Acropora cervicornis, commonly known as the staghorn coral has historically been a major contributor to reef structural complexity, providing habitat for many functionally important fish species throughout Florida and the Caribbean. Unfortunately, due to disease, bleaching, and local anthropogenic stressors, A. cervicornis populations have suffered drastic declines that have negatively impacted associated reef fish populations. In order to promote recovery, A. cervicornis fragments can be cultivated in nurseries and outplanted back onto reefs. This practice can effectively increase A. cervicornis abundance, but the long-term effects on local fish assemblages, and specifically functionally important grazing fishes, has not been assessed. Fish assemblages at natural (control) sites were compared to outplanted A. cervicornis sites in Southeast Florida. Fish surveys were conducted each summer at four locations from 2012 to 2017. Each location contained three outplanted A. cervicornis and one or two control sites. Outplant sites were defined by 50 A. cervicornis colonies in a 36 m2 area. Control sites occupied the same area but did not contain outplanted colonies. The fish assemblage structure was assessed in terms of composition, demography, and functional temporal trends as well as with the increasing structural complexity of the outplanted corals, defined as total linear extension (TLE). Significant temporal trends were recorded for total fish abundance, grazer abundance, and diversity. Structural complexity (outplanted A. cervicornis measured in TLE m-2) was found to be a significant predictor of total fish abundance, grazer abundance and diversity. Fishes 2-5 cm total length were most numerous indicating that the outplant sites may be providing habitat for juvenile reef fishes, particularly algae consumers. These findings suggest that A. cervicornis restoration may be creating a positive feedback loop in which outplanted corals create habitat for grazing fishes that in turn reduce algae competition, potentially providing new habitat for coral settlement.

