Finding the Knysna Seahorse: Mini-blog 4

We are 5 days into sampling environmental DNA of the Knysna seahorse (Hippocampus capensis) and I continue to be impressed by the landscapes and nature of South Africa. After sampling at the southern Eastern Cape we traveled to the Knysna estuary in the Western Cape. We not only collected water samples along our way, but also passed through a national park to get a look at some of the wildlife.

ElephantAnd oh my, how lovely that was. I might be a marine scientist, but seeing the impressive wildlife here is pretty amazing as well. Obviously seeing elephants, zebras, lions and all the other cool animals roaming around is awesome, but there is so much more than that. There’s all the different kinds of gazelles, the warthogs (might be a personal favourite) and the very diverse birdlife. Unfortunately there won’t be enough time this trip to really experience it all, so I will just have to come back!

The focus of the trip is still very much on the endangered Knysna seahorse.  But what does it mean when we say that an animal is endangered? And why are the Knysna seahorse and the estuarine pipefish endangered?

The easiest way to explain what “Endangered” means, is that an animal or plant has a high chance of becoming extinct in the near future. This can be caused by directly killing the animals/plants, such as overfishing or hunting (think rhinos and the ivory trade), but also by more indirect threats. For example: if you cut down the rainforest, the animals that need the forest to live in will disappear as well, even if you do not kill the animal directly.

20180811_075851

Swartvlei estuary

In the case of the two species we are working on, two big factors are responsible for their high extinction risk. Both the Knysna seahorse and the Estuarine pipefish only occur in a very, very small area of the world. The seahorse only lives in 3 estuaries and the pipefish in 4 estuaries in the southern tip of South Africa. They do not live in the ocean or the rivers, but only in the small area of mix salt and fresh water where the rivers go into the ocean.

The other big factor is that both species only live in a particular habitat. That is, they don’t just live anywhere in those estuaries, that would be too easy! No no, the species we study aren’t happy anywhere else than in areas where there is enough seagrass. So even though there might be a lot of space in the estuaries they live, they only live in a very small area in that space.

Seahorse

Can you spot the Knysna seahorse (Hippocampus capensis) in the seagrass?

What this means is that small changes to the seagrass can have a very big effect on the seahorses or pipefishes. As you may or may not know, seagrass is disappearing all over the world, including South Africa. Some of the most important causes are poor water quality, coastal development, and climate change (Here is a great site for more info on threats to seagrass meadows).

For our two species, even a small, localised decrease of seagrass means they can go extinct in those estuaries where the seagrass is affected. The estuarine pipefish has in fact already disappeared from two estuaries where it used to live. This might also already have happened to the Knysna seahorse, but there is very little information about where it used to live and where it lives now, so it is hard to be certain about this.

Hopefully our work will help to protect these beautiful, but vulnerable animals. How the results of our research might help is for one of the next mini-blogs.

Sampling

Early morning water sampling

Finding the Knysna Seahorse: Mini-blog 3

IMG_1714

Kleine Monde

Today was busy, so not enough time to properly write. Instead, to give you an idea of what I do all day,  here is the schedule of today’s fieldwork.

  • 6:00 – Wake up
  • 6:30 – Drive to first site (Kleine Monde)
  • 7:50 – Collect samples (Kleine Monde West, 2 locations)
  • 8:10 – Collect samples (Kleine Monde East, 2 locations)
  • 10:00 – Back at room, start filtering samples
  • 12:30 – Drive to site (Bushmans estuary)
  • 13:15 – Collect samples (Bushmans, 2 locations)
  • 14:50 – Back at room, start filtering samples
  • 19:30 – Realise samples contained more sediment than expected and that filtering will take twice as long as planned, eat food, drink some wine
  • 21:40 – Still filtering, drink tea, lots of tea
  • 23:25 – Finished filtering samples, time to clean up
  • 23:50 – Off to bed!
38704899_290774851475043_3374615427203203072_n

Louw on her way to sample Bushmans estuary

 

Finding the Knysna Seahorse: Mini-blog 2

IMG_1677

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.

38777316_2086748234922179_5249979198688198656_n

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.

38668211_1926695760728222_5584027590168936448_n

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.

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.

20180806_135439

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).

20180806_173815

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.