http://lod.bco-dmo.org/id/dataset/767022
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
2019-05-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phosphohydrolysis rates from samples collected in the coastal western North Atlantic on R/V Endeavor cruise EN588 during September 2016
2019-05-08
publication
2019-05-08
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2019-05-14
publication
https://doi.org/10.1575/1912/bco-dmo.767022.1
Julia Diaz
Skidaway Institute of Oceanography
principalInvestigator
Yuanzhi Tang
Georgia Institute of Technology
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: Diaz, J., Tang, Y. (2019) Phosphohydrolysis rates from samples collected in the coastal western North Atlantic on R/V Endeavor cruise EN588 during September 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2019-05-08 [if applicable, indicate subset used]. doi:10.1575/1912/bco-dmo.767022.1 [access date]
Phosphohydrolysis rates in the coastal western North Atlantic Dataset Description: <p>Seawater samples were collected at five field sites and amended with inorganic polyphosphate to determine maximum potential hydrolysis rates compared to a common fluorogenic probe, 4-methylumbelliferyl phosphate (MUF-P).</p> Methods and Sampling: <p><strong>Field sampling:</strong> Surface seawater (5–35 m) was collected in September 2016 during two sampling campaigns in the coastal western North Atlantic (Diaz et al., 2018; Supplementary Table S1). Three sites were sampled aboard the R/V Endeavor using a Niskin rosette sampler and incubated immediately in order to determine rates of P hydrolysis. Two sites accessible by small boat in Woods Hole Harbor and Buzzard's Bay, MA, were sampled utilizing a peristaltic pump. These samples were transported on ice packs and analyzed for P hydrolysis rates within 5–6 hours of collection. Additional samples were preserved and analyzed for chlorophyll, bacteria and phytoplankton abundance, and soluble reactive P (SRP), as detailed below.</p>
<p><strong>Chlorophyll:</strong> In the dark, 250 mL of seawater was filtered onto 25 mm GF/F filters. Samples were stored in the dark at -20C until analyzed according to protocols adapted from Strickland and Parsons (1972). Briefly, samples were extracted in 90% acetone in the dark (4C, 9 hr) and measured using a 10AU fluorometer (Turner). Sample signals were calibrated using a chlorophyll-a standard (Sigma) and were corrected for phaeopigments by accounting for the fluorescence of extracts before and after acidification to 0.003 M HCl.</p>
<p><strong>Abundance of bacteria and phytoplankton:</strong> Seawater samples were preserved for flow cytometry with 0.5% glutaraldehyde (final concentration), flash frozen in liquid nitrogen and stored at -80°C until analysis. Bacteria and group-specific phytoplankton counts were conducted on a Guava EasyCyte HT flow cytometer (Millipore). Instrument-specific beads were used to calibrate the cytometer. Samples were analyzed at a low flow rate (0.24 µL s⁻¹) for 3 min. To enumerate bacteria, samples were diluted (1:100) with filtered seawater (0.01 µm). Samples and filtered seawater blanks were stained with SYBR Green I (Invitrogen) according to the manufacturer's instructions and incubated in a 96-well plate in the dark at room temperature for 1 hr. Bacterial cells were counted based on diagnostic forward scatter vs. green fluorescence signals. Major phytoplankton groups were distinguished based on plots of forward scatter vs. orange (phycoerythrin-containing Synechococcus sp.), and forward scatter vs. red (eukaryotes). Size classes of eukaryotic phytoplankton were further distinguished based on forward scatter (pico-, nano- and large eukaryotes).</p>
