Ambon and Halmahera fieldwork: Mini-blog 3 – Surveying Ambon’s reefs

In the previous fieldwork blog I wrote that we were about to leave on the boat to survey coral reefs around Ambon. So let me walk you through how our first week went.

Leaving Ambon took a bit more effort than expected, getting the necessary pre-departure paperwork signed off took 6 hours instead of 10 minutes, but we finally managed to leave late afternoon. We left under a rather gloomy sky, with grey clouds and scattered rain showers seeing us out of the bay instead of the bright sunshine we hoped for. But with an overnight boat trip ahead of us to get to the first sites, we could maybe wake up to blue skies.

That, unfortunately, was not meant to be…

Leaving Ambon

Gloomy Ambon skies

When I mention “dive expedition in Indonesia”, most people tend not to imagine grey skies and unrelenting rain, but the lush tropics wouldn’t be quite as lush without lots and lots of rain! Throughout the week we had plenty of rain, sometimes so much we had to postpone dives because of the limited visibility at the surface: the boat driver needs to be able to see the divers at the surface to pick them up when surveys are done.

 

But we had come to Ambon to study coral reefs, so (mostly) undeterred by the rain, we hopped in and started our work! The first thing we noticed was a conspicuous lack of…coral. We started surveys in an area with a lot of human fishing activity, and it showed, big time. We did not hear any blasts while diving, but there was a lot of evidence of dynamite fishing. Entire reefs were reduced to rubble, some places even had large bomb craters, something I had never seen before. I dread to think about the size of the bomb and the immediate impacts of its blast. A lot of explosive power is required to leave a 40cm deep, 1.5m wide crater underwater!

It wasn’t all bad news though, some places were showing slow signs of recovery, which could mean they hadn’t been bombed for a while. There were still some large fish left, nowhere near as many as there should be, but I did spot a few large groupers and emperors, and even a few adult blacktip reef sharks. We saw encrusting algae and small coral slowly starting to take hold in some places, although they were still a long way from becoming a real coral reef again. I would estimate it could easily take another 50-100 years for these sites to become a fully functional reef, even if they were left in peace and there were no other impacts.

 

After a couple of days of rain and survey dives that made our hearts ache, the team’s morale (or at least mine) had seen better days. Luckily, two things happened: we moved on to sites that had less fishing pressure and the sun started shining!

This part of the trip brought home just how rich coral reefs can be if you just use them in a less destructive way. Sites with very high and diverse coral cover, big schools of fish, lots of invertebrates, funky critters, everything you could want in a dive. This time our only regret was that the tight schedule didn’t give us time to explore each site more thoroughly. Between trying to count and identify large schools of mixed fish species, processing eDNA samples and entering data, little time was left to do anything else than eat and prepare for the next dive. Not that I’m complaining though, being able to work on reefs like this is a privilege that never gets old.

We were also privileged to see some of Ambon’s funky critters. During quite a few dives we came across ghostpipefish (Solenostomus paradoxus and S. cyanopterus), a rare sight on standard coral reef surveys. Our invertebrate expert had his work cut out counting a variety of nudibranchs, shrimp, cowries, and anything in between. Even the algae crew got more fish than they bargained for when a giant frogfish (Antennarius commersoni) decided to swim by and say hello.

 

Despite some adverse weather and a slow start, we finished surveys within the planned time and arrived back in Ambon Bay two days ago. Our two days on land were put to good use, catching up on data entry and admin, meetings, and even catching a movie last night (Joker, pretty good actually). Tomorrow we leave at first light for a longer trip. We are headed to Halmahera, an area where precious little information exists on the health of coral reefs. If all goes according to plan, I should be able to write an update from Ternate in about 6 days!

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Ambon and Halmahera fieldwork: Mini-blog 2 – Logistics

I have made my way to Ambon since the last blog, where I have been preparing the last logistics with my local colleagues from Pattimura University before the actual fieldwork begins. In the last 3 days, the other team members have also started arriving, with the final team member (and master fish counter) landing tomorrow morning. The main things that had to happen before our boat leaves port (besides recovering from jetlag), was organising a detailed plan, training new team members, and preparing all the gear. 

