Niche partitioning between planktivorous fish in the pelagic Baltic Sea assessed by DNA metabarcoding, qPCR and microscopy: Data and Analyses

Marine communities undergo rapid changes because of human-induced
ecosystem pressures. The Baltic Sea pelagic food web has experienced
several regime shifts during the past century, resulting in a system where
competition between planktivorous mesopredators is assumed to be high.
While the two clupeids sprat and herring reveal signs of competition, the
stickleback population has increased drastically during the past decades.
Here, we investigate diet overlap between the three dominating
planktivorous fish in the Baltic Sea, utilizing DNA metabarcoding on the
18S rRNA gene and the COI gene, targeted qPCR, and microscopy. Our results
show niche differentiation between clupeids and stickleback and that
rotifers play an important function in niche partitioning of stickleback,
as a resource that is not being used, neither by the clupeids nor by other
zooplankton. We further show that all the diet assessment methods used in
this study are consistent but DNA metabarcoding describes the
plankton-fish link at the highest taxonomic resolution. This study
suggests that rotifers and other understudied soft-bodied prey may have an
important function in the pelagic food web and that the growing population
of pelagic stickleback is supported by the unutilized feeding niche
offered by the rotifers.