Analysing diet of small herbivores: the efficiency of DNA barcoding coupled with high-throughput pyrosequencing for deciphering the composition of complex plant mixtures.
BACKGROUND
In order to understand the role of herbivores in trophic webs, it is essential to know what they feed on. Diet analysis is, however, a challenge in many small herbivores with a secretive life style. In this paper, we compare novel (high-throughput pyrosequencing) DNA barcoding technology for plant mixture with traditional microhistological method. We analysed stomach contents of two ecologically important subarctic vole species, Microtus oeconomus and Myodes rufocanus, with the two methods. DNA barcoding was conducted using the P6-loop of the chloroplast trnL (UAA) intron.


RESULTS
Although the identified plant taxa in the diets matched relatively well between the two methods, DNA barcoding gave by far taxonomically more detailed results. Quantitative comparison of results was difficult, mainly due to low taxonomic resolution of the microhistological method, which also in part explained discrepancies between the methods. Other discrepancies were likely due to biases mostly in the microhistological analysis.


CONCLUSIONS
We conclude that DNA barcoding opens up for new possibilities in the study of plant-herbivore interactions, giving a detailed and relatively unbiased picture of food utilization of herbivores.
Soininen
Eeva M
EM
Department of Biology, University of Tromsø, N-9037 Tromsø, Norway. eeva.soininen@uit.no.
Valentini
Alice
A
Coissac
Eric
E
Miquel
Christian
C
Gielly
Ludovic
L
Brochmann
Christian
C
Brysting
Anne K
AK
Sønstebø
Jørn H
JH
Ims
Rolf A
RA
Yoccoz
Nigel G
NG
Taberlet
Pierre
P
Trends Ecol Evol. 2009 Feb;24(2):110-7
19100655
Proc Biol Sci. 2003 Aug 7;270 Suppl 1:S96-9
12952648
Plant Mol Biol. 1991 Nov;17(5):1105-9
1932684
Proc Natl Acad Sci U S A. 1988 Apr;85(8):2444-8
3162770
Nucleic Acids Res. 2007;35(3):e14
17169982
Genome Biol. 2007;8(7):R143
17659080
Biotechniques. 1996 Oct;21(4):700-9
8891224
Appl Environ Microbiol. 2001 Feb;67(2):880-7
11157258
Nature. 2008 Nov 6;456(7218):93-7
18987742
Am J Primatol. 2007 Jun;69(6):699-705
17216626
Science. 2003 Oct 31;302(5646):866-8
14593179
PLoS One. 2007 Sep 05;2(9):e831
17786203
Front Zool. 2006 Aug 16;3:11
16911807
Biol Lett. 2008 Aug 23;4(4):419-22
18482904
Mar Biotechnol (NY). 2006 Nov-Dec;8(6):686-96
16924375
Mol Ecol Resour. 2009 Jan;9(1):51-60
21564566
Nature. 2005 Sep 15;437(7057):376-80
16056220
Mol Ecol. 2003 Dec;12(12):3467-75
14629361
Oecologia. 2008 May;156(2):333-40
18274778
Proc Biol Sci. 2006 Sep 22;273(1599):2299-304
16928631
Biotechniques. 1996 Jun;20(6):1004-6, 1008-10
8780871
Mol Ecol. 1993 Dec;2(6):405-6
8162230