<p><strong>Soluble reactive P:</strong> Seawater samples were collected from Niskin rosette bottles or the peristaltic pump into acid cleaned, high density polyethylene bottles. Samples used for determining in situ SRP concentrations were frozen and stored upright at -20°C until analysis. Field samples and diatom filtrates were both analyzed for SRP using a standard colorimetric method (Hansen and Koroleff, 1999). To determine in situ SRP concentrations in field samples, SRP analysis was conducted using a 4 cm glass spectrophotometry cell on triplicate subsamples, and the detection limit, defined as three times the standard deviation of replicate blank measurements, was 115 nmol L⁻¹ SRP. For incubations to determine P hydrolysis rates (see below), replicate samples were analyzed in clear 96-well plates on a multimode plate reader (Molecular Devices) with a detection limit of 800 nmol L⁻¹ P.</p>
<p><strong>P-hydrolysis of model DOP substrates:</strong> Field samples were incubated with the fluorogenic probe 4-methylumbeliferone phosphate (MUF-P) and two inorganic polyphosphate compounds with an average chain length of 3 or 45 P atoms.</p>
<p>Samples were amended with each substrate at a final concentration of 20 M P. This concentration was assumed to be rate-saturating based on preliminary experiments. Hydrolysis of polyphosphates was determined from the production of phosphate using the colorimetric protocol outlined above. Hydrolysis of the fluorogenic probe MUF-P was monitored using a standard fluorescence technique. Briefly, hydrolysis of MUF-P to 4-methylumbellierone (MUF) was measured (excitation: 359 nm, emission: 449 nm) and calibrated with a multi-point standard curve of MUF (10–500 nmol L⁻¹). In both methods, samples were corrected for substrate autohydrolysis by accounting for negative controls, which were filtered (0.2 m) and boiled (99C, 15 min) prior to P amendment in order to eliminate enzyme activity. See Diaz et al. 2018 Frontiers in Marine Science 5: 380 for full methods.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559124 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559124
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1559087 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1559087
completed
Julia Diaz
Skidaway Institute of Oceanography
j2diaz@ucsd.edu
pointOfContact
Yuanzhi Tang
Georgia Institute of Technology
404-894-3814
311 Ferst Drive
Atlanta
GA
30332
USA
yuanzhi.tang@eas.gatech.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Station
Lat
Long
Depth
Temperature
Salinity
Inorganic_poly_P_hydrolysis
MUF_P_hydrolysis
Soluble_reactive_P
Chlorophyll
Bacterial_abundance
Total_phytoplankton
Synechococcus_spp
Picoeukaryotic_phytoplankton
Nanoeukaryotic_phytoplankton
Large_eukaryotic_phytoplankton
Bacterial_abundance_to_Total_phytoplankton
Guava EasyCyte HT flow cytometer (Millipore)
multimode plate reader (Molecular Devices)
peristaltic pump
10AU fluorometer (Turner)
theme
None, User defined
station
latitude
longitude
depth
water temperature at measurement depth
salinity
Phosphorus
chlorophyll a
abundance
featureType
BCO-DMO Standard Parameters
Flow Cytometer
Niskin bottle
plate reader
Pump
Turner Designs Fluorometer 10-AU
instrument
BCO-DMO Standard Instruments
EN588
service
Deployment Activity
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: Exploring the role of exogenous polyphosphate in the precipitation of calcium phosphate minerals in the marine environment
https://osprey.bco-dmo.org/project/757061
Collaborative Research: Exploring the role of exogenous polyphosphate in the precipitation of calcium phosphate minerals in the marine environment
<p><em>NSF Award Abstract:</em><br />
Phosphorous is an important nutrient sustaining all forms of life. In particular, in the ocean, phosphorous is a key limiting nutrient, controlling levels of primary productivity across large swaths of the ocean. Removal of phosphorous occurs largely via formation of stable apatite minerals in ocean sediments. However, average ocean conditions generally inhibit the formation of apatite, thus the abundance of apatite minerals in marine sediments is a mystery. This research aims to determine the mechanisms of apatite formation in the ocean to answer this century-old question. Evaluating these mechanisms will greatly advance