http://lod.bco-dmo.org/id/dataset/839985
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
2021-02-05
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sample log recorded during cruise LMG1801 on R/V Laurence M. Gould from January to February 2018
2021-04-08
publication
2021-04-08
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-04-08
publication
https://doi.org/10.26008/1912/bco-dmo.839985.1
James T. Hollibaugh
University of Georgia
principalInvestigator
Brian N. Popp
University of Hawaiʻi at Mānoa
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: Hollibaugh, J. T., Popp, B. N. (2021) Sample log recorded during cruise LMG1801 on R/V Laurence M. Gould from January to February 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-04-08 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.839985.1 [access date]
LMG1801 Sample Log Dataset Description: Methods and Sampling: <p><strong>Sample Collection</strong>. Samples were collected on the Antarctic continental shelf and slope west of the Antarctic Peninsula within the PAL-LTER sampling domain (<a href="http://pal.lternet.edu/" target="_blank">http://pal.lternet.edu/</a>) during summer (cruise dates 30 Dec 2017 through 12 Feb 2018; sampling dates 5 Jan to 4 Feb 2018) from the ARSV Laurence M Gould (LMG 1801, PAL-LTER cruise 26, DOI:&nbsp;<a href="http://dx.doi.org/10.7284/907858" target="_blank">10.7284/907858</a>). Sampling focused on three or 4 depths at each station chosen to represent the Antarctic Surface Water (ASW, 0 -34 m depth), the Winter Water (WW, the water column temperature minimum, generally between 35 and 174 m) the Circumpolar Deep Water (CDW, 175-1000 m) and slope water (SLOPE, &gt;1000 m, generally ~10 m above the bottom at deep stations on the slope, 2500-3048m). Water samples were collected from Niskin bottles (General Oceanics Inc., Miami, FL, USA) into opaque 2 L HDPE plastic bottles or into aged, acid-washed, sample-rinsed 250 ml polycarbonate bottles (Nalge) completely filled (~270 mL) directly from Niskin bottles as soon as possible after the rosette was secured on deck. Subsequent processing took place in an adjacent laboratory.</p>
<p>Samples for DNA analysis were taken from the 2 L opaque HDPE bottles and were filtered under pressure through 0.22 um pore size Sterivex GVWP filters (EMD Millipore, Billerica, MA, USA) using a peristaltic pump. Residual seawater was expelled from the filter using a syringe filled with air, then ~1.8 ml of lysis buffer (0.75 M sucrose, 40 mM EDTA, 50 mM Tris, pH 8.3) was added to the filter capsule, which was capped and placed in a -20 °C freezer. The frozen samples were aggregated into Ziploc Freezer Bags and transferred to a -80 °C freezer for the remainder of the cruise and for shipping to the laboratory.</p>
<p>Two samples of the Sterivex filtrate (40 mL each into new 50 mL disposable centrifuge tubes, VWR, rinsed 3x with sample) were frozen immediately at -20 °C, then aggregated into Ziploc Freezer Bags and transferred to a -80 ° freezer for the remainder of the cruise and for shipping to the laboratory. These were used for subsequent determination of 1) urea concentration and 2) the natural abundance of&nbsp;<sup>15</sup>N in the nitrite plus nitrate pools (<sup>15</sup>NOₓ hereinafter). An additional sample of the Sterivex filtrate was stored in a polycarbonate bottle at 4 °C for subsequent onboard determination of ammonia concentration by the Holmes et al (1999) o-phthaldialdehyde method and nitrite concentration by the diazo-coupling method (Strickland and Parsons 1972). Technical difficulties encountered during onboard analysis resulted in the loss of ammonium and nitrite data for some samples.</p>
<p>Samples for DNA and chemical analyses were shipped on dry ice from Punta Arenas, Chile to the Hollibaugh laboratory at the University of Georgia. Upon arrival they were stored in a -80 °C freezer until analyzed. Samples for&nbsp;<sup>15</sup>N analysis were shipped on dry ice from Punta Arenas, Chile to the Popp laboratory at the University of Hawaii. Upon arrival they were stored in a -40 °C freezer until analyzed.</p>
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: OPP-1643466 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1643466
Funding provided by NSF Office of Polar Programs (formerly NSF PLR) (NSF OPP) Award Number: OPP-1643345 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1643345
completed
James T. Hollibaugh
University of Georgia
706-542-7671
Department of Marine Sciences, University of Georgia
Athens
GA
30602
USA
aquadoc@uga.edu
pointOfContact
Brian N. Popp
University of Hawaiʻi at Mānoa
808-956-6206
Department of Earth Sciences 1680 East-West Road
Honolulu
HI
96822
USA
popp@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Event_Log_Number
Cast_Start_ISO_DateTime_UTC
Latitude
Longitude
Station_Description
LTER_Grid_Station
Sample_Depth
Niskin_Bottle_Number
Sample_Temp
Sample_Salinity
