Dataset: AE1703 bottles: Biogeochemical and Microbial data

Name: Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1703 in the Bermuda Atlantic Time-series Study site from Mar/April 2016
Published: 2019-01-23
Keywords: oceans

Cite This Dataset

DOI:10.1575/1912/bco-dmo.753679.1

Spatial Extent: N:32.53 E:-64.138 S:31.656 W:-77.427

Temporal Extent: 2017-03-30 - 2017-04-04

Project:

Dissolved Organic Carbon Cycling by SAR11 Marine Bacteria (Bacterial DOC cycling)

Principal Investigator:

Stephen Giovannoni (Oregon State University, OSU)

Co-Principal Investigator:

Craig A. Carlson (University of California-Santa Barbara, UCSB-MSI)

BCO-DMO Data Manager:

Nancy Copley (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2019-01-23

Restricted:

Release Date:

2019-09-30

Validated:

Yes

Current State:

Final no updates expected

Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1703 in the Bermuda Atlantic Time-series Study site from Mar/April 2016

Abstract:

Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1703 in the Bermuda Atlantic Time-series Study site from Mar/April 2016.

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2019-01-23	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.1575/1912/bco-dmo.753679.1	2019-09-30

Description

Nutrient concentrations and microbial counts from Niskin bottle collections on R/V Atlantic Explorer A1703 in the Bermuda Atlantic Time-series Study site from Mar/April 2016.

Methods & Sampling

See Supplemental Documents below.

Data Processing Description

BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- replaced blank cells with ‘nd’ (no data)
- changed sign of longitude (lon) so negative values represent west

Data Files

File
AE1703_bottle.csv (Comma Separated Values (.csv), 74.04 KB) MD5:fb2b8c7dce3dfde303debd9fe15f38ab Primary data file for dataset ID 753679

Supplemental Files

File
DOC and TDN methodology (UCSB) filename: DOC-TDN_UCSB_method.pdf (Portable Document Format (.pdf), 122.71 KB) MD5:310f5c86b897d43276e8ad27a3873e50 Methodology for measuring Dissolved Organic Carbon and Total Dissolved Nitrogen
Methodology for bacterial abundance - DAPI filename: bact_abun_DAPI_method.pdf (Portable Document Format (.pdf), 70.83 KB) MD5:3393f21489687d12bc5c6621ebbb23ac Determination of Bacterial Abundance using DAPI DNA binding stain and Epifluorescence microscopy
Methodology for bacterial production measurement filename: BactProd_method.pdf (Portable Document Format (.pdf), 128.90 KB) MD5:181de3ce9c9037073127e41d36a2219b Microcentrifuge Method Protocol for Determination of Bacterial Production Rates via 3H-Leucine incorporation

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1436865

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AE1703		2017-03-29	R/V Atlantic Explorer	Stephen Giovannoni (Chief Scientist)	data info

Instruments

CTD - profiler

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

Fluorescence Microscope

Supplied Name: Epifluorescence microscope

Supplied Description:

Used to enumerate bacterial abundance

Instrument Type

Generic Name: Fluorescence Microscope

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB06/

Generic Description:

Instruments that generate enlarged images of samples using the phenomena of fluorescence and phosphorescence instead of, or in addition to, reflection and absorption of visible light. Includes conventional and inverted instruments.

Liquid Scintillation Counter

Supplied Name:

Supplied Description:

Used to count microbial cells

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.

Niskin bottle

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic Description:

A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc.

Shimadzu TOC-V Analyzer

Supplied Name: Shimadzu High Temperature Combustion system

Supplied Description:

Used to measure non-purgeable Organic Carbon (NPOC) and Total Dissolved Nitrogen (TDN)

Instrument Type

Generic Name: Shimadzu TOC-V Analyzer

Acronym: Shimadzu TOC-V

Community Identifier: http://onto.nerc.ac.uk/CAST/124

Generic Description:

A Shimadzu TOC-V Analyzer measures DOC by high temperature combustion method.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
sample_id	Unique Identified Code for each sample collected	unitless	sample
Cruise	cruise name	unitless	cruise_id
Cast	cast number	unitless	cast
Niskin	Niskin bottle number	unitless	bottle
date	Date (yyyymmdd)	unitless	date
date_decyr	Date (decimal year)	unitless	date
time_UTC	Timestamp (UTC) hh:mm	unitless	time
lat	Latitude; north is positive	decimal degrees	lat
lon	Longitude; east is positive	decimal degrees	lon
Depth	Sampling depth in meters	meters	depth
Temp	CTD temperature	degrees celsius	temp
CTD_S	CTD salinity	pratical salinity units (PSU)	sal
Pressure	CTD Pressure	decibars	press
Sigma_theta	CTD sigma theta (potental density)	kilogram/meter^3	sigma_t
Conductivity	CTD Conductivity	Siemens per meter	cond
Fluor	CTD Fluorescence	milligram per Liter	fluor
Par	CTD photosynthetically available radiation	micro-Einsteins/meter^2/second (uE/m^2/sec)	PAR
O2	CTD Oxygen	millimole per kilogram	O2
beam_trans_CStarTr0	CTD beam transmission as percent	unitless	trans
NO3_NO2	Nitrate+Nitrite concentration by flow injection autoanalyzer (Lachat QuikChem 8000)	millimole per Liter	NO3_NO2
NO3_NO2_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
PO4	ortho-Phosphate concentration by flow injection autoanalyzer (Lachat QuikChem 8000)	millimole per Liter	PO4
PO4_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
NH4	Ammonium ion concentration by flow injection autoanalyzer (Lachat QuikChem 8000)	millimole per liter	NH4
NH4_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
POC_mg_L	Particulate organic carbon measured by combustion analysis (CEC 440HA). Collected on Glass fiber filter type GF/F (Whatman)	milligram per Liter	POC
POC_mmol_L	Particulate organic carbon	millimole per Liter	POC
POC_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
PON_mg_L	Particulate organic nitrogen measured by combustion analysis (CEC 440HA). Collected on Glass fiber filter type GF/F (Whatman)	milligram per Liter	PON
PON_mmol_L	Particulate organic nitrogen	millimole per Liter	PON
PON_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
DOC	Dissolved organic carbon concentration by HTCO. Glass fiber filtrate type GF/F (Whatman). Methodological reference is Carlson et al. 2010 DSRII	micromolar	DOC
DOC_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
TDN	Total dissolved nitrogen concentration by HTCO. Glass fiber filtrate type GF/F (Whatman).	micromolar	TDN
TDN_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
Bact	Bacterioplankton abundance by microscopy. Methodological reference: K.G. Porter and Y.S. Feig (1980). The use of DAPI for identifying and counting aquatic microflora. Limnol. Oceanogr 25(5): 943-948.	cells per milliliter	cell_concentration
Bact_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag
Bact_Prod	Heterotrophic bacterial production by 3H Leu uptake. Methodological reference: Smith DC & Azam F (1992) A simple economical method for measuring bacterial protein synthesis rates in seawater using 3H-leucine. Mar Microb Food Webs 6: 107_114.	picomoles per liter per hour	leuc_incorp
Bact_Prod_QF	Quality Flags (QF): 0 good; 1 unknown; 4 questionable measurement; 8 bad measurement	unitless	q_flag