Skip to main content
SpringerLink
Log in

Novel Rumen Bacterial Diversity in Two Geographically Separated Sub-Species of Reindeer

  • Published:
Microbial Ecology Aims and scope Submit manuscript

Abstract

Svalbard reindeer (Rangifer tarandus platyrhynchus) live under austere nutritional conditions on the high-arctic archipelago of Svalbard, while semi-domesticated Norwegian reindeer (R. tarandus tarandus) migrate between lush coastal summer pastures and inland winter pastures with lichens on mainland Norway. Svalbard reindeer are known to have high rumen concentrations of cellulolytic bacteria, ranging from 15% of the viable population in summer to 35% in winter, compared to only 2.5% in Norwegian reindeer. Their rumen bacterial diversity was investigated through comparative analyses of 16S rRNA gene sequences (∼1.5 kb in length) generated from clone libraries (n = 121) and bacterial isolates (n = 51). LIBSHUFF comparisons of the composition of the two 16S rRNA libraries from Norwegian reindeer showed a significant effect of artificial feeding compared to natural pasture, but failed to yield significant differences between libraries from Norwegian reindeer and Svalbard reindeer. The combined sequences from reindeer were not significantly different from those reported in wild Thompson’s gazelle in Kenya but did differ from those reported in domestic cattle in Japan. A total of 90 distinct operational taxonomic units (OTUs) were identified by employing a criterion of 97% similarity, while the Chao1 index estimated the reindeer bacterial rumen population richness at 698 OTUs. The majority of the clone library sequences (92.5%) represented novel strains with <97% identity to any known sequence in the public database, most of them affiliated with the bacterial phylum Firmicutes (low G+C Gram-positives) related to the order Clostridiales (76.7%), while Gram-negative bacteria in the Bacteriodales (Prevotella–Bacteroides group) contributed to 22.5%. Also, six of the isolates were putatively novel strains, possibly representing new species in the Clostridium subphylum (cluster XIVa), Actinomyces and Butyrivibrio.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Figure 1
Figure 2
Figure 3

Similar content being viewed by others

References

  1. Aagnes, TH, Sørmo, W, Mathiesen, SD (1995) Ruminal microbial digestion in free-living, in captive-fed, and in starved reindeer (Rangifer tarandus tarandus) in winter. Appl Environ Microbiol 61: 583–591

    PubMed  CAS  Google Scholar 

  2. Aagnes, TH, Blix, AS, Mathiesen, SD (1996) Food intake, digestibility and rumen fermentation in reindeer fed baled timothy silage in summer and winter. J Agric Sci 127: 517–523

    Article  Google Scholar 

  3. Altschul, SF, Madden, TL, Schäffer, AA, Zhang, J, Chang, Z, Miller, W, Lipman, DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res 25: 3389–3402

    Article  PubMed  CAS  Google Scholar 

  4. Amann, RI, Ludwig, W, Schleifer, KH (1995) Phylogenetic identification and in situ detection of individual microbial cells without cultivation. Microbiol Rev 59: 143–169

    PubMed  CAS  Google Scholar 

  5. Avguštin, G, Wright, F, Flint, H (1994) Genetic diversity and phylogenetic relationships among strains of Prevotella (Bacteroides) ruminicola from the rumen. Int J Syst Bacteriol 44: 246–255

    PubMed  Google Scholar 

  6. Banfield, AWF (1961) A revision of the reindeer and caribou, genus Rangifer. National Museum of Canada, Bulletin No. 177. Biol Ser 66: 1–137

    Google Scholar 

  7. Benson, DA, Karsch-Mizrachi, I, Lipman, DJ, Ostell, J, Wheeler, DL (2005) GenBank. Nucleic Acids Res 33: D34–D38

    Article  PubMed  CAS  Google Scholar 

  8. Bonnet, R, Suau, A, Doré, J, Gibson, GR, Collins, MD (2002) Differences in rDNA libraries of faecal bacteria derived from 10- and 25-cycle PCRs. Int J Syst Evol Microbiol 52: 757–763

    Article  PubMed  CAS  Google Scholar 

  9. Bryant, MP, Small, N, Bouma, C, Chu, H (1958) Bacteroides ruminicola n. sp. and Succinomonas amylolytica, the new genus and species. J Bacteriol 76: 15–23