Yeung, Chung Wing. / Thesis (M.Phil.)--Chinese University of Hong Kong, 2010. / Includes bibliographical references (leaves 143-156). / Abstracts in English and Chinese. / Acknowledgements --- p.i / Abstract (English) --- p.iii / Abstract (Chinese) --- p.vi / Contents --- p.vii / List of Tables --- p.xii / List of Figures --- p.xii / Chapter Chapter 1 --- Introduction / Chapter 1.1 --- Ecological and economic importance of coral reef habitats --- p.1 / Chapter 1.2 --- D egradation of coral reefs --- p.2 / Chapter 1.2.1 --- Natural recovery --- p.3 / Chapter 1.2.2 --- Restoration of disturbed reefs --- p.3 / Chapter 1.2.2.1 --- Whole colony transplantation --- p.4 / Chapter 1.2.2.2 --- Fragment transplantation --- p.4 / Chapter 1.2.2.3 --- Coral nursery --- p.5 / Chapter 1.3 --- Studies on octocorals --- p.6 / Chapter 1.3.1 --- Functional ecology of octocorals --- p.7 / Chapter 1.3.2 --- Biodiversity of octocorals in Hong Kong --- p.9 / Chapter 1.3.3 --- Threats on octocorals in Hong Kong --- p.10 / Chapter 1.4 --- The focus and significance of the present study --- p.12 / Chapter 1.4.1 --- "Lobophytum sarcophytoides, the study organism" --- p.14 / Chapter 1.4.2 --- Objectives --- p.15 / Chapter 1.5 --- Thesis Outline --- p.16 / Chapter Chapter 2 --- Seasonal Variation and Size-dependent Eco-physiological Performances of the Soft Coral Lobophytum sarcophytoides / Chapter 2.1 --- Introduction --- p.19 / Chapter 2.1.1 --- Damage recovery --- p.20 / Chapter 2.1.2 --- Photosynthetic activity --- p.21 / Chapter 2.1.3 --- Reproductive biology --- p.22 / Chapter 2.1.4 --- Growth rate --- p.23 / Chapter 2.1.5 --- Significance and objectives --- p.23 / Chapter 2.2 --- Study Sites --- p.24 / Chapter 2.2.1 --- Lan Guo Shui (LGS) --- p.24 / Chapter 2.2.2 --- Tolo Harbour (MSL) --- p.25 / Chapter 2.3 --- Methodologies --- p.27 / Chapter 2.3.1 --- Sample collection --- p.27 / Chapter 2.3.2 --- Treatment of samples --- p.27 / Chapter 2.3.3 --- Health condition --- p.28 / Chapter 2.3.4 --- Damage recovery --- p.29 / Chapter 2.3.5 --- Growth rate --- p.29 / Chapter 2.3.6 --- Photosynthetic activity --- p.30 / Chapter 2.3.7 --- Reproductive biology --- p.30 / Chapter 2.3.8 --- Statistical Analysis --- p.31 / Chapter 2.4 --- Results --- p.32 / Chapter 2.4.1 --- Acclimation of transplanted corals --- p.32 / Chapter 2.4.2 --- Health condition --- p.33 / Chapter 2.4.3 --- Growth rate --- p.34 / Chapter 2.4.4 --- Photosynthetic activity --- p.38 / Chapter 2.4.5 --- Damage recovery --- p.39 / Chapter 2.4.6 --- Reproductive biology --- p.40 / Chapter 2.5 --- Discussion --- p.41 / Chapter 2.5.1 --- Diurnal expansion and contraction of colonies --- p.41 / Chapter 2.5.2 --- Size fluctuation of the colonies --- p.42 / Chapter 2.5.3 --- Possible factors for the high initial mortality of corals --- p.43 / Chapter 2.5.4 --- Causes of bleaching and the harmful effects --- p.44 / Chapter 2.5.5 --- Energy allocation between reproduction and growth --- p.47 / Chapter 2.5.6 --- Quick healing of cut fragments and its ecological implication --- p.48 / Chapter 2.5.7 --- Choice of suitable fragment size for nursery use --- p.49 / Chapter 2.5.8 --- Suitable season for conducting the experiment --- p.50 / Chapter 2.6 --- Summary --- p.51 / Chapter Chapter 3 --- Effects of Temperature on the Health Condition and Photosytnthetic Activity of the Soft Coral Lobophytum sarcophytoides / Chapter 3.1 --- Introduction --- p.69 / Chapter 3.2 --- Methodologies --- p.73 / Chapter 3.2.1 --- Sample collection --- p.73 / Chapter 3.2.2 --- Experimental set-up of aquaria for growing corals --- p.73 / Chapter 3.2.2.1 --- Temperature experiment I --- p.74 / Chapter 3.2.2.2 --- Temperature experiment II --- p.74 / Chapter 3.2.2.3 --- Temperature experiment III --- p.76 / Chapter 3.2.3 --- Health condition --- p.76 / Chapter 3.2.4 --- Photosynthetic activity --- p.77 / Chapter 3.2.5 --- Statistical analysis --- p.78 / Chapter 3.3 --- Results --- p.79 / Chapter 3.3.1 --- Temperature experiment I --- p.79 / Chapter 3.3.1.1 --- Health condition --- p.79 / Chapter 3.3.1.2 --- Photosynthetic activity --- p.80 / Chapter 3.3.2 --- Temperature experiment IIA --- p.81 / Chapter 3.3.2.1 --- Health condition --- p.81 / Chapter 3.3.2.2 --- Photosynthetic activity --- p.83 / Chapter 3.3.3 --- Temperature experiment IIB --- p.84 / Chapter 3.3.3.1 --- Health condition --- p.84 / Chapter 3.3.3.2 --- Photosynthetic activity --- p.85 / Chapter 3.3.4 --- Temperature experiment III --- p.85 / Chapter 3.3.4.1 --- Health condition --- p.85 / Chapter 3.3.4.2 --- Photosynthetic activity --- p.86 / Chapter 3.4 --- Discussion --- p.87 / Chapter 3.4.1 --- The effect of acclimation --- p.87 / Chapter 3.4.2 --- Temperature tolerance range of L. sarcophytoides --- p.90 / Chapter 3.4.3 --- Indicators of coral health --- p.92 / Chapter 3.4.3.1 --- Photosynthetic activity --- p.92 / Chapter 3.4.3.2 --- Colony contraction --- p.94 / Chapter 3.4.3.3 --- Bleaching --- p.95 / Chapter 3.4.3.4 --- Algal overgrowth --- p.97 / Chapter 3.4.3.5 --- Attachment of transplanted corals --- p.99 / Chapter 3.5 --- Summary --- p.100 / Chapter Chapter 4 --- Reproductive Biology of Lobophytum sarcophytoides / Chapter 4.1 --- Introduction --- p.114 / Chapter 4.2 --- Methodologies --- p.117 / Chapter 4.2.1 --- Study site --- p.117 / Chapter 4.2.2 --- Sample collection and treatments --- p.117 / Chapter 4.3 --- Results --- p.119 / Chapter 4.3.1 --- Gametogenic development: Size changes --- p.119 / Chapter 4.3.2 --- Gametogenic development: Developmental stages --- p.120 / Chapter 4.3.2.1 --- Oogenesis --- p.120 / Chapter 4.3.2.2 --- Spermatogenesis --- p.121 / Chapter 4.4 --- Discussion --- p.122 / Chapter 4.4.1 --- Unusual oogenic development pattern in L sarcophytoides --- p.122 / Chapter 4.4.2 --- Possible effect of lack of a temperature cue on gametogenic development --- p.123 / Chapter 4.4.3 --- Alternative explanation: Energy allocation --- p.126 / Chapter 4.5 --- Summary --- p.128 / Chapter Chapter 5 --- Summary and Perspectives --- p.137 / References --- p.143

