Changing times: back to Australia and more eDNA

It’s been quiet here for a while, which I fully intend to change in the coming weeks. To get people up to speed, I’ll start by giving an update on what’s happened in the last months.

As you might remember, last time I wrote, I was doing research for the University of Leeds into the biodiversity of central Indonesia’s marine environment. We had some very interesting fieldwork trips and were using environmental DNA to describe the health of coral reefs. Unfortunately, COVID happened and the world got turned upside down. Fieldwork got cancelled, Europe went into lockdown, life slowed down.

Just before that happened though, my partner started her PhD in Australia. What was supposed to be a few months of separation turned into an indeterminate period of uncertainty when Australia decided to close its borders for anyone besides citizens and their immediate family. I made the decision to try to move back to Australia asap under the immediate family rule, just before the government introduced flight caps. This massively limited how many people could fly into the country and resulted in my booked flights being cancelled (and rebooked) 4 times.

It’s great to be back in Australia – “Look at me now” headland

Eventually I got lucky and landed in Sydney in mid August 2020. Two delightful weeks of quarantine later, I was declared COVID-free and released out into the wide Australian east coast. More specifically, Tanika and me are now living near Coffs Harbour, a lovely place midway between Sydney and Brisbane. While it’s not a lively city like Leeds or Perth, it more than makes up for that in nature. Its great to be living close to the ocean again, with ancient Gondwana rainforests nearby for hikes, and even a nice creek next door ideal for morning (or evening) kayaks.

Early morning kayak on the creek next door

Moving back to Australia did create logistical issues for my job in Leeds. Working from home might be the norm in many countries at the moment, the situation was not viable long-term. As soon as I arrived in Australia, I started applying for jobs and I am very glad to share that I got offered a position working for CSIRO, Australia’s national science organisation. CSIRO does a lot of exciting research, but might be best known (and celebrated) for inventing WiFi, Australia’s ocean-proof plastic bank notes, and coining the term petrichor: the smell of rain in the air.

Sunset surf at Diggers beach

I won’t be inventing new words at CSIRO (I think), but I am doing very exciting work at the intersection of hardcore scientific research and management. For the next 3 years I will be preparing a roadmap on how environmental DNA (eDNA) can be used to monitor Australia’s marine parks. If you have been following the blog, you’ll know that eDNA is an amazing new method to study the marine environment, but so far the use of eDNA is still mostly restricted to fundamental research. Together with members of Oceans and Atmosphere and the Environomics Future Science Platform, I’ll be turning the many findings and recommendations of eDNA researchers into a realistic pathway for managers of marine parks who want to start using eDNA. A big challenge, but an exciting one which will be research focused on direct, real world applications.

In the coming months I’ll try to get back to regular blogging, hopefully including updates on my new research, explainers of exciting new upcoming papers, and plenty of critters news!

New place, new critters! A juvenile pineapple fish (Cleidopus gloriamaris)

More fieldwork discoveries in corona times: Sangihe

In the previous blog I described how my colleague Alessia and me explored Alor, on a mission to collect environmental DNA and study Indonesia’s remote reefs. I am still stuck at home in corona times, so what follows is the next leg of our trip. After we left Alor, we headed to an island that’s been a tempting dot on Indonesia’s map for a while: Sangihe. This particular trip was supported by a National Geographic grant to investigate Indonesia’s remote reefs.

Map

The tiny speck on the map that is Sangihe Island

To get to Sangihe, you have to pass through Manado, from there you can either take a long ferry ride or a tiny plane very early in the morning. Flying to the island is a great way to admire the volcanic activity that has formed the islands. Multiple volcanoes surround the airport in Manado and you fly over a few more dotted in the Celebes sea before landing in Sangihe, which has its own large volcano (Gunung Awu).

Sangihe fisherman

Fisherman in Sangihe. Photo credit: Maarten De Brauwer

The island itself is gorgeous, covered in forest with deep blue water around it. Being so remote, the place gets few divers, so dive facilities are nearly non-existing. When we were there (March 2020), the only place to rent equipment was the tourist info centre in Tahuna. Jemmy, who runs the shop is a great guy who went out of his way to help out were possible. Logistics were not quite on point yet since he only started in the scuba business a few weeks before we got there, but fieldwork logistics rarely are on point, so we still got to explore and collect the data we needed.

