1887

Abstract

Structures of free-living and protozoa-associated methanogen (PAM) communities from forage-fed cattle were investigated by comparative sequence analysis of 16S rRNA and methyl coenzyme M reductase () gene clone libraries. The free-living and protozoa-associated communities were composed of the same three genera [namely , and rumen cluster C (RCC), which is distantly related to ]; however, the distribution of the methanogen genera differed between the two communities. Despite previous reports of potential bias for the degenerate primer set, the 16S rRNA ( = 100 clones) and ( = 92 clones) gene libraries exhibited a similar distribution pattern for the three methanogenic genera. RCC was more abundant in the free-living community and represented 72 and 42 % of the 16S rRNA and gene sequences, respectively, versus 54 and 13 % of the 16S rRNA and gene sequences from the PAM community, respectively. The majority of RCC sequences from the free-living and protozoa-associated communities belonged to different species-level operational taxonomic units. species were more abundant in the PAM community and represented 42 and 79 % of clones for the 16S rRNA and gene libraries, respectively, versus 9 and 27 % of 16S rRNA and gene clones from the free-living community, respectively. species were predominantly free-living. Primers for quantitative PCR were designed to target specific methanogen groups and used to assess the effect of a high-grain diet on methanogen species composition. Switching the ruminant diet from forage to high-grain resulted in reduced protozoal diversity, along with a profound overall reduction in the relative abundance of RCC and an increase in the relative abundance of free-living spp. It was unclear whether the reduced abundance of RCC in grain-fed animals was due to the loss of symbiotic protozoa species or due to broader changes in the rumen environment that affected both RCC and protozoa. Importantly, results from this study emphasize the need to consider the different methanogen communities when developing strategies for mitigating methane emissions in ruminants.

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2012-07-01
2019-10-17
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References