Vol_Filtered_for_DNA
Ammonium_oxidation_incubation_Start_Time_GMT
Ammonium_oxidation_incubation_End_Time_GMT
Nitrite_oxidation_incubation_Start_Time_GMT
Nitrite_oxidation_incubation_End_Time_GMT
Urea_oxidation_incubation_Start_Time_GMT
Urea_oxidation_incubation_End_Time_GMT
Putrescine_oxidation_incubation_Start_Time_GMT
Putrescine_oxidation_incubation_End_Time_GMT
C14_Incubation_Start_Time_GMT
C14_Incubation_End_Time_GMT
Other_Notes
CTD rosette
Niskin bottles (General Oceanics Inc., Miami, FL, USA)
theme
None, User defined
event
ISO_DateTime_UTC
latitude
longitude
site description
station
depth
bottle
water temperature at measurement depth
salinity
volume of water filtered
date
Date and time
comments
featureType
BCO-DMO Standard Parameters
CTD - profiler
Niskin bottle
instrument
BCO-DMO Standard Instruments
LMG1801
service
Deployment Activity
Palmer LTER
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: Chemoautotrophy in Antarctic Bacterioplankton Communities Supported by the Oxidation of Urea-derived Nitrogen
https://osprey.bco-dmo.org/project/775717
Collaborative Research: Chemoautotrophy in Antarctic Bacterioplankton Communities Supported by the Oxidation of Urea-derived Nitrogen
<p><em>NSF Award Abstract:</em><br />
Part 1: The project addresses fundamental questions regarding the role of nitrification (the conversion of ammonium to nitrate by a two-step process involving two different guilds of microorganisms: ammonia- and nitrite-oxidizers) in the Antarctic marine ecosystem. Specifically, the project seeks to evaluate the contribution of primary production supported by the energy in nitrogen compounds to the overall supply of organic carbon to the food web of the Southern Ocean. Previous measurements indicate that nitrification could contribute about 9% to primary production supporting the Antarctic food web on an annual basis, but those measurements did not include the additional production associated with nitrite oxidation. Additionally, the project will aim to determine the significance of the contribution of other sources of nitrogen, (specifically organic nitrogen and urea released by other organisms) to nitrification because these contributions may not be assessed by standard protocols. Such work will aid in better understanding the basis of the energy for the Antarctic marine ecosystems on an annual basis as well as better aid in understanding the energetics of the ecosystem in times and places where primary production based on light energy is limited (i.e. during the polar night or under sea ice cover).</p>
<p>This project will result in training a postdoctoral researcher and provide undergraduate students opportunities to gain hand-on experience with research on microbial geochemistry. The Palmer Long Term Ecological Research (LTER) activities have focused largely on the interaction between ocean climate and the marine food web affecting top predators. Relatively little effort has been devoted to studying processes related to the microbial geochemistry of nitrogen cycling, yet these are a major themes at other LTER sites. This work will contribute substantially to understanding an important aspect of nitrogen cycling and bacterioplankton production in the study area. The team will be working synergistically and be participating fully in the education and outreach efforts of the Palmer LTER, including making highlights of the findings available for posting to their project web site and participating in any special efforts they have in the area of outreach.</p>
<p>Part 2: The proposed work will quantify oxidation rates of 15N supplied as ammonium, urea and nitrite, allowing the estimation of the contribution of urea-derived N and complete nitrification (ammonia to nitrate) to chemoautotrophy and bacterioplankton production in Antarctic coastal waters. The project will compare these estimates to direct measurements of the incorporation of 14C into organic matter in the dark for an independent estimate of chemoautotrophy. The team aims to collect samples spanning the water column: from surface water (~10 m), winter water (50-100 m) and circumpolar deep water (>150 m); on a cruise surveying the continental shelf and slope west of the Antarctic Peninsula in the austral summer of 2018. Other samples will be taken to measure the concentrations of nitrate, nitrite, ammonia and urea, for qPCR analysis of the abundance of relevant microorganisms, and for studies of related processes. The project will rely on collaboration with the existing Palmer LTER to ensure that ancillary data (bacterioplankton abundance and production, chlorophyll, physical and chemical variables) will be available. The synergistic activities of this project along with the LTER activities will provide a unique opportunity to assess chemoautotrophy in context of the overall ecosystem's dynamics- including both primary and secondary production processes.</p>
Oxidation of Urea N
