http://lod.bco-dmo.org/id/dataset/538091
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
2014-11-17
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Biogeochemistry of microbial phosphorus uptake from cruises in the Sargasso Sea; Bermuda Atlantic Time-Series Station from 2011-2013 (Biological C:N:P ratios project)
2021-02-05
publication
2021-02-05
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-12-03
publication
https://doi.org/10.26008/1912/bco-dmo.538091.1
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
principalInvestigator
Dr Juan A. Bonachela
University of Strathclyde
principalInvestigator
Simon Levin
Princeton University
principalInvestigator
Adam Martiny
University of California-Irvine
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: Lomas, M. W., Bonachela, J. A., Levin, S., Martiny, A. (2021) Biogeochemistry of microbial phosphorus uptake from cruises in the Sargasso Sea; Bermuda Atlantic Time-Series Station from 2011-2013 (Biological C:N:P ratios project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-02-05 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.538091.2 [access date]
Bulk phosphorus uptake by microbes Dataset Description: <p>Biogeochemistry of microbial phosphorus uptake from cruises in the Sargasso Sea; Bermuda Atlantic Time-Series Station from 2011-2013 (Biological C:N:P ratios project).This data was published in&nbsp;Lomas et al. 2014 PNAS.</p> Methods and Sampling: <p><strong>Sample collection:&nbsp;</strong><br />
The data presented in this study were collected on 7 cruises throughout the Western North Atlantic Ocean (cruise X0606, X0705, X0804, BVAL 39, BVAL 46, AE1206, and AE1319). Data for kinetics experiments were collected from throughout the western North Atlantic, from roughly 55oN in the Labrador Sea to ~21oN, just north of Puerto Rico. All sample depths were &lt;200m. All samples for Pi uptake rates and kinetics experiments were collected in acid-cleaned Niskin bottles attached to a CTD rosette and kept in subdued lighting until experiments were initiated (&lt; 1 h). &nbsp;Samples for whole community ambient uptake rates were collected from ~4 depths in the upper 60 m, while samples for taxon-specific ambient uptake rates were collected from 5 m, 40 m, and the deep chlorophyll maximum (DCM; ranging from 80 to 120 m) (27). <em>Trichodesmium</em> colonies were collected from the near surface (roughly within the top 20 m) by vertically hauling a handheld 100 µm net. &nbsp;Single colonies were transferred a second time into fresh 0.2 µm-filtered water to reduce contamination of closely associated organisms, and subsequently separated by morphotype (either ‘puff’ with radial trichomes or ‘raft’ with parallel trichomes); only data for ‘rafts’ are presented here.</p>
<p><strong>Dissolved inorganic and organic, and particulate nutrients:</strong><br />
Samples for NO3-/NO2-, NO2- and PO4-3 are gravity filtered through 0.8 µm Nucleopore polycarbonate filters using acid cleaned in-line polycarbonate filter holders, then frozen (-20oC) in HDPE bottles until analysis (Dore et al., 1996). &nbsp;Tests of frozen versus refrigerated samples have indicated no significant difference between storage methods (Dore et al., 1996). &nbsp;Nutrient samples prior to ~2003 were analyzed on a modified Technicon Autoanalyzer and samples post ~2003 were analyzed on an Alpkem Flow Solution IV; both instrumental setups have comparable sensitivity and method detection limits validated by 6-month sample overlap on both instruments. During every sample run, commercially available certified standards, OSIL and Wako Chemical, are analyzed to maintain data quality, as well as ‘standard water’ from 3000 m which serves as an internal standard.</p>
<p>Soluble reactive phosphate (SRP) concentrations in the euphotic zone of the Sargasso Sea are below analytical detection limits (~20 nmol kg-1) of standard nutrient autoanalyzer configurations. &nbsp;To resolve the low concentrations of SRP in the surface waters at BATS the Magnesium Induced Co-precipitation method, referred to as MAGIC-SRP measurements (Karl and Tien, 1992; Rimmelin and Moutin, 2005), was used starting in late 2004. &nbsp;Several modifications to the method were made and detailed in Lomas et al. (2010a). &nbsp;Sample accuracy was checked on each run with a certified OSIL nutrient standard. &nbsp;The method detection limit following this protocol is ~1 nmol kg-1 with a precision of + 5% at 5 nmol kg-1.</p>
