http://lod.bco-dmo.org/id/dataset/745449
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2018-08-30
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Physiochemical data from samples collected along the coast of Louisiana, USA during 2018
2020-02-13
publication
2020-02-13
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-06-11
publication
https://doi.org/10.1575/1912/bco-dmo.745449.1
J. Cameron Thrash
University of Southern California
principalInvestigator
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Thrash, J. C., Kujawinski, E. (2020) Physiochemical data from samples collected along the coast of Louisiana, USA during 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2020-02-13 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.745449.2 [access date]
Physiochemical data from samples collected along the coast of Louisiana, USA during 2018. Dataset Description: <p>Physiochemical data from samples collected along the coast of Louisiana in the Gulf of Mexico.</p> Methods and Sampling: <p>Samples were collected manually by filling an acid-washed and autoclaved 20L carboy after three rinses. Temperature, pH, and salinity were taken using a handheld YSI. Cell counts were obtained by filtering water through a 2.7 µm Whatman GF/D filter, fixing with 10% formaldehyde, placing on ice, and then counting using flow cytometry (Thrash et al., 2015, Hydrocarbon and Lipid Microbiology Protocols). Inorganic nutrients were measured at the University of Washington Marine Chemistry Laboratory after sequential filtration through 2.7 Whatman GF/D and 0.22 µm Sterivex filters. Samples were initially placed on ice in the field, and then refrigerated until shipment with ice packs.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1747681 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1747681
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1747722 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1747722
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1931113 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1931113
completed
J. Cameron Thrash
University of Southern California
510-292-7785
3616 Trousdale Pkwy AHF 209
Los Angeles
CA
90089
USA
thrash@usc.edu
pointOfContact
Elizabeth Kujawinski
Woods Hole Oceanographic Institution
508-289-3493
266 Woods Hole Rd. MS #4
Woods Hole
MA
02543
USA
ekujawinski@whoi.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Site
Lat
Lon
Date
Time_Central
Offset
Time_UTC
Temp
Cond
Salinity
pH
Cell_counts
PO4
SiOH4
NO3
NO2
NH4
ISO_DateTime_UTC
Millipore Guava 5HT HPL benchtop flow cytometer
YSI 556 MPS handheld meter
Masterflex I/P peristaltic pump
theme
None, User defined
site
latitude
longitude
date
time of day
time difference
temperature of sample or a generic measurement (not in-situ water temp)
conductivity
salinity
pH
count
reactive phosphorus (PO4)
Silicate, Si(OH)4, silicic acid
Nitrate
Nitrite
Ammonium
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Multi Parameter Portable Meter
Pump
instrument
BCO-DMO Standard Instruments
Coastal_SAR11
service
Deployment Activity
Coastal Louisiana
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Collaborative Research: EAGER: Salinity-based selection between sister clades of abundant coastal bacterioplankton
https://osprey.bco-dmo.org/project/707006
Collaborative Research: EAGER: Salinity-based selection between sister clades of abundant coastal bacterioplankton
<p><em>NSF award abstract:</em><br />
Adaptation to new environments is a fundamental challenge for organisms, including microbes, in expanding their habitat range. It is important to investigate the cellular mechanisms underlying salinity tolerance in coastal bacterioplankton and their different responses to salinity in nature because (i) it will provide fundamental understanding for how microorganisms evolve to inhabit environments with different salinities, and (ii) alterations in coastal salinity are connected to climate change, so the way these alterations affect abundant coastal microorganisms also alters the biogeochemical cycling of, e.g., carbon. The project will examine microbial adaptations to salinity and determine how changes in salinity affect microbial metabolism using two closely related groups of abundant coastal bacterioplankton as model taxa. In addition, the research will continue and expand microbiology Course-based Undergraduate Research Experiences (mCUREs) in high-throughput cultivation and microbial characterization at the Lousiana State University. Sections of freshman biology laboratories will learn how to isolate, characterize, and molecularly identify microorganisms from local aquatic systems. mCURE sections will lead to newly isolated strains, genome sequences, and physiological data, these results will be published with the contributing students as co-authors. The relative success of mCURE sections will be assessed compared to traditional freshman biology sections. mCURE sections will offer unique opportunities for LSU students by creating excitement about research through discovery of new organisms and generating knowledge of the coastal habitats that are essential to the livelihood of the Gulf Coast.</p>