current understanding of phosphorous cycling in the ocean. A more detailed understanding of phosphorous cycling can be applied across the disciplines of ocean science, and because of the importance of phosphorous as a nutrient and an element with a variety of interactions with other elements, it will be applicable to a variety of other research questions. The researchers are dedicated to promoting diversity in ocean science and plan to include undergraduate students from underrepresented groups in the study. They will also mentor a postdoc and communicate their science to the public and K-12 teachers via a blog entitled "Britannica Blog", the Atlanta Science Festival, a rock show, and educational material, the latter two to be developed as part of this work.</p>
<p>Marine phosphorous burial via authigenic stable apatite formation in sediments is a major pathway for phosphorous removal in the ocean. However, in most marine environments, under natural conditions, this process is kinetically inhibited. It has been a mystery for more than a century as to how it is therefore possible for apatite to be oversaturated in large areas of marine sediments. A possible mechanism that could explain 95% of the apatite burial flux is that apatite minerals are precipitated as fine-grained particles from exogenous polyphosphate intermediates. Exogenous polyphosphates have been understudied, despite this possible importance as a mechanism for phosphorous removal. As a consequence this research could revolutionize current understanding of phosphorous cycling in the ocean for the major aim is to make a thorough and detailed study of the mechanisms behind marine apatite formation, focusing on the role of exogenous polyphosphate particles. Phosphorous is an element with widespread importance in ocean sciences, and more clearly understanding its burial will have applications across the disciplines.</p>
PolyP and P-minerals
largerWorkCitation
project
eng; USA
oceans
-73.24917
-70.66917
39.41208
41.54397
2016-09-01
2016-09-30
0
BCO-DMO catalogue of parameters from Phosphohydrolysis rates from samples collected in the coastal western North Atlantic on R/V Endeavor cruise EN588 during September 2016
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/767163.rdf
Name: Station
Units: unitless
Description: <p>Station name</p>
http://lod.bco-dmo.org/id/dataset-parameter/767164.rdf
Name: Lat
Units: decimal degrees
Description: <p>Latitude North</p>
http://lod.bco-dmo.org/id/dataset-parameter/767165.rdf
Name: Long
Units: decimal degrees
Description: <p>Longitude East (negative values = West)</p>
http://lod.bco-dmo.org/id/dataset-parameter/767166.rdf
Name: Depth
Units: meters (m)
Description: <p>Depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/767167.rdf
Name: Temperature
Units: degrees Celsius
Description: <p>Temperature</p>
http://lod.bco-dmo.org/id/dataset-parameter/767168.rdf
Name: Salinity
Units: PSU?
Description: <p>Salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/767169.rdf
Name: Inorganic_poly_P_hydrolysis
Units: nanomoles P per liter per hour (nmol P/L/hr)
Description: <p>Inorganic poly-P hydrolysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/767170.rdf
Name: MUF_P_hydrolysis
Units: nmol P/L/hr
Description: <p>MUF-P hydrolysis</p>
http://lod.bco-dmo.org/id/dataset-parameter/767171.rdf
Name: Soluble_reactive_P
Units: nanomoles per liter (nmol/L)
Description: <p>Soluble reactive P</p>
http://lod.bco-dmo.org/id/dataset-parameter/767172.rdf
Name: Chlorophyll
Units: micrograms per liter (ug/L)
Description: <p>Chlorophyll</p>
http://lod.bco-dmo.org/id/dataset-parameter/767173.rdf
Name: Bacterial_abundance
Units: 10^5 cells per milliiter (10^5 cells/mL)
Description: <p>Bacterial abundance</p>
http://lod.bco-dmo.org/id/dataset-parameter/767174.rdf
Name: Total_phytoplankton
Units: 10^4 cells/mL
Description: <p>Total phytoplankton</p>
http://lod.bco-dmo.org/id/dataset-parameter/767175.rdf
Name: Synechococcus_spp
Units: 10^4 cells/mL
Description: <p>Synechococcus spp.</p>