<p>Particulate organic carbon (POC) and nitrogen (PON) samples are filtered on precombusted (450oC, 4h) Whatman GF/F filters and frozen until analysis Steinberg et al., 2001a. &nbsp;Samples are analyzed on a Control Equipment 240-XA or 440-XA elemental analyzer standardized to acetanilide. &nbsp;Particulate phosphorus samples (PPhos) are analyzed using a ash-hydrolysis method (Lomas et al., 2010a). &nbsp;Oxidation efficiency and standard recovery is tested with each sample run using an ATP standard solution and a certified phosphate standard (OSIL Phosphate Nutrient Standard Solution). &nbsp;Method precision is ~9% at 2.5 nmol kg-1 (the lowest concentrations typically observed well below the euphotic zone), and ~1% at 15 nmol kg-1 (typical euphotic zone concentrations). &nbsp;The method detection limit, defined as three times the standard deviation of the lowest standard (2.5 nmol kg-1) is ~0.5 nmol kg-1. &nbsp; &nbsp;</p>
<p><strong>33Phosphate incubations:</strong><br />
The approach for ambient whole community and population-specific uptake rate measurements were previously published (<span style="font-size:12.7272720336914px">Casey et al, 2009</span>). Briefly, duplicate aliquots of 10 ml seawater were amended with 0.15 µCi (~80 pmol L-1) additions of H333PO4 (3000 Ci mol-1; PerkinElmer, USA), and incubated for 30 - 60 min in subdued lighting (~100 µmol photons m-2 s-1) at ~23oC. This temperature was within ~3oC of the coolest/warmest in situ temperature from which the samples were collected. The duration of each incubation varied depending on turnover time of the added isotope, such that efforts were made to keep uptake to &lt;25% of the tracer added. &nbsp;Duplicate killed control incubations were conducted for each station. Killed controls were amended with paraformaldehyde (0.5% final concentration) for 30 min prior to the addition of isotopic tracer and incubation. Whole community incubations were terminated by filtration onto 0.2 µm polycarbonate filters that were subsequently placed in glass scintillation vials. &nbsp;Population-specific ambient uptake incubations were terminated by the addition of paraformaldehyde (0.5% final concentration), and stored at 4oC until sorting (&lt;12 h) as described in the next section.&nbsp;</p>
<p>Whole community and population-specific kinetics experiments were conducted by adding 0.15 µCi (~80 pM) of H333PO4 to ~10 replicate 10 ml seawater samples that were further amended by increasing additions of ‘cold’ KH2PO4 up to 100 nM. &nbsp;Samples were incubated as above, but the incubations were terminated by the addition of KH2PO4 to a final concentration of 100 µM (28). Whole community samples were filtered onto 0.2 µm polycarbonate filters, and rinsed with an oxalate wash (29). Surface bound phosphate in population-specific samples was accounted for by subtracting 33P counts for sorted populations to which 100 µM phosphate had been added prior to addition of the isotopic tracer. It is assumed that addition of such a high level of phosphate would result in negligible uptake of radioactive phosphate and thus any signal was attributed to surface absorption; this correction was always &lt;2-3%. Population-specific kinetics experiments for samples collected in the deep chlorophyll maximum were first gravity concentrated and resuspended in phosphate-free Sargasso Sea surface water prior to incubation as described. Population-specific samples were stored at 4oC in the dark until sorting (&lt;3 h) as described in the next section. Kinetics experiments for Trichodesmium spp. were conducted in the same manner as above for whole community samples but with picked and rinsed colonies and increasing additions of ‘cold’ KH2PO4 up to 1000 nM.&nbsp;</p>
<p><strong>Flow cytometry analysis and cell sorting:</strong><br />
