Magnitude and extent of chemical contamination and toxicity in sediments of Biscayne Bay and vicinity

The toxicity of sediments in Biscayne Bay and many adjoining tributaries was determined as part of a bioeffects assessments program managed by NOAA’s National Status and Trends Program. The objectives of the survey were to determine: (1) the incidence and degree of toxicity of sediments throughout the study area; (2) the spatial patterns (or gradients) in chemical contamination and toxicity, if any, throughout the study area; (3) the spatial extent of chemical contamination and toxicity; and (4) the statistical relationships between measures of toxicity and concentrations of chemicals in the sediments. The survey was designed to characterize sediment quality throughout the greater Biscayne Bay area. Surficial sediment samples were collected during 1995 and 1996 from 226 randomly-chosen locations throughout nine major regions. Laboratory toxicity tests were performed as indicators of potential ecotoxicological effects in sediments. A battery of tests was performed to generate information from different phases (components) of the sediments. Tests were selected to represent a range in toxicological endpoints from acute to chronic sublethal responses. Toxicological tests were conducted to measure: reduced survival of adult amphipods exposed to solid-phase sediments; impaired fertilization success and abnormal morphological development in gametes and embryos, respectively, of sea urchins exposed to pore waters; reduced metabolic activity of a marine bioluminescent bacteria exposed to organic solvent extracts; induction of a cytochrome P-450 reporter gene system in exposures to solvent extracts; and reduced reproductive success in marine copepods exposed to solid-phase sediments. Contamination and toxicity were most severe in several peripheral canals and tributaries, including the lower Miami River, adjoining the main axis of the bay. In the open basins of the bay, chemical concentrations and toxicity generally were higher in areas north of the Rickenbacker Causeway than south of it. Sediments from the main basins of the bay generally were less toxic than those from the adjoining tributaries and canals. The different toxicity tests, however, indicated differences in severity, incidence, spatial patterns, and spatial extent in toxicity. The most sensitive test among those performed on all samples, a bioassay of normal morphological development of sea urchin embryos, indicated toxicity was pervasive throughout the entire study area. The least sensitive test, an acute bioassay performed with a benthic amphipod, indicated toxicity was restricted to a very small percentage of the area. Both the degree and spatial extent of chemical contamination and toxicity in this study area were similar to or less severe than those observed in many other areas in the U.S. The spatial extent of toxicity in all four tests performed throughout the bay were comparable to the “national averages” calculated by NOAA from previous surveys conducted in a similar manner. Several trace metals occurred in concentrations in excess of those expected in reference sediments. Mixtures of substances, including pesticides, petroleum constituents, trace metals, and ammonia, were associated statistically with the measures of toxicity. Substances most elevated in concentration relative to numerical guidelines and associated with toxicity included polychlorinated biphenyls, DDT pesticides, polynuclear aromatic hydrocarbons, hexachloro cyclohexanes, lead, and mercury. These (and other) substances occurred in concentrations greater than effects-based guidelines in the samples that were most toxic in one or more of the tests. (PDF contains 180 pages)

An assessment of chemical contaminants, toxicity and benthic infauna in sediments from the St. Thomas East End Reserves (STEER)

