Abstract
Biogas digesters contain microbial assemblages that process a mass of extracellular polymeric substances from animal manure and domestic wastewater; however, due to the limitation of available technology in cultivation of majority of the micro-organisms in biogas digesters, the enzymatic potential of these microbial communities remains largely unexplored. In this study, to evaluate subtilase gene diversity in a biogas digester, the partial sequences of the gene were directly amplified from the metagenomic DNA by using consensus-degenerate primers. The desired PCR products were cloned into pGEM-T Easy vector, and thirty positive clones were chose for Polymerase chain reaction–restriction fragment length polymorphism (PCR–RFLP) analysis, from which thirteen distinguished patterns were obtained and then sequenced. Phylogenetic analysis showed that ten out of the thirteen sequences were related to the subtilase genes in GenBank and were grouped into three families of the subtilases superfamily. The nucleotide sequences analysis through BLAST search revealed that none of the partial genes the authors isolated showed significant similarity against the non-redundant Nucleotide database of NCBI. Meanwhile, the deduced amino acid sequences of ten partial subtilase genes showed moderate identities to the previously identified sequences in GenBank, with a range from 39 to 61%. Collectively, the data indicate that there is a great diversity of subtilase genes in the biogas digester; and may be a rich reservoir for novel subtilase genes.
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Acevedo JP, Reyes F, Parra LP et al (2008) Cloning of complete genes for novel hydrolytic enzymes from Antarctic sea water bacteria by use of an improved genome walking technique. J Biotechnol 133:277–286
Amann R, Ludwig W, Schleifer K (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59:143–169
Chen X, Xie B, Lu J et al (2007) A novel type of subtilase from the psychrotolerant bacterium Pseudoalteromonas sp. SM9913: catalytic and structural properties of deseasin MCP-01. Microbiology 153:2116–2125
Chen Y, Yang GH, Sandra S et al (2010) Household biogas use in rural China: a study of opportunities and constraints. Renew Sust Energ Rev 1:545–549
Cheng G, Zhao P, Tang X et al (2009) Identification and characterization of a novel spore-associated subtilase from Thermoactinomyces sp. CDF. Microbiology 155:3661–3672
Cheng XJ, Qiu TL, Wang M et al (2010) Screening of microbial community in biogas fermentation under low temperature and construction of its metagenome library. China biotechnol 30:50–55
Deublein D, Steinhauser A (2008) Biogas from waste and renewable resources—an introduction. Wiley-VCH, Weinheim
Don RH, Cox PT, Wainwright BJ et al (1991) ‘Touchdown’ PCR to circumvent spurious priming during gene amplification. Nucleic Acids Res 19:4008
Ekici ÖD, Paetzel M, Dalbey RE (2008) Unconventional serine proteases: variations on the catalytic Ser/His/Asp triad configuration. Protein Sci 17:2023–2037
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Ferrer M, Martínez-Abarca F, Golyshin PN (2005) Mining genomes and ‘metagenomes’ for novel catalysts. Curr Opin Biotechnol 16:588–593
Gupta R, Beg Q, Lorenz P (2002) Bacterial alkaline proteases: molecular approaches and industrial applications. Appl Microbio Biotechnol 59:15–32
Harmsen HJM, Van Kuijk BLM, Plugge CM et al (1998) Syntrophobacter fumaroxidans sp. nov., a syntrophic propionate-degrading sulfate-reducing bacterium. Int J Syst Bacteriol 48:1383–1387
Hill DT, Taylor SE, Grift TE (2001) Simulation of low temperature anaerobic digestion of dairy and swine manure. Bioresour Technol 78:127–131
Kindaichi T, Ito T, Okabe S (2004) Ecophysiological interaction between nitrifying bacteria and heterotrophic bacteria in autotrophic nitrifying biofilms as determined by microautoradiography-fluorescence in situ hybridization. Appl Environ Microbiol 70:1641–1650
Korbie DJ, Mattick JS (2008) Touchdown PCR for increased specificity and sensitivity in PCR amplification. Nat Protocol 3:1452–1456
Larkin MA, Blackshields G, Brown NP et al (2007) Clustal W and Clustal X version 2.0. Bioinformatics 23:2947–2948
McKeown RM, Scully C, Enright A-M et al (2009) Psychrophilic methanogenic community development during long-term cultivation of anaerobic granular biofilms. ISME J 11:1231–1242
