Joey’s Blog

Blog Summary:

A blog by Dr. Joseph DiBattista from a recent Curtin University research trip highlighting some of the cultural and scientific curiosities both above and below the waterline in Okinawa, Japan

Installment #1 - Arrive in Okinawa

Installment#2  - Sampling eDNA at Mizugama

The search for pristine coral reefs, butterflyfish, and environmental DNA in Okinawa 

July 7, 2016:

I arrive in Naha, Okinawa under the wind shadow of the foreboding Super Typhoon Nepartak, which by all accounts is set to steamroll over the heavily populated Taiwan. I am hoping it will veer south and west of course, and dissolve out at sea. Its far reaching effects can be seen from the window of my plane as we taxi on the tarmac to our assigned gate. Deep grey clouds unfurl on the horizon and unleash an army of rain bands that restrict our visibility to tens of meters. No doubt a menacing outlook of things to come.

unconventional and uncomplicated. For this trip I have packed minimal gear, I have a clear scientific mandate to fulfil (sampling of environmental DNA, more details to come), and I will be working from the respected home base of the University of the Ryukyus, which is rife with amenities and provides ideal sleeping arrangements. I will not be wanting for food or comforts from home. The only confusion that I encounter is upon exiting the airport; apparently I am not Chinese. It appears that the car company I enlisted is shocked that I cannot read or speak Cantonese, which is understandable given that 99% of the passengers on my Dragonair flight are prospective holidaymakers from Hong Kong. The remote rental car office is similarly perplexed, and struggles to find the attendant reserved for English speaking clients. In these situations tact, understanding, and patience are requisite virtues.


A rental car is not a luxury in Okinawa as I will need one to regularly stock up on supplies off campus, and transport people and tanks to prospective dive sites in the coming days. The GPS that I am provided with is less than ideal though, the voice prompt is in English but the touch screen interface is not; Japanese is instead a perplexing mix of hiragana, katakana, and kanji. Okinawa, it seems, is also not known for their logical road system. Two hours into what should be a thirty minute journey I arrive on campus, and only because I have been here once before. The winding inland highway and narrow laneways, peppered with everything from barber poles to yuru-chara (Japanese mascots) heralding car dealerships, were at last familiar leading up to my destination.     

      The sign posted on my guesthouse door is confronting but not entirely unexpected. It warns of the “habu”, a highly venomous (but not so uncommon) pit viper species complex (Trimeresurus and Ovophis spp.) that enjoys hiding amongst the tall grasses that envelop this sprawling, verdant campus. An irate snake was spotted here last week, and although bites are rarely fatal, an extended stay in the local hospital to receive anti-venom treatment is far from ideal.

      An hour later and I am greeted by my gregarious host, Associate Professor James Reimer (a fellow Canadian), who picks me up for dinner and treats me to a sushi train. Reimer-sensei has been based in Okinawa for nine years, and is one of the foremost experts in this region (if not the entire tropics) on “Molecular Invertebrate Systematics and Ecology”. Over the years he has hosted an army of students, postdocs, and interns (30 current members at last count) to help maintain a highly productive and interactive lab environment despite operating on a tight budget. His research group collectively pumps out taxonomic publications at a frenzied pace on all that is marine and invertebrate. His local knowledge, benthic survey data, and genetic voucher sequences for everything from corals to cucumbers (of the animal variety) will serve as an excellent point of calibration for our novel approach to sampling biodiversity. As James drops me off at my guesthouse for the evening I am buzzed by a pair of Ryukyu flying foxes (Pteropus dasymallus), whom, now threatened on the island, are surely in search of sweet treats (fruits and flowers). This close encounter heralds in the fact that I am now firmly planted in the tropics.

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.

© mike bunce 2015