Most coral reef studies focus on scleractinian (stony) corals to indicate reef condition, but there are other prominent assemblages that play a role in ecosystem structure and function. In Puerto Rico these include fish, gorgonians, and sponges. The U.S. Environmental Protection Agency conducted unique surveys of coral reef communities across the southern coast of Puerto Rico that included simultaneous measurement of all four assemblages. Evaluating the results from a community perspective demands endpoints for all four assemblages, so patterns of community structure were explored by probabilistic clustering of measured variables with Bayesian networks. Most variables were found to have stronger associations within than between taxa, but unsupervised structure learning identified three cross-taxa relationships with potential ecological significance. Clusters for each assemblage were constructed using an expectation-maximization algorithm that created a factor node jointly characterizing the density, size, and diversity of individuals in each taxon. The clusters were characterized by the measured variables, and relationships to variables for other taxa were examined, such as stony coral clusters with fish variables. Each of the factor nodes were then used to create a set of meta-factor clusters that further summarized the aggregate monitoring variables for the four taxa. Once identified, taxon-specific and meta-clusters represent patterns of community structure that can be examined on a regional or site-specific basis to better understand risk assessment, risk management and delivery of ecosystem services.

A goal of coral reef management is to provide habitat and nursery areas for fish populations. This requires simple and reliable methods for characterizing biological and physical reef features that contribute to fish habitat. Most attempts to establish this relationship have been performed on small-scale, site-specific study areas where variability in fish populations and reef structure is limited and results may be insufficiently robust for extrapolation beyond those sites. Most studies also include geological structures, like ridges and rock formations that provide fish habitat but are not amenable to management action. A focus on the role of Scleractinia (stony corals) may better inform decisions aimed at improving fish habitat. Stony corals provide the structural foundation of coral reefs and are the target of numerous management actions. Data from three broad-area, multi-station reef surveys of fish and stony coral colonies were examined to identify correlations between fish population measures (density, taxa richness and biomass) and both biological (taxa richness and live surface area) and physical (number, size and structural complexity) attributes of scleractinian coral populations. Strongest correlations were found with physical coral features, particularly coral colony height. Characterizing this relationship will improve fishery management tools and support status and trend assessment of the worldwide decline in the physical stature of reefs.

Shallow-water coral reefs of the Florida Reef Tract compose the third largest reef in the world, but during the last several decades, scleractinian (stony) corals have suffered unprecedented declines from global and local stressors. A program to evaluate the effects of high-temperature bleaching events was initiated by The Nature Conservancy's Florida Reef Resilience Program in 2005 and surveys have been completed across at least some portion of the entire region every year since. The program adopted a demographic (colony-based) assessment approach, which records colony species, size (height and maximum diameter), and estimated partial mortality (percent barren skeleton). Because reef structure is critical to ecosystem functioning and services, data from 2005 to 2020 were analyzed to describe the abundance, size, and morphological complexity of stony coral colonies forming the biogenic reef. Colony height, footprint, surface area, and volume summed for 6016 transects were used to describe reef structure and averages were used to characterize the components that contributed to the structure. Nearly 150,000 colonies representing 49 species were reported during this period and results demonstrated both spatial and temporal changes for the region and for geographic subregions. Some subregions showed increasing colony density, especially for three small, hemispheric species, and declining average colony size.

The Biological Condition Gradient (BCG) is a conceptual model used to describe incremental changes in biological condition along a gradient of increasing anthropogenic stress. As coral reefs collapse globally, scientists and managers are focused on how to sustain the crucial structure and functions, and the benefits that healthy coral reef ecosystems provide for many economies and societies. We developed a numeric (quantitative) BGC model for the coral reefs of Puerto Rico and the US Virgin Islands to transparently facilitate ecologically meaningful management decisions regarding these fragile resources. Here, reef conditions range from natural, undisturbed conditions to severely altered or degraded conditions. Numeric decision rules were developed by an expert panel for scleractinian corals and other benthic assemblages using multiple attributes to apply in shallow-water tropical fore reefs with depths <30 m. The numeric model employed decision rules based on metrics (e.g., % live coral cover, coral species richness, pollution-sensitive coral species, unproductive and sediment substrates, % cover by Orbicella spp.) used to assess coral reef condition. Model confirmation showed the numeric BCG model predicted the panel's median site ratings for 84% of the sites used to calibrate the model and 89% of independent validation sites. The numeric BCG model is suitable for adaptive management applications and supports bioassessment and criteria development. It is a robust assessment tool that could be used to establish ecosystem condition that would aid resource managers in evaluating and communicating current or changing conditions, protect water and habitat quality in areas of high biological integrity, or develop restoration goals with stakeholders and other public beneficiaries.

