Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations
Article first published online: 7 SEP 2012
© 2012 The Authors Journal of Applied Microbiology © 2012 The Society for Applied Microbiology
Journal of Applied Microbiology
Volume 113, Issue 5, pages 1065–1075, November 2012
How to Cite
Klieve, A.V., Ouwerkerk, D. and Maguire, A.J. (2012), Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations. Journal of Applied Microbiology, 113: 1065–1075. doi: 10.1111/j.1365-2672.2012.05428.x
- Issue published online: 17 OCT 2012
- Article first published online: 7 SEP 2012
- Accepted manuscript online: 16 AUG 2012 06:44AM EST
- Manuscript Accepted: 6 AUG 2012
- Manuscript Revised: 20 JUL 2012
- Manuscript Received: 8 JUN 2012
- DNA sequence;
- Kangaroo forestomach
To investigate, using culture-independent techniques, the presence and diversity of methanogenic archaea in the foregut of kangaroos.
Methods and Results
DNA was extracted from forestomach contents of 42 kangaroos (three species), three sheep and three cattle. Four qualitative and quantitative PCR assays targeting the archaeal domain (16S rRNA gene) or the functional methanogenesis gene, mcrA, were used to determine the presence and population density of archaea in kangaroos and whether they were likely to be methanogens. All ruminal samples were positive for archaea, produced PCR product of expected size, contained high numbers of archaea and high numbers of cells with mcrA genes. Kangaroos were much more diverse and contradictory. Fourteen kangaroos had detectable archaea with numbers 10- to 1000-fold fewer than sheep and cattle. Many kangaroos that did not possess archaea were positive for the mcrA gene and had detectable numbers of cells with this gene and vice versa. DNA sequence analysis of kangaroos' archaeal 16S rRNA gene clones show that many methanogens were related to Methanosphaera stadmanae. Other sequences were related to non-methanogenic archaea (Thermoplasma sp.), and a number of kangaroos had mcrA gene sequences related to methane oxidising archaea (ANME).
Discrepancies between qualitative and quantitative PCR assays for archaea and the mcrA gene suggest that the archaeal communities are very diverse and it is possible that novel species exist.
Significance and Impact of the Study
Archaea (in general) were below detectable limits in many kangaroos, especially Red kangaroos; when present they are in lower numbers than in ruminants, and the archaea are not necessarily methanogenic. The determination of why this is the case in the kangaroo foregut could assist in reducing emissions from other ecosystems in the future.