A comparison of animal abundance and distribution in similar habitats in Rookery Bay, Marco Island and Fakahatchee on the southwest coast of Florida, 1971 - 1972

The three areas in Rookery Bay, near Marco Island and Fakahatchee Bay were sampled from July 1971 through July 1972, and 1,006,640 individual animals were collected, of which the majority (55%) came from the Marco area. The large disparity between the catches at Marco and the remaining study areas was due mainly to the appearance of high numbers of species of polychaetes and echinoderms that were of very minor importance or absent from the catches in Rookery Bay and Fakahatchee Bay. When only the major classes of animals in the catch are considered (i.e., crustaceans, fish and mollusks) the total counts for Fakahatchee (298,830) and Marco (275,075) are quite comparable but both exceed Rookery Bay (119,388) by a considerable margin. The effects of the red tide outbreak in the summer of 1971 were apparently restricted to the Rookery Bay Sanctuary and may account for some of the observed differences. For the purposes of making controlled comparisons between the study areas, three common habitats were selected in each area so that a mud bottom habitat, a sand-shell bottom habitat and a vegetated bottom habitat were located in each of the study areas. Total catches by habitat types for crustaceans, fish and mollusks and certain of the more abundant species show clearly the overwhelming importance of the vegetated bottom as a habitat for animals. By habitat the vegetated areas had the most "indicator species" with five, the mud habitat was next with three and the sand-shell habitat third with two. Thus the vegetated habitat would be the best choice if a single habitat were to be used to detect environmental changes between study areas. (PDF contains 137 pages)

Tidal creek habitats: sentinels of coastal health

Tidal creek ecosystems are the primary aquatic link between stormwater runoff form the land and estuaries. Small tidal creeks begin in upland areas and drain into larger creeks forming a network. The creeks increase in size until they join a tidal river, sound, bay, or harbor that ultimately conect to the coastal ocean. The upper regions or headwaters of tidal creeks are "first responders" to stormwater runoff and are an important habitat for evaluating the impacts of coastal development on aquatic ecosystems. (PDF contains 22 pages)

Science-based restoration monitoring of coastal habitats, Volume One: A framework for monitoring plans under the Estuaries and Clean Waters Act of 2000 (Public Law 160-457)

Executive Summary: The Estuary Restoration Act of 2000 (ERA), Title I of the Estuaries and Clean Waters Act of 2000, was created to promote the restoration of habitats along the coast of the United States (including the US protectorates and the Great Lakes). The NOAA National Centers for Coastal Ocean Science was charged with the development of a guidance manual for monitoring plans under this Act. This guidance manual, titled Science-Based Restoration Monitoring of Coastal Habitats, is written in two volumes. It provides technical assistance, outlines necessary steps, and provides useful tools for the development and implementation of sound scientific monitoring of coastal restoration efforts. In addition, this manual offers a means to detect early warnings that the restoration is on track or not, to gauge how well a restoration site is functioning, to coordinate projects and efforts for consistent and successful restoration, and to evaluate the ecological health of specific coastal habitats both before and after project completion (Galatowitsch et al. 1998). The following habitats have been selected for discussion in this manual: water column, rock bottom, coral reefs, oyster reefs, soft bottom, kelp and other macroalgae, rocky shoreline, soft shoreline, submerged aquatic vegetation, marshes, mangrove swamps, deepwater swamps, and riverine forests. The classification of habitats used in this document is generally based on that of Cowardin et al. (1979) in their Classification of Wetlands and Deepwater Habitats of the United States, as called for in the ERA Estuary Habitat Restoration Strategy. This manual is not intended to be a restoration monitoring “cookbook” that provides templates of monitoring plans for specific habitats. The interdependence of a large number of site-specific factors causes habitat types to vary in physical and biological structure within and between regions and geographic locations (Kusler and Kentula 1990). Monitoring approaches used should be tailored to these differences. However, even with the diversity of habitats that may need to be restored and the extreme geographic range across which these habitats occur, there are consistent principles and approaches that form a common basis for effective monitoring. Volume One, titled A Framework for Monitoring Plans under the Estuaries and Clean Waters Act of 2000, begins with definitions and background information. Topics such as restoration, restoration monitoring, estuaries, and the role of socioeconomics in restoration are discussed. In addition, the habitats selected for discussion in this manual are briefly described. (PDF contains 116 pages)

