http://lod.bco-dmo.org/id/dataset/842944
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
2021-03-02
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Natural abundance of 15N and 18O measured in samples collected over the continental shelf west of the Antarctic Peninsula on cruise LMG1801 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.842944.1
Brian N. Popp
University of Hawaiʻi at Mānoa
principalInvestigator
James T. Hollibaugh
University of Georgia
principalInvestigator
Natalie J. Wallsgrove
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: Popp, B. N., Wallsgrove, N. J., Hollibaugh, J. T. (2021) Natural abundance of 15N and 18O measured in samples collected over the continental shelf west of the Antarctic Peninsula on cruise LMG1801 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.842944.1 [access date]
Natural abundance of 15N and 18O from LMG1801 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: <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 <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 <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>
<p><strong>Nitrogen oxidation rates.</strong> Oxidation rates of N supplied as ammonium, nitrite, urea and putrescine (1,4 diaminobutane) were measured in ~48 h incubations using <sup>15</sup>N-labeled substrates (&gt;98 at% <sup>15</sup>N, Cambridge Isotope Laboratories, Tewksbury,MA, USA) added within ~1 hr of sample collection to yield ~44 nM amendments (Santoro et al., 2010; Beman et al., 2012). Labeled substrates were added to duplicate bottles that were placed in cardboard boxes and incubated in the dark in a Percival incubator (Perry, IA, USA). Incubation temperature was recorded at 5-minute time steps with HOBO TidBit data loggers (Onset Computer Corp., Bourne MA, Figure 1) placed in bottles of filtered seawater incubated in cardboard boxes identical to those used for experiments (see the "<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Incubator_Temperature.xlsx" target="_blank">Incubator_Temperature.xlsx</a>" Supplemental File). Incubations were terminated after ~48 hr by decanting 40 mL subsamples from each bottle into new, sample rinsed, 50 mL polypropylene centrifuge tubes that were immediately frozen at -80 °C. Water in these tubes was used for subsequent analysis of <sup>15</sup>NOₓ. The natural abundance of <sup>15</sup>N in NOₓ was taken as the initial (time = 0) value for calculating the amount of <sup>15</sup>N oxidized to nitrate or nitrite during the incubations.</p>
<p><strong>Chemical analyses.</strong> Urea content was determined by the diacetyl monoxime method (Rahmatullah and Boyde 1980, Mulvenna and Savidge 1992). Subsamples from samples that were also used to determine oxidation of <sup>15</sup>N supplied as putrescine were sent to Dr. X. Mou’s laboratory at Kent State University where they were analyzed to determine polyamine and DFAA content as described previously (Lu et al 2014).</p>
<p><strong><sup>15</sup>N in nitrite plus nitrate</strong>. The <sup>15</sup>NOₓ in samples was measured using the ‘denitrifier method’ (Sigman et al., 2001) with <em>Pseudomonas aureofaciens</em> as described in Popp et al. (1995), Dore et al. (1998) and Beman et al. (2011). The nitrous oxide produced was analyzed using a Gas Bench II coupled to a MAT 252 mass spectrometer following the recommendations of Casciotti et al. (2002). Typically nineteen samples plus one sample duplicate was analyzed along with duplicate reference materials USGS 32, USGS 34 and USGS 35 (or NIST 3), which were used to normalize the measured d<sup>15</sup>N values to AIR. In addition, a laboratory reference solution made from analytical grade NaNO₃ with d<sup>15</sup>N value (-52.2‰) that was known through extensive characterization using NIST/USGS reference materials was also analyzed in duplicate with each batch of 19 samples.</p>
