Metabarcoding the benthic boundary layer: the role of sampling method and marker characteristics in the DNA signatures obtained at the interface between benthos and plankton
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1
University of Barcelona, Spain
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2
Center for Advanced Studies of Blanes, Superior Council of Scientific Investigations, Spain
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3
UiT The Arctic University of Norway, Norway
The study of community structure is crucial for monitoring and managing marine ecosystems. Metabarcoding has been used to assess the biodiversity of benthic and planktonic marine communities. However, the DNA dynamics in the benthic boundary layer has not been analysed yet. The signal recovered in this transition depends crucially on the type of sampling performed: community DNA (comDNA) vs environmental DNA (eDNA), and the characteristics of the primers used to generate amplicons: universal vs group-specific primers. The aim of this study, performed in the Cabrera National Park, is to characterize with metabarcoding two different benthic littoral communities (photophilic and sciaphilous) and the adjacent water column at four distances (from 0 centimetres to 20 metres) from the benthos. We compared the signal obtained from comDNA sampled by quadrat scraping in the benthos and eDNA obtained from the water by filtering at 0.22 µm. We used two different primer sets, one universal (COI, Wangensteen et al. 2018), and a second one specific for vertebrates (12S, Miya et al., 2015) targeting the fish communities. The results of both primers were markedly different. With COI, only 14% of the reads obtained in the water could be assigned to eukaryotes, as opposed to ca. 99% in the benthos. A high diversity was found, with 1,883 MOTUs detected in the benthos and 839 in the water. The structure of the communities in benthos and water was markedly different both in terms of main groups and MOTU composition, and significant differences between photophilic and sciaphilous samples (both in benthos and water) were also detected. The interaction interchange between benthos and water was weak, with only ca. 2% of MOTUs shared. The number of shared MOTUs decreased from the benthic boundary to distances of up to 20 m. With 12S, 31 fish MOTUs were detected, and ca. 30% of them were shared between benthos and water. Again, the highest number of shared MOTUs was found adjacent to the benthos and the percentage diminished with distance. This marker showed significant differentiation between photophilic and sciaphilous communities, but not between benthos and water samples. By ecological categories, benthic fish were more abundant in the benthos and water column close to it, while pelagic fish were more abundant in the external samples and benthopelagic fish were ubiquitous. We conclude that the benthic signal is highly local and cannot be adequately assessed in water samples, even adjacent to the benthos, due to fast dilution of benthic DNA. Moreover, unspecific amplification rendered the universal primers poorly efficient for eukaryote amplification in eDNA samples rich in prokaryote DNA such as those from the filters. The specific primers performed better, but high stochasticity in fish DNA presence in the samples makes it necessary a high level of replication to obtain reliable estimates of fish diversity in both benthic and water samples.
Acknowledgements
We thank Raül González and Emma Cebrian for help with the sampling. This work was supported by the Spanish Government project PopCOmics CTM2017-88080 (MCIU, AEI/FEDER, UE). This is a contribution from the Consolidated Research Group “Benthic Biology and Ecology” SGR2017-1120 (Catalan Government).
References
Miya, M., Sato, Y., Fukunaga, T., Sado, T., Poulsen, J. Y., Sato, K., … Iwasaki, W. (2015). MiFish, a set of universal PCR primers for metabarcoding environmental DNA from fishes: detection of more than 230 subtropical marine species. Royal Society Open Science, 2(7), 150088. https://doi.org/10.1098/rsos.150088
Wangensteen, O. S., Palacín, C., Guardiola, M., & Turon, X. (2018). DNA metabarcoding of littoral hard-bottom communities: high diversity and database gaps revealed by two molecular markers. PeerJ, 6, e4705. https://doi.org/10.7717/peerj.4705
Keywords:
COI,
12S,
metabarcoding,
Benthic boundary layer,
Community DNA,
eDNA,
Biodiversity
Conference:
XX Iberian Symposium on Marine Biology Studies (SIEBM XX) , Braga, Portugal, 9 Sep - 12 Sep, 2019.
Presentation Type:
Oral Presentation
Topic:
Ecology, Biodiversity and Vulnerable Ecosystems
Citation:
Antich
A,
Palacín
C,
San Roman
D,
Wangensteen
OS and
Turon
X
(2019). Metabarcoding the benthic boundary layer: the role of sampling method and marker characteristics in the DNA signatures obtained at the interface between benthos and plankton.
Front. Mar. Sci.
Conference Abstract:
XX Iberian Symposium on Marine Biology Studies (SIEBM XX) .
doi: 10.3389/conf.fmars.2019.08.00046
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Received:
15 May 2019;
Published Online:
27 Sep 2019.
*
Correspondence:
Mx. Adrià Antich, University of Barcelona, Barcelona, Spain, adriantich@gmail.com