largerWorkCitation
project
eng; USA
oceans
Palmer LTER
-78.20207
-64.03196
-69.25615
-64.03196
2018-01-05
2018-02-04
Coastal, shelf and slope waters off the West Antarctic Peninsula, PAL-LTER sampling grid, Lawrence M Gould cruise 18-01
0
BCO-DMO catalogue of parameters from Sample log recorded during cruise LMG1801 on R/V Laurence M. Gould from January to February 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/839998.rdf
Name: Event_Log_Number
Units: unitless
Description: <p>Sequential numbers keyed to the bridge log of activities</p>
http://lod.bco-dmo.org/id/dataset-parameter/839999.rdf
Name: Cast_Start_ISO_DateTime_UTC
Units: unitless
Description: <p>Date and time of day for beginning CTD cast = sample collection; 24-hour clock; formatted to ISO8601 standard (UTC/GMT): YYYY-MM-DDThh:mmZ</p>
http://lod.bco-dmo.org/id/dataset-parameter/840000.rdf
Name: Latitude
Units: degrees North
Description: <p>Latitude in decimal degrees (negative values = South)</p>
http://lod.bco-dmo.org/id/dataset-parameter/840001.rdf
Name: Longitude
Units: degrees East
Description: <p>Longitude in decimal degrees (negative values = West)</p>
http://lod.bco-dmo.org/id/dataset-parameter/840002.rdf
Name: Station_Description
Units: unitless
Description: <p>PAL-LTER category for the station</p>
http://lod.bco-dmo.org/id/dataset-parameter/840003.rdf
Name: LTER_Grid_Station
Units: unitless
Description: <p>Station location on the PAL-LTER sampling grid (<a href="http://pal.lternet.edu">http://pal.lternet.edu</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/840004.rdf
Name: Sample_Depth
Units: meters (m)
Description: <p>Depth sampled in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/840005.rdf
Name: Niskin_Bottle_Number
Units: unitless
Description: <p>The number of the Niskin bottle from which the sample was taken</p>
http://lod.bco-dmo.org/id/dataset-parameter/840006.rdf
Name: Sample_Temp
Units: degrees Celsius
Description: <p>Water temperature from the CTD in Centigrade degrees from CTD data</p>
http://lod.bco-dmo.org/id/dataset-parameter/840007.rdf
Name: Sample_Salinity
Units: PSU
Description: <p>Salinity calculated from water temperature and conductivity from the ship's CTD, practical salinity units</p>
http://lod.bco-dmo.org/id/dataset-parameter/840008.rdf
Name: Vol_Filtered_for_DNA
Units: liters (L)
Description: <p>The amount of water filtered under pressure from a peristaltic pump through a Millipore Sterivex GV filter capsule (0.22 micron pore size)</p>
http://lod.bco-dmo.org/id/dataset-parameter/840009.rdf
Name: Ammonium_oxidation_incubation_Start_Time_GMT
Units: unitless
Description: <p>Time when 15N NH4 was added to subsamples to initiate the ammonia oxidation rate measurements: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840010.rdf
Name: Ammonium_oxidation_incubation_End_Time_GMT
Units: unitless
Description: <p>Time when ammonia oxidation rate measurements were terminated by freezing a 45 mL susample: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840011.rdf
Name: Nitrite_oxidation_incubation_Start_Time_GMT
Units: unitless
Description: <p>Time when 15N nitrite was added to subsamples to initiate thenitrite oxidation rate measurements: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840012.rdf
Name: Nitrite_oxidation_incubation_End_Time_GMT
Units: unitless
Description: <p>Time when nitrite oxidation rate measurements were terminated by freezing a 45 mL susample: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840013.rdf
Name: Urea_oxidation_incubation_Start_Time_GMT
Units: unitless
Description: <p>Time when 15N urea was added to subsamples to initiate the urea N oxidation rate measurements: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840014.rdf
Name: Urea_oxidation_incubation_End_Time_GMT
Units: unitless
Description: <p>Time when urea-N oxidation rate measurements were terminated by freezing a 45 mL susample: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840015.rdf
Name: Putrescine_oxidation_incubation_Start_Time_GMT
Units: unitless
Description: <p>Time when 15N NH4 was added to subsamples to initiate the ammonia oxidation rate measurements: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840016.rdf
Name: Putrescine_oxidation_incubation_End_Time_GMT
Units: unitless
Description: <p>Time when putrescine-N oxidation rate measurements were terminated by freezing a 45 mL susample: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840017.rdf
Name: C14_Incubation_Start_Time_GMT
Units: unitless
Description: <p>Time when 14C NaHCO3 was added to subsamples to initiate the chemoautotrophy measurements: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840018.rdf
Name: C14_Incubation_End_Time_GMT
Units: unitless
Description: <p>Time when chemoautotrophy samples were vacuum filtered through Millipore GS (0.22 micron pore size) filters: MMDDYY hh:mm format, 24-hour clock, Greenwich Mean Time</p>
http://lod.bco-dmo.org/id/dataset-parameter/840019.rdf