Samples were sorted on an InFlux cell sorter (BD, Seattle, WA) at an average flow rate of ~40 µL min-1. &nbsp;Samples were sorted for <em>Prochlorococcus</em>, <em>Synechococcus</em>, and an operationally defined eukaryotic algae size fraction (eukaryotes &gt;2 µm). A 100 mW blue (488 nm) excitation laser was used. After exclusion of laser noise gated on pulse width and forward scatter, autotrophic cells were discriminated by chlorophyll fluorescence (&gt;650 nm), PE (585/30 nm), and granularity (side scatter). Sheath fluid was made fresh daily from distilled deionized water (Millipore, Billerica, MA) and molecular grade NaCl (Mallinckrodt Baker, Phillipsburg, NJ), pre-filtered through a 0.2 µm capsule filter (Pall, East Hills, NY), and a STERIVEX sterile 0.22 µm inline filter (Millipore, Billerica, MA). Mean coincident abort rates were &lt; 1% and mean recovery from secondary sorts (n = 25) was 97.5 ± 1.1% (data not shown). &nbsp;Spigot™ (BD Seattle, WA) and FCS Express V3™ (DeNovo Software, Seattle, WA) were used for data acquisition and post acquisition analysis, respectively. Sorted cells from each sample were gently filtered onto 0.2 µm Nucleopore polycarbonate filters, rinsed with copious amounts of 0.2 µm filtered seawater, an oxalate wash(29), and placed in a 7 ml scintillation vial for &nbsp;liquid scintillation counting.&nbsp;</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046001 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046001
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046368 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046368
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1046297 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1046297
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1045966 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1045966
completed
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext 311
60 Bigelow Drive PO Box 380
East Boothbay
ME
04544
United States
mlomas@bigelow.org
pointOfContact
Dr Juan A. Bonachela
University of Strathclyde
MASTS marine population modeling group, Department of Mathematics and Statistics 26 Richmond Street
Glasgow
Scotland
G1 1XH
UK
jabo@Princeton.EDU
pointOfContact
Simon Levin
Princeton University
609-258-6880
Dept. of Ecology & Evolutionary Biology 203 Eno Hall
Princeton
NJ
08544-1003
USA
slevin@princeton.edu
pointOfContact
Adam Martiny
University of California-Irvine
949-824-9713
Earth System Science & Ecology and Evolutionary Biology 3208 Croul Hall
Irvine
CA
92697
USA
amartiny@uci.edu
pointOfContact
asNeeded
Dataset Version: 2
Unknown
cruise_id
date
station
lon
lat
depth
chl_a
NO3_NO2
NO2
PO4
SiO4
SRP
POC
PON
POP
Pro
Syn
Peuks
Neuks
Flow Cytometer
Niskin bottle
Nutrient Autoanalyzer
Plankton Net
theme
None, User defined
Cruise identfier
date
station
longitude
latitude
depth
chlorophyll a
nitrate plus nitrite
Nitrite
reactive phosphorus (PO4)
Silicate (reactive silica)
SRP
particulate organic Carbon (POC)
particulate organic nitrogen
particulate organic phosphorus
prochlorococcus abundance
synechococcus abundance
pico_euks
nano eukaryotic phytoplankton
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Niskin bottle
Nutrient Autoanalyzer
Plankton Net
instrument
BCO-DMO Standard Instruments
AE1206
AE1319
AE1123
service
Deployment Activity
Sargasso Sea; Bermuda Atlantic Time-Series Station; 31 N 64 S
NW Atlantic
western North Atlantic transect 19 to 39N
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.
Dimensions of Biodiversity
http://www.nsf.gov/funding/pgm_summ.jsp?pims_id=503446
Dimensions of Biodiversity
(adapted from the NSF Synopsis of Program)
Dimensions of Biodiversity is a program solicitation from the NSF Directorate for Biological Sciences. FY 2010 was year one of the program. [MORE from NSF]
The NSF Dimensions of Biodiversity program seeks to characterize biodiversity on Earth by using integrative, innovative approaches to fill rapidly the most substantial gaps in our understanding. The program will take a broad view of biodiversity, and in its initial phase will focus on the integration of genetic, taxonomic, and functional dimensions of biodiversity. Project investigators are encouraged to integrate these three dimensions to understand the interactions and feedbacks among them. While this focus complements several core NSF programs, it differs by requiring that multiple dimensions of biodiversity be addressed simultaneously, to understand the roles of biodiversity in critical ecological and evolutionary processes.
