Coral restoration

Abstract

The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and evolutionary implications. Epigenetic gene regulation alters gene function in response to environmental cues without changes to the underlying genetic sequence and likely mediates phenotypic variation. DNA methylation is currently the most well described epigenetic mechanism and is related to transcriptional homeostasis in invertebrates. However, evidence quantitatively linking variation in DNA methylation with that of phenotype is lacking in some taxa, including reef-building corals. In this study, spatial and seasonal environmental variation in Bonaire, Caribbean Netherlands was utilized to assess relationships between physiology and DNA methylation profiles within genetic clones across different genotypes of Acropora cervicornis and A. palmata corals. The physiology of both species was highly influenced by environmental variation compared to the effect of genotype. GxE effects on phenotype were only apparent in A. cervicornis. DNA methylation in both species differed between genotypes and seasons and epigenetic variation was significantly related to coral physiological metrics. Furthermore, plastic shifts in physiology across seasons were significantly positively correlated with shifts in DNA methylation profiles in both species. These results highlight the dynamic influence of environmental conditions and genetic constraints on the physiology of two important Caribbean coral species. Additionally, this study provides quantitative support for the role of epigenetic DNA methylation in mediating phenotypic plasticity in invertebrates.

Contact details:

Francesca Virdis (Reef Renewal Bonaire) ->  francesca@reefrenewalbonaire.org

Serena Hackerott (FIU) -> shack013@fiu.edu

Full text available here: https://pubmed.ncbi.nlm.nih.gov/37454286/

Abstract

The plastic ability for a range of phenotypes to be exhibited by the same genotype allows organisms to respond to environmental variation and may modulate fitness in novel environments. Differing capacities for phenotypic plasticity within a population, apparent as genotype by environment interactions (GxE), can therefore have both ecological and evolutionary implications. Epigenetic gene regulation alters gene function in response to environmental cues without changes to the underlying genetic sequence and likely mediates phenotypic variation. DNA methylation is currently the most well described epigenetic mechanism and is related to transcriptional homeostasis in invertebrates. However, evidence quantitatively linking variation in DNA methylation with that of phenotype is lacking in some taxa, including reef-building corals. In this study, spatial and seasonal environmental variation in Bonaire, Caribbean Netherlands was utilized to assess relationships between physiology and DNA methylation profiles within genetic clones across different genotypes of Acropora cervicornis and A. palmata corals. The physiology of both species was highly influenced by environmental variation compared to the effect of genotype. GxE effects on phenotype were only apparent in A. cervicornis. DNA methylation in both species differed between genotypes and seasons and epigenetic variation was significantly related to coral physiological metrics. Furthermore, plastic shifts in physiology across seasons were significantly positively correlated with shifts in DNA methylation profiles in both species. These results highlight the dynamic influence of environmental conditions and genetic constraints on the physiology of two important Caribbean coral species. Additionally, this study provides quantitative support for the role of epigenetic DNA methylation in mediating phenotypic plasticity in invertebrates.