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Cloudy Ambon days

One of the things we will be doing, is collecting environmental DNA (eDNA) to study biodiversity on coral reefs. If you want to know more about eDNA, I have written more about it here or here. In short: eDNA are tiny fragments of DNA in the water column that come from poop, mucus, etc. By filtering and analysing a scoop of water, we can tell what lives in the area we took water from. Because eDNA is such a new method, most people have not used it before. So in a great mutual benefit arrangement, our Pattimura University colleagues took us (my colleague Dom and me) out for a dive and in return we showed them how to collect water 😉

We obviously did more than just collecting seawater, we also went back to the lab to teach them the protocols on how to filter samples while avoiding contamination. Since eDNA analysis is so good at picking up the tiniest fragments of DNA, a careless brush of a fingertip can render the entire sample useless. We are collecting data from a boat instead of a high-tech lab, so being aware of how things can go wrong is absolutely crucial to get reliable data.

Tomorrow morning we set sail (start engine?) for 10 days of research around Ambon. So today we had make sure all the equipment got to the boat, for us to leave at first light in the morning. Between dive gear (including compressors, tanks, etc), survey tools, eDNA equipment, and other random practical bits and pieces, it took multiple returns trips with the pickup to get everything to the boat. Science is of course hungry work and feeding 16 people takes a lot of grocery shopping, which was luckily taken care of by our local team. Gino (our Ambon trip leader) has assured me we have an excellent chef on board, so be aware that there is a decent chance that the rest of these fieldwork blogs will mostly be about tasty Indonesian food!

As we will be on a boat for quite a while in the next weeks, I am not sure yet if I will be able to post blogs until we are back on the mainland. If I can snatch up some 4G signal along the way, you’ll be able to read an update on the fieldwork in a couple of days. Otherwise, the next blog will be online around the 11th of October.

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Sunny Ambon days

Ambon and Halmahera fieldwork: Mini-blog 1 – Departure

It’s that time again! I am on my way to do fieldwork and I will try to post regular, small updates so everyone can follow along with what we’re up to. In the coming month I’m hoping to post at least 4 – 5 mini-blogs (depending on internet speed), so keep an eye out for updates.

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It’s fieldwork time! Photo: Luke Gordon

I am writing this first blog from an airport hotel in Makassar. It took me a train ride and 3 flights (Manchester – Doha – Jakarta – Makassar) to get this far, but I’m not quite where I should be yet. A ridiculously early flight (4:00am) tomorrow will get me to Ambon, where the fieldwork will start. Doing research in remote areas is fun, but it also means 3-day trips to get where you want to be.

The reason our team (more on them later) wants to be in Ambon, is to do research on the biodiversity of Indonesian coral reefs. We are trying to investigate how coral reefs function (or stop to function) when they are affected by human actions like overfishing or pollution.

To do this, we will be working from a boat for most of October, hopefully visiting more than 30 different sites in Ambon and Halmahera. We’ve got a team that is specialised in different topics, people will be counting fish, identifying corals, collecting environmental DNA, mapping reefs, etc. Exciting stuff with hopefully some useful results!

Survey sites Ambon

Survey sites for the upcoming fieldwork

Getting everybody at the right place at the right time can be challenging enough. I flew in from Leeds (UK), but other people are flying in from Germany, Jakarta, and Makassar. Our aim is to leave Ambon harbour on the 1st of October, with most of the team arriving the day before. But sometimes nature can get in the way of even the best planning…

Today two earthquakes have rocked Ambon, causing quite a lot of structural damage. The boat (as far as I am aware) is fine, but unfortunately the damage to the city is quite large. Luckily human casualties seem low at the moment. In any case it is likely that organising the food and other practical matters in the next few days will be more complicated than expected.

In the next post I will go into a bit more detail about the science behind this trip, and ideally I will also have some updates about the situation Ambon.

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Marine science fieldwork and packing lightly don’t go well together

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.

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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!