<p>We calculated oxidation rates from d<sup>15</sup>N enrichment of the NOₓ pool in the bottles at the ends of the incubations compared to the initial value in the unamended seawater sample ("natural abundance"). We assumed that the d<sup>15</sup>N of naturally occurring ammonia, urea and putrescine is the same as that of N in bulk organic matter, and that the d<sup>15</sup>N value of nitrite is our samples is -30 o/oo as reported by Smart et al. (2015). Samples with low or no activity sometimes yielded negative rates because the d<sup>15</sup>NOₓ "natural abundance" value for that sample was greater than the d<sup>15</sup>NOₓ value of amended sample. We analyzed control samples consisting of filtered seawater taken at the beginning of the cruise, amended with <sup>15</sup>NO₂, then immediately frozen at -80 °C, or "time zero" samples from time course experiments performed throughout the cruise, to determine the contribution of autooxidation or isotope exchange to the apparent rate of nitrite oxidation. These samples were treated with sulfamic acid to remove unreacted <sup>15</sup>NO₂ (Granger and Sigman 2009). The analysis indicated that about 7.9% of the <sup>15</sup>N supplied as NO₂ had been converted to <sup>15</sup>NO₃ by the time we analyzed the samples. We also performed an independent chemical analysis of nitrite and nitrate (Strickland and Parsons 1972) in the (nominally) 0.125 mM <sup>15</sup>NO₂ working stock solution a few months after the cruise. This analysis indicated that about 14.3% of the of the nitrite plus nitrate in the stock was nitrate. Because this stock had been handled and shipped separately from the cruise samples, we used 7.9% as the best estimate of the amount of <sup>15</sup>N label converted to nitrate. We have incorporated corrections for this reaction into rates calculated from field data.</p>
<p>We ran time-course incubations with samples from 2 or 3 depths at 34 stations to verify that oxidation rates did not change significantly during incubations, for example, due to substrate depletion or changes in the population of ammonia oxidizers. These experiments were set up in 250 ml polycarbonate bottles as above. Two bottles were sampled at each time point over time courses of 72 to 96 h. These data are presented in <a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Table1.pdf" target="_blank">Table 1</a> (PDF; see Supplemental Files). AO rates determined from the slope of linear regressions of the data from a given sample were compared to rates determined from samples taken at the 48 hr time point. We performed analogous experiments to examine the effect on N oxidation rates of variation in incubation temperature and in substrate concentration.</p>
<p>Summary Statistics for d15NOx (mean, median, maximum, minimum, and standard error of d15NOx measurements grouped by the water mass depth ranges) are provided in the Supplemental File&nbsp;<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/842944/d15NOx_Summary_Statistics.JPG" target="_blank">d15NOx_Summary_Statistics.JPG</a>.</p>
<p><strong>Precision</strong>. Analytical uncertainty in d<sup>15</sup>N values was determined from duplicate analyses of USGS reference materials, our laboratory reference solution and samples analyzed in duplicate and ranged from 0.36‰ to 0.56‰ (<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Table1.pdf" target="_blank">Table 1</a> (PDF) Supplemental File). All rate measurements were also performed in duplicate (biological replicates) and their uncertainty is also presented in Table 1. Accuracy was determined based on isotope analysis of the laboratory reference solution, which was not used to normalize the isotopic results of samples and was found to be 0.42‰ (at% <sup>15</sup>N = 0.00019, n = 56).</p>
<p><strong>Rate calculations.</strong> We integrated the data we collected to calculate oxidation rates of N supplied as ammonia and urea as described in Popp et al. (1995), Dore et al. (1998) and Beman et al. (2011). We used ammonium concentration data from shipboard analyses. Nitrite + nitrate concentrations were determined by PAL-LTER personnel and were obtained from their database. Urea concentrations were measured on samples shipped frozen to the University of Georgia (Hollibaugh lab). Chemical data needed for rate calculations were not available for some samples so we substituted water mass averages determined from other samples taken on the cruise.</p>
