A guide to monitoring reef fish in the National Park Service's South Florida/Caribbean Network

Reef fishes are conspicuous and essential components of coral reef ecosystems and economies of southern Florida and the United States Virgin Islands (USVI). Throughout Florida and the USVI, reef fish are under threat from a variety of anthropogenic and natural stressors including overfishing, habitat loss, and environmental changes. The South Florida/Caribbean Network (SFCN), a unit of the National Park Service (NPS), is charged with monitoring reef fishes, among other natural and cultural resources, within six parks in the South Florida - Caribbean region (Biscayne National Park, BISC; Buck Island Reef National Monument, BUIS; Dry Tortugas National Park, DRTO; Everglades National Park, EVER; Salt River Bay National Historic Park and Ecological Preserve, SARI; Virgin Islands National Park, VIIS). Monitoring data is intended for park managers who are and will continue to be asked to make decisions to balance environmental protection, fishery sustainability and park use by visitors. The range and complexity of the issues outlined above, and the need for NPS to invest in a strategy of monitoring, modeling, and management to ensure the sustainability of its precious assets, will require strategic investment in long-term, high-precision, multispecies reef fish data that increases inherent system knowledge and reduces uncertainty. The goal of this guide is to provide the framework for park managers and researchers to create or enhance a reef fish monitoring program within areas monitored by the SFCN. The framework is expected to be applicable to other areas as well, including the Florida Keys National Marine Sanctuary and Virgin Islands Coral Reef National Monument. The favored approach is characterized by an iterative process of data collection, dataset integration, sampling design analysis, and population and community assessment that evaluates resource risks associated with management policies. Using this model, a monitoring program can adapt its survey methods to increase accuracy and precision of survey estimates as new information becomes available, and adapt to the evolving needs and broadening responsibilities of park management.

Integration of fisheries acoustics surveys and bathymetric mapping to characterize midwater-seafloor habitats of US Virgin Islands and Puerto Rico (2008-2010)

NOAA’s Coral Reef Conservation program (CRCP) develops coral reef management priorities by bringing together various partners to better understand threats to coral reef ecosystems with the goal of conserving, protecting and restoring these resources. Place-based and ecosystem-based management approaches employed by CRCP require that spatially explicit information about benthic habitats and fish utilization are available to characterize coral reef ecosystems and set conservation priorities. To accomplish this, seafloor habitat mapping of coral reefs around the U.S. Virgin Islands (USVI) and Puerto Rico has been ongoing since 2004. In 2008, fishery acoustics surveys were added to NOAA survey missions in the USVI and Puerto Rico to assess fish distribution and abundance in relation to benthic habitats in high priority conservation areas. NOAA’s National Centers for Coastal Ocean Science (NCCOS) have developed fisheries acoustics survey capabilities onboard the NOAA ship Nancy Foster to complement the CRCP seafloor habitat mapping effort spearheaded by the Center for Coastal Monitoring and Assessment Biogeography Branch (CCMA-BB). The integration of these activities has evolved on the Nancy Foster over the three years summarized in this report. A strategy for improved operations and products has emerged over that time. Not only has the concurrent operation of multibeam and fisheries acoustics surveys been beneficial in terms of optimizing ship time and resources, this joint effort has advanced an integrated approach to characterizing bottom and mid-water habitats and the fishes associated with them. CCMA conducts multibeam surveys to systematically map and characterize coral reef ecosystems, resulting in products such as high resolution bathymetric maps, backscatter information, and benthic habitat classification maps. These products focus on benthic features and live bottom habitats associated with them. NCCOS Centers (the Center for Coastal Fisheries and Habitat Research and the Center for Coastal Environmental Health and Biomolecular Research) characterize coral reef ecosystems by using fisheries acoustics methods to capture biological information through the entire water column. Spatially-explicit information on marine resources derived from fisheries acoustics surveys, such as maps of fish density, supports marine spatial planning strategies and decision making by providing a biological metric for evaluating coral reef ecosystems and assessing impacts from pollution, fishing pressure, and climate change. Data from fisheries acoustics surveys address management needs by providing a measure of biomass in management areas, detecting spatial and temporal responses in distribution relative to natural and anthropogenic impacts, and identifying hotspots that support high fish abundance or fish aggregations. Fisheries acoustics surveys conducted alongside multibeam mapping efforts inherently couple water column data with information on benthic habitats and provide information on the heterogeneity of both benthic habitats and biota in the water column. Building on this information serves to inform resource managers regarding how fishes are organized around habitat structure and the scale at which these relationships are important. Where resource managers require place-based assessments regarding the location of critical habitats along with high abundances of fish, concurrent multibeam and fisheries acoustics surveys serve as an important tool for characterizing and prioritizing coral reef ecosystems. This report summarizes the evolution of fisheries acoustics surveys onboard the NOAA ship Nancy Foster from 2008 to 2010, in conjunction with multibeam data collection, aimed at characterizing benthic and mid-water habitats in high priority conservation areas around the USVI and Puerto Rico. It also serves as a resource for the continued development of consistent data products derived from acoustic surveys. By focusing on the activities of 2010, this report highlights the progress made to date and illustrates the potential application of fisheries data derived from acoustic surveys to the management of coral reef ecosystems.

