http://lod.bco-dmo.org/id/dataset/835741
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
2021-01-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Phytoplankton carbon biomass by taxa from NOAA Ship R/V Nancy Foster cruises NF1704 and NF1802 in the Gulf of Mexico, May 2017 and 2018
2021-01-07
publication
2021-01-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-02-09
publication
https://doi.org/10.26008/1912/bco-dmo.835741.1
Karen E. Selph
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: Selph, K. E. (2021) Phytoplankton carbon biomass by taxa from NOAA Ship R/V Nancy Foster cruises NF1704 and NF1802 in the Gulf of Mexico, May 2017 and 2018. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-01-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.835741.1 [access date]
Phytoplankton carbon biomass Dataset Description: Methods and Sampling: <p>Phytoplankton samples for flow cytometry, HPLC and microscopy were collected pre-dawn from Niskin bottles mounted on a 24-place rosette system equipped with a Seabird SBE911 CTD and a Seapoint fluorometer.&nbsp;</p>
<p>Flow cytometry samples (2-mL) for pico-phytoplankton abundance were preserved (0.5% paraformaldehyde) and frozen in LN2, then stored at -80°C until shore-based analyses.&nbsp; On-shore, flow cytometry samples were thawed and stained for 1 h with the DNA stain Hoechst 33342 (1 µg/ml, Monger and Landry, 1993), then analyzed with a Beckman Coulter EPICS Altra flow cytometer (Selph et al., 2011).&nbsp; Listmode data were processed using FlowJo (version 9.7.7, Treestar, Inc.) to delineate Prochlorococcus (PRO), Synechococcus (SYN), and eukaryotic phytoplankton (PEUK).&nbsp; PRO and SYN abundances were converted to carbon using 32 and 101 fg C/cell, respectively (Garrison et al., 2000; Brown et al., 2008).&nbsp; PEUK were mainly ≤2 µm cells, however some were larger and therefore microscopic counts for cells from 2-5 µm were subtracted from the total PEUK abundance, and the remaining cells were converted to carbon and scaled to be that of a cell twice the diameter of SYN (808 fg C/cell).</p>
<p>HPLC pigment samples (2.2-L) were filtered onto GF/F filters, frozen in LN2 and stored at -85°C until shore-based analyses.&nbsp; On shore, samples were sent to Horn Point Analytical Services Laboratory (University of Maryland Center for Environmental Science).&nbsp; There they were extracted, and analyzed using an automated 1100 HPLC system with Agilent temperature-controlled autosampler, Peltier temperature-controlled column oven compartment, PDA detector and ChemStation software.&nbsp; The HPLC method uses a C8 column and a reversed phase, methanol-based solvent system (Van Heukelem and Thomas, 2001; Hooker et al., 2012).&nbsp; MVCHLa and DVCHLa are detected at 665 nm.&nbsp; Carotenoid and xanthophyll accessory pigments are detected at 450 nm.</p>
<p>The pigments used for phytoplankton taxonomic identification were MVCHLa and DVCHLa (sum = TCHLa), monovinyl chlorophyll b (MVCHLb), divinyl chlorophyll b (DVCHLb), chlorophyll c3 (CHLc3), zeaxanthin (ZEAX), fucoxanthin (FUCO), 19’-hex-fucoxanthin (HEX), 19’-but-fucoxanthin (BUT), allophycocyanin (ALLO), peridinin (PER), neoxanthin (NEO), and prasinoxanthin (PRAS).&nbsp; Chlorophyll a contributions for PRO and SYN were subtracted from HPLC pigment data (estimated from flow cytometry and DVCHLa).&nbsp; Similarly, Trichodesmium MVCHLa was assigned from separately collected samples (Selph et al., 2021).&nbsp; The remaining HPLC pigments, except for ZEAX, were entered into the CHEMTAX program (v. 1.95, Wright, 2008) for partitioning into eukaryotic groups.</p>