<p>We determined the limits of detection and precision of nutrient analyses as follows. The precision of nitrate plus nitrite analyses run by LTER personnel (<a href="https://oceaninformatics.ucsd.edu/datazoo/catalogs/pallter/datasets/27" target="_blank">https://oceaninformatics.ucsd.edu/datazoo/catalogs/pallter/datasets/27</a>) was reported to be 100 nM. The precision and limit of detection of putrescine (polyamine) analysis is given in Lu et al. (2018) as 1 nM. We determined the precision of ammonium, urea and nitrite analyses as the mean standard deviation of replicate (2 or 3) analyses of a given sample. They are: ammonium, 65 nM; urea, 10 nM; and nitrite, 70 nM. The limits of detection were taken as 1.96 times the precision of the relevant measurements.</p>
<p>We ran Monte Carlo simulations to estimate the precision and the limits of detection of rate measurements. The models incorporated the estimates of precision given above and the means of the measured <em>in situ</em> concentrations of the reactants, the mean <em>in situ</em> concentration of NOₓ (from PAL-LTER data), the precision of the measured d<sup>15</sup>NOₓ in the experiments at the beginning (natural abundance) and end of the incubations. We ran 10,000 trials using random numbers generated with population means and standard deviations (assuming normally distributed variance and produced using an Excel spreadsheet in the EasyFit<sup>®</sup> app) ) equivalent to the test values. The standard deviation of the 10,000 rates calculated in this manner was taken as an overall estimate of the precision of the rates we report. The results of these models are summarized in Supplemental Table 3. Our estimates of the precision of the rate measurements (oxidation of <sup>15</sup>N supplied as ammonium urea, putrescine or nitrite to <sup>15</sup>NOₓ, nmol L<sup>-1</sup> d<sup>-1</sup>) are: ammonia, 2.18; urea 0.31; putrescine, 0.51; nitrite, 4.6, for relative standard deviations (RSD; ((standard deviation/mean)*100)) of: 15.3%; 11.3%; 8.2% and 32%, respectively, of the calculated rates. Model runs, which also tested the sensitivity of the calculated rates to the accuracy of estimates of some variables, are summarized in Supplemental <a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Table3_Summary_of_Monte_Carlo_Models.xlsx" target="_blank">Table 3</a> (.xlsx file), which also includes the equations used to calculate rates.</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
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
James T. Hollibaugh
University of Georgia
706-542-7671
Department of Marine Sciences, University of Georgia
Athens
GA
30602
USA
aquadoc@uga.edu
pointOfContact
Natalie J. Wallsgrove
University of Hawaiʻi at Mānoa
Isotope Biogeochemistry Lab University of Hawaii at Manoa
Honolulu
HI
96822
USA
nw@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Event_Log_Number
Cast_Start_Time_GMT
Latitude
Longitude
Station_Description
LTER_Grid_Station
Sample_Depth
d15N
d18O
Analytical_Batch
Percival incubator
Gas Bench II coupled to a MAT 252 mass spectrometer
Niskin bottles (General Oceanics Inc., Miami, FL, USA)
HOBO TidBit data loggers
theme
None, User defined
event
ISO_DateTime_UTC
latitude
longitude
site description
station
depth
delta 15N NO3+NO2
oxygen 16 to oxygen 18 ratio
sample identification
featureType
BCO-DMO Standard Parameters
In-situ incubator
Isotope-ratio Mass Spectrometer
Niskin bottle
Temperature Logger
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 Natural abundance of 15N and 18O measured in samples collected over the continental shelf west of the Antarctic Peninsula on cruise LMG1801 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/845137.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/845138.rdf
Name: Cast_Start_Time_GMT
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/845139.rdf
Name: Latitude
Units: degrees North
Description: <p>Latitude in decimal degrees (negative values = South)</p>
http://lod.bco-dmo.org/id/dataset-parameter/845140.rdf
Name: Longitude
Units: degrees East
Description: <p>Longitude in decimal degrees (negative values = West)</p>
http://lod.bco-dmo.org/id/dataset-parameter/845141.rdf
Name: Station_Description
Units: unitless
Description: <p>PAL-LTER category for the station</p>
http://lod.bco-dmo.org/id/dataset-parameter/845142.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/845143.rdf
