This book summarizes what is known about mesophotic coral ecosystems (MCEs) geographically and by major taxa. MCEs are characterized by light-dependent corals and associated communities typically found at depths ranging from 30-40 m. and extending to over 150 m. in tropical and subtropical ecosystems. They are populated with organisms typically associated with shallow coral reefs, such as macroalgae, corals, sponges, and fishes, as well as specialist species unique to mesophotic depths. During the past decade, there has been an increasing scientific and management interest in MCEs expressed by the exponential increase in the number of publications studying this unique environment. Despite their close proximity to well-studied shallow reefs, and the growing evidence of their importance, our scientific knowledge of MCEs is still in its early stages. The topics covered in the book include: regional variation in MCEs; similarities and differences between mesophotic and shallow reef taxa, biotic and abiotic conditions, biodiversity, ecology, geomorphology, and geology; potential connectivity between MCEs and shallow reefs; MCE disturbances, conservation, and management challenges; and new technologies, key research questions/knowledge gaps, priorities, and future directions in MCE research.

Mesophotic coral ecosystems (MCE) are defined as phototrophic coral habitats found deeper than 30 m. Despite being aware of these ecosystems for over 200 years, surprisingly little information is available on their ecology and biology. Recently, MCE have received renewed interest, as it appears that depth and distance from shore have the potential to buffer coral organisms from the detrimental effects of coastal development and climate change. The "deep reef refugia hypothesis" (DRRH) is an umbrella term for a collection of hypotheses concerning the role of MCE in the uncertain future of coral reefs, yet our predictions are limited by shortcomings in our understanding of some very basic effects of depth on corals and associated communities. In order to investigate the effects of depth on coral reproductive biology, sampling of Montastraea faveolata and Porites astreoides coral tissues was conducted along a depth gradient from 5 to 40 m during coral reproductive seasons in the Northern United States Virgin Islands (USVI), and observations of coral spawning and planulation were made. Samples were histologically analyzed for gamete development, reproductive activity and fecundity. Mesophotic populations of both M. faveolata and P. astreoides were reproductively active in MCE with similar gametogenic cycles to nearby shallow coral populations. There was evidence of M. faveolata split spawning in August and September at all depths, and oocyte development was delayed but more rapid in mesophotic corals. M. faveolata fecundities were significantly higher in MCE (35-40 m) than in shallow (5-10 m) sites, but the differences were not significant between mid-depth (15-22 m) and either shallow or mesophotic sites. There was no difference found in P. astreoides fecundity between mesophotic, mid-depth and shallow sites, however planulation appeared to be delayed in mesophotic colonies by 1-2 weeks. Differences in fecundity per area and coral cover between depths determine the number of propagules a unit reef will produce at different depths. In the case of M. faveolata, ova production is likely an order of magnitude greater at 35 m than at 10 m. The Connectivity Modeling System, an individual-based stochastic biophysical model of larval dispersal, parameterized with depth-specific productivity estimates and species-specific reproductive seasons and larval traits, was used to evaluate the vertical connectivity of M. faveolata and P. astreoides larvae between MCE and shallow coral habitats in the Northern USVI. Sensitivity analyses were performed to test the sensitivity of mesophotic larval subsidy into shallow habitats to depth-specific productivity, pelagic larval mortality, depth-specific fertilization rates and depth-specific post-settlement survivorship. Simulated mesophotic subsidies to shallow recruitment were found to be considerably robust, and mesophotic subsidy to shallow recruitment accounted for a greater proportion of total recruitment as shallow productivity was reduced. Even when modeled mesophotic fertilization rates and larval post-settlement survivorship were dramatically reduced, the model predicted what would likely be demographically significant mesophotic larval subsidy into shallow habitat. Mesophotic M. faveolata skeletal density, extension and calcification were estimated using micro-computed tomography. Results suggest that rates of linear extension of M. faveolata in USVI MCE may be quite fast compared to other Caribbean MCE, and that total calcification in MCE may rival shallow coral calcification. Lastly, consistencies and inconsistencies in the population connectivity of two coral and three fish constituent species in Caribbean coral reef assemblages were investigated using a nested biophysical model. Connectivity networks of coral species were more fragmented than fish, and the networks of corals and fish showed different patterns of betweenness centrality. This suggests that populations of corals and fish will likely be affected by habitat fragmentation in different ways, and that they require specific management consideration. This dissertation suggests that MCE are integral to the population connectivity of corals in the USVI and likely to wider Caribbean metapopulation connectivity as well. Further study of these highly productive ecosystems is necessary to better understand the DRRH and the role of MCE in the past, present and future of coral reefs.

