Responses of anaerobic rumen fungal diversity (phylum Neocallimastigomycota) to changes in bovine diet

Journal of Applied Microbiology

Volumn 114, Issue 3, 2013, Pages 626-635

  Boots, B ^a   Lillis, L ^a   Clipson, N ^a   Petrie, K ^a   Kenny, D A ^a   Boland, T M ^a   Doyle, E ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

Anaerobic fungi; Diet; Diversity; Neocallimastigales; Rumen; Soya oil

Indexed keywords

MICROORGANISMS; OILSEEDS; VEGETABLE OILS; VOLATILE FATTY ACIDS;

ANAEROBIC FUNGUS; ANAEROBICS; CELLULOSE-RICH MATERIALS; DECOMPOSITION PRODUCTS; DIETARY CHANGES; DIVERSITY; FUNGAL DIVERSITY; NEOCALLIMASTIGALE; RUMEN; SOYA OIL;

FUNGI;

ACETIC ACID; BUTYRIC ACID; PROPIONIC ACID; SOYBEAN OIL; VOLATILE FATTY ACID;

ANOXIC CONDITIONS; DIET; DNA FINGERPRINTING; FUNGUS; METHANOGENESIS; POLYMERASE CHAIN REACTION; SPECIES DIVERSITY; VEGETABLE OIL;

ANAEROBIC RUMEN FUNGUS; ARTICLE; BIODIVERSITY; FORAGE; NEOCALLIMASTIGOMYCOTA; NONHUMAN; POLYMERASE CHAIN REACTION; RUMINANT STOMACH;

BOVINAE; FUNGI; NEOCALLIMASTIGALES;

EID: 84874001214     PISSN: 13645072     EISSN: 13652672     Source Type: Journal    
DOI: 10.1111/jam.12067     Document Type: Article

References (45)