Name: Sample_Depth
Units: meters (m)
Description: <p>Depth sampled in meters</p>
http://lod.bco-dmo.org/id/dataset-parameter/845144.rdf
Name: d15N
Units: parts per thousand (o/oo or per mil)
Description: <p>d15N value of the NO2 + NO3 in the sample as determined by the denitrifier method, units of parts per thousand (o/oo or per mil). Replicate determinations are retained but were averaged for use in calculating oxidation rates.</p>
http://lod.bco-dmo.org/id/dataset-parameter/845145.rdf
Name: d18O
Units: parts per thousand (o/oo or per mil)
Description: <p>d18O value of the NO2 + NO3 in the sample as determined by the denitrifier method, units of parts per thousand (o/oo or per mil).</p>
http://lod.bco-dmo.org/id/dataset-parameter/845146.rdf
Name: Analytical_Batch
Units: unitless
Description: <p>Samples were run in batches of 20 samples with 10 standards, this column identifies the batch that included a specific 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
11143
https://darchive.mblwhoilibrary.org/bitstream/1912/26924/1/dataset-842944_d15nox-natural-abundance__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.842944.1
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: <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 <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 <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>
<p><strong>Nitrogen oxidation rates.</strong> Oxidation rates of N supplied as ammonium, nitrite, urea and putrescine (1,4 diaminobutane) were measured in ~48 h incubations using <sup>15</sup>N-labeled substrates (&gt;98 at% <sup>15</sup>N, Cambridge Isotope Laboratories, Tewksbury,MA, USA) added within ~1 hr of sample collection to yield ~44 nM amendments (Santoro et al., 2010; Beman et al., 2012). Labeled substrates were added to duplicate bottles that were placed in cardboard boxes and incubated in the dark in a Percival incubator (Perry, IA, USA). Incubation temperature was recorded at 5-minute time steps with HOBO TidBit data loggers (Onset Computer Corp., Bourne MA, Figure 1) placed in bottles of filtered seawater incubated in cardboard boxes identical to those used for experiments (see the "<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Incubator_Temperature.xlsx" target="_blank">Incubator_Temperature.xlsx</a>" Supplemental File). Incubations were terminated after ~48 hr by decanting 40 mL subsamples from each bottle into new, sample rinsed, 50 mL polypropylene centrifuge tubes that were immediately frozen at -80 °C. Water in these tubes was used for subsequent analysis of <sup>15</sup>NOₓ. The natural abundance of <sup>15</sup>N in NOₓ was taken as the initial (time = 0) value for calculating the amount of <sup>15</sup>N oxidized to nitrate or nitrite during the incubations.</p>
<p><strong>Chemical analyses.</strong> Urea content was determined by the diacetyl monoxime method (Rahmatullah and Boyde 1980, Mulvenna and Savidge 1992). Subsamples from samples that were also used to determine oxidation of <sup>15</sup>N supplied as putrescine were sent to Dr. X. Mou’s laboratory at Kent State University where they were analyzed to determine polyamine and DFAA content as described previously (Lu et al 2014).</p>
<p><strong><sup>15</sup>N in nitrite plus nitrate</strong>. The <sup>15</sup>NOₓ in samples was measured using the ‘denitrifier method’ (Sigman et al., 2001) with <em>Pseudomonas aureofaciens</em> as described in Popp et al. (1995), Dore et al. (1998) and Beman et al. (2011). The nitrous oxide produced was analyzed using a Gas Bench II coupled to a MAT 252 mass spectrometer following the recommendations of Casciotti et al. (2002). Typically nineteen samples plus one sample duplicate was analyzed along with duplicate reference materials USGS 32, USGS 34 and USGS 35 (or NIST 3), which were used to normalize the measured d<sup>15</sup>N values to AIR. In addition, a laboratory reference solution made from analytical grade NaNO₃ with d<sup>15</sup>N value (-52.2‰) that was known through extensive characterization using NIST/USGS reference materials was also analyzed in duplicate with each batch of 19 samples.</p>
