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High throughput shotgun sequencing of eRNA reveals taxonomic and derived functional shifts across a benthic productivity gradient
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  • Elias Broman,
  • Stefano Bonaglia,
  • Alf Norkko,
  • Simon Creer,
  • Francisco Nascimento
Elias Broman
Stockholm University
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Stefano Bonaglia
Stockholm University
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Alf Norkko
University of Helsinki
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Simon Creer
Bangor University
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Francisco Nascimento
Stockholm University
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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.

Peer review status:ACCEPTED

31 Jan 2020Submitted to Molecular Ecology
01 Feb 2020Submission Checks Completed
01 Feb 2020Assigned to Editor
20 Feb 2020Reviewer(s) Assigned
26 Mar 2020Review(s) Completed, Editorial Evaluation Pending
31 Mar 2020Editorial Decision: Revise Minor
29 Apr 2020Review(s) Completed, Editorial Evaluation Pending
29 Apr 20201st Revision Received
13 May 2020Reviewer(s) Assigned
26 Jun 2020Editorial Decision: Revise Minor
29 Jun 2020Review(s) Completed, Editorial Evaluation Pending
29 Jun 20202nd Revision Received
18 Jul 2020Editorial Decision: Accept