Methods

The three major types of geophysical data acquired during the Hudson River Benthic Mapping Program were multibeam bathymetry, side scan sonar, and Chirp sub-bottom seismic data. These acoustic methods were supplemented by an extensive program of cores and grab sampling. A shallow-water geophysics program comparing Chirp sub-bottom seismic profiles and ground-penetrating radar was also conducted.

(1) Multibeam Bathymetry: Bathymetry provides basic information on riverbed morphology including the variations in channel structure that control sediment transport through the estuarine system (Hughes Clarke, Mayer, and Wells, 1996; Gardner et al., 1998; Flood, 2002; Fig. 5.2). Multi-beam bathymetry can be presented as contoured maps (usually with 1 m contours) or as sun-illuminated maps that show smaller-scale relief as it would be revealed by shining a synthetic sun across the riverbed. Multibeam bathymetry provides high-resolution imaging of the riverbed and shows the locations and dimensions of riverbed features, including rock outcrops and sediment bedforms (Fig. 5.3) as well as smaller features such as anchor drag scars, cable crossings, and other anthropogenic features.

We used the Simrad EM 3000 multibeam system to map with 100 percent coverage the portion of the river deeper than 5 m (ca. 15 feet) where this technique is most appropriate. The EM 3000 system transmits at 300 kHz in a fan-shaped pattern perpendicular to the survey track imaging a band or swath of the riverbed about four times water depth. Bottom depths are measured at up to 125 points across the swath, each beam nominally 1.5° wide and spaced 0.9° apart. The maximum ping rate is 25 times a second, decreasing to 13 times a second as water depth increases to 10 m. In water depths of 10 m and at a ship speed of 8 knots (kts) (4 m/s), depth measurements are acquired at about 30 cm intervals along and across track with a vertical accuracy of 5-10 cm. The amplitude of the reflected sound (which is converted into backscatter) is also measured at these points.

Multibeam bathymetry requires accurate navigation and orientation information. This information was provided by a TSS POS/MV model 320 v2 which uses three accelerometers and three gyroscopes to correct the multibeam data for heading, roll, pitch, and heave, and includes a differential GPS system (supplemented by inertial navigation; also part of the POS/MV system) to determine position to about 1 m. The real time differential GPS corrections were provided by Omnistar because we were generally out of range of the U.S. Coast Guard (USCG) station at Sandy Hook, New Jersey that transmits differential corrections. Other system components include: a separate display to guide the boat along precise survey lines; a CTD for determining the sound velocity profile; tide gauges for determining local sea level during a survey; Sun and SGI computers for logging, storing, processing, and displaying the data; and multibeam processing software. Near-final survey products can be generated within a short time after the survey is completed, and the resulting products generally meet hydrographic mapping standards. Seabed elevations were calculated relative to the NAVD88 geoid through the

Figure 5.3. Upper: Multibeam backscatter data from the channel of the Hudson River (lighter areas have higher backscatter). There is azone of higher backscatter from the center of the channel axis with variable (and generally lower) backscatter both east and west). North is up, bar shows scale. Lower: Multibeam bathymetry (viewed as sun-illuminated bathymetry) for the same area as the upper image. The channel axis (area of higher backscatter) is generally smooth but with some drag marks. Sediment waves of a variety of scales are imaged both east and west of the channel axis. Also visible are at least two debris deposits, several obstacles and one possible sunken barge. The trough on the eastern edge of the image is part of a dredged channel to the former GM plant in Tarrytown. The backscatter image shows that this is a region of low backscatter.

Figure 5.4. Example side-scan sonar record from the Hudson River. The ship track is in the center, and areas of higher backscatter are darker. This record shows the river bank (observed from underwater) on the right-hand side.

use of tide gauges. The NAVD88 datum is about 30 cm below mean sea level in the Hudson River. The EM 3000 multibeam system was mounted on the R/V Onrust, a research vessel operated by the State University of New York at Stony Brook. The multibeam data was processed using the SwathEd software toolkit developed at the University of New Brunswick (http://www.omg.unb. ca/omg/research/swath_sonar_analysis_software. html).

(2) Side-scan Sonar and Multibeam Back-

scatter: Backscatter is related to the amplitude of an acoustic signal scattered off the riverbed back toward the sound transducer (Nitsche et al., 2001). As part of the Hudson River Benthic Mapping Project these data were collected both with a dual frequency sidescan sonar system and with the multibeam bathymetry system. Backscatter data are ideally suited for distinguishing among sediment types based on differing acoustic properties. Properties which can be distinguished include fine versus coarse grained sediments and hard versus soft bottom. Side-scan sonar systems are effective in all water depths, including in water shallower than 5 m where multibeam systems are not efficient, and can be used to map the shoreline from underwater.

For this study the side-scan sonar study was conducted from the R/V Walford operated by the New Jersey Marine Consortium. We used the Edge Tech DF-1000 dual frequency side-scan sonar simultaneously operating at 384 kHz and 100 kHz (Fig. 5.4). The 1.8 m side-scan sonar tow fish was deployed from a boom off the bow of the ship to place the system in quiet water for optimal instrument performance. The fish was towed at a depth of 2 m. The fish has transducers and receivers on either side of it, and the transducers transmit and receive both frequencies simultaneously. The acoustic signals are digitized in the tow fish and sent to the shipboard acquisition system through a high-speed digital uplink. A swath width of 200 m was used so that together a total width of 400 m of riverbed was surveyed with a single survey track. Full saturation of the riverbed for the side-scan sonar was accomplished in two directions using track lines with an approximate 85 m lateral spacing in a north-south orientation and with a 185 m lateral spacing east to west (Fig. 5.5). Orthogonal coverage was obtained in order to investigate the acoustic response of the riverbed as a function of look direction of the imaging sonar source.

The data acquisition topside unit was the ISIS system from Triton Elics. Side-scan data were time tagged in the ISIS system and recorded to hard disk. The Triton Elics system also recorded several auxiliary data streams including the ship's compass heading, single beam bathymetry and navigation. The Lamont - Doherty Earth Observatory (LDEO) ship compass was mounted in a magnetically quiet location amidships. The depth sounder used was the R/ V Walford's Raytheon DE-719C with a hull-mounted transducer. The transducer (Raytheon model 200TSHAD) operates at 208 kHz, with 8° beam width at half power points. The DE-719C system produces an analog

Figure 5.5. Side-scan sonar mosaic from Area 1 north of the Tappan Zee bridge. Note the east-west zones of high backscat-ter (old oyster reefs) and the zone of higher backscatter in the channel axis. The zone of lower backscatter in the channel appears to be a region of recent sediment deposition. The dots and triangles show the locations of core and grab samples, respectively.

Area 1 Tappan Zee

Figure 5.5. Side-scan sonar mosaic from Area 1 north of the Tappan Zee bridge. Note the east-west zones of high backscat-ter (old oyster reefs) and the zone of higher backscatter in the channel axis. The zone of lower backscatter in the channel appears to be a region of recent sediment deposition. The dots and triangles show the locations of core and grab samples, respectively.

Area 1 Tappan Zee

10 0 1 Kilometers output and was interfaced with an "Odom Digi-trace" system. The transducer was mounted amidships and a bar check was performed daily to determine system offsets. The navigation data recorded in the ISIS system were DGPS positions from an Ashtech Z-12 receiver. The Ashtech Z-12 is a 12 channel dual-frequency, geodetic caliber GPS receiver. The real time corrections were provided by Omnistar and received by a Trimble AgGPS-132 unit. The Trimble unit was selected to enable the flexibility of using either the satellite broadcast corrections or the real time correction transmitted by the U.S. Coast Guard. During operations, only the satellite broadcast corrections were used to prevent the introduction of offsets between the two corrections.

(3) Sub-bottom Chirp Data: Sub-bottom or seismic profiles are made by recording acoustic energy reflected from sediment layers and other structures beneath the riverbed (Carbotte et al., 2001). The sub-bottom profile data reveal the relative age relationships between different sedimentary layers and can be used to study the erosion and deposition of sediments through time (Fig. 5.6).

Sub-bottom data were acquired simultaneously with the side-scan sonar data using an EdgeTech X-Star topside data acquisition unit and SB 4_24 tow fish. This is a Chirp or swept frequency sonar system, which emits a broadband FM source pulse with low frequencies providing depth penetration into the sub-bottom and higher frequencies providing high vertical resolution. The X-Star acquisition unit controls all data transmission, recording, and signal processing including Analogue to Digital (A to D) conversion, compression of the FM pulse, and spherical divergence correction. The recorded signal is the output of the correlation filter used for pulse compression and is stored in SEG-Y format. Data were acquired at a transmission rate of 5-6 pings s-1. At survey speeds of 5 knots these transmission rates provide one trace for each 0.83 m of ship motion. Transmit pulse length was 10 m s-1. Pulse power was set at 50-60 percent of maximum available output in order to avoid ringing and generation of cross-talk interference with the side-scan sonar data. The SB 4_24 tow vehicle offers the ability to transmit a variety of pulses with a frequency range from 4 to 24 kHz. After