    PubMed  CAS  Google Scholar 

  10. Chao, A (1984) Non-parametric estimation of the number of classes in a population. Scand J Statist 11: 783–791

    Google Scholar 

  11. Collins, MD, Lawson, PA, Willems, A, Cordoba, JJ, Fernandezgarayzabal, J, Carcia, P, Cai, J, Hippe, H, Farrow, JAE (1994) The phylogeny of the genus Clostridium: proposal of five new genera and eleven new species combinations. Int J Syst Bacteriol 44: 812–826

    PubMed  CAS  Google Scholar 

  12. Edwards, JE, McEwan, NR, Travis, AJ, Wallace, RJ (2004) 16S rDNA library-based analysis of ruminal bacterial diversity. Antonie van Leeuwenhoek 86: 263–281

    Article  CAS  Google Scholar 

  13. Felsenstein, J (1985) Confidence limits on phylogenies: an approach using the bootstrap. Evolution 39: 783–791

    Article  Google Scholar 

  14. Felsenstein, J (2004) PHYLIP (phylogenetic inference package) documentation files. Version 3.62c, Department of Genetics, University of Washington, Seattle, Washington.

  15. Hazelwood, GP, Davidson, K, Laurie, JI, Romaniec, MPM, Gilbert, HJ (1990) Cloning and sequencing of the celA gene encoding endoglucanases A of Butyrivibrio fibrisolvens strain A46. J Gen Microbiol 136: 2089–2097

    Google Scholar 

  16. Huber, T, Faulkner, G, Hugenholtz, P (2004) Bellerophon: a program to detect chimeric sequences in multiple sequence alignments. Bioinformatics 20: 2317–2319

    Article  PubMed  CAS  Google Scholar 

  17. Hungate, RE (1966) The rumen and its microbes. Adacemic Press, Inc., New York

    Google Scholar 

  18. Josefsen, TD, Aagnes, TH, Mathiesen, SD (1996) Influence of diet on the morphology of the ruminal papillae in reindeer calves (Rangifer tarandus tarandus L.). Rangifer 16: 119–128

    Google Scholar 

  19. Kopecný, J, Zorec, M, Mrázek, J, Kobayashi, Y, Marinšek-Logar, R (2003) Butyrivibrio hungatei sp. nov. and Pseudoburyrivibrio xylanivorans sp. nov., butyrate-producing bacteria from the rumen. Int J Syst Evol Microbiol 53: 201–209

    Article  PubMed  CAS  Google Scholar 

  20. Koike, S, Kabayashi, Y (2001) Development and use of competitive PCR assay for the rumen cellulolytic bacteria: Fibrobacter succinogenes, Ruminococcus albus and Ruminococcus flavefaciens. FEMS Microbiol Lett 204: 361–366

    Article  PubMed  CAS  Google Scholar 

  21. Koike, S, Yoshitani, S, Kobayashi, Y, Tanaka, K (2003) Phylogenetic analysis of fiber-associated rumen bacterial community and PCR detection of uncultured bacteria. FEMS Microbiol Lett 229: 23–30

    Article  PubMed  CAS  Google Scholar 

  22. Lane, DJ (1991) 16S/23S rRNA sequencing. In: Stackebrandt, E, Goodfellow, M (Eds.) Nucleic Acid Techniques In Bacterial Systematics, John Wiley and Sons, New York, N.Y., pp 115–175

    Google Scholar 

  23. Larue, R, Yu, Z, Parisi, VA, Egan, AR, Morrison, M (2005) Novel microbial diversity adherent to plant biomass in the herbizvore gastrointestinal tract, as revealed by ribosomal intergenic spacer analysis and rrs gene sequencing. Environ Microbiol 7: 530–543

    Article  PubMed  CAS  Google Scholar 

  24. Lauterwein, M, Oethinger, M, Belsner, K, Peters, T, Marre, R (1995) In vitro activities of the lichen secondary metabolites vulpinic acid, (+)-usnic acid, and (−)-usnic acid against aerobic and anaerobic microorganisms. Antimicrob Agents Chemother 39: 2541–2543

    PubMed  CAS  Google Scholar 

  25. Leser, TD, Amenuvor, JZ, Jensen, TK, Lindecrona, RH, Boye, M, Moller, K (2002) Culture-independent analysis of gut bacteria: the pig gastrointestinal tract microbiota revisited. Appl Environ Microbiol 68: 673–690

    Article  PubMed  CAS  Google Scholar 

  26. Mackie, RI, Aminov, RI, Hu, W, Klieve, AV, Ouwerkerk, D, Sundset, MA, Kamagata, Y (2003) Ecology of uncultivated Oscillospira species in the rumen of cattle, sheep and reindeer as assessed by microscopy and molecular approaches. Appl Environ Microbiol 69: 6808–6815

