Skip to main content

Rumen protozoa and methanogenesis: not a simple cause–effect relationship

  • Diego P. Morgavi (a1), Cécile Martin (a1), Jean-Pierre Jouany (a1) and Maria José Ranilla (a2)

Understanding the interactions between hydrogen producers and consumers in the rumen ecosystem is important for ruminant production and methane mitigation. The present study explored the relationships between rumen protozoa, methanogens and fermentation characteristics. A total of six donor sheep harbouring (F, faunated) or not (D, defaunated) protozoa in their rumens (D animals were kept without protozoa for a period of a few months (D − ) or for more than 2 years (D+)) were used in in vitro and in vivo experiments. In vitro the absence of protozoa decreased NH3 and butyrate production and had no effect on methane. In contrast, the liquid-associated bacterial and methanogens fraction of D+ inocula produced more methane than D −  and F inoculum (P < 0·05). In vivo fermentation parameters of donor animals showed the same trend on NH3 and butyrate and showed that D+ animals were high methane emitters, while D −  were the lowest ( − 35 %). The concentration of dissolved dihydrogen measured after feeding followed the opposite trend. Methane emissions did not correlate with the relative abundance of methanogens in the rumen measured by quantitative PCR, but there was a trend for higher methanogens concentration in the solid-associated population of D+ animals compared with D −  animals. In contrast, PCR-denaturing gradient gel electrophoresis profiles of methanogens' methyl coenzyme-M reductase A gene showed a clear clustering in liquid-associated fractions for all three groups of donors but fewer differences in solid-associated fractions. These results show that the absence of protozoa may affect differently the methanogen community and methane emissions in wethers.

  • View HTML
    • Send article to Kindle

      To send this article to your Kindle, first ensure is added to your Approved Personal Document E-mail List under your Personal Document Settings on the Manage Your Content and Devices page of your Amazon account. Then enter the ‘name’ part of your Kindle email address below. Find out more about sending to your Kindle. Find out more about sending to your Kindle.

      Note you can select to send to either the or variations. ‘’ emails are free but can only be sent to your device when it is connected to wi-fi. ‘’ emails can be delivered even when you are not connected to wi-fi, but note that service fees apply.

      Find out more about the Kindle Personal Document Service.

      Rumen protozoa and methanogenesis: not a simple cause–effect relationship
      Available formats
      Send article to Dropbox

      To send this article to your Dropbox account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Dropbox.

      Rumen protozoa and methanogenesis: not a simple cause–effect relationship
      Available formats
      Send article to Google Drive

      To send this article to your Google Drive account, please select one or more formats and confirm that you agree to abide by our usage policies. If this is the first time you use this feature, you will be asked to authorise Cambridge Core to connect with your <service> account. Find out more about sending content to Google Drive.

