Scaling up Coral Reef Arks for reef restoration: phase 2 testing in Biosphere 2 Ocean

Coral Reef Arks is an innovative concept that is currently funded by the Department of Defense (RC20-5175), National Science Foundation (2133474), and Gordon and Betty Moore Foundation (GBMF9207 and GBMF9344) grants to achieve initial deployment. The concept has been shared amongst a network of interdisciplinary researchers studying coral reef ecology, microbiology, virology, biogeochemistry, hydrodynamics, and modeling and mathematics with the goal of it becoming a fully mature and publicly accessible coral restoration tool. Incorporating the mesocosm facility, Biosphere 2, is the next step toward optimizing the specifics of this tool and scaling this solution to meet reef restoration needs worldwide.

Despite covering only 0.5 percent of the ocean, reef-building corals create habitat for numerous different animals, including one-third of all marine fish (Birkeland et al. 2015). Coral reefs are one of the most highly productive, biodiverse ecosystems on earth, rendering them of great economic and ecological importance. Tropical coral reefs have experienced significant declines globally, in some regions upwards of 50%, due to anthropogenic stressors (Eddy et al. 2021). Reefs have been degraded by local impacts, such as eutrophication from pollution and overfishing of herbivorous fish, and the global impacts of ocean warming and acidification from climate change (Eddy et al. 2021, Hughes et al. 2003, Hughes et al. 2017). Whereas reefs have undergone climatic changes previously in their geologic history, the current rate of change is unprecedented (Pandolfi et al. 2014a). Coral reef degradation is initiated by human activities, but is ultimately microbially-mediated: a process we call microbialization (Haas et al 2016). Removal of reef grazers and excess nutrient inputs cause the overgrowth of fleshy algae, which produce dissolved organic carbon (DOC) that fuels the growth of pathogenic and rapidly growing microbial communities and destabilizes viral communities (Haas et al 2011, Knowles et al 2016, Nelson et al 2013). These viruses and microbes cause coral death through disease and by drawing down oxygen levels in the water (Dinsdale et al 2008, Haas et al 2013, Silveira et al 2019), freeing up space for more algae and creating a positive feedback loop that shifts the ecosystem from coral-dominated to algal/microbe-dominated states.  

Coral reef degradation leads to changes/loss of critical ecosystem services like reef accretion (Andersson and Gledhill, 2013; Kleypas et al., 1999; Wisshak et al., 2012), nutrient cycling (Hollibaugh and Azam, 1983; Van Duyl and Gast, 2001; Wild et al., 2004), and energy metabolism (Haas et al., 2013; Roach et al., 2017; Smith et al., 2013). The changes/loss of these functions create positive feedbacks that result in further reef degradation. Conservation and restoration efforts must break these detrimental positive feedback loops to be successful. 

The current coral reef restoration paradigm is centered around relocating nursery-reared corals to existing reef habitats (Rinkevich, 2005). These efforts typically have low success rates and do not restore ecosystem services (Forrester et al., 2014; Garrison and Ward, 2012; Palomar et al., 2009). Most coral restoration efforts ignore the vast majority of coral reef organisms and their associated ecosystem services. These ecosystem services are essential for coral survival and this is one reason why coral translocation efforts have experienced limited success in the long term (e.g., >50% mortality after 3 years and 90% mortality after 12 years; Casey et al., 2015; Forrester et al., 2014; Garrison and Ward, 2012; Palomar et al., 2009). Placing corals on degraded benthos also contributes to microbialization and lowers the chances of success. Restoration efforts need to incorporate reef biodiversity and reinstate ecosystem services to restore the reef community and the economic benefits they provide (Lirman and Schopmeyer, 2016; Rodgers et al., 2017). 

Imagine massive midwater structures colonized with luminescent corals, anemones, crabs, and urchins, and circled by giant schools of fish. These are Coral Reef Arks. We have previously used a tool, called ARMS (Autonomous Reef Monitoring Structures), that aggregates millions of reef species into one-square-foot structures. Like building blocks, ARMS can be aggregated onto Coral Reef Arks to assemble large reef communities. 

“Coral Reef Arks,” developed by the Rohwer Laboratory at San Diego State University, are a new technology that can translocate more than 80% of coral reef biodiversity to create a “floating coral reef” and can be used to support conservation and restoration goals. The majority of reef biodiversity can be harvested using ARMS (Plaisance et al., 2011; please see our white paper at <coralarks.org> for experimental details), which have been used as a survey tool to capture and enumerate much of the diversity of coral reefs (Carvalho et al., 2019; Pearman et al., 2019, 2018, 2016). The Coral Reef Arks project uses ARMS to seed larger structures and get this diversity off the benthos and into the water column. Elevation off the seafloor circumvents the poor conditions (suboxia and sedimentation) associated with degraded reefs and has been shown to increase coral growth and survival rates in coral nurseries. 

