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

New publication: Critter diversity on the sand

It turns out that moving halfway across the world and diving into a new job is more time consuming than I expected, so I haven’t been keeping up with the blog recently. I’m slowly starting to get more organised and in the coming weeks I will try to catch up with summaries of papers that I’ve published recently.

The paper “High diversity, but low abundance of cryptobenthic fishes on soft sediment habitats in Southeast Asia” was published almost a year ago in the journal Estuarine, Coastal and Shelf Science. It was one of the key papers of my PhD and describes the diversity of critters on sandy habitats in Indonesia and the Philippines.


If you have ever been muck diving it won’t come as a surprise to you that there is some very exciting marine life to be found on sandy bottoms. When you mention places like Lembeh Strait, Anilao, or Dauin to keen divers – especially photographers – they either get lyrical about the amazing pictures they took there, or will tell you about their plans for visiting any of the above places to go see some crazy marine life.

Froggie yawning

Species like this painted frogfish (Antennarius pictus) are popular with muck divers

In fact, the popularity of these sandy critters is so great, that the divers visiting Southeast Asia for muck diving bring in more than $150 million of revenue each year, supporting thousands of sustainable jobs! With so much money and jobs involved, it would be normal to expect researchers and conservationists to be interested in knowing which animals live on tropical sandy slopes. Unfortunately, that assumption would be wrong, surprisingly little is known about soft sediment (=sandy) habitats in the tropics. Even basic knowledge such as which animals live where is often unknown.

Luckily things are changing! Scientific interest in “cryptobenthic species” – the small, camouflaged critters this site is all about – is definitely increasing, with excellent work being doing on coral reefs by colleagues from across the world. We are starting to understand just how important they are for coral reefs and how very diverse cryptobenthic species can be.

What I am interested in though, is what is going on with the critters that live away from reefs. Are the critters living on the sand as diverse as those one coral reefs? Which species are most common? What causes species to live in one area, but not another? To answer these questions I set of with my good friend Luke for a 3 month dive survey trip that took us to Lembeh Strait, the north coast of Bali, and the sandy slopes of Dauin.

Maarten Smile

Surveying soft sediment critters in Dauin. Photo: Luke Gordon

During our survey dives, we not only counted and identified the fish we saw, we also measured a bunch of other factors that could have an effect on the presence of critters. We wanted to know whether depth, benthic cover (growth of algae, coral, sponges etc), or the characteristics of the sediment played a role in which species we found.

So what did we find?

One of the most interesting results is that the diversity (number of species) of cryptobenthic species was very high, higher in fact than the cryptobenthic fish diversity on many coral reefs! In contrast, the abundance (number of individuals) was much, much lower than what is found on coral reefs. To put it in perspective, if a normal coral reef would be an aquarium with 300 cryptobenthic fish of 15 different species crammed inside, soft sediment habitats would be the same aquarium with 30 fish of 16 species.

When looking at environmental factors, one of the most important factors that influenced where species lived, was the characteristics of the sediment. For small critters it makes a big difference whether the sand is powdery fine, or coarse like gravel. There seems to be a middle ground where the size of the sediment seems ideal for many critters. The tricky part is that the characteristics of sediment are in a large part determined by other processes such as currents or wave action. For now it is too early to conclude whether critters are found in these places because of the type of sediment or because of other factors that shape the sediment!

The amount of growth on the bottom played a role as well, particularly when algae or sponges were present, which makes sense as it offers variation in the habitat and potential hiding places for some species. Depth differences played a minor role in some regions (Daiun, Bali), but did not make a real difference in Lembeh. The limited effect of depth could partially be due to the fact that we did not survey deeper than 16m (university diving regulations are quite restrictive). It would be a great follow-up study to compare with deeper depths, as I am sure they will give very different results.

What does it all mean?

This study was (as far as I know) the first one ever to investigate the cryptobenthic fish in soft sediment habitats. The unexpectedly high diversity and very low abundance means there is a lot more  species out there than what was assumed, but that we have to look much harder to find them. I mostly see our results as a starting point to guide further research. We have only uncovered a fraction of what is out there and are not even close to really understanding how tropical soft sediment systems function. While this provides an exciting opportunity for scientists like me to new research, it also means that we do not yet know how environmental threats such climate change or overfishing will impact  species living on soft sediment. We do not know yet if the species that muck dive tourism depends on need protection, or how to best protect them if they do.