<p>Initial pigment ratios (accessory pigment:MVCHLa) used in CHEMTAX were those of oceanic species (Higgens et al., 2011) and indicative of the following groups: chlorophytes (CHLOR), diatoms (DIAT), prymnesiophytes - type 6 (PRYM), pelagophytes (PELAG), cryptophytes (CRYPT), prasinophytes - type 3 (PRAS3), and dinoflagellates (A-DINO).&nbsp; Data were divided into 2 groups: shallower and deeper than 60 m, since some of the accessory pigments were only present in deep samples (NEO and ALLO) and the general pattern of pigments showed a different community at depth.&nbsp; The initial ratio matrix was randomized into 60 matrices (0.7 x random number between -0.5 and +0.5), which were then applied to the data sets (Supp. Table I).&nbsp; The resulting partitioning of MVCHLa into these phytoplankton taxa was used to estimate the percent of total carbon biomass in each group.</p>
<p>Microscopy samples from the top two depths (~80%I0 and 40%I0) and the bottom 2 depths (~5%I0 and 1%I0) sampled were used to estimate the biomass of eukaryotic phytoplankton taxa.&nbsp; Phytoplankton taxonomic structure was assessed to the extent possible, separating cells into dinoflagellates, diatoms, and unidentified flagellates. Microscope slides were prepared from 500 mL of preserved sample (260 µL alkaline Lugol’s solution (0.1% final), 10 mL 10% buffered formalin, 500 µL 3% sodium thiosulfate; modified protocol from Sherr and Sherr, 1993), to which 1 mL 0.33% proflavine (w/v) and 1 mL of 4’,6-diamidino-2-phenylindole (DAPI, 0.01 mg/mL) were added.&nbsp; For analysis of cells &lt;10-µm, a slide was prepared from 50 mL subsamples filtered onto a 25-mm, 0.8-µm pore size, black PCTE filter and mounted on a glass slide.&nbsp; For larger (10- to ~50-µm) cells, the remaining sample was filtered onto a 25-mm, 8-µm pore size, black PCTE filter.&nbsp; Slides were frozen (-80°C) until image analysis as detailed in Taylor et al. (2015).&nbsp; Cell biovolumes (BV, µm3) were calculated from length (L) and width (W) according to Taylor et al. (2011).&nbsp; BV was converted to carbon (C, pg/cell) using C = 0.216 x BV0.939 for non-diatoms and C = 0.288 x BV0.811 for diatoms (Menden-Deuer and Lessard, 2000).&nbsp; The FCM-derived PEUK abundance were assumed to represent cells &lt;5 µm, therefore 2-5 µm cells from microscopy were subtracted from total PEUK cells, leaving cells ≤2 µm (not counted with microscopy), and their carbon contents were added to the microscope slide-estimated carbon for a total phytoplankton community carbon estimate. These data were also used to determine carbon:chlorophyll (C:CHL) ratios at the depths where both measurements were taken.&nbsp; Missing intermediate depths (for carbon) were estimated using the 5%I0 C:CHL ratio.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851558 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851558
Funding provided by National Oceanic and Atmospheric Administration (NOAA) Award Number: NA16NMF4320058 Award URL: https://grantsonline.rdc.noaa.gov/flows/publicSearch/showAwardDetails.do?awdNum=NA16NMF4320058
completed
Karen E. Selph
University of Hawaiʻi at Mānoa
808-956-7941
Department of Oceanography 1000 Pope Road, MSB 205
Honolulu
HI
96822
USA
selph@hawaii.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Station
Date
Lon
Lat
Cycle
CTD
Depth
PRO
SYN
PRYM
DIAT
A_DINO
PELAG
CHLOR
PRAS3
CRYPT
interp
Beckman Coulter EPICS Altra flow cytometer
HPLC
Dissecting microscope
theme
None, User defined
Cruise identfier
station
date
latitude
longitude
No BCO-DMO term
cast
depth
wet_weight_biomass
featureType
BCO-DMO Standard Parameters
Flow Cytometer
High-Performance Liquid Chromatograph
Microscope - Optical
instrument
BCO-DMO Standard Instruments
NF1704
NF1802
service
Deployment Activity
Gulf of Mexico
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.
