bacteria, actinomycetes and fungi) during composting is well established. However, the microbial diversity during composting may vary with the variety of composting materials and nutrient supplements. Therefore, it is necessary to study the diversity of microorganisms during composting of different agricultural byproducts like wheat bran, rice bran, rice husk, along with grass clippings and bulking agents. Here it has been attempted to assess the diversity of culturable bacteria during composting of agricultural byproducts.

Results

The culturable bacterial diversity was assessed during the process by isolating the most prominent bacteria. Bacterial population was found to be maximum during the mesophilic phase, but decreased during the thermophilic phase and declined further in the cooling and maturation phase of composting. The bacterial population ranged from 10⁵ to 10⁹ cfu g^-1 compost. The predominant bacteria were characterized biochemically, followed by 16S rRNA gene sequencing. The isolated strains, both Gram-positive and Gram-negative groups belonged to the order Burkholderiales, Enterobacteriales, Actinobacteriales and Bacillales, which includes genera e.g. Staphylococcus, Serratia, Klebsiella, Enterobacter, Terribacillus, Lysinibacillus Kocuria, Microbacterium, Acidovorax and Comamonas. Genera like Kocuria, Microbacterium, Acidovorax, Comamonas and some new species of Bacillus were also identified for the first time from the compost made from agricultural byproducts.

Conclusion

The use of appropriate nitrogen amendments and bulking agents in composting resulted in good quality compost. The culture based strategy enabled us to isolate some novel bacterial isolates like Kocuria, Microbacterium, Acidovorax and Comamonas first time from agro-byproducts compost. These bacteria can be used as potential compost inoculants for accelerating composting process.

【 授权许可】

   
2013 Chandna et al.; licensee BioMed Central Ltd.

【 图 表 】

Figure 1.

Figure 2.

Figure 3.

Figure 4.

【 参考文献 】

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