Colorful Coral Gardens that Flourish Entirely out of Our Sight 
Date of publication: Oct 27, 2022

With the ability of building complex 3D habitats, corals as sessile animals harbor high levels of biodiversity, similar to plants on land. While iconic ecosystems like tropical coral reefs and seagrass meadows occur in light-flooded zones of the ocean, deep coral assemblages populate oceanic regions where light is scarce or even absent, and therefore remain entirely out of sight. Together with tropical coral reefs, seagrass meadows and macroalgae forests, these habitats are commonly termed marine forests and have crucial ecological functions in the marine environment. 

Within the group of marine forests, I would like to shed some light on temperate corals, often referred to as forming coral gardens. Coral gardens are a type of coral formation occurring from 20 up to 500 m depth that are less well known than their shallow-water counterparts, mainly due to the hindered accessibility. Observations from accidental coral catches by fisheries, the use of remotely operated vehicles (ROV) and to some extent diving, only provide fragmented information on these habitats. Thus, their importance as a functioning ecosystem has only been recently revealed and further investigations are crucial to learn more about these corals and the habitats they form in order to manage their conservation. Along the continental shelf and slope, coral gardens provide shelter, food sources, a nursery ground and contribute to the blue carbon budget by immobilizing carbon as long living organisms. Corals act as ecosystem engineers by building physical structures that reach into the water column, forming natural sediment traps for further seafloor consolidation and space for organisms. As coral gardens are dominated by filter feeding organisms, they facilitate a trophic link between benthic and pelagic communities. Not only are these habitats flourishing areas for many organisms, they are also of great interest for the fishing industry. In a nutshell, coral gardens are essential biodiverse ecosystems and their effective conservation and restoration is urgently needed. Yet, they are being destroyed at a rate much faster than they need to recover.

As all multicellular life forms, corals live in association with a diverse community of microorganisms, a so-called microbiome. With my Master thesis I aim to study the role of microbiomes on the health of their coral hosts, as well as their potential use in coral restoration projects. In particular, I aim to monitor healthy microbiomes of corals as close as possible to their natural environment, compare those with microbiomes of corals in captivity and study how the microbial community changes over time in short-term captivity, before being outplanted for restoration. The results will help us to define a natural coral microbiome baseline, as well as microbial responses to a changing environment in order to improve aquarium conditions for restoration efforts. The crew of a fishing vessel based in Sagres has been collaborating with researchers of the Biogeographical Ecology and Evolution team from the Center of Marine Sciences (CCMAR), University of Algarve. Within the scope of that collaboration, the fisher collect coral specimens that  get accidently entangled in the fishing nets. These corals are rescued and used for various research purposes, including for habitat restoration actions. 

The coral by-catch in fishing nets around Cape St. Vicente of the Portuguese continental shelf give a glimpse on the distribution of coral gardens and dominant species in that region. Cape St. Vicente (Sagres, Algarve) is the most southwestern point of mainland Europe. There, seasonal hydrodynamics and an important upwelling regime shape unique marine habitats. Together with my advisor from CCMAR, Dr. Márcio Coelho, we accompanied the fishers twice on their working day to sample coral by-catch.

Fig. 1. Left: Dr. Márcio Coelho and me sampling corals on the fishing boat. Right: Large specimen of the yellow tree coral Dendrophyllia cornigera. (Picture by Dr. Márcio Coelho)

But first we need to talk about microbes – defining a “healthy coral” is a key prerequisite to develop efficient nature-based tools to conserve healthy coral gardens and to gearing restoration efforts. All multicellular life is associated with a functional community of internal and surface-dwelling microorganisms, consisting of bacteria, fungi, archaea, viruses and protists. Together with the host, this unit is termed a holobiont. The characteristic microbes play a key role in nutrient cycling and with that maintain a dynamic holobiont homeostasis that changes along with the surrounding environmental conditions. However, a restricted group of residential microbes build up a core microbiome, whereas other microbial lineages are found to be more transient.