As I compose this message in 2022, reflecting on Reef Renewal Bonaire’s accomplishments during 2021, and during its first ten years of operation – I find it impossible not to be captivated by the impact that RRFB’s work has had on the shores of Bonaire and Klein Bonaire. For the diver and snorkeler, this work is now easy to see - acres of restored Staghorn corals, stands of majestic Elkhorns thriving and spawning, and providing habitat for a teeming biodiversity of reef life. If you have been lucky enough to tour the Jeff Davis Memorial dive site, just a few yards off Bonaire’s northern coast, you get a sense of what years of hard work and actively managed, successful restoration work can achieve on Bonaire. When RRFB started, these accomplishments were the dream of our Board of Directors, and specifically of our founding President, Martien Van der Valk. As I assume the role of President in 2022 from Martien, I want to take this opportunity to thank him for his hard work, his broad vision, his get-things-done attitude, and for his ability to assemble the diverse team that has executed on behalf of Bonaire’s coral reefs for the past decade. From the beginning, Martien insisted that this vision could not succeed if it was the initiative of a single dive operation or resort. Rather, the whole of Bonaire needed to embrace the restoration vision for RRFB to succeed. Today, RRFB boasts more than 9 dive operators and resort partners who work together on the mission of protecting, restoring, and giving the reefs of Bonaire a helping hand. Together with the Bonaire government, hundreds of volunteer divers and donors, the Bonaire Tourism Board, STINAPA, DCNA, WWF, and other key island partners, the work of RRFB can truly be categorized as a whole, island-wide initiative. Martien helped define RRFB’s “Secret Sauce” – focus on practical goals that are informed by science but made successful and sustainable by a powerful engine of cooperation between local businesses, government, NGOs, volunteers, and the dive community. As we move forward into 2022 and our next decade,  we are setting some very ambitious goals, but we will be guided by Martien’s recipe and his standards as we move forward. Our second secret – in this case, our Secret Weapon - is our Chief Operating Officer, Francesca Virdis. From day one of RRFB, she has been making RRFB’s ambitious vision a reality. She has tirelessly led RRFB’s efforts, pushing it forward in the water, in the lab, and with the scientific community. You will see the impressive results of Francesca’s and her team’s work in this report on our activities in 2021 – but know that RRFB is just getting started. Yes, we will grow more and get more corals in the water but are also looking to significantly scale our outplanting efforts, to push restoration science with new partnerships and new techniques (including building Bonaire’s first full-featured coral Wet Lab), and to continue the push to make Bonaire the global Center of Excellence for coral reef restoration. Thank you to all our partners, donors, and volunteers. As a team, we will continue to execute for Bonaire’s coral reefs and their biodiversity.

David J. Fishman President, RRFB Board of Directors 

Abstract

The dire state of coral reefs demands a rapid increase in the scale and efficiency of coral restoration methods in addition to mitigating local and global stressors. Larval propagation can provide vast numbers of coral propagules from an individual spawning event and increased genetic diversity in restored populations. The conversion of embryos collected from wild, broadcast-spawning populations to settlers that can be outplanted to the reef is a key component of this production process. We present preliminary results on settlement yield (i.e. % embryos converted to settled polyps on outplantable substrates) following in situ mass culture in floating mesocosms (Coral Rearing In-situ Basins, or CRIBs; 5.6 m3 volume, 5.4 m2 surface area) that can be implemented independent of land-based facilities. Ten trials over 2 years were conducted in three locations using five Caribbean broadcast-spawning species. Embryos were added at different stocking densities and settlement was scored 2–4 weeks after fertilization. Two trials failed, resulting in no effective settlement, but the remaining eight trials resulted in between 1% and 11% settlement yield (overall mean 5.3%) and 77–100% of substrates exposed to larvae acquired settlers (average production: 700 substrates trial−1). Parallel land-based trials showed a similar range (<1–14%) and mean (3.6%) settlement yield over nine trials. These values are also similar to the previously published lab and field-based trials using Pacific Acropora spp. Continued optimization of CRIB design and execution is expected to improve consistency, overall yield, and efficiency in the production of sexual propagules for restoration.

Full text available here:  Settlement yields in large‐scale in situ culture of Caribbean coral larvae for restoration - Miller - 2022 - Restoration Ecology - Wiley Online Library

Elkhorn (Acropora palmata) and staghorn (A. cervicornis) corals were listed as threatened under the ESA on May 9, 2006. Elkhorn and staghorn corals were once the most abundant and important species on Atlantic/Caribbean coral reefs in terms of building reef structure. Both elkhorn and staghorn corals underwent precipitous declines in abundance throughout their ranges. No single or collective group of threats may impact all regions of these species’ ranges equally. Multiple threats acting synergistically or cumulatively likely compound impediments to recovery among elkhorn and staghorn coral populations. The threats to these species that are impeding recovery are: disease, increasing
temperature, depensatory population effects, loss of recruitment habitat, sedimentation, anthropogenic abrasion and breakage, predation, inadequacy of existing regulatory mechanisms, natural abrasion and breakage, ocean acidification, and nutrients and contaminants.