Dimensions of Biodiversity
largerWorkCitation
program
Ocean Carbon and Biogeochemistry
http://us-ocb.org/
Ocean Carbon and Biogeochemistry
The Ocean Carbon and Biogeochemistry (OCB) program focuses on the ocean's role as a component of the global Earth system, bringing together research in geochemistry, ocean physics, and ecology that inform on and advance our understanding of ocean biogeochemistry. The overall program goals are to promote, plan, and coordinate collaborative, multidisciplinary research opportunities within the U.S. research community and with international partners. Important OCB-related activities currently include: the Ocean Carbon and Climate Change (OCCC) and the North American Carbon Program (NACP); U.S. contributions to IMBER, SOLAS, CARBOOCEAN; and numerous U.S. single-investigator and medium-size research projects funded by U.S. federal agencies including NASA, NOAA, and NSF.
The scientific mission of OCB is to study the evolving role of the ocean in the global carbon cycle, in the face of environmental variability and change through studies of marine biogeochemical cycles and associated ecosystems.
The overarching OCB science themes include improved understanding and prediction of: 1) oceanic uptake and release of atmospheric CO2 and other greenhouse gases and 2) environmental sensitivities of biogeochemical cycles, marine ecosystems, and interactions between the two.
The OCB Research Priorities (updated January 2012) include: ocean acidification; terrestrial/coastal carbon fluxes and exchanges; climate sensitivities of and change in ecosystem structure and associated impacts on biogeochemical cycles; mesopelagic ecological and biogeochemical interactions; benthic-pelagic feedbacks on biogeochemical cycles; ocean carbon uptake and storage; and expanding low-oxygen conditions in the coastal and open oceans.
OCB
largerWorkCitation
program
Biological Controls on the Ocean C:N:P ratios
https://osprey.bco-dmo.org/project/2178
Biological Controls on the Ocean C:N:P ratios
<p>One of the fundamental patterns of ocean biogeochemistry is the Redfield ratio, linking the stoichiometry of surface plankton with the chemistry of the deep ocean. There is no obvious mechanism for the globally consistent C:N:P ratio of 106:16:1 (Redfield ratio), especially as there is substantial elemental variation among plankton communities in different ocean regions. Thus, knowing how biodiversity regulates the elemental composition of the ocean is important for understanding the ocean and climate as a whole -- now and in the future.</p>
<p>The conceptual hypotheses for this study are as follows: 1. The C:N:P ratio of a cell is constrained by its broad taxonomic group, which determines, for example, whether it has an outer shell, its size, functional metabolism, membrane lipid composition. 2. Within a taxon, there is high genetic diversity. Some of this genetic diversity is potentially laterally transferred, or can be lost within taxa, and confers various functional abilities (organic phosphate assimilation, nitrate assimilation, photoheterotrophy, etc.). Functional diversity provides the cell with further flexibility, such as the ability to respond to varying nutrient supply rates/ratios, and affects a cell's C:N:P ratio within the range specified by the taxon. 3. Given these taxonomic and genetic constraints, a cell is physiologically plastic and modifies how it allocates cellular resources in response to nutrient supply rates/ratios in the environment. 4. The microbial diversity (taxonomic, genetic, and functional) of the surface ocean varies over time and space, driven by many factors in addition to nutrients. The sum of this mixture composes the ecosystem C:N:P, the ratio that Redfield described.</p>
<p>Based on this framework, the CoPIs will make field observations of taxon-specific stoichiometry and growth rates, genomic analyses, and conduct laboratory chemostat experiments to improve understanding of how ocean taxonomic, genetic, and functional biodiversity control the stoichiometry of the surface ocean plankton. Their analyses of these data would lead to a mechanistic understanding of variations in the Redfield ratio, both spatially and temporally.</p>
