Document Type

Research Data

Publication Date

2010

Keywords

benthic community, sediments, Peconic Bays Estuary NY, GIS data

Abstract

Benthic habitat maps of the estuary seafloor can increase our knowledge of the range and variability in benthic habitats, assist managers in their efforts to protect and/or restore commercially and recreationally important finfish and shellfish, link land usage (e.g. developed vs. undeveloped areas) and water quality data to benthic habitat quality, and make it possible to utilize faunal data as a long-term indicator of the overall “health” of the estuary. This study combined high-resolution sonar surveys with physical and faunal characteristics at point locations in different seafloor areas of the Peconic Bays Estuary. Sonar mapping used multibeam swath bathymetry to generate backscatter images that allowed visual classification of the seabed into provinces. Samples for sediment and macrofauna were collected within each province to provide "ground truth" for the sonar maps. Results suggest that the acoustic provinces identified represent areas of similar faunal and sedimentary characteristics. In addition, analysis of species richness of the combined Phase I-III data sets indicated that no west to east spatial gradient in species richness exists in the Peconics.

Comments

This .zip file contains ground truth results for the Phase I-III Peconic Bays Estuary benthic mapping project. Sonar multibeam mapping, sediment, and benthic macrofauna were collected in three stages (Phases I-III) with support from various funding sources. Final reports for each phase are in the Report folder.

Important note: Because of the large size of the sonar data files, the GIS might be slow opening and/or moving to a different bookmarked location. This may also happen when trying to open the main geodatabase (PeconicsBenthic.gdb).

The principal GIS project file is PeconicsPI-III.mxd in ArcMap and PeconicsPI-III.aprx in ArcGIS Pro. These project files contain data layers for all Phase I-III data (except for ½ phi grain size data which are saved in GrainSizeInHalfPhi.xls). All data layers are loaded from a geodatabase called PeconicsBenthic.gdb.

Provinces feature classes attempt to subdivide areas into homogeneous bottom types based on a visual interpretation of backscatter acoustic data. Two feature classes contain provinces. The one listed as "GeophysicalProvinces_PI-III_Seperate" contains the province polygons generated during each phase of the study. The one listed as "GeophysicalProvinces_PI-IIIMerged" contains the final set of provinces after adjusting polygons that overlapped between phases and after merging adjacent polygons if backscatter properties were continuous across province boundaries. Thus, for example, SR_K from Phase II and LP_J from Phase III were merged into a single province. Similarly, O_I from Phase I and OD_B from Phase II were merged. Please see the attribute table for fields that list the names of the original provinces.

Note that merged provinces have sampling stations from multiple phases within them. We did not alter the station ID of any sampling location. Since the three phases of the study were conducted in different years, please remember that combining faunal data from different phases could be problematic because of natural interannual variability.

The following is a breakdown of the contents of each folder:

DataTables - Contains files with field, sediment, and faunal summary data in spreadsheet (Excel) format. Phase I, II, and III data are included. Print areas in Excel spreadsheets are set to print only Phase III results; adjust "File", "Print Area", "Adjust Print Area" to change the setting.

Geodatabase - This folder contains the PeconicsBenthic.gdb geodatabase with data tables, all feature classes, and raster files loaded into it. It is an ArcGIS file geodatabase. The complete set of GIS data from Phase I, II and III are present in tables, feature classes, raster files, and raster mosaics.

PeconicsCharts - This folder contains raster files of two Peconics charts. These were also loaded into the geodatabase as raster files.

Report - Contains .pdf files of Phase I, II, and III reports.

Shapefiles - Contains shapefiles of the shoreline and station locations. These were loaded into the geodatabase.

SonarData - This folder has georeferenced raster files of each of the regions. These were loaded into the geodatabase as a mosaic dataset.

GPMessages and DefaultToolBox.atbx were generated by ArcGIS Pro internally.