Our oceans have experienced an alarming accelerated and intensified pattern of changes over the last decades. General marine habitat stressors, that also act on coral gardens, include ocean acidification, nutrient pollution, overfishing and rising seawater temperatures, along with rising sea levels as a result of global warming. Especially, continental margins suffer from a high fishery exploitation and the use of bottom-contact fishing gears have destructive effects on those habitats.

Microbiome analyses can be used as a monitoring tool and to improve restoration and conservation efforts. All forms of environmental changes subsequently alter microbial communities that naturally occur in the water column and in the host species. Moreover, different microbes show different patterns of adaptation to environmental changes, such as temperature changes or nutrient availability. With that, the microbiome can equip the host with a broader capacity for adaptation. Thus, the characteristic microbial communities give insights into the host’s health status, indicate disturbances on higher environmental scales and provide resilience and adaptation. 

Due to their limited accessibility, there are only a few techniques to collect samples from coral gardens. Little by little, we can gain a more detailed picture of their biology and use new discoveries to eventually enhance conservation and restoration techniques. Accidental coral by-catches from fisheries give us a chance to gradually answer research questions that remain unknown compared to their well-studied tropical counterpart. For over three years now, the fisher crew in Sagres takes the time to detangle corals, provides them to the CCMAR and offers researchers to accompany them on their working day. With that, we were able to collect coral samples as close as possible to their natural environment to gain insights into natural microbial compositions of coral gardens.

Fig. 2. Left: The vessel in the harbour of Sagres before departure at 3am on the 19th of August. (Picture by Márcio Coelho) Right: Sunrise above the Algarve drystone walls of Cape St. Vicente

Every day, the fishers start their working day at a time that can be better described as night time rather than early morning. Arriving at the harbour, we found the captain already planning the day in the fishing logbook. Immediately, he kindly offered us a seat on the bench in his cabin. While he steered the boat offshore and deployed the first net, we tried to prepare our sense of balance for the journey that was ahead of us. On time with the sunrise, the first fishing net was pulled in. Over two sampling days, we monitored in total 8 sets of bottom-set trammel nets and collected 68 samples of 12 different coral species. 

Coral gardens in Sagres are populated by a diverse range of coral species, including hard corals of the order Scleractinia (e.g., the tree corals Dendrophyllia ramea and Dendrophyllia cornigera) and most dominantly by several orders of soft corals (subclass Octocorallia) like sea fans, that are also known as gorgonians (Fig. 3). The species composition varies along depth ranges and seabed conditions in the sampling area. Active sediment transport and erosion maintain rocky surfaces and with increasing distance to the drystone walls, the seabed develops into a soft sandy and muddy substrate. The fishing nets are mostly deployed over or near hard substrate with an average depth of 80 – 90 m, bringing a certain collection of by-catch species on deck. The most abundant species found entangled in the net are the gorgonians Eunicella verrucosa and Paramuricea grayi. Accompanied by these gorgonians, many other species are accidentally collected, for example filter feeding ophiurids, that profit from the branching physical structure of sea fans. The tree corals (D. cornigera and D. ramea), belonging to the group of stony corals, are common representatives of coral gardens and therefore frequently found in the nets, as is the giant gorgonian (Ellisella paraplexauroides), a very tall coral that can form brick-red colonies up to 2 m high. Aside from the by-catch that they accidentally gather along the way, the fishers actually target species like monkfish, or black-bellied angler (Lophius budegassa), the blonde ray (Raja brachyura) and the John Dory (Zeus faber). 

Fig. 3. Overview of dominant coral species found along the coast of Algarve

One net that was deployed in the deep sea reached a depth of around 472 m. Here, the coral by-catch was mainly dominated by a bamboo coral species (Isidella cf. elongata). Similar to the ophiurids, feather stars (Crinoidea) anchor themselves to the branches of the coral to enhance their feeding success on plankton, detritus and other small particles. When reaching more sandy areas, one inhabitant that will be frequently pulled out of the sediment is the sea pen Pennatula rubra. Hotspots of biomass production also attract a range of cetaceans and on the second trip we were lucky to see a large pod of short beaked common dolphins (Delphinus delphis) gathering around the vessel.

