|Wethey, David S||University of South Carolina||Co-Principal Investigator|
|Woodin, Sarah A||University of South Carolina||Co-Principal Investigator|
|Volkenborn, Nils||University of Southern California (USC-HIMS)||Contact|
|Rauch, Shannon||Woods Hole Oceanographic Institution (WHOI BCO-DMO)||BCO-DMO Data Manager|
This dataset includes results from experiments investigating the hydraulic activities of the lugworm, Arenicola marina, in different sediment types. Porewater pressure sensing, time-lapse photography, and planar optode imaging methods were used. MP4 movies and NetCDF files are avialable for download. Each file contains 7.5 h of porewater pressure data and nikon images or oxygen planar optode images.
Quick-look files are MP4 movies (with H264 codec) that incorporate simultaneous visible light and optode imagery and pressure records. The movie files provide a "quick look" of what exactly can be found in the NetCDF files.
Netcdf optode files include optode imagery as time-resolved matrices, and a time series of pressure records. Oxygen images are matrices of percent air saturation values. All times are in unix format (seconds since 1970-01-01). Data are in 2.5 hour blocks.
Netcdf Nikon files include visible light imagery as time-resolved matrices and a time series pressure records. Nikon images are matrices of 24 bit RGB values. All times are in unix format (seconds since 1970-01-01). Data are in 2.5 hour blocks.
Experimental set-up and sediment characteristics:
internal tank dimensions: 40 cm wide, 30 cm high, 1.2 cm deep,
30 cm x 20 cm sediment,
3 cm overlying water,
overlying water flow rate: 10 mL min-1
pressure sensors: 15 deep in the sediment in the center of aquarium, for dataset 070601 data from 3 pressure sensors are provided (all 15 cm deep).
Experiments were conducted at the Alfred Wegener Institute for Polar and Marine Research in the Helmholtz Association, Wadden Sea Station Sylt, Hafenstrasse 43, 25992 List, Germany.
Planar Optode Imaging:
The lifetime imaging system is modified after Holst and Grunwald (2001). It comprises a cooled CCD camera (pco.1600MOD, PCO AG, Donaupark 11, 93309 Kelheim, Germany), a pulse delay generator (T560, Highland Technology, 18 Otis St, San Francisco CA), an array of blue-light emitting diodes (LEDs; lambda max = 455 nm, LXHL-LR5C, Philips Lumileds, 370 W Trimble Rd, San Jose, CA) attached to a heat sink (~5×5×2.5 cm), and a custom-made power supply. The camera accumulates multiple exposures with a programmable modulation time. By using the output of the exposure synchronization of the camera as a trigger for the pulse delay generator and subsequently the LED light pulse, any jitter between the camera exposure time and the preceding light flash can be avoided. The timing parameters is chosen as follows. After the LED pulse of 20 µs duration and a given delay, delta, the electronic shutter for camera exposure opens for D = 10 µs. The delays of delta_1 = 1 µs and delta_2 = 11 µs are applied for the accumulation of the first (I1) and second (I2) intensity window images (gates), respectively, which are acquired sequentially. Summing up all times to 41 µs for the longest delay reveals the minimum time interval for the accumulations of single exposures. Typically an interval of 44 µs is chosen, corresponding to a repetition rate of almost 23 kHz. Using the first and second intensity window images, the luminescence lifetime image is calculated as t = D/ln(I1/I2) (Holst and Grunwald 2001). The peak current through the LEDs (typically 200–300 mA) and the integration time during which both intensity windows are accumulated (typically 250–1000 ms) are adjusted to optimize image quality. The control of the camera and image acquisition through the IEEE 1394 (firewire) interface, and of the delay pulse generator through the RS232 (serial) interface, are done by a laptop computer using software developed by Lubos Polercky (Microsensors Group, Max Planck Institute for Marine Microbiology, Bremen, 28359, Germany) and Uli Henne (German Aerospace Center, Institute of Aerodynamics and Flow Technology, Göttingen, 37073, Germany) in Borland Delphi and C++. Optodes were calibrated using the lifetime values measured in the anoxic sediment and in the air-saturated overlying water. For details see Matsui, GY et al. 2011.
Porewater Pressure Sensing:
The differential pressure sensors (Honeywell 27PC) are piezoresistive bridges that provide a differential voltage proportional to the pressure difference between the 2 sides of the sensor. While one side of the sensor is indirect contact with the sediment porewater (gage pressure), the ambient (hydrostatic) pressure isdetected within a water-filled space within the PVC channels (plenum) that is in direct contact with the overlying water and isolated from the porewater. Data are typically collected at 200 Hz using autonomous 8-channel 16-bit data loggers (CF2, Persistor Instruments, 153-A Lovells Lane, Marston Mills MA). Amplifiers on the boards allow adjustment of the dynamic range of the sensors. Sensors are calibrated by varying the water heights on both sides of the sensors, i.e. the plenum and sediment side. Twelve positive and negative pressures are typically applied to each sensor, and the linear calibration between the gauge pressure and measured voltage has typically R2 > 0.95. The 200 Hz raw data are downscaled to 1Hz by taking the median of all values in each 1-second interval. The median of each 60 minute block was calculated, and linearly interpolated values of this median time series was subtracted from each 1Hz data value to remove long term drift from the signals.
Images of the tanks are taken with digital SLR cameras (Nikon D200 and D300) using flash, triggered by time-lapse controllers (Digi-Snap, Harbortronics) or by a digital delay generator (T560 Highland Technology). Images are typically taken at 15 to 30 s intervals.
Related files and references:
Matsui, GY, N Volkenborn, L Polerecky, U Henne, DS Wethey, CR Lovell, SA Woodin. 2011. Mechanical imitation of bidirectional bioadvection in aquatic sediments. Limnology and Oceanography: Methods 9: 84-96. DOI: 10.4319/lom.2011.9.84
These data are related to Figures 2 and 4 in the following paper:
Volkenborn N., Polerecky L., Wethey D.S, Woodin S.A (2010) Oscillatory porewater bioadvection in marine sediments induced by hydraulic activities of Arenicola marina. Limnology and Oceanography 55(3), 2010, 1231–1247. DOI: 10.4319/lo.2010.55.3.1231
Programs in R statistics language that were used to make the netcdf files:
|species||Name of the species.||text|
|date||Date of the experiment.||mmddYYYY|
|weight||Weight of the worm, in grams.||grams|
|press_sensor||Identification of the pressure sensor.||text|
|sediment_permeability||Permeability of the sediment in the experimental tank (m^2).||meters squared|
|sediment_porosity||Sediment porosity.||volume fraction|
|tot_org_matter||% weight total organic matter.||% weight|
|O2_consump_rate||O2 consumption rate (umol cm-3 h-1).||micromoles per cubic centimeter per hour|
|movie||Link to the movie (mp4) file. Movies provide a "quick look" of what is in the NetCDF files, incorporating simultaneous visible light and optode imagery and pressure records. The vertical red line marks the time point in the 20 min pressure record that corresponds to the images.||dimensionless|
|nikon_NetCDF_files||Link to the Nikon NetCDF files (.zip). Nikon NetCDF files include visible light imagery as time-resolved matrices, and a time series of pressure records. 10 hour time series were split in four 2.5 h blocks. Nikon images are matrices of 24 bit RGB values. All times are in unix format (seconds since 1970-01-01).||dimensionless|
|O2_NetCDF_files||Link to the NetCDF optode files, which include optode imagery as time-resolved matrices, and a time series of pressure records. Oxygen images are matrices of percent air saturation values. 10 hour time series were split in four 2.5 hour blocks. All times are in unix format (seconds since 1970-01-01).||dimensionless|
|R_files||Link to R files, which show how the NetCDF files were created.||dimensionless|
|Dataset-specific Instrument Name|| |
|Generic Instrument Name|| |
|Dataset-specific Description|| |
Images of the tanks are taken with digital SLR cameras (Nikon D200 and D300) using flash, triggered by time-lapse controllers (Digi-Snap, Harbortronics) or by a digital delay generator (T560 Highland Technology).
|Generic Instrument Description|| |
All types of photographic equipment including stills, video, film and digital systems.
Wadden Sea Station Sylt
|Start Date|| |
|End Date|| |
Experiments were conducted at the Alfred Wegener Institute for Polar and Marine Research in the Helmholtz Association, Wadden Sea Station Sylt, Hafenstrasse 43, 25992 List, Germany for the project, "Linking infaunal hydraulic activities, porewater flow and biogeochemical processes in marine sediments" during May and June 2007.
This document is created by info v 4.1f 5 Oct 2018 from the content of the BCO-DMO metadata database. 2020-02-24 15:59:57