    Article  PubMed  CAS  Google Scholar 

  27. Mann, SO (1986) An improved method of determining cellulolytic activity in anaerobic bacteria. J Appl Bacteriol 31: 241–246

    Google Scholar 

  28. Mathiesen, SD, Sørmo, W, Aagnes, Utsi, TH (1999) Forage chemistry and the digestive system in reindeer (Rangifer tarandus tarandus) in northern Norway and on South Georgia. Rangifer 20: 91–101

    Google Scholar 

  29. Mathiesen, SD, Haga, ØE, Kaino, T, Tyler, NJC (2000a) Diet composition, rumen papillation and the maintenance of carcass mass in female Norwegian reindeer (Rangifer tarandus tarandus) in winter. J Zool Lond 251: 129–138

    Article  Google Scholar 

  30. Mathiesen, SD, Sørmo, W, Aagnes, Utsi, TH (2000b) Comparative aspects of volatile fatty acid production in reindeer (Rangifer tarandus tarandus) in northern Norway and on South Georgia. Rangifer 20: 201–210

    Google Scholar 

  31. Mathiesen, SD, Mackie, RI, Aschfalk, A, Ringø, E, Sundset, MA (2005) Microbial ecology of the gastrointestinal tract in reindeer—changes through season. In: Holzapfel, W, Naughton, P (Eds.) Microbial Ecology of the Growing Animal; Biology of the Growing Animals, Vol. 3, Elsevier Press, Oxford, pp 73–100

    Google Scholar 

  32. Nelson, KE, Zinder, SH, Hance, I, Burr, P, Odongo, D, Wasawo, D, Odenyo, A, Bishop, R (2003) Phylogenetic analysis of the microbial populations in the wild herbivore gastrointestinal tracts: insight into an unexplored niche. Environ Microbiol 5: 1212–1220

    Article  PubMed  Google Scholar 

  33. Niemann, S, Puehler, A, Tichy, TV, Simon, R, Selbitschka, W (1997) Evaluation of the resolving power of three different DNA fingerprinting methods to discriminate among isolates of a natural Rhizobium meliloti population. J Appl Microbiol 82: 477–489

    Article  PubMed  CAS  Google Scholar 

  34. Nili, N, Brooker, JD (1997) Lack of methionine biosynthesis de novo in Butyrivibrio fibrisolvens strain E14. Lett Appl Microbiol 25: 85–90

    Article  CAS  Google Scholar 

  35. Olsen, MA, Aagnes, TH, Mathiesen, SD (1994) Digestion of herring by indigenous bacteria in the minke whale forestomach. Appl Environ Microbiol 60: 4445–4455

    PubMed  CAS  Google Scholar 

  36. Olsen, MA, Aagnes, TH, Mathiesen, SD (1997) The effect of timothy silage on the bacterial population in rumen fluid of reindeer (Rangifer tarandus tarandus) from natural summer and winter pasture. FEMS Microbiol Ecol 24: 127–136

    Article  CAS  Google Scholar 

  37. Olsen, MA, Mathiesen, SD (1998) The bacterial populations adherent to plant particles in the rumen of reindeer fed lichen, timothy hay or silage. Rangifer 18: 55–64

    Google Scholar 

  38. Orpin, CG, Mathiesen, SD, Greenwood, Y, Blix, AS (1985) Seasonal changes in the ruminal microflora of the high-arctic Svalbard reindeer (Rangifer tarandus platyrhynchus). Appl Environ Microbiol 30: 144–151

    Google Scholar 

  39. Orpin, CG, Jordan, JD, Mathiesen, SD, Yeal, NL, Hazlewood, GP, Mann, SP (1987) Plasmid profiles in the rumen bacteria Selenomonas ruminantium and Butyrivibrio fibrisolvens. Appl Bacteriol XIII (Abst.)

