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Chemical markers for rumen methanogens and methanogenesis

  • C. A. McCartney (a1) (a2), I. D. Bull (a2) and R. J. Dewhurst (a1)

Abstract

The targeting of mcrA or 16S rRNA genes by quantitative PCR (qPCR) has become the dominant method for quantifying methanogens in rumen. There are considerable discrepancies between estimates based on different primer sets, and the literature is equivocal about the relationship with methane production. There are a number of problems with qPCR, including low primer specificity, multiple copies of genes and multiple genomes per cell. Accordingly, we have investigated alternative markers for methanogens, on the basis of the distinctive ether lipids of archaeal cell membranes. The membranes of Archaea contain dialkyl glycerol ethers such as 2,3-diphytanayl-O-sn-glycerol (archaeol), and glycerol dialkyl glycerol tetraethers (GDGTs) such as caldarchaeol (GDGT-0) in different proportions. The relationships between estimates of methanogen abundance using qPCR and archaeol measurements varied across primers. Studies in other ecosystems have identified environmental effects on the profile of ether lipids in Archaea. There is a long history of analysing easily accessible samples, such as faeces, urine and milk, to provide information about digestion and metabolism in livestock without the need for intrusive procedures. Purine derivatives in urine and odd-chain fatty acids in milk have been used to study rumen function. The association between volatile fatty acid proportions and methane production is probably the basis for empirical relationships between milk fatty acid profiles and methane production. However, these studies have not yet identified consistent predictors. We have evaluated the relationship between faecal archaeol concentration and methane production across a range of diets in studies on beef and dairy cattle. Faecal archaeol is diagnostic for ruminant faeces being below the limit of detection in faeces from non-ruminant herbivores. The relationship between faecal archaeol and methane production was significant when comparing treatment means across diets, but appears to be subject to considerable between-animal variation. This variation was also evident in the weak relationship between archaeol concentrations in rumen digesta and faeces. We speculate that variation in the distribution and kinetics of methanogens in the rumen may affect the survival and functioning of Archaea in the rumen and therefore contribute to genetic variation in methane production. Indeed, variation in the relationship between the numbers of micro-organisms present in the rumen and those leaving the rumen may explain variation in relationships between methane production and both milk fatty acid profiles and faecal archaeol. As a result, microbial markers in the faeces and milk are unlikely to relate well back to methanogenesis in the rumen. This work has also highlighted the need to describe methanogen abundance in all rumen fractions and this may explain the difficulty interpreting results on the basis of samples taken using stomach tubes or rumenocentesis.

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Bessa, RJB, Maia, MRG, Jeronimo, E, Belo, AT, Cabrita, ARJ, Dewhurst, RJ, Fonseca, AJM 2009. Using microbial fatty acids to improve understanding of the contribution of solid associated bacteria to microbial mass in the rumen. Animal Feed Science and Technology 150, 197206.
Bhagwat, AM, De Baets, B, Steen, A, Vlaeminck, B, Fievez, V 2012. Prediction of ruminal volatile fatty acid proportions of lactating dairy cows based on milk odd- and branched-chain fatty acid profiles: new models, better predictions. Journal of Dairy Science 95, 39263937.
Brulc, JM, Antonopoulos, DA, Miller, ME, Wilson, MK, Yannarell, AC, Dinsdale, EA, Edwards, RE, Emerson, JB, Wacklin, P, Coutinho, PM, Henrissat, B, Nelson, KE, White, BA 2009. Gene-centric metagenomics of fiber-adherent bovine rumen microbiome reveals forage specific glycoside hydrolases. Proceedings of the National Academy of Sciences 106, 19481953.
Casto Montoya, JM, Bhagwat, AM, Peiren, N, De Campeneere, S, De Baets, B, Fievez, V 2011. Relationship between odd- and branched-chain fatty acid profiles in milk and calculated enteric methane production for lactating dairy cows. Animal Feed Science and Technology 166–167, 596602.
Chen, XB, Ørskov, ER, Hovell, FDD 1990. Excretion of purine derivatives by ruminants: endogenous excretion differences between cattle and sheep. British Journal of Nutrition 63, 121129.
Chilliard, Y, Martin, C, Rouel, J, Doreau, M 2009. Milk fatty acids in dairy cows fed whole crude linseed, extruded linseed, or linseed oil, and their relationship with methane output. Journal of Dairy Science 92, 51995211.