<p>This study will greatly expand knowledge of the genomic diversity among ocean microbes and how this diversity affects biogeochemistry. The stoichiometry of the ocean's microbes is a parameter that nearly every chemical or biological oceanographer uses, from converting measurements made in one element to another, to estimating regional and global nitrogen budgets. The research also has important implications for the global carbon budget and any changes that might result from climate change.</p>
<p>To understand mechanistically temporal and spatial variability of the plankton C:N:P ratio, biodiversity must be studied not only at the traditional taxonomic level, but at the genetic and functional levels which dictate organism response to their environment. Data will be integrated into a combined ocean ecological, evolutionary, and biogeochemical model, with flexible stoichiometry, including cellular biochemical allocations. Seeding a coupled physical-biological model of the oceans with multiple competing genotypes enables the exploration of ecological and evolutionary patterns of resource acquisition and C:N:P ratios. Developing a more mechanistic examination of the course of ecology and evolution, in which laboratory and field data define tradeoffs between different growth and nutrient acquisition strategies, would estabblish the framework of adaptive dynamics for determining "evolutionarily convergence". Finally, model outcomes will be evaluated against field data.</p>
<p>The field work planned for this project includes several cruises: BV46 (September/October 2011), BV48 (September 2012), a June 2013 cruise from Bermuda to the Labrador Sea, and a cruise from Hawaii to Tahiti (May 2014). Additionally, samples will be be acquired during cruises of opportunity.</p>
Biological C:N:P ratios
largerWorkCitation
project
eng; USA
biota
oceans
Sargasso Sea; Bermuda Atlantic Time-Series Station; 31 N 64 S; NW Atlantic; western North Atlantic transect 19 to 39N
-69.21
-40.01
19.667
55
2011-09-28
2013-09-08
western North Atlantic; 60N to 20N along 66W longitude; 20N to 15S in the tropical Pacific
0
BCO-DMO catalogue of parameters from Biogeochemistry of microbial phosphorus uptake from cruises in the Sargasso Sea; Bermuda Atlantic Time-Series Station from 2011-2013 (Biological C:N:P ratios 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
http://lod.bco-dmo.org/id/dataset-parameter/538105.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/538106.rdf
Name: date
Units: yyyy-mm-dd
Description: <p>date of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/538107.rdf
Name: station
Units: unitless
Description: <p>station number or identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/538108.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/538109.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/538110.rdf
Name: depth
Units: meters
Description: <p>depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/538111.rdf
Name: chl_a
Units: micrograms/liter
Description: <p>CTD Chlorophyll a</p>
http://lod.bco-dmo.org/id/dataset-parameter/538112.rdf
Name: NO3_NO2
Units: umol/kg
Description: <p>combined oxidized nitrogen concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/538113.rdf
Name: NO2
Units: umol/kg
Description: <p>nitrite concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/538114.rdf
Name: PO4
Units: umol/kg
Description: <p>phosphate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/538115.rdf
Name: SiO4
Units: umol/kg
Description: <p>silicate concentration</p>
http://lod.bco-dmo.org/id/dataset-parameter/538116.rdf
Name: SRP
Units: nmol/kg
Description: <p>soluble reactive phosphate</p>
http://lod.bco-dmo.org/id/dataset-parameter/538117.rdf
Name: POC
Units: umol/L
Description: <p>particulate organic carbon</p>
http://lod.bco-dmo.org/id/dataset-parameter/538118.rdf
Name: PON
Units: umol/L
Description: <p>particulate organic nitrogen</p>
http://lod.bco-dmo.org/id/dataset-parameter/538119.rdf
Name: POP
Units: umol/kg
Description: <p>particulate organic phosphorus</p>
http://lod.bco-dmo.org/id/dataset-parameter/538120.rdf
Name: Pro
Units: cells/ml
