Survey report of NOAA Ship McArthur II cruises AR-04-04, AR-05-05 and AR-06-03: Habitat classification of side scan sonar imagery in support of deep-sea coral/sponge explorations at the Olympic Coast National Marine Sanctuary

Habitat mapping and characterization has been defined as a high-priority management issue for the Olympic Coast National Marine Sanctuary (OCNMS), especially for poorly known deep-sea habitats that may be sensitive to anthropogenic disturbance. As a result, a team of scientists from OCNMS, National Centers for Coastal Ocean Science (NCCOS), and other partnering institutions initiated a series of surveys to assess the distribution of deep-sea coral/sponge assemblages within the sanctuary and to look for evidence of potential anthropogenic impacts in these critical habitats. Initial results indicated that remotely delineating areas of hard bottom substrate through acoustic sensing could be a useful tool to increase the efficiency and success of subsequent ROV-based surveys of the associated deep-sea fauna. Accordingly, side scan sonar surveys were conducted in May 2004, June 2005, and April 2006 aboard the NOAA Ship McArthur II to: (1) obtain additional imagery of the seafloor for broader habitat-mapping coverage of sanctuary waters, and (2) help delineate suitable deep-sea coral/sponge habitat, in areas of both high and low commercial-fishing activities, to serve as sites for surveying-in more detail using an ROV on subsequent cruises. Several regions of the sea floor throughout the OCNMS were surveyed and mosaicked at 1-meter pixel resolution. Imagery from the side scan sonar mapping efforts was integrated with other complementary data from a towed camera sled, ROVs, sedimentary samples, and bathymetry records to describe geological and biological (where possible) aspects of habitat. Using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999), we created a preliminary map of various habitat polygon features for use in a geographical information system (GIS). This report provides a description of the mapping and groundtruthing efforts as well as results of the image classification procedure for each of the areas surveyed. (PDF contains 60 pages.)

Habitat mapping effort at the Olympic Coast National Marine Sanctuary – Current status and future needs

With elevating interest to establish conservation efforts for groundfish stocks and continued scrutiny over the value of marine protected areas along the west coast, the importance of enhancing our knowledge of seabed characteristics through mapping activities is becoming increasingly more important, especially in a timely manner. Shortly after the inception of the Seabed Mapping Initiative instituted with the US Geological Survey (USGS), the National Marine Sanctuary Program (NMSP) assembled a panel of habitat mapping experts. They determined that the status of existing data sets and future data acquisition needs varied widely among the individual sanctuaries and that more detailed site assessments were needed to better prioritize mapping efforts and outline an overall joint strategy. To assist with that specific effort and provide pertinent information for the Olympic Coast National Marine Sanctuary’s (OCNMS) Management Plan Review, this report summarizes the mapping efforts that have taken place at the site to date; calculates a timeframe for completion of baseline mapping efforts when operating under current data acquisition limitations; describes an optimized survey strategy to dramatically reduce the required time to complete baseline surveying; and provides estimates for the needed vessel sea-days (DAS) to accomplish baseline survey completion within a 2, 5 and 10 year timeframe. (PDF contains 38 pages.)

Olympic Coast National Marine Sanctuary Habitat Mapping: Survey report and classification of side scan sonar data from surveys HMPR-114-2004-02 and HMPR-116-2005-01.

The Olympic Coast National Marine Sanctuary (OCNMS) continues to invest significant resources into seafloor mapping activities along Washington’s outer coast (Intelmann and Cochrane 2006; Intelmann et al. 2006; Intelmann 2006). Results from these annual mapping efforts offer a snapshot of current ground conditions, help to guide research and management activities, and provide a baseline for assessing the impacts of various threats to important habitat. During the months of August 2004 and May and July 2005, we used side scan sonar to image several regions of the sea floor in the northern OCNMS, and the data were mosaicked at 1-meter pixel resolution. Video from a towed camera sled, bathymetry data, sedimentary samples and side scan sonar mapping were integrated to describe geological and biological aspects of habitat. Polygon features were created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). For three small areas that were mapped with both side scan sonar and multibeam echosounder, we made a comparison of output from the classified images indicating little difference in results between the two methods. With these considerations, backscatter derived from multibeam bathymetry is currently a costefficient and safe method for seabed imaging in the shallow (<30 meters) rocky waters of OCNMS. The image quality is sufficient for classification purposes, the associated depths provide further descriptive value and risks to gear are minimized. In shallow waters (<30 meters) which do not have a high incidence of dangerous rock pinnacles, a towed multi-beam side scan sonar could provide a better option for obtaining seafloor imagery due to the high rate of acquisition speed and high image quality, however the high probability of losing or damaging such a costly system when deployed as a towed configuration in the extremely rugose nearshore zones within OCNMS is a financially risky proposition. The development of newer technologies such as intereferometric multibeam systems and bathymetric side scan systems could also provide great potential for mapping these nearshore rocky areas as they allow for high speed data acquisition, produce precisely geo-referenced side scan imagery to bathymetry, and do not experience the angular depth dependency associated with multibeam echosounders allowing larger range scales to be used in shallower water. As such, further investigation of these systems is needed to assess their efficiency and utility in these environments compared to traditional side scan sonar and multibeam bathymetry. (PDF contains 43 pages.)