Monitoring Hawaii’s marine protected areas: examining spatial and temporal trends using a seascape approach

Hawaii’s coastal marine resources have declined dramatically over the past 100 years due to multiple anthropogenic stressors including overfishing, coastal development, pollution, overuse, invasive species and climate change. It is now becoming evident that ecosystem-based management, in the form of marine protected areas (MPAs), is necessary to conserve biodiversity, maintain viable fisheries, and deliver a broad suite of ecosystem services. Over the past four decades, Hawaii has developed a system of MPAs to conserve and replenish marine resources around the state. These Marine Life Conservation Districts (MLCDs) vary in size, habitat quality, and management regimes, providing an excellent opportunity to test hypotheses concerning MPA design and function using multiple discreet sampling units. NOAA/NOS/NCCOS/Center for Coastal Monitoring and Assessment’s Biogeography Branch used digital benthic habitat maps coupled with comprehensive ecological studies between 2002 and 2004 to evaluate the efficacy of all existing MLCDs using a spatially-explicit stratified random sampling design. The results from this work have shown that areas fully protected from fishing had higher fish biomass, larger overall fish size, and higher biodiversity than adjacent areas of similar habitat quality. Other key findings demonstrated that top predators and other important fisheries species were more abundant and larger in the MPAs, illustrating the effectiveness of these closures in conserving these populations. Habitat complexity, protected area size and habitat diversity were the major factors in determining effectiveness among MPAs.

Assessment and monitoring of marine debris in Gray's Reef National Marine Sanctuary