Miyamoto K, Tsujibo H, Nukui E et al (2002) Isolation and characterization of the genes encoding two metalloproteases (MprI and MprII) from a Marine Bacterium, Alteromonas sp. Strain O-7. Biosci Biotechnol Biochem 66:416–421
Miyazaki M, Nogi Y, Usami R et al (2006) Shewanella surugensis sp. nov., Shewanella kaireitica sp. nov. and Shewanella abyssi sp. nov., isolated from deep-sea sediments of Suruga Bay, Japan. Int J Syst Evol Microbiol 56:1607–1613
Møller HB, Sommer SG, Ahring BK (2004) Methane productivity of manure, straw and solid fractions of manure. Biomass Bioenergy 26:485–495
Ollivier BM, Mah RA, Ferguson TJ et al (1985) Emendation of the genus Thermobacteroides: Thermobacteroides proteolyticus sp. nov., a proteolytic acetogen from a methanogenic enrichment. Int J Syst Bacteriol 35:425–428
Polgár L (2005) The catalytic triad of serine peptidases. Cell Mol Life Sci 62:2161–2172
Rainey FA, Stackebrandt E (1993) Transfer of the type species of the genus Thermobacteroides to the genus Thermoanaerobacter as Thermoanaerobacter acetoethylicus(Ben-Bassat and Zeikus 1981) comb. nov., description of Coprothermobacter gen. nov., and reclassification of Thermobacteroides proteolyticus as Coprothermobacter proteolyticus(Ollivier et al. 1985) comb. nov. Int J Syst Bacteriol 43:857–859
Ramos C, Grilo A, Sousa S et al (2010) A new methodology combining PCR, cloning, and sequencing of clones discriminated by RFLP for the study of microbial populations: application to an UASB reactor sample. Appl Microbiol Biotechnol 85:801–806
Raunkjær K, Hvitved-Jacobsen T, Nielsen PH (1994) Measurement of pools of protein, carbohydrate and lipid in domestic wastewater. Water Res 28:251–262
Ravena RPJM, Gregersenb KH (2007) Biogas plants in Denmark: successes and setbacks. Renew Sust Energ Rev 1:116–132
Riviere D, Desvignes V, Pelletier E et al (2009) Towards the definition of a core of microorganisms involved in anaerobic digestion of sludge. ISME J 6:700–714
Safley LM Jr, Westerman PW (1994) Low-temperature digestion of dairy and swine manure. Bioresour Technol 47:165–171
Saitou N, Nei M (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425
Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual. Cold Spring Harbor Laboratory, New York
Siezen RJ, Renckens B, Boekhorst J (2007) Evolution of prokaryotic subtilases: genome-wide analysis reveals novel subfamilies with different catalytic residues. Protein Struct Funct Bioinf 67:681–694
Siezen RJ, Leunissen JAM (1997) Subtilases: the superfamily of subtilisin-like serine proteases. Protein Sci 6:501–523
Sokolova TG, Kostrikina NA, Chernyh NA et al (2005) Thermincola carboxydiphila gen. nov., sp. nov., a novel anaerobic, carboxydotrophic, hydrogenogenic bacterium from a hot spring of the lake Baikal area. Int J Syst Evol Microbiol 55:2069–2073
Tamura K, Dudley J, Nei M et al (2007) MEGA4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599
Yoon J, Matsuo Y, Adachi K et al (2008) Description of Persicirhabdus sediminis gen. nov., sp. nov., Roseibacillus ishigakijimensis gen. nov., sp. nov., Roseibacillus ponti sp. nov., Roseibacillus persicicus sp. nov., Luteolibacter pohnpeiensis gen. nov., sp. nov. and Luteolibacter algae sp. nov., six marine members of the phylum ‘Verrucomicrobia’, and emended descriptions of the class Verrucomicrobiae, the order Verrucomicrobiales and the family Verrucomicrobiaceae. Int J Syst Evol Microbiol 58:998–1007
Zhou J, Bruns M, Tiedje J (1996) DNA recovery from soils of diverse composition. Appl Environ Microbiol 62:316–322
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The authors are very grateful to the reviewers of this article for their careful review, constructive suggestions and language improving. The authors wish to thank Wen-jun Shen for her help in English correcting of the manuscript.
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This study was supported by the Key Program of Beijing Municipal Natural Science Foundation (no. 5081001).
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Cheng, X., Gao, M., Wang, M. et al. Subtilase Genes Diversity in the Biogas Digester Microbiota. Curr Microbiol 62, 1542–1547 (2011). https://doi.org/10.1007/s00284-011-9876-6
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DOI: https://doi.org/10.1007/s00284-011-9876-6