Finding the Knysna Seahorse: Mini-blog 2

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Sunrise in Kariega

Today was the first day of collecting samples in South Africa and the first sampling location was the Kariega estuary, near Kenton-On-Sea. We were joined by two researcher from SAIAB (South African Institute for Aquatic Biodiversity), who study a relative of the Knysna seahorse: the estuarine pipefish (Syngnathus watermeyeri). A species which is critically endangered, it is in fact so rare, that it was thought to be extinct in the early nineties until it was re-sighted in 1995. Since we are collecting environmental DNA (eDNA) samples in this area, we decided to temporarily team up with Paul and Nikki to see if this rare species can be detected with eDNA.

But what exactly is eDNA, or more precisely, how does it work?

The basis of this method is that all living beings contain DNA in their cells, and that all living beings “shed” this DNA in their environment. On land this can for example be through hair or feces, for fish this can happen through mucus, excrement, scales, etc.  These tiny bits of DNA then float in the environment (the water in our case), which brings us to the actual sampling.

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Kariega estuary, full of tiny bits of environmental DNA

Collecting eDNA is pretty simple, we just scoop up water. That’s it. Really. But the actual work begins after the water is collected. The first step is to filter the water using a very fine filter which (hopefully) traps all the DNA in the water. At this point there is a LOT of DNA on the filter paper, most of which will be from bacteria, or larger species you may or may not be interested in.

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Filtering water, exciting stuff!

The tricky next step (which will be done in the TrEnD laboratory at Curtin University), is to find the DNA you are looking for, which is very much like searching for a needle in a haystack. But both the hay and the needle are so small you can’t actually see it with a microscope. Scientists much smarter than me found a very clever solution to this: they invented a kind of magnet that basically pulls out the needle.

This magnet is called a “primer” and is based on how the DNA of different species (or families, or genera) is different from each other. These differences make it possible for geneticists to develop primers (=magnets) that can detect different things. Some primers are used to detect multiple species, for example: there are primers that will detect (almost) all bony fishes, others could be used to detect sharks. Other primers are more specific, like in our case, where we try to detect only 1 species. Alternatively, another project at Curtin University is currently working on a true “seahorse-magnet”: a primer that will detect all seahorse DNA in the water, regardless which species of seahorse.

As you can imagine, eDNA is a very exciting method with lots of potential uses. It is also a relatively new method, so lots of finer details still need to be studied to make the most of this technique.

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Finding the Knysna Seahorse: Mini-blog 1

Yesterday I wrote about the exciting projects that are coming up, one of which looks at the Knysna Seahorse (Hippocampus capensis). The next two weeks I will be in the south of South Africa, where my friend Louw and I will to try to learn more about this endangered species. I promised I would try to give you frequent updates about what is going on, so here is the first of this fieldwork-mini-blog series.

I am extremely lucky that I get to travel to amazing places for my work, but sometimes the traveling alone is almost as much adventure as the actual work. Last night’s flight was late (not too much, just over an hour), but it meant that I’d struggle to make my connecting flight. It turned out there was no need to worry, since the domestic flight I was supposed to take had been cancelled altogether! Luckily I got a place on a different flight a few hours later (with “Mango Air”) which brought me to my final destination, George. In George I got picked up by Louw, and after a minor struggle to get all our equipment in the car, we drove off to the first fieldwork location, another 5 hour drive from the airport.

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Arrival in George, with the very orange plane of Mango Air

Which brings us to the reason why we are doing this project, the Knysna seahorse. This species is quite special, but not necessarily for the right reasons. It only occurs in a few estuaries in the very southern tip of South Africa, in the Knysna region. Since it is so isolated, and only occurs in so few places, any environmental impacts can have a big effect on the species. Because of this unique situation, the species is listed as “Endangered” in the IUCN Red List.

You might be wondering “That’s all fine, but what are you two going to do about it?”. The main goal of this project is to figure out exactly WHERE the seahorses live, and if there are places where they are present that might have been overlooked in the past. Finding (or just as important, NOT finding) these new places are important for managing this species. We will do this not by diving and looking for them, but by using a shiny new method called “Environmental DNA” (or “eDNA” for short).

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The eDNA mobile

I will explain what exactly eDNA is in a future blog, but we will basically be scooping up water and then filtering that water to find traces of seahorse DNA. These traces will tell us whether or not seahorses are present in the estuary we just visited. The benefit of this method is that there is no need to go in the water, where it is easy to miss camouflaged species like seahorses. It also avoids using other, more destructive methods, like using fish poison to find out what is around you.

Exciting things ahead

I may not have been blogging much recently, but a lot has happened in the last few months. First and foremost, I completed and handed in my PhD-thesis. Since then I have been teaching, writing grant and job applications, and I’ve had a nice long holiday relaxing and traveling in Europe and diving in Indonesia.

In all honesty, handing in my PhD-thesis isn’t really news anymore since it’s been almost four months ago. That does not change anything about how happy and relieved I am that I managed to finish this epic project. Although this happiness might also have a slight tinge of regret as it means the end of more than 3 fantastic years of being absorbed by something that I love doing very much. By now I have also received the examiners’ comments back from my thesis, which were very positive, meaning that the whole process of finalising the PhD might be even quicker than I’d really like to.