Description: <p>Prochlorococcus abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/538121.rdf
Name: Syn
Units: cells/ml
Description: <p>Synechococcus abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/538122.rdf
Name: Peuks
Units: cells/ml
Description: <p>Picoeukaryote abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/538123.rdf
Name: Neuks
Units: cells/ml
Description: <p>Nanoeukaryote abundance</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
34999
https://darchive.mblwhoilibrary.org/bitstream/1912/26651/1/dataset-538091_phosphorus-uptake-biogeochemistry__v2.tsv
download
24992
https://darchive.mblwhoilibrary.org/bitstream/1912/26436/1/dataset-538091_phosphorus-uptake-biogeochemistry__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.538091.1
download
onLine
dataset
<p><strong>Sample collection:&nbsp;</strong><br />
The data presented in this study were collected on 7 cruises throughout the Western North Atlantic Ocean (cruise X0606, X0705, X0804, BVAL 39, BVAL 46, AE1206, and AE1319). Data for kinetics experiments were collected from throughout the western North Atlantic, from roughly 55oN in the Labrador Sea to ~21oN, just north of Puerto Rico. All sample depths were &lt;200m. All samples for Pi uptake rates and kinetics experiments were collected in acid-cleaned Niskin bottles attached to a CTD rosette and kept in subdued lighting until experiments were initiated (&lt; 1 h). &nbsp;Samples for whole community ambient uptake rates were collected from ~4 depths in the upper 60 m, while samples for taxon-specific ambient uptake rates were collected from 5 m, 40 m, and the deep chlorophyll maximum (DCM; ranging from 80 to 120 m) (27). <em>Trichodesmium</em> colonies were collected from the near surface (roughly within the top 20 m) by vertically hauling a handheld 100 µm net. &nbsp;Single colonies were transferred a second time into fresh 0.2 µm-filtered water to reduce contamination of closely associated organisms, and subsequently separated by morphotype (either ‘puff’ with radial trichomes or ‘raft’ with parallel trichomes); only data for ‘rafts’ are presented here.</p>
<p><strong>Dissolved inorganic and organic, and particulate nutrients:</strong><br />
Samples for NO3-/NO2-, NO2- and PO4-3 are gravity filtered through 0.8 µm Nucleopore polycarbonate filters using acid cleaned in-line polycarbonate filter holders, then frozen (-20oC) in HDPE bottles until analysis (Dore et al., 1996). &nbsp;Tests of frozen versus refrigerated samples have indicated no significant difference between storage methods (Dore et al., 1996). &nbsp;Nutrient samples prior to ~2003 were analyzed on a modified Technicon Autoanalyzer and samples post ~2003 were analyzed on an Alpkem Flow Solution IV; both instrumental setups have comparable sensitivity and method detection limits validated by 6-month sample overlap on both instruments. During every sample run, commercially available certified standards, OSIL and Wako Chemical, are analyzed to maintain data quality, as well as ‘standard water’ from 3000 m which serves as an internal standard.</p>
<p>Soluble reactive phosphate (SRP) concentrations in the euphotic zone of the Sargasso Sea are below analytical detection limits (~20 nmol kg-1) of standard nutrient autoanalyzer configurations. &nbsp;To resolve the low concentrations of SRP in the surface waters at BATS the Magnesium Induced Co-precipitation method, referred to as MAGIC-SRP measurements (Karl and Tien, 1992; Rimmelin and Moutin, 2005), was used starting in late 2004. &nbsp;Several modifications to the method were made and detailed in Lomas et al. (2010a). &nbsp;Sample accuracy was checked on each run with a certified OSIL nutrient standard. &nbsp;The method detection limit following this protocol is ~1 nmol kg-1 with a precision of + 5% at 5 nmol kg-1.</p>