Gray’s Reef National Marine Sanctuary (GRNMS) is located 32.4 km offshore of Sapelo Island, Georgia. The ecological importance of this area is related to the transition between tropical and temperate waters, and the existence of a topographically complex system of ledges. Due to its central location, GRNMS can be used as a focal site to study the accumulation and impacts of marine debris on the Atlantic continental shelf offshore of the Southeast United States. Previously, researchers characterized marine debris in GRNMS and reported that incidence of the debris at the limited densely colonized ledge sites was significantly greater than at sand or sparsely colonized live bottom, and is further influenced by the level of boating activity and physiographic characteristics (e.g., ledge height). Information gleaned from the initial marine debris characterization was used to devise a strategy for prioritizing cleanup and monitoring efforts. However, a significant gap in knowledge was the rate of debris accumulation. The primary objective of this study was to select, mark, and perform initial marine debris surveys at permanent monitoring sites within GRNMS to quantify long-term trends in types, abundance, impacts, and accumulation rates of debris. Ledge sites were selected to compare types, abundance, and accumulation rates of marine debris between a) areas of high and low use and b) short and tall ledges. Nine permanent monitoring sites were marked and initially surveyed in 2007/2008. Surveys were conducted within a 50 x 4 m transect for a total survey area of 200 square meters. All debris was removed and detailed information was taken on the types of debris, quantity, and associations with benthic fauna. Information on associations with benthic fauna included degree of entanglement, type of organism with which it is entangled or resting on, degree of fouling, and visible impacts such as tissue abrasions. Sites were re-surveyed approximately one year later to quantify new accumulation. During the initial survey, a total of ten debris items, totaling 16.3 kg in weight, were removed from two monitoring stations, both “tall” sites within the area of high boat use. Year-one accumulation totaled five items and approximately 7 kg in weight. Similar to the initial survey, all debris was found at sites in the area of high boat use. However, in contrast to the initial survey, two of these items were found on medium-height ledges. Removed items included fishing line, leaders, rope, plastic, and fabric. Although items were often encrusted in benthic biota or entangled on the ledge, impacts such as abrasions or other injuries were not observed. During the 2009 monitoring efforts, volunteer divers were trained to conduct the survey. Monitoring protocols were documented for GRNMS staff and included as an appendix of this report to enable long-term monitoring of sites. Additionally, national reconnaissance data (e.g. satellite, radar, aerial surveys) and other information on known fishing locations were examined for patterns of resource use and correlations with debris occurrence patterns. A previous model predicting the density of marine debris based on ledge features and boat use was refined and the results were used to generate a map of predicted debris density for all ledges.

Long-term monitoring of habitats and reef fish found inside and outside the U.S. Virgin Islands Coral Reef National Monument: a comparative assessment

The primary objective of this study was to assess the efficacy of the Virgin Islands Coral Reef National Monument (VICR), a marine protected area in St John, US Virgin Islands. Surveys of habitat and fishes inside and outside of VICR were conducted in 2003-2008. Areas outside the VICR had significantly more scleractinian corals, greater habitat complexity, and greater species richness and density of reef fishes than areas inside., Areas inside and outside the VICR exhibited significant decreases in percent scleractinian coral coverage over the study period. A contrasting trend of increasing macroalgal cover was also observed. No clear effect of the severe 2005 coral bleaching event was observed suggesting other causal factors. No obvious trends in the fish community were observed across the study period. The significant decline in habitat condition, coupled with the initial incorporation of some of the more degraded reefs into the marine protected area may result in a longer time period necessary to detect positive changes in the St. John coral reef ecosystem and associated reef fish abundance and community structure.

Northeast Fisheries Observer Program manual, 2013

The National Marine Fisheries Service (NMFS) Northeast Fisheries Science Center (NEFSC) Fisheries Sampling Branch (FSB) collects, maintains, and distributes data for scientific and management purposes in the northwest Atlantic Ocean. FSB manages three separate but related observer programs: the Northeast Fisheries Observer Program (NEFOP), the Industry Funded Scallop (IFS) Observer Program, and the At Sea Monitoring (ASM) Program. For the purposes of this manual, “observers” refers to any observer/monitor working for the FSB. In 2011, FSB trained and deployed over 200 observers, provided coverage on a variety of fisheries, and completed over 15,000 sea days. Observed trips are required under many of the region's fishery management plans, and for some fisheries by other federal laws and authorities such as Amendment 16 and Framework 44, Magnuson-Stevens Fishery Conservation and Management Act, Marine Mammal Protection Act, the Endangered Species Act, the and the Sustainable Fisheries Act. The purpose of this guide is to provide FSB observers, as well as end users of NEFSC Observer Program data, with a detailed description of each data field collected. In addition to this manual, the NEFSC Observer Program Biological Sampling and Catch Estimation Manual provides summaries and tables intended to enable observers to quickly determine the correct sampling protocols and methods while at sea. This manual represents a revision of the data forms, collection procedures, and protocols described in the 1996 NEFSC Observer Program Manual. For documentation of other changes see Documentation of changes made to the NEFSC Fisheries Observer Program Manual, 2013.