Contributors | Affiliation | Role |
---|---|---|
Ward, Bess B. | Princeton University | Principal Investigator, Contact |
Allen, Andrew E. | J. Craig Venter Institute (JCVI) | Co-Principal Investigator |
Sigman, Daniel M. | Princeton University | Scientist |
Van Oostende, Nicolas C. | Princeton University | Contact |
Copley, Nancy | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
Rauch, Shannon | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
This dataset includes pico- and nanoplankton cell concentrations from CTD casts made during the August-September 2013 EN532 and April-May 2014 EN358 cruises aboard R/V Endeavor. Study sites were located in the subarctic Atlantic Ocean along the 20 °W meridian between 50 °N and 60 °N in September 2013 and May 2014. Two transects from the US East coast to the subarctic study sites were performed as well.
See the "Related Datasets" section for several related BCO-DMO datasets from the same cruises.
The cell abundance of pico- and nanophytoplankton (<~14 micrometers (µm) cell diameter) was determined by flow cytometric analysis of 1500 microliters (µl) of glutaraldehyde-preserved (1% v/v) (Marie et al. 1997) samples using a BD Accuri C6 flow cytometer equipped with a blue laser (488 nanometers (nm)), at a flow rate of 100 µl per minute, and a core diameter of 22 µm. Standard fluorescent bead solutions were prepared daily and used as an internal standard to assess instrument performance, to standardize scatter and fluorescence measurements (Rainbow Calibration Particles (8 peaks), BD Biosciences), and to validate the flow rate (TruCount, BD Biosciences) for quantitative applications. Each sample was run with fluorescent beads (YG beads, 0.94 µm Fluoresbrite® Yellow Green Microspheres, Polysciences, Inc.) as an internal standard for forward scatter measurements.
We distinguished several phytoplankton groups based on their forward (FSC) and side scatter (SSC), Chla, and phycoerythrin (PE) fluorescence signals: the picophytoplankton (<~2.5 µm) group comprised PE-containing Synechococcus and non-PE-containing picoeukaryotes (picoEuk), the nanophytoplankton groups (nanoEuk, >~2.5 - 14 µm) included PE-containing nanophytoplankton (PE_Euk), non-PE-containing phytoplankton, and coccolithophores (Cocco) (the latter group was identified based on their enhanced side scatter signal). The total concentration of nanoeukaryote phytoplankton (totnanoEuk) is the sum of PE_Euk, Cocco, and non-PE-containing phytoplankton other than Cocco.
The picoplanktonic Prochlorococcus cells were counted in SYBR Green I-stained samples (Marie et al. 1997), according to (Heywood et al. 2006), because of the difficulty of discriminating unstained cells from background noise. The concentration of heterotrophic bacterial cells was determined by flow cytometric analysis of 250 µl of glutaraldehyde-preserved (1% v/v) and SYBR Green I-stained (1:7500) samples according to Marie et al. (1997) and Gasol and Del Giorgio (2000). The Prochlorococcus and heterotrophic bacteria samples were analysed using a BD Accuri C6 flow cytometer, at a flow rate of 35 µl per minute, and a core diameter of 16 µm. All plankton groups were gated and their abundance quantified using FlowJo software (Tree Star, Inc., www.flowjo.com).
The biovolume of phytoplankton cells analyzed by flow cytometry was derived from forward scatter measurements of individual cells based on the polynomial relationship between the log10 of measured biovolumes of pico- and nanophytoplankton cells and the log10 of the peak area of their forward scatter signal (FSC-A) (Laney & Sosik 2014). A calibration procedure, using bead stocks and an unidentified cultured picoeukaryote from the Sosik Lab at Woods Hole Oceanographic Institution, confirmed the inter-lab agreement of flow cytometry-derived biovolume estimates. Since the largest phytoplankton cell in the empirical relationship of Laney & Sosik (2014) had a cell diameter of 14 µm and the number of cells larger than this in our samples was negligible, only cells up to ~14 µm in diameter were included in the cell abundance and biovolume calculations. Cellular biomass was estimated according to the relationship between cellular biovolume (cubic micrometers per cell (µm3 cell-1)) and carbon content (picomoles per cell (pmol cell-1)) for glutaraldehyde preserved pico- and nanophytoplankton cells from (Verity et al. 1992): C = (0.433 ⁄ 12) × biovolume^0.863.
