Abstract
Two euryarchaeota-specific 16S rRNA gene clone libraries (MT1 and MT2) and two bacterial 16S rRNA gene clone libraries (HW1 and HW2) were constructed using DNA isolated from two sludge samples (sample 1 and sample 2) collected from two separate tanks of commercial biogas plant operating at the methanogenesis stage, each receiving the same feedstock, after heat pretreatment for an hour at 70 °C, located near Holsworthy, Devon, UK. In the euryarchaeotal-based libraries, both samples revealed clone sequenses assigned to Methanomicrobiales and Methanosarcinales of the phylum Euryarchaeota. Although not much difference was observed in the Archaeal diversity, phylogenetic tree analysis demonstrates that 25 % of clone sequences of sample 1 and 42 % of clone sequences of sample 2 formed separate clades from cultured diversity. 16S rRNA gene-based bacterial libraries also revealed the ubiquitous presence of phyla Firmicutes and Proteobacteria. Cellulolytic bacterial clone sequences were abundant in both the samples. Fluorescent in situ hybridisation (FISH) results also revealed the presence of Methanomicrobiales and Methanosarcinales as a dominant group.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Similar content being viewed by others
References
APHA (1992) Standard methods for the examination of water and wastewater, 18th edn. American Public Health Association, American Water Works Association and Water Environment Federation, Washington, DC
Bala Subramanian S, Yan S, Tyagi RD et al (2010) Extracellular polymeric substances (EPS) producing bacterial strains of municipal wastewater sludge: isolation, molecular identification, EPS characterization and performance for sludge settling and dewatering. Water Res 44:2256–2266
Chachkiani M, Dabert P, Abzianidze T et al (2004) 16S rDNA characterization of bacterial and archaeal communities during start-up of anaerobic thermophilic digestion of cattle manure. Bioresour Technol 93:227–232
Chen S, Niu L, Zhang Y (2010) Saccharofermentans acetigenes gen. nov., sp. nov., an anaerobic bacterium isolated from sludge treating brewery wastewater. Int J Syst Evol Microbiol 60:2735–2738
Chouari R, Paslier DL, Daegelen P et al (2005) Novel predominant archaeal and bacterial groups revealed by molecular analysis of an anaerobic sludge digester. Environ Microbiol 7:1104–1115
Dagar SS, Kumar S, Mudgil P et al (2011) D1/D2 domain of large-subunit ribosomal DNA for differentiation of Orpinomyces spp. Appl Environ Microbiol 77:6722–6725
Deborah T, Silvia V, Marco A et al (2011) The role of different methanogen groups evaluated by Real-Time qPCR as high-efficiency bioindicators of wet anaerobic co-digestion of organic waste. AMB Express 1:28
Demirel B, Scherer P (2008) The roles of acetotrophic and hydrogenotrophic methanogens during anaerobic conversion of biomass to methane: a review. Rev Environ Sci Biotech 7:173–190
Demirel B, Scherer P (2011) Trace element requirements of agricultural biogas digesters during biological conversion of renewable biomass to methane. Biomass Bioenerg 35:992–998
Edelmann W, Joss A, Engeli H (1999) Two step anaerobic digestion of organic solid wastes. In: Mata Alvarez J, Tilehe A, Cecchi J (eds) 11 international symposium on anaerobic digestion of solid wastes. International Association of Water Quality, Barcelona, pp 150–153
Feng XM, Karlsson A, Svensson BH et al (2010) Impact of trace element addition on biogas production from food industrial waste-linking process to microbial communities. FEMS Microbiol Ecol 74:226–240
Goebel BM, Stackebrandt E (1994) Cultural and phylogenetic analysis of mixed microbial populations found in natural and commercial bioleaching environments. Appl Environ Microbiol 60:1614–1621
Handelsman J (2004) Metagenomics: application of genomics to uncultured microorganisms. Microbiol Mol Biol Rev 68:669–685
Higgins MJ, Novak JT (1997) Characterization of exocellular protein and its role in bioflocculation. J Environ Eng 123:479–485
Hofman-Bang J, Zhang D, Westermann P et al (2003) Molecular ecology of anaerobic reactor systems. Adv Biochem Eng Biotechnol 81:151–203
