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

Finding the Knysna Seahorse: Mini-blog 2


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.


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.


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.

Seahorse and pipefish blog collection

syngbioI am currently in Florida at the University of Tampa, to attend Syngbio 2017. Syngbio is the global conference about Syngnathidae. “Syngnathidae” is the scientific name for the group of animals that consists of seahorses, pipefishes, etc. The conference is being attended by over 100 experts from across the world, who are discussing topics ranging from behaviour, to genetics, husbandry and conservation.

Once the conference is over, I will write a blog about the main conclusions of the conference. But since I am currently in a syngnathid mind-set, I figured it made sense to have a look at previous blog posts I wrote about seahorses and their relatives and combine them for anyone interested to learn more about these fascinating animals.

  • Little known seahorse facts: an overview of interesting facts about seahorses you might not have heard of before
  • Winged pipefish: one of my favourite pipefish species that I feel deserves more attention
  • Seadragons and other critters found in the cold waters around Sydney
  • Ruby seadragons, deep sea seahorses and other critters beyond the reach of divers
  • Keeping seahorses in tanks: a rant on how I struggled keeping West Australian seahorses in tanks. Read this blog if you are considering keeping seahorses in tanks yourself
  • Ornate ghostpipefish: ghostpipefishes are gorgeous animals, but very understudied. This blog is an overview of what we know about the ornate ghostpipefish.
  • Fluo seahorses: A photo compilation of some of the fluoresence work I’ve done, including fluo seahorse shots


Winged Pipefish

As the research that I am doing looks at some of the strangest critters you can find in the ocean, it seems only right to give them a space on this blog. The little guy who kicks of the page is a little known pipefish: the “Winged Pipefish”.

Adult Winged Pipefish

Winged Pipefish

While doing surveys on the Critters@Lembeh housereef, I found a large (15cm) Winged pipefish (Halicampus macrorhynchus) chilling out on a patch of rubble. I have seen this species a few times before on dives in Indonesia, and always liked it a lot, even if you don’t hear or read about them very often. Maybe I like them just because it’s less of an in your face – “take a picture of me now, I’m AWESOME” – kind of critter than some of the more popular ones, but they still manage to be pretty cool creatures. As with most other pipefishes, little is known about their life history and behaviour. Besides the original description, I found a grand total of 0 (=zero) scientific papers that focus on the ins and outs of this amazing fish…

Juvenile Winged Pipefish

Juvenile Winged Pipefish

So here is what we do know: The juveniles are beautiful, mimicking algae or bits of seagrass. The tiny juvies have got large appendages resembling wings, hence the name. The wings don’t serve many other purposes besides looks (more on that later). They can be found on sand or rubble, often in areas with a lot of plant debris or seagrass. I think they are cutest juvenile pipefish you can find, but they are a very rare find, in 12 years of diving I only ever managed to find a single one.

With age the wings appear to get smaller (they grow into them). In big adults the only things that can be seen are small skin flaps on the side. The adult pipefish still look quite amazing, and can display all kinds of colours, ranging from brown to yellow to pink. At this stage, they are more commonly found on coral rubble or coral reefs.

The biggest adults can get overgrown with algae and are extremely well camouflaged, like the one on the housereef. The big ones I’ve seen were always on coral rubble and looked kind of gritty and tough (as far as pipefishes can look tough).

Halicampus macrorhynchus

Halicampus macrorhynchus

For those if you interested in finding or photographing one of these guys, Winged Pipefish range from the Red Sea to as far as Hawaii and Panama. Look in rubble, sand or seagrass patches between 3m and 25m.

Spot the pipefish...

Spot the pipefish…

Oh, and the function of the skin flaps and wings? It is assumed that they help to break up the shape of the fish, making it even harder to find for predators or divers.