Second International Indian Ocean Expedition
https://web.whoi.edu/iioe2/
Second International Indian Ocean Expedition
Description from the program website:
The Second International Indian Ocean Expedition (IIOE-2) is a major global scientific program which will engage the international scientific community in collaborative oceanographic and atmospheric research from coastal environments to the deep sea over the period 2015-2020, revealing new information on the Indian Ocean (i.e. its currents, its influence upon the climate, its marine ecosystems) which is fundamental for future sustainable development and expansion of the Indian Ocean's blue economy. A large number of scientists from research institutions from around the Indian Ocean and beyond are planning their involvement in IIOE-2 in accordance with the overarching six scientific themes of the program. Already some large collaborative research projects are under development, and it is anticipated that by the time these projects are underway, many more will be in planning or about to commence as the scope and global engagement in IIOE-2 grows.
Focused research on the Indian Ocean has a number of benefits for all nations. The Indian Ocean is complex and drives the region's climate including extreme events (e.g. cyclones, droughts, severe rains, waves and storm surges). It is the source of important socio-economic resources (e.g. fisheries, oil and gas exploration/extraction, eco-tourism, and food and energy security) and is the background and focus of many of the region's human populations around its margins. Research and observations supported through IIOE-2 will result in an improved understanding of the ocean's physical and biological oceanography, and related air-ocean climate interactions (both in the short-term and long-term). The IIOE-2's program will complement and harmonise with other regional programs underway and collectively the outcomes of IIOE-2 will be of huge benefit to individual and regional sustainable development as the information is a critical component of improved decision making in areas such as maritime services and safety, environmental management, climate monitoring and prediction, food and energy security.
IIOE-2 activities will also include a significant focus on building the capacity of all nations around the Indian Ocean to understand and apply observational data or research outputs for their own socio-economic requirements and decisions. IIOE-2 capacity building programs will therefore be focused on the translation of the science and information outputs for societal benefit and training of relevant individuals from surrounding nations in these areas.
A Steering Committee was established to support U.S. participation in IIOE-2. More information is available on their website at https://web.whoi.edu/iioe2/.
IIOE-2
largerWorkCitation
program
Collaborative Research: Mesoscale variability in nitrogen sources and food-web dynamics supporting larval southern bluefin tuna in the eastern Indian Ocean
https://osprey.bco-dmo.org/project/819488
Collaborative Research: Mesoscale variability in nitrogen sources and food-web dynamics supporting larval southern bluefin tuna in the eastern Indian Ocean
<p><em>NSF Award Abstract:</em><br />
The small area between NW Australia and Indonesia in the eastern Indian Ocean (IO) is the only known spawning ground of Southern Bluefin Tuna (SBT), a critically endangered top marine predator. Adult SBT migrate thousands of miles each year from high latitude feeding areas to lay their eggs in these tropical waters, where food concentrations on average are below levels that can support optimal feeding and growth of their larvae. Many critical aspects of this habitat are poorly known, such as the main source of nitrogen nutrient that sustains system productivity, how the planktonic food web operates to produce the unusual types of zooplankton prey that tuna larvae prefer, and how environmental differences in habitat quality associated with ocean fronts and eddies might be utilized by adult spawning tuna to give their larvae a greater chance for rapid growth and survival success. This project investigates these questions on a 38-day expedition in early 2021, during the peak time of SBT spawning. This project is a US contribution to the 2nd International Indian Ocean Expedition (IIOE-2) that advances understanding of