This report contains a chemical and biological characterization of sediments from the St. Thomas East End Reserves (STEER) in St. Thomas, U.S. Virgin Islands (USVI). The STEER Management Plan (published in 2011) identified chemical contaminants and habitat loss as high or very high threats and called for a characterization of chemical contaminants as well as an assessment of their effects on natural resources. The baseline information contained in this report on chemical contaminants, toxicity and benthic infaunal community composition can be used to assess current conditions, as well as the efficacy of future restoration activities. In this phase of the project, 185 chemical contaminants, including a number of organic (e.g., hydrocarbons and pesticides) and inorganic (e.g., metals) compounds, were analyzed from 24 sites in the STEER. Sediments were also analyzed using a series of toxicity bioassays, including amphipod mortality, sea urchin fertilization impairment, and the cytochrome P450 Human Reporter Gene System (HRGS), along with a characterization of the benthic infaunal community. Higher levels of chemical contaminants were found in Mangrove Lagoon and Benner Bay in the western portion of the study area than in the eastern area. The concentrations of polychlorinated biphenyls (PCBs), DDT (dichlorodiphenyltrichloroethane), chlordane, zinc, copper, lead and mercury were above a NOAA sediment quality guideline at one or more sites, indicating impacts may be present in more sensitive species or life stages in the benthic environment. Copper at one site in Benner Bay, however, was above a NOAA guideline indicating that effects on benthic organisms were likely. The antifoulant boat hull ingredient tributyltin, or TBT, was found at the third highest concentration in the history of NOAA’s National Status and Trends (NS&T) Program, which monitors the Nation’s coastal and estuarine waters for chemical contaminants and bioeffects. Unfortunately, there do not appear to be any established sediment quality guidelines for TBT. Results of the bioassays indicated significant sediment toxicity in Mangrove Lagoon and Benner Bay using multiple tests. The benthic infaunal communities in Mangrove Lagoon and Benner Bay appeared severely diminished.

Sediment Quality Triad assessment in Kachemak Bay: characterization of soft bottom benthic habitats and contaminant bioeffects assessment

A baseline environmental characterization of the inner Kachemak Bay, Alaska was conducted using the sediment quality triad approach based on sediment chemistry, sediment toxicity, and benthic invertebrate community structure. The study area was subdivided into 5 strata based on geophysical and hydrodynamic patterns in the bay (eastern and western intertidal mud flats, eastern and western subtidal, and Homer Harbor). Three to seven locations were synoptically sampled within each stratum using a stratified random statistical design approach. Three sites near the village of Port Graham and two sites in the footprint of a proposed Homer Harbor expansion were also collected for comparison. Concentrations of over 120 organic and metallic contaminants were analyzed. Ambient toxicity was assessed using two amphipod bioassays. A detailed benthic community condition assessment was performed. Habitat parameters (depth, salinity, temperature, dissolved oxygen, sediment grain size, and organic carbon content) that influence species and contaminant distribution were also measured at each sampling site. Sediments were mostly mixed silt and sand; characteristic of high energy habitats, with pockets of muddy zones. Organic compounds (PAHs, DDTs, PCBs, cyclodienes, cyclohexanes) were detected throughout the bay but at relatively low concentrations. Tributyltin was elevated in Homer Harbor relative to the other strata. With a few exceptions, metals concentrations were relatively low and probably reflect the input of glacial runoff. Relative to other sites, Homer Harbor sites were shown to have elevated concentrations of metallic and organic contaminants. The Homer Harbor stratum however, is a deep, low energy depositional environment with fine grained sediment. Concentrations of organic contaminants measured were five to ten times higher in the harbor sites than in the open bay sites. Concentration of PAHs is of a particular interest because of the legacy of oil spills in the region. There was no evidence of residual PAHs attributable to oil spills, outside of local input, beyond the confines of the harbor. Concentrations were one to ten times below NOAA sediment quality guidelines. Selected metal concentrations were found to be relatively elevated compared to other data collected in the region. However, levels are still very low in the scale of NOAA’s sediment quality guidelines, and therefore appear to pose little or no ecotoxicity threat to biota. Infaunal assessment showed a diverse assemblage with more than 240 taxa recorded and abundances greater than 3,000 animals m-22 in all but a few locations. Annelid worms, crustaceans, snails, and clams were the dominant taxa accounting for 63 %, 19%, 5%, and 7 % respectively of total individuals. Specific benthic community assemblages were identified that were distributed based on depth and water clarity. Species richness and diversity was lower in the eastern end of the bay in the vicinity of the Fox River input. Abundance was also generally lower in the eastern portion of the study area, and in the intertidal areas near Homer. The eastern portions of the bay are stressed by the sediment load from glacial meltwater. Significant toxicity was virtually absent. Conditions at the sites immediately outside the existing Homer Harbor facility did not differ significantly from other subtidal locations in the open Kachemak Bay. The benthic fauna at Port Graham contained a significant number of species not found in Kachemak Bay. Contaminant conditions were variable depending on specific location. Selected metal concentrations were elevated at Port Graham and some were lower relative to Kachemak Bay, probably due to local geology. Some organic contaminants were accumulating at a depositional site.

