Analysis of methanogenic archaeal communities of rumen fluid and rumen particles from Korean black goats

Animal Science Journal

Volumn 82, Issue 5, 2011, Pages 663-672

  Gu, Min Jung ^a   Alam, Md Jahangir ^a   Kim, Seon Ho ^a   Jeon, Che Ok ^b   Chang, Moon Baek ^b   Oh, Young Kyoon ^c   Lee, Sang Cheol ^c   Lee, Sang Suk ^a  

^a Sunchon National University   (South Korea)

^b Chung Ang University   (South Korea)

^c National Institute of Animal Science   (South Korea)

Author keywords

Korean black goat; Methanobacteriaceae; Methanogens; Rumen; Thermoplasmatales

Indexed keywords

RNA 16S;

AGE; ANIMAL; ANIMAL FOOD; ARTICLE; GENE LIBRARY; GENETIC VARIABILITY; GENETICS; GOAT; ISOLATION AND PURIFICATION; METHANOBACTERIACEAE; MICROBIOLOGY; PHYLOGENY; REAL TIME POLYMERASE CHAIN REACTION; RUMINANT STOMACH; SEQUENCE ANALYSIS; THERMOPLASMATALES;

AGE FACTORS; ANIMAL FEED; ANIMALS; GENE LIBRARY; GENETIC VARIATION; GOATS; METHANOBACTERIACEAE; PHYLOGENY; REAL-TIME POLYMERASE CHAIN REACTION; RNA, RIBOSOMAL, 16S; RUMEN; SEQUENCE ANALYSIS, RNA; THERMOPLASMALES;

ARCHAEA; CAPRA HIRCUS; METHANOBACTERIACEAE; THERMOPLASMATALES; UNCULTURED METHANOGENIC ARCHAEON;

EID: 80053216434     PISSN: 13443941     EISSN: 17400929     Source Type: Journal    
DOI: 10.1111/j.1740-0929.2011.00890.x     Document Type: Article

References (55)