  1. Beauchemin K. A., McAllister T. A., McGinn S. M.. ( 2009;). Dietary mitigation of enteric methane from cattle. . CAB Reviews 4:, 1–18. [CrossRef]
    [Google Scholar]
  2. Cadillo-Quiroz H., Yashiro E., Yavitt J. B., Zinder S. H.. ( 2008;). Characterization of the archaeal community in a minerotrophic fen and terminal restriction fragment length polymorphism-directed isolation of a novel hydrogenotrophic methanogen. . Appl Environ Microbiol 74:, 2059–2068. [CrossRef][PubMed]
    [Google Scholar]
  3. Chagan I., Tokura M., Jouany J. P., Ushida K.. ( 1999;). Detection of methanogenic archaea associated with rumen ciliate protozoa. . J Gen Appl Microbiol 45:, 305–308. [CrossRef][PubMed]
    [Google Scholar]
  4. Dehority B. A.. ( 1993;). Laboratory Manual for Classification and Morphology of Rumen Ciliate Protozoa. Boca Raton, FL:: CRC Press;.
    [Google Scholar]
  5. Evans P. N., Hinds L. A., Sly L. I., McSweeney C. S., Morrison M., Wright A. D.. ( 2009;). Community composition and density of methanogens in the foregut of the Tammar wallaby (Macropus eugenii). . Appl Environ Microbiol 75:, 2598–2602. [CrossRef][PubMed]
    [Google Scholar]
  6. Finlay B. J., Fenchel T.. ( 1989;). Hydrogenosomes in some anaerobic protozoa resembling mitochondria. . FEMS Microbiol Lett 65:, 311–314. [CrossRef]
    [Google Scholar]
  7. Finlay B. J., Esteban G., Clarke K. J., Williams A. G., Embley T. M., Hirt R. P.. ( 1994;). Some rumen ciliates have endosymbiotic methanogens. . FEMS Microbiol Lett 117:, 157–161. [CrossRef][PubMed]
    [Google Scholar]
  8. Hegarty R. S.. ( 1999;). Reducing rumen methane emissions through elimination of rumen protozoa. . Aust J Agric Res 50:, 1321–1327. [CrossRef]
    [Google Scholar]
  9. Huber T., Faulkner G., Hugenholtz P.. ( 2004;). Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. . Bioinformatics 20:, 2317–2319. [CrossRef][PubMed]
    [Google Scholar]
  10. IPCC ( 2007;). Climate Change 2007: the Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change. Edited by Solomon S., Qin D., Manning M., Marquis M., Averyt K., Tignor M. M. B., Miller H. L. Jr, Chen Z... Cambridge:: Cambridge University Press;.
    [Google Scholar]
  11. Irbis C., Ushida K.. ( 2004;). Detection of methanogens and proteobacteria from a single cell of rumen ciliate protozoa. . J Gen Appl Microbiol 50:, 203–212. [CrossRef][PubMed]
    [Google Scholar]
  12. Janssen P. H., Kirs M.. ( 2008;). Structure of the archaeal community of the rumen. . Appl Environ Microbiol 74:, 3619–3625. [CrossRef][PubMed]
    [Google Scholar]
  13. Johnson K. A., Johnson D. E.. ( 1995;). Methane emissions from cattle. . J Anim Sci 73:, 2483–2492.[PubMed]
    [Google Scholar]
  14. Livak K. J., Schmittgen T. D.. ( 2001;). Analysis of relative gene expression data using real-time quantitative PCR and the method. . Methods 25:, 402–408. [CrossRef][PubMed]
    [Google Scholar]
  15. Lozupone C., Hamady M., Knight R.. ( 2006;). UniFrac – an online tool for comparing microbial community diversity in a phylogenetic context. . BMC Bioinformatics 7:, 371. [CrossRef][PubMed]
    [Google Scholar]
  16. Lueders T., Friedrich M. W.. ( 2003;). Evaluation of PCR amplification bias by terminal restriction fragment length polymorphism analysis of small-subunit rRNA and mcrA genes by using defined template mixtures of methanogenic pure cultures and soil DNA extracts. . Appl Environ Microbiol 69:, 320–326. [CrossRef][PubMed]
    [Google Scholar]
  17. Mosoni P., Martin C., Forano E., Morgavi D. P.. ( 2011;). Long-term defaunation increases the abundance of cellulolytic ruminococci and methanogens but does not affect the bacterial and methanogen diversity in the rumen of sheep. . J Anim Sci 89:, 783–791. [CrossRef][PubMed]
    [Google Scholar]
  18. Ohene-Adjei S., Teather R. M., Ivan M., Forster R. J.. ( 2007;). Postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen. . Appl Environ Microbiol 73:, 4609–4618. [CrossRef][PubMed]
    [Google Scholar]
  19. Olfert E. D., Cross B. M., McWilliam A. A.. ( 1993;). Guide to the Care and Use of Experimental Animals, 2nd edn, vol. 1.. Ottawa: Canadian Council on Animal Care. http://www.ccac.ca/en_/standards/guidelines
    [Google Scholar]
  20. Regensbogenova M., McEwan N. R., Javorsky P., Kisidayova S., Michalowski T., Newbold C. J., Hackstein J. H., Pristas P.. ( 2004;). A re-appraisal of the diversity of the methanogens associated with the rumen ciliates. . FEMS Microbiol Lett 238:, 307–313. [CrossRef][PubMed]
    [Google Scholar]
  21. Schloss P. D., Larget B. R., Handelsman J.. ( 2004;). Integration of microbial ecology and statistics: a test to compare gene libraries. . Appl Environ Microbiol 70:, 5485–5492. [CrossRef][PubMed]
    [Google Scholar]
  22. Schloss P. D., Westcott S. L., Ryabin T., Hall J. R., Hartmann M., Hollister E. B., Lesniewski R. A., Oakley B. B., Parks D. H.. & other authors ( 2009;). Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. . Appl Environ Microbiol 75:, 7537–7541. [CrossRef][PubMed]
    [Google Scholar]
  23. Sharma R., John S. J., Damgaard M., McAllister T. A.. ( 2003;). Extraction of PCR-quality plant and microbial DNA from total rumen contents. . Biotechniques 34:, 92–94, 96–97.[PubMed]
    [Google Scholar]
  24. Sharp R., Ziemer C. J., Stern M. D., Stahl D. A.. ( 1998;). Taxon-specific associations between protozoal and methanogen populations in the rumen and a model rumen system. . FEMS Microbiol Ecol 26:, 71–78. [CrossRef]
    [Google Scholar]
  25. Skillman L. C., Evans P. N., Strömpl C., Joblin K. N.. ( 2006;). 16S rDNA directed PCR primers and detection of methanogens in the bovine rumen. . Lett Appl Microbiol 42:, 222–228. [CrossRef][PubMed]
    [Google Scholar]
  26. Smoot M. E., Ono K., Ruscheinski J., Wang P. L., Ideker T.. ( 2011;). Cytoscape 2.8: new features for data integration and network visualization. . Bioinformatics 27:, 431–432. [CrossRef][PubMed]
    [Google Scholar]
  27. Stackebrandt E., Goebel B. M.. ( 1994;). Taxonomic note: a place for DNA-DNA reassociation and 16S rRNA sequence analysis in the present species definition in bacteriology. . Int J Syst Bacteriol 44:, 846–849. [CrossRef]
    [Google Scholar]
  28. Tajima K., Nagamine T., Matsui H., Nakamura M., Aminov R. I.. ( 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 Microbiol Lett 200:, 67–72. [CrossRef][PubMed]
    [Google Scholar]
  29. Tamura K., Peterson D., Peterson N., Stecher G., Nei M., Kumar S.. ( 2011;). mega5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. . Mol Biol Evol 28:, 2731–2739. [CrossRef][PubMed]
    [Google Scholar]
  30. Thompson J. D., Higgins D. G., Gibson T. J.. ( 1994;). clustal w: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. . Nucleic Acids Res 22:, 4673–4680. [CrossRef][PubMed]
    [Google Scholar]
  31. Tokura M., Chagan I., Ushida K., Kojima Y.. ( 1999;). Phylogenetic study of methanogens associated with rumen ciliates. . Curr Microbiol 39:, 123–128. [CrossRef][PubMed]
    [Google Scholar]
  32. Tymensen L. D., McAllister T. A.. ( 2012;). Community structure analysis of methanogens associated with rumen protozoa reveals bias in universal archaeal primers. . Appl Environ Microbiol 78:, 4051–4056. [CrossRef][PubMed]
    [Google Scholar]
  33. Wright A. D., Toovey A. F., Pimm C. L.. ( 2006;). Molecular identification of methanogenic archaea from sheep in Queensland, Australia reveal more uncultured novel archaea. . Anaerobe 12:, 134–139. [CrossRef][PubMed]
    [Google Scholar]
  34. Wright A. D., Auckland C. H., Lynn D. H.. ( 2007;). Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. . Appl Environ Microbiol 73:, 4206–4210. [CrossRef][PubMed]
    [Google Scholar]
  35. Zhang Z., Schwartz S., Wagner L., Miller W.. ( 2000;). A greedy algorithm for aligning DNA sequences. . J Comput Biol 7:, 203–214. [CrossRef][PubMed]
    [Google Scholar]
  36. Zhou M., Hernandez-Sanabria E., Guan L. L.. ( 2009;). Assessment of the microbial ecology of ruminal methanogens in cattle with different feed efficiencies. . Appl Environ Microbiol 75:, 6524–6533. [CrossRef][PubMed]
    [Google Scholar]
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