Houghton JI, Quarmby J, Stephenson T (2001) Municipal wastewater sludge dewaterability and the presence of microbial extracellular polymer. Water Sci Technol 44:373–379
Jaenicke S, Ander C, Bekel T et al (2011) Comparative and joint analysis of two metagenomic datasets from a biogas fermenter obtained by 454-pyrosequencing. PLoS One 6:e14519
Karr EA, Ng JM, Belchik SM, Sattley WM, Madigan MT, Achenbach LA (2006) Biodiversity of methanogenic and other archaea in the permanently frozen Lake Fryxell, Antarctica. Appl Environ Microbiol 72:1663–1666
Kato S, Haruta S, Cui ZJ et al (2004) Clostridium straminisolvens sp. nov., a moderately thermophilic, aerotolerant and cellulolytic bacterium isolated from a cellulose-degrading bacterial community. Int J Syst Evol Microbiol 54:2043–2047
Klocke M, Mähnert P, Mundt K et al (2007) Microbial community analysis of a biogas producing completely stirred tank reactor fed continuously with fodder beet silage as mono-substrate. Syst Appl Microbiol 30:139–151
Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J (2008) Phylogenetic classification of short environmental DNA fragments. Nucleic Acids Res 36:2230–2239
Kröber M, Bekel T, Diaz NN et al (2009) Phylogenetic characterization of biogas plant microbial community integrating clone library 16S-rDNA sequences and methagenome sequence data obtained by 454-pyrosequencing. J Biotechnol 142:38–49
Kumar S, Puniya AK, Puniya M et al (2009) Factors affecting rumen methanogens and methane mitigation strategies. World J Microbiol Biotechnol 25:1557–1566
Kumar S, Sumit SD, Mohanty AK et al (2011) Enumeration of methanogens with a focus on fluorescence in situ hybridization. Naturwissenschaften 98:457–472
Kumar S, Sumit SD, Puniya AK (2012) Isolation and characterization of methanogens from rumen of Murrah buffalo. Ann Microbiol 62:345–350
Kumar S, Sumit SD, Puniya AK et al (2013) Changes in methane emission, rumen fermentation in response to diet and microbial interactions. Res Vet Sci 94:263–268
Leclerc M, Delgènes JP, Godon JJ (2004) Diversity of the archaeal community in 44 anaerobic digesters as determined by single strand conformation polymorphism analysis and 16S rDNA sequencing. Environ Microbiol 6:809–819
Lefauconnier B, Hagen JO, Rudant JP (1994) Flow speed and calving rate of Kongsbreen glacier, 70°N Spitsbergen, Svalbard, using SPOT images. Polar Res 13:59–66
Leung K, Topp E (2001) Bacterial community dynamics in liquid swine manure during storage: molecular analysis using DGGE/PCR of 16S rDNA. FEMS Microbiol Ecol 38:169–177
Liu H, Fang HH (2002) Extraction of extracellular polymeric substances (EPS) of sludges. J Biotechnol 95:249–256
Liu Y, Whitman WB (2008) Metabolic, phylogenetic, and ecological diversity of the methanogenic archaea. Ann N Y Acad Sci 1125:171–189
McHugh S, Carton M, Mahony T et al (2003) Methanogenic population structure in a variety of anaerobic bioreactors. FEMS Microbiol Lett 219:297–304
Nettmann E, Bergmann I, Mundt K et al (2008) Archaea diversity within a commercial biogas plant utilizing herbal biomass determined by 16S rDNA and mcrA analysis. J Appl Microbiol 105:1835–1850
Nettmann E, Bergmann I, Pramschufer S et al (2010) Polyphasic analyses of methanogenic archaeal communities in agricultural biogas plants. Appl Environ Microbiol 76:2540–2548
Nicholas A, Ravella SR, Hobbs PJ (2012) Optimizing anaerobic digestion by selection of the immobilizing surface for enhanced methane production. Bioresour Technol 120:248–255
Pradhan S, Srinivas TNR, Pindi PK et al (2010) Bacterial diversity from Roopkund Glacier, Himalayan Mountain ranges, India. Extremophiles 14:377–395
Reddy GSN, Aggarwal RK, Matsumoto GI, Shivaji S (2000) Arthrobacter flavus sp. nov., a psychrophilic bacterium isolated from a pond in McMurdo Dry Valley, Antarctica. Int J Syst Evol Microbiol 50:1553–1561
Riesenfield SC, Goodman RM, Handelsman J (2004) Uncultural soil bacteria are a reservoir of new antibiotic resistance genes. Environ Microbiol 6:981–989
Schattauer A, Abdoun E, Weiland P et al (2011) Abundance of trace elements in demonstration biogas plants. Biosyst Eng 108:57–65