 

Sangihe

Sangihe boat views. Photo credit: Maarten De Brauwer

What stuck with me most about the sites, is the incredible visibility, which was 30m at the worst of times and up to 50m at some of the best spots. Otherwise, the health of the reefs was not as good as I hoped it would be. Some sites had extensive dynamite damage, others looked like they had bleached, and the northern sites were strangely devoid of coral, but also lacked the evidence of any typical human impacts. Bare in mind that we were exploring, and neither our fixer Jemmy, nor the boat driver had taken divers or snorkelers to most of the places we sampled. So there was a lot of searching, looking for spots, and the times we got it right, diving was as good as some of the very best Indonesia’s got to offer.

Sangihe island_boat_cave

Not a bad place to sample eDNA. Photo credit: Maarten De Brauwer

One of the cooler experiences during our time in Sangihe was exploring a small freshwater creek that entered the sea at the beach where we were having a surface interval. This small, fast-flowing river wasn’t only absolutely stunning to look at, it was also home to some very exciting fish life. Besides some very cute blue streamgoby (Sicyopterus lagocephalus), it also sheltered a healthy population of freshwater pipefish (Microphis retzii)!!! While I knew they existed, I had never seen them myself, so discovering a creek full of them definitely made my day!

Unfortunately, the next leg of the trip was cancelled due to the spread of COVID19. We were planning to head to an ever more remote island (Pulau Talaud), but the risk of getting stuck there grew a bit too serious. We managed to get a short sampling trip in at the more accessible Bangka island, but eventually had to cut our time short there as well. After only 2 nights on the island, we were told by both the university and friends in the government that the safest course of action would be to leave the country and head back to Europe. Where, at the time of writing, I still am…


A small word of warning for those of you reading this and feel like going for a diving adventure. Sangihe is proper frontier diving with lots of exploring to do. The island has few other sources of income than fishing and coconut farming, so tourism could boost livelihoods in the areas. Just be aware that safety protocols are not as well-established as they are in other, more touristy areas of Indonesia. You should be an experienced scuba diver who can deal with strong currents, basic conditions, and limited to no safety backup from operators.

Fish market Tahuna_yellowfin tuna

Yellowfin tuna for sale at Tahuna market. Photo credit: Maarten De Brauwer

Fish market Tahuna_tuna head

Tuna head was had. Photo credit: Maarten De Brauwer

Fishmarket

A man and his skipjack tuna. Photo credit: Maarten De Brauwer

Fieldwork discoveries in corona times: Alor

It’s July 2020 and more than 3 months of COVID19 isolation is starting to grate on me. Time to relive fieldwork from earlier this year, when travel was still possible and exciting research was happening!

My fieldwork season for 2020 promised to be a very exciting one. Not only were we planning to survey coral reefs in Flores with a great team, I even got support from National Geographic to explore some of Indonesia’s most remote reefs.

In the start of March I picked up my genetically-inclined colleague Alessia Bani from the airport in Bali for what turned out to be quite the adventure. We had 2 months of eDNA sampling and exploring ahead of us, mostly in places I had never visited, let alone dived before! Our first destination was Alor, a spot where I had been dying to get to for years.

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Heading to a survey site

Alor is fast becoming known as a place for great muck diving, but also for excellent reefs and even big stuff (hammerhead sharks!). It’s still not the easiest place to get to, but once you get there, oh boy does it deliver! I can honestly say that it has been one of the most enjoyable places I visited in the last 3 years of fieldwork.

We stayed at the very hospitable Air Dive, where our host Acionk and the rest of the team made us feel not just welcome, but part of the Air Dive family. They made our surveys into the easiest and most pleasant fieldwork we’ve done for this entire project.

Solenostomus cyanopterus_pair

A pair of robust ghost pipefish (Solenostomus cyanopterus). Photo credit: Maarten De Brauwer

Our reason for being in Alor was obviously more than just good company. We were in Alor to study coral reefs and collect eDNA. This method is great to get fantastic amounts of data on the diversity of life on coral reefs, but unfortunately it also means very short dives and lots of time spent filtering water at the surface. And trust me, when you’re in Alor, you want to spend as much time as you can under water. While we purposely visited healthy and damaged sites, the abundance of life was great. We had amazing coral reefs, plenty of fish, some very cool critters (frogfishes, ghost pipefishes, plenty of nudibranchs,…). If we could have spent an extra week just fun diving we definitely would have.

The place wasn’t just great under water, there is SO MUCH action on top as well. Alor Strait is home to two resident dolphin pods, one of which frequently hangs out just out front of the place we were staying. We were also lucky enough to see a strong upwelling event, where (very) cold water rises to the surface. As a result, many smaller fish get a cold shock and die or get temporarily paralysed. The sudden abundance of motionless tasty morsels meant a free feast for the dolphins, as well as the local people, who came out with every pot, pan, net, or other random scooping implement of choice.

