The first Field Identification Guide of Seychelles’ deeper reefscapes

The deep ocean is the last frontier on our planet. It is home to creatures beyond our imagination and filled to the brim with life. Coastal communities have known the value of a healthy ocean for centuries, yet much of its life remains unknown, sitting beyond the reach of most research programs due to the hostility of its depth and vastness. With current research and monitoring activities in the region mostly focussing on shallow reefs, our Field Identification Guide, published in the peer-reviewed, open-access Biodiversity Data Journal, aims to showcase the benthic organisms that inhabit the Seychelles’ deeper reefscapes. The research cruise that gathered the imagery data used to create the guide, Nekton’s “First Descent: Seychelles Expedition”, was the first of its kind to systematically survey deeper reefs in Seychelles waters, bringing to light previously little-known ecosystems and their inhabitants.

Guest blog post by Nico Fassbender, Zoleka Filander, Carlos Moura, Paris Stefanoudis and Lucy Woodall

 “We cannot protect something we do not love, we cannot love what we do not know, and we cannot know what we do not see.”

These compelling words by author Richard Louv perfectly describe the importance of taxonomy in today’s conservation efforts.

A fan coral of the genus Annella surrounded by various smaller fans and encrusting benthic organisms. Photograph taken at 60m depth. © Nekton.

The deep ocean is the last frontier on our planet. It is home to creatures beyond our imagination and filled to the brim with life. Coastal communities have known the value of a healthy ocean for centuries, yet much of its life remains unknown, sitting beyond the reach of most research programs due to the hostility of its depth and vastness. 

More recently, the importance of deeper ecosystems started moving into the focus of modern marine research as many scientists across the globe are now working to unriddle the mysteries and processes that drive the patterns of life down in the deep.

Deeper reef habitats, starting at ~30m depth beyond SCUBA diving limits, are of crucial importance for coastal communities and adjacent ecosystems alike. They have been found to not only support coral and fish larval supply, aiding shallower reefs, but also to act as a refuge for many species in times of disturbance. Yet, going back to the start of this post – you cannot protect what you don’t know – and we currently know very little about these deeper reefs, especially ones in the Western Indian Ocean region.

We are many nations, but together we are one ocean.

Zoleka Filander – Department of Forestry, Fisheries and Environment, Branch Oceans and Coasts, Cape Town, South Africa

With current research and monitoring activities in the region mostly focussing on shallow reefs, our Field Identification Guide, published in the peer-reviewed, open-access Biodiversity Data Journal, aims to showcase the benthic organisms that inhabit the Seychelles’ deeper reefscapes. The research cruise that gathered the imagery data used to create the guide, Nekton’s “First Descent: Seychelles Expedition”, was the first of its kind to systematically survey deeper reefs in Seychelles waters, bringing to light previously little-known ecosystems and their inhabitants.

All species play relevant roles in trophic relations, in the functioning of ecosystems, and all have a potential biotechnological interest.

Carlos Moura – OKEANOS/DOP, University of the Azores, Horta, Portugal
A grouper (Cephalopholis miniate) hovering above encrusting benthic communities at Aldabra, dominated by the scleractinian coral Pachyseris. Photograph taken at 30m depth. © Nekton.

Our Field Identification Guide is one of the first efforts to describe the mesophotic and sub-mesophotic reefs in the Western Indian Ocean. To effectively protect these ecosystems, stakeholders need to be able to visualise them and scientists need to be able to identify and classify the organisms they observe. Displaying the diversity of the benthic organisms we encountered is only the first step in a complex and long process, allowing us to categorize, study, monitor and thus effectively protect these habitats. 

The correct identification of life is a fundamental building block of ecological knowledge. This international collaboration provided an important place to start from when considering the life on deeper reefs in Seychelles and the wider Western Indian Ocean region.

Lucy Woodall – University of Oxford, and Nekton

To survey the benthic flora and fauna of the Seychelles, we used a variety of methods, including submersibles, remotely operated vehicles and SCUBA diving teams equipped with stereo-video camera systems. We then recorded benthic communities during transect surveys conducted at 10 m, 30 m, 60 m, 120 m, 250 m and 350 m depths. This way, we ended up with 45 h of video footage and enough images to be able to present a photographic guide for the visual identification of the marine macrophytes, corals, sponges and other common invertebrates that inhabit Seychelles’ reefs.

We encountered coral fan gardens on steep slopes, boulders entirely encrusted with sponges of all colours and textures, corals of all shapes and sizes, and an amazing variety of critters. The images in our guide cannot do justice to the beauty of these habitats, and more than one tear was shed encountering these intact ecosystems teeming with life. Especially in times of increasingly frequent disturbance events and quickly shifting baselines (i.e., what we would see as a pristine, healthy reef in the 21st century), intact reef systems become increasingly rare. So much so that they are often confined to extremely remote and/or long and heavily protected areas. Finding these deeper reefs intact and with little to no signs of anthropogenic disturbance means hope – hope that there are yet undiscovered and unexplored reefs in the Western Indian Ocean region that show similar traits; and hope that we will discover even more novel habitats worth protecting.

An overview of how habitat composition changes across depths at Astove Island. © Nekton.

We hope that this guide will help the public to discover the beauty of Seychelles’ deeper reefs and aid current and future monitoring and research activities in Seychelles and the Western Indian Ocean region.

Currently, there are few formalised training materials available to new marine researchers working in mesophotic and deeper reef habitats, especially for the Indian Ocean. The present benthic field ID guide will hopefully be of use to marine researchers, managers, divers and naturalists with the identification of organisms as seen in marine imagery or live in the field.