As coral reef condition and sustainability continue to decline worldwide, losses of critical habitat and their ecosystem services have generated an urgency to understand and communicate reef response to management actions, environmental contamination, and natural disasters. Increasingly, coral reef protection and restoration programs emphasize the need for robust assessment tools for protecting high-quality waters and establishing conservation goals. Of equal importance is the need to communicate assessment results to stakeholders, beneficiaries, and the public so that environmental consequences of decisions are understood. The Biological Condition (BCG) model provides a structure to evaluate the condition of a coral reef in increments of change along a gradient of human disturbance. Communication of incremental change, regardless of direction, is important for decision makers and the public to better understand what is gained or lost depending on what actions are taken. We developed a narrative (qualitative) Biological Condition Gradient (BCG) from the consensus of a diverse expert panel to provide a framework for coral reefs in US Caribbean Territories. The model uses narrative descriptions of biological attributes for benthic organisms to evaluate reefs relative to undisturbed or minimally disturbed conditions. Using expert elicitation, narrative decision rules were proposed and deliberated to discriminate among six levels of change along a gradient of increasing anthropogenic stress. Narrative rules for each of the BCG levels are presented to facilitate the evaluation of benthic communities in coral reefs and provide specific narrative features to detect changes in coral reef condition and biological integrity. The BCG model can be used in the absence of numeric, or quantitative metrics, to evaluate actions that may encroach on coral reef ecosystems, manage endangered species habitat, and develop and implement management plans for marine protected areas, watersheds, and coastal zones. The narrative BCG model is a defensible model and communi-cation tool that translates scientific results so the nontechnical person can understand and support both regu-latory and non-regulatory water quality and natural resource programs.

Accretion and erosion of scleractinian (stony coral) carbonate skeletons determine whether a colony will increase or decrease in size with potential consequences for ecosystem processes, functions and services. The capacity for skeletal growth can be estimated by comparing a colony's rate of calcification with its rate of erosion. Calcification depends on the species-specific metabolic activity of living tissue, and erosion depends primarily on the availability and density of barren skeleton, those areas on the colony where polyps have died. Assessment of skeletal growth capacity requires data on calcification rates, erosion rates and both live and barren colony surface area. Rates of calcification and erosion are documented for many Caribbean species and others can be estimated from existing data. Three-dimensional surface area of colonies can be determined from data collected during demographic surveys, which identify species, measure dimensions, and estimate the proportion of live tissue on a colony. Data from demographic surveys conducted in the U.S. Virgin Islands are used to calculate the skeletal growth capacity (GC) as an indicator of coral species and community resilience. Scleractinia are the primary architects of coral reefs, and the gain or loss of skeletal framework is vitally important to reef ecosystem processes that lead to valued goods and services. Estimates of GC reflect stony coral resilience, which is the capacity to recover from disturbances by returning to previous physical and functional levels. GC can also provide insight to the effects of stressors such as ocean acidification, and can inform several management decisions, including restoration site selection and threatened species designation.