biogeochemical and ecological dynamics in the poorly studied eastern IO. This is the first detailed study of nitrogen and carbon cycling in the region linking Pacific and IO waters. The shared dietary preferences of SBT larvae with those of other large tuna and billfish species may also make the insights gained broadly applicable to understanding larval recruitment issues for top consumers in other marine ecosystems. New information from the study will enhance international management efforts for SBT. The shared larval dietary preferences of large tuna and billfish species may also extend the insights gained broadly to many other marine top consumers, including Atlantic bluefin tuna that spawn in US waters of the Gulf of Mexico. The end-to-end study approach, highlights connections among physical environmental variability, biogeochemistry, and plankton food webs leading to charismatic and economically valuable fish production, is the theme for developing educational tools and modules through the "scientists-in-the-schools" program of the Center for Ocean-Atmospheric Prediction Studies at Florida State University, through a program for enhancing STEM learning pathways for underrepresented students in Hawaii, and through public outreach products for display at the Birch Aquarium in San Diego. The study also aims to support an immersive field experience to introduce talented high school students to marine research, with the goal of developing a sustainable marine-related educational program for underrepresented students in rural northwestern Florida.</p>
<p>Southern Bluefin Tuna (SBT) migrate long distances from high-latitude feeding grounds to spawn exclusively in a small oligotrophic area of the tropical eastern Indian Ocean (IO) that is rich in mesoscale structures, driven by complex currents and seasonally reversing monsoonal winds. To survive, SBT larvae must feed and grow rapidly under environmental conditions that challenge conventional understanding of food-web structure and functional relationships in poor open-ocean systems. The preferred prey of SBT larvae, cladocerans and Corycaeidae copepods, are poorly studied and have widely different implications for trophic transfer efficiencies to larvae. Differences in nitrogen sources - N fixation vs deep nitrate of Pacific origin - to sustain new production in the region also has implications for conditions that may select for prey types (notably cladocerans) that enhance transfer efficiency and growth rates of SBT larvae. The relative importance of these N sources for the IO ecosystem may affect SBT resiliency to projected increased ocean stratification. This research expedition investigates how mesoscale variability in new production, food-web structure and trophic fluxes affects feeding and growth conditions for SBT larvae. Sampling across mesoscale features tests hypothesized relationships linking variability in SBT larval feeding and prey preferences (gut contents), growth rates (otolith analyses) and trophic positions (TP) to the environmental conditions of waters selected by adult spawners. Trophic Positions of larvae and their prey are determined using Compound-Specific Isotope Analyses of Amino Acids (CSIA-AA). Lagrangian experiments investigate underlying process rates and relationships through measurements of water-column 14C productivity, N2 fixation, 15NO3- uptake and nitrification; community biomass and composition (flow cytometry, pigments, microscopy, in situ imaging, genetic analyses); and trophic fluxes through micro- and mesozooplankton grazing, remineralization and export. Biogeochemical and food web elements of the study are linked by CSIA-AA (N source, TP), 15N-constrained budgets and modeling. The project elements comprise an end-to-end coupled biogeochemistry-trophic study as has not been done previously for any pelagic ecosystem.</p>
<p>This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.</p>
BLOOFINZ-IO
largerWorkCitation
project
Effects of Nitrogen Sources and Plankton Food-Web Dynamics on Habitat Quality for the Larvae of Atlantic Bluefin Tuna in the Gulf of Mexico
https://osprey.bco-dmo.org/project/834957
Effects of Nitrogen Sources and Plankton Food-Web Dynamics on Habitat Quality for the Larvae of Atlantic Bluefin Tuna in the Gulf of Mexico