1. Amann RI, Ludwig W, Schleifer K. 1995. Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiological Reviews 59, 143-169.
2. An D, Dong X, Dong Z. 2005. Prokaryote diversity in the rumen of yak (Bos grunniens) and Jinnan cattle (Bos taurus) estimated by 16S rDNA homology analyses. Anaerobe 11, 207-215.
3. Archimède H, Sauvant D, Hervieu J, Ternois F, Poncet C. 1996. Effects of the nature of roughage and concentrate and their proportion on rumina1 characteristics of non lactating goats, consequence on digestive interactions. Animal Feed Science and Technology 58, 267-282.
4. Australian Greenhouse Office (AGO). 2003. National Greenhouse Gas Inventory 2001 with Methodology Supplements. Australian Greenhouse Office, Canberra, Australia.
5. Bergey DH. 1994. The methanogens. In: Holt JG (ed.), Bergey's Manual of Determinative Bacteriology, 9th edn, pp. 719-725. Williams and Wilkins Co., Baltimore, MD.
6. Chaney AL, Marbach EP. 1962. Modified reagents for determination of urea and ammonia. Clinical Chemistry 8, 130-132.
7. Chao A. 1984. Non-parametric estimation of the number of classes in a population. Scandinavian Journal of Statistics 11, 783-791.
8. Cheng YF, Edwards JE, Allison GG, Zhu WY, Theodorou MK. 2009. Diversity and activity of enriched ruminal cultures of anaerobic fungi and methanogens grown together in consecutive batch culture. Bioresource Technology 100, 4821-4828.
9. Cheng YF, Mao SY, Pei CX, Liu JX, Zhu WY. 2006. Detection and diversity analysis of rumen methanogens in co-cultures with anaerobic fungi. Acta Microbiologica Sinica 46, 879-883.
10. Christophersen CT. 2007. Grain and artificial stimulation of the rumen change the abundance and diversity of methanogens and their association with ciliates. Ph.D. thesis. University of Western Australia, Perth, Western Australia, Australia.
11. Hughes JB, Hellmann JJ, Ricketts TH, Bohannan BJ. 2001. Counting the uncountable: statistical approaches to estimating microbial diversity. Applied and Environmental Microbiology 67, 4399-4406.
12. Intergovernmental Panel on Climate Change (IPCC). 2001. Climate change. In: Houghton JT, Ding Y (eds), The Scientific Basis, Intergovernmental Panel on Climate Change, pp. 85-98. Cambridge University Press, New York.
13. Janssen PH, Kirs M. 2008. Structure of the archaeal community of the rumen. Applied and Environmental Microbiology 74, 3619-3625.
14. Jarvis GN, Strompl C, Burgess DM, Skillman LC, Moore ERB, Joblin KN. 2000. Isolation and identification of ruminal methanogens from grazing cattle. Current Microbiology 40, 327-332.
15. Johnson KA, Johnson DE. 1995. Methane emissions from cattle. Journal of Animal Science 73, 2483-2492.
16. Kemnitz D, Kolb S, Conrad R. 2005. Phenotypic characterization of rice cluster III archaea without prior isolation by applying quantitative polymerase chain reaction to an enrichment culture. Environmental Microbiology 7, 553-565.
17. Kimura M. 1980. A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. Journal of Molecular Evolution 16, 111-120.
18. Kocherginskaya SA, Aminov RI, White BA. 2001. Analysis of the rumen bacterial diversity under two different diet conditions using denaturing gradient gel electrophoresis, random sequencing, and statistical ecology approaches. Anaerobe 7, 119-134.
19. Kumar S, Puniya AK, Puniya M, Dagar SS, Sirohi SK, Singh K, Griffith GW. 2009. Factors affecting rumen methanogens and methane mitigation strategies. World Journal of Microbiology and Biotechnology 25, 1557-1566.
20. Lana RP, Russell JB, Van Amburgh ME. 1998. The role of pH in regulating ruminal methane and ammonia production. Journal of Animal Science 76, 2190-2196.
21. Leadbetter JR, Breznak JA. 1996. Physiological ecology of Methanobrevibacter cuticularis sp. nov. and Methanobrevibacter curvatus sp. nov., isolated from the hindgut of the termite Reticulitermes flavipes. Applied and Environmental Microbiology 62, 3620-3631.
22. Leadbetter JR, Crosbyand LD, Breznak JA. 1998. Methanobrevibacter filiformis sp. nov., a filamentous methanogen from termite hindguts. Archives of Microbiology 169, 287-292.
23. Lin C, Miller TL. 1998. Phylogenetic analysis of Methanobrevibacter isolated from feces of humans and other animals. Archives of Microbiology 169, 397-403.
24. Magurran AE. 1996. Ecological Diversity and Its Measurement. Chapman and Hall, London.
25. McAllister TA, Okine EK, Mathison GW, Cheng KJ. 1996. Dietary, environmental, and microbiological aspects of methane production in ruminants. Canadian Journal of Animal Science 76, 231-243.
26. Miller TL, Lin C. 2002. Description of Methanobrevibacter gottschalkii sp. nov., Methanobrevibacter thaueri sp. nov., Methanobrebibacter woesei sp. nov. and Methanobrevibacter wolinii sp. nov. International Journal of Systematic and Evolutionary Microbiology 52, 819-822.
