Abstract
- Prey metabarcoding has become a popular tool in molecular ecology for
resolving trophic interactions at high resolution, from various sample
types and animals. To date, most predator-prey studies of small-sized
animals (<1 mm) have met the problem of overabundant
predator DNA in dietary samples by adding blocking primers/peptide
nucleic acids. These primers aim to limit the PCR amplification and
detection of the predator DNA but may introduce bias to the prey
composition identified by interacting with sequences that are similar
to those of the predator.
- Here we demonstrate the use of an alternative method to explore the
prey of small marine copepods using whole-body DNA extracts and deep,
brute force metabarcoding of an 18S rDNA fragment.
- After processing and curating raw data from two sequencing runs of
varying depth (0.4 and 5.4 billion raw reads), we isolated 1.3 and
52.2 million prey reads, with average depths of
~15 900 and ~120 000 prey reads per
copepod individual, respectively. While data from both sequencing runs
were sufficient to distinguish dietary compositions from disparate
seasons, locations and copepod species, greater sequencing depth led
to better separation of clusters.
- As computation and sequencing are becoming ever more powerful and
affordable, we expect the brute force approach to become a general
standard for prey metabarcoding, as it offers a simple and affordable
solution to consumers that are impractical to dissect or unknown to
science.