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BOTTOMS UP Benthic Observatory


Despite their widespread occurrence (Emery 1968), and the significance of ocean margin systems in the ocean carbon cycle (Wollast 1991), coarse-grained, sandy shelf environments have not been widely studied.While low organic carbon contents suggested little diagenetic importance of shelf sediments to earlier investigators, more recent studies have shown that permeable shelf sediments support high rates of mineralization and nutrient recycling (e.g., Jahnke et al. 2005).Key to the efficiency of this permeable sediment "bioreactor" is the occurrence of advective transport through the sands.Advective exchange allows the bed to filter particles from the water column (i.e., delivery of labile organic matter does not depend solely on particle sedimentation), and transports oxygen into surface sediments and products of organic matter remineralization out of the bed.This combination results in a high rate of organic matter cycling despite relatively low organic content.


Benthic exchange of solutes and particles in shelf environments is controlled by a diverse set of abiotic and biotic forcings and responses that operate over a wide range of characteristic time scales.Factors that can impose variability in benthic exchanges include wind-generated surface waves, bottom currents, bed roughness, light reaching the seafloor, temperature, and the abundance and activities of benthic microorganisms and macrofauna.In many cases it is likely the interactions of multiple factors that will result in significant impact on benthic exchange processes.


The BOTTOMS-UP project (Benthic Observatory and Technology Testbed on the Mid Shelf – Understanding Processes) was designed to address these issues in an observatory setting. The BOTTOMS-UP benthic observatory was deployed on the seafloor at the R2 Navy tower from 4/07 to 12/09.The observatory instrumentation was used to characterize the seabed response to physical forces acting across a spectrum of time scales. The frequency, intensity, and timing of energetic events are detected within the water column, and their manifestation within the BBL followed. BBL instrumentation measured thresholds of bed motion and characterized near-bed suspended loads, and will be used to estimate pressure fields and advective fluxes at the interface. In situ geochemical sensors were used to characterize rates of advection of properties within the sediment and connect those properties to both physical forcing above the interface and biological forcing driven by seasonal and diurnal cues. The combination of instrumentation and observational strategies will produce a holistic portrait of the causes and consequences of benthic exchange processes in permeable sediments.A summary of the observatory instrumentation and some recent results can be found in a recent issue of the TOS journal (Savidge et al. 2008).


At the largest scale, Dr. Dana Savidge has been using permanently installed physical oceanographic instrumentation to measure the regional scale forcing in the water column. WERA HF radar data from SABSOON was used to document surface currents across the entire shelf directional wave field within a more delimited sector, including the area around R2. Currents above the observatory were monitored with a Teledyne/RDI 600kHz 5 beam ADCP (VADCP). The unit transmitted data to the R2 tower via an underwater cable, and the data was relayed to shore hourly via a high bandwith microwave link. The 5th vertical beam of the VADCP resolved turbulent vertical velocities in the water column.Initial observations have revealed that the “Langmuir supercells” first observed by Gargett et al. (2004) in shallow (15m) waters off New Jersey are a ubiquitous feature of shelf circulation during high energy events

Changes in backscatter during the passage of a storm at R2. Each panel in this figure is a two hour window of BOTTOMS-UP VADCP backscatter, taken at 1 second intervals. Time progresses left to right in each panel, the vertical axis is depth in the water, with the water surface at the top of each panel, and the ocean bottom about 2 meters below the bottom of each panel. High backscatter at the surface is due to bubble entrainment by breaking waves. In the lower panels, plumes of high (sediment) backscatter emanate from the bottom. Diminishing storm winds toward the end of the record are associated with diminishing backscatter intensity.

The evolution of bedforms (sand waves and ripples) on the seafloor in response to wave forcing were monitored with a Imaginex rotating sonar.The sonar imaged a 10m diameter circle of seafloor every hour and transmitted the images back to the tower via a seafloor cable.The sonar images reveal changes in the size and orientation of bedforms in response to water column forcing (09.15.07 through 09.21.07).Bedform geometry will be used to estimate the pressure gradients over the sediment surface that drive advective circulation of porewater.

09.15.07 through 09.21.07

Two instrumented tripods were placed on the sea floor to sample intensively processes occurring in the bottom boundary layer. Dr. George Voulgaris of the University of South Carolina measured near-bottom velocity gradients and suspended sediment concentrations with a downward-looking Nortek Aquadopp Acoustic Backscatter Sensor (ABS:1, 2.5, & 5 MHz). An upward looking ABS mounted on the top of the frame measured water velocities and suspended particulates in the outer boundary layer.Near-bed turbulence was measured by a pair of ADVs mounted to the tripod legs.To help quantify resuspension events, a WetLabs EcoPuck fluorometer was coupled to one of the ADVs to produce an eddy correlation sensor for suspended chlorophyll-bearing particles (right side of image).

Dr. Jim Nelson of SkIO designed a second tripod to measure gradients in suspended chlorophyll and their response to boundary layer forcing using a stacked array of five WetLabs shuttered FLNTU fluorometers.

The near-bed chlorophyll and turbidity time-series were coordinated with the benthic boundary layer velocity/turbulence measurements (benthic tripod) and bed imaging sonar obtained by USC colleagues.Five deployments of the near-bed chlorophyll fluorescence/turbidity array were conducted in 2007-2008, with measurements at 5 or 6 levels (initially between 0.5 – 2.0 meters elevation above the sea floor, 0.25 m added for the last deployment). Near-continuous time-series measurements of chlorophyll/turbidity measurements were also obtained in the water column (near-bottom at ~5 m elevation and near-surface at ~22 m elevation) as part of instrument packages deployed from the R2 tower.One focus of the pre- and post-deployment effort has been to ensure consistent between-instrument calibrations of the chlorophyll fluorometers (while factory turbidity calibrations are consistent, we have found it necessary to establish chlorophyll calibration factors for each fluorometer).


Among the major interdisciplinary findings from the multiple instrument package deployments are those centering on the dynamic relationships between surface forcing (wind, waves), density and velocity structure through the water column, mobilization of the bed, resuspension of fine particles into the benthic boundary layer, and mixing of resuspended material through the shelf water column.Results from the near-bed optical package were combined with tower instruments to provide combined benthic boundary layer and water column time series.The near-bed turbidity signal, which we interpret to be predominantly associated with fine particles, indicated fine particle resuspension began to occur with the initial mobilization of the bed during a storm event.However, subsequent distinct pulses in the near-bed chlorophyll and turbidity signals (and formation of steep near-bed gradients) were observed at times when the sediment bed-form became reoriented into parallel linear ripples.This suggests formation of organized small-scale features in the near-bed velocity field (vortex shedding) that can mobilize sand-associated benthic diatoms into the benthic boundary layer as well as enhance resuspension of fine material (e.g., Savidge et al. 2008).

Estimates of depth-integrated turbidity and chlorophyll (obtained by combining near-bed measurements with those obtained higher in the water column with tower-deployed packages) show rapid increases in the fine particle concentrations through the water column during storm events.Ongoing analyses are examining the association of the optical signal of fine particle resuspension through the water column with occurrence of Langmuir Super-cells observed by Ann Gargett and Dana Savidge with the VADCP deployed for this project.Initial analyses of ocean color satellite imagery bracketing several major storm events (particulate backscatter and other particle-related products) indicate that the major resuspension/mixing events observed at the R2 mid-shelf location were representative of shelf-wide conditions.Thus, for at least some major events (where sufficient cloud-free imagery is obtained) we can evaluate the event-driven biogeochemical exchange between the sediment and water column on a shelf-wide basis.

Within the seabed, physical and chemical exchanges with the overlying water were investigated using shorter-term deployments of in situ instrumentation.Estimates of the flux of overlying water through the sand took advantage of tidal variations of temperature in the overlying water.A vertical array of thermistors was used to measure the propagation of those temperature changes into the seabed, and hence to estimate the advective flux of seawater into the sands.

Porewater temperatures during the July 2008 TRIP deployment. The tidal fluctuations are overlain by longer period intrusions of different water masses across the site. The inset shows an ~ 3 days segment of the record. Note the time lag in temperature propagation to depth.

Water exchange is rapid, but appears to show considerable spatial variability:

The in situ chemical environment was probed by an array of redox electrodes on the same instrument.Interpretation of the redox sensor data is more problematic, but the data reveal occasional strong, tidally-driven fluctuations in the interstitial chemical environment.

Redox potential in sands at aR2.Note the tidal fluctuations in redox potential at -3 and -6 cm.

Results of the August 08 MIMS deployment. Depth-time contours of calibrated data in sediment porewater. a) Methane concentration (umol/kg). b) Nitrogen-argon ratio (no units). c) Oxygen concentration (umol/kg). d) Carbon dioxide concentration (umol/kg). The horizontal line at 0 cm represents the sediment-water interface as determined by time lapse photography. The ‘•’ markers represent sample locations in time and depth.

A more elegant probing of interstitial chemistry was conducted by Tim Short and Ryan Bell of the Stanford Research Institute.They deployed an autonomous Membrane Inlet Mass Spectrometer (MIMS) with a specially designed sampling lance for obtaining profiles of dissolved gas concentrations in porewater.The MIMS collected a time series of observations on the August and October 2008 cruises to R2.The data revealed rapid depletion of oxygen in porewaters, despite the high fluid exchange rates.Slightly elevated concentrations of N2 and CH4 were detected as well, suggesting that denitrification and methanogenesis are active within the upper sediment column. We are combining the results from the temperature and the MIMS instruments to model rates of photosynthesis, respiration, denitrification and methanogenesis in this system.

Biological and sedimentological data from R2 were collected during each of the 16 cruises of the project.Cores reveal a sparse, small, and mobile infauna dominated by errant polychaetes and amphipods. Sediment chlorophyll concentrations were measured at cm intervals in the upper 15 cm of cores and finer scale measurements were taken in the upper 3 cm.These data are part of a long-term data record for sediment chlorophyll that dates back to 1999. Integrated chlorophyll in the uppermost 3 cm of sediment is equal to that of the integrated 30m water column (Nelson et al. 1999). In addition, the total quantity of fine particulates (<63 um) in the upper 15 cm has been quantified.Concentrations of fines increase with depth as a result of winnowing and decay in the uppermost sediment layers.Relatively high concentrations of fines in the upper (0-5 cm) sediments in 2007 were not seen in 2008.

(Photos of Georgia shelf infauna taken from NOAA Gray’s Reef website: )

Part of the SABSOON data archive from the Navy towers was a long record of acoustic backscatter from 300 kHz ADCP’s at R2, R8, and R4.A large nocturnal backscatter signal was often visible in the summer and fall.

The fact that there was a strong scattering signal at 300 kHz also indicated the possibility that scattering targets were relatively large (e.g., Holliday and Pieper 1980, Kringel et al 2003).In estuarine habitats, nocturnal vertical migration by benthic mysids can lead to an order of magnitude increase in water column biomass (Abello et al. 2005, Taylor et al. 2005).The vertical migration observed on the GA shelf was a result of similar processes. Migrating fauna could represent a significant vector of carbon transfer across the sediment-water interface, either by feeding in the water column at night and defecation on the bed during the day, or by grazing on benthic chlorophyll during the day and transferring that carbon into the water column at night.

To investigate the sources of nocturnal backscatter, the water column was sampled day and night on every cruise with a 1m diameter, 500 um mesh plankton net.Samples were collected from ~10 minute tows at the surface, near the bottom, and at mid-depth.Plankton tows were augmented with day and night tows with an epibenthic sled.The sled consisted of a stainless steel structure around a 0.5 x 0.75 m rectangular mouth plankton net with a 500um mesh. Three replicate tows were made during at least one day and one night interval during each cruise.The objective of this sampling was to sample the interface to determine if there was a distinct assemblage of epibenthic organisms that were present at the interface during the day but absent at night.

The huge trove of ADCP data is only beginning to be examined.Dr. Atsushi Kaneda has examined a fraction of the historical 4-beam data and has produced a manuscript describing the seasonal backscatter associated with sediment resuspension after the fall transition (Kaneda et al., in prep.).Shelf-wide patterns of biological vertical migration, and its responses to environmental variables such as water clarity, stratification, temperature, chlorophyll content, etc. have not yet been examined.

References and other literature.

This research project was awarded to SkIO by NSF's Division of Ocean Sciences and Directorate for Geosciences.

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