The search for pristine coral reefs, butterflyfish, and environmental DNA in Okinawa
July 8, 2016:
I wake up to the deafening drone of millions of male cicadas calling out to their prospective mates. The riotous din is tempered only by the lyrical sounds of songbirds, among them the handsome blue rock thrush (Monticola solitarius) and Ryukyu robin (Larvivora komadori), which heartily trill away amongst the chaos. As I open my balcony door to collect some field gear I am enveloped by a wave of heat and forced to engulf the thick and mealy air. I am not pleased by my morning find either, a giant African land snail (Achatina fulica, an invasive species in Japan) has decided to ooze a syrupy trail of mucus across my dive booties.
Despite the inclement conditions we have a weather window to visit our first site at Mizugama on the western coast of Okinawa, a reef system impacted by coastal development and freshwater outflow from a nearby river mouth. The first aim of my research on this trip is to collect sea water samples from a gradient of impacted to pristine coral reefs in order to sequence its eDNA. This catch-all term refers to the preserved, but often degraded genetic material that is suspended in the soupy seas and sediments. Indeed, all marine animals and plants regularly shed cellular material, scales, faeces, and so on. When combined with next generation sequencing (NGS) technology, which is capable of simultaneously sequencing millions of copies of DNA from complex samples, eDNA can provide a wealth of information for studies of biodiversity, food web dynamics, diet analysis, and invasive marine pests. eDNA metabarcoding (as it’s known) is a fairly new technology, having been applied to seawater for the first time in 2012 to detect multiple species of fish and marine mammals.
Foote, A.D., Thomsen, P.F., Sveegaard, S., Wahlberg, M., Kielgast, J., Kyhn, L.A., Salling, A.B., Galatius, A., Orlando, L. and Gilbert, M.T.P. (2012) Investigating the potential use of environmental DNA (eDNA) for genetic monitoring of marine mammals. PloS one, 7, e41781.
Thomsen, P.F., Kielgast, J., Iversen, L.L., Møller, P.R., Rasmussen, M. and Willerslev, E. (2012) Detection of a diverse marine fish fauna using environmental DNA from seawater samples. PLoS one, 7, e41732.
In my case, I am interested in auditing species composition and trophic communities at a given location (from phytoplankton right on up to apex predators) simply by sequencing all of the DNA in replicate water samples. This innovative work is only possible because of a close collaboration with the Trace and Environmental DNA (TrEnD) laboratory at Curtin University in Western Australia, particularly Professor Michael Bunce, who has extensive experience in isolating DNA from a variety of substrates including bulk bone, faecal material, and, more recently, samples sourced from the marine sector. The TrEnD Lab now has an active presence in the waters off Western Australia with recent Australia Research Council funding and profitable links with industry partners such as the Department of Fisheries and BMT Oceanica.
Our sampling is short and sweet at Mizugama. We collect several litres of sea water near the end of the day but are restricted to snorkelling in the lagoon due to heavy sets of waves that appear to blindly throw themselves up and over the shallow reef crest.