It is well established that sedimentary margins grow by sediments bypassing through shelf-and slope-incising canyons onto the basin floor and by sediments being deposited incrementally across clinoforming and pro-grading margins. However, we argue that these two distinctive types of deep-water sediment supply to the basin floor and to the margin are generally not operating at the same time and should not be seen as integral parts of a single model. When shelf-incising canyons were actively bypassing sediments across the margin, the margin itself was not prograding, and vice versa. We present stratigraphic data for some 111 global examples of shelf-and slope-incising canyons and their linked basin-floor sediments, and we provide criteria to distinguish them from prograding margins fed by shelf-edge deltas and their linked slope channels and toe-of-slope fans. The defining character of the canyon feeding system is basin-floor sediment aggradation and the onlapping of this stratigraphy against an eroded basin margin. For many of our examples this onlap persists for millions to tens of millions of years and is especially prolonged in periods of persistent high eustatic sea level. This is in clear contrast to the downlapping stratigraphy that dominates during intervals of high sediment supply from the shelf, and active margin accretion. Some 60% of the ancient canyon/basin-floor fan systems are inferred to have been sourced by canyons tapping longshore drift in littoral cells; they are inferred because with canyon capture, tapped littoral cells are generally depleted and not preserved. In other cases, shelf-incising canyons tapped documented deltas on the inner or middle shelf, but in some other cases, a deltaic or riverine source was inferred. Canyon cutting and initial sediment bypass through the canyons are chiefly associated with initially ?out-of-grade? margins?for example, where a carbonate margin has foundered and oversteepened or where large-scale collapse of aggradational and oversteepened clastic shelf edges occurred. Canyon feeding onto the basin floor is linked with runout of basin-floor fans to the basin center, in contrast to direct-fed prograding margins, where sediment is continuously partitioned onto and across the entire shelf-edge, slope, and toe-of-slope areas.

Coastal acidification in southeastern U.S. estuaries and coastal waters is influenced by biological activity, run-off from the land, and increasing carbon dioxide in the atmosphere. Acidification can negatively impact coastal resources such as shellfish, finfish, and coral reefs, and the communities that rely on them. Organismal responses for species located in the U.S. Southeast document large negative impacts of acidification, especially in larval stages. For example, the toxicity of pesticides increases under acidified conditions and the combination of acidification and low oxygen has profoundly negative influences on genes regulating oxygen consumption. In corals, the rate of calcification decreases with acidification and processes such as wound recovery, reproduction, and recruitment are negatively impacted. Minimizing the changes in global ocean chemistry will ultimately depend on the reduction of carbon dioxide emissions, but adaptation to these changes and mitigation of the local stressors that exacerbate global acidification can be addressed locally. The evolution of our knowledge of acidification, from basic understanding of the problem to the emergence of applied research and monitoring, has been facilitated by the development of regional Coastal Acidification Networks (CANs) across the United States. This synthesis is a product of the Southeast Coastal and Ocean Acidification Network (SOCAN). SOCAN was established to better understand acidification in the coastal waters of the U.S. Southeast and to foster communication among scientists, resource managers, businesses, and governments in the region. Here we review acidification issues in the U.S. Southeast, including the regional mechanisms of acidification and their potential impacts on biological resources and coastal communities. We recommend research and monitoring priorities and discuss the role SOCAN has in advancing acidification research and mitigation of and adaptation to these changes.

Quantifying ecosystem goods and services can help evaluate policies aimed at protecting present and future generations from losing ecosystem benefits. Explicating and quantifying the relationships among risk factors, ecological structure and function, and delivery of ecosystem goods and services requires analytical methodologies that propagate uncertainties. The capabilities of Bayesian networks in generating predictions and accounting for uncertainty are explored with a focus on coral reef ecosystem service assessments. The qualitative aspects of Bayesian networks can be applied to conceptual frameworks developed for coral reef ecosystem service assessments. This is demonstrated using qualitative graphs that describe the relationships between coral reef condition endpoints and benefits from ecosystem services including property protection, recreational opportunities, fish for fisheries, and biochemical metabolites for commercial products developed from reef organisms. Bayesian networks help weigh uncertainties between management decision impacts on stressors and the corresponding delivery of ecosystem services. Quantitative capabilities for inferences are examined in hypothetical scenarios evaluating how decisions affect coral reef ecosystem services and economic benefits and resilience to episodic stress. The described methods facilitate visualizing the potential impacts on ecosystem services from alternative scenarios.