Whiteface whaspfish

We might not know yet what the future holds for sand-specialists like this whiteface waspfish (Richardsonichthys leaucogaster), but I am hoping to find out!

New publication: Flash photography impacts on fish – To flash or not to flash?

The final paper of my PhD thesis has just been published online in the journal Scientific Reports. The paper, titled “Behavioural and pathomorphological impacts of flash photography on benthic fishes” explains the effects of typical diver behaviour while photographing small critters such as seahorses or frogfishes.

The paper itself can be a tad technical, so with the help of two co-authors (Dr. Ben Saunders and Tanika Shalders), I wrote this summary of the research, which was published first at The Conversation (original article here).


We all enjoy watching animals, whether they’re our own pets, birds in the garden, or elephants on a safari during our holidays. People take pictures during many of these wildlife encounters, but not all of these photographic episodes are harmless.

There is no shortage of stories where the quest for the perfect animal picture results in wildlife harassment. Just taking photos is believed to cause harm in some cases – flash photography is banned in many aquariums as a result.

But it’s not always clear how bright camera flashes affect eyes that are so different from our own. Our latest research, published in Nature Scientific Reports, shows that flash photography does not damage the eyes of seahorses, but touching seahorses and other fish can alter their behaviour.

Look but don’t touch

In the ocean it is often easier to get close to your subject than on land. Slow-moving species such as seahorses rely on camouflage rather than flight responses. This makes it very easy for divers to approach within touching distance of the animals.

Previous research has shown that many divers cannot resist touching animals to encourage them to move so as to get a better shot. Additionally, the high-powered strobes used by keen underwater photographers frequently raise questions about the welfare of the animal being photographed. Do they cause eye damage or even blindness?

_MG_6706

Does flash harm fishes? Photo: Luke Gordon

Aquariums all around the world have taken well-meaning precautionary action. Most of us will have seen the signs that prohibit the use of flash photography.

Similarly, a variety of guidelines and laws exist in the scuba-diving community. In the United Kingdom, flash photography is prohibited around seahorses. Dive centres around the world have guidelines that include prohibiting flash or limiting the number of flashes per fish.

While all these guidelines are well-intended, none are based on scientific research. Proof of any damage is lacking. Our research investigated the effects of flash photography on slow-moving fish using three different experiments.

What our research found

During the first experiment we tested how different fish react to the typical behaviour of scuba-diving photographers. The results showed very clearly that touching has a very strong effect on seahorses, frogfishes and ghost pipefishes. The fish moved much more, either by turning away from the diver, or by swimming away to escape the poorly behaving divers. Flash photography, on the other hand, had no more effect than the presence of a diver simply watching the fishes.

For slow-moving fishes, every extra movement they make means a huge expense of energy. In the wild, seahorses need to hunt almost non-stop due to their primitive digestive system, so frequent interruptions by divers could lead to chronic stress or malnutrition.

The goal of the second experiment was to test how seahorses react to flash without humans present. To do this we kept 36 West Australian seahorses (Hippocampus subelongatus) in the aquarium facility at Curtin University. During the experiment we fed the seahorses with artemia (“sea monkeys”) and tested for changes in their behaviour, including how successful seahorses were at catching their prey while being flashed with underwater camera strobes.

img_8812

The aquaria were the seahorses were housed during the experiment

An important caveat to this experiment: the underwater strobes we used were much stronger than the flashes of normal cameras or phones. The strobes were used at maximum strength, which is not usually done while photographing small animals at close range. So our results represent a worst-case scenario that is unlikely to happen in the real world.

14808071_10154728145537608_910910029_o

West Australian seahorses (Hippocampus subelongatus) in their aquarium at Curtin University

The conclusive, yet somewhat surprising, result of this experiment was that even the highest flash treatment did not affect the feeding success of the seahorses. “Unflashed” seahorses spent just as much time hunting and catching prey as the flashed seahorses. These results are important, as they show that flashing a seahorse is not likely to change the short-term hunting success (or food intake) of seahorses.

We only observed a difference in the highest flash treatment (four flashes per minute, for ten minutes). Seahorses in this group spent less time resting and sometimes showed “startled” reactions. These reactions looked like the start of an escape reaction, but since the seahorses were in an aquarium, escape was impossible. In the ocean or a large aquarium seahorses would simply move away, which would end the disturbance.