      Rumen protozoa and methanogenesis: not a simple cause–effect relationship
      Available formats
Corresponding author
*Corresponding author: D. P. Morgavi, fax +33 4 73 62 42 73, email
Hide All
1 Steinfeld, H, Gerber, P, Wassenaar, T, et al. (2006) Livestock's Long Shadow Environmental Issues and Options, pp. 390. Rome: FAO.
2 Lassey, KR (2008) Livestock methane emission and its perspective in the global methane cycle. Aust J Exp Agric 48, 114118.
3 Forster, P, Ramaswamy, V, Artaxo, P, et al. (2007) Changes in atmospheric constituents and in radiative forcing. In Climate Change 2007: The Physical Science Basis. Contribution of Working Group I to the Fourth Assessment Report of the Intergovernmental Panel on Climate Change [Solomon, S, Qin, D, Manning, M, Chen, Z, Marquis, M, Averyt, KB, Tignor, M and Miller, HL, editors]. Cambridge/New York: Cambridge University Press.
4 Shindell, DT, Faluvegi, G, Koch, DM, et al. (2009) Improved attribution of climate forcing to emissions. Science 326, 716718.
5 Morgavi, DP, Forano, E, Martin, C, et al. (2010) Microbial ecosystem and methanogenesis in ruminants. Animal 4, 10241036.
6 Boadi, D, Benchaar, C, Chiquette, J, et al. (2004) Mitigation strategies to reduce enteric methane emissions from dairy cows: update review. Can J Anim Sci 84, 319335.
7 Hegarty, RS (1999) Reducing rumen methane emissions through elimination of rumen protozoa. Aust J Agric Res 50, 13211327.
8 Machmüller, A, Soliva, CR & Kreuzer, M (2003) Effect of coconut oil and defaunation treatment on methanogenesis in sheep. Reprod Nutr Dev 43, 4155.
9 Bird, SH, Hegarty, RS & Woodgate, R (2008) Persistence of defaunation effects on digestion and methane production in ewes. Aust J Exp Agric 48, 152155.
10 Hegarty, RS, Bird, SH, Vanselow, BA, et al. (2008) Effects of the absence of protozoa from birth or from weaning on the growth and methane production of lambs. Br J Nutr 100, 12201227.
11 Williams, YJ, Popovski, S, Rea, SM, et al. (2009) A vaccine against rumen methanogens can alter the composition of archaeal populations. Appl Environ Microbiol 75, 18601866.
12 Eugène, M, Archimède, H & Sauvant, D (2004) Quantitative meta-analysis on the effects of defaunation of the rumen on growth, intake and digestion in ruminants. Livest Prod Sci 85, 8197.
13 Mosoni, P, Martin, C, Forano, E, et al. (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, 783791.
14 Williams, AG & Withers, SE (1993) Changes in the rumen microbial population and its activities during the refaunation period after the reintroduction of ciliate protozoa into the rumen of defaunated sheep. Can J Microbiol 39, 6169.
15 Ozutsumi, Y, Tajima, K, Takenaka, A, et al. (2006) Real-time PCR detection of the effects of protozoa on rumen bacteria in cattle. Curr Microbiol 52, 158162.
16 Janssen, PH (2010) Influence of hydrogen on rumen methane formation and fermentation balances through microbial growth kinetics and fermentation thermodynamics. Anim Feed Sci Technol 160, 122.
17 Jouany, JP & Senaud, J (1979) Defaunation of the sheep rumen. Ann Biol Anim Biochim Biophys 19, 619624.
18 Goering, HK & VanSoest, PJ (1970) Forage Fibre Analysis. Washington, DC: Agricultural Research Service, US Department of Agriculture.
19 Johnson, K, Huyler, M, Westberg, H, et al. (1994) Measurement of methane emissions from ruminant livestock using a SF6 tracer technique. Environ Sci Technol 28, 359362.
20 Martin, C, Rouel, J, Jouany, JP, et al. (2008) Methane output and diet digestibility in response to feeding dairy cows crude linseed, extruded linseed, or linseed oil. J Anim Sci 86, 26422650.
21 Denman, SE, Tomkins, NW & McSweeney, CS (2007) Quantitation and diversity analysis of ruminal methanogenic populations in response to the antimethanogenic compound bromochloromethane. FEMS Microbiol Ecol 62, 313322.
22 Edwards, JE, Huws, SA, Kim, EJ, et al. (2007) Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen. FEMS Microbiol Ecol 62, 323335.
23 Edwards, JE, Huws, SA, Kim, EJ, et al. (2008) Characterization of the dynamics of initial bacterial colonization of nonconserved forage in the bovine rumen. FEMS Microbiol Ecol 63, 141142.
24 Denman, SE & McSweeney, CS (2006) Development of a real-time PCR assay for monitoring anaerobic fungal and cellulolytic bacterial populations within the rumen. FEMS Microbiol Ecol 58, 572582.
25 Schmittgen, TD & Livak, KJ (2008) Analyzing real-time PCR data by the comparative C(T) method. Nat Protoc 3, 11011108.
26 Luton, PE, Wayne, JM, Sharp, RJ, et al. (2002) The mcrA gene as an alternative to 16S rRNA in the phylogenetic analysis of methanogen populations in landfill. Microbiology 148, 35213530.
27 Muyzer, G, de Waal, EC & Uitterlinden, AG (1993) Profiling of complex microbial populations by denaturing gradient gel electrophoresis analysis of polymerase chain reaction-amplified genes coding for 16S rRNA. Appl Environ Microbiol 59, 695700.
28 Janse, I, Bok, J & Zwart, G (2004) A simple remedy against artifactual double bands in denaturing gradient gel electrophoresis. J Microbiol Methods 57, 279281.
29 Fromin, N, Hamelin, J, Tarnawski, S, et al. (2002) Statistical analysis of denaturing gel electrophoresis (DGE) fingerprinting patterns. Environ Microbiol 4, 634643.