Although Synechococcus cells could readily be counted based on their size and their characteristic PE fluorescence the high signal-to-noise ratio in the FSC-A channel of the Accuri precluded a reliable cell size estimate for particles smaller than 1 µm. Therefore, the biomass of Synechococcus was estimated using a conversion factor of 140 femtograms carbon per cell (fg C cell-1) assuming a cell diameter of 1 µm and 270 fg C µm-3 (Bertilsson et al. 2003). The biomass of Prochlorococcus cells was calculated by using an average cellular carbon content of 53.5 fg C cell-1 (Bertilsson et al. 2003), which is very similar to the range of cellular carbon content determined by Casey et al. (2013) for Prochlorococcus in the euphotic zone.
Quality Flags:
The data quality flag scheme used is that of SEADATANET, where:
no quality control = 0
good value = 1
probably good value = 2
probably bad value = 3
bad value = 4
changed value = 5
value below detection = 6
value in excess = 7
interpolated value = 8
missing value = 9
value phenomenon uncertain = A
BCO-DMO Processing & Version History:
Version 1 (date: 2016-07-15)
- added conventional header with dataset name, PI name, version date.
- renamed parameters to BCO-DMO standard.
- replaced blank cells with "nd".
- replaced blanks with underscores.
- formatted lat and long to 4 decimal places.
Version 1 contained some incorrect values in column "totnanoEuk_biomass_nMC". These values have been corrected in version 2.
Version 2 (date: 2025-01-08)
- Imported original file "FCM_Ward_Dimensions_2024.xlsx" into the BCO-DMO system.
- Marked "nd" as a missing data identifier; all missing data are empty/blank in the final csv file.
- Added a trailing "Z" to the ISO_DateTime_UTC column to indicate UTC time zone.
- Added column for longitude in -180 to 180 degrees; renamed the original longitude column "lon_360"
- Saved the final file as "651890_v2_pico_nano_abund_fcm_en532_en538.csv".
In this version, values in the column "totnanoEuk_biomass_nMC" have been corrected.
Parameter | Description | Units |
cruise_id | cruise identification | unitless |
cast | cast number | unitless |
ISO_DateTime_UTC | Date and time (UTC) in ISO 8601 format | unitless |
lat | latitude; positive values = North | decimal degrees |
lon | longitude; negative values = West | decimal degrees |
lon_360 | longitude from 0 to 360 degrees | decimal degrees |
depth_w | depth of the water | meters |
depth | sample depth | meters |
Syn_biomass_nMC | concentration of Synechococcus carbon biomass | nanomoles Carbon per liter (nmol C/liter) |
Syn_cells_per_ml | concentration of Synechococcus cells | cells/milliliter |
Syn_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
picoEuk_biomass_nMC | concentration of picoeukaryote phytoplankton carbon biomass | nanomoles Carbon per liter (nmol C/liter) |
picoEuk_cells_per_ml | concentration of picoeukaryote phytoplankton cells | cells/milliliter |
picoEuk_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
PE_Euk_biomass_nMC | concentration of phycoerythrin-containing nanoeukaryote phytoplankton carbon biomass | nanomoles Carbon per liter (nmol C/liter) |
PE_Euk_cells_per_ml | concentration of phycoerythrin-containing nanoeukaryote phytoplankton cells | cells/milliliter |
PE_Euk_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
totnanoEuk_biomass_nMC | concentration of nanoeukaryote phytoplankton carbon biomass | nanomoles Carbon per liter (nmol C/liter) |
totnanoEuk_cells_per_ml | concentration of nanoeukaryote phytoplankton cells | cells/milliliter |
totnanoEuk_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
cocco_biomass_nMC | concentration of coccolithophore carbon biomass | nanomoles Carbon per liter (nmol C/liter) |
cocco_cells_per_ml | concentration of coccolithophore cells | cells/milliliter |
cocco_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
Prochlor_biomass_nMC | concentration of Prochlorococcus carbon biomass | nanomoles Carbon per liter (nmol C/liter) |
Prochlor_cells_per_ml | concentration of Prochlorococcus cells | cells/milliliter |