Science-based restoration monitoring of coastal habitats, Volume Two: Tools for monitoring coastal habitats

Healthy coastal habitats are not only important ecologically; they also support healthy coastal communities and improve the quality of people’s lives. Despite their many benefits and values, coastal habitats have been systematically modified, degraded, and destroyed throughout the United States and its protectorates beginning with European colonization in the 1600’s (Dahl 1990). As a result, many coastal habitats around the United States are in desperate need of restoration. The monitoring of restoration projects, the focus of this document, is necessary to ensure that restoration efforts are successful, to further the science, and to increase the efficiency of future restoration efforts.

Self-recruiting species (SRS) from farmer managed aquatic systems: are they important to the livelihoods of rural communities?

Why are SRS important? The answer is to be found in this well-structured survey under: SRS as food source; SRS as additional source of cash income; Role of SRS in social capital. An analysis of the threats to SRS and the potential management options for farmer managed aquatic systems are also available in this survey along with the following definition of SRS: SRS are defined as aquatic animals that can be harvested from farmer managed aquatic systems without regular stocking. (PDF contains 4 pages)

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.)

Automated, objective texture segmentation of multibeam echosounder data - Seafloor survey and substrate maps from James Island to Ozette Lake, Washington Outer Coast

Without knowledge of basic seafloor characteristics, the ability to address any number of critical marine and/or coastal management issues is diminished. For example, management and conservation of essential fish habitat (EFH), a requirement mandated by federally guided fishery management plans (FMPs), requires among other things a description of habitats for federally managed species. Although the list of attributes important to habitat are numerous, the ability to efficiently and effectively describe many, and especially at the scales required, does not exist with the tools currently available. However, several characteristics of seafloor morphology are readily obtainable at multiple scales and can serve as useful descriptors of habitat. Recent advancements in acoustic technology, such as multibeam echosounding (MBES), can provide remote indication of surficial sediment properties such as texture, hardness, or roughness, and further permit highly detailed renderings of seafloor morphology. With acoustic-based surveys providing a relatively efficient method for data acquisition, there exists a need for efficient and reproducible automated segmentation routines to process the data. Using MBES data collected by the Olympic Coast National Marine Sanctuary (OCNMS), and through a contracted seafloor survey, we expanded on the techniques of Cutter et al. (2003) to describe an objective repeatable process that uses parameterized local Fourier histogram (LFH) texture features to automate segmentation of surficial sediments from acoustic imagery using a maximum likelihood decision rule. Sonar signatures and classification performance were evaluated using video imagery obtained from a towed camera sled. Segmented raster images were converted to polygon features and attributed using a hierarchical deep-water marine benthic classification scheme (Greene et al. 1999) for use in a geographical information system (GIS). (PDF contains 41 pages.)

Developing alternatives for optimal representation of seafloor habitats and associated communities in Stellwagen Bank National Marine Sanctuary

