Shoffiana Noor (1) , Hendro Pramono (2) , Saefuddin Aziz (3)

(1) Fakultas Biologi, Universitas Jenderal Soedirman
(2) Fakultas Biologi, Universitas Jenderal Soedirman
(3) Fakultas Biologi, Universitas Jenderal Soedirman


Ruminants produce methane gas which contributes to enhanced greenhouse effect in the atmosphere. Cattle issued the highest methane during the fermentation of feed in the rumen. Methane gas produced by methanogen bacteria in carbohydrates anaerobic fermentation. Methanogen bacteria are difficult to obtain diversity information because difficult cultured. One technique can be used is molecular rRNA 16S gene cloning and sequencing. This study was aims to determine the species diversity of methanogen bacteria in cattle's rumen using rRNA 16S gene cloning and sequencing technique by survey method. The results obtained 51 clones with 800 bp insert size length. The sequencing resulted 2 different sequences, ie 8-3L21 clone bacterium uncultured and BBS-12 clone methanogens rumen uncultured rRNA 16S gene partial sequence with 99% and 100% similarity. The Genus sequences for gene 1 and 3 were Prevotella (24%), Clostridium (1.5%), and other uncultured bacteria, whereas the 2 gene sequences of species was Methanobrevibacter ruminantium (21.83%), M. millerae (29.17%), M. gottschalkii (6.47%), Methanosphaera stadtmanae, and Methanobacterium alcaliphilum. This research provides scientific information about cattle rumen methanogen bacteria species diversity which can be used as a basis for control of cattle rumen methanogen bacteria. 


cattle rumen methanogens; rRNA 16S; gene cloning

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Amann RI, Ludwig W, Schleifer KH. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59: 143-169.

Applied Biosystem. 2000. Automated DNA sequencing: chemistry guide. Applera Copporation, Foster City, hlm. 246.

Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Sturhl K, Albright LM, Coen DM, Varki A, Jamsen K. 1995. Qurrent protocols in molecular biology. 2nd ed. John Wiley and Sons. Inc., Massachusetts 24(3): 1-9.

Ausubel FM, Brent R, Kingston RE, Moore DD, Seidman JG, Smith JA, Struhl K. 2002. Current protocol in molecular biology 1. John Wiley and Sons Inc., Canada 26(8): 1-2.

Borneman TD, Madigan MT, Martinko JM, Parker J. 1996. Biology of microorganism. 7th ed. Prentice-Hall, New Jersey 7: 909.

Brooker RJ. 2005. Genetics: analysis and principles. McGraw Hill Companies, Inc., Boston 26: 842.

Brown TA. 2006. Gene cloning and DNA analysis: An Introduction. 5th ed. Blackwell Publishing, Oxford 20: 386.

Chromas Lite. 2013. Version 2.1.1., Technelysium Pty Ltd, Australia.

Crustal W. 2012. Foster City. Ltd.

Davis LG, Kuehl WM, Battey JF. 1994. Basic methods in molecular biology. 2nd ed. Appleton and Lange. Connecticut 12: 777.

Ditjennak. 2007. Statistik peternakan. Direktorat Jenderal Peternakan, Departemen Pertanian, Jakarta.

Fairbanks DF, Andersen WR. 1999. Genetics: Continuity of Life. Brooks/Cole Publishing Company, New York 19: 820.

Fanani MZ. 2011. Eksplorasi novel gen glikosida hidrolase untuk degradasi biomassa: pendekatan secara metagenomik. Surabaya: Fakultas Sains dan Teknologi Universitas Airlangga.

Felske T, Akratanakul P, Nettanomsak S, Huntamai S. 1998. Larval habitats and distribution patterns of Aedes aegypti (Linnaeus) and Aedes albopictus (Skuse), in Thailand. Southeast Asian J. Tropical Medical Public Health 34(3): 529-535.

GeneJet™ Plasmid Kit. USA. 2013.

Hall BG. 2001. Phylogenetic trees made easy: a how to manual for molecular biologist. Sinaeur Associates, Inc., Sunderland 12: 179.

Hanahan D. 1983. Studies on transformation of Escherichia coli with plasmids. In: Sambrook, J. S. and D. W. Russell. 2001. Molecular Cloning : A Laboratory Manual. J. Mol. Biol 166: 557-580.