<p>Particulate organic carbon (POC) and nitrogen (PON) samples are filtered on precombusted (450oC, 4h) Whatman GF/F filters and frozen until analysis Steinberg et al., 2001a. &nbsp;Samples are analyzed on a Control Equipment 240-XA or 440-XA elemental analyzer standardized to acetanilide. &nbsp;Particulate phosphorus samples (PPhos) are analyzed using a ash-hydrolysis method (Lomas et al., 2010a). &nbsp;Oxidation efficiency and standard recovery is tested with each sample run using an ATP standard solution and a certified phosphate standard (OSIL Phosphate Nutrient Standard Solution). &nbsp;Method precision is ~9% at 2.5 nmol kg-1 (the lowest concentrations typically observed well below the euphotic zone), and ~1% at 15 nmol kg-1 (typical euphotic zone concentrations). &nbsp;The method detection limit, defined as three times the standard deviation of the lowest standard (2.5 nmol kg-1) is ~0.5 nmol kg-1. &nbsp; &nbsp;</p>
<p><strong>33Phosphate incubations:</strong><br />
The approach for ambient whole community and population-specific uptake rate measurements were previously published (<span style="font-size:12.7272720336914px">Casey et al, 2009</span>). Briefly, duplicate aliquots of 10 ml seawater were amended with 0.15 µCi (~80 pmol L-1) additions of H333PO4 (3000 Ci mol-1; PerkinElmer, USA), and incubated for 30 - 60 min in subdued lighting (~100 µmol photons m-2 s-1) at ~23oC. This temperature was within ~3oC of the coolest/warmest in situ temperature from which the samples were collected. The duration of each incubation varied depending on turnover time of the added isotope, such that efforts were made to keep uptake to &lt;25% of the tracer added. &nbsp;Duplicate killed control incubations were conducted for each station. Killed controls were amended with paraformaldehyde (0.5% final concentration) for 30 min prior to the addition of isotopic tracer and incubation. Whole community incubations were terminated by filtration onto 0.2 µm polycarbonate filters that were subsequently placed in glass scintillation vials. &nbsp;Population-specific ambient uptake incubations were terminated by the addition of paraformaldehyde (0.5% final concentration), and stored at 4oC until sorting (&lt;12 h) as described in the next section.&nbsp;</p>
<p>Whole community and population-specific kinetics experiments were conducted by adding 0.15 µCi (~80 pM) of H333PO4 to ~10 replicate 10 ml seawater samples that were further amended by increasing additions of ‘cold’ KH2PO4 up to 100 nM. &nbsp;Samples were incubated as above, but the incubations were terminated by the addition of KH2PO4 to a final concentration of 100 µM (28). Whole community samples were filtered onto 0.2 µm polycarbonate filters, and rinsed with an oxalate wash (29). Surface bound phosphate in population-specific samples was accounted for by subtracting 33P counts for sorted populations to which 100 µM phosphate had been added prior to addition of the isotopic tracer. It is assumed that addition of such a high level of phosphate would result in negligible uptake of radioactive phosphate and thus any signal was attributed to surface absorption; this correction was always &lt;2-3%. Population-specific kinetics experiments for samples collected in the deep chlorophyll maximum were first gravity concentrated and resuspended in phosphate-free Sargasso Sea surface water prior to incubation as described. Population-specific samples were stored at 4oC in the dark until sorting (&lt;3 h) as described in the next section. Kinetics experiments for Trichodesmium spp. were conducted in the same manner as above for whole community samples but with picked and rinsed colonies and increasing additions of ‘cold’ KH2PO4 up to 1000 nM.&nbsp;</p>
<p><strong>Flow cytometry analysis and cell sorting:</strong><br />
Samples were sorted on an InFlux cell sorter (BD, Seattle, WA) at an average flow rate of ~40 µL min-1. &nbsp;Samples were sorted for <em>Prochlorococcus</em>, <em>Synechococcus</em>, and an operationally defined eukaryotic algae size fraction (eukaryotes &gt;2 µm). A 100 mW blue (488 nm) excitation laser was used. After exclusion of laser noise gated on pulse width and forward scatter, autotrophic cells were discriminated by chlorophyll fluorescence (&gt;650 nm), PE (585/30 nm), and granularity (side scatter). Sheath fluid was made fresh daily from distilled deionized water (Millipore, Billerica, MA) and molecular grade NaCl (Mallinckrodt Baker, Phillipsburg, NJ), pre-filtered through a 0.2 µm capsule filter (Pall, East Hills, NY), and a STERIVEX sterile 0.22 µm inline filter (Millipore, Billerica, MA). Mean coincident abort rates were &lt; 1% and mean recovery from secondary sorts (n = 25) was 97.5 ± 1.1% (data not shown). &nbsp;Spigot™ (BD Seattle, WA) and FCS Express V3™ (DeNovo Software, Seattle, WA) were used for data acquisition and post acquisition analysis, respectively. Sorted cells from each sample were gently filtered onto 0.2 µm Nucleopore polycarbonate filters, rinsed with copious amounts of 0.2 µm filtered seawater, an oxalate wash(29), and placed in a 7 ml scintillation vial for &nbsp;liquid scintillation counting.&nbsp;</p>