A quantitative survey of the benthic infauna of northern Monterey Bay, California: Annual report, Part 8, 1973

(PDF contains 241 pages)

Selected Cenozoic Benthic Foraminifera from Florida : poster

(1 poster - no publication date on poster, but since early in series likely to be early 1990's))

Fish Habitat Utilization Patterns and Evaluation of the Efficacy of Marine Protected Areas in Hawaii: Integration of NOAA Digital Benthic Habitat Mapping and Coral Reef Ecological Studies

Over the past four decades, the state of Hawaii has developed a system of eleven Marine Life Conservation Districts (MLCDs) to conserve and replenish marine resources around the state. Initially established to provide opportunities for public interaction with the marine environment, these MLCDs vary in size, habitat quality, and management regimes, providing an excellent opportunity to test hypotheses concerning marine protected area (MPA) design and function using multiple discreet sampling units. NOAA/NOS/NCCOS/Center for Coastal Monitoring and Assessment’s Biogeography Team developed digital benthic habitat maps for all MLCD and adjacent habitats. These maps were used to evaluate the efficacy of existing MLCDs for biodiversity conservation and fisheries replenishment, using a spatially explicit stratified random sampling design. Coupling the distribution of habitats and species habitat affinities using GIS technology elucidates species habitat utilization patterns at scales that are commensurate with ecosystem processes and is useful in defining essential fish habitat and biologically relevant boundaries for MPAs. Analysis of benthic cover validated the a priori classification of habitat types and provided justification for using these habitat strata to conduct stratified random sampling and analyses of fish habitat utilization patterns. Results showed that the abundance and distribution of species and assemblages exhibited strong correlations with habitat types. Fish assemblages in the colonized and uncolonized hardbottom habitats were found to be most similar among all of the habitat types. Much of the macroalgae habitat sampled was macroalgae growing on hard substrate, and as a result showed similarities with the other hardbottom assemblages. The fish assemblages in the sand habitats were highly variable but distinct from the other habitat types. Management regime also played an important role in the abundance and distribution of fish assemblages. MLCDs had higher values for most fish assemblage characteristics (e.g. biomass, size, diversity) compared with adjacent fished areas and Fisheries Management Areas (FMAs) across all habitat types. In addition, apex predators and other targeted resources species were more abundant and larger in the MLCDs, illustrating the effectiveness of these closures in conserving fish populations. Habitat complexity, quality, size and level of protection from fishing were important determinates of MLCD effectiveness with respect to their associated fish assemblages. (PDF contains 217 pages)

Fish assemblages and benthic habitats of Buck Island Reef National Monument (St. Croix, U.S. Virgin Islands) and the surrounding seascape: A characterization of spatial and temporal patterns