The purpose of this recovery plan is to identify a strategy for rebuilding and assuring the long-term viability of elkhorn coral and staghorn coral populations in the wild, allowing ultimately for the species’ removal from the federal list of endangered and threatened species. Actions must be taken to address ocean warming and acidification impacts on these species. Simultaneously, local threat reductions, mitigation strategies, and in and ex situ conservation and restoration actions must be pursued.

The goal of this recovery plan is to increase the abundance and to protect the genetic diversity of elkhorn and staghorn coral populations throughout their geographical ranges while sufficiently abating threats to warrant delisting of both species.

Coral reef protection is the process of modifying human activities to avoid damage to healthy coral reefs and to help damaged reefs recover. The key strategies used in reef protection include defining measurable goals and introducing active management and community involvement to reduce stressors that damage reef health. It is difficult to create a substantial plan for the protection of coral reefs due to their location out in open water; there is no distinct ownership over certain parts of the ocean, which creates difficulty in delegating responsibility. Private and government groups whose purpose is to help the environment have made steps towards the restoration of coral reefs [wikipedia, retrieved Ferbruary 2018]. Today, coral restoration is recognized as a promising strategy for preserving the genetic diversity of endangered coral species, enhancing coral populations and increasing the likelihood of successful sexual reproduction in short timeframes (National Marine Fisheries Service, 2015).

Since 2012, Coral Restoration Foundation Bonaire (CRFB) has developed a large scale reef restoration program, promoting awareness and engaging tourists and local volunteers. To date 50 different genotypes of A. cervicornis and A. palmata are growing in the nurseries and more than 15,000 coral colonies have been already transplanted back to the reef. The restoration of Acropora corals as practiced by CRFB is shown to be highly successful in terms of growth and survival of new colonies in both nurseries and transplant sites. Coral restoration is expected to contribute to ecosystem services and increase coastal protection, biodiversity, fish biomass, and tourism (Meesters et al. 2015).

The above figure shows a sequence of pictures taken at one of the restoration locations at Klein Bonaire. The corals were selected after having grown 6-8 months in off-shore nurseries and then “glued” onto the substrate. The pictures show one coral cluster, which consists of 10 A. cervicornis coral colonies of the same genotype, transplanted on March 2016. Different clusters are strategically placed in the same general area, in order to promote genetic diversity and enhance the chances of having successful sexual reproductions between different strains.

Please contact the DCBD administrator for access to the photographs or find them at Project baseline. 