Coral Reef Arks deployed in Curacao and Puerto Rico have demonstrated that Arks generate immediate economic benefits in the form of fisheries, carbon sequestration, and environmental mitigation, and deployed en masse, will stimulate tourism and protect coastlines. They create an entirely new way to study coral reefs, allow for the continued discovery of pharmaceutical molecules, and serve as midwater zoos and reservoirs to restore reef communities following damage or degradation. To be applied at scale, the Arks project needs to answer some fundamental questions about how the Arks drive community development at both microbial and macrobial scales, how ecological processes on Arks can influence the surrounding ecosystem, and how material composition, geometry, and hydrodynamics of the Arks can improve coral reef outcomes.  
During phase 2, Arks are being introduced to a 2.6-million-liter coral reef mesocosm, the Biosphere 2 ocean, to undergo further testing and design iteration in a controlled environment and to seek answers to these fundamental questions. Biosphere 2 captures the scale and control to provide a unique opportunity to develop, test, and deploy such solutions to the coral reef crisis. In Biosphere 2, Arks will be replicated in order to identify the optimal size, materials, and geometries of Arks that maximize coral reef community growth and to determine how multiple Arks interact with each other and the surrounding ecosystem. For example, phase 2 testing in the Biosphere 2 ocean will explore the hydrodynamics of modular shapes and sizes to optimize flow across the coral reef arks. 

The ARMS project in Madagascar (armsrestore.com), led by Dr. Aaron Hartmann (who, along with Dr. Forest Rohwer, conceived of the Arks idea) integrates the Arks concept and the capacity of ARMS to collect and move biodiversity into a reef restoration strategy. In Madagascar, declining fish catches as a result of overfishing have led to a critical protein deficiency in the local diet, causing greater strain on dwindling marine resources and exacerbating malnutrition in the local community. The ARMS Restore project is building novel artificial reef systems that provide the same beneficial conditions provided by Arks for corals and fish, and use ARMS to transfer healthy reef communities to these artificial reef systems, with the goal of enhancing fisheries and bolstering food provisions for the surrounding communities. This project, funded by the Belmont Forum, engages international partners of scientists, nutritionists, and restoration practitioners to provide the science, but is ultimately community-implemented. Two major questions being asked in this project are: (1) do the artificial reefs produce enough fish (as food) to improve the health of the local peoples? And (2) are artificial reefs increasing the abundance of fish or are they merely aggregating existing fish and making it easier to catch them, thus amplifying overfishing? The team includes ecologists, fisheries scientists, and nutritionists, who together are studying the impacts of this technology across ecological health, fisheries production, and human health outcomes to address the two pressing questions above. 

Arks serve as a mid-water seed bank for recruitment and habitat for economically important fish species. Studying Arks in Biosphere 2 is essential to scaling up these community-implemented solutions with potential to serve numerous communities that rely on healthy reefs for their sustenance and coastal protection.  

The Arks project, which originated at San Diego State University, has expanded to include collaborators at the U.S. Navy, numerous U.S. academic institutions (Harvard University, Scripps Institute of Oceanography, University of Illinois at Urbana Champagne), and international universities and organizations across the globe (Sri Lanka, Netherlands, Saudi Arabia, Curacao, Madagascar). This year, Biosphere 2 (B2), the world’s largest controlled ecosystem facility, including an ocean system that has been in place for nearly 35 years and sealed off from the outside world, hosted this working group for the third annual Coral Arks consortium meeting to discuss the future of the project and its scalability. General consensus from this group identified Biosphere 2 as an ideal site for iterative design and scalability analysis for the Arks.  

Although investment in field observatories has increased in the recent years from federal agencies such as NSF and DOE (in projects such as LTER, CZO and NEON), experimental facilities for evaluating ecosystem responses to climate change remain scarce. The Biosphere 2 Ocean (B2O) is a 2.6-million-liter ocean mesocosm featuring an experimental coral reef ecosystem. The system replicates a typical barrier reef system, with a turbulent fore-reef with 6-7m vertical relief, a reef crest and back reef sloping down to 2m, and a large 1-2m lagoon with diverse substrates. As the largest experimental ocean on Earth, the B2O provides a unique opportunity to develop, test, and deploy solutions to the coral reef crisis. We aim to build a reef that can survive future climate change, at the scale of an ecological community that is sufficiently complex to have its own emergent properties. We will perturb this reef in specific and highly controlled ways, and track the response at unprecedented resolution, from the genomic through the community and biogeochemical scales. The B2O holds unique strengths for the study of coral reef restoration and environmental stress. We are not bound by existing ecological associations or biogeographical constraints and can explore solutions that cannot be undertaken on a natural reef, as the potential consequences for an existing vulnerable ecosystem are too great; nor can they be done in a small aquarium or a meter-scale mesocosm, which lack the requisite scale and complexity. The unique combination of scale, control, and accessibility of B2 enables us to address key grand challenges in the restoration of resilient coral reef ecosystems. 