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Yours truly during my PhD-presentation, very happy days!

Why quicker than I’d like to? Mostly because it means I have to find a job now! I really, really like doing research, especially when it involves little critters or sandy ocean floors. So I will try my very best to keep on doing research on this, but post-PhD research jobs (so called “post-docs”) are hard to come by. Even harder when you study sand and animals that look like sand 😉 So I have been applying for positions all over the world, ranging from Australia, to Germany, the UK, Indonesia, etc.

This is all very exciting, since I might literally end up anywhere in the world. But as you can imagine, it also means a fair amount of insecurity of what life will look like in a few months time. The excitement about new projects and adventure always wins over the worries though 😀

But, just in case you’d happen to know someone who is looking for a researcher who knows his way around Southeast Asia, soft sediment, and cryptobenthic fauna, do give me a ring 😉

There are more exciting thing going on than just job-hunting! As a matter of fact, August will be a pretty busy, action-packed month. At the moment I am in Perth airport, almost ready to fly to South Africa. As you may or may not remember, a few months ago we (my friend Louw and me) received a grant from the Mohammed bin Zayed Species Conservation Fund to conduct research on the endangered Knysna Seahorse (Hippocampus capensis). We have been working behind the scenes and preparing since, but now it is finally time to do the fieldwork portion of the work!

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The species we’ll be studying: the Knysna seahorse (Hippocampus capensis)

To try and give everyone who is interested an idea  of what marine science fieldwork is like, I am planning to blog frequently during the next 2 weeks. No promises about just of frequently, but I will do my very best to document trip and give you an insight of what it’s  like (for me) to do the data collecting that is behind most of the stories I share here.

If you do not want to miss anything, you can always follow the blog (there’s a button on the site somewhere), you don’t need an account, you can just get the updates via email. Alternatively, I’ll try to post (almost) daily pictures on Instagram (crittersresearch) and Twitter (@DeBrauwerM) as well if you can’t be bothered reading and just want to see what it all looks like.

 

Musings on the 4th Asia-Pacific Coral Reef Symposium

downloadI am writing this blog while in transit in Kuala Lumpur, traveling from Cebu (the Philippines) to Perth. I was in Cebu to attend the Asia-Pacific Coral Reef Symposium (APCRS 2018). In the past I have written about the reasons why as a scientist I like visiting conferences, such as IPFC or ICRS. Those reasons have not changed: hearing about new research, meeting up with colleagues and friends, discussing new collaborations, and sharing my own research with people working on similar topics.

What was different atthis conference, is that it was my first international conference after submitting my PhD thesis. This was also the first time that I was invited as a  keynote speaker (for a mini-symposium that was part of the bigger conference). The conference had a strong regional focus, so many of the people attending conduct their research in the same region as I do. So there were a lot more opportunities for developing new collaborative projects than on larger conferences.

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Presenting my first keynote on the Sustainable Coral Reef mini-Symposium parallel to APCRS 2018 (Photo credit: Sugbu Turismo)

Here are some of my impressions while the last days are still fresh in mind….kind of fresh at least, the conference organisation was very generous in the amount of free San Miguel beer provided at the dinner last night 😉

More than other conferences I attended, APCRS 2018 had a strong management and practical feel to it. Many conversations I had and most of the presentations I heard had a strong underlying theme of developing solutions that could actually be used for managing reefs. What really made it interesting was that not only scientists, but also some managers and conservation organisations were presenting their work. I might be a bit too optimistic, but I feel that in the last years, many of the idealistic, but completely unrealistic ideas are being replaced by a more realistic approach that does not turn a blind eye to the real problems.

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Presenters of the Sustainable Coral Reef Tourism session (Photo credit: Sugbu Turismo)

Talking about how to use research results for management with the people working for organisations like Reefcheck, GreenFins, or CMAS was sometimes confronting, but also a great way to start having an impact beyond mere suggestions in scientific papers. Besides discussing future projects that will result in helping management, I also had some very inspiring talks with other researchers. If all goes well, the end of 2018 could become even more fun than I already expected. Hopefully more on that later!

There was another interesting theme that kept on coming back through many of the conversation I had: “What are we trying to achieve as scientists?” Or even more fundamental: “Why are we REALLY doing what we do”? It might seem obvious; most scientific papers will state that one way or another they want to understand the world better, and usually that they want to make a positive difference. But it can be interesting to ask if that’s what we are really doing? To what extent are we actually making a difference, or just following our curiosity? Are we willing to do the extra effort that is needed to truly have a positive impact? Or are we sometimes forgetting about the world beyond academia and writing papers because that is what you do when you want a career in science?

There is no judgement in any of these motivations, most of the scenarios are equally valuable. But realising why you do the research that you do, might help you to be more focused and get the results you aim for. At least it does for me…

This conference was probably one of the most productive and inspirational conferences I have attended since I started my PhD in 2014. I am very much looking forward to the next one in Singapore in 2022, and the new projects that I’ll be working on in between!

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Audience at the sustainable tourism session – APCRS 2018 (Photo credit: Sugbu Turismo)