Since 1999, NOAA’s Biogeography Branch of the Center for Coastal Monitoring and Assessment (CCMA-BB) has been working with federal and territorial partners to characterize, monitor, and assess the status of the marine environment around northeastern St. Croix, U.S. Virgin Islands. This effort is part of the broader NOAA Coral Reef Conservation Program’s (CRCP) National Coral Reef Ecosystem Monitoring Program (NCREMP). With support from CRCP’s NCREMP, CCMA conducts the “Caribbean Coral Reef Ecosystem Monitoring project” (CREM) with goals to: (1) spatially characterize and monitor the distribution, abundance, and size of marine fauna associated with shallow water coral reef seascapes (mosaics of coral reefs, seagrasses, sand and mangroves); (2) relate this information to in situ fine-scale habitat data and the spatial distribution and diversity of habitat types using benthic habitat maps; (3) use this information to establish the knowledge base necessary for enacting management decisions in a spatial setting; (4) establish the efficacy of those management decisions; and (5) develop data collection and data management protocols. The monitoring effort in northeastern St. Croix was conducted through partnerships with the National Park Service (NPS) and the Virgin Islands Department of Planning and Natural Resources (VI-DPNR). The geographical focal point of the research is Buck Island Reef National Monument (BIRNM), a protected area originally established in 1961 and greatly expanded in 2001; however, the work also encompassed a large portion of the recently created St. Croix East End Marine Park (EEMP). Project funding is primarily provided by NOAA CRCP, CCMA and NPS. In recent decades, scientific and non-scientific observations have indicated that the structure and function of the coral reef ecosystem around northeastern St. Croix have been adversely impacted by a wide range of environmental stressors. The major stressors have included the mass Diadema die off in the early 1980s, a series of hurricanes beginning with Hurricane Hugo in 1989, overfishing, mass mortality of Acropora corals due to disease and several coral bleaching events, with the most severe mass bleaching episode in 2005. The area is also an important recreational resource supporting boating, snorkeling, diving and other water based activities. With so many potential threats to the marine ecosystem and a dramatic change in management strategy in 2003 when the park’s Interim Regulations (Presidential Proclamation No. 7392) established BIRNM as one of the first fully protected marine areas in NPS system, it became critical to identify existing marine fauna and their spatial distributions and temporal dynamics. This provides ecologically meaningful data to assess ecosystem condition, support decision making in spatial planning (including the evaluation of efficacy of current management strategies) and determine future information needs. The ultimate goal of the work is to better understand the coral reef ecosystems and to provide information toward protecting and enhancing coral reef ecosystems for the benefit of the system itself and to sustain the many goods and services that it offers society. This Technical Memorandum contains analysis of the first six years of fish survey data (2001-2006) and associated characterization of the benthos (1999-2006). The primary objectives were to quantify changes in fish species and assemblage diversity, abundance, biomass and size structure and to provide spatially explicit information on the distribution of key species or groups of species and to compare community structure inside (protected) versus outside (fished) areas of BIRNM. (PDF contains 100 pages).

Long-Term Monitoring of Ecological Conditions In Gray’s Reef National Marine Sanctuary: Comparison of soft-bottom benthic assemblages and contaminant levels in sediments and biota in Spring 2000 and 2005

As part of an ongoing program of benthic sampling and related assessments of sediment quality at Gray’s Reef National Marine Sanctuary (GRNMS) off the coast of Georgia, a survey of soft-bottom benthic habitats was conducted in spring 2005 to characterize condition of macroinfaunal assemblages and levels of chemical contaminants in sediments and biota relative to a baseline survey carried out in spring 2000. Distribution and abundance of macrobenthos were related foremost to sediment type (median particle size, % gravel), which in turn varied according to bottom-habitat mesoscale features (e.g., association with live bottom versus flat or rippled sand areas). Overall abundance and diversity of soft-bottom benthic communities were similar between the two years, though dominance patterns and relative abundances of component species were less repeatable. Seasonal summer pulses of a few taxa (e.g., the bivalve Ervilia sp. A) observed in 2000 were not observed in 2005. Concentrations of chemical contaminants in sediments and biota, though detectable in both years, were consistently at low, background levels and no exceedances of sediment probable bioeffect levels or FDA action levels for edible fish or shellfish were observed. Near-bottom dissolved oxygen levels and organic-matter content of sediments also have remained within normal ranges. Highly diverse benthic assemblages were found in both years, supporting the premise that GRNMS serves as an important reservoir of marine biodiversity. A total of 353 taxa (219 identified to species) were collected during the spring 2005 survey. Cumulatively, 588 taxa (371 identified to species) have been recorded in the sanctuary from surveys in 2000, 2001, 2002, and 2005. Species Accumulation Curves indicate that the theoretical maximum should be in excess of 600 species. Results of this study will be of value in advancing strategic science and management goals for GRNMS, including characterization and long-term monitoring of sanctuary resources and processes, as well as supporting evolving interests in ecosystem-based management of the surrounding South Atlantic Bight (SAB) ecosystem. (PDF contains 46 pages)