Dehareng, F, Delfosse, C, Froidmont, E, Soyeurt, H, Martin, C, Gengler, N, Vanlierde, A, Dardenne, P 2012. Potential use of milk mid-infrared spectra to predict individual methane emissions of dairy cows. Animal 6, 16941701.
Dehority, BA, Tirabasso, PA 1998. Effect of ruminal celluloytic bacterial concentrations on in situ digestion of forage cellulose. Journal of Animal Science 76, 29052911.
Dewhurst, RJ, Davies, DR, Merry, RJ 2000. Microbial protein supply from the rumen. Animal Feed Science and Technology 85, 121.
Dewhurst, RJ, Moorby, JM, Vlaeminck, B, Van Nespen, T, Fievez, V 2007. Apparent recovery of duodenal odd- and branched-chain fatty acids in milk. Journal of Dairy Science 90, 17751780.
Diedrich, M, Henschel, KP 1990. The natural occurrence of unusual fatty acids. 1. Odd numbered fatty acids. Nahrung 34, 935943.
Dijkstra, J, Van Zijderveld, SM, Apajalahti, JA, Bannink, A, Gerrits, WJJ, Newbold, JR, Perdock, HB, Berends, H 2011. Relationships between methane production and milk fatty acid profiles in dairy cattle. Animal Feed Science and Technology 166, 590595.
Ding, X, Long, R, Zhang, Q, Huang, X, Guo, X, Mi, J 2012. Reducing methane emissions and the methanogen population in the rumen of Tibetan sheep by dietary supplementation with coconut oil. Tropical Animal Health and Production 44, 15411545.
Fievez, V, Colman, E, Castro-Montoya, JM, Stefanov, I, Vlaeminck, B 2012. Milk odd- and branched-chain fatty acids as biomarkers of rumen function – an update. Animal Feed Science and Technology 172, 5165.
Firkins, JL, Yu, Z 2006. Characterisation of quantification of the microbial populations of the rumen. In Ruminant physiology: digestion, metabolism and impact of nutrition on gene expression, immunology and stress (ed. K Sejrsen, T Hvelplund and MO Nielson), pp. 1954. Wageningen Academic Publishers, The Netherlands.
Frey, JC, Pell, AN, Berthiaume, R, Lapierre, H, Lee, S, Ha, JK, Mendell, JE, Angert, ER 2010. Comparative studies of microbial populations in the rumen, duodenum, ileum and faeces of lactating dairy cows. Journal of Applied Microbiology 108, 19821993.
Fritze, H, Tikka, P, Pennanen, T, Saano, A, Jurgens, G, Nilsson, M, Bergman, I, Kitunen, V 1999. Detection of archaeal diether lipid by gas chromatography from humus and peat. Scandinavian Journal of Forest Research 14, 545551.
Gill, FL, Dewhurst, RJ, Evershed, RP, McGeough, E, O'Kiely, P, Pancost, RD, Bull, ID 2011. Analysis of archaeal ether lipids in bovine faeces. Animal Feed Science and Technology 166, 8792.
Gill, FL, Dewhurst, RJ, Dungait, JAJ, Evershed, RP, Ives, L, Li, CS, Pancost, RD, Sullivan, M, Bera, S, Bull, ID 2010. Archaeol – a biomarker for foregut fermentation in modern and ancient herbivorous mammals? Organic Geochemistry 41, 467472.
Gu, MJ, Alam, MJ, Kim, SH, Jeon, CO, Chang, MB, Oh, YK, Lee, SC, Lee, SS 2011. Analysis of methanogenic archaeal communities of rumen fluid and rumen particles from Korean black goats. Animal Science Journal 82, 663672.
Guo, YQ, Liu, JX, Lu, Y, Zhu, WY, Denman, SE, McSweeney, CS 2008. Effect of tea saponin on methanogenesis, microbial community structure and expression of mcrA gene, in cultures of rumen micro-organisms. Letters in Applied Microbiology 47, 421426.
Hegarty, RS 2004. Genotype differences and their impact on digestive tract function of ruminants: a review. Australian Journal of Experimental Agriculture 44, 459467.
Hildenbrand, C, Stock, T, Lange, C, Rother, M, Soppa, J 2011. Genome copy numbers and gene conversion in methanogenic Archaea. Journal of Bacteriology 193, 734743.
Hook, SE, Northwood, KS, Wright, ADG, McBride, BW 2009. Long-term monensin supplementation does not significantly affect the quantity or diversity of methanogens in the rumen of the lactating dairy cow. Applied and Environmental Microbiology 75, 374380.