<p>Amendment #136: Current stock assessments for the Gulf of Mexico require better ecosystem understanding to effectively evaluate how bottom-up processes limit or enhance Atlantic Bluefin Tuna recruitment. The objective of this proposal is to elucidate the underlying mechanisms that link variability in nitrogen sources and food-web fluxes in the Gulf of Mexico to habitat quality, feeding, growth and survival for Atlantic Bluefin Tuna larvae. This proposal addresses the Program Priority: Comprehensive understanding of living coastal and marine resources, food web dynamics, habitat utilization, protected areas, and carbon flows, specifically "(d) Food web structure and dynamics, trophic linkages, and/or predator-prey relationships, especially projects that develop and/or apply new techniques or technologies".</p>
GoMex Tuna Foodweb B
largerWorkCitation
project
eng; USA
biota
oceans
Gulf of Mexico
-90.1775
-87.3032
25.721
28.3358
2017-05-11
2018-05-18
From projects that focused on the following 2 locations: 1. Eastern Indian Ocean, Indonesian Throughflow area, and the Gulf of Mexico 2. Gulf of Mexico
0
BCO-DMO catalogue of parameters from Phytoplankton carbon biomass by taxa from NOAA Ship R/V Nancy Foster cruises NF1704 and NF1802 in the Gulf of Mexico, May 2017 and 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/835756.rdf
Name: Cruise
Units: unitless
Description: <p>cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/835757.rdf
Name: Station
Units: unitless
Description: <p>station identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/835758.rdf
Name: Date
Units: unitless
Description: <p>cast date, UTC</p>
http://lod.bco-dmo.org/id/dataset-parameter/835759.rdf
Name: Lon
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/835760.rdf
Name: Lat
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/835761.rdf
Name: Cycle
Units: unitless
Description: <p>Series of stations following a Lagrangian drift array, as described in Gerard et al., 2021.</p>
http://lod.bco-dmo.org/id/dataset-parameter/835762.rdf
Name: CTD
Units: unitless
Description: <p>cast number</p>
http://lod.bco-dmo.org/id/dataset-parameter/835764.rdf
Name: Depth
Units: meters
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/835765.rdf
Name: PRO
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Prochlorococcus biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835766.rdf
Name: SYN
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Synechococcus biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835767.rdf
Name: PRYM
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Prymnesiophytes-Type 6 biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835768.rdf
Name: DIAT
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Diatom biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835769.rdf
Name: A_DINO
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Autotrophic dinoflagellates biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835770.rdf
Name: PELAG
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Pelagophytes biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835771.rdf
Name: CHLOR
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Chlorophytes biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835772.rdf
Name: PRAS3
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Prasinophytes-Type 3 biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835773.rdf
Name: CRYPT
Units: micrograms Carbon/liter (ug C/L)
Description: <p>Cryptophytes biomass</p>
http://lod.bco-dmo.org/id/dataset-parameter/835774.rdf
Name: interp
Units: unitless
Description: <p>Interpolated Data flag: Y (Yes); N (No). Interpolated data refers to carbon biomass data calculated from HPLC pigment data multiplied by the carbon:chlorophyll (C:CHL) ratio of the deepest available data. For instance, for CTD 8, the C:CHL ratio of the 70 m (5% of incident irradiance) sample was multiplied by the HPLC pigment data of the 25 and 50 m samples to obtain C for those samples.</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
6987
https://darchive.mblwhoilibrary.org/bitstream/1912/26655/1/dataset-835741_gomex-phytoplankton-carbon-biomass__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.835741.1
download
onLine
dataset
<p>Phytoplankton samples for flow cytometry, HPLC and microscopy were collected pre-dawn from Niskin bottles mounted on a 24-place rosette system equipped with a Seabird SBE911 CTD and a Seapoint fluorometer.&nbsp;</p>