http://lod.bco-dmo.org/id/dataset-parameter/767176.rdf
Name: Picoeukaryotic_phytoplankton
Units: 10^3 cells/mL
Description: <p>Picoeukaryotic phytoplankton</p>
http://lod.bco-dmo.org/id/dataset-parameter/767177.rdf
Name: Nanoeukaryotic_phytoplankton
Units: 10^3 cells/mL
Description: <p>Nanoeukaryotic phytoplankton</p>
http://lod.bco-dmo.org/id/dataset-parameter/767178.rdf
Name: Large_eukaryotic_phytoplankton
Units: 10^2 cells/mL
Description: <p>Large eukaryotic phytoplankton</p>
http://lod.bco-dmo.org/id/dataset-parameter/767179.rdf
Name: Bacterial_abundance_to_Total_phytoplankton
Units: unitless
Description: <p>Ratio of Bacterial abundance:Total phytoplankton</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
786
https://darchive.mblwhoilibrary.org/bitstream/1912/24131/1/dataset-767022_phosphohydrolysis-rates-coastal-western-north-atlantic__v1.tsv
download
https://doi.org/10.1575/1912/bco-dmo.767022.1
download
onLine
dataset
<p><strong>Field sampling:</strong> Surface seawater (5–35 m) was collected in September 2016 during two sampling campaigns in the coastal western North Atlantic (Diaz et al., 2018; Supplementary Table S1). Three sites were sampled aboard the R/V Endeavor using a Niskin rosette sampler and incubated immediately in order to determine rates of P hydrolysis. Two sites accessible by small boat in Woods Hole Harbor and Buzzard's Bay, MA, were sampled utilizing a peristaltic pump. These samples were transported on ice packs and analyzed for P hydrolysis rates within 5–6 hours of collection. Additional samples were preserved and analyzed for chlorophyll, bacteria and phytoplankton abundance, and soluble reactive P (SRP), as detailed below.</p>
<p><strong>Chlorophyll:</strong> In the dark, 250 mL of seawater was filtered onto 25 mm GF/F filters. Samples were stored in the dark at -20C until analyzed according to protocols adapted from Strickland and Parsons (1972). Briefly, samples were extracted in 90% acetone in the dark (4C, 9 hr) and measured using a 10AU fluorometer (Turner). Sample signals were calibrated using a chlorophyll-a standard (Sigma) and were corrected for phaeopigments by accounting for the fluorescence of extracts before and after acidification to 0.003 M HCl.</p>
<p><strong>Abundance of bacteria and phytoplankton:</strong> Seawater samples were preserved for flow cytometry with 0.5% glutaraldehyde (final concentration), flash frozen in liquid nitrogen and stored at -80°C until analysis. Bacteria and group-specific phytoplankton counts were conducted on a Guava EasyCyte HT flow cytometer (Millipore). Instrument-specific beads were used to calibrate the cytometer. Samples were analyzed at a low flow rate (0.24 µL s⁻¹) for 3 min. To enumerate bacteria, samples were diluted (1:100) with filtered seawater (0.01 µm). Samples and filtered seawater blanks were stained with SYBR Green I (Invitrogen) according to the manufacturer's instructions and incubated in a 96-well plate in the dark at room temperature for 1 hr. Bacterial cells were counted based on diagnostic forward scatter vs. green fluorescence signals. Major phytoplankton groups were distinguished based on plots of forward scatter vs. orange (phycoerythrin-containing Synechococcus sp.), and forward scatter vs. red (eukaryotes). Size classes of eukaryotic phytoplankton were further distinguished based on forward scatter (pico-, nano- and large eukaryotes).</p>
<p><strong>Soluble reactive P:</strong> Seawater samples were collected from Niskin rosette bottles or the peristaltic pump into acid cleaned, high density polyethylene bottles. Samples used for determining in situ SRP concentrations were frozen and stored upright at -20°C until analysis. Field samples and diatom filtrates were both analyzed for SRP using a standard colorimetric method (Hansen and Koroleff, 1999). To determine in situ SRP concentrations in field samples, SRP analysis was conducted using a 4 cm glass spectrophotometry cell on triplicate subsamples, and the detection limit, defined as three times the standard deviation of replicate blank measurements, was 115 nmol L⁻¹ SRP. For incubations to determine P hydrolysis rates (see below), replicate samples were analyzed in clear 96-well plates on a multimode plate reader (Molecular Devices) with a detection limit of 800 nmol L⁻¹ P.</p>
