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.)

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.)

Patterns of succession in benthic infaunal communities following dredging and dredged material disposal in Monterey Bay

This report is the final product of a two-year study conducted for the Office, Chief of Engineers, by the Moss Landing Marine Laboratories, Moss Landing, California, under Contract No. DACW39-74-C-OI51 with the Environmental Effects Laboratory (EEL), U. S. Army Engineer Waterways Experiment Station (WES), Yicksburg, Mississippi. (PDF contains 192 pages)

Benthic Macrofauna of the New York Bight, 1979-89

The benthic macrofauna of the New York Bight has been monitored extensively, primarily to determine trends over space and time in biological effects of waste inputs. In the present study, from 44 to 48 stations were sampled each summer from 1980-1985. Data from other Bight benthic studies are included to· extend the temporal coverage from 1979 to 1989. Numbers of species and amphipods per sample, taken as relatively sensitive indicators of environmental stress, showed consistent spatial patterns. Lowest values were found in the Christiaensen Basin and other inshore areas, and numbers increased toward the outermost shelf and Hudson Shelf Valley stations. There were statistically significant decreases in species and amphipods at most stations from 1980 to 1985. (Preliminary data from a more recent study suggest numbers of species increased again between 1986 and 1989.) Cluster analysis of 1980-85 data indicated several distinct assemblages-sewage sludge dumpsite, sludge accumulation area, inner Shelf Valley, outer Shelf Valley, outer shelf-with little change over time. The "enriched" and "highly altered" assemblages in the Basin appear similar to those reported since sampling began there in 1968. No consistently defaunated areas have been found in any sampling programs over the past 20 years. On a gross level, therefore, recent faunal responses to any environmental changes are not evident, but the more sensitive measures used, i.e. numbers of species and amphipods, do indicate widespread recent effects. Causes of the faunal changes are not obvious; some possibilities, including increasing effects of sewage sludge or other waste inputs, natural factors, and sampling artifacts, are discussed. (PDF file contains 54 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.)

Effects of beach remourishment on the benthic macrofauna and the fishes of the nearshore zone at Sebastian Inlet State Recreation Area

Approximately 100,000 cubic yards of sand was transported to the ocean beach to renourish the eroded beach front during the period December 1985 through May 1986. The ocean beach at Sebastian Inlet SRA was previously studied in a project examining the benthic macrofauna and the fishes of the nearshore zone during 1981-1982 (Allenbaugh, 1984; Peters, 1984; Nelson, unpublished). In view of the existing data, the US Army Corps of Engineers provided funding to study the effects of the beach renourishment activities at Sebastian Inlet SRA on the benthic macrofauna and the fishes of the nearshore zone. This is the report on the results of this study.

Assessing the quality of water quality assessments: An analytical quality control protocol for benthic diatoms

In this paper, the background to the development of an analytical quality control procedure for the Trophic Diatom Index (TDI) is explained, highlighting some of the statistical and taxonomic problems encountered, and going on to demonstrate how the system works in practice. Most diatom-based pollution indices, including the TDI, use changes in the relative proportions of different taxa to indicate changing environmental conditions. The techniques involved are therefore much simpler than those involved in many studies of phytoplankton, for example, where absolute numbers are required.

Description of sampling stations, methods of benthic sampling and biological water quality assessment; with some consideration of the influence of sample variation on the assessment values obtained

The first bilateral study of methods of biological sampling and biological methods of water quality assessment took place during June 1977 on selected sampling sites in the catchment of the River Trent (UK). The study was arranged in accordance with the protocol established by the joint working group responsible for the Anglo-Soviet Environmental Agreement. The main purpose of the bilateral study in Nottingham was for some of the methods of sampling and biological assessment used by UK biologists to be demonstrated to their Soviet counterparts and for the Soviet biologists to have the opportunity to test these methods at first hand in order to judge the potential of any of these methods for use within the Soviet Union. This paper is concerned with the nine river stations in the Trent catchment.

A bibliography of samplers for benthic invertebrates

This annotated bibliography covers literature to the end of November 1977, and includes references to samplers that could be used for the rapid removal of benthic invertebrates from natural substrata of rivers and streams. Marine samplers which have been, or could be, used in freshwater. Coverage of Russian literature is incomplete, although a selection of recent and important references are included. The references are arranged under the following headings, Reviews; Nets and quadrat samplers; Scoops, shovels and dredges; Grabs; Corers; Suction and air-lift samplers; Electroshocking samplers; Efficiencies and comparisons; and Samplers from catalogues. There is an index to samplers (by the common name) and an author index.

