Fieldwork discoveries in corona times: Alor

July 3, 2020July 3, 2020 / Maarten De Brauwer / 2 Comments

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!

Survey site – Ternate selatan

Fisherman at a survey site

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.

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.

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.

Scooping up frozen fish

One scoop catch

Dolphins joining the feast

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…

Mawar cuddling the boat

Mawar REALLY loved that boat

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

June 24, 2020 / Maarten De Brauwer / Leave a comment

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.

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.

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.

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

Ambon and Halmahera fieldwork: Mini-blog 2 – Logistics

September 30, 2019September 30, 2019 / Maarten De Brauwer / 1 Comment

I have made my way to Ambon since the last blog, where I have been preparing the last logistics with my local colleagues from Pattimura University before the actual fieldwork begins. In the last 3 days, the other team members have also started arriving, with the final team member (and master fish counter) landing tomorrow morning. The main things that had to happen before our boat leaves port (besides recovering from jetlag), was organising a detailed plan, training new team members, and preparing all the gear.

Cloudy Ambon days

One of the things we will be doing, is collecting environmental DNA (eDNA) to study biodiversity on coral reefs. If you want to know more about eDNA, I have written more about it here or here. In short: eDNA are tiny fragments of DNA in the water column that come from poop, mucus, etc. By filtering and analysing a scoop of water, we can tell what lives in the area we took water from. Because eDNA is such a new method, most people have not used it before. So in a great mutual benefit arrangement, our Pattimura University colleagues took us (my colleague Dom and me) out for a dive and in return we showed them how to collect water 😉

We obviously did more than just collecting seawater, we also went back to the lab to teach them the protocols on how to filter samples while avoiding contamination. Since eDNA analysis is so good at picking up the tiniest fragments of DNA, a careless brush of a fingertip can render the entire sample useless. We are collecting data from a boat instead of a high-tech lab, so being aware of how things can go wrong is absolutely crucial to get reliable data.

Getting ready to dive. Photo: Dominic Muenzel

Getting ready to filter. Photo: Dominic Muenzel

Tomorrow morning we set sail (start engine?) for 10 days of research around Ambon. So today we had make sure all the equipment got to the boat, for us to leave at first light in the morning. Between dive gear (including compressors, tanks, etc), survey tools, eDNA equipment, and other random practical bits and pieces, it took multiple returns trips with the pickup to get everything to the boat. Science is of course hungry work and feeding 16 people takes a lot of grocery shopping, which was luckily taken care of by our local team. Gino (our Ambon trip leader) has assured me we have an excellent chef on board, so be aware that there is a decent chance that the rest of these fieldwork blogs will mostly be about tasty Indonesian food!

As we will be on a boat for quite a while in the next weeks, I am not sure yet if I will be able to post blogs until we are back on the mainland. If I can snatch up some 4G signal along the way, you’ll be able to read an update on the fieldwork in a couple of days. Otherwise, the next blog will be online around the 11th of October.

Sunny Ambon days

New research project: diversity in Wallacea

June 11, 2019June 11, 2019 / Maarten De Brauwer / 6 Comments

A few weeks ago I wrote about starting an exciting new project at the University of Leeds. At the time I didn’t go into details, but now that I’m a few months in and I am starting to understand what is going, so it’s time to enlighten you as well.

Coral reef critter research coming up!

For the next two years I’m part of a team that will study marine biodiversity on coral reefs in central Indonesia. The overarching goal of of the project is to improve the management and conservation of coral reefs by discovering how impacts such as pollution or overfishing change the way coral reefs function. After all, the best way to start solving a problem is by properly understanding it.

Obviously, there’s a lot more to it than the lofty big goal as the title of the project indicates: “Gradients of marine biodiversity and linkages with eDNA across the Wallacea Region”. There are two components to the project: traditional visual surveys and environmental DNA (“eDNA”) surveys. We will use both methods to create ecological networks and see how they differ when they are threatened by different impacts.

At this point you might be asking a few (logical) questions:

Where is the Wallacea region and why do you go there?
What is eDNA?
What is an ecological network?
Why should I care? I came to this site to read about critters!

The Wallacea region is the central part of Indonesia, from Lombok eastward almost all the way to Papua, and up all the way to Halmahera (check out the map below). It was named after Alfred Russel Wallace, the scientist who, together with Darwin, developed the theory of evolution. The region represents an interesting boundary area where fauna and flora from the Asian and Australian continents meet. So it is home to some amazing wildlife, but also to a large human population that depends on natural resources to survive. The marine diversity in the region has not been studied very well (except for a few local exceptions), so finding out how healthy the marine ecosystems are is quite important.

The Wallacea Region

Environmental DNA (eDNA for short), is a relatively new method to detect species. I have written about it extensively here if you want a long explanation and background. The method detects tiny fragments of DNA in the water column that are shed through poop, mucus, etc. By filtering and analysing a scoop of water, we can tell what animals (and plants, microbes, etc) live in the water nearby. It’s pretty powerful and very exciting, but still needs a lot of additional testing to know just how precise it is compared to other survey methods.

I will then build ecological network models with all the data we collect. The easiest way to imagine what those are, is to see them as a different kind of food web. Where food webs focus on who eats who, we are more interested in who lives close to who, and who interacts with who. In the ideal situation I will include all the information on fish, corals, algae, invertebrates (crabs, sea stars, etc.) in one big model which will show how they rely on each other. More importantly, it will also show what happens with the networks if sites are overfished or polluted and how that differs from untouched sites.

Species-interaction-networks-at-Norwood-Farm-Somerset-UK-revised-from-Pocock-et-al

Example of an interaction network on land, figure by Bohal et al. 2013. Source here.

So yes, my job for the next few years is less critter-focused than before, but it doesn’t mean I will be ignoring them! Besides the obvious fact that there’s a lot of cool critters to be found on the coral reefs I’ll be visiting, I am still involved in a few very cool projects on the side. It’s too early to go into details, but more seahorse and seadragon work is coming up, and even some exciting pygmy seahorse news as well! I’ll regularly be posting updates on the Wallacea project, as well as more critter features, so stay tuned 🙂