We finished our non-diving day with a visit to the local dugong, Mawar. Mawar’s name (=Rose) turned out to be a bit of an awkward choice, as this particular rose was a hefty male dugong with anything but delicate flowers on his mind. As we were told, he is the only dugong in the area and gets quite lonely. So any visitors are greeted with overly enthusiastic hugs, which is why nobody is allowed to swim with him anymore. In absence of humans in the water, dear Mawar seems to have taken a fancy for boats. If you want to know just how much of a fancy, let’s say that if I posted some of the pictures I took on this blog, it would probably get taken offline for inappropriate content…

In short, we had a fantastic time in Alor, seeing 9 dive sites was nowhere near enough and I hope to get back sooner rather than later. A big thank you to the Air Dive team, while I am normally not one to advertise dive centres on this blog, they helped us out far beyond what was needed and were just the friendliest bunch of people. Sampai jumpa lagi!

Guestblog: Environmental DNA allows for the detection of cryptic seahorse species

I’m very proud to publish this guestblog by Georgia Nester. Georgia is a PhD-candidate at Curtin University, where she focuses on the use of environmental DNA on species that are otherwise hard to study. She has just published her first paper, which could be a game changer on how we detect and study seahorses and their relatives in the future.


Seahorses (members of the Syngnathidae family) have never been detected using environmental DNA (eDNA), despite the fact that globally there are 14 species classified as “Threatened” by the IUCN. We compared the ability to detect a wide range of fish including Syngnathidae of two existing fish metabarcoding assays (= methods to detect eDNA and two new fish metabarcoding assays which we developed. With our new assays, we detected three Syngnathidae species in eDNA survey of the Perth metropolitan area (Western Australia), while the existing assays did not detect any Syngnathidae. These detections include the seahorse species Hippocampus subelongatus and Hippocampus breviceps, which represents the first time a seahorse has been detected using eDNA.

 

H subelongatus

The West Australian Seahorse (Hippocampus subelongatus). Photo credit: Maarten De Brauwer

With increasing human pressures and climate change resulting in a continuous decline of global biodiversity, there is a growing demand for rapid and sensitive conservation and monitoring programs. Using traditional methods, accurate data on species presence/absence and distribution is often difficult to obtain in aquatic environments. Environmental DNA metabarcoding is an increasingly popular solution. eDNA metabarcoding is capable of revealing what species are present in an environment by detecting traces of DNA they leave behind in the environment (e.g. shed skin cells, scales, blood, faeces etc). While eDNA metabarcoding surveys have been applied to a wide range of aquatic environments, no one has reported the detection of a seahorse to the best of our knowledge.

Many Syngnathidae species are considered threatened, however many more species (over 30%) lack the data necessary to assess their extinction risk. With the risk of a ‘silent extinction’ for many Syngnathidae species, the design of a non-invasive method for monitoring and managing these cryptic species may be critical to their survival. False negatives (failure to detect a species when they are in fact present) are significant in conservation management. For this reason, we aimed to determine if the Syngnathidae family (seahorses, seadragons and pipefish) were being inadvertently missed in current eDNA surveys.

H breviceps (1)

Camouflaged species such as the shorthead seahorse (Hippocampus breviceps) can be hard to detect with the naked eye. Photo credit: Maarten De Brauwer

Australia is home to 128 species of Syngnathidae in 40 genera, 65 of which are found in Western Australian waters. The Perth metropolitan area in Western Australia was chosen as our study site as it encompasses several habitat types, including brackish and salt water. We sampled from five locations across the Perth metropolitan area and processed the samples back at the TrEnD Laboratory in Curtin University. The results of this study have recently been published in the scientific journal environmental DNA.

In total, we detected four species of Syngnathidae using our newly developed metabarcoding assays “16S_FishSyn_Short” and “16S_FishSyn_Long”. The Syngnathidae species we detected were the Western Australian seahorse (Hippocampus subelongatus), the shorthead seahorse (Hippocampus breviceps), the spotted pipefish (Stigmatopora argus) and the tiger pipefish (Filicampus tigris). With Syngnathidae populations declining due to exploitation for the aquarium trade and habitat degradation, we have shown that eDNA methodologies are capable of detecting Syngnathidae taxa in the environment. This will help inform conservation and management strategies by providing a much-needed non-invasive method for monitoring these populations. Importantly, our study represents the first time a seahorse species has been detected using eDNA methodologies.

H subelongatus_Dave

The Western Australia seahorse (Hippocampus subelongatus, one of the first seahorse species to be detected with eDNA. Photo credit: David Harasti