<p>We calculated oxidation rates from d<sup>15</sup>N enrichment of the NOₓ pool in the bottles at the ends of the incubations compared to the initial value in the unamended seawater sample ("natural abundance"). We assumed that the d<sup>15</sup>N of naturally occurring ammonia, urea and putrescine is the same as that of N in bulk organic matter, and that the d<sup>15</sup>N value of nitrite is our samples is -30 o/oo as reported by Smart et al. (2015). Samples with low or no activity sometimes yielded negative rates because the d<sup>15</sup>NOₓ "natural abundance" value for that sample was greater than the d<sup>15</sup>NOₓ value of amended sample. We analyzed control samples consisting of filtered seawater taken at the beginning of the cruise, amended with <sup>15</sup>NO₂, then immediately frozen at -80 °C, or "time zero" samples from time course experiments performed throughout the cruise, to determine the contribution of autooxidation or isotope exchange to the apparent rate of nitrite oxidation. These samples were treated with sulfamic acid to remove unreacted <sup>15</sup>NO₂ (Granger and Sigman 2009). The analysis indicated that about 7.9% of the <sup>15</sup>N supplied as NO₂ had been converted to <sup>15</sup>NO₃ by the time we analyzed the samples. We also performed an independent chemical analysis of nitrite and nitrate (Strickland and Parsons 1972) in the (nominally) 0.125 mM <sup>15</sup>NO₂ working stock solution a few months after the cruise. This analysis indicated that about 14.3% of the of the nitrite plus nitrate in the stock was nitrate. Because this stock had been handled and shipped separately from the cruise samples, we used 7.9% as the best estimate of the amount of <sup>15</sup>N label converted to nitrate. We have incorporated corrections for this reaction into rates calculated from field data.</p>
<p>We ran time-course incubations with samples from 2 or 3 depths at 34 stations to verify that oxidation rates did not change significantly during incubations, for example, due to substrate depletion or changes in the population of ammonia oxidizers. These experiments were set up in 250 ml polycarbonate bottles as above. Two bottles were sampled at each time point over time courses of 72 to 96 h. These data are presented in <a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Table1.pdf" target="_blank">Table 1</a> (PDF; see Supplemental Files). AO rates determined from the slope of linear regressions of the data from a given sample were compared to rates determined from samples taken at the 48 hr time point. We performed analogous experiments to examine the effect on N oxidation rates of variation in incubation temperature and in substrate concentration.</p>
<p>Summary Statistics for d15NOx (mean, median, maximum, minimum, and standard error of d15NOx measurements grouped by the water mass depth ranges) are provided in the Supplemental File&nbsp;<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/842944/d15NOx_Summary_Statistics.JPG" target="_blank">d15NOx_Summary_Statistics.JPG</a>.</p>
<p><strong>Precision</strong>. Analytical uncertainty in d<sup>15</sup>N values was determined from duplicate analyses of USGS reference materials, our laboratory reference solution and samples analyzed in duplicate and ranged from 0.36‰ to 0.56‰ (<a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Table1.pdf" target="_blank">Table 1</a> (PDF) Supplemental File). All rate measurements were also performed in duplicate (biological replicates) and their uncertainty is also presented in Table 1. Accuracy was determined based on isotope analysis of the laboratory reference solution, which was not used to normalize the isotopic results of samples and was found to be 0.42‰ (at% <sup>15</sup>N = 0.00019, n = 56).</p>
<p><strong>Rate calculations.</strong> We integrated the data we collected to calculate oxidation rates of N supplied as ammonia and urea as described in Popp et al. (1995), Dore et al. (1998) and Beman et al. (2011). We used ammonium concentration data from shipboard analyses. Nitrite + nitrate concentrations were determined by PAL-LTER personnel and were obtained from their database. Urea concentrations were measured on samples shipped frozen to the University of Georgia (Hollibaugh lab). Chemical data needed for rate calculations were not available for some samples so we substituted water mass averages determined from other samples taken on the cruise.</p>