1. Anderson, M.J. (2001) A new method for non-parametric multivariate analysis of variance. Austral Ecol 26, 31-46.
2. Anderson, M.J. and Willis, T.J. (2003) Canonical analysis of principal coordinates: a useful method of constrained ordination for ecology. Ecology 84, 511-525.
3. Bray, J.R. and Curtis, J.T. (1957) An ordination of the upland forest communities of Southern Wisconsin. Ecol Monogr 27, 325-349.
4. Broudiscou, L., van Nevel, C.J. and Demeyer, D.I. (1990) Effect of soya oil hydrolysate on rumen digestion in defaunated and refaunated sheep. Anim Feed Sci Tech 30, 51-67.
5. Calsamiglia, S., Busquet, M., Cardozo, P.W., Castillejos, L. and Ferret, A. (2007) Invited review:essential oils as modifiers of rumen microbial fermentation. J Dairy Sci 90, 2580-2595.
6. Denman, S.E., Nicholson, M.J., Brookman, J.L., Theodorou, M.K. and McSweeney, C.S. (2008) Detection and monitoring of anaerobic rumen fungi using an ARISA method. Lett Appl Microbiol 47, 492-499.
7. Dunbar, J., Ticknor, L.O. and Kuske, C.R. (2001) Phylogenetic specificity and reproducibility and new new method for analysis of terminal restriction fragment profiles of 16S rRNA genes from bacterial communities. Appl Environ Microb 67, 190-197.
8. Edwards, J.E., Kingston-Smith, A.H., Jimenez, H.R., Huws, S.A., Skøt, K.P., Griffith, G.W., McEwan, N.R. and Theodorou, M.K. (2008) Dynamics of initial colonization of nonconserved perennial ryegrass by anaerobic fungi in the bovine rumen. FEMS Microbiol Ecol 66, 537-545.
9. Fliegerova, K., Mrázek, J., Hoffmann, K., Zábranská, J. and Voigt, K. (2010) Diversity of anaerobic fungi within cow manure determined by ITS1 analysis. Folia Microbiol 55, 319-325.
10. Galbraith, H., Miller, T.B., Paton, A.M. and Thompson, J.K. (1971) Antibacterial activity of long chain fatty acids and the reversal with calcium, magnesium, ergocalciferol and cholesterol. J Appl Bacteriol 34, 803-813.
11. Gleeson, D.B., Clipson, N., Melville, K., Gadd, G.M. and McDermott, F.P. (2005) Characterization of fungal community structure on a weathered pegmatite granite. Microb Ecol 50, 360-368.
12. Gordon, G.L.R. and Phillips, M.W. (1998) The role of anaerobic fungi in ruminants. Nutr Res Rev 11, 133-168.
13. Grainger, C., Williams, R., Clarke, T., Wright, A.-D.G. and Eckard, R.J. (2010) Supplementation with whole cottonseed causes long-term reduction of methane emissions from lactating dairy cows offered a forage and cereal grain diet. J Dairy Sci 93, 2612-2619.
14. Griffith, G.W., Baker, S., Fliegerova, K., Liggenstoffer, A.S., van der Giezen, M., Voigt, K. and Beakes, G. (2010) Anaerobic fungi: Neocallimastigomycota. IMA Fungus 1, 181-185.
15. Hammond, E.G., Johnson, L.A., Su, C., Wang, T. and White, P.J. (2005) Soybean oil. In Bailey's Industrial Oil and Fat Products, Vol. 2. ed. Shahidi, F. Hoboken, NJ: John Wiley & Sons, Inc.
16. Hibbett, D.S., Binder, M., Bischoff, J.F., Blackwell, M., Cannon, P.F., Eriksson, O.E., Huhndorf, S., James, T. etal. (2007) A higher-level phylogenetic classification of the fungi. Mycol Res 111, 509-547.
17. Hobson, P.N. and Stewart, C.S. (1997) The Rumen Microbial Ecosystem, 2nd edn, pp. 744. London, UK: Blackie.
18. Joblin, K.N. (1999) Ruminal acetogens and their potential to lower ruminant methane emissions. Aust J Agr Res 50, 1037-1313.
19. Joblin, K.N. and Naylor, G.E. (1993) Inhibition of the rumen anaerobic fungus Neocallimastix frontalis by fermentation products. Lett Appl Microbiol 16, 254-256.
20. Joblin, K.N., Cambell, G.P., Richardson, A.J. and Stewart, C.S. (1989) Fermentation of barley straw by anaerobic rumen bacteria and fungi in axenic culture and in co-culture with methanogens. Lett Appl Microbiol 9, 195-197.
21. Johnson, K.A. and Johnson, D.E. (1995) Methane emissions from cattle. J Anim Sci 73, 2483-2492.
22. Johnson, K.A., Huyler, M., Westberg, H., Lamb, B. and Zimmerman, P. (1994) Measurement of methane emissions from ruminant livestock using a SF6 tracer technique. Environ Sci Technol 28, 359-362.
23. Jordan, E., Kenney, D., Hawkins, M., Malone, R., Lovett, D.K. and O'Mara, F.P. (2006) Effect of refined soy oil or whole soybean on intake, methane output, and performance of young bulls. J Anim Sci 84, 2418-2425.