Specified by the Principal Investigator(s)
<p><strong>P uptake Rate Calculations:</strong><br />
Whole community and taxon-specific assimilation rates were calculated using the same equation as follows:<br />
--&nbsp; [see formula in Supplemental Files section]<br />
where Vpi is the cell-specific utilization rate (amol 33Pi cell-1 hr-1); ßsample and ßTA are the ß-emission activities (counts min-1) for the sorted sample and the total activity added, respectively; n is the number of cells sorted; Delta-T is the elapsed time from 33P isotopic tracer addition to counting; To is the incubation duration; Lambda is the decay constant of 33P (half life = 25.4 d); P is the ambient concentration of the P source (nmol L-1). The method detection limit following this protocol is ~0.5 nM with a precision of + 5% at 5 nM.</p>
<p><strong>Data analysis:</strong><br />
Parameters for the hyperbolic nutrient uptake curves from all samples were estimated in SigmaPlot (Systat Software, San Jose, CA, Version 10) using an iteratively fit hyperbolic equation.&nbsp;</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- reformated data from m/d/yyyy to yyyy-mm-dd<br />
- changed -9.9 and -9.99 to nd<br />
- replaced blank cells with nd<br />
- replaced spaces and other special characters with underscore<br />
- changed positive longitudes to negative values</p>
<p>Version 1 (2014-11-19): originally submitted data<br />
Version 2 (2021-02-05):&nbsp;Update the AE1319 cruise: updated chl-a for AE1319 station 4 and station 9; updated POC and PON for stations 4, 9, 12, and 16; added AE1319 stations 1-3, 5-8, and 13-15.</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
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info@bco-dmo.org
http://www.bco-dmo.org
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For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Flow Cytometer
Flow Cytometer
PI Supplied Instrument Name: Flow Cytometer PI Supplied Instrument Description:InFlux cell sorter (BD, Seattle, WA) 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/
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:Acid washed Niskin bottles attached to a CTD rosette 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/
Nutrient Autoanalyzer
Nutrient Autoanalyzer
PI Supplied Instrument Name: Nutrient Autoanalyzer PI Supplied Instrument Description:Modified Technicon Autoanalyzer and an Alpkem Flow Solution IV Instrument Name: Nutrient Autoanalyzer Instrument Short Name:Nutrient Autoanalyzer Instrument Description: Nutrient Autoanalyzer is a generic term used when specific type, make and model were not specified. In general, a Nutrient Autoanalyzer is an automated flow-thru system for doing nutrient analysis (nitrate, ammonium, orthophosphate, and silicate) on seawater samples. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB04/
Plankton Net
Plankton Net
PI Supplied Instrument Name: Plankton Net PI Supplied Instrument Description:Handheld 100 µm net Instrument Name: Plankton Net Instrument Short Name:Plankton Net Instrument Description: A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/22/
Cruise: AE1206
AE1206
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1206
Tammi Richardson
University of South Carolina
Cruise: AE1319
AE1319
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1319
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
http://dmoserv3.whoi.edu/data_docs/Bio_CNP_Ratios/AE1319_Cruise_Report_09182013_reduced2.pdf
Report describing AE1319
Cruise: AE1123
AE1123
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1123
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel