High throughput shotgun sequencing of eRNA reveals taxonomic and derived
functional shifts across a benthic productivity gradient
Abstract
Benthic macrofauna is regularly used in monitoring programmes, however
the vast majority of benthic eukaryotic biodiversity lies mostly in
microscopic organisms, such as meiofauna (invertebrates < 1
mm) and protists, that rapidly responds to environmental change. These
communities have traditionally been hard to sample and handle in the
laboratory, but DNA sequencing has made such work less time consuming.
Compared to DNA sequencing that captures both alive and dead organisms,
environmental RNA (eRNA) can be used to better target alive communities.
Here, we assessed the biodiversity of three known bioindicator
microeukaryote groups (nematodes, foraminifera, and ciliates) in
sediment samples collected at seven coastal sites along an organic
carbon (OC) gradient. We aimed to investigate if eRNA shotgun sequencing
can be used to simultaneously detect differences in 1) biodiversity of
multiple microeukaryotic communities, and 2) functional feeding traits
of nematodes. Results showed that biodiversity was lower for nematodes
and foraminifera in high OC (6.2–6.9 %), when compared to low OC
sediments (1.2–2.8 %). The beta diversity for all three groups were
different along the OC gradient, as well as the classified feeding type
of nematode genera (with more non-selective deposit feeders in high OC
sediment). High relative abundant genera included nematode
Sabatieria and foraminifera Elphidium in high OC, and
Cryptocaryon-like ciliates in low OC sediments. Considering that
future sequencing technologies are likely to decrease in cost, the use
of eRNA shotgun sequencing to assess biodiversity of living benthic
microeukaryotes could be a powerful tool in recurring monitoring
programmes.