CALICE Calibrating Plant Biodiversity in Glacier Ice

Molecular biology techniques nowadays allow DNA analyses from so-called environmental samples (Taberlet et al. 2012), i.e. samples originating from different matrices such as water, air, soil, sediment, permafrost and ice. After extracting the entire DNA fraction, a metabarcoding approach is adopted for simultaneously identifying large sets of taxa occurring in the single environmental sample. The rationale of this approach is straightforward: within the genome there are stretches of DNA whose nucleotide sequence is expected to be species-specific and that have been deemed as barcode markers (Hebert et al. 2003). The analyses of these markers allow identifying the taxa of a field-collected sample to species level. 
While for some organisms, such as birds and mammals, a single barcode marker is required for accomplishing this goal (Valentini et al.2009), there is growing evidence that in plants (Hollingsworth 2011) a combination of differentbarcode markers is required for single species identification.
Another relevant feature of barcodemarkers is their flexibility in terms of nucleotide length. Some are 650 base pairs (bp) long but others can be as short as about 100 bp. This makes it possible to apply barcoding to DNA retrieved from ancient specimens dating back from decades to thousands of years before present. Usually, DNA extracted from ancient remains (aDNA) is highly fragmented in sequences no longer than about 150-200 bp.
The recent developments in sequencing techniques (Taberlet et al. 2012) have opened up new promising opportunities to DNA barcoding: the millions of DNA reads usually produced in a single Next Generation Sequencing (NGS) run of DNA from an environmental sample (eDNA) permit to reveal even less abundant species, thus significantly increasing the information in terms of taxonomic composition of the sample (Wilcox et al. 2013). At the same time with NGS the amount of contamination from exogenous DNA can be tracked (Overballe-Petersen et al. 2012).
Our aim is to apply eDNA metabarcoding to identify plant species diversity in the 40 m ice core extracted from the Adamello Glacier. The biodiversity estimates from eDNA will integrate those obtained through morphological pollen analyses and together they will be compared to biodiversity assessments in the catchment area of the glacier obtained by means of surveys such as remote sensing and vegetational maps.

Hebert P., Cywinska A., Ball S.L., de Waard JR. 2003: Biological identifications through DNA barcodes. Proceeedings of the Royal Society of London, series B 270, 313–321.

Hollingsworth P.M. 2011: Refining the DNA barcode for land plants. Proceedings of the National Academy of Science USA, 108 (49): 19451-19452.

Overballe-Petersen S., Orlando L., Willerslev E. 2012: Next-generation sequencing offers newinsights into DNA degradation. Trends in Biotechnology, 30 (7): 364-368

Taberlet P., Coissac E., Hajiababei M., Rieseberg L. 2012: Environmental DNA. Molecular Ecology,21: 1789-1793.

Valentini A., Pompanon F., Taberlet P. 2009: DNA barcoding for ecologists. Trends in Ecology and Evolution, 24 (2): 110-117

Wilcox T.M., McKelvey K.S., Young M.K., Jane S.F., Lowe W.H., Whiteley, AR., Schwartz, MK., 2013: Robust detection of rare species using environmental DNA: the importance of primer specificity.PLosONE 8(3): e59520.