The heterogeneity provided by structured habitats is important in supporting diverse and dense fish communities. The biogenic reefs created by the native Eastern Oyster, Crassostrea virginica, were once the dominant structural habitat in Chesapeake Bay, and have since declined to less than 1% of historic estimates. Conflicting results on the effects of oyster reef restoration on pelagic fish assemblages make further investigation necessary. Incorporating multiple sampling strategies may help elucidate oyster reef habitat influence on fish assemblages. This study used multi-panel gillnets, hydroacoustic technology, and day-night sampling to describe pelagic fish assemblages on and off oyster reef habitat in the lower Piankatank River, VA. Data from oyster reef habitat, adjacent sandy-mud bottom habitat, and unstructured sandy habitat outside of a reef restoration area compared fish diversity, species composition, and density among habitat types. A multivariate analysis using day of the year, day or night, and habitat type as model terms found temporal factors explained variation in fish distribution more than habitat. Fish diversity varied significantly with day or night and habitat type. Diversity and density were significantly higher at night, demonstrating the necessity of nocturnal sampling in fish assemblage research. Results from this study conclude that fish assemblages were not significantly more diverse or denser on reef than non-reef habitat. We suggest that future work should concentrate on studying areas where oyster reef habitat comprises a larger proportion of the study area.

Oyster reef habitats have declined from historic levels due to a variety of reasons, including overharvest, disease, and degraded water quality. The harvesting of oysters has led to a loss of reef habitat for both oysters and reef-associated fauna. When oysters spawn, the larval oysters, or spat, depend on hard substrate for settlement and growth. Oyster shell is the preferred substrate for use in restoration because it most closely matches natural reef habitat, but it is often expensive and in limited supply. This study incorporated field and laboratory experiments to assess the relative habitat value of alternative substrates (crushed concrete, porcelain, crushed limestone, and river rock, as well as oyster shell) for larval oyster recruitment as well as reef resident fishes and macro-invertebrates. Replicate trays of each substrate type were deployed in St. Charles Bay, TX for four months during spring and summer 2012 and assessed for oyster recruitment and faunal diversity and density. Concrete, river rock, limestone and porcelain had similar spat recruitment densities compared to oyster shell (1300-2300 spat). Spat shell heights were also larger on these substrates (13-16 mm), while spat on porcelain substrates were slightly smaller (10-13 mm). All substrates except bare sediment had similar fauna species densities (200-500 individuals m-2). Limestone had lower fauna diversity (H’; 0-1) than concrete and shell (1-2). Laboratory experiments compared the effectiveness of these substrates in providing prey refuge from pinfish and blue crab predators. All substrates performed similarly resulting in very low (<20 %) prey mortality rates for either predator. Results may enable future restoration plans to be implemented at a lower cost while providing similar habitat functions.

Octocorals are important components of many reef benthic communities, and efforts to restore populations following damage events and relocating colonies preceding permitted activities is becoming part of regulatory processes. Because many octocorals have regenerative capabilities ideal for removing branch clippings (fragments), they may make excellent donors, sources of transplants, for restoration efforts. This study examined the effect of fragment size, fragmentation timing, and transplantation on the survivorship, growth, and fecundity of Eunicea flexuosa clippings and donor colonies. Eunicea flexuosa clippings 20 cm in height were transplanted to a ship grounding site offshore southeast Florida in April 2010 and November 2010. Data collected during the June through September spawning months in 2010 and 2011 revealed high survivorship among all transplants (85%), however partial mortality from encrustation by bio-fouling organisms ensued. Growth rates among donor colonies was high. The fecundity of fragments transplanted in May was not negatively affected in 2010; however the fecundity of all transplants was lower than that of donor colonies in 2011, with oocytes failing to reach reproductive size. Re-allocation of energy resources towards tissue repair may account for the low growth and loss in fecundity. This study highlights the importance of evaluating fragment size and collection time in promoting growth and propagation of transplanted octocorals following damage and prior to marine construction events.