<p>The evolutionary transition between salt- and freshwater environments occurs rarely in microorganisms. In one of the most abundant aquatic groups, SAR11, the transition between salt- and freshwater environments has happened only once: all freshwater SAR11 belong to subclade IIIb/LD12, which has also been found to inhabit coastal environments where salinity varies widely. The first reported isolates of the SAR11 freshwater clade LD12 and a member of the sister clade IIIa from the same region are now available. These pure culture representatives provide a powerful model for experimentally investigating adaptations to new environments in microorganisms, specifically (i) the genomic pathway and regulatory distinctions that arise during the evolutionary transition from marine to freshwater environments, and (ii) the physiological mechanisms that underlie the ecological restrictions imposed on microorganisms by ionic strength in coastal and freshwater environments. Furthermore, because these organisms have distinct differences in metabolic potential, the isolates facilitate testing (iii) the effects of changing coastal salinity on microbial contributions to other biogeochemical cycles, such as that for carbon. The project will test the hypothesis that the relative ionic strength tolerances between the sister lineages (LD12, IIIa) result from fundamental differences in metabolic flexibility at a genomic and regulatory level. To do so it will assess transcriptional and metabolic responses to varied ionic strength for both taxa and measure the distribution and activity of both groups in nature to translate laboratory findings to the field. The research will provide new understanding of LD12 habitat range and insights into how the "freshwater" lineage evolved from a SAR11 common ancestor. The project will also more generally provide important information on microbial responses to salinity changes in coastal systems and the evolutionary paths separating freshwater and marine microorganisms.</p>
<p>This award is co-funded by Biological Oceanography, Division of Ocean Sciences in the Directorate for Geosciences and by Systems and Synthetic Biology, Division of Molecular and Cellular Biosciences in the Directorate for Biological Sciences.</p>
CoastalSAR11
largerWorkCitation
project
eng; USA
oceans
Coastal Louisiana
-93.340714
-89.676029
29.243342
29.867989
2018-01-27
2018-11-16
Coastal Louisiana, northern Gulf of Mexico
0
BCO-DMO catalogue of parameters from Physiochemical data from samples collected along the coast of Louisiana, USA during 2018
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/745457.rdf
Name: Site
Units: unitless
Description: <p>Sampling site designation</p>
http://lod.bco-dmo.org/id/dataset-parameter/745458.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude of site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745459.rdf
Name: Lon
Units: decimal degrees
Description: <p>Longitude of site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745460.rdf
Name: Date
Units: unitless
Description: <p>Date of sampling; format: yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/745461.rdf
Name: Time_Central
Units: unitless
Description: <p>Time of sampling in the Central Time Zone, USA; format: HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/745462.rdf
Name: Offset
Units: unitless
Description: <p>Universal time coordinated (UTC) offset, corrected for daylight savings</p>
http://lod.bco-dmo.org/id/dataset-parameter/745463.rdf
Name: Time_UTC
Units: unitless
Description: <p>Universal Time Coordinated (UTC) subtracting Central Time from the UTC offset; format: HH:MM</p>
http://lod.bco-dmo.org/id/dataset-parameter/745464.rdf
Name: Temp
Units: degrees Celsius
Description: <p>Temperature measured via YSI at the sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745465.rdf
Name: Cond
Units: ms/cm
Description: <p>Conductivity measured via YSI at the sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745466.rdf
Name: Salinity
Units: unitless
Description: <p>Calculated salinity based on the conductivity measurement from the YSI</p>