Arks and Biosphere 2’s connections with international institutions open opportunities to work in close proximity to our target populations. For example, the Arks team in Puerto Rico works directly with the local community to identify community values and desired outcomes for an Arks installation so as to best align the design of the Arks with the surrounding community. To do this, the team hosts local community workshops and discussion sessions to show results from the Arks projects, collect community perspectives, enhance transparency, and increase community involvement. 

Coral Reef Arks is between the Pilot and Growth phases, with first-generation designs deployed in a few communities (San Diego, Curacao, Puerto Rico, Madagascar) with promising results. However, though the potential is there, no life cycle cost analysis has been done nor has scalability been explored. 

Three Coral Reef Arks have been deployed in Curacao for approximately 3 years on a reef where coral cover is not as high as others, yet fish still thrive in great numbers. These midwater reef mesocosms have been used in a series of tests studying the response of reef communities (from the viruses and microbes to the coral and fish) to different perturbations (i.e., adding/removing biological components, manipulating geometries and materials, and moving the Arks to manipulate environmental conditions). The goal of these tests is to identify interventions that push reef communities towards healthy outcomes, which can then be scaled to the surrounding reef in restoration efforts. 

Paper – Baer et al 2023 (https://www.jove.com/t/64778/c...) 

Paper – Baer et al 2024 (in prep) – “A control theoretic framework and in situ experimental platform for active restoration of coral reefs” 

Two Coral Reef Arks have been deployed in Puerto Rico for approximately 2 years. These Arks were designed to serve as a home for corals and other reef biota impacted by an underwater munitions cleanup by the U.S. Navy. The goal of this project was to determine the feasibility of Arks as a mitigation strategy for projects that require coral transplantation or conservation of reef biodiversity. In addition to improving coral survival outcomes, Arks also attracted abundant fish communities.  

Paper – Baer et al 2023 (https://www.jove.com/t/64778/c...) 

Paper – Carilli and Baer et al 2024 (in press) – “Escaping the benthos with Coral Reef Arks – Effects on coral translocation and fish biomass” 

Paper – Baer et al 2024 (in review) – “Coral reef microbialization drives survival outcomes for translocated corals”  

At both sites, Arks are monitored for colonization by reef organisms and coral health. After 9 months 80% of corals were alive on the Arks compared to only 42% of corals at seafloor control sites due to the Arks having higher average flow speeds, higher average light availability and higher average dissolved oxygen.

Though first-generation designs are already installed in several locations, the Coral Reef Arks team and its collaborators are scientists primarily interested in answering fundamental science questions and thus have not explored potential scalability or business avenues. This group has established the potential of this tool using basic science and some measurement, reporting and verification but has not optimized the scalability and developed a life cycle cost analysis of the Arks at any reasonable scale.

Fundraising support is also necessary for the next steps in bringing Arks to the Biosphere 2 ocean and the associated costs with testing the hydrodynamics, biology, and engineering for meaningful replication. To support the increased biomass of the Coral Reef Arks in Biosphere 2, we need to upgrade the life-support systems to include substrate, protein fractionators, and additional circulation support to maintain water quality and clarity of tropical, oligotrophic reefs. These upgrades are estimated at $4 million.

Coral Reef Arks are innovative for inventing a unique approach to coral reef restoration that includes more benefits such as increased oxygenation, light, biodiversity, and ecosystem services. Therefore, Arks contribute to greater coral survival and reef ecosystem health for longer periods of time. Current conservation and restoration efforts typically focus solely on corals. This paradigm does not restore ecosystem services or break detrimental positive feedback loops. Ignoring the vast majority of coral reef organisms deprives corals of critical ecosystem services for their survival and leads to low success rates. Additionally, placing corals on degraded benthos contributes to microbialization and lowers the chances of success.  

Arks incorporate reef biodiversity and reinstate ecosystem services to restore the reef community and the economic benefits they provide. This is achieved through using ARMS (another Coral Reef Arks team innovation) to collect important reef biodiversity and translocate it to the Ark which resides midwater, away from the poor conditions of degraded substrate which has been shown to increase coral growth and survival rates in coral nurseries.  