27. Miller TL, Wolin MJ, Kusel EA. 1986. Isolation and characterization of methanogens from animal feces. Systematic and Applied Microbiology 8, 234-238.
28. Ministry of Agriculture and Forestry (MAF). 2008. Statistical Yearbook of Agriculture. Forestry and Fisheries; MAF, Seoul, Republic of Korea.
29. Miron J, Ben-Ghedalia D, Morrison M. 2001. Adhesion mechanisms of rumen cellulolytic bacteria. Journal of Dairy Science 84, 1294-1309.
30. Nicholson MJ, Evans PN, Joblin KN. 2007. Analysis of methanogen diversity in the rumen using temporal temperature gradient gel electrophoresis: identification of uncultured methanogens. Microbial Ecology 54, 141-150.
31. Pei CX, Mao SY, Cheng YF, Zhu WY. 2010. Diversity, abundance and novel 16S rRNA gene sequences of methanogens in rumen liquid, solid and epithelium fractions of Jinnan cattle. Animal 4, 20-29.
32. Pitchford P. 1993. Healing with Whole Foods-Oriental Tradition and Modern Nutrition, p. 338. North Atlantic Books, Berkeley, CA.
33. Ramsak A, Peterka M, Tajima K, Martin JC, Wood J, Johnston MEA, Aminov RI, Flint HJ, Avgustin G. 2000. Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiology Ecology 33, 69-79.
34. Rea S, Bowman JP, Popovski S, Pimm C, Wright ADG. 2007. Methanobrevibacter millerae sp. nov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth. International Journal of Systematic and Evolutionary Microbiology 57, 450-456.
35. SAS Institute. 2003. SAS User's Guide. Version 9.1. SAS Institute, Cary, NC.
36. Shannon CE, Weaver W. 1949. The Mathematical Theory of Communication. University of Illinois Press, Urbana, IL.
37. Sharp R, Ziemer CJ, Stern MD, Stahl DA. 1998. Taxon-specific associations between protozoal and methanogen populations in the rumen and model rumen system. FEMS Microbiology Ecology 26, 71-78.
38. Shin EC, Choi BR, Lim WJ, Hong SY, An CL, Cho KM, Kim YK, An JM, Kang JM, Lee SS, Kim H. 2004. Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence. Anaerobe 10, 313-319.
39. Son YS. 1999. Production and uses of Korean Native Black Goat. Small Ruminant Research 34, 303-308.
40. Stewart CS, Flint HJ, Bryant MP. 1997. The rumen bacteria. In: Hobson PN, Stewart CS (eds), The Rumen Microbial Ecosystem, 2nd edn, pp. 10-72. Blackie Academic and Professoressional, New York.
41. Sundset MA, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Præsteng KE, Glad T, Mathiesen SD, Wright ADG. 2009. Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea. FEMS Microbiology Letters 70, 553-562.
42. Tajima K, Arai S, Ogata K, Nagamine T, Matsui H, Nakamura M, Aminov RI, Benno Y. 2000. Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6, 273-284.
43. Tajima K, Nagamine T, Matsui H, Nakamura M, Aminov RI. 2001. Phylogenetic analysis of archaeal 16S rRNA libraries from the rumen suggests the existence of a novel group of archaea not associated with known methanogens. FEMS Microbiology Letters 200, 67-72.
44. Theodorou MK, Zhu WY, Rickers A, Nielsen BB, Gull K, Trinci APJ. 1996. Biochemistry and ecology of anaerobic fungi. In: Mycota VI, Howard DH, Miller JD (eds), Human and Animal Relationships, pp. 265-295. Springer-Verlag, Berlin.
45. Thompson JD, Higgins DG, Gibson TJ. 1994. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22, 4673-4680.
46. Ushida K, Ohashi Y, Tokura M, Miyazaki K, Kojima Y. 1995. Sulphate reduction and methanogenesis in the ovine rumen and porcine caecum: a comparison of two microbial ecosystems. Dtsch Tierarztl Wochenschr 102, 154-156.
47. Whitford MF, Teather RM, Forster RJ. 2001. Phylogenetic analysis of methanogens from the bovine rumen. BMC Microbiology 1, 5-9.
48. Woese CR, Kandler O, Wheelis ML. 1990. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proceedings of the National Academy of Sciences of the United States of America 87, 4576-4579.
49. Wolin MJ, Miller TL, Stewart CS. 1997. Microbe-microbe interactions. In: Hobson PN, Stewart CS (eds), The Rumen Microbial Ecosystem, 2nd edn, pp. 467-491. Blackie Academic and Professoressional, New York.
50. Wright ADG, Auckland CH, Lynn DH. 2007. Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Applied and Environmental Microbiology 73, 4206-4210.
51. Wright ADG, Ma X, Obispo NE. 2008. Methanobrevibacter phylotypes are the dominant methanogens in sheep from Venezuela. Microbial Ecology 56, 390-394.
52. Wright ADG, Pimm C. 2003. Improved strategy for presumptive identification of methanogens using 16S riboprinting. Journal of Microbiological Methods 55, 337-349.
53. Wright ADG, Toovey AF, Pimm CL. 2006. Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveals more uncultured novel archaea. Anaerobe 12, 134-139.
54. Wright ADG, Williams AJ, Winder B, Christophersen CT, Rodgers SL, Smith KD. 2004. Molecular diversity of rumen methanogens from sheep in Western Australia. Applied and Environmental Microbiology 70, 1263-1270.
55. Wuebbles DJ, Hayhoe K. 2002. Atmospheric methane and global change. Earth-Science Reviews 57, 117-210.