Soft-bottom benthic assemblages and levels of contaminants in sediments and biota at Gray's Reef National Marine Sanctuary and nearby shelf waters off the coast of Georgia (2000 and 2001)

A series of studies was initiated to assess the condition of benthic macroinfauna and chemical contaminant levels in sediments and biota of the Gray’s Reef National Marine Sanctuary (GRNMS) and nearby shelf waters off the coast of Georgia. Four key objectives of the research are (1) to document existing environmental conditions within the sanctuary in order to provide a quantitative benchmark for tracking any future changes due to either natural or human disturbances; (2) to examine broader cross-shelf spatial patterns in benthic fauna and sediment contaminant concentrations and to identify potential controlling factors associated with the observed patterns; (3) to assess any between-year temporal variability in benthic fauna; and (4) to evaluate the importance of benthic fauna as prey for higher trophic levels. Such questions are being addressed to help fulfill long-term science and management goals of the GRNMS. However, it is anticipated that the information will be of additional value in broadening our understanding of the surrounding South Atlantic Bight (SAB) ecosystem and in bringing the knowledge to bear on related resourcemanagement issues of the region. We have begun to address the first three of these objectives with data from samples collected in spring 2000 at stations within GRNMS, and in spring 2001 at stations within the sanctuary and along three cross-shelf transects extending from the mouths of Sapelo, Doboy, and Altamaha Sounds out to sanctuary depths (about 17-20 m). This report provides a description of baseline conditions within the sanctuary, based on results of the spring 2000 survey (Section II), and uses data from both 2000 and 2001 to examine overall spatial and temporal patterns in biological and chemical variables within the sanctuary and surrounding inner-shelf environment (Section III). (PDF contains 65 pages)

Extent and toxicity of contaminated marine sediments in Southeastern Florida

Thirty sites were sampled in southern Biscayne Bay and Manatee Bay in December 1999 to determine the extent of toxicity in sediments. Analyses and assays included: pesticides and phenols in seawater; chemical contaminants in sediment; amphipod mortality, HRGS P450, sea urchin sperm fertilization and embryology, MicrotoxTM, MutatoxTM, grass shrimp AChE and juvenile clam mortality assays; sea urchin sperm, amphipod and oyster DNA damage; and benthic community assessment. Sediment sites near the mouth of canals showed evidence of contamination. Contaminant plumes and associated toxicity do not appear to extend seaward of the mouth of the canals in an appreciable manner. Concentrations of contaminants in the sediments in open areas of Biscayne and Manatee Bays are generally low. (PDF contains 140 pages)