A Brief Summary of Sampling Methods

Sampling Locations

Stratification of the sonar maps into acoustic provinces was carried out by visual examination of multibeam backscatter data. In this process, backscatter was taken as a proxy for bottom type, and our goal was to subdivide or stratify each region into separate provinces, each consisting of a homogeneous bottom type. Sampling stations were randomly positioned within each acoustic province, although we did modify target positions such that sampling stations were at least 100 meters from any boundary or any other station if possible. It should be noted that letters associated with acoustic provinces are for identification purposes only and were arbitrarily assigned, i.e., there is no correspondence between provinces labeled "A" among regions.

Fauna and Sediment sampling

Fauna and sediment sampling was conducted aboard the R/V Pritchard operated by Stony Brook University. Subsamples of sediments for organic content and grain size were drawn from each grab sample. The remaining sediment was washed through a 0.5 mm sieve for fauna. All material left on the sieve was preserved in 10% buffered formalin and stained with rose bengal. Fauna samples were rewashed in the lab and transferred to 70% ethanol before sorting and identification. Individual organisms were identified to species level whenever possible and the total for each taxon enumerated. Unless otherwise noted, all abundances are expressed as the number of individuals per sample (i.e., per 0.04 m2).

Sediment organic content was estimated by weight loss on ignition (LOI) when dry sediment samples were combusted at 450o C for at least 4 hours. Sediment grain-size analyses measured percent composition by weight of major size-fractions (gravel, sand, silt, clay), as well as the detailed grain-size distribution in ½ phi intervals. We used a combination of dry sieve, settling column, and sedigraph analyses for the gravel, sand, and silt-clay fractions, respectively. Samples were initially partitioned into three size-fractions by wet sieving with distilled water through a combination of 1 mm and 63 micron sieves. The >1 mm and 1 mm-63 micron fractions were placed in a drying oven at 60o C for at least 48 hours to obtain dry weights. Water containing the <63 micron fraction (silt-clay) was brought up to 1000ml total volume in a graduated cylinder, mixed thoroughly, and subsampled with a 20 ml pipette at a depth of 20 cm, 20 seconds after mixing (Folk 1964). Pipette samples were placed in a drying oven at 60o C for at least 48 hours to obtain dry weight estimates of the silt-clay fraction. The remaining water containing the <63 micron fraction (silt-clay) was reserved for later grain-size analysis in the sedigraph.

The detailed grain-size distribution of the >1 mm fraction was determined by dry sieving samples through a stack of sieves with the following sizes: 12.5 mm, 9.5 mm, 6.3 mm, 4.75 mm, 3.35 mm, 2 mm, 1.42 mm, and 1mm. Material remaining on each sieve was weighed.

The grain-size distribution of the 1 mm-63 micron fraction was determined by settling column analysis. The settling column consisted of a 193.5 cm tall PVC tube with an internal diameter of 15.2 cm filled with distilled water. Samples were introduced at the top of the column and a collecting pan connected to a balance registered weight as particles settled through the water. A computer connected to the balance recorded cumulative weight and elapsed time for each sample. Weight-time data were converted to sedimentation diameter using an empirical equation in Gibbs et al. (1971). A particle roughness correction suggested by Baba and Komar (1981) was also applied.

A Micromeritics SediGraph 5100 was used to analyze the <63 micron (silt-clay) fraction. Water containing the <63 micron fraction was centrifuged for approximately ten minutes. Water was then decanted from the sample, and the sedimented material was rewetted with a 0.5% Calgon solution to reduce coagulation of clay particles. Samples were run using standard techniques obtained from the manufacturer. As a final step in the sediment analysis, results from the dry sieve, settling column, and sedigraph analyses were combined, and grain-size distribution in ½ phi intervals was obtained by linear interpolation. Mean grain-size and sorting (standard deviation) measures were computed from the cumulative distribution.

Baba, J. and P.D. Komar 1981. Measurements and analysis of settling velocities of natural quartz sand grains. J. Sed. Petrol. 51: 631-640.

Folk, R.L. 1964. Petrology of Sedimentary Rocks. Hemphill Pub. Co., Austin, Texas.

Gibbs, R.J., M.D. Matthews, and D.A. Link. 1971. The relationship between sphere size and settling velocity. J. Sed. Petrol. 41: 7-18.

Creative Commons License

Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License
This work is licensed under a Creative Commons Attribution-Noncommercial-No Derivative Works 3.0 License.

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