  40. Ozutsumi, Y, Tajima, K, Takenaka, A, Itabashi, H (2005) The effect of protozoa on the composition of rumen bacteria in cattle using 16S rRNA gene clone libraries. Biosci Biotechnol Biochem 69: 499–506

    Article  PubMed  CAS  Google Scholar 

  41. Palo, RT (1993) Usnic acid, a secondary metabolite of lichens and its effect on in vitro digestibility in reindeer. Rangifer 13: 39–43

    Google Scholar 

  42. Præsteng, KE, Mathiesen, SD, Mackie, RI, Cann, IKO, Sundset, MA (2004) Novel rumen bacterial isolates from reindeer (Rangifer tarandus tarandus). J Anim Feed Sci 13(Suppl. 1): 183–186

    Google Scholar 

  43. Ramsak, A, Peterka, M, Tajima, K, Martin, JC, Wood, J, Johnston, MEA, Aminov, RI, Flint, HJ, Avguštin, G (2000) Unravelling the genetic diversity of ruminal bacteria belonging to the CFB phylum. FEMS Microbiol Ecol 33: 69–79

    Article  PubMed  CAS  Google Scholar 

  44. Randi, E, Mucci, N, Pierpaoli, M, Douzery, E (1998) New phylogenetic perspectives on the Cervidae (Artiodactyla) are provided by the mitochondrial cytochrome b gene. Proc Roy Soc Lond B 265: 793–801

    Article  CAS  Google Scholar 

  45. Roché, C, Albertyn, H, van Gylswyk, NO, Kistner, A (1973) The growth response of celluloytic acetate-utilizing and acetate-producing Butyrivibrios to volatile fatty acids and other nutrients. J Gen Microbiol 78: 253–260

    PubMed  Google Scholar 

  46. Roux, V, Raoult, D (2004) Paenibacillus massiliensis sp. nov., Paenibacillus sanguinis sp. nov. and Paenibacillus timonensis sp. nov., isolated from blood cultures. Int J Syst Evol Microbiol 54: 1049–1054

    Article  PubMed  CAS  Google Scholar 

  47. Saito, N, Nei, M (1987) The neighbour-joining method: a new method for constructing phylogenetic trees. Mol Biol Evol 4: 406–425

    Google Scholar 

  48. Shannon, CE, Weaver, W (1949) The mathematical theory of communication. University of Illinois Press, Urbana

    Google Scholar 

  49. Singleton, DR, Furlong, MA, Rathbun, SL, Whitman, WB (2001) Quantitative comparisons of 16S rRNA gene sequence libraries from environmental samples. Appl Environ Microbiol 67: 4374–4376

    Article  PubMed  CAS  Google Scholar 

  50. Stackebrandt, E, Goebel, BM (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

    Article  CAS  Google Scholar 

  51. Storeheier, PV, Mathiesen, SD, Tyler, NJC, Olsen, MA (2002a) Nutritive value of terricolous lichens for reindeer in winter. The Lichenologist 34: 247–257

    Article  Google Scholar 

  52. Storeheier, PV, Mathiesen, SD, Tyler, NJC, Schelderup, I, Olsen, MA (2002b) Utilisation of nitrogen and mineral-rich vascular plants by reindeer in winter. J Agric Sci Cambr 139: 151–160

    Article  Google Scholar 

  53. Storeheier, PV, Sehested, J, Diernæs, L, Sundset, MA, Mathiesen, SD (2003) Effects of seasonal changes of food quality and food intake on the transport of sodium and butyrate across ruminal epithelium of reindeer. J Comp Physiol 173: 391–399

    CAS  Google Scholar 

  54. Štyriak, I, Lauková, A, Ljungh, Å (2002) Binding of extracellular matrix molecules by Staphylococci from wild herbivores. Acta Vet Brno 71: 369–374

    Google Scholar 

  55. Sørmo, W, Haga, ØE, Gaare, E, Langvatn, R, Mathiesen, SD (1999) Forage chemistry and fermentation chambers in Svalbard reindeer (Rangifer tarandus platyhynchus). J Zool Lond 247: 247–256

    Google Scholar 

  56. Tajima, K, Aminov, RI, Nagamine, T, Ogata, K, Nakamura, M, Benno, Y (1999) Rumen bacterial diversity as determined by sequence analysis of 16S rDNA libraries. FEMS Microbiol Ecol 29: 159–169

    Article  CAS  Google Scholar 

  57. Tajima, K, Arai, S, Ogata, K, Nagamine, T, Matsui, H, Nakamura, M, Aminov, RI, Benno, Y (2000) Rumen bacterial community transition during adaptation to high-grain diet. Anaerobe 6: 273–284

    Article  CAS  Google Scholar 

  58. 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

    Article  PubMed  CAS  Google Scholar 

  59. Teather, RM, Wood, PJ (1982) Use of congo red-polysaccharide interactions in enumerating and characterization of cellulolytic bacteria from the bovine rumen. Appl Environ Microbiol 43: 777–780

    PubMed  CAS  Google Scholar 

  60. Turi, JM (2002) The world reindeer livelihood current situation, threats and possibilities. In: Kankaanpää, S, Wüller-Wille, L, Susiluoto, P, Sutinen, ML (Eds.) Northern Timberline Forests: Environmental and Socio-Economic Issues and Concerns, The Finnish Forest Res Inst, Research Paper 862: 70–75

