Finding the Knysna Seahorse: Mini-blog 5

It’s already been a week since I arrived in South Africa to study the endangered Knysna seahorse with Dr. Louw Claassens from the Knysna Basin Project. Together we are testing if environmental DNA (eDNA) can be used to find rare seahorses and pipefishes.

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eDNA filtering in progress

To do this, we have been travelling along the southern coast of South Africa, taking water samples along the way in estuaries where our focal species lives, where it used to live, or where it might live. Yesterday we left Knysna to sample water in Klein Brak and Groot Brak. We are especially interested in the Klein Brak estuary, since there are multiple anecdotes that the Knysna seahorse (Hippocampus capensis) used to live here. Nobody has checked recently if it really was the Knysna seahorses and it seems that the most recent sighting has been many years ago. Because of this, it is usually assumed that there are no more Knysna seahorses in Klein Brak.

This brings me to a very important (maybe the most important?) question about this whole endeavour: WHY are we actually doing this? It’s all good an well to say that we want to help these endangered animals, but what exactly are we hoping to achieve? What will our results mean for managing the endangered Knysna seahorse, the critically endangered Estuarine pipefish, or any other endangered small fish for that matter?

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Knysna estuary, just imagine all the seahorses down there!

What we are hoping to achieve can be summarised in three main points.

  1. We want to test if the eDNA method can really be used to find small, endangered fishes (particularly seahorses and their relatives). So far, previous research has shown that eDNA work on large fishes such as sawfish, but it is not sure yet if this will work for seahorses, which are obviously much smaller.
  2. The best case scenario would be that we could also find seahorses in estuaries where it was thought to have disappeared. This would be great news for the conservation status for the species, as it would mean that it occurs in a wider area than we thought, which would mean that it is less likely to go extinct.
  3. If this would happen, it would mean two things. First of all, the new locations would have to be studied, so we can find out how many live in these estuaries. It would also mean that those new places need extra protection and monitoring to ensure the species do not disappear from their newly discovered homes.

Ultimately, if the eDNA method works for small, endangered seahorses (or their relatives), it could be used to monitor small fishes worldwide. This would help solving one of the biggest problems with studying small species, especially those that are rare or hard to find.

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Louw looking for Knysna seahorses in the Thesen Island Marina (she found 3!)

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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.

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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.

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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

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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!
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Louw on her way to sample Bushmans estuary

 

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.