The implementation of various types of marine protected areas is one of several management tools available for conserving representative examples of the biological diversity within marine ecosystems in general and National Marine Sanctuaries in particular. However, deciding where and how many sites to establish within a given area is frequently hampered by incomplete knowledge of the distribution of organisms and an understanding of the potential tradeoffs that would allow planners to address frequently competing interests in an objective manner. Fortunately, this is beginning to change. Recent studies on the continental shelf of the northeastern United States suggest that substrate and water mass characteristics are highly correlated with the composition of benthic communities and may therefore, serve as proxies for the distribution of biological biodiversity. A detailed geo-referenced interpretative map of major sediment types within Stellwagen Bank National Marine Sanctuary (SBNMS) has recently been developed, and computer-aided decision support tools have reached new levels of sophistication. We demonstrate the use of simulated annealing, a type of mathematical optimization, to identify suites of potential conservation sites within SBNMS that equally represent 1) all major sediment types and 2) derived habitat types based on both sediment and depth in the smallest amount of space. The Sanctuary was divided into 3610 0.5 min2 sampling units. Simulations incorporated constraints on the physical dispersion of sampling units to varying degrees such that solutions included between one and four site clusters. Target representation goals were set at 5, 10, 15, 20, and 25 percent of each sediment type, and 10 and 20 percent of each habitat type. Simulations consisted of 100 runs, from which we identified the best solution (i.e., smallest total area) and four nearoptimal alternates. We also plotted total instances in which each sampling unit occurred in solution sets of the 100 runs as a means of gauging the variety of spatial configurations available under each scenario. Results suggested that the total combined area needed to represent each of the sediment types in equal proportions was equal to the percent representation level sought. Slightly larger areas were required to represent all habitat types at the same representation levels. Total boundary length increased in direct proportion to the number of sites at all levels of representation for simulations involving sediment and habitat classes, but increased more rapidly with number of sites at higher representation levels. There were a large number of alternate spatial configurations at all representation levels, although generally fewer among one and two versus three- and four-site solutions. These differences were less pronounced among simulations targeting habitat representation, suggesting that a similar degree of flexibility is inherent in the spatial arrangement of potential protected area systems containing one versus several sites for similar levels of habitat representation. We attribute these results to the distribution of sediment and depth zones within the Sanctuary, and to the fact that even levels of representation were sought in each scenario. (PDF contains 33 pages.)

A review of marine zones in the Monterey Bay National Marine Sanctuary

This report reviews marine zoning in the Monterey Bay National Marine Sanctuary (MBNMS). The 72 zoned areas in the MBNMS are of 13 different zone types. Each marine zone type has associated regulations that restrict or promote specific activities. For example, recreational activities such as boating, fishing, tidepooling, snorkeling, and SCUBA diving are limited in some zones. Scientific research is allowed at all sites, with appropriate permits, and is specifically promoted in a few sites. In addition, motorized personal watercraft use, dredge material disposal, large vessel traffic, jade collection, and aircraft overflight are allowed only in specific zones. The effectiveness of the marine zoning in the MBNMS is difficult to determine for two reasons. Firstly, many of the zones lack a clearly stated purpose or have confusing regulations. Secondly, the majority of the zones have not been evaluated formally by the managing agencies. Of the zones that have been evaluated, such as Dredge Material Disposal zones, Big Creek MRPA Ecological Reserve, and Pt. Lobos State/Ecological Reserve, the majority appear to be achieving their mandated purpose to some extent. Many of the zones in the MBNMS fall under the title "marine reserve." Marine reserves have recently received significant attention internationally, nationally, and in California due to their potential for: improving the status of exploited species; protecting marine habitats and ecosystems from degradation; facilitating scientific research and fisheries management; and increasing ecotourism. However, reserves must be well designed and managed to reach this potential. A well designed and managed reserve will have clearly defined goals, scientifically-based design, proper enforcement of regulations, rigorous evaluation of the reserve's effectiveness, and adaptive management. Based on these criteria, the majority of the marine reserves in California are not well designed or managed. However, the State of California has recognized this problem and is in the process of re-evaluating the California system of marine managed areas. (PDF contains 137 pages.)

Detecting fish aggregations from reef habitats mapped with high resolution side scan sonar imagery

As part of a multibeam and side scan sonar (SSS) benthic survey of the Marine Conservation District (MCD) south of St. Thomas, USVI and the seasonal closed areas in St. Croix—Lang Bank (LB) for red hind (Epinephelus guttatus) and the Mutton Snapper (MS) (Lutjanus analis) area—we extracted signals from water column targets that represent individual and aggregated fish over various benthic habitats encountered in the SSS imagery. The survey covered a total of 18 km2 throughout the federal jurisdiction fishery management areas. The complementary set of 28 habitat classification digital maps covered a total of 5,462.3 ha; MCDW (West) accounted for 45% of that area, and MCDE (East) 26%, LB 17%, and MS the remaining 13%. With the exception of MS, corals and gorgonians on consolidated habitats were significantly more abundant than submerged aquatic vegetation (SAV) on unconsolidated sediments or unconsolidated sediments. Continuous coral habitat was the most abundant consolidated habitat for both MCDW and MCDE (41% and 43% respectively). Consolidated habitats in LB and MS predominantly consisted of gorgonian plain habitat with 95% and 83% respectively. Coral limestone habitat was more abundant than coral patch habitat; it was found near the shelf break in MS, MCDW, and MCDE. Coral limestone and coral patch habitats only covered LB minimally. The high spatial resolution (0.15 m) of the acquired imagery allowed the detection of differing fish aggregation (FA) types. The largest FA densities were located at MCDW and MCDE over coral communities that occupy up to 70% of the bottom cover. Counts of unidentified swimming objects (USOs), likely representing individual fish, were similar among locations and occurred primarily over sand and shelf edge areas. Fish aggregation school sizes were significantly smaller at MS than the other three locations (MCDW, MCDE, and LB). This study shows the advantages of utilizing SSS in determining fish distributions and density.