Schnürer A, Zellner G, Svensson BH (1999) Mesophilic syntrophic acetate oxidation during methane formation in biogas reactors. FEMS Microbiol Ecol 29:249–261
Shivaji S, Reddy GSN, Aduri RP et al (2004) Bacterial diversity of a soil sample from Schirmacher Oasis, Antarctica. Cell Mol Biol 50:525–536
Shivaji S, Kumari K, Kishore KH et al (2011) Vertical distribution of bacteria in a lake sediment from Antarctica by culture-independent and culture-dependent approaches. Res Microbiol 162:191–203
Sirohi SK, Pandey N, Singh B et al (2010) Rumen methanogens: a review. Indian J Microbiol 50:253–262
Sirohi SK, Singh N, Dagar SS et al (2012) Molecular tools for deciphering the microbial community structure and diversity in rumen ecosystem. Appl Microbiol Biotechnol 95:1135–1154
Sirohi SK, Chaudhary PP, Singh N et al (2013) The 16S rRNA and mcrA gene based comparative diversity of methanogens in cattle fed on high fibre based diet. Gene 523:161–166
Subramanian B, Yan S, Tyagi RD et al (2008) Isolation and molecular identification of extracellular polymeric substances (EPS) producing bacterial strains for sludge settling and dewatering. J Environ Sci Heal-A 43:1495–1503
Tolvanen KES, Karp MT (2011) Molecular methods for characterizing mixed microbial communities in hydrogen-fermenting systems. Int J Hydrog Energy. doi:10.1016/j.ijhydene.2011.01.029
Traversi D, Villa S, Acri M, Pietrangeli B, Degan R, Gilli G (2011) The role of different methnogen groups evaluated by real-time qPCR as high-efficiency bioindicators of wet anaerobic co- digestion of organic waste. AMB Express 1:28
Tsai YL, Olson BH (1991) Rapid method for direct extraction of DNA from soil and sediments. Appl Environ Microbiol 57:1070–1074
Tsai YL, Olson BH (1992) Rapid method for separation of bacterial DNA from humic substances in sediments for polymerase chain reaction. Appl Environ Microbiol 58:2292–2295
Urbain V, Block JC, Manem J (1993) Bioflocculation in activated sludge: an analytical approach. Water Res 27:829–838
Weiss A, Jerome V, Burghardt D et al (2009) Investigation of factors influencing biogas production in a large-scale thermophilic municipal biogas plant. Appl Microbiol Biotechnol 84:987–1001
Westerholm M, Roos S, Schnürer A (2010) Syntrophaceticus schinkii gen. nov., sp. nov., an anaerobic, syntrophic acetate-oxidizing bacterium isolated from a mesophilic anaerobic filter. FEMS Microbiol Lett 309:100–104
Wirth R, Kovács E, Maróti G et al (2012) Characterization of a biogas-producing microbial community by short-read next generation DNA sequencing. Biotechnol Biofuels 5:41
Woese CR, Kandler O, Wheelis ML (1990) Towards a natural system of organisms: proposal for the domains of Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A 87:4576–4579
Yeates C, Gillings MR, Davison AD et al (1998) Methods for microbial DNA extraction from soil for PCR amplification. Biol Proced Online 1:40–47
Yu Z, Morrison M, Schanbacher FL (2010) Production and utilization of methane biogas as renewable fuel. In: Vertes AA, Qureshi N, Yukawa H, Blaschek H (eds) Biomass to biofuels: strategies for global industries. Wiley, New York
Zinder SH (1993) Physiological ecology of methanogens. In: Ferry JG (ed) Methanogenesis: ecology, physiology, biochemistry, and genetics. Chapman & Hall, New York, pp 128–206
Acknowledgements
We thank the Biotechnology and Biological Sciences Research Council (BBSRC), UK, for the financial support. Sreenivas would like to thank Welsh European Funding Office (WEFO) for financial support.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2015 Springer India
About this chapter
Cite this chapter
Arunasri, K., Shivaji, S., Hobbs, P.J., Potu, M., Kishore, S., Ravella, S.R. (2015). Molecular Characterisation of Euryarchaeotal Community Within an Anaerobic Digester. In: Puniya, A., Singh, R., Kamra, D. (eds) Rumen Microbiology: From Evolution to Revolution. Springer, New Delhi. https://doi.org/10.1007/978-81-322-2401-3_20
Download citation
DOI: https://doi.org/10.1007/978-81-322-2401-3_20
Publisher Name: Springer, New Delhi
Print ISBN: 978-81-322-2400-6
Online ISBN: 978-81-322-2401-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)