Prochlor_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
total_FC_phyto_biomass_nMC | concentration of total flow cytometrically determined phytoplankton carbon biomass | nanomoles Carbon per liter (nmol C/liter) |
total_FC_phyto_cells_per_ml | concentration of total flow cytometrically determined phytoplankton cells | cells/milliliter |
total_FC_phyto_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
total_het_bact_cells_per_ml | concentration of non-chlorophyll a containing bacterial cells | cells/milliliter |
total_het_bact_cells_per_ml_flag | quality flag - see description in the Data Processing section of metadata | unitless |
comment | comments | unitless |
Dataset-specific Instrument Name | |
Generic Instrument Name | CTD Sea-Bird SBE 911plus |
Generic Instrument Description | The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics |
Dataset-specific Instrument Name | |
Generic Instrument Name | Flow Cytometer |
Dataset-specific Description | BD Accuri C6 flow cytometer |
Generic 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) |
Dataset-specific Instrument Name | |
Generic Instrument Name | Niskin bottle |
Generic 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. |
Website | |
Platform | R/V Endeavor |
Report | |
Start Date | 2013-08-22 |
End Date | 2013-09-15 |
Description | Study sites in the subtropical North-Atlantic Ocean near the Bermuda Atlantic Time Series in February 2012 and August 2012, and in the subarctic Atlantic Ocean along the 20W meridian between 50N and 60N in September 2013 and May 2014. Two transects from the US East coast to the subarctic study sites were performed as well. |
Website | |
Platform | R/V Endeavor |
Report | |
Start Date | 2014-04-29 |
End Date | 2014-05-22 |
Description | Study sites in the subarctic Atlantic Ocean along the 20 °W meridian between 58 °N and 60 °N in May 2014. A transect from the US East coast (RI) to the subarctic study sites was performed as well. |
This project will investigate the taxonomic, genetic and functional diversity of eukaryotic phytoplankton at two North Atlantic sites (subarctic and subtropical) in two seasons. The PIs will use diagnostic microarrays for community analysis based on functional genes (both DNA and RNA) and next generation sequencing (i.e., transcriptomics using 454 technology) to identify the players, both in terms of community composition and activity, and to explore the functional diversity of the natural assemblage. In order to identify which groups are active in C and N assimilation and which N source is being utilized by the different size and functional groups, both filter-separated and flow cytometry-sorted samples will be used to 1) measure 13C primary production and 15N assimilation by incubations with isotope tracers, 2) measure the natural stable N isotope signatures of different taxonomic groups and 3) link the molecular diversity to the functional diversity in C and N transformations. Using flow cytometry linked to mass spectrometry, these investigators have found an unexpectedly strong differentiation in the form of N assimilated by prokaryotes and eukaryotes, with eukaryotes being more dynamic.
This project will investigate the taxonomic, genetic and functional diversity of eukaryotic phytoplankton and to link this diversity and assemblage composition to the carbon and nitrogen biogeochemistry of the surface ocean. Taxonomic diversity will be investigated by identifying the components of the phytoplankton assemblages using molecular, chemical and microscope methods. Genetic diversity will be explored at several levels, including direct sequencing of clone libraries of key functional genes and metatranscriptomic sequencing and microarray analysis of size fractionated/sorted phytoplankton assemblages. Using natural abundance and tracer stable isotope methods, genetic and taxonomic diversity will be linked to functional diversity in C and N assimilation in size- fractionated and taxon-sorted populations.
(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.
Funding Source | Award |
---|---|
NSF Division of Ocean Sciences (NSF OCE) |