Paris Stefanoudis – University of Oxford, and Nekton

Taxonomic paper:

Fassbender N, Stefanoudis PV, Filander ZN, Gendron G, Mah CL, Mattio L, Mortimer JA, Moura CJ, Samaai T, Samimi-Namin K, Wagner D, Walton R, Woodall LC (2021) Reef benthos of Seychelles – A field guide. Biodiversity Data Journal 9: e65970. https://doi.org/10.3897/BDJ.9.e65970

From an amateur nature video to a unique study on Antarctic jellyfish

Sometimes research emerges from the strangest turns of events. In this case, an online video created by an amateur videographer on life under the sea ice in McMurdo Sound, Antarctica, resulted in a unique taxonomic study on Antarctic jellyfish and an image-based training set for machine learning. This study was published in the open-access Biodiversity Data Journal.

Sometimes, scientific discoveries emerge from the strangest turns of events.

It all started in 2018, when Dr. Emiliano Cimoli, postdoctoral researcher at the University of Tasmania, joined a field campaign to McMurdo Sound in the Ross Sea, Antarctica – to study not jellyfish, but rather the algal communities that thrive beneath the ice. 

This crystal-like comb jelly species, Callianira cristata, has been reported for the first time in the Ross Sea by the team of researchers. Photo by Dr. Emiliano Cimoli

“These algae are like the plants of the under-ice world and are very important for the Antarctic food chain,” Dr. Cimoli says.  The research team he was part of focused on the development of new sensing technologies to monitor these algal communities (e.g. optical techniques and chemical microsensors).

“We usually have a nice large tent to be able to work and operate such instruments in the harsh Antarctic environment. The cool part is that inside this tent, we have a massive 2 x 2 m hole in the sea ice that allows us to deploy these instruments to the under-ice world.”

It’s kind of like a magic portal to another world filled with mysterious and wondrous jellyfish-like creatures that live down there.

Besides working as an engineer and remote sensing scientist, Dr. Cimoli is also a passionate amateur nature and wildlife photographer and videographer, and in his free time he decided to document all sightings of these creatures with his camera. The researcher used a combination of macro photography equipment and a set of light sources, along with underwater robots for filming underwater. 

This brownish-orange comb jelly of the genus Beroe is likely one of the five undescribed species characterized by the team of researchers. Photo by Dr. Emiliano Cimoli

“Finally, I ended up having a massive amount of jellyfish footage, did not know what to do with it, then lockdown hit and suddenly I found myself working on a trippy video composition of all these creatures,” he adds.

The value of his video was soon picked up by biologist Dr. Gerlien Verhaegen, postdoctoral researcher at the Japan Agency for Marine-Earth Science and Technology (JAMSTEC):

“When I came across Emiliano’s video, I was amazed by the image quality of his underwater footage. You could clearly distinguish some key morphological features.” Unlike hard-bodied animals, the fragile body of jellyfishes and comb jellies (i.e. “sea gooseberries”) are easily destroyed when sampled with nets, which is why photography and videography of specimens are crucial to describing them taxonomically.

“Life Beneath the Ice”, a short musical film about light and life beneath the Antarctic sea-ice by Dr. Emiliano Cimoli

The two postdocs soon joined forces to produce a collaborative study. 

“I think I underestimated the time needed to produce a jellyfish taxonomic paper,” laughs Dr. Verhaegen. “Most of the original descriptions of Antarctic jellies date back to the so-called Heroic Age of Antarctic Exploration in the early 20th century, and are written in English, French, and German. Furthermore, due to the high-water content of jellies, it is extremely difficult to fix and preserve them in formalin or ethanol. We therefore could not compare our specimens to physical specimens preserved in museums but had to rely on the century old descriptions and drawings. Luckily, we were in good hands with my project host, Dr. Dhugal Lindsay, senior scientist at JAMSTEC, a jellyfish taxonomist expert, and last author of our paper”.

Filming creatures in their natural environment can yield valuable information on their trophic interactions with other organisms. For example, this picture of a Diplulmaris antarctica jellyfish shows it feeds on comb jellies, with a Beroe present in its stomach, whereas numerous hyperiid amphipods (small parasitic crustaceans) are observed scattered around on the bell of the jellyfish. Photo by Dr. Emiliano Cimoli

Despite the small geographical and temporal scale of this study, which was published in the open-access Biodiversity Data Journal, a total of 12 species were reported, with two jellyfish and three comb jellies likely representing undescribed species.

Besides revealing new morphological traits for every species, including some behavior and trophic traits, this study was also the first to include a training image set for video annotation of Antarctic jellyfish through machine learning. 

“Machine learning is being applied to numerous fields nowadays, from voice recognition software and translation through to detection of typhoon formation,” comments Dr. Lindsay.

“In marine biology, annotating species from underwater videos can be both time-consuming and financially costly, with very few experts able to give names to the high diversity of species invariably encountered. Machine learning techniques could help solve these issues by enabling automatic first-pass annotation of videos. However, taxonomically accurate image-based datasets are needed to train these learning algorithms, and this study is a valuable first step.”

Watch the video “Life Beneath the Ice” by Dr. Emiliano Cimoli on YouTube and Vimeo.

Original source

Verhaegen, G., Cimoli, E., & Lindsay, D. J. (2021). Life beneath the ice: jellyfish and ctenophores from the Ross Sea, Antarctica, with an image- based training set for machine learning. Biodiversity Data Journal, 9, e69374. https://doi.org/10.3897/BDJ.9.e69374