Our last experiment tested if seahorses indeed “go blind” by being exposed to strong flashes. In scientific lingo: we tested if flash photography caused any “pathomorphological” impacts. To do this we euthanised (following strict ethical protocols) some of the unflashed and highly flashed seahorses from the previous experiments. The eyes of the seahorses were then investigated to look for any potential damage.

The results? We found no effects in any of the variables we tested. After more than 4,600 flashes, we can confidently say that the seahorses in our experiments suffered no negative consequences to their visual system.

What this means for scuba divers

A potential explanation as to why flash has no negative impact is the ripple effect caused by sunlight focusing through waves or wavelets on a sunny day. These bands of light are of a very short duration, but very high intensity (up to 100 times stronger than without the ripple effect). Fish living in such conditions would have evolved to deal with such rapidly changing light conditions.

This of course raises the question: would our results be the same for deep-water species? That’s a question for another study, perhaps.

So what does this mean for aquariums and scuba diving? We really should focus on not touching animals, rather than worrying about the flash.

Flash photography does not make seahorses blind or stop them from catching their prey. The strobes we used had a higher intensity than those usually used by aquarium visitors or divers, so it is highly unlikely that normal flashes will cause any damage. Touching, on the other hand, has a big effect on the well-being of marine life, so scuba divers should always keep their hands to themselves.

Luke_Snoot_Black Hairy

Look, take pictures, but don’t touch!


NOTE: I realise that this is a controversial topic in underwater photography. If you have relevant questions, comments, or thoughts you want to share, feel free to add them in the comment section below. If you are interested, I would highly advise you to read the original research paper via this link. The paper is open access, so anyone can read and download it. If you have specific questions about the paper, you can always contact me via email here.

Marine biodiversity in Oman: Mini-blog 2 – Meet the team

In the previous blog I wrote how I joined a great team of researchers to study fish diversity in Oman. The scientists I’m working with are experts in their fields, and form a very complimentary group, perfect to be studying fish diversity with. It’s fantastic to be collaborating with them, especially since this kind of work is new to me, which means I am learning loads at the moment! So it’s only fair to introduce the people that are really driving this trip.

Amanda

Ms. Amanda Hay: Amanda is Acting Ichthyology Collection Manager at the Australian Museum. She is a taxonomy expert, specialised in larval fishes. While she considers herself a jack-of-all-trades, she is the most organised member of the team who makes sure all the fish are named and catalogued properly.

 

Chris

Dr. Chris Goatley: Chris is a postdoctoral research fellow at University of New England who specialises in reef fish ecology. In particular, Chris is interested in the ecology of the smallest coral reef fishes, including gobies and blennies. He is particularly interested in the roles of these small fishes in maintaining coral reef food webs.

 

DarrenDr. Darren Coker:  Darren is a Research Scientist in the Red Sea Research Center and Saudi Aramco-KAUST center for Marine Environmental Observations at King Abdullah University of Science and Technology in Saudi Arabia. Here he focuses on reef fish communities along environmental gradients and how local and global stresses influence fish groups that are important to reef health.

Alyssa MarshellDr. Alyssa Marshell: Alyssa is an Assistant Professor in the College of Agricultural and Marine Sciences at Sultan Qaboos University. She is on of the lead investigators on the DFAT CAAR grant that funds this research project. Alyssa is an expert in marine and spatial ecology, with particular interests in the movement and behaviour of herbivorous reef fishes.

JoeyDr. Joey DiBattista: Joey is the new Curator of Ichthyology at the Australian Museum and standing member of the TrEnD Lab at Curtin University. Joey is the other lead investigator on this research project. His name might sound familiar if you follow this blog, since he has written a very interesting guest blog in the past. Joey is interested in developing next generation-sequencing tools to aid in  fisheries management. His new position role at the museum will allow him to build up genetic “barcode” libraries for fishes across Australia.

These are not the only team members working on this project, other researchers involved include remote marine field specialist Tane Sinclair-Taylor, PhD student Mark Priest, and Director of the Red Sea Research Center at KAUST – Professor Michael Berumen. Their contribution is at least as important as the other members, but they are unfortunately not close enough at the moment to hassle them for info.

Lastly, the newest, honorary member of the team is our Musandam captain Ali! Ali owns  Ras Mudandam Diver, the dive centre that was taking us out for our work here. He’s been an absolute legend, and if you’re considering diving here, you should definitely look him up!

Ali

Captain Ali