Figure 5.6. Example of Chirp sub-bottom profiles from north of the Tappan Zee Bridge. The upper profile shows a buried oyster bed (the high-amplitude sub-bottom layer on the left-hand side of the profile) as well as the unconformity produced where sediments deposited in the channel lie on top of older channel margin sediments. In the lower profile the oyster bed is at the sediment surface in some places. The identifications of the surficial and buried oyster beds have been confirmed by sampling.

Figure 5.6. Example of Chirp sub-bottom profiles from north of the Tappan Zee Bridge. The upper profile shows a buried oyster bed (the high-amplitude sub-bottom layer on the left-hand side of the profile) as well as the unconformity produced where sediments deposited in the channel lie on top of older channel margin sediments. In the lower profile the oyster bed is at the sediment surface in some places. The identifications of the surficial and buried oyster beds have been confirmed by sampling.

comparison of data quality obtained with the range of pulse options, we chose the lowest frequency sweep pulse (4 to 16 KHz) to obtain maximum possible penetration with this fish.

All processing was carried out using a combination of in-house code for reading the raw data files and the Seismic Unix package maintained by the Colorado School of Mines (Stockwell, 1999). The raw data were combined and scaled during initial processing to output the envelope amplitude for each sample. SEG-Y data files were written for each profile and a gif image was produced to allow immediate assessment of data quality. The Chirp fish was towed from the stern of the boat.

(4) Sediment Cores and Grab Samples: An extensive suite of core and grab samples were collected to ground truth the geophysical data sets (McHugh et al., 2001; Fig. 5.7). Cores provide a key link with the sub-bottom data and are useful in regions of fine grained sediments (Fig. 5.8). The grabs provide ground truth information in the coarser grained and bedrock portions of the river where the coring device could not penetrate. Both sediment cores and grab samples were recovered from the Tappan Zee, Newburgh Bay, and Kingston-Saugerties Areas (Areas 1, 2, and 3). Only grab samples were obtained from the Stockport Flats Area (Area 4) where sediment was sand dominated and poor core recovery was expected.

A gravity corer with a weight of 750 lbs. was used to penetrate the sediment. The core liners were 4 inches in inside diameter, providing more sediment volume for sampling than the traditional 2.5-inch diameter cores. The longest core recovered was 180 cm and the average length was 100 cm. The grab samples were collected with a Shipeck or Smith-MacIntyre grab. All cores and grab samples are being curated at the LDEO Core Laboratory under the support of the National Science Foundation. The processing of the cores included the following steps. Physical properties were measured on the unsplit cores including magnetic susceptibility, bulk density, and p-wave velocity. Cores were then split, photographed and described, grain size analysis of the core tops was carried out, and the cores were archived within the Lamont Core Archive. Grab samples were described and the presence of major components (e.g., slag: zebra mussels: oysters: and wood) was noted. For the grab samples, grain size analysis of the sand fraction was done by sonic sifter at MSRC, and, where present, the silt/clay fraction was analyzed by sedigraph at Wesleyan College.

Bottom photographs of the sediment-water interface were taken in Areas 1 to 3 using a sediment

Figure 5.7. Shipboard crews collecting grab samples (upper) and gravity cores (lower).

profile imagery (SPI) camera system (Rhoads and Germano, 1982; Iocco, Wilbur, and Diaz, 2000; Fig. 5.9). This system uses a prism inserted in the sediment to photograph a vertical profile or cross-section of about the upper 10 cm of the sediment to showsedimentaryfeatures such as ripples as well as any large animals living in the sediments or on the sediment surface. SPI images also show the depth of the oxygenated layer, the nature of and number of burrows, and sediment structures. SPI images were collected from the R/V Onrust through a collaborative program with the NOAA Coastal Services Center.

In 2001, we began a pilot study in which sediment samples from different bottom types in Areas 1 and 3 are being analyzed to determine invertebrate animal populations. This kind of interaction between biologists, geophysicists, geologists, and geochemists is important to be able to use our acoustic images to map benthic habitats.

Figure 5.8. Photographs of split cores from the Hudson River. The cores show finer layering (perhaps a layer every few years) plus some thicker layers. The thicker layers may represent storm deposits.
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