Ichthyoplankton Adjacent to Live-Bottom Habitats in Onslow Bay, North Carolina

The abundance and distribution of ichthyoplankton adjacent to live-bottom habitats (rock outcroppings containing rich, sessile invertebrate communities and many species of tropical and subtropical fishes) in open-shelf waters « 55-m isobath) in Onslow Bay, North Carolina, were investigated. Larvae of reef-associated genera, especially the economically important subtropical and tropical members of the families Haemulidae (Haemulon), Lutjanidae (Lutjanus and Rltomboplites), Serranidae (Mycteroperca and Epinephelus), and Sparidae (Calamus and Pagrus) were targeted. Larvae representing 40 families were collected in neuston tows. Commonly collected reef-associated families were Balistidae, Blenniidae (dominated by the reef-associated Parablennius marmoreus) , Mullidae, and Gobiidae. Larvae representing 70 families were collected in subsurface tows. Reef-associated families commonly collected included Apogonidae, Balistidae, Gobiidae, Haemulidae, LutJanidae, Scaridae, and Serranidae. Larval Haemulon sp (p)., Lutjanus sp(p)., and Rltomboplites aurorubens were commonly collected and thus it is likely that these taxa spawn in Onslow Bay and recruit to live-bottom sites within the area. Other families of fishes commonly collected but generally not considered reef-associated included Bothidae, Callionymidae, Carangidae, Clupeidae, Engraulidae, and Ophidiidae. Estuarine-dependent species (e.g. the clupeid Brevoortia tyrannus and the sciaenids Leiostomus xanthurus and Micropogonias undulatus) were an important component of the ichthyoplankton during late fall and winter. The frequent occurrence of larvae from oceanic species (e.g. gonostomatids and myctophids) indicated that Gulf Stream waters had intruded onto the shelf, transporting these larvae to open-shelf waters off North Carolina.(PDF file containes 36 pages.)

A temporal and spatial study of invertebrate communities associated with hard-bottom habitats in the South Atlantic Bight

Species composition, biomass, density, and diversity of benthic invertebrates from six bard-bottom areas were evaluated. Seasonal collections using a dredge, trawl, and suction and grab samplers yielded 432, 525, and 845 taxa, respectively. Based on collections wltb the different gear types, species composition of invertebrates was found to change bathymetrically. Inner- and mlddle-shelf sites were more similar to each other in terms of invertebrate species composition than they were to outer-shelf sites, regardless of season. Sites on the inner and outer shelf were grouped according to latitude; however, results suggest that depth is apparently a more important determinant of invertebrate species composition than either season or latitude. Sponges generally dominated dredge and trawl collections in terms of biomass. Generally, cnidarians, bryozoans, and sponges dominated at sites In terms of number of taxa collected. The most abundant smaller macrofauna collected in suction and grab samples were polychaetes, amphipods, and mollusks. Densities of the numerically dominant species changed botb seasonally and bathymetrically, with very few of these species restricted to a specific bathymetrlc zone. The high diversity of invertebrates from hard-bottom sites is attributed to the large number of rare species. No consistent seasonal changes in diversity or number of species were noted for individual stations or depth zones. In addition, H and its components showed no definite patterns related to depth or latitude. However, more species were collected at middle-shelf sites than at inner- or outer-shelf sites, which may be related to more stable bottom temperature or greater habitat complexity in that area. (PDF file contains 110 pages.)