In this review the following three reef restoration techniques are discussed: 1. Coral gardening, 2. Larval seeding, and 3. Reef balls. These techniques are commonly used in the Caribbean and have widely different approaches. Coral gardening utilize the natural process of asexual reproduction through fragmentation to provide new coral clones for population growth. Healthy wild colonies are once clipped/fragmented and further grown (and cloned multiple times) in an underwater nursery and ultimately transplanted to the reef.
In contrast, larval seeding is based on the sexual reproduction of corals, where large amounts of coral eggs and sperm are collected in the field with subsequent fertilization in the lab. The coral recruits are then made to settle and grown in aquaria until a certain size, after which they are transplanted to the reef. Reef balls are artificial concrete structures designed to provide shoreline protection and sometimes shelter for fish, while at the same time providing substrate for natural recruitment and attachment of benthic organisms such as corals.
A general introduction to coral reproduction is provided to show how life history characteristics are used in restoration efforts and how these can affect the genetic variation within coral populations. The three approaches are compared based on:
1. Survival of fragments and larvae before transplantation to the reef.
2. Survival of transplants at the restoration site.
3. Introduction of exogenous material.
4. Indirect effects of coral restoration on the reef.
5. Genetic diversity.
6. Feasibility and effectiveness.
The main advantages of the production of colonies from fragments are that it bypasses the early larval stages where mortality is high and that new colonies can be grown completely in the field. Generally, the asexual reproduction technique demands less advanced expertise and the public outreach of this method is high because volunteers can easily be incorporated into the program. Furthermore, results become apparent relatively soon since the used species are relatively fast growing. However, there is the risk of creating populations with little genetic variability and the method is only applicable to branching coral species. Presently the method is mainly used for one single species, namely staghorn coral (Acropora cervicornis).
Larval seeding (sexual reproduction) is arguably the best method since it ensures natural genetic diversity and can be used with many species. The disadvantage with this method is that it demands a reasonably high level of expertise and takes more time than the asexual production of new colonies by fragmentation. Also a high percentage of new colonies is lost during the early stages. It is still mostly in the development phase.
Reef balls may increase fish biomass and protect shorelines, but their potential for coral reef restoration is judged to be limited due to the generally low levels of natural recruitment to these structures.
The restoration techniques suffer presently from a lack of independent scientific publications with good data to validate survival, regeneration, and growth rates of colonies in the different phases of the restoration program.
Different populations of the branching Acropora species can differ fundamentally in reproductive characteristics and may respond differently to environmental change. Their difference in strategy may also be a result of adaptation to local environmental factors. All studies and protocols thus stress the necessity to adapt methods to specific locations and environments.
Consideration of genetic factors is essential because the long-term success of restoration efforts (depending on resilience of the populations) may be influenced by genetic diversity of restored coral populations. The use of molecular tools may aid managers in the selection of appropriate propagule sources, guide spatial arrangement of transplants, and help in assessing the success of coral restoration projects by tracking the performance of transplants, thereby generating important data for future coral reef conservation and restoration projects.
It is proposed to study genetic variation in the natural populations around the islands of the Dutch Caribbean and within the various restoration projects in progress. Additionally, it is recommended to assess survival, growth and regeneration of fragments ánd mother colonies in the field. We recommend to combine characteristics of the two main coral restoration techniques (fragmentation and larval rearing) to create a new hybrid approach to increase survival of sexually derived colonies and genetic diversity. In addition, the cost-effectiveness of the larval seeding method should be ascertained and compared with the fragmentation method.
We conclude by pointing out that reef restoration can only be successful if environmental conditions are adequate for survival and growth of coral colonies. This will mean that presently the selection of restoration sites with good environmental conditions is crucial. Thus, active management of anthropogenic stressors is a prerequisite for reef restoration — if a reef is not effectively managed and chronic stressors persist or develop, restoration will ultimately fail. Reef restoration must only be considered as complementary to management tools that address the wider causes of reef degradation.

This month’s issue focuses on coral reef restoration efforts; research by SECORE and CARMABI on Curaçao and a private initiative by the Coral Restoration Foundation and Buddy Dive Resort on Bonaire. Since the decimation of Staghorn and Elkhorn coral colonies by whiteband disease in the early 1980s and because of their slow natural recovery rates throughout the Caribbean, there is a strong interest in human-assisted restoration efforts, which may help speed up the natural process of recovery. In addition to coral reef restoration, this edition profiles the ongoing flora monitoring on the Leeward Islands and showcases the historical taxonomic collections from the Dutch Caribbean held at Naturalis Biodiversity Center in Leiden, the Netherlands.

Amongst others, you will find in this fifth issue:

• Overview of Research and Monitoring Efforts
• Bonaire Deep Reef Exploration (by Lisa Becking)
• ‘Research of the Month‘: Coral Restoration Initiatives on Curaçao and Bonaire (by Valérie Chamberland and March Storm)
• Flora of Aruba, Bonaire and Curaçao (by André van Proosdij)
• Historical Collections on Dutch Caribbean Biodiversity (by Frank Wesselingh, Tinde van Andel and André van Proosdij)
• Calendar of Upcoming Events, Meetings and Workshops