<p>We determined the limits of detection and precision of nutrient analyses as follows. The precision of nitrate plus nitrite analyses run by LTER personnel (<a href="https://oceaninformatics.ucsd.edu/datazoo/catalogs/pallter/datasets/27" target="_blank">https://oceaninformatics.ucsd.edu/datazoo/catalogs/pallter/datasets/27</a>) was reported to be 100 nM. The precision and limit of detection of putrescine (polyamine) analysis is given in Lu et al. (2018) as 1 nM. We determined the precision of ammonium, urea and nitrite analyses as the mean standard deviation of replicate (2 or 3) analyses of a given sample. They are: ammonium, 65 nM; urea, 10 nM; and nitrite, 70 nM. The limits of detection were taken as 1.96 times the precision of the relevant measurements.</p>
<p>We ran Monte Carlo simulations to estimate the precision and the limits of detection of rate measurements. The models incorporated the estimates of precision given above and the means of the measured <em>in situ</em> concentrations of the reactants, the mean <em>in situ</em> concentration of NOₓ (from PAL-LTER data), the precision of the measured d<sup>15</sup>NOₓ in the experiments at the beginning (natural abundance) and end of the incubations. We ran 10,000 trials using random numbers generated with population means and standard deviations (assuming normally distributed variance and produced using an Excel spreadsheet in the EasyFit<sup>®</sup> app) ) equivalent to the test values. The standard deviation of the 10,000 rates calculated in this manner was taken as an overall estimate of the precision of the rates we report. The results of these models are summarized in Supplemental Table 3. Our estimates of the precision of the rate measurements (oxidation of <sup>15</sup>N supplied as ammonium urea, putrescine or nitrite to <sup>15</sup>NOₓ, nmol L<sup>-1</sup> d<sup>-1</sup>) are: ammonia, 2.18; urea 0.31; putrescine, 0.51; nitrite, 4.6, for relative standard deviations (RSD; ((standard deviation/mean)*100)) of: 15.3%; 11.3%; 8.2% and 32%, respectively, of the calculated rates. Model runs, which also tested the sensitivity of the calculated rates to the accuracy of estimates of some variables, are summarized in Supplemental <a href="https://datadocs.bco-dmo.org/docs/302/Oxidation_of_Urea_N/data_docs/840629/Table3_Summary_of_Monte_Carlo_Models.xlsx" target="_blank">Table 3</a> (.xlsx file), which also includes the equations used to calculate rates.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing:</strong><br />
- renamed fields to comply with BCO-DMO naming conventions;<br />
- 2021-03-16: replaced with data file received on 2021-03-14; converted latitude and longitude values to negative; formatted date/time field to ISO8601 format.<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
Percival incubator
Percival incubator
PI Supplied Instrument Name: Percival incubator Instrument Name: In-situ incubator Instrument Short Name:in-situ incubator Instrument Description: A device on a ship or in the laboratory that holds water samples under controlled conditions of temperature and possibly illumination. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/82/
Gas Bench II coupled to a MAT 252 mass spectrometer
Gas Bench II coupled to a MAT 252 mass spectrometer
PI Supplied Instrument Name: Gas Bench II coupled to a MAT 252 mass spectrometer Instrument Name: Isotope-ratio Mass Spectrometer Instrument Short Name:IR Mass Spec; IRMS Instrument Description: The Isotope-ratio Mass Spectrometer is a particular type of mass spectrometer used to measure the relative abundance of isotopes in a given sample (e.g. VG Prism II Isotope Ratio Mass-Spectrometer). Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB16/
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/
HOBO TidBit data loggers
HOBO TidBit data loggers
PI Supplied Instrument Name: HOBO TidBit data loggers Instrument Name: Temperature Logger Instrument Short Name: Instrument Description: Records temperature data over a period of time.
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