The giant barrel sponge, Xestospongia muta is a prominent component in southeast Florida reef communities and is often injured from anthropogenic or natural disturbances. The resulting complete or partial shearing of X. muta barrels frequently leads to mortality of loose fragments that do not typically reattach. This study examines the degree to which sponge size and injury severity affects recovery and growth, and explores artificial reattachment success and growth of fragments. In June 2008, 65 sponges were subjected to injury treatments of approximately 50% or 90% barrel removal. A new, simple method was developed to secure these removed barrels (fragments) to the substrate. For 15 months, all donor, fragment and control sponges were monitored for survival, recovery and growth (change in height), and fragments were additionally monitored for reattachment. All injured sponges showed signs of recovery within 1 month. Within 7 months the reattachment method had already proved successful with more than 80% of all fragments becoming attached; final reattachment success after 15 months was 87%. Survival remained high for donors (97%), fragments (94%) and controls (97%). Size class and injury treatment did not significantly affect survival for donors. However, larger fragments had significantly lower survival and reduced reattachment success. Fragment growth rates were significantly lower than donor and control sponges. All sponges showed significant increase in height from post-cutting to the final monitoring. No injured donors reached pre-cut heights, however those from the smaller size class are projected to reach pre-injury heights faster than the larger size class.

In the Caribbean, Acropora cervicornis (staghorn coral) exemplifies the worldwide anthropogenic decline of reef-building corals. From the mid-Pleistocene through the mid-1900s, A. cervicornis was a dominant framework builder, providing complex habitat for reef organisms. Since the 1980s, populations of A. cervicornis have declined by as much as 98%. Despite the overall decline, scattered remnants persist, and some appear to be thriving. As in recent studies on other acroporids, if we can identify variation in traits related to resilience in the remaining A. cervicornis, and understand the genetic basis of such variation, we could better forecast the species’ future response to climate change, and inform ongoing restoration efforts. Here, I compare phenotypic and transcriptomic indicators of resilience in A. cervicornis from two nearby but environmentally-disparate habitats on Turneffe Atoll, Belize: Calabash Caye forereef and Blackbird Caye backreef. Blackbird exhibits significantly higher flow, light, average temperature, and temperature variation. Over four years, I conducted a longitudinal study of 122 tagged coral colonies. Corals from Blackbird and Calabash, which I confirmed to be genetically distinct based upon single nucleotide polymorphisms, exhibited pronounced differences in traits related to resilience including the proportion of healthy tissue, chlorophyll, growth, and wound-healing. By most measures, Blackbird corals displayed superior indicators of resilience. Through a two-year reciprocal transplant study involving 120 corals, I identified substantial environmental plasticity in these traits, e.g., Blackbird corals transplanted to Calabash exhibited higher chlorophyll levels and more rapid wound healing than when grown in Blackbird, exceeding the native Calabash corals. RNA sequencing and assembly of site-specific transcriptomes revealed greater diversity of transcripts and genes from photosynthetic symbionts at Blackbird but greater diversity of bacterial associates at Calabash. Single nucleotide polymorphism (SNP) analyses using RNAseq data determined that corals from the two sites were separate putative populations. Principal components analysis of gene expression in natives and transplants revealed a clear distinction based on site of origin, but also a clear effect of environment. Thousands of differentially expressed genes distinguished the sites, including many genes implicated in heat stress, oxidative stress and UV-light stress. This genetic and phenotypic diversity of remnant staghorn populations on Turneffe represents a potential basis for future re-expansion of this important framework builder through natural or assisted shifts toward resilient populations. / 2023-02-03T00:00:00Z

This study aims to review thirteen coastal restoration projects considering the various ecosystem services provided by restoration and estimates the economic value of one of the ecosystem services of restoration. These ecosystem services include water quality improvement, fish and benthic species productivity, shoreline stabilization, oyster abundance, and marsh growth. The projects represent a set of large-scale projects within Alabama and Mississippi, with construction and monitoring costs ranging from $2.3 million to $50 million per project. To determine the economic value of one of the ecosystem services of coastal restoration projects, I used the meta-analysis method to estimate the willingness to pay (WTP) for coastal water quality improvements. The estimated function from the meta-analysis is applied to parameters specific to the study area. The WTP for improved coastal water quality, from a baseline of fishable but likely to degrade, to an improved fishing catch rate, is $203 per household annually among residents of Alabama and Mississippi.

