Abstract
Non-lactating dairy cattle were transitioned to a high-concentrate diet to investigate the effect of ruminal pH suppression, commonly found in dairy cattle, on the density, diversity, and community structure of rumen methanogens, as well as the density of rumen protozoa. Four ruminally cannulated cows were fed a hay diet and transitioned to a 65% grain and 35% hay diet. The cattle were maintained on an high-concentrate diet for 3 weeks before the transition back to an hay diet, which was fed for an additional 3 weeks. Rumen fluid and solids and fecal samples were obtained prior to feeding during weeks 0 (hay), 1, and 3 (high-concentrate), and 4 and 6 (hay). Subacute ruminal acidosis was induced during week 1. During week 3 of the experiment, there was a significant increase in the number of protozoa present in the rumen fluid (P = 0.049) and rumen solids (P = 0.004), and a significant reduction in protozoa in the rumen fluid in week 6 (P = 0.003). No significant effect of diet on density of rumen methanogens was found in any samples, as determined by real-time PCR. Clone libraries were constructed for weeks 0, 3, and 6, and the methanogen diversity of week 3 was found to differ from week 6. Week 3 was also found to have a significantly altered methanogen community structure, compared to the other weeks. Twenty-two unique 16S rRNA phylotypes were identified, three of which were found only during high-concentrate feeding, three were found during both phases of hay feeding, and seven were found in all three clone libraries. The genus Methanobrevibacter comprised 99% of the clones present. The rumen fluid at weeks 0, 3, and 6 of all the animals was found to contain a type A protozoal population. Ultimately, high-concentrate feeding did not significantly affect the density of rumen methanogens, but did alter methanogen diversity and community structure, as well as protozoal density within the rumen of nonlactating dairy cattle. Therefore, it may be necessary to monitor the rumen methanogen and protozoal communities of dairy cattle susceptible to depressed pH when methane abatement strategies are being investigated.
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Altschul SF, Madden TL, Schaffer AA, Zhang J, Chang J, Miller W, Lipman DI (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25:3389–3402
AlZahal O, Kebreab E, France J, McBride BW (2007) A mathematical approach to predicting biological values from ruminal pH measurements. J Dairy Sci 90:3777–3785
AlZahal O, Rustomo B, Odongo NE, Duffield TF, McBride BW (2007) Technical note: a system for continuous recording of ruminal pH in cattle. J Anim Sci 85:213–217
de Rijk P, de Wachter R (1993) DCSE, an interactive tool for sequence alignment and secondary structure research. Comput Appl Biosci 9:735–740
Dehority BA (1993) Laboratory manual for classification and morphology of rumen ciliate protozoa. CRC Press, Florida
Dehority BA (2005) Effect of pH on viability of Entodinium caudatum, Entodinium exiguum, Epidinium caudatum, and Ophryoscolex purkynjei in vitro. J Eukaryot Microbiol 52:339–342
Dehority BA, Orpin CG (1997) Development of, and natural fluctuations in, rumen microbial populations. In: Hobson PN, Stewart CS (eds) The rumen microbial ecosystem, 2nd edn. Chapman & Hall, Great Britain, pp 196–245
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 62:313–322
Felsenstein J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39:783–791
Franzolin R, Dehority BA (1996) Effect of prolonged high-concentrate feeding on ruminal protozoa concentrations. J Anim Sci 74:2803–2809
Goad DW, Goad CL, Nagaraja TG (1998) Ruminal microbial and fermentative changes associated with experimentally induced subacute acidosis in steers. J Anim Sci 76:234–241
Gozho GN, Plaizier JC, Krause DO, Kennedy AD, Wittenberg KM (2005) Subacute ruminal acidosis induces ruminal lipopolysaccharide release and triggers an inflammatory response. J Dairy Sci 88:1399–1403
Hook SE, Northwood KS, Wright A-DG, 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. Appl Environ Microbiol 75:374–380
Huber T, Faulkner G, Hugenholtz P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20:2317–2319
Jarvis GN, Strompl C, Burgess DM, Skillman LC, Moore ERB, Joblin KN (2000) Isolation and identification of ruminal methanogens from grazing cattle. Curr Microbiol 40:327–332
Khafipour E, Li S, Plaizier JC, Krause DO (2009) Rumen microbiome composition determined using two nutritional models of subacute ruminal acidosis. Appl Environ Microbiol 75:7115–7124
Kimura M (1980) A simple method of estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences. J Mol Evol 16:111–120
Krumholz LR, Forsberg CW, Veira DM (1983) Association of methanogenic bacteria with rumen protozoa. Can J Microbiol 29:676–680
Miller TL, Wolin MJ (1985) Methanosphaera stadtmaniae gen. nov., sp. nov.: a species that forms methane by reducing methanol with hydrogen. Arch Microbiol 141:116–122
Nagaraja TG, Bartley EE, Fina LR, Anthony HD (1978) Relationship of rumen gram-negative bacteria and free endotoxin to lactic acidosis in cattle. J Anim Sci 47:1329–1336
Nocek JE (1997) Bovine acidosis: implications on laminitis. J Dairy Sci 80:1005–1028