Coral reefs are increasingly under threat, necessitating an emphasis to identify coral reefs with reduced susceptibilities to local and/or global anthropogenic impacts. Mesophotic coral reefs (MCEs; >30m) are proposed as potential refugia and/or propagule sources, yet little information is known about deep reefs' abilities to harbor, replenish, or conserve shallow species. In this dissertation, I examine the plausibility of MCEs to act as refugia for shallow reef fishes in the Hawaiian Islands. Chapter One explores reef fish community structure and habitat composition along a 3-50m gradient in West Hawai'i. Reef fish communities change gradually with depth, with >78% of species observed at mesophotic depths (>30m) found at shallow depths. Changes in community structure are linked closely with feeding behavior, with shallow reefs dominated by herbivores, while mesophotic reefs are dominated by invertivore and planktivore trophic assemblages. Changes in fish assemblages are tied to indirect effects of depth and available coral habitat, as deeper reefs contain more patchily-distributed habitat. Chapter Two examines mechanisms underlying herbivorous fish distributions using a suite of observational and experimental field and laboratory techniques. Herbivorous fishes are not limited by food resources at MCE depths, as MCE algae had similar nutritional content, species assemblages, and appears to be highly palatable from algal choice experiments. Instead, changes with depth are likely the result of top-down, non-consumptive predation effects and behavioral choices. Chapter Three undertakes a critical analysis of the deep refugia hypothesis for coral reef fishes across the Main Hawaiian Islands. Upper MCEs (30-60m) may act as refugia for shallow reef fishes, as we found they are more thermally stable and >70% of reef fishes encountered were shallow species. Conversely, MCEs contain reduced densities of reef fishes and communities are comprised almost solely of invertivore and planktivore trophic groups. The near-absence of herbivorous fishes below 30m indicate MCEs will have a limited capacity to re-seed shallow reefs with species of ecological or economic importance. Overall, MCEs may act as refugia for biodiversity conservation but their ability to restock shallow reef fish communities will result in fundamentally different community compositions that shift towards smaller-bodied and less economically/ecologically valuable species.

Coral reef habitats in Hawai'i are common in shallow waters and extend into mesophotic depths (30-150 m). However, habitat monitoring efforts have been concentrated in depths constrained by safe dive limits of 0-30 m. Mesophotic coral ecosystems (MCEs), located in depths of 30-150 m, are important components of the coral reef ecosystem, but only a small number of surveys have been conducted in these depths. Data for these deep-water habitats are essential for evaluating and monitoring their health and resilience. Classifying benthic habitats in mesophotic depths is challenging due to dive safety limits and water penetration capabilities of remote sensing options, such as satellite imagery and Light Detection and Ranging (LiDAR). The results of this effort show that acoustic data can be used to provide detailed substrate and biological cover maps that include mesophotic coral ecosystems. Here we employ a combination of principal component analyses and unsupervised classification techniques to derive six substrate and five biological cover classes from multi-beam acoustic data, which are validated by optical seafloor imagery to create a complete benthic habitat map for the West Hawai'i Habitat Focus Area (WHHFA). Our results show that the overall accuracy of the benthic habitat maps is 59% for substrate classification and 61% for biological cover classification. Accuracy was higher for the following individual classes; 76% Complex Reef, 86% Sand, and 88% Coral. These habitat maps are the first within the WHHFA to incorporate mesophotic data and provide important information for evaluating and managing the coral reef ecosystem as a whole. [doi:10.7289/V5/TM-PIFSC-61 (https://doi.org/10.7289/V5/TM-PIFSC-61)]

Mesophotic coral ecosystems (MCEs) are deep, light-dependent communities that are abundant in the northern US Virgin Islands. Compared to their shallow water counterparts, MCEs remain understudied. South of St. Thomas, mesophotic coral cover on Orbicella dominated reefs can reach 50%, but observations of the northern shelf at similar depths suggest limited coral cover. The cause and extent of these deferences is unknown. Usually spatially explicit observations of coral health, species abundances, and coral population densities, we compared northern shelf bank MCEs to previously studied MCEs south of St. Thomas. We predict slower growth rates of mesophotic corals north of St. Thomas, corresponding to increased turbidity and lower light conditions, more frequent disturbance such as chronic swell, as well as nutrient loading and thermal stress associated with upwelling.