States and other jurisdictions may protect coral reefs using biological water quality standards outlined by the United States Clean Water Act (CWA). Such protection will require long-term, regional monitoring of the resource using biological indicators and a probability-based sampling design. A 60-station survey targeting nearshore linear coral reef was conducted across southern Puerto Rico in December 2011 to document the status of reef inhabitants using a probabilistic, regional sampling design. The quantity, type and condition of stony corals, fish, gorgonians and sponges were documented from each station, providing a robust representation of linear reef status and composition across the region. Fish represented 106 unique taxa and stony corals 32 unique taxa. Benthic organisms (stony corals, sponges and gorgonians) averaged nearly 12 colonies per square meter, more than half of which were gorgonians. Assessment results can be used as a baseline to compare with future regional surveys to quantify change in reef condition over time (trend). Both temporal and spatial changes can be expected after large-scale disturbances like hurricanes Maria and Irma in 2017. The indicators and probabilistic sampling design support the long-term regional monitoring envisioned by the Environmental Protection Agency to implement CWA protections in Puerto Rico and elsewhere.

The geothermal energy of the earth is diffuse, diverse, and by any measure immense. Geothermal resources are generally classed in three main categories: hydrothermal systems, including both vapor-and-liquid-dominated systems, hot dry rock systems, and geopressured systems. In many deposits, water temperatures are too low for efficient flash separation. In such instances a different geothermal power process—the vapors turbine or binary system has been developed. The largest volume of geothermal water is too cool for power production. Past and future use is largely limited to local space heating and certain agricultural uses. In 1975, the US Geological Survey published an assessment of the Gulf Basin geopressured-geothermal resources as a part of their overall assessment of geothermal resources throughout the US The U.S.G.S. assessed about 145,000 square kilometers or a little less than one-half the area they consider underlain by geopressured zones.

Coral reef condition on the south shore of St. Thomas, U.S. Virgin Islands, was assessed at various distances from Charlotte Amalie, the most densely populated city on the island. Human influence in the area includes industrial activity, wastewater discharge, cruise ship docks, and impervious surfaces throughout the watershed. Anthropogenic activity was characterized using a landscape development intensity (LDI) index, sedimentation threat (ST) estimates, and water quality (WQ) impairments in the near-coastal zone. Total three-dimensional coral cover, reef rugosity, and coral diversity had significant negative coefficients for LDI index, as did densities of dominant species Orbicella annularis , Orbicella franksi , Montastraea cavernosa , Orbicella faveolata , and Porites porites . However, overall stony coral colony density was not significantly correlated with stressors. Positive relationships between reef rugosity and ST, between coral diversity and ST, and between coral diversity and WQ were unexpected because these stressors are generally thought to negatively influence coral growth and health. Sponge density was greater with higher disturbance indicators (ST and WQ), consistent with reports of greater resistance by sponges to degraded water quality compared to stony corals. The highest FoRAM (Foraminifera in Reef Assessment and Monitoring) indices indicating good water quality were found offshore from the main island and outside the harbor. Negative associations between stony coral metrics and LDI index have been reported elsewhere in the Caribbean and highlight LDI index potential as a spatial tool to characterize land-based anthropogenic stressor gradients relevant to coral reefs. Fewer relationships were found with an integrated stressor index but with similar trends in response direction.

Projected increases in ocean pCO2 levels are anticipated to affect calcifying organisms more rapidly and to a greater extent than other marine organisms. The effects of ocean acidification (OA) have been documented in numerous species of corals in laboratory studies, largely tested using flow-through exposure systems. We developed a recirculating ocean acidification exposure system that allows precise pCO2 control using a combination of off-gassing measures including aeration, water retention devices, venturi injectors, and CO2 scrubbing. We evaluated the recirculating system performance in off-gassing effectiveness and maintenance of target pCO2 levels over an 84-day experiment. The system was used to identify changes in calcification and tissue growth in response to elevated pCO2 (1000 μatm) in three reef-building corals of the Caribbean: Pseudodiploria clivosa, Montastraea cavernosa, and Orbicella faveolata. All three species displayed an overall increase in net calcification over the 84-day exposure period regardless of pCO2 level (control +0.28- 1.12 g, elevated pCO2 +0.18- 1.16 g), and the system was effective at both off-gassing acidified water to ambient pCO2 levels, and maintaining target elevated pCO2 levels over the 3-month experiment.