Sediment Quality in Puget Sound Year 3 - Southern Puget Sound

As a component of a three-year cooperative effort of the Washington State Department of Ecology and the National Oceanic and Atmospheric Administration, surficial sediment samples from 100 locations in southern Puget Sound were collected in 1999 to determine their relative quality based on measures of toxicity, chemical contamination, and benthic infaunal assemblage structure. The survey encompassed an area of approximately 858 km2, ranging from East and Colvos Passages south to Oakland Bay, and including Hood Canal. Toxic responses were most severe in some of the industrialized waterways of Tacoma’s Commencement Bay. Other industrialized harbors in which sediments induced toxic responses on smaller scales included the Port of Olympia, Oakland Bay at Shelton, Gig Harbor, Port Ludlow, and Port Gamble. Based on the methods selected for this survey, the spatial extent of toxicity for the southern Puget Sound survey area was 0% of the total survey area for amphipod survival, 5.7% for urchin fertilization, 0.2% for microbial bioluminescence, and 5- 38% with the cytochrome P450 HRGS assay. Measurements of trace metals, PAHs, PCBs, chlorinated pesticides, other organic chemicals, and other characteristics of the sediments, indicated that 20 of the 100 samples collected had one or more chemical concentrations that exceeded applicable, effects-based sediment guidelines and/or Washington State standards. Chemical contamination was highest in eight samples collected in or near the industrialized waterways of Commencement Bay. Samples from the Thea Foss and Middle Waterways were primarily contaminated with a mixture of PAHs and trace metals, whereas those from Hylebos Waterway were contaminated with chlorinated organic hydrocarbons. The remaining 12 samples with elevated chemical concentrations primarily had high levels of other chemicals, including bis(2-ethylhexyl) phthalate, benzoic acid, benzyl alcohol, and phenol. The characteristics of benthic infaunal assemblages in south Puget Sound differed considerably among locations and habitat types throughout the study area. In general, many of the small embayments and inlets throughout the study area had infaunal assemblages with relatively low total abundance, taxa richness, evenness, and dominance values, although total abundance values were very high in some cases, typically due to high abundance of one organism such as the polychaete Aphelochaeta sp. N1. The majority of the samples collected from passages, outer embayments, and larger bodies of water tended to have infaunal assemblages with higher total abundance, taxa richness, evenness, and dominance values. Two samples collected in the Port of Olympia near a superfund cleanup site had no living organisms in them. A weight-of-evidence approach used to simultaneously examine all three “sediment quality triad” parameters, identified 11 stations (representing 4.4 km2, 0.5% of the total study area) with sediment toxicity, chemical contamination, and altered benthos (i.e., degraded sediment quality), 36 stations (493.5 km2, 57.5% total study area) with no toxicity or chemical contamination (i.e., high sediment quality), 35 stations (274.1 km2, 32.0% total study area) with one impaired sediment triad parameter (i.e., intermediate/high sediment quality), and 18 stations (85.7km2, 10.0% total study area) with two impaired sediment parameters (i.e., intermediate/degraded quality sediments). Generally, upon comparison, the number of stations with degraded sediments based upon the sediment quality triad of data was slightly greater in the central Puget Sound than in the northern and southern Puget Sound study areas, with the percent of the total study area degraded in each region decreasing from central to north to south (2.8, 1.3 and 0.5%, respectively). Overall, the sediments collected in Puget Sound during the combined 1997-1999 surveys were among the least contaminated relative to other marine bays and estuaries studied by NOAA using equivalent methods. (PDF contains 351 pages)

Benthic sampling program in Biscayne Bay, 1981-1982

The Biscayne Bay Benthic Sampling Program was divided into two phases. In Phase I, sixty sampling stations were established in Biscayne Bay (including Dumfoundling Bay and Card Sound) representing diverse habitats. The stations were visited in the wet season (late fall of 1981) and in the dry season (midwinter of 1982). At each station certain abiotic conditions were measured or estimated. These included depth, sources of freshwater inflow and pollution, bottom characteristics, current direction and speed, surface and bottom temperature, salinity and dissolved oxygen, and water clarity was estimated with a secchi disk. Seagrass blades and macroalgae were counted in a 0.1-m2 grid placed so as to best represent the bottom community within a 50-foot radius. Underwater 35-mm photographs were made of the bottom using flash apparatus. Benthic samples were collected using a petite Ponar dredge. These samples were washed through a 5-mm mesh screen, fixed in formalin in the field, and later sorted and identified by experts to a pre-agreed taxonomic level. During the wet season sampling period, a nonquantitative one-meter wide trawl was made of the epibenthic community. These samples were also washed, fixed, sorted and identified. During the dry season sampling period, sediment cores were collected at each station not located on bare rock. These cores were analyzed for sediment size and organic composition by personnel of the University of Miami. Data resulting from the sampling were entered into a computer. These data were subjected to cluster analyses, Shannon-Weaver diversity analysis, multiple regression analysis of variance and covariance, and factor analysis. In Phase II of the program, fifteen stations were selected from among the sixty of Phase I. These stations were sampled quarterly. At each quarter, five Petite Ponar dredge samples were collected from each station. As in Phase I, observations and measurements, including seagrass blade counts, were made at each station. In Phase II, polychaete specimens collected were given to a separate contractor for analysis to the species level. These analyses included mean, standard deviation, coefficient of dispersion, percent of total, and numeric rank for each organism in each station as well as number of species, Shannon-Weaver taxa diversity, and dominance (the compliment of Simpson's Index) for each station. Multiple regression analysis of variance and covariance, and factor analysis were applied to the data to determine effect of abiotic factors measured at each station. (PDF contains 96 pages)