24. Kittelmann, S., Naylor, G.E., Koolaard, J.P. and Janssen, P.H. (2012) A proposed taxonomy of anaerobic fungi (Class Neocallimastigomycetes) suitable for large-scale sequence-based community structure analysis. PLoS One 7, e36866.
25. Legendre, P. and Anderson, M.J. (1999) Distance-based redundancy analysis: testing multispecies responses in multifactorial ecological experiments. Ecol Monogr 69, 1-24.
26. Liggenstoffer, A.S., Youssef, N.H., Couger, M.B. and Elshahed, M.S. (2010) Phylogenetic diversity and community structure of anaerobic gut fungi (phylum Neocallimastigomycota) in ruminant and non-ruminant herbivores. ISME J 4, 1225-1235.
27. Lillis, L., Boots, B., Kenny, D.A., Petrie, K., Boland, T.M., Clipson, N. and Doyle, E.M. (2011) The efect of dietary concentrate and soya oil inclusion on microbial diversity in the rumen of cattle. J Appl Microbiol 111, 1426-1435.
28. Lovett, D., Lovell, S., Stack, L., Callan, J., Finlay, M., Conolly, J. and O'Mara, F.P. (2003) Effect of forage/concentrate ratio and dietary coconut oil level on methane output and performance of finishing beef heifers. Livest Prod Sci 84, 135-146.
29. Lowe, S.E., Theodorou, M.K. and Trinci, A.P. (1987) Cellulases and xylanase of an anaerobic rumen fungus grown on wheat straw, wheat straw holocellulose, cellulose, and xylan. Appl Environ Microb 53, 1216-1223.
30. Machmüller, A., Ossowski, D.A. and Kreuzer, M. (2000) Comparative evaluation of the effects of coconut oil, oilseeds and crystalline fat on methane release, digestion and energy balance in lambs. Anim Feed Sci Tech 85, 41-60.
31. Martin, C., Morgavi, D.P. and Doreau, M. (2010) Methane mitigation in ruminants: from microbe to the farm scale. Animal 4, 351-365.
32. Matsumoto, M., Kobayashi, T., Takenaka, A. and Itabashi, H. (1991) Defaunation effects of medium-chain fatty acids and their derivates on goat rumen protozoa. J Gen Appl Microbiol 37, 439-445.
33. McArdle, B.H. and Anderson, M.J. (2001) Fitting multivariate models to community data: a comment on distance-based redundancy analysis. Ecology 82, 290-297.
34. deMenezes, A.B., Lewis, E., O'Donovan, M., O'Neill, B.F., Clipson, N. and Doyle, E.M. (2011) Microbiome analysis of dairy cows fed pasture or total mixed ration diets. FEMS Microbiol Ecol 78, 256-265.
35. Orpin, C.G. and Joblin, K.N. (1997) The rumen anaerobic fungi. In The Rumen Microbial Ecosystem ed. Hobson, P.N. and Stewart, C.S. pp. 140-195. London, UK: Chapman & Hall.
36. Petrie, K.J., Boland, T.M., Hart, K.J., Mccarney, C.M., Waters, S.M. and Kenny, D.A. (2010) Effect of level of dietary soy oil supplementation and concentrate to forage ratio on feed intake, methane production and rumen fermentation variables of beef steers. In Proceedings of the Annual Conference of the British Society of Animal Science, Belfast, April 2010.
37. R Core Team (2010). R: A language and environment for statistical computing. Vienna, Austria: R foundation for Statistical Computing. ISBN 3-900051-07-0, URL: http://www.R-project.org/.
38. Russell, J.B. and Rychlik, J.L. (2001) Factors that alter rumen microbial ecology. Science 292, 1119-1122.
39. Scallan, Ú., Liliensiek, A., Clipson, N. and Conolly, J. (2008) Ribosort: a program for automated data preparation and exploratory analysis of microbial community fingerprints. Mol Ecol Resour 8, 95-98.
40. Williams, A.G. and Orpin, C.G. (1987) Polysaccharide-degrading enzymes formed by three species of anaerobic rumen fungi grown on a range of carbohydrate substrates. Can J Microbiol 33, 418-426.
41. Wolin, M.J. and Miller, H.J. (1997) Microbe-microbe interactions. In The Rumen Microbial Ecosystem ed. Hobson, P.N. and Stewart, C.S. pp. 467-491. London, UK: Chapman & Hall.
42. Wuebbles, D.J. and Hayhoe, K. (2002) Atmospheric methane and global change. Earth-Sci Rev 57, 177-210.
43. Yang, S.L., Bu, D.P., Wang, J.Q., Hu, Z.Y., Li, D., Wei, H.Y., Zhou, L.Y. and Loor, J.J. (2009) Soybean oil and linseed oil supplementation affect profiles of ruminal microorganisms in dairy cows. Animal 3, 1562-1569.
44. Yu, Z.T. and Morrison, M. (2004) Improved extraction of PCR-quality community DNA from digesta and fecal samples. Biotechniques 36, 808-812.
45. Zoetendal, E.G., Collier, C.T., Koike, S., Mackie, R.I. and Gaskins, H.R. (2004) Molecular ecological analysis of the gastrointestinal microbiota: a review. J Nutr 134, 465-472.