Name: Other_Notes
Units: unitless
Description: <p>Notes relevant to the activities performed at this station or with this sample</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
23342
https://darchive.mblwhoilibrary.org/bitstream/1912/26920/1/dataset-839985_lmg1801-sample-log__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.839985.1
download
onLine
dataset
<p><strong>Sample Collection</strong>. Samples were collected on the Antarctic continental shelf and slope west of the Antarctic Peninsula within the PAL-LTER sampling domain (<a href="http://pal.lternet.edu/" target="_blank">http://pal.lternet.edu/</a>) during summer (cruise dates 30 Dec 2017 through 12 Feb 2018; sampling dates 5 Jan to 4 Feb 2018) from the ARSV Laurence M Gould (LMG 1801, PAL-LTER cruise 26, DOI:&nbsp;<a href="http://dx.doi.org/10.7284/907858" target="_blank">10.7284/907858</a>). Sampling focused on three or 4 depths at each station chosen to represent the Antarctic Surface Water (ASW, 0 -34 m depth), the Winter Water (WW, the water column temperature minimum, generally between 35 and 174 m) the Circumpolar Deep Water (CDW, 175-1000 m) and slope water (SLOPE, &gt;1000 m, generally ~10 m above the bottom at deep stations on the slope, 2500-3048m). Water samples were collected from Niskin bottles (General Oceanics Inc., Miami, FL, USA) into opaque 2 L HDPE plastic bottles or into aged, acid-washed, sample-rinsed 250 ml polycarbonate bottles (Nalge) completely filled (~270 mL) directly from Niskin bottles as soon as possible after the rosette was secured on deck. Subsequent processing took place in an adjacent laboratory.</p>
<p>Samples for DNA analysis were taken from the 2 L opaque HDPE bottles and were filtered under pressure through 0.22 um pore size Sterivex GVWP filters (EMD Millipore, Billerica, MA, USA) using a peristaltic pump. Residual seawater was expelled from the filter using a syringe filled with air, then ~1.8 ml of lysis buffer (0.75 M sucrose, 40 mM EDTA, 50 mM Tris, pH 8.3) was added to the filter capsule, which was capped and placed in a -20 °C freezer. The frozen samples were aggregated into Ziploc Freezer Bags and transferred to a -80 °C freezer for the remainder of the cruise and for shipping to the laboratory.</p>
<p>Two samples of the Sterivex filtrate (40 mL each into new 50 mL disposable centrifuge tubes, VWR, rinsed 3x with sample) were frozen immediately at -20 °C, then aggregated into Ziploc Freezer Bags and transferred to a -80 ° freezer for the remainder of the cruise and for shipping to the laboratory. These were used for subsequent determination of 1) urea concentration and 2) the natural abundance of&nbsp;<sup>15</sup>N in the nitrite plus nitrate pools (<sup>15</sup>NOₓ hereinafter). An additional sample of the Sterivex filtrate was stored in a polycarbonate bottle at 4 °C for subsequent onboard determination of ammonia concentration by the Holmes et al (1999) o-phthaldialdehyde method and nitrite concentration by the diazo-coupling method (Strickland and Parsons 1972). Technical difficulties encountered during onboard analysis resulted in the loss of ammonium and nitrite data for some samples.</p>
<p>Samples for DNA and chemical analyses were shipped on dry ice from Punta Arenas, Chile to the Hollibaugh laboratory at the University of Georgia. Upon arrival they were stored in a -80 °C freezer until analyzed. Samples for&nbsp;<sup>15</sup>N analysis were shipped on dry ice from Punta Arenas, Chile to the Popp laboratory at the University of Hawaii. Upon arrival they were stored in a -40 °C freezer until analyzed.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- replaced 'NAN' with 'nd' as missing data identifier;<br />
- renamed fields to comply with BCO-DMO naming conventions;<br />
- corrected dates where month and day were reversed;<br />
- converted cast start date/time field to ISO8601 format;<br />
- replaced commas with semi-colons in the Other_Notes column;<br />
- 2021-03-02: revised/updated the Acquisition Description section of the metadata;<br />
- 2021-04-08: replaced data file with copy received on 2021-03-18.</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
CTD rosette
CTD rosette
PI Supplied Instrument Name: CTD rosette Instrument Name: CTD - profiler Instrument Short Name: Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/130/
Niskin bottles (General Oceanics Inc., Miami, FL, USA)
Niskin bottles (General Oceanics Inc., Miami, FL, USA)
PI Supplied Instrument Name: Niskin bottles (General Oceanics Inc., Miami, FL, USA) Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument 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. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
Cruise: LMG1801
LMG1801
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel
ARSV Laurence M. Gould
Community Standard Description
International Council for the Exploration of the Sea
ARSV Laurence M. Gould
vessel