Over the last 40 years, the Caribbean has lost half of its live coral cover, mostly in the form of Acropora cervicornis and A. palmata, due to disease, bleaching from rising water temperatures, and other stressors. To help restore these corals to reefs in Florida, the Coral Restoration Foundation (CRF) created nearshore nurseries and transplanted over 30,000 acroporid colonies across the Florida Keys. The objective of this thesis was to evaluate the growth, survivorship, and condition of nursery-raised A. cervicornis colonies that were part of two transplant projects: 1) photographic analyses of 17 past CRF transplant projects over the last seven years; and 2) a transplant experiment at Little Conch Reef to additionally assess the effects of depth, colony density, and the genetic composition of transplants. The photographic analyses included 2,428 individual colonies, 38 genotypes, and six reefs from 2007 to 2013. Results from the photographs were combined with one in situ monitoring effort that used SCUBA in 2014. In the Little Conch Reef experiment, 1,288 colonies from 14 genotypes were transplanted in October and November, 2013 at two depths (5m and 12m) in either cluster or thicket configurations. At each depth, clusters comprised 14 colonies, each placed within in 1m diameter radius, with ten monogenetic and six multigenetic structures. Thickets were 3.5m by 1.5m in size, with 10 colonies from each genotype forming its own subunit within the larger configuration. In June 2014, 963 additional colonies were added to the shallow site by stacking them on top of six existing clusters and one thicket to evaluate whether larger three-dimensional structures affected growth or survival. The Little Conch Reef experiment was monitored through January 2015. Results from the photographic analyses were: 1) maximum size of A. cervicornis transplants was approximately 40cm in diameter; 2) mortality increased after approximately two years; 3) despite high mortality, some colonies survived the duration of each project; and 4) frequent and long-term monitoring is required to assess factors that affect survival and condition. Results from the Little Conch Reef experiment suggest: 1) maximum skeletal diameter was unaffected by any of the treatments; 2) percent survival and percent live tissue were higher at the shallow site compared to the deep site, and similarly, the clusters outperformed the thickets, and multigenetic clusters outperformed their monogenetic counterparts; 3) location within the shallow site had an impact on survival and condition, with clusters doing better on the south side than on the north; and 4) stacking did not positively impact growth, survival, or condition. In general, the sizes and condition of natural populations of A. cervicornis throughout the Florida Keys are similar to results from both experiments and with other transplant projects conducted in the Caribbean. Remarkably, despite high mortality in nearly all of the projects, small numbers of colonies transplanted for most projects, a few colonies survived to 2014/2015. These colonies have the potential to act as a “seed population” that might produce sexually dispersed larvae better adapted at surviving mortality events and asexual fragments that may be better acclimated to the stressors related to their location. Evidence of persistence in this species and expansion northward in Florida suggest that it is too early to consider coral reefs a lost cause, and that coral restoration holds promise for enhancing recovery of A. cervicornis.

Knowledge of effective reef restoration techniques are necessary in this age of worldwide coral reef decline. Coral transplantation is a restoration technique employed after natural (i.e. hurricanes) and anthropogenic (i.e. vessel groundings) physical disturbance events. The study was conducted to compare the efficacy of propagating small colony fragments in laboratory and field conditions in terms of survival and growth. Fragment growth and survival were assessed for six scleractinian boulder corals common to Florida and Caribbean reefs: Montastraea annularis, M. cavernosa, Diploria clivosa, Siderastrea siderea, S. radians and Dichocoenia stokesii. Broken coral colonies were salvaged from vessel grounding sites and marine debris, fragmented into pucks and secured to travertine tiles. One hundred and fifty-three coral colony fragments were cultivated in an ex situ laboratory nursery and 133 coral colony fragments were cultivated in an in situ field nursery and monitored for 13 months. Survival of all colonies was 94%, with 98% survival in the laboratory treatment and 89% survival in the field treatment. Complete colony mortality was documented in three S. radians colonies, all in the laboratory treatment. All colony loss in the field treatment was due to colony pucks being detached from the tiles. Overall mean percent change in colony tissue area from initial to final monitoring events was calculated to determine growth. Across species, growth was greater in the laboratory treatment (76 ± 4 % SEM) in comparison to the field treatment (27 ± 5 % SEM). Positive growth was observed in D. clivosa, D. stokesii, M. annularis, M. cavernosa and S. siderea in the laboratory treatment. In the field treatment, D. clivosa, M. annularis and M. cavernosa were the only species that exhibited positive growth. Negative growth was observed in both the laboratory and field treatments for S. radians. In conclusion, colonies propagated in the ex situ nursery (laboratory treatment) had higher growth and survival than colonies propagated in the in situ nursery (field treatment). A critical acclimation period accomplished through the use of stable laboratory conditions will produce healthier, more secure coral colonies that may be used to repopulate disturbed reef sites.