Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations

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 5: 1065-1075.


Author Klieve, A. V.
Ouwerkerk, D.
Maguire, A. J.
Title Archaea in the foregut of macropod marsupials: PCR and amplicon sequence-based observations
Journal name Journal of Applied Microbiology  (ERA 2012 Listed)    (ERA 2010 Rank B)   Check publisher's open access policy
Publication date 2012-11
Sub-type Article
DOI 10.1111/j.1365-2672.2012.05428.x
Volume number 113
Issue number 5
ISSN 1364-5072; 1365-2672
Start page 1065
End page 1075
Total pages 11
Place of publication Chichester, West Sussex, United Kingdom
Publisher Wiley-Blackwell
Collection year 2013
Language eng
Formatted abstract Aims: 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).

Conclusions: 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.
Keyword Archaea
DNA sequence
Kangaroo forestomach
Q-Index Code C1
Q-Index Status Confirmed Code
Institutional Status UQ

 
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