Hopmans, EC, Weijers, JWH, Schefub, E, Herfort, L, Sinninghe Damste, JS, Schouten, S 2004. A novel proxy for terrestrial organic matter in sediments based on branched and isoprenoid tetraether lipids. Earth and Planetary Science Letters 224, 107116.
Huguet, A, Fosse, C, Metzger, P, Fritsch, E, Derenne, S 2010. Occurrence and distribution of extractable glycerol dialkyl glycerol tetraethers in podzols. Organic Geochemistry 41, 291301.
Janssen, PH, Kirs, M 2008. Structure of the archaeal community of the rumen. Applied and Environmental Microbiology 74, 36193625.
Jenkins, TC 2005. Butylsoyamide protects soybean oil from ruminal biohydrogenation: effects of butylsoyamide on plasma fatty acids and nutrient digestion in sheep. Journal of Animal Science 73, 23762381.
Kim, EJ, Sanderson, R, Dhanoa, MS, Dewhurst, RJ 2005. Fatty acid profiles associated with microbial colonization of freshly ingested grass and rumen biohydrogenation. Journal of Dairy Science 88, 32203230.
Koga, Y, Nishihara, M, Morii, H, Akagawa-Matsushita, M 1993. Ether polar lipids of methanogenic bacteria: structures, comparative aspects, and biosyntheses. Microbiological Reviews 57, 164182.
Koga, Y, Kyruagi, T, Nishihara, M, Sone, N 1998. Did archaeal and bacterial cells arise independently from noncellular precursors? A hypothesis stating that the advent of membrane phospholipid with enantiomeric glycerophosphate backbones caused the separation of the two lines of descent. Journal of Molecular Evolution 46, 5463.
Lee, HJ, Jung, JY, Oh, YK, Lee, SS, Madsen, EL, Jeon, CO 2012. Comparative survey of rumen microbial communities and metabolites across one caprine and three bovine groups, using bar-coded pyrosequencing and 1H nuclear magnetic resonance spectroscopy. Applied and Environmental Microbiology 78, 59835993.
Leng, RA, Gill, M, Kempton, TJ, Rowe, BJ, Nolan, JV, Stachiw, SJ, Preston, TR 1981. Kinetics of large ciliate protozoa in the rumen of cattle given sugar cane diets. British Journal of Nutrition 46, 371384.
Liu, C, Zhu, ZP, Liu, YF, Guo, TJ, Dong, HM 2012. Diversity and abundance of the rumen and fecal methanogens in Altay sheep native to Xinijang and the influence of diversity of methane emissions. Archives of Microbiology 194, 353361.
Mao, HL, Wang, JK, Zhou, YY, Liu, JX 2010. Effects of addition of tea saponins and soybean oil on methane production, fermentation and microbial population in the rumen of growing lambs. Livestock Science 129, 5662.
Mathai, JC, Sprott, GD, Zeidel, ML 2001. Molecular mechanisms of water and solute transport across archaebacterial lipid membranes. Journal of Biological Chemistry 275, 2726627271.
McCartney, CA 2012. Ether lipids as biomarkers for methanogenic Archaea in the ruminant gastro-intestinal tract. PhD Thesis, University of Bristol, Bristol, UK.
McCartney, CA, Bull, ID, Yan, T, Dewhurst, RJ 2013. Assessment of archaeol as a molecular proxy for methane production in cattle. Journal of Dairy Science 96, 12111217.
McGeough, EJ, O'Kiely, PO, Hart, KJ, Moloney, AP, Boland, TM, Kenny, DA 2010. Methane emissions, feed intake, performance, digestibility, and rumen fermentation of finishing beef cattle offered whole-crop wheat silages differing in grain content. Journal of Animal Science 88, 27032716.
Mohammed, R, McGinn, SM, Beauchemin, JA 2011. Prediction of enteric methane output from milk fatty acids concentrations and rumen fermentation parameters in dairy cows fed sunflower, flax or canola seeds. Journal of Dairy Science 94, 60576068.
Morgavi, DP, Martin, C, Jouany, JP, Ranilla, MJ 2012. Rumen protozoa and methanogenesis: not a simple cause-effect relationship. British Journal of Nutrition 107, 388397.
Mosoni, P, Martin, C, Forano, E, Morgavi, DP 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. Journal of Animal Science 89, 783791.