Healthy coral reefs provide value to coastal communities through ecosystem services such as shoreline protection, food provisions through fisheries, and tourism. On Coral Arks, our goal is to build systems that provide these ecosystem services or enhance them on the surrounding reef. We will measure the calcification rate of the Arks by weighing them using strain gauges to determine if they are accreting and actively building reef. We will also measure the hydrodynamics to determine if Arks can help protect shorelines by dissipating wave energy. We will measure fish biomass to determine if the Arks are attracting or enhancing fish populations or other fishery target species (i.e., lobster, crabs, urchins), which provide food resources to local communities. We will measure microbial metrics including the virus-to-microbe ratio to determine the microbialization state (healthy coral reefs are not microbialized). We will also use imaging methods to extract visual information from the systems, such as changes in shape/volume/color due to biological growth, and visual census methods to document changes in biodiversity. 

Preliminary results show calcification values of 690 g/m^2/year, exceeding the goal point of 500g/m^2/year for a healthy reef. Fish biomass similarly exceeded goals with the preliminary studies reporting 200 g/m^2 on the Arks compared to the goal of 50g/m^2 to constitute a healthy reef. Virus-to-microbe ratios of 15 on the Arks also surpassed the goal value of 10 for a healthy ecosystem. 

Coral Reef Arks are a nature-based solution. The design of the Arks is based on fractals commonly seen in nature such as viruses. In one of our Curacao Arks, San Diego artist Ben Darby created a midwater sculpture from real reef materials. He chose to model this Ark after the canonical bacteriophage (or "phage," meaning a virus that infects bacteria) capsid, lining the inside with a DNA double helix and surrounding it with supporting proteins, all made from limestone.

These shapes are hydrodynamically stable, while also providing plenty of 3D structure/surfaces for settlement and growth of reef species.

Coral Reef Arks: An In Situ Mesocosm and Toolkit for Assembling Reef Communities

The Arks and Biosphere 2 teams include PIs, research technicians, graduate and undergraduate student workers, and maintenance staff. Team members have varying levels of involvement alongside their other obligations. In summary, Coral Arks has 25 full-time researchers, 18 part-time student workers, and 6 full-time maintenance staff. Biosphere 2 has 4 full-time researchers, 5 part-time ocean student workers, and 5 full-time B2 maintenance staff. These teams combined will be tackling the proposed solution of bringing the Coral Arks concept to Biosphere 2 Ocean and supporting the mission of the organization moving forward.  

5 years

As an officially designated Hispanic serving institution and as the home for large numbers of Native American students, the University of Arizona has an especially significant moral responsibility to provide equitable opportunities and inclusive environments for all students, regardless of background.  This responsibility applies not only to undergraduate students, but to graduate students, postdoctoral fellows, staff, and faculty. The Biosphere 2 Ocean team works closely with the Honors College, ASEMS program, and individual departments to broaden participation in the Biosphere Ocean education and research programs. Nearly 100% of the interns in the program have been from underrepresented groups in oceanography (including women, LGBTQ+, minority, and first-generation students). We strive to increase the number of underrepresented minorities participating in these programs and have applied for a number of grants to reduce barriers to participation in these activities. We will continue working with our partners to achieve these goals over the coming years. The Biosphere 2 JEDI (Justice, Equitability, Diversity, and Inclusion) Committee provides oversight to ensure that these plans are successfully implemented, to develop and implement surveys to assess climate, to provide a place for anonymous feedback, and to propose new activities to address problems as they arise.  They will also be responsible for assessing training needs, such as in bystander interventions or better understanding of concepts such as implicit bias and stereotype threat, and finding/developing resources to meet these needs. The leadership of B2 is ultimately responsible for ensuring that Biosphere 2 is a place where everyone is welcomed, has equal opportunity, and is encouraged and supported to succeed.   

Coral Reef Arks lacks a clearly defined business model. This is an area we would like to explore more with insight from someone with expertise as the technology is not intended to generate capital. Our goal is to provide a concept that people are welcome to adapt and improve for restoration success. Our business model would involve refining the technology, bringing down the cost, streamlining the methods, and verifying the benefits so that potentially disadvantaged end users can apply it and improve their livelihoods. This solution will primarily provide a product (Coral Reef Arks) to reef communities in need worldwide. Our team will provide some services to assist these teams in troubleshooting deployment, monitoring, or long-term maintenance of the Arks.

Since Coral Reef Arks has its roots in academic research, we are used to being, by definition, financially unstable and rely on grants and donations to fund projects. Exploring Arks as a social enterprise using a “Low-income client” revenue model seems to be a possible way forward. Again, we do not intend to gain capital from this and want to remove barriers to accessing the technology for disadvantaged communities. We look forward to developing a fitting plan for financial sustainability with the help of valuable expertise.