Ohene-Adjei S, Teather RM, Ivan M, Forster RJ (2007) Postinoculation protozoan establishment and association patterns of methanogenic archaea in the ovine rumen. Appl Environ Microbiol 73:4609–4618
Purser DB, Moir RJ (1966) Variations in rumen volume and associated effects as factors influencing metabolism and protozoa concentrations in the rumen of sheep. J Anim Sci 15:516–520
Rea S, Bowman JP, Popovski S, Pimm C, Wright A-DG (2007) Methanobrevibacter millerae sp. ov. and Methanobrevibacter olleyae sp. nov., methanogens from the ovine and bovine rumen that can utilize formate for growth. Int J Syst Evol Microbiol 57:450–456
Saito N, Nei M (1987) The neighbor-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4:406–425
Schloss PD, Westcott SL, Ryabin T, Hall JR, Hartmann M, Hollister EB, Lesniewski RA, Oakley BB, Parks DH, Robinson CJ, Sahl JW, Stres B, Thallinger GG, Van Horn DJ, Weber CF (2009) Introducing mothur: open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol 75:7537–7541
Shannon CE, Weaver W (1949) The mathematical theory of communication. University of Illinois Press, Urbana
Singleton DR, Furlong MA, Rathburn SL, Whitman WB (2001) Quantitative comparisons of 16S rDNA sequence libraries from environmental samples. Appl Environ Microbiol 67:4373–4376
Skillman LC, Toovey AF, Williams AJ, Wright A-DG (2006) Development and validation of a real-time PCR method to quantify rumen protozoa and examination of variability between Entodinium populations in sheep offered a hay-based diet. Appl Environ Microbiol 72:200–206
Steele MA, AlZahal O, Hook SE, Croom J, McBride BW (2009) Ruminal acidosis and the rapid onset of ruminal parakeratosis in a mature dairy cow: a case report. Acta Vet Scand 51:39
Steele MA, Croom J, Kahler M, AlZahal O, Hook SE, Plaizier K, McBride BW (2011) Bovine rumen epithelium undergoes rapid structural adaptations during grain-induced subacute ruminal acidosis. Am J Physiol Regul Integr Comp Physiol. doi:10.1152/ajpregu.00120.2010
Steele MA, Vandervoort G, AlZahal O, Hook SE, Matthews JC, McBride BW (2011) Rumen epithelial adaptation to high grain diets involves the coordinated regulation of genes involved in cholesterol homeostasis. Physiol Genomics 43:308–316
Sundset MA, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Præsteng KE, Glad T, Mathiesen SD, Wright A-DG (2009) Molecular diversity of the rumen microbiome of Norwegian reindeer on natural summer pasture. Microb Ecol 57:335–348
Sundset MA, Edwards JE, Cheng YF, Senosiain RS, Fraile MN, Northwood KS, Præsteng KE, Glad T, Mathiesen SD, Wright A-DG (2009) Rumen microbial diversity in Svalbard reindeer, with particular emphasis on methanogenic archaea. FEMS Microbiol Ecol 70:553–562
Swindell SR, Plasterer TN (1997) SEQMAN. Contig assembly. Methods Mol Biol 70:75–89
Sylvester JT, Karnati SKR, Yu Z, Morrison M, Firkins JL (2004) Development of an assay to quantify rumen ciliate protozoal biomass in cows using real-time PCR. J Nutr 134:3378–3384
Tajima K, Aminov RI, Nagamine T, Matsui H, Nakamura M, Benno Y (2001) Diet-dependent shifts in the bacterial population of the rumen revealed with real-time PCR. Appl Environ Microbiol 67:2766–2774
Teather RM, Mahadevan S, Erfle JD, Sauer FD (1984) Negative correlation between protozoal and bacterial levels in rumen samples and its relation to the determination of dietary effects on the rumen microbial population. Appl Environ Microbiol 47:566–570
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 Res 22:4673–4680
Towne G, Nagaraja TG, Brandt RT Jr, Kemp KE (1990) Ruminal ciliated protozoa in cattle fed finishing diets with or without supplemental fat. J Anim Sci 68:2150–2155
Van Kessel JAS, Russell JB (1996) The effect of pH on ruminal methanogenesis. FEMS Microbiol Ecol 20:205–210
Wang Z, Goonewardene LA (2004) The use of MIXED models in the analysis of animal experiments with repeated measures data. Can J Anim Sci 84:1–11
Wright A-DG, Pimm CL (2003) Improved strategy for presumptive identification of methanogens using 16S riboprinting. J Microbiol Methods 55:337–349
Wright A-DG, Auckland CH, Lynn DH (2007) Molecular diversity of methanogens in feedlot cattle from Ontario and Prince Edward Island, Canada. Appl Environ Microbiol 73:4206–4210
Wright A-DG, Dehority BA, Lynn DH (1997) Phylogeny of the rumen ciliates Entodinium, Epidinium and Polyplastron (Litostomatea: Entodiniomorphida) inferred from small subunit ribosomal RNA sequences. J Eukaryot Microbiol 44:61–67
Acknowledgments
The authors wish to acknowledge the barn staff at the University of Guelph, Dr. Ousama AlZahal for the pH monitoring and Dr. Margaret Quinton for the statistical consultation. Support from the Natural Science and Engineering Research Council (BWM) is gratefully acknowledged.
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Hook, S.E., Steele, M.A., Northwood, K.S. et al. Impact of High-Concentrate Feeding and Low Ruminal pH on Methanogens and Protozoa in the Rumen of Dairy Cows. Microb Ecol 62, 94–105 (2011). https://doi.org/10.1007/s00248-011-9881-0
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DOI: https://doi.org/10.1007/s00248-011-9881-0