The effects of stress on benthic algal communities

The effects of stress on both microalgal and macroalgal communities are considered. On one hand the contrasting approaches of studies of these two communities reflect intrinsic differences in plant size, longevity and ease of handling. On the other hand they reveal that biological monitoring of the potentially deleterious effects of man's activities has focused largely on freshwater environments in which macroalgae only occasionally dominate. Large conspicuous plants can be readily investigated as individuals, whereas it is virtually impossible to trace effects of stress on an individual cell of a vegetatively-reproducing microalga; a population approach is almost inevitably necessary. However, rapid turnover rates, a spectrum of ecological characteristics distributed between many taxa, and the potential for statistical analysis, have facilitated the use of microalgae in environmental impact studies. Failure to extend such investigations into marine systems rests as much on man's ability to ignore environmental deterioration until it affects his quality of life as on the visual dominance of seaweeds around our coasts. However, large gaps remain in our knowledge of both large and small algae; some reported community changes over time are suspect, and the causes of even blatant changes are not always apparent.

A supplement to a bibliography of samplers for benthic invertebrates

A supplement to the earlier bibliography compiled by Elliott and Tullett 1978 (FBA Occas. Publ. No. 4) covering literature from December 1977 - December 1982 on samplers that could be used for the rapid removal of benthic intertebrates from the natural substrata of rivers and streams. In addition it includes papers on marine samplers that have been or could be used in freshwater.

Effects of a large fishing closure on benthic communities in the western Gulf of Maine: recovery from the effects of gillnets and otter trawls

The recovery of benthic communities inside the western Gulf of Maine fishing closure area was evaluated by comparing invertebrate assemblages at sites inside and outside of the closure four to six years after the closure was established. The major restriction imposed by the closure was a year-round prohibition of bottom gillnets and otter trawls. A total of 163 seafloor sites (~half inside and half outside the closure) within a 515-km2 study area were sampled with some combination of Shipek grab, Wildco box corer, or underwater video. Bottom types ranged from mud (silt and clay) to boulders, and the effects of the closure on univariate measures (total density, biomass, taxonomic richness) of benthos varied widely among sediment types. For sites with predominantly mud sediments, there were mixed effects on inside and outside infauna and no effect on epifauna. For sites with mainly sand sediments, there were higher density, biomass, and taxonomic richness for infauna inside the closure, but no significant effects on epifauna. For sites dominated by gravel (which included boulders in some areas), there were no effects on infauna but strong effects on epifaunal density and taxonomic richness. For fishing gear, the data indicated that infauna recovered in sand from the impacts of otter trawls operated inside the closure but that they did not recover in mud, and that epifauna recovered on gravel bottoms from the impact of gillnets used inside the closure. The magnitudes of impact and recovery, however, cannot be inferred directly from our data because of a confounding factor of different fishing intensities outside the closure for a direct comparison of preclosure and postclosure data. The overall negative impact of trawls is likely underestimated by our data, whereas the negative impact of gillnets is likely overestimated.

Changes in a benthic megafaunal community due to disturbance from bottom fishing and the establishment of a fishery closure

Trawling and dredging on Georges Bank (northwest Atlantic Ocean) have altered the cover of colonial epifauna, as surveyed through in situ photography. A total of 454 photographs were analyzed from areas with gravel substrate between 1994 and 2000 at depths of 40–50 m and 80–90 m. The cover of hydroids, bushy bryozoans, sponges, and tubeworms was generally higher at sites undisturbed by fishing than at sites classified as disturbed. The magnitude and significance of this effect depended on depth and year. Encrusting bryozoans were the only type of colonial epifauna positively affected by bottom fishing. Species richness of noncolonial epifauna declined with increased bottom fishing, but Simpson’s index of diversity typically peaked at intermediate levels of habitat disturbance. Species that were more abundant at undisturbed sites possessed characteristics that made them vulnerable to bottom fishing. These characteristics include emergent growth forms, soft body parts, low motility, use of complex microhabitats, long life spans, slow growth, and larval dispersal over short distances. After the prohibition of bottom fishing at one site, both colonial and noncolonial species increased in abundance. Populations of most taxa took two years or more to increase after the fishing closure. This finding indicates that bottom fishing needs to be reduced to infrequent intervals to sustain the benthic species composition of Georges Bank at a high level of biodiversity and abundance.

Whole-gear efficiency of a benthic survey trawl for flatfish

Whole-gear efficiency (the proportion of fish passing between the otter doors of a bottom trawl that are subsequently captured) was estimated from data collected during experiments to measure the herding efficiency of bridles and doors, the capture efficiency of the net, and the length of the bridles sufficiently close to the seafloor to elicit a herding response. The experiments were focused on four species of flatfish: arrowtooth flounder (Atheresthes stomias), flathead sole (Hippoglossoides elassodon), rex sole (Glyptocephalus zachirus), and Dover sole (Microstomus pacificus). Whole-gear efficiency varied with fish length and reached maximum values between 40% and 50% for arrowtooth flounder, flathead sole, and rex sole. For Dover sole, however, whole-gear efficiency declined from a maximum of 33% over the length range sampled. Such efficiency estimates can be used to determine catchability, which, in turn, can be used to improve the accuracy of stock assessment models when the time series of a survey is short.