Dataset: Effects of mussels on seawater chemistry

Name: Average conditions and chemical fluxes during mussel bed experiments at the Bodega Marine Laboratory, University of California, Davis in 2017.
Published: 2022-02-24
Keywords: Mytilus californicus, mussel bed, biogenic habitat, foundation species, carbonate chemistry, chemical gradients, calcification, respiration, flow speed, pH, oxygen, oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.869361.1

Spatial Extent: N:38.33325 E:-123.04805 S:38.33325 W:-123.04805

Temporal Extent: 2017-01-27 - 2017-02-13

Project:

Trophic consequences of ocean acidification: Intertidal sea star predators and their grazer prey (BOAR Trophic)

Principal Investigator:

Brian Gaylord (University of California-Davis, UC Davis-BML)

Contact:

Aaron T. Ninokawa (University of California-Davis, UC Davis-BML)

BCO-DMO Data Manager:

Taylor Heyl (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Shannon Rauch (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2022-02-24

Restricted:

Validated:

Yes

Current State:

Final no updates expected

Average conditions and chemical fluxes during mussel bed experiments at the Bodega Marine Laboratory, University of California, Davis in 2017.

Abstract:

This dataset represents average conditions and chemical fluxes during mussel bed experiments where chemistry (pH and O2) was measured at defined heights within and above the mussel bed. These data describe average conditions outside of the mussel bed during each profile sampled at the Bodega Marine Laboratory, University of California, Davis in 2017.

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2022-02-24	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.869361.1	2022-03-15

Methods & Sampling

These data were generated by establishing a mussel bed in a laboratory flow tunnel. Each profile represents a period where chemistry (pH and O2) was measured at defined heights within and above the mussel bed. These profiles occurred at two places in the mussel bed. These data describe average conditions outside of the mussel bed during each profile. Freestream velocities and shear velocities were assumed constant during a profile.

Calcification and respiration rates were calculated as the fluxes of alkalinity and oxygen, respectively. Flux calculations were modified from McGillis et al, 2011 and Takeshita et al, 2016.

Methods described in detail in Ninokawa et al. (2020).

Known Issues: No oxygen data was collected for profiles 1-7. This also prohibits the calculation of alkalinity profiles, calcification rates, and respiration rates. Zero freestream velocities also prohibits the calculation of calcification and respiration rates due to the lack of sufficient turbulent mixing.

Data Processing Description

All data analyses were performed with R Statistical Software. The seacarb package was used for carbonate chemistry calculations and the marelac package was used for estimating oxygen flux out of the surface of the flow tunnel.

BCO-DMO Processing:
- Adjusted field/parameter names to comply with BCO-DMO naming conventions
- Missing data identifier ‘NA’ replaced with 'nd' (BCO-DMO's default missing data identifier)
- Added a conventional header with dataset name, PI names, version date

Data Files

File
effects_of_mussels_on_seawater_chemistry_-_summary_data.csv (Comma Separated Values (.csv), 1.75 KB) MD5:96bf120f1a3f09064b53612789656455 Primary data file for dataset ID 869361

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1636191

Deployments

None available yet

Instruments

Acoustic Doppler Current Profiler

Supplied Name: Nortek acoustic doppler profiler (ADP)

Supplied Description:

Nortek acoustic doppler profiler (ADP). Freestream velocity and u* were extracted from velocity profiles. A relationship between flow tunnel speed setting and freestream velocity and u* was used during period the ADP lacked sufficient particles in the water for accurate velocity measurements.

Instrument Type

Generic Name: Acoustic Doppler Current Profiler

Acronym: ADCP

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/115/

Generic Description:

The ADCP measures water currents with sound, using a principle of sound waves called the Doppler effect. A sound wave has a higher frequency, or pitch, when it moves to you than when it moves away. You hear the Doppler effect in action when a car speeds past with a characteristic building of sound that fades when the car passes. The ADCP works by transmitting "pings" of sound at a constant frequency into the water. (The pings are so highly pitched that humans and even dolphins can't hear them.) As the sound waves travel, they ricochet off particles suspended in the moving water, and reflect back to the instrument. Due to the Doppler effect, sound waves bounced back from a particle moving away from the profiler have a slightly lowered frequency when they return. Particles moving toward the instrument send back higher frequency waves. The difference in frequency between the waves the profiler sends out and the waves it receives is called the Doppler shift. The instrument uses this shift to calculate how fast the particle and the water around it are moving. Sound waves that hit particles far from the profiler take longer to come back than waves that strike close by. By measuring the time it takes for the waves to bounce back and the Doppler shift, the profiler can measure current speed at many different depths with each series of pings. (More from WHOI instruments listing).

Oxygen Microelectrode Sensor

Supplied Name: Presens Microx 4 with needle-type microsensor

Supplied Description:

O2 and temperature calibrate by the manufacturer. O2 calibration verified in seawater equilibrated with atmospheric O2 and sensors deviating from 100% were replaced.

Instrument Type

Generic Name: Oxygen Microelectrode Sensor

Acronym: O2 Microelectrode

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/351/

Generic Description:

Any microelectrode sensor that measures oxygen.

pH Sensor

Supplied Name: Honeywell Durafet III combination electrode

Supplied Description:

Top pH sensor: Honeywell Durafet III combination electrode calibrated to total scale with spectrophotometric pH determination on discrete water samples

Profiling pH sensor: Honeywell Durafet III combination electrode calibrated to total scale by holding adjacent to the top pH sensor

Instrument Type

Generic Name: pH Sensor

Generic Description:

An instrument that measures the hydrogen ion activity in solutions.

The overall concentration of hydrogen ions is inversely related to its pH. The pH scale ranges from 0 to 14 and indicates whether acidic (more H+) or basic (less H+).

YSI Sonde 6-Series

Supplied Name: Yellow Springs Instruments 6920 Multiparameter Sonde

Supplied Description:

Top O2, salinity, and temperature sensor: Yellow Springs Instruments 6920 Multiparameter Sonde. O2 calibrated by holding adjacent to the profiling O2 sensor. Salinity calibrated with YSI 50 uS/cm Conductivity Standard. Temperature calibrated by manufacturer.

Instrument Type

Generic Name: YSI Sonde 6-Series

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0737/

Generic Description:

YSI 6-Series water quality sondes and sensors are instruments for environmental monitoring and long-term deployments. YSI datasondes accept multiple water quality sensors (i.e., they are multiparameter sondes). Sondes can measure temperature, conductivity, dissolved oxygen, depth, turbidity, and other water quality parameters. The 6-Series includes several models. More from YSI.

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
bed_position	location of profile in the bed, 1=95 cm downstream of leading edge, 2=145 cm downstream of leading edge	unitless	site_descrip
calcification_rate	bed calcification rate calculated for the mussel bed as the areal flux of alkalinity during the profile	mmol hr-1 m-2	calcification
date	date when the profile was measured in format: YYYY-MM-DD Format: %Y-%m-%d	unitless	date
freestream_velocity	freestream velocity held during the profile, calculated from a relationship with flow tunnel speed setting	m s-1	no_bcodmo_term
max_diff_o2	maximum observed difference in oxygen concentration during the profile	µmol kg-1	O2
max_diff_ph	maximum observed difference in pH during the profile	unitless	pH
profile	profile identifier	unitless	cast
respiration_rate	bed respiration rate calculated for the mussel bed as the areal flux of oxygen during the profile	mmol hr-1 m-2	resp
salinity	average top salinity during the profile	PSU	sal_nis
temperature	average top temperature during the profile	degrees celsius (°C)	temp
top_o2	average top oxygen concentration during the profile	µmol kg-1	O2
top_ph	average top pH during the profile	unitless	pH
u_star	shear velocity during the profile, calculated from a relationship with flow tunnel speed setting	m s-1	no_bcodmo_term

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Database

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Dataset: Effects of mussels on seawater chemistry