The lowland dry zone of Sri Lanka: site for study of aquaculture development within farmer-managed irrigation systems and methodology for participatory situation appraisal

The aims of this paper are twofold. Firstly to characterise rural poverty and to give a broad overview of the agro-ecological, climatic and socio-economic conditions in Sri Lanka which shape poverty. Secondly to present the methodology employed to screen suitable field research areas and the techniques subsequently used to carry out Rapid Rural Appraisal in two upper-watersheds villages. Also presented are details of a concurrent stakeholder analysis that aimed to investigate the capacity of secondary stakeholders to promote sustainable aquatic resource development and to invite their participation in the formulation of a participatory research agenda.[PDF contains 58 pages]

The nature of small-scale farmer managed irrigation systems in North West Province, Sri Lanka and potential for aquaculture

RRAs were carried out in two Small Tank Cascade systems (STCs) of North West Province, Sri Lanka (less than 1000 ha total watershed area). A total of 21 tanks and 7 villages were investigated with primary emphasis on two upper watershed communities. The two systems differ primarily in their resource base; namely rainfall, natural forests and proximity to large scale perennial irrigation resources. [PDF contains 86 pages]

Optical Remote Sensing of Coastal Habitats, Moss Landing, California, 9-11 January, 2006: workshop proceedings

The Alliance for Coastal Technologies (ACT) Workshop on Optical Remote Sensing of Coastal Habitats was convened January 9-11, 2006 at Moss Landing Marine Laboratories in Moss Landing, California, sponsored by the ACT West Coast regional partnership comprised of the Moss Landing Marine Laboratories (MLML) and the Monterey Bay Aquarium Research Institute (MBARI). The "Optical Remote Sensing of Coastal Habitats" (ORS) Workshop completes ACT'S Remote Sensing Technology series by building upon the success of ACT'S West Coast Regional Partner Workshop "Acoustic Remote Sensing Technologies for Coastal Imaging and Resource Assessment" (ACT 04-07). Drs. Paul Bissett of the Florida Environmental Research Institute (FERI) and Scott McClean of Satlantic, Inc. were the ORS workshop co-chairs. Invited participants were selected to provide a uniform representation of the academic researchers, private sector product developers, and existing and potential data product users from the resource management community to enable development of broad consensus opinions on the role of ORS technologies in coastal resource assessment and management. The workshop was organized to examine the current state of multi- and hyper-spectral imaging technologies with the intent to assess the current limits on their routine application for habitat classification and resource monitoring of coastal watersheds, nearshore shallow water environments, and adjacent optically deep waters. Breakout discussions focused on the capabilities, advantages ,and limitations of the different technologies (e.g., spectral & spatial resolution), as well as practical issues related to instrument and platform availability, reliability, hardware, software, and technical skill levels required to exploit the data products generated by these instruments. Specifically, the participants were charged to address the following: (1) Identify the types of ORS data products currently used for coastal resource assessment and how they can assist coastal managers in fulfilling their regulatory and management responsibilities; (2) Identify barriers and challenges to the application of ORS technologies in management and research activities; (3) Recommend a series of community actions to overcome identified barriers and challenges. Plenary presentations by Drs. Curtiss 0. Davis (Oregon State University) and Stephan Lataille (ITRES Research, Ltd.) provided background summaries on the varieties of ORS technologies available, deployment platform options, and tradeoffs for application of ORS data products with specific applications to the assessment of coastal zone water quality and habitat characterization. Dr. Jim Aiken (CASIX) described how multiscale ground-truth measurements were essential for developing robust assessment of modeled biogeochemical interpretations derived from optically based earth observation data sets. While continuing improvements in sensor spectral resolution, signal to noise and dynamic range coupled with sensor-integrated GPS, improved processing algorithms for georectification, and atmospheric correction have made ORS data products invaluable synoptic tools for oceanographic research, their adoption as management tools has lagged. Seth Blitch (Apalachicola National Estuarine Research Reserve) described the obvious needs for, yet substantial challenges hindering the adoption of advanced spectroscopic imaging data products to supplement the current dominance of digital ortho-quad imagery by the resource management community, especially when they impinge on regulatory issues. (pdf contains 32 pages)