30 Savelkoul, PH, Aarts, HJ, de Haas, J, et al. (1999) Amplified-fragment length polymorphism analysis: the state of an art. J Clin Microbiol 37, 30833091.
31 Larsen, N, Olsen, GJ, Maidak, BL, et al. (1993) The ribosomal database project. Nucleic Acids Res 21, 30213023.
32 Ogimoto, K & Imai, S (1981) Atlas of Rumen Microbiology. Tokyo: Japan Scientific Societies Press.
33 Morgavi, DP, Boudra, H, Jouany, JP, et al. (2003) Prevention of patulin toxicity on rumen microbial fermentation by SH-containing reducing agents. J Agric Food Chem 51, 69066910.
34 Weatherburn, MW (1967) Phenol-hypochlorite reaction for determination of ammonia. Anal Chem 39, 971974.
35 Davies, AW & Taylor, K (1965) Application of the autoanalyser in a river authority laboratory. Symposium Technicon 294300.
36 Broudiscou, L-P, Papon, Y & Broudiscou, A (1999) Effects of inorganic nitrogen and amino acids on the degradation of ammonia-treated barley straw and proteosynthesis in a continuous culture of rumen microbes. Anim Feed Sci Technol 77, 149162.
37 Robinson, JA, Strayer, RF & Tiedje, JM (1981) Method for measuring dissolved hydrogen in anaerobic ecosystems: application to the rumen. Appl Environ Microbiol 41, 545548.
38 Demeyer, DI (1991) Quantitative aspects of microbial metabolism in the rumen and hindgut. In Rumen Microbial Metabolism and Ruminant Digestion, pp. 217237 [Jouany, JP, editor]. Versailles: INRA Editions.
39 Imachi, H, Sakai, S, Sekiguchi, Y, et al. (2008) Methanolinea tarda gen. nov., sp. nov., sp. nov., a methane-producing archaeon isolated from a methanogenic digester sludge. Int J Syst Evol Microbiol 58, 294301.
40 Beauchemin, KA, McGinn, SM, Benchaar, C, et al. (2009) Crushed sunflower, flax, or canola seeds in lactating dairy cow diets: effects on methane production, rumen fermentation, and milk production. J. Dairy Sci 92, 21182127.
41 Machmüller, A, Soliva, CR & Kreuzer, M (2003) Methane-suppressing effect of myristic acid in sheep as affected by dietary calcium and forage proportion. Br J Nutr 90, 529540.
42 Martin, C, Ferlay, A, Chilliard, Y, et al. (2007) Rumen methanogenesis of dairy cows in response to increasing levels of dietary extruded linseeds. In Energy and Protein Metabolism and Nutrition, EAAP Publication, pp. 609610 [Ortigues-Marty, I, Miraux, N and Brand-Williams, W, editors]. Wageningen: Wageningen Academic Publishers.
43 Mao, H-L, Wang, J-K, Zhou, Y-Y, et al. (2010) Effects of addition of tea saponins and soybean oil on methane production, fermentation and microbial population in the rumen of growing lambs. Lives Sci 129, 5662.
44 Guan, H, Wittenberg, KM, Ominski, KH, et al. (2006) Efficacy of ionophores in cattle diets for mitigation of enteric methane. J Anim Sci 84, 18961906.
45 Ranilla, MJ, Jouany, JP & Morgavi, DP (2007) Methane production and substrate degradation by rumen microbial communities containing single protozoal species in vitro. Lett Appl Microbiol 45, 675680.
46 Morgavi, DP, Jouany, JP & Martin, C (2008) Changes in methane emission and rumen fermentation parameters induced by refaunation in sheep. Aust J Exp Agric 48, 6972.
47 Newbold, CJ, Lassalas, B & Jouany, JP (1995) The importance of methanogens associated with ciliate protozoa in ruminal methane production in vitro. Lett Appl Microbiol 21, 230234.
48 Williams, AG & Coleman, GS (1992) The Rumen Protozoa. New York, NY: Springer-Verlag New York Inc.
49 Hungate, RE (1967) Hydrogen as an intermediate in the rumen fermentation. Arch Microbiol 59, 158164.
50 van Nevel, CJ & Demeyer, DI (1996) Control of rumen methanogenesis. Environ Monit Assess 42, 7397.
51 Thauer, RK, Jungermann, K & Decker, K (1977) Energy conservation in chemotrophic anaerobic bacteria. Microbiol Mol Biol Rev 41, 100180.
52 Finlay, BJ, Esteban, G, Clarke, KJ, et al. (1994) Some rumen ciliates have endosymbiotic methanogens. FEMS Microbiol Lett 117, 157162.
53 Stumm, CK, Gijzen, HJ & Vogels, GD (1982) Association of methanogenic bacteria with ovine rumen ciliates. Br J Nutr 47, 9599.
54 Morgavi, DP, Jouany, JP, Martin, C, et al. (2006) Archaeal community structure diversity in the rumen of faunated and defaunated sheep. Int Congr Ser 1293, 127130.
55 Watanabe, T, Asakawa, S, Nakamura, A, et al. (2004) DGGE method for analyzing 16S rDNA of methanogenic archaeal community in paddy field soil. FEMS Microbiol Lett 232, 153163.
Recommend this journal

Email your librarian or administrator to recommend adding this journal to your organisation's collection.

British Journal of Nutrition
  • ISSN: 0007-1145
  • EISSN: 1475-2662
  • URL: /core/journals/british-journal-of-nutrition
Please enter your name
Please enter a valid email address
Who would you like to send this to? *


Type Description Title
Supplementary Figure

Morgavi Supplementary Material
Morgavi Supplementary Figure

 Unknown (301 KB)
301 KB


Full text views

Total number of HTML views: 0
Total number of PDF views: 0 *
Loading metrics...

Abstract views

Total abstract views: 0 *
Loading metrics...

* Views captured on Cambridge Core between <date>. This data will be updated every 24 hours.

Usage data cannot currently be displayed