The societal benefits of coral reef ecosystems include shoreline protection, habitat provision for reef fish, tourism, and recreation. Rarely considered in valuation of reefs is the considerable contribution of marine natural products (MNPs) to both human health and the economy. To better understand the relation of MNP discovery with the characteristics and condition of coral reef ecosystems, we initiated a study to track the collection location and taxonomic identity of organisms that have provided pharmacological products. We reviewed collection information and associated data from 298 pharmacological products originating from marine biota during the past 47 years. The products were developed from 232 different marine species representing 15 phyla, and the 1296 collections of these specimens occurred across 69 countries and seven continents. Our evaluation of the collection data was hampered by sundry observational and reporting issues, including imprecise location descriptions and omission of collection dates. Nonetheless, the study provides an important synopsis and appraisal of years of study and exploration by the marine natural product community. Understanding and quantifying the benefits of MNP discovery will depend upon improved reporting of collections, including accurate taxonomic identification, collection dates, and locations.

Policies to protect coastal resources may lead to greater social, economic, and ecological returns when they consider potential co-benefits and trade-offs on land. In Guánica Bay watershed, Puerto Rico, a watershed management plan is being implemented to restore declining quality of coral reefs due to sediment and nutrient runoff. However, recent stakeholder workshops indicated uncertainty about benefits for the local community. A total of 19 metrics were identified to capture stakeholder concerns, including 15 terrestrial ecosystem services in the watershed and 4 metrics in the coastal zone. Ecosystem service production functions were applied to quantify and map ecosystem service supply in 1) the Guánica Bay watershed and 2) a highly engineered upper multi-watershed area connected to the lower watershed via a series of reservoirs and tunnels. These two watersheds were compared to other watersheds in Puerto Rico. Relative to other watersheds, the Upper Guánica watershed had high air pollutant removal rates, forest habitat area, biodiversity of charismatic and endangered species, but low farmland quality and low sediment retention. The Lower Guánica watershed had high rates of denitrification and high levels of marine-based recreational and fishing opportunities compared to other watersheds, but moderate to low air pollutant removal, soil carbon content, sediment and nutrient retention, and terrestrial biodiversity. Our results suggest that actions in the watershed to protect coral reefs may lead to improvements in other ecosystem services that stakeholders care about on land. Considering benefits from both coastal and terrestrial ecosystems in making coastal management decisions may ultimately lead to a greater return on investment and greater stakeholder acceptance, while still achieving conservation goals.

通过研究,根据测井数据编制的地层厚度、孔隙度和孔隙度-产层厚度图,评估了Fort Worth盆地Barnett页岩天然气主采区的储层物性和游离气的贮藏能力.在Barnett页岩层,密度孔隙度(DPHI)测井曲线对于定量评估页岩气资源非常有用,而伽马(GR)和中子孔隙度测井曲线对于识别页岩气藏至关重要.关键数据是根据GR和密度测井曲线的有效性、测井品质以及良好的空间分布从146口井的数字测井中选择的.依据以下条件确定Barnett页岩的产层:(1)DPHI ＞5％;(2)高GR值(通常＞～90API单位);(3)没有明显的富含碳酸盐岩夹层;(4)产层的单层厚度足以能使现行水平井的设计实现商业上的成功.研究区内,Barnett页岩产层的厚度(H)是变化的,从165 ft (50 m)至420 ft(128 m).单井产层的平均DPHI值为8.5％～14.0％.孔隙度与产层厚度关系(DPHI-H)图表明,高DPHI-H值区域与天然气高产区一致,说明测井导出的DPHI-H图是评估Barnett页岩产层储集特性和天然气资源量的一个很好的方法.研究区西北角运用该方法有一定局限性,因为该区域位于富含液体的窗口,热成熟度较低.