Techniques for spatial analysis and visualization of benthic mapping data: final report

The mapping and geospatial analysis of benthic environments are multidisciplinary tasks that have become more accessible in recent years because of advances in technology and cost reductions in survey systems. The complex relationships that exist among physical, biological, and chemical seafloor components require advanced, integrated analysis techniques to enable scientists and others to visualize patterns and, in so doing, allow inferences to be made about benthic processes. Effective mapping, analysis, and visualization of marine habitats are particularly important because the subtidal seafloor environment is not readily viewed directly by eye. Research in benthic environments relies heavily, therefore, on remote sensing techniques to collect effective data. Because many benthic scientists are not mapping professionals, they may not adequately consider the links between data collection, data analysis, and data visualization. Projects often start with clear goals, but may be hampered by the technical details and skills required for maintaining data quality through the entire process from collection through analysis and presentation. The lack of technical understanding of the entire data handling process can represent a significant impediment to success. While many benthic mapping efforts have detailed their methodology as it relates to the overall scientific goals of a project, only a few published papers and reports focus on the analysis and visualization components (Paton et al. 1997, Weihe et al. 1999, Basu and Saxena 1999, Bruce et al. 1997). In particular, the benthic mapping literature often briefly describes data collection and analysis methods, but fails to provide sufficiently detailed explanation of particular analysis techniques or display methodologies so that others can employ them. In general, such techniques are in large part guided by the data acquisition methods, which can include both aerial and water-based remote sensing methods to map the seafloor without physical disturbance, as well as physical sampling methodologies (e.g., grab or core sampling). The terms benthic mapping and benthic habitat mapping are often used synonymously to describe seafloor mapping conducted for the purpose of benthic habitat identification. There is a subtle yet important difference, however, between general benthic mapping and benthic habitat mapping. The distinction is important because it dictates the sequential analysis and visualization techniques that are employed following data collection. In this paper general seafloor mapping for identification of regional geologic features and morphology is defined as benthic mapping. Benthic habitat mapping incorporates the regional scale geologic information but also includes higher resolution surveys and analysis of biological communities to identify the biological habitats. In addition, this paper adopts the definition of habitats established by Kostylev et al. (2001) as a “spatially defined area where the physical, chemical, and biological environment is distinctly different from the surrounding environment.” (PDF contains 31 pages)

Guidance for benthic habitat mapping: an aerial photographic approach

This document, Guidance for Benthic Habitat Mapping: An Aerial Photographic Approach, describes proven technology that can be applied in an operational manner by state-level scientists and resource managers. This information is based on the experience gained by NOAA Coastal Services Center staff and state-level cooperators in the production of a series of benthic habitat data sets in Delaware, Florida, Maine, Massachusetts, New York, Rhode Island, the Virgin Islands, and Washington, as well as during Center-sponsored workshops on coral remote sensing and seagrass and aquatic habitat assessment. (PDF contains 39 pages) The original benthic habitat document, NOAA Coastal Change Analysis Program (C-CAP): Guidance for Regional Implementation (Dobson et al.), was published by the Department of Commerce in 1995. That document summarized procedures that were to be used by scientists throughout the United States to develop consistent and reliable coastal land cover and benthic habitat information. Advances in technology and new methodologies for generating these data created the need for this updated report, which builds upon the foundation of its predecessor.