The structural complexity and geomorphic diversity of coral reefs are vital foundational characteristics responsible for the many ecological and economic benefits these ecosystems provide. Shallow-water coral reef geomorphology and structural sustainability is mostly determined by varying reef sedimentary components including: (1) sediment production (matrix) and deposition, (2) framework production and secondary carbonate accretion; (3) bioerosion; and (4) cementation. However, little is known regarding the variability and influence of these sedimentary processes in mesophotic coral ecosystems (MCEs), deep reef communities 30-150 m below sea-level. Despite recent increases in biological and ecological MCE studies, many crucial sedimentological research questions remain unaddressed. These unaddressed questions impede a greater understanding of mesophotic reef structural sustainability and potentially related habitat heterogeneity, carbonate reef shelf development and variability in mesophotic depths, and the general origins of modern coral reef biodiversity. Critical gaps in knowledge of mesophotic coral reef geomorphology and structural sustainability were addressed in this dissertation by conducting one of the first extensive sedimentological analyses of a mesophotic coral reef ecosystem. Beyond a general exploration of MCEs, the overall research goal was to identify basic sedimentary processes integral to the development, modification, and sustainability of mesophotic coral reef structure. The goal was also to determine the variability of the identified processes at different mesophotic reef habitats and investigate how these processes and potential variability impact shelf-wide habitat heterogeneity and long-term accretion. To address these goals, sedimentary analyses and ecological surveys were conducted at mesophotic coral reef habitats with distinct structurally characteristics, and neighboring shallow-water reef counterparts in the northern U.S. Virgin Islands (USVI). Analyses at all reefs were designed to address four specific aims: (1) categorization and comparison of various mesophotic reef sediment and cement attributes; (2) determination of exposed consolidated substrate reef bioerosion rates, and the distribution and variability of bioeroding groups; (3) quantification and determination of primary coral mesophotic reef framework builder linear growth and calcification rate variability, and comparison to live mesophotic framework bioerosion and secondary accretion rates; and (4) application of study results for carbonate budget analysis and assessment of geomorphic carbonate production status. Sediment and cement analysis (first aim) indicated that distinct MCE habitats produce subfacies. The interpreted hydrodynamic and biological interactions controlling mesophotic USVI subfacies have implications towards paleoenvironmental interpretations of ancient mesophotic reef deposits with similar sediment and cement characteristics. Significant differences in exposed consolidated substrate bioerosional processes were discovered between the analyzed habitats. These differences were found to primarily result from variation in parrotfish biomass and related controls on substrate exposure time and location in macroboring succession. Results also broadly confirm pervious hypothesizes that bioerosion decreases with depth along a carbonate shelf and have implications leaning toward rejection of traditional reef accretion theories. Analysis of coral growth identified statistically significant differences in mesophotic coral reef calcification rates, implying another potential long-term mechanism for enhancing mesophotic reef structural heterogeneity. However, on a larger scale, linear extension rates were found to fit within previously proposed models of decreasing coral growth rate with increasing depth. Mesophotic coral reef sedimentary analyses were compared in a newly developed carbonate budget model to analyze structural sustainability and consider implications of these analyses on mesophotic reef habitat heterogeneity and Holocene carbonate shelf accretion. All USVI mesophotic habitats examined were identified with net positive carbonate production despite significant variability in geomorphic production states. Additionally, comparisons with earlier benthic surveys suggest higher net USVI mesophotic reef carbonate production in the recent past, potentially implying these deeper reefs are not fully immune to modern global stressors impacting shallow-water reefs. Results indicated that mesophotic reef accretion was not the main driver of shelf-scale topographic relief. However, mesophotic carbonate production variability substantially contributes to habitat-scale structural relief and complexity and relatedly to overall ecosystem diversity. Specific mesophotic reef sedimentology research methods and the need for similar studies at other mesophotic reef habitats were suggested. Comprehensive sedimentology analysis of mesophotic coral reefs in the USVI provide new insight into reef structural sustainability, geomorphic status, and potential impacts from global stressors, and should be considered when developing specific reef sustainability models and management strategies.

"This document summarizes the results of the first Mesophotic Coral Ecosystems Workshop held in Jupiter, Florida on July 12-15, 2008. The workshop was hosted by the Perry Institute for Marine Science (PIMS) and organized by the National Oceanic and Atmospheric Administration (NOAA) National Centers for Coastal Ocean Science's Center for Sponsored Coastal Ocean Research and the Office of Ocean Exploration and Research's NOAA Undersea Research Program, and the U.S. Geological Survey (USGS). This meeting brought together researchers, managers, and nongovernmental agents active in mesophotic coral ecosystem issues to determine the current state of knowledge and establish research priorities for these ecosystems"--Title page verso.

"Using the archive of available video and photographic records from the Hawaiʻi Undersea Research Laboratory (HURL) and the Pacific Islands Fisheries Science Center (PIFSC), we developed a model to predict the occurrence of two dominant mesophotic coral genera, Leptoseris and Montipora, across the main Hawaiian Islands. The overall prediction success (73.6% and 74.3%, respectively) was relatively high, and these predictions were translated to spatially independent habitat suitability maps of the main Hawaiian Islands at 25 m2 resolution. Montipora presence peaks in the middle mesophotic zone (50 - 80 m) in areas sheltered from high intensity winter swells, whereas Leptoseris tends to colonize steep, rugose, well-flushed areas in the lower mesophotic zone (> 80 m)"--Executive Summary.