<p>Flow cytometry samples (2-mL) for pico-phytoplankton abundance were preserved (0.5% paraformaldehyde) and frozen in LN2, then stored at -80°C until shore-based analyses.&nbsp; On-shore, flow cytometry samples were thawed and stained for 1 h with the DNA stain Hoechst 33342 (1 µg/ml, Monger and Landry, 1993), then analyzed with a Beckman Coulter EPICS Altra flow cytometer (Selph et al., 2011).&nbsp; Listmode data were processed using FlowJo (version 9.7.7, Treestar, Inc.) to delineate Prochlorococcus (PRO), Synechococcus (SYN), and eukaryotic phytoplankton (PEUK).&nbsp; PRO and SYN abundances were converted to carbon using 32 and 101 fg C/cell, respectively (Garrison et al., 2000; Brown et al., 2008).&nbsp; PEUK were mainly ≤2 µm cells, however some were larger and therefore microscopic counts for cells from 2-5 µm were subtracted from the total PEUK abundance, and the remaining cells were converted to carbon and scaled to be that of a cell twice the diameter of SYN (808 fg C/cell).</p>
<p>HPLC pigment samples (2.2-L) were filtered onto GF/F filters, frozen in LN2 and stored at -85°C until shore-based analyses.&nbsp; On shore, samples were sent to Horn Point Analytical Services Laboratory (University of Maryland Center for Environmental Science).&nbsp; There they were extracted, and analyzed using an automated 1100 HPLC system with Agilent temperature-controlled autosampler, Peltier temperature-controlled column oven compartment, PDA detector and ChemStation software.&nbsp; The HPLC method uses a C8 column and a reversed phase, methanol-based solvent system (Van Heukelem and Thomas, 2001; Hooker et al., 2012).&nbsp; MVCHLa and DVCHLa are detected at 665 nm.&nbsp; Carotenoid and xanthophyll accessory pigments are detected at 450 nm.</p>
<p>The pigments used for phytoplankton taxonomic identification were MVCHLa and DVCHLa (sum = TCHLa), monovinyl chlorophyll b (MVCHLb), divinyl chlorophyll b (DVCHLb), chlorophyll c3 (CHLc3), zeaxanthin (ZEAX), fucoxanthin (FUCO), 19’-hex-fucoxanthin (HEX), 19’-but-fucoxanthin (BUT), allophycocyanin (ALLO), peridinin (PER), neoxanthin (NEO), and prasinoxanthin (PRAS).&nbsp; Chlorophyll a contributions for PRO and SYN were subtracted from HPLC pigment data (estimated from flow cytometry and DVCHLa).&nbsp; Similarly, Trichodesmium MVCHLa was assigned from separately collected samples (Selph et al., 2021).&nbsp; The remaining HPLC pigments, except for ZEAX, were entered into the CHEMTAX program (v. 1.95, Wright, 2008) for partitioning into eukaryotic groups.</p>
<p>Initial pigment ratios (accessory pigment:MVCHLa) used in CHEMTAX were those of oceanic species (Higgens et al., 2011) and indicative of the following groups: chlorophytes (CHLOR), diatoms (DIAT), prymnesiophytes - type 6 (PRYM), pelagophytes (PELAG), cryptophytes (CRYPT), prasinophytes - type 3 (PRAS3), and dinoflagellates (A-DINO).&nbsp; Data were divided into 2 groups: shallower and deeper than 60 m, since some of the accessory pigments were only present in deep samples (NEO and ALLO) and the general pattern of pigments showed a different community at depth.&nbsp; The initial ratio matrix was randomized into 60 matrices (0.7 x random number between -0.5 and +0.5), which were then applied to the data sets (Supp. Table I).&nbsp; The resulting partitioning of MVCHLa into these phytoplankton taxa was used to estimate the percent of total carbon biomass in each group.</p>
<p>Microscopy samples from the top two depths (~80%I0 and 40%I0) and the bottom 2 depths (~5%I0 and 1%I0) sampled were used to estimate the biomass of eukaryotic phytoplankton taxa.&nbsp; Phytoplankton taxonomic structure was assessed to the extent possible, separating cells into dinoflagellates, diatoms, and unidentified flagellates. Microscope slides were prepared from 500 mL of preserved sample (260 µL alkaline Lugol’s solution (0.1% final), 10 mL 10% buffered formalin, 500 µL 3% sodium thiosulfate; modified protocol from Sherr and Sherr, 1993), to which 1 mL 0.33% proflavine (w/v) and 1 mL of 4’,6-diamidino-2-phenylindole (DAPI, 0.01 mg/mL) were added.&nbsp; For analysis of cells &lt;10-µm, a slide was prepared from 50 mL subsamples filtered onto a 25-mm, 0.8-µm pore size, black PCTE filter and mounted on a glass slide.&nbsp; For larger (10- to ~50-µm) cells, the remaining sample was filtered onto a 25-mm, 8-µm pore size, black PCTE filter.