Our working station onboard was located on the vessel’s bow. While the fishing net was pulled in from the ocean with a net hauler we had to quickly spot adequate specimens before the net was passed on to a secondary hauler where the fisher processed their catches. Sometimes, spotting specimens was quite challenging while processing previous samples. At a certain point the entire crew helped out, stopping the net hauler on “pára” (portuguese for stop) to give us time to collect corals from the net. After four to five fishing nets, one crew member generally starts preparing a pot of pasta or rice stew with the catch of the day. A shared lunch is served on deck as the boat slowly makes its way back to the harbour.

Fig. 4. Left: The captain’s cabin with GPS devices, radar and steering wheel. Middle: Steering back to the harbour of Sagres. Right: A school of short beaked common dolphins (Delphinus delphis) (Picture by Márcio Coelho)

A selection of coral specimens from the last sampling trip are now kept in the aquaria system at CCMAR’s Marine Station Ramalhete. The corals were regularly sampled for one month to survey potential responses of the coral microbiome to changing environmental conditions, such as the effect of captivity. The results will help us improve aquaria conditions to facilitate the restoration success of these corals. Finally, another sampling of corals previously rescued from by-catch is being conducted on specimens that are now cultivated for four months at the tank systems of  Zoomarine Algarve (Guia) and for over a year at the Oceanário de Lisboa (Lisbon). These samples will state an important baseline by allowing us to identify a resident microbiome that is always present despite changing conditions. In the next step of this work, I will be taking the samples to the Natural History Museum (NHM) in Vienna, to begin the second phase of my master thesis project under the supervision of Dr. Pedro Frade. With the molecular work, we will steadily get closer to gathering the first results that will contribute to the project goals of RESTORESEAS. 

Written by Marcellina Rola, NHMW

References & Further Readings

Dias, Vítor, Frederico Oliveira, Joana Boavida, Ester A. Serrão, Jorge M. S. Gonçalves, and Márcio A. G. Coelho. 2020. “High Coral Bycatch in Bottom-Set Gillnet Coastal Fisheries Reveals Rich Coral Habitats in Southern Portugal.” Frontiers in Marine Science 7 (November): 603438.

Dittami, Simon M., Enrique Arboleda, Jean-Christophe Auguet, Arite Bigalke, Enora Briand, Paco Cárdenas, Ulisse Cardini, et al. 2021. “A Community Perspective on the Concept of Marine Holobionts: Current Status, Challenges, and Future Directions.” PeerJ 9 (February): e10911.

Frade, Pedro R., Bettina Glasl, Samuel A. Matthews, Camille Mellin, Ester A. Serrão, Kennedy Wolfe, Peter J. Mumby, Nicole S. Webster, and David G. Bourne. 2020. “Spatial Patterns of Microbial Communities across Surface Waters of the Great Barrier Reef.” Communications Biology 3 (1): 442.

Hernandez-Agreda, Alejandra, William Leggat, Pim Bongaerts, and Tracy D. Ainsworth. 2016. “The Microbial Signature Provides Insight into the Mechanistic Basis of Coral Success across Reef Habitats.” Edited by Eugene Rosenberg and Farooq Azam. MBio 7 (4): e00560-16.

Nestorowicz, Iga-Maria, Frederico Oliveira, Pedro Monteiro, Luís Bentes, Nuno Sales Henriques, Ricardo Aguilar, Barbara Horta e Costa, and Jorge M. S. Gonçalves. 2021. “Identifying Habitats of Conservation Priority in the São Vicente Submarine Canyon in Southwestern Portugal.” Frontiers in Marine Science 8 (September): 672850.

Peixoto, Raquel S., Phillipe M. Rosado, Deborah Catharine de Assis Leite, Alexandre S. Rosado, and David G. Bourne. 2017. “Beneficial Microorganisms for Corals (BMC): Proposed Mechanisms for Coral Health and Resilience.” Frontiers in Microbiology 8 (March)., Paulo, E.D. Barton, Jesús Dubert, Paulo B. Oliveira, Álvaro Peliz, J.C.B. da Silva, and A. Miguel P. Santos. 2007. “Physical Oceanography of the Western Iberia Ecosystem: Latest Views and Challenges.” Progress in Oceanography 74 (2–3): 149–73.