http://lod.bco-dmo.org/id/dataset-parameter/745467.rdf
Name: pH
Units: unitless
Description: <p>pH of the seawater at the sampling site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745468.rdf
Name: Cell_counts
Units: cells/mL
Description: <p>Number of cells passing through a 2.7 µm filter (Whatman GF/D) determined via flow cytometry</p>
http://lod.bco-dmo.org/id/dataset-parameter/745469.rdf
Name: PO4
Units: umol/L
Description: <p>Concentration of phosphate in seawater from the site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745470.rdf
Name: SiOH4
Units: umol/L
Description: <p>Concentration of silicate in seawater from the site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745471.rdf
Name: NO3
Units: umol/L
Description: <p>Concentration of nitrate in seawater from the site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745472.rdf
Name: NO2
Units: umol/L
Description: <p>Concentration of nitrite in seawater from the site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745473.rdf
Name: NH4
Units: umol/L
Description: <p>Concentration of ammonium in seawater from the site</p>
http://lod.bco-dmo.org/id/dataset-parameter/745474.rdf
Name: ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time of sampling (UTC) formatted to ISO 8601 standard; format: yyyy-mm-ddTHH:MMZ</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
5361
https://darchive.mblwhoilibrary.org/bitstream/1912/25376/1/dataset-745449_coastal-sar11-physiochemical-data__v2.tsv
download
3755
https://darchive.mblwhoilibrary.org/bitstream/1912/24252/1/dataset-745449_coastal-sar11-physico-chemical-data__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.745449.1
download
onLine
dataset
<p>Samples were collected manually by filling an acid-washed and autoclaved 20L carboy after three rinses. Temperature, pH, and salinity were taken using a handheld YSI. Cell counts were obtained by filtering water through a 2.7 µm Whatman GF/D filter, fixing with 10% formaldehyde, placing on ice, and then counting using flow cytometry (Thrash et al., 2015, Hydrocarbon and Lipid Microbiology Protocols). Inorganic nutrients were measured at the University of Washington Marine Chemistry Laboratory after sequential filtration through 2.7 Whatman GF/D and 0.22 µm Sterivex filters. Samples were initially placed on ice in the field, and then refrigerated until shipment with ice packs.</p>
Specified by the Principal Investigator(s)
<p><strong>Data Problem Report:&nbsp;</strong><br />
pH is not reported for the first time points because a crack was noticed in the housing of the YSI cable that seemed to be associated with calibration. This was subsequently replaced and all values were also checked in the lab with a Fisherbrand pH meter.</p>
<p>Sample ARD 9/19/18 was not filtered on site because of bad weather. Therefore, the filtration steps for nutrients were conducted back at the lab after a 2.5 hour transit time</p>
<p>Sample ARD 11/16/18 was filtered for nutrients after a 3 hour delay at site CJ because of power supply issues at the ARD site.</p>
<p><strong>BCO-DMO Data Processing Notes:</strong><br />
-Reformatted column names&nbsp;to comply with BCO-DMO standards;<br />
-Replaced blank cells with nd;<br />
-Reformatted dates;<br />
-Added ISO DateTime column.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Millipore Guava 5HT HPL benchtop flow cytometer
Millipore Guava 5HT HPL benchtop flow cytometer
PI Supplied Instrument Name: Millipore Guava 5HT HPL benchtop flow cytometer PI Supplied Instrument Description:Used for sampling Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument 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) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
YSI 556 MPS handheld meter
YSI 556 MPS handheld meter
PI Supplied Instrument Name: YSI 556 MPS handheld meter PI Supplied Instrument Description:YSI 556 MPS handheld meter, calibrated with salinity and pH standards immediately prior to use Instrument Name: Multi Parameter Portable Meter Instrument Short Name: Instrument Description: An analytical instrument that can measure multiple parameters, such as pH, EC, TDS, DO and temperature with one device and is portable or hand-held.
Masterflex I/P peristaltic pump
Masterflex I/P peristaltic pump
PI Supplied Instrument Name: Masterflex I/P peristaltic pump PI Supplied Instrument Description:Used for sampling Instrument Name: Pump Instrument Short Name: Instrument 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
Deployment: Coastal_SAR11
Coastal_SAR11
shoreside Gulf of Mexico
shoreside
shoreside Gulf of Mexico
shoreside