<p><strong>P-hydrolysis of model DOP substrates:</strong> Field samples were incubated with the fluorogenic probe 4-methylumbeliferone phosphate (MUF-P) and two inorganic polyphosphate compounds with an average chain length of 3 or 45 P atoms.</p>
<p>Samples were amended with each substrate at a final concentration of 20 M P. This concentration was assumed to be rate-saturating based on preliminary experiments. Hydrolysis of polyphosphates was determined from the production of phosphate using the colorimetric protocol outlined above. Hydrolysis of the fluorogenic probe MUF-P was monitored using a standard fluorescence technique. Briefly, hydrolysis of MUF-P to 4-methylumbellierone (MUF) was measured (excitation: 359 nm, emission: 449 nm) and calibrated with a multi-point standard curve of MUF (10–500 nmol L⁻¹). In both methods, samples were corrected for substrate autohydrolysis by accounting for negative controls, which were filtered (0.2 m) and boiled (99C, 15 min) prior to P amendment in order to eliminate enzyme activity. See Diaz et al. 2018 Frontiers in Marine Science 5: 380 for full methods.</p>
Specified by the Principal Investigator(s)
<p>BCO-DMO Processing:&nbsp;modified parameter names (replaced spaces and hyphens with underscores, removed units)</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
Guava EasyCyte HT flow cytometer (Millipore)
Guava EasyCyte HT flow cytometer (Millipore)
PI Supplied Instrument Name: Guava EasyCyte HT flow cytometer (Millipore) 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/
PI Supplied Instrument Name: 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/
multimode plate reader (Molecular Devices)
multimode plate reader (Molecular Devices)
PI Supplied Instrument Name: multimode plate reader (Molecular Devices) Instrument Name: plate reader Instrument Short Name: Instrument Description: Plate readers (also known as microplate readers) are laboratory instruments designed to detect biological, chemical or physical events of samples in microtiter plates. They are widely used in research, drug discovery, bioassay validation, quality control and manufacturing processes in the pharmaceutical and biotechnological industry and academic organizations. Sample reactions can be assayed in 6-1536 well format microtiter plates. The most common microplate format used in academic research laboratories or clinical diagnostic laboratories is 96-well (8 by 12 matrix) with a typical reaction volume between 100 and 200 uL per well. Higher density microplates (384- or 1536-well microplates) are typically used for screening applications, when throughput (number of samples per day processed) and assay cost per sample become critical parameters, with a typical assay volume between 5 and 50 µL per well. Common detection modes for microplate assays are absorbance, fluorescence intensity, luminescence, time-resolved fluorescence, and fluorescence polarization. From: http://en.wikipedia.org/wiki/Plate_reader, 2014-09-0-23.
peristaltic pump
peristaltic pump
PI Supplied Instrument Name: peristaltic pump Instrument Name: Pump Instrument Short Name: Instrument Description: A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps
10AU fluorometer (Turner)
10AU fluorometer (Turner)
PI Supplied Instrument Name: 10AU fluorometer (Turner) Instrument Name: Turner Designs Fluorometer 10-AU Instrument Short Name:Turner Fluorometer 10-AU Instrument Description: The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA). Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/
Cruise: EN588
EN588
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN588
Colleen Hansel
Woods Hole Oceanographic Institution
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel