Dataset: water_samples
Deployment: LDZ1

Depth profiles of oceanographic parameters from Chesapeake Bay in Spring and Summer of 2010-2011

Principal Investigator:

Dr Byron C Crump (University of Maryland Center for Environmental Science, UMCES/HPL)

Co-Principal Investigator:

Jeffrey Cornwell (University of Maryland Center for Environmental Science, UMCES/HPL)

Ian Hewson (Cornell University, Cornell)

Contact:

Dr Byron C Crump (University of Maryland Center for Environmental Science, UMCES/HPL)

BCO-DMO Data Manager:

Ms Dicky Allison (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Project:

Life in the Dead Zone: Microbial respiration, production, diversity and gene expression in seasonally anoxic estuarine waters (LiDZ)

Current State:

Final with updates expected

Version:

final

Version Date:

2014-05-20

Data URL:

https://osprey.bco-dmo.org/dataset-deployment/515371/data

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Description

Oceanographic data from the middle region of the Chesapeake Bay, especially water column depth profiles of seasonally anoxic bottom waters, collected in spring and summer of 2010-2011.

Water samples and sensor-based measurements were made during sixteen research cruises in 2010-2012: two 1-week cruises aboard the UNOLS vessel R/V Hugh R. Sharp, and fourteen 1-day cruises aboard the R/V Terrapin, which is a 25' Parker outboard motorboat with davit for deploying a CTD package.

Methods & Sampling

Dataset acquisition description

SAMPLE COLLECTION

Deployment-specific acquisition description

Vertical profiles at sampling stations were conducted from surface to near bottom depth with a Sea-Bird conductivity-temperature-depth (CTD) system with dissolved oxygen (SBE 25 on the R/V Terrapin); Sea-Bird Electronics and fluorescence (WETStar, WET Labs) sensors.

Data Processing Description

Dataset Processing Description

SAMPLE ANALYSES

REFERENCES

RELATED FILES AND REFERENCES:

16S amplicon DNA sequences to the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI) under Accession SAMN02863536-SAMN02863970.

Metatranscriptomic sequence data to the BioProject Archive at NCBI under Accession PRJNA222777. http://www.ncbi.nlm.nih.gov/bioproject/PRJNA222777

Lee, D. Y., M. S. Owens, B. C. Crump, and J. C. Cornwell. 2014. The Effects of Oxygen Transition on Community Respiration and Potential Chemoautotrophic Production in a Seasonally Stratified Anoxic Estuary. Estuaries and Coasts. DOI 10.1007/s12237-014-9803-8. http://link.springer.com/article/10.1007/s12237-014-9803-8

Hewson, I., E. Eggleston, M. Doherty, D. Y. Lee, M. Owens, J. P. Shipleigh, J. C. Cornwell, and B. C. Crump. 2014. Metatranscriptomic analyses of plankton communities inhabiting surface and sub-pycnocline waters of the Chesapeake Bay during oxic-anoxic-oxic transitions. Applied And Environmental Microbiology 80:328-338. http://aem.asm.org/content/early/2013/10/21/AEM.02680-13

DMO notes:
Format or vocabulary adjustments to metadata primarily involved controlling the vocabulary and adding UNOLS names for the cruises.
Date changed to date_local
Time -> time_local
Vessel -> platform
Cruise -> cruise [Inserted cruise_new to give column for UNOLS name]
Lowercase Filtered, Cast, Depth [added cast_new to separate alpha and numeric for mapper]
Abbreviated Latitude, Longiture, Conductivity, Temperature, Salinity, Fluorescence
Decoded Oxygen1 -> O2_conc and Oxygen2 -> O2_rate

In keeping with BCO-DMO best practices, ISODateTime has been added as a formatted time column. At this time it is local time.

More information about this dataset deployment

Funding

Award Number	Funding Source
OCE-0961920	NSF Division of Ocean Sciences

Instruments

Box Corer

Supplied Description:

Sediment cores were collected with an acrylic/PVC Soutar-design box corer to determine sediment-water fluxes.

Instrument Type

Generic Name: Box Corer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/51/

Generic Description:

General description of a box corer:

A box corer is a marine geological tool that recovers undisturbed soft surface sediments. It is designed for minimum disturbance of the sediment surface by bow wave effects. Traditionally, it consists of a weighted stem fitted to a square sampling box. The corer is lowered vertically until it impacts with the seabed. At this point the instrument is triggered by a trip as the main coring stem passes through its frame. While pulling the corer out of the sediment a spade swings underneath the sample to prevent loss. When hauled back on board, the spade is under the box. (definition from the SeaVox Device Catalog)

Box corers are one of the simplest and most commonly used types of sediment corers. The stainless steel sampling box can contain a surface sediment block as large as 50cm x 50cm x 75cm with negligible disturbance. Once the sediment is recovered onboard, the sediment box can be detached from the frame and taken to a laboratory for subsampling and further analysis. The core sample size is controlled by the speed at which the corer is lowered into the ocean bottom. When the bottom is firm, a higher speed is required to obtain a complete sample. A depth pinger or other depth indicator is generally used to determine when the box is completely filled with sediment. Once the core box is filled with sediment, the sample is secured by moving the spade-closing lever arm to lower the cutting edge of the spade into the sediment, until the spade completely covers the bottom of the sediment box. (definition from Woods Hole Oceanographic Institution).

Discrete water sampler

Supplied Name: oxycline sampling device

Supplied Description:

Samples were collected at 7 depths across the oxycline using a syringe-sampling device that simultaneously fills a total of 28 syringes (4 syringes every 20cm vertically) using a mechanical feature that gradually pulls the water into the syringes when triggered. In 2012, a new “oxycline sampling device” was developed that uses a multi-channel peristaltic pump to draw water from 8 depths across a 3m range.

Instrument Type

Generic Name: Discrete water sampler

Generic Description:

A device that collects an in-situ discrete water sample from any depth and returns it to the surface without contamination by the waters through which it passes, such as a water bottle.

Flow Cytometer

Supplied Description:

Enumeration was performed using a FACSCalibur flow cytometer (Becton Dickinson) using green fluorescence as an incident trigger, with a target range for sample event rates at 100-1000 particles s-1 to prevent incident coincidence.

(http://www.bdbiosciences.com/instruments/facscalibur/features/index.jsp)

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Inorganic Carbon Analyzer

Supplied Name: Apollo SciTech infrared-based analyzer

Supplied Description:

Dissolved inorganic carbon (DIC = [H2CO3] + [HCO3-] + [CO32-]) was measured with an infrared-based analyzer (Apollo SciTech)

http://www.apolloscitech.com/DIC.htm

Instrument Type

Generic Name: Inorganic Carbon Analyzer

Generic Description:

Instruments measuring carbonate in sediments and inorganic carbon (including DIC) in the water column.

Liquid Scintillation Counter

Supplied Name: Liquid Scintillation Analyzer

Supplied Description:

Radioactivity, expressed as disintegration per minute (DPM), was counted in a liquid scintillation analyzer (Tri-Carb 3100TR, Packard). The Tri-Carb® 3100TR is a computer-controlled
benchtop liquid scintillation analyzer for detecting
small amounts of alpha, beta and gamma radioactivity. (http://shop.perkinelmer.com/Content/relatedmaterials/specificationsheets/spc_tricarb3100trlowactliquidscint.pdf)

Instrument Type

Generic Name: Liquid Scintillation Counter

Acronym: LSC

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB21/

Generic Description:

Liquid scintillation counting is an analytical technique which is defined by the incorporation of the radiolabeled analyte into uniform distribution with a liquid chemical medium capable of converting the kinetic energy of nuclear emissions into light energy. Although the liquid scintillation counter is a sophisticated laboratory counting system used the quantify the activity of particulate emitting (ß and a) radioactive samples, it can also detect the auger electrons emitted from 51Cr and 125I samples.

Mass Spectrometer

Supplied Name: membrane inlet mass spectrometer

Supplied Description:

"A membrane inlet mass spectrometer was modified to perform rapid, high-precision measurements of dissolved 02, and Ar in water. The instrument pumps water at < 1 mL per min through semipermeable microbore silicone; tubing positioned inside an inlet vacuum line of a quadrupole mass spectrometer. Precise pumping and temperature control of the water sample contribute to high signal stability and reproducibility. Dissolved gas concentrations are determined from intensities of the mass spectrometer signals in the multiple ion detection mode.

Precision (coefficient of variation) is <0.5% for N2, 02, and Ar concentrations and <0.05% for N2/Ar and O/Ar ratio data. Deviation from expected values was between 0.5 and 1.5% for air-equilibrated water of widely ranging temperature and salinity. Advantages of the instrument over existing methods include rapid throughput (-20- 30 samples h-l), lack of sample water preparation (e.g., no degassing step), small sample size (<10 mL), and high- precision measurement of both concentration and gas ratio data. A limitation of the present instrument is the difficulty in measuring water with significantly supersaturated gas concentrations."

from Kana et al., 1994.

Instrument Type

Generic Name: Mass Spectrometer

Acronym: Mass Spec

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/

Generic Description:

General term for instruments used to measure the mass-to-charge ratio of ions; generally used to find the composition of a sample by generating a mass spectrum representing the masses of sample components.

Pump

Supplied Name: Diaphragm Pump

Supplied Description:

Water samples for chemistry and biological rate measurements were collected with a diaphragm pump with a 2.54 cm diameter hose attached to the CTD frame and ended with a conical PVC manifold distributing water to 16 tubings to fill sample vials.

Instrument Type

Generic Name: Pump

Generic Description:

A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps

Pump

Supplied Name: Submersible Well Pump

Supplied Description:

Water samples for DNA and RNA were collected with a submersible well pump (Tornado Pump, Groundwater Essentials) attached to the CTD Frame (R/V Sharp) or deployed by hand separately from the CTD (R/V Terrapin).

http://www.groundwateressentials.com/pumps/plastic-pumps-standard/tornado-dtw-100ft

Instrument Type

Generic Name: Pump

Generic Description:

Parameters

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_num	arbitrary	nd	no_bcodmo_term
date_local	Date	Eastern Daylight Time	date
time_local	HH:MM	24-hour clock	time
platform	Ship used to collect samples	nd	platform
cruise	Internal cruise number	text	cruise_name
cruise_new	UNOLS cruise identifier	text	cruise_name
filtered	indicates whether a sample was prefiltered before measuring N2_rate;O2_rate; and DIC_rate	text	no_bcodmo_term
cast	Depth station number for each CTD and pump cast; WC1 is near surface and WC8 is near bottom.	alphanumeric	cast
cast_new	Depth station number for each CTD and pump cast without the alpha	numeric	cast
depth	Sampling depth	meters	depth
lat	Latitude	degrees	lat
lon	Longitude	degrees	lon
cond	Conductivity: Measured with a SBE 25 on the R/V Terrapin and SBE 911plus on R/V Hugh R. Sharp; Sea-Bird Electronics	microsiemens per centimeter	cond
temp	Temperature: Measured with a SBE 25 on the R/V Terrapin and SBE 911plus on R/V Hugh R. Sharp; Sea-Bird Electronics	degrees celsius	temp
sal	Salinity: Measured with a SBE 25 on the R/V Terrapin and SBE 911plus on R/V Hugh R. Sharp; Sea-Bird Electronics	salinity	sal
O2_conc	oxygen concentration: Measured with a SBE 25 on the R/V Terrapin and SBE 911plus on R/V Hugh R. Sharp; Sea-Bird Electronics	milligrams per liter	O2_ml_L
O2_sat	oxygen saturation: Measured with a SBE 25 on the R/V Terrapin and SBE 911plus on R/V Hugh R. Sharp; Sea-Bird Electronics	percent saturation	O2_sat_pcnt
fluor	Fluorescence: Measured with a WETStar sensor; WET Labs	milligrams per cubic meter	fluor
N2_rate	Nitrogen production rate: (TF-T0) / hr (Importantly this is the number which is multiplied by -2 to make unit of uM N2-N/h)	micromoles per liter hour	no_bcodmo_term
O2_rate	Oxygen consumption rate: Measured with membrane inlet mass spectrometer during short incubations in gas-tight BOD bottles	micromoles per liter hour	O2_consum
DIC_rate	Dissolved inorganic carbon production rate: Measured with an infrared CO2 detector during short incubations in gas-tight BOD bottles	micromoles per liter hour	no_bcodmo_term
NO2	Nitrite: Measured with segmented flow analysis after cadmium reduction (Lane et al. 2000)	micromolar	NO2
NO3	Nitrate: Measured with segmented flow analysis after cadmium reduction (Lane et al. 2000)	micromolar	NO3
NH4	Ammonium: Measured colorimetrically (Brewer and Spencer 1971; Parsons et al. 1984)	micromolar	NH4
SRP	Soluble reactive phosphorous: Measured colorimetrically (Brewer and Spencer 1971; Parsons et al. 1984)	micromolar	SRP
H2S	Total dissolved sulfide (DS = [S2-] + [HS-] + [H2S]): Measured colorimetrically (Brewer and Spencer 1971; Parsons et al. 1984)	micromolar	sulfide
Fe	Dissolved iron (II): Measured colorimetrically (Brewer and Spencer 1971; Parsons et al. 1984)	milligrams per liter	Fe
Mn	Dissolved manganese (III and II): Measured colorimetrically (Brewer and Spencer 1971; Parsons et al. 1984)	micromolar	Mn
BP	Bacterial Production: Calculated from the rate of incorporation of tritiated L-leucine in 1-hour incubations at ambient temperature and redox conditions	micrograms carbon per liter hour	no_bcodmo_term
Chla	Chlorophyll a: Measured with a fluorometric method (Arar & Collins 1997)	micrograms per liter	chl_a
Pheophytin_a	Phaeophytin a: Measured with a fluorometric method (Arar & Collins 1997)	micrograms per liter	p_phytin
Cell_Counts	flow cytometry counts of prokaryotic cells	cells per milliliter	no_bcodmo_term
ISO_DateTime_Local	ISO8601-compliant date/time standard	YYYY-mm-ddTHH:MM:SS.ss	ISO_DateTime_Local

Database

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Dataset: water_samples
Deployment: LDZ1

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Database

Contribute Data

Dataset: water_samplesDeployment: LDZ1

Dataset acquisition description

Deployment-specific acquisition description

Dataset Processing Description

Dataset: water_samples
Deployment: LDZ1