Odongo, NE, Or-Rashid, MM, Kebreab, E, France, J, McBride, BW 2007. Effect of supplementing myristic acid in dairy cow rations on ruminal methanogenesis and fatty acids profile in milk. Journal of Dairy Science 90, 18511858.
Pancost, RD, McClymont, EL, Bingham, EM, Roberts, Z, Charman, DJ, Hornibrook, ERC, Blundell, A, Chambers, FM, Lim, KLH, Evershed, RP 2011. Archaeol as a methanogen biomarker in ombrotrophic bogs. Organic Geochemistry 42, 12791287.
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, 2029.
Pinares-Patiño, CS, Clark, H 2008. Reliability of the sulfur hexafluoride tracer technique for methane emission measurement from individual animals: an overview. Australian Journal of Experimental Agriculture 48, 223229.
Polidori, P, Maggi, GL, Moretti, VM, Valfre, F, Navarotto, P 1993. A note of the effect of the use of bovine somatotrophin on the fatty acid composition of milk fat in dairy cows. Animal Production 57, 319322.
Schouten, S, Hopmans, EC, Sinninghe Damsté, JS 2013. The organic geochemistry of glycerol dialkyl tetraether lipids: a review. Organic Geochemistry 54, 1961.
Schouten, S, Hopmans, EC, Schefuβ, E, Sinninghe Damsté, JS 2002. Distributional variations in marine crenarchaeotal membrane lipids: a new tool for reconstructing ancient sea water temperatures? Earth and Planetary Science Letters 204, 265274.
Sharp, R, Ziemer, CJ, Stern, MD, Stahl, DA 1998. Taxon-specific associations between protozoal and methanogen populations in the rumen and a model rumen system. FEMS Microbiology Ecology 26, 7178.
Shimada, H, Nemoto, N, Shida, Y, Oshima, T, Yamagishi, A 2008. Effects of pH and temperature on the composition of polar lipids in Thermoplasma acidophilum HO-62. Journal of Bacteriology 190, 54045411.
Shin, EC, Choi, BR, Lim, WJ, Hong, SY, An, CL, Cho, KM, Kim, YK, An, JM, Kang, JM, Lee, SS, Kim, H, Yun, HD 2004. Phylogenetic analysis of archaea in three fractions of cow rumen based on the 16S rDNA sequence. Anaerobe 10, 313319.
Shingfield, KJ, Offer, NW 1998. Evaluation of milk allantoin excretion as an index of microbial protein supply in lactating dairy cows. Animal Science 67, 371385.
Stouthamer, AH, Bettenhaussen, C 1973. Utilization of energy for growth and maintenance in continuous and batch cultures of microorganisms. Biochemica et Biophysica Acta 301, 5370.
Thauer, RK 1998. Biochemistry of methanogenesis: a tribute to Marjory Stephenson. Microbiology 144, 23772406.
Tymensen, LD, McAllister, TA 2012. Community structure analysis of methanogens associated with rumen protozoa reveals bias in universal archaeal primers. Applied and Environmental Microbiology 78, 40514056.
Valentine, DL 2007. Adaptations to energy stress dictate the ecology and evolution of the Archaea. Nature Reviews Microbiology 5, 316323.
Vlaeminck, B, Fievez, F 2005. Potential of milk odd- and branched-chain fatty acids to predict ruminal methanogenesis in dairy cows. In Proceedings of the second international conference on greenhouse gases and animal agriculture Zurich, Switzerland, 393396.
Vlaeminck, B, Fievez, V, Cabrita, ARJ, Fonseca, AJM, Dewhurst, RJ 2006. Factors affecting odd- and branched-chain fatty acids in milk: a review. Animal Feed Science and Technology 131, 389417.
Weijers, JWH, Schouten, S, van Den Donker, JC, Hopmans, EC, Sinninghe Damsté, JS 2007. Environmental controls on bacterial tetraether membrane lipid distribution in soils. Geochimica et Cosmochimica Acta 71, 703713.
Zhou, YY, Mao, HL, Jiang, F, Wang, JX, McSweeney, CS 2011a. Inhibition of rumen methanogenesis by tea saponins with reference to fermentation pattern and microbial communities in Hu sheep. Animal Feed Science and Technology 166–167, 93100.
Zhou, M, Chung, YH, Beauchemin, KA, Holtshausen, L, Oba, M, McAllister, TA, Guan, LL 2011b. Relationship between rumen methanogens and methane production in dairy cows fed diets supplemented with a feed enzyme additive. Journal of Applied Microbiology 111, 11481158.

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