Predicting species distributions at the landscape level has many applications in fish ecology, management, and conservation, yet generating accurate predictions remains a challenge to fish ecologists. Areas of the landscape with higher environmental suitability should have higher relative abundance, although the predictive capability of this relationship might be limited because environmental suitability ignores other factors such as biotic interactions and stochastic events. These factors could contribute to a species being absent or at low abundance in a site with high environmental suitability. Owing to the potential influence of non-environmental and stochastic factors on relative abundance, modelled environmental suitability should be a better predictor of maximum abundance (i.e. the ceiling of scattered data) than mean relative abundance because ecosystem complexities often preclude a simple monotonic response. To evaluate this assumption, environmental suitability was predicted for 55 944 stream reaches in New York State using native brook trout (Salvelinus fontinalis) and non-native brown trout (Salmo trutta) occurrence data and a suite of four broad-scale habitat factors. Estimates of suitability were then used to test the relationship with the upper limits of abundance using quantile regression. As predicted, there was a significant positive relationship with maximum abundance for native brook trout at the upper quantiles; however, this relationship did not extend to non-native brown trout. These findings indicate that broad-scale habitat factors can predict maximum abundance of a native stream-dwelling trout and produced environmental suitability maps that could be useful for brook trout conservation. These findings could be used to predict trout occurrence in unsurveyed stream reaches with the highest abundance limits, which could be used to set conservation priorities and provide benchmarks of habitat potential for monitoring programmes as well as identify threats to environmental suitability from anthropogenic sources. Copyright © 2014 John Wiley & Sons, Ltd.

We sampled 16 water bodies on Tishomingo National Wildlife Refuge (TNWR) in south- central Okla ho ma to document the occurrence of fi sh species, to describe habitat types, and to eval u ate fi sh-habitat relationships. Water bodies were sampled by using electrofi sh- ing, ex per i men tal gill nets, seines, and trap nets during 1996 and 1997. We collected 52 species and report the occurrence of the American eel (Anguilla rostrata species and report the occurrence of the American eel (Anguilla rostrata species and report the occurrence of the American eel ( ) upstream from Denison Dam of Lake Texoma. We used cluster analysis of the habitat features (water depth, conductivity, water clarity) to group the water bodies into three types: riverine, lacus trine, and palustrine. Similarity analysis of fi sh assemblages (co ef fi cient of com- munity) and habitat features (principal components analysis) revealed that palustrine water bodies had the highest similarity followed by lacustrine and riv er ine water bodies, respectively. We interpret differences in similarity to be related to variation in habitat of the water body types in the three groups. Information from this study should benefi t management of fi sh assemblages and aquatic habitats at TNWR. © 2005 Proceedings of the Oklahoma Academy of Science.

The U.S. Environmental Protection Agency (EPA) has recently realigned its research enterprise around the concept of sustainability, including improving understanding of benefits derived from ecosystems. We provide an example of how EPA is applying structured decision-making (SDM) as a framework for guiding development of scientific information, data, and models to support watershed and marine-based management in coastal communities. In particular, we have been using the Driver–Pressure–State–Impact–Response (DPSIR) model as a tool in the SDM process to identify and assemble a broadly applicable suite of information with relevancy for coastal management, including 1) development of conceptual models to clarify the decision context, 2) identification of measurements of ecosystem attributes, ecosystem goods and services, and their connection to stakeholder objectives, 3) elaboration of potential decision alternatives, and 4) identification of ecosystem production and valuation functions for modeling consequences of decision alternatives on benefits derived from coral reefs. Finally, we overview how this information is being applied for two case studies: development of water quality criteria and watershed management to protect coastal resources. We posit that applying a systems thinking framework, such as DPSIR, within a structured decision-making approach will better enable marine ecosystem managers to utilize scientific information toward more sustainable decision-making.