&nbsp; Slides were frozen (-80°C) until image analysis as detailed in Taylor et al. (2015).&nbsp; Cell biovolumes (BV, µm3) were calculated from length (L) and width (W) according to Taylor et al. (2011).&nbsp; BV was converted to carbon (C, pg/cell) using C = 0.216 x BV0.939 for non-diatoms and C = 0.288 x BV0.811 for diatoms (Menden-Deuer and Lessard, 2000).&nbsp; The FCM-derived PEUK abundance were assumed to represent cells &lt;5 µm, therefore 2-5 µm cells from microscopy were subtracted from total PEUK cells, leaving cells ≤2 µm (not counted with microscopy), and their carbon contents were added to the microscope slide-estimated carbon for a total phytoplankton community carbon estimate. These data were also used to determine carbon:chlorophyll (C:CHL) ratios at the depths where both measurements were taken.&nbsp; Missing intermediate depths (for carbon) were estimated using the 5%I0 C:CHL ratio.</p>
Specified by the Principal Investigator(s)
<p>Flow cytometry listmode files: On flow cytometer, listmode files are generated by Expo32 software (Beckman-Coulter); offline these listmode files were processed using FlowJo, version 9.7.7, Treestar, Inc.</p>
<p>HPLC:&nbsp; ChemStation software for generated raw data, whereas the program CHEMTAX was used for partitioning MVCHLa into taxonomic groups (CHEMTAX, v. 1.95,Wright, 2008).</p>
<p>Microscopy:&nbsp; Zeiss Axiovision software</p>
<p><strong>BCO-DMO Processing Notes:</strong><br />
- data submitted in Excel file "GoM phytoplankton carbon.csv"&nbsp;extracted to csv<br />
- added conventional header with dataset name, PI name, version date<br />
- renamed columns to conform with BCO-DMO naming conventions (removed spaces and special characters)<br />
- formatted&nbsp;Date to ISO (yyyy-mm-dd)<br />
- replaced blank cells with no data value 'nd', the default missing data identifier in the BCO-DMO system.</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
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Beckman Coulter EPICS Altra flow cytometer
Beckman Coulter EPICS Altra flow cytometer
PI Supplied Instrument Name: Beckman Coulter EPICS Altra flow cytometer 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/
HPLC
HPLC
PI Supplied Instrument Name: HPLC PI Supplied Instrument Description:Automated 1100 HPLC system with Agilent temperature-controlled autosampler, Peltier temperature-controlled column oven compartment, PDA detector and ChemStation software. Instrument Name: High-Performance Liquid Chromatograph Instrument Short Name:HPLC Instrument Description: A High-performance liquid chromatograph (HPLC) is a type of liquid chromatography used to separate compounds that are dissolved in solution. HPLC instruments consist of a reservoir of the mobile phase, a pump, an injector, a separation column, and a detector. Compounds are separated by high pressure pumping of the sample mixture onto a column packed with microspheres coated with the stationary phase. The different components in the mixture pass through the column at different rates due to differences in their partitioning behavior between the mobile liquid phase and the stationary phase. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB11/
Dissecting microscope
Dissecting microscope
PI Supplied Instrument Name: Dissecting microscope PI Supplied Instrument Description:Dissecting microscope (10X-30X) with a NightSea SFA adaptor and Royal Blue light head (EX 440-460 nm, EM >500 nm); Olympus BX-41 epifluorescence microscope (200X, EX 450-480 nm, dichroic 500 nm, EM >515 nm); Chlorophyll fluorescence of Trichodesmium - 10AU fluorometer. Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
Cruise: NF1704
NF1704
R/V Nancy Foster
Community Standard Description
International Council for the Exploration of the Sea
R/V Nancy Foster
vessel
NF1704
Estrella Malca
University of Miami
https://datadocs.bco-dmo.org/docs/302/BLOOFINZ_IO/data_docs/cruise_reports/NF1704_CRUISE_REPORT.pdf
Report describing NF1704
Cruise: NF1802
NF1802
R/V Nancy Foster
Community Standard Description
International Council for the Exploration of the Sea
R/V Nancy Foster
vessel
NF1802
John Lamkin
NOAA Southeast Fisheries Science Center
https://datadocs.bco-dmo.org/docs/302/BLOOFINZ_IO/data_docs/cruise_reports/NF1802_CRUISE_REPORT.pdf
Report describing NF1802
R/V Nancy Foster
Community Standard Description
International Council for the Exploration of the Sea
R/V Nancy Foster
vessel