Benthic habitat mapping in the Olympic Coast National Marine Sanctuary: Classification of side scan sonar data from survey HMPR-108-2002-01: Version I

In September 2002, side scan sonar was used to image a portion of the sea floor in the northern OCNMS and was mosaiced at 1-meter pixel resolution using 100 kHz data collected at 300-meter range scale. Video from a remotely-operated vehicle (ROV), bathymetry data, sedimentary samples, and sonar mapping have been integrated to describe geological and biological aspects of habitat and polygon features have been created and attributed with a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999). The data can be used with geographic information system (GIS) software for display, query, and analysis. Textural analysis of the sonar images provided a relatively automated method for delineating substrate into three broad classes representing soft, mixed sediment, and hard bottom. Microhabitat and presence of certain biologic attributes were also populated into the polygon features, but strictly limited to areas where video groundtruthing occurred. Further groundtruthing work in specific areas would improve confidence in the classified habitat map. (PDF contains 22 pages.)

Juvenile and small resident fishes of Florida Bay, a critical habitat in the Everglades National Park, Florida

This compendium presents information on the life history, diet, and abundance and distribution of 46 of the more abundant juvenile and small resident fish species, and data on three species of seagrasses in Florida Bay, Everglades National Park. Abundance and distribution of fish data were derived from three sampling schemes: (1) an otter trawl in basins (1984–1985, 1994–2001), (2) a surface trawl in basins (1984–1985), and (3) a surface trawl in channels (1984–1985). Results from surface trawling only included pelagic species. Collections made with an otter trawl in basins on a bi-monthly basis were emphasized. Nonparametric statistics were used to test spatial and temporal differences in the abundance of species and seagrasses. Fish species accounts were presented in four sections – Life history, Diet, Abundance and distribution, and Length-frequency distributions. Although Florida Bay is a subtropical estuary, the majority of fish species (76%) had warm-temperate affinities; i.e., only 24% were solely tropical species. The five most abundant species collected, in descending order, by (1) otter trawl in basins were: Eucinostomus gula, Lucania parva, Anchoa mitchilli, Lagodon rhomboides, and Syngnathus scovelli; (2) surface trawl in basins were: Hyporhamphus unifasciatus, Strongylura notata, Chriodorus atherinoides, Anchoa hepsetus, and Atherinomorus stipes; (3) surface trawl in channels were: Hypoatherina harringtonensis, A. stipes, A. mitchelli, H. unifasciatus, and C. atherinoides. (PDF file contains 219 pages.)

Acoustic signatures of the seafloor: Tools for predicting grouper habitat

Groupers are important components of commercial and recreational fisheries. Current methods of diver-based grouper census surveys could potentially benefit from development of remotely sensed methods of seabed classification. The goal of the present study was to determine if areas of high grouper abundance have characteristic acoustic signatures. A commercial acoustic seabed mapping system, QTC View Series V, was used to survey an area near Carysfort Reef, Florida Keys. Acoustic data were clustered using QTC IMPACT software, resulting in three main acoustic classes covering 94% of the area surveyed. Diver-based data indicate that one of the acoustic classes corresponded to hard substrate and the other two represented sediment. A new measurement of seabed heterogeneity, designated acoustic variability, was also computed from the acoustic survey data in order to more fully characterize the acoustic response (i.e., the signature) of the seafloor. When compared with diver-based grouper census data, both acoustic classification and acoustic variability were significantly different at sites with and without groupers. Sites with groupers were characterized by hard bottom substrate and high acoustic variability. Thus, the acoustic signature of a site, as measured by acoustic classification or acoustic variability, is a potentially useful tool for stratifying diver sampling effort for grouper census.

Southeastern U.S. Deepwater Reef Fish Assemblages, Habitat Characteristics, Catches, and Life History Summaries

There are 19 economically important reef fish species in the deepwater (l00-300 m) fishery of the southeastern United States. Five species make up the majority (over 97% by weight) of the catch. In descending order of total landings for 1995, they are: tilefish, Lopholatilus chamaeleonticeps, snowy grouper, Epinephelus niveatus, blueline tilefish, Caulolatilus microps, warsaw grouper, Epinephelus nigritus, and yellowedge grouper, E. flavolimbatus. Life history summaries and estimates of catches from 1972 through 1995 for 14 species are described. (PDF file contains 45 pages.)

Benthic macrofauna and habitat monitoring on the Continental Shelf of the northeastern United States: I. Biomass

Information on long-term temporal variability of and trends in benthic community-structure variables, such as biomass, is needed to estimate the range of normal variability in comparison with the effects of environmental change or disturbance. Fishery resource distribution and population growth will be influenced by such variability. This study examines benthic macrofaunal biomass and related data collected annually between 1978 and 1985 at 27 sites on the continental shelf of the northwestern Atlantic, from North Carolina to the southern Gulf of Maine. The study was expanded at several sites with data from other studies collected at the same sites prior to 1978. Results indicate that although there was interannual and seasonal variability, as expected, biomass levels over the study period showed few clear trends. Sites exhibiting trends were either in pollution-stressed coastal areas or influenced by the population dynamics of one or a few species, especially echinoderms. (PDF file contains 34 pages.)

Species composition, distribution, and relative abundance of fishes in the coastal habitat off the southeastern United States

Ichthyofauna of the coastal «10 m depth) habitat of the South Atlantic Bight were investigated between Cape Fear, North Carolina, and the St. John's River, Florida. Trawl collections from four nonconsecutive seasons in the period July 1980 to December 1982 indicated that the fish community is dominated by the family Sciaenidae, particularly juvenile forms. Spot (Leiostomus xanthurus) and Atlantic croaker (Micropogonias undulatus) were the two most abundant species and dominated catches during all seasons. Atlantic menhaden (Brevoortin tyrannus) was also very abundant, but only seasonally (winter and spring) dominant in the catches. Elasmobranch fIShes, especially rajiforms and carcharinids, contributed to much of the biomass of fishes collected. Total fish abundance was greatest in winter and lowest in summer and was influenced by the seasonality of Atlantic menhaden and Atlantic croaker in the catches. Biomass was highest in spring and lowest in summer, and was influenced by biomass of spot. Fish density ranged from 321 individuals and 12.2 kg per hectare to 746 individuals and 25.2 kg per hectare. Most species ranged widely throughout the bight, and showed some evidence of seasonal migration. Species assemblages were dominated by ubiquitous year-round residents of the coastal waters of the bight. Diversity (H') was highest in summer, and appeared influenced by the evenness of distribution of individuals among species. (PDF file contains 56 pages.)

Codend selection of winter flounder Pseudopleuronectes americanus

Codend selection of winter flounder (Pseudopleuronectes americanus) in 76-127 mm mesh codends was examined from experiments conducted in Long Island Sound during the spring of 1986-87. The results show a slightly larger size at selection than was found in earlier work as indicated by the selection factor, 2.31 in the present study compared with 2.2 and 2.24 from previous studies. Diamond mesh was found to have a length at 50% retention about 1 cm longer (Lso =22.6 cm), and a selection range (3.4 cm) about 1 cm narrower, than square mesh in 102-mm codends. Tow duration varied from 1 to 2 hours using 114-mm diamond mesh. As has been found in previous studies, tow duration and Lso are positively related, with I-hour tows averaging 24.6 cm and 2-hour tows averaging 26.6 cm. The importance of the slope of the selection curve was examined in yield-per-recruit analyses by comparing knife-edge and stepwise recruitment. In all mesh sizes, stepwise recruitment provides a more conservative estimate of yield in the presence of a minimum size limit. Differences in yield estimates between the two models were generally small (1-7%), except in the largest mesh size, 127 mm, where yield is overestimated by 10% when assuming knife-edge recruitment. (PDF file contains 16 pages.)

Evaluation of salmon and steelhead spawning habitat quality in the South Fork Trinity River Basin, 1997

Sediment sampling was used to evaluate chinook salmon (Oncorhynchus tshawytscha) and steelhead (O. mykiss) spawning habitat quality in the South Fork Trinity River (SFTR) basin. Sediment samples were collected using a McNeil-type sampler and wet sieved through a series of Tyler screens (25.00 mm, 12.50 mm, 6.30 mm, 3.35 mm, 1.00 mm, and 0.85 mm). Fines (particles < 0.85 mm) were determined after a l0-minute settling period in Imhoff cones. Thirteen stations were sampled in the SFTR basin: five stations were located in mainstem SFTR between rk 2.1 and 118.5, 2 stations each were located in EF of the SFTR, Grouse Creek, and Madden Creek, and one station each was located in Eltapom and Hayfork Creeks. Sample means for fines(particles < 0.85 mm) fer SFTR stations ranged between 14.4 and 19.4%; tributary station sample mean fines ranged between 3.4 and 19.4%. Decreased egg survival would be expected at 4 of 5 mainstem SFTR stations and at one station in EF of SFTR and Grouse Creek where fines content exceed 15%. Small gravel/sand content measured at all stations were high, and exceed levels associated with reduced sac fry emergence rates. Reduction of egg survival or sac fry emergence due to sedimentation in spawning gravels could lead to reduced juvenile production from the South Fork Trinity River. (PDF contains 18 pages.)

A study of the length at maturity and hooks/gill net mesh selection in Clarias lazera from Lake Chad

The minimum length at first maturity of Clarias lazera was found to be 24 cm (4.8%) for females and 20 cm (1.8%) for males. Fifty percent maturity was attained at length of 28 cm to 30 cm for both sexes; there being little difference among the sexes at this level of maturity. The modal retention lengths for gill nets were: 13 cm for 25.5 mm mesh; 18 cm for 32 mm mesh; 28 cm for 57 mm mesh; and 38 cm for 76 mm mesh. Modal lengths of Clarias lazera caught by various hooks sizes were No. 10 (28 cm); No. 11 (33 cm); Nos. 15 and 16 (28 cm). It is recommended that to protect the clarias fishery in Lake Chad, the use of gill nets of less than 57 mm mesh size and fishing hook No. 16 (and smaller sizes) which caught 43.94% of immature fishes should be discouraged

Limited resources? Let the habitat priority planner help!

In this time of scarce resources, coastal resource managers must find ways to prioritize conservation, land use, and restoration efforts. The Habitat Priority Planner (HPP) is a free geospatial tool created by the National Oceanic and Atmospheric Administration’s Coastal Services Center that has received wide praise for its ease of use and broad applicability to conservation strategic planning, restoration, climate change scenarios, and other natural resource management actions. Not a geographic information system (GIS) user? Don’t worry―this tool was designed to be used in a team setting. One intermediate-level GIS user can push the buttons to show quick results while a roomful of resource managers and stakeholders provide input criteria that determine the results. The Habitat Priority Planner is a toolbar for ESRI’s ArcGIS platform that is composed of three modules: Habitat Classification, Habitat Analysis, and Data Explorer. The tool calculates basic ecological statistics that are used to examine how habitats function within a landscape. The tool pre‐packages several common landscape metrics into a user‐friendly interface for intermediate GIS users. In addition, HPP allows the user to build queries interactively using a graphical interface for demonstrating criteria selections quickly in a visual manner that is useful in stakeholder interactions. Tool advocates and users include land trusts, conservation alliances, nonprofit organizations, and select National Estuarine Research Reserves and refuges of the U.S. Fish and Wildlife Service. Participants in this session will learn the basic requirements for HPP use and the multiple ways the HPP has been applied to geographies nationwide. (PDF contains 5 pages)

Habitat enhancing marine structures: Creating habitat in urban waters

Although maritime regions support a large portion of the world’s human population, their value as habitat for other species is overlooked. Urban structures that are built in the marine environment are not designed or managed for the habitat they provide, and are built without considering the communities of marine organisms that could colonize them (Clynick et al., 2008). However, the urban waterfront may be capable of supporting a significant proportion of regional aquatic biodiversity (Duffy-Anderson et al., 2003). While urban shorelines will never return to their original condition, some scientists think that the habitat quality of urban waterfronts could be significantly improved through further research and some design modifications, and that many opportunities exist to make these modifications (Russel et al., 1983, Goff, 2008). Habitat enhancing marine structures (or HEMS) are a potentially promising approach to address the impact of cities on marine organisms including habitat fragmentation and degradation. HEMS are a type of habitat improvement project that are ecologically engineered to improve the habitat quality of urban marine structures such as bulkheads and docks for marine organisms. More specifically, HEMS attempt to improve or enhance the physical habitat that organisms depend on for survival in the inter- and sub-tidal waterfronts of densely populated areas. HEMS projects are targeted at areas where human-made structures cannot be significantly altered or removed. While these techniques can be used in suburban or rural areas restoration or removal is preferred in these settings, and HEMS are resorted to only if removal of the human-made structure is not an option. Recent research supports the use of HEMS projects. Researchers have examined the communities found on urban structures including docks, bulkheads, and breakwaters. Complete community shifts have been observed where the natural shoreline was sandy, silty, or muddy. There is also evidence of declines in community composition, ecosystem functioning, and increases in non-native species abundances in assemblages on urban marine structures. Researchers have identified two key differences between these substrates including the slope (seawalls are vertical; rocky shores contain multiple slopes) and microhabitat availability (seawalls have very little; rocky shores contain many different types). In response, researchers have suggested designing and building seawalls with gentler slopes or a combination of horizontal and vertical surfaces. Researchers have also suggested incorporating microhabitat, including cavities designed to retain water during low tide, crevices, and other analogous features (Chapman, 2003; Moreira et al., 2006) (PDF contains 4 pages)

Predicting the effects of climate change on sea turtle nesting habitat in Florida

Rising global temperatures threaten the survival of many plant and animal species. Having already risen at an unprecedented rate in the past century, temperatures are predicted to rise between 0.3 and 7.5C in North America over the next 100 years (Hawkes et al. 2007). Studies have documented the effects of climate warming on phenology (timing of seasonal activities), with observations of early arrival at breeding grounds, earlier ends to the reproductive season, and delayed autumnal migrations (Pike et al. 2006). In addition, for species not suited to the physiological demands of cold winter temperatures, increasing temperatures could shift tolerable habitats to higher latitudes (Hawkes et al. 2007). More directly, climate warming will impact thermally sensitive species like sea turtles, who exhibit temperature-dependent sexual determination. Temperatures in the middle third of the incubation period determine the sex of sea turtle offspring, with higher temperatures resulting in a greater abundance of female offspring. Consequently, increasing temperatures from climate warming would drastically change the offspring sex ratio (Hawkes et al. 2007). Of the seven extant species of sea turtles, three (leatherback, Kemp’s ridley, and hawksbill) are critically endangered, two (olive ridley and green) are endangered, and one (loggerhead) is threatened. Considering the predicted scenarios of climate warming and the already tenuous status of sea turtle populations, it is essential that efforts are made to understand how increasing temperatures may affect sea turtle populations and how these species might adapt in the face of such changes. In this analysis, I seek to identify the impact of changing climate conditions over the next 50 years on the availability of sea turtle nesting habitat in Florida given predicted changes in temperature and precipitation. I predict that future conditions in Florida will be less suitable for sea turtle nesting during the historic nesting season. This may imply that sea turtles will nest at a different time of year, in more northern latitudes, to a lesser extent, or possibly not at all. It seems likely that changes in temperature and precipitation patterns will alter the distribution of sea turtle nesting locations worldwide, provided that beaches where the conditions are suitable for nesting still exist. Hijmans and Graham (2006) evaluate a range of climate envelope models in terms of their ability to predict species distributions under climate change scenarios. Their results suggested that the choice of species distribution model is dependent on the specifics of each individual study. Fuller et al. (2008) used a maximum entropy approach to model the potential distribution of 11 species in the Arctic Coastal Plain of Alaska under a series of projected climate scenarios. Recently, Pike (in press) developed Maxent models to investigate the impacts of climate change on green sea turtle nest distribution and timing. In each of these studies, a set of environmental predictor variables (including climate variables), for which ‘current’ conditions are available and ‘future’ conditions have been projected, is used in conjunction with species occurrence data to map potential species distribution under the projected conditions. In this study, I will take a similar approach in mapping the potential sea turtle nesting habitat in Florida by developing a Maxent model based on environmental and climate data and projecting the model for future climate data. (PDF contains 5 pages)