19:I[42426,["/_next/static/immutable/chunks/1xctgzqre-wsy.js","/_next/static/immutable/chunks/06_-wz6pdtp2b.js","/_next/static/immutable/chunks/30e52g49hg40p.js","/_next/static/immutable/chunks/02yq6tul2z-oh.js","/_next/static/immutable/chunks/10bx_ec2vj7n_.js","/_next/static/immutable/chunks/33bfn03fo8xnt.js","/_next/static/immutable/chunks/0tfjf78scu61b.js","/_next/static/immutable/chunks/31xnvej4n1bi9.js"],"default"] 1a:Tb36,

Analytical procedure:

Microbial cell abundances were determined using an Influx flow cytometer. Briefly, pigmented groups (Prochlorococcus, Synechococcus, and picoalgae) were enumerated in unstained samples by their chlorophyll and forward scatter signatures (Marie et al. 1999). The high phycoerythrin signal in