A comparison of seafloor habitats and associated benthic fauna in areas open and closed to bottom trawling along the central California Continental Shelf

Executive Summary: A number of studies have shown that mobile, bottom-contact fishing gear (such as otter trawls) can alter seafloor habitats and associated biota. Considerably less is known about the recovery of these resources following such disturbances, though this information is critical for successful management. In part, this paucity of information can be attributed to the lack of access to adequate control sites – areas of the seafloor that are closed to fishing activity. Recent closures along the coast of central California provide an excellent opportunity to track the recovery of historically trawled areas and to compare recovery rates to adjacent areas that continue to be trawled. In June 2006 we initiated a multi-year study of the recovery of seafloor microhabitats and associated benthic fauna inside and outside two new Essential Fish Habitat (EFH) closures within the Cordell Bank and Gulf of the Farallones National Marine Sanctuaries. Study sites inside the EFH closure at Cordell Bank were located in historically active areas of fishing effort, which had not been trawled since 2003. Sites outside the EFH closure in the Gulf of Farallones were located in an area that continues to be actively trawled. All sites were located in unconsolidated sands at equivalent water depths. Video and still photographic data collected via a remotely operated vehicle (ROV) were used to quantify the abundance, richness, and diversity of microhabitats and epifaunal macro-invertebrates at recovering and actively trawled sites, while bottom grabs and conductivity/temperature/depth (CTD) casts were used to quantify infaunal diversity and to characterize local environmental conditions. Analysis of still photos found differences in common seafloor microhabitats between the recovering and actively trawled areas, while analysis of videographic data indicated that biogenic mound and biogenic depression microhabitats were significantly less abundant at trawled sites. Each of these features provides structure with which demersal fishes, across a wide range of size classes, have been observed to associate. Epifaunal macro-invertebrates were sparsely distributed and occurred in low numbers in both treatments. However, their total abundance was significantly different between treatments, which was attributable to lower densities at trawled sites. In addition, the dominant taxa were different between the two sites. Patchily-distributed buried brittle stars dominated the recovering site, and sea whips (Halipteris cf. willemoesi) were most numerous at the trawled site though they occurred in only five of ten transects. Numerical classification (cluster analysis) of the infaunal samples also revealed a clear difference between benthic assemblages in the recovering vs. trawled areas due to differences in the relative abundances of component species. There were no major differences in infaunal species richness, H′ diversity, or J′ evenness between recovering vs. trawled site groups. However, total infaunal abundance showed a significant difference attributable to much lower densities at trawled sites. This pattern was driven largely by the small oweniid polychaete Myriochele gracilis, which was the most abundant species in the overall study region though significantly less abundant at trawled sites. Other taxa that were significantly less abundant at trawled sites included the polychaete M. olgae and the polychaete family Terebellidae. In contrast, the thyasirid bivalve Axinopsida serricata and the polychaetes Spiophanes spp. (mostly S. duplex), Prionospio spp., and Scoloplos armiger all had significantly to near significantly higher abundances at trawled sites. As a result of such contrasting species patterns, there also was a significant difference in the overall dominance structure of infaunal assemblages between the two treatments. It is suggested that the observed biological patterns were the result of trawling impacts and varying levels of recovery due to the difference in trawling status between the two areas. The EFH closure was established in June 2006, within a month of when sampling was conducted for the present study, however, the stations within this closure area are at sites that actually have experienced little trawling since 2003, based on National Marine Fishery Service trawl records. Thus, the three-year period would be sufficient time for some post-trawling changes to have occurred. Other results from this study (e.g., similarly moderate numbers of infaunal species in both areas that are lower than values recorded elsewhere in comparable habitats along the California continental shelf) also indicate that recovery within the closure area is not yet complete. Additional sampling is needed to evaluate subsequent recovery trends and persistence of effects. Furthermore, to date, the study has been limited to unconsolidated substrates. Ultimately, the goal of this project is to characterize the recovery trajectories of a wide spectrum of seafloor habitats and communities and to link that recovery to the dynamics of exploited marine fishes. (PDF has 48 pages.)