Handoyo D, Ari R. 2001. Manipulation and expression of recombinant DNA: A Laboratory Manual. 2nd ed. London: Elsevier Academic Press 16: 151.

Herison C, Rustikawati, Eliyanti. 2003. Penentuan protokol yang tepat untuk menyiapkan DNA genom cabai (Capsicum sp.). Jurnal Akta Agrosia 6(2): 38-43.

IPCC. 2006. Emission from Livestock and Manure Management. Guidelines for National Greenhouse Gas Inventories. Ch. 10.

Johnson KA, Johnson DE. 1995. Methane emissions from cattle. J. Anim. Sci 73: 2483-2492.

Lorenz K, Schleper A. 2002. Bioimformatics tools and guideline to PCR primer design. Afr. J. Biotechnol. 2(5): 91-95.

Mackie AT, Bryant DA. 1984. Identification of a novel group of bacteria in sludge from a deteriorated biological phosphorus removal reactor. AEM J. 65(3): 1251-1258.

Martin C, Doreau M, Morgavi DP. 2008. Methane mitigation in ruminants: from rumen microbes to the animal. Inra, Ur 1213, Herbivores Research Unit, Research Centre of Clermont-Ferrand-Theix. France: F-63122 St Genes Champanelle.

Moss AR. 1993. Methane Global Warming and Production by Animals. Chalcombe Publications, Canterbury.

NCBI. 2013. The BLAST sequence analysis tool, 1 November 2013.

Nercessian O, Bienvenu N, Moreira D, Prieur D, Jeanthon C. 2005. Diversity of functional genes of methanogens, methanotrophs, and sulfate reducers in deep-sea hydrothermal environments. Environ. Microbiol. 7(1): 118-132.

Old RW. Primrose SB. 2003. Prinsip-Prinsip Manipulasi Gen: Pengantar rekayasa genetika. Edisi ke-4. Terjemahan dari Principles of gene manipulation: an introduction to genetic engineering. 4th ed, oleh Susilo H, Oorebima AD. Jakarta: UI Press 8: 446.

Philekorea Technology INC. Xprep Plant DNA Mini Kit (RNase A Included). Gasan-dong, Geumcheon-gu, Seoul, Korea Selatan pp: 153-803.

Promega. 2008. pGEM®-T Easy vector systems: technical manual 42: 30.

Queen BJ. 2000. The transformation lab: experiment using E. coli and pFluoroGreen. MdBioLab hlm. 19.

Reeve G. 1994. Molecular biology of dengue viruses. New York: CAB International 175-198.

Riesenfeld CS, Goodman RM, Handelsman J. 2004. Uncultured soil bacteria are a reservoir of new antibiotic resistance genes. Environ. Microbiol. 6(9): 981-989.

Sambrook J, Fritsch EF, Manniatis T. 1989. Molecular cloning: a laboratory manual. 2nd ed. New York: Cold Spring Harbour Laboratory Press 38(31): 9.

Sambrook JS, Russell DW. 2001. Molecular cloning: a laboratory manual. Volume 1-3. 3rd ed. New York: Cold Spring Harbor Laboratory Press: xxvii + 18.136 + A. 14. 1 + R. 22 + 1. 44 hlm.

Shiddieqy CH. 2009. 16S rDNA fingerprinting of rhizosphere bacterial communities associated with healthy and phytophthora infected avocado roots. FEMS Microbiol. Ecol. 35: 129-136.

Schmeisser S, Talamin A, Debruyne M, Falconar A, Deubel V, Flamand M. 2007. Enzyme-linked immunosorbent assay spesific to dengue virus type-1 nonstructural protein ns1 reveals circulation of the antigen in the blood during the acute phase of disease in patients experiencing primary or secondary infections. J. of Clinical Microbiol. 40(2): 376-381.

Skillman LC, Evans PN, Naylor GE, Morvan B, Jarvis GN, Joblin KN. 2004. 16S Ribosomal DNA-directed PCR primers for ruminal methanogens and identi?cation of methanogens colonising young lambs. Anaerobe 10: 277-285.

Skillman LC, Evans PN, Strompl C, Joblin KN. 2006. 16S rDNA directed PCR primers and detection of methanogens in the bovine rumen. Lett. J. of Appl. Microbiol. 42: 222-228.

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