  61. Tyler, NJC, Øritsland, NA (1989) Why don’t Svalbard reindeer migrate? Holarctic Ecol 12: 369–376

    Google Scholar 

  62. Tyler, NJC, Turi, JM, Sundset, MA, Strøm, Bull K, Sara, MN, Reindert, E, Oskal, N, Nellemann, C, McCarthy, JJ, Mathiesen, SD, Martello, ML, Magga, OH, Hovelsrud, GK, Hanssen-Bauer, I, Eira, NI, Eira, IMG, Corell, RW (2006) Saami reindeer pastoralism under climate change: applying a generalized framework for vulnerability studies to a sub-arctic social–ecological system. Global Environ Change doi: 10.1016/j.gloenvcha.2006.06.001

  63. Velázquez, E, de Miguel, T, Poza, M, Rivas, R, Rosselló-Mora, R, Villa, RG (2004) Paenibacillus favisporus sp. nov., a xylanolytic bacterium isolated from cow faeces. Int J Syst Evol Microbiol 54: 59–64

    Article  PubMed  CAS  Google Scholar 

  64. Whitford, MF, Forster, RJ, Beard, CE, Gong, J, Theather, RM (1998) Phylogenetic analysis of rumen bacteria by comparative sequence analysis of cloned 16S rRNA genes. Anaerobe 4: 153–163

    Article  PubMed  CAS  Google Scholar 

  65. Wood, J, Scott, KP, Avguštin, G, Newbold, CJ, Flint, HJ (1998) Estimation of the relative abundance of different Bacteroides and Prevotella ribotypes in gut samples by restiction enzyme profiling of PCR-amplified 16S rRNA gene sequences. Appl Environ Microbiol 64: 3683–3689

    PubMed  CAS  Google Scholar 

  66. Yu, Y, Breitbart, M, McNairnie, P, Rohwer, F (2006) FastGroupII: a web-based bioinformatics platform for analyses of large 16S rDNA libraries. BMC Bioinformatics 7: 57–65

    Article  PubMed  CAS  Google Scholar 

Download references

Acknowledgments

This study was funded by The University of Tromsø, The Reindeer Husbandry Research Fund, The Norwegian Research Council, The Roald Amundsen Centre for Arctic Research (University of Tromsø), and the Centre for Sámi Studies (University of Tromsø). We thank Dr. Samuel Ohene-Adjei for his invaluable help through the various statistical software comparing 16S rDNA clone libraries, Dr. Rustam I. Aminov for his contribution in developing a protocol for DNA isolation from the reindeer rumen samples, Dr. Hisao Itabashi for providing data on clone libraries from domestic cattle, and Dr. Tove H. Aagnes Utsi for allowing access to her rumen bacterial isolates from reindeer on natural pasture. We are grateful to Dr. Andre Wright for critically reviewing the manuscript and for his helpful suggestions.

Author information

Authors and Affiliations

  1. Department of Arctic Biology and Institute of Medical Biology, University of Tromsø, 9037, Tromsø, Norway

    Monica A. Sundset & Kirsti E. Præsteng

  2. Department of Animal Sciences, University of Illinois, Urbana-Champaign, IL, 61801, USA

    Monica A. Sundset, Isaac K. O. Cann & Roderick I. Mackie

  3. Department of Microbiology, University of Illinois, Urbana-Champaign, IL, 61801, USA

    Isaac K. O. Cann

  4. Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, 61801, USA

    Isaac K. O. Cann & Roderick I. Mackie

  5. Section of Arctic Veterinary Medicine, The Norwegian School of Veterinary Science, 9292, Tromsø, Norway

    Svein D. Mathiesen

  6. Saami University College, 9520, Guovdageaidnu, Norway

    Svein D. Mathiesen

Authors
  1. Monica A. Sundset
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Kirsti E. Præsteng
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Isaac K. O. Cann
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Svein D. Mathiesen
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Roderick I. Mackie
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Monica A. Sundset.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Sundset, M.A., Præsteng, K.E., Cann, I.K.O. et al. Novel Rumen Bacterial Diversity in Two Geographically Separated Sub-Species of Reindeer. Microb Ecol 54, 424–438 (2007). https://doi.org/10.1007/s00248-007-9254-x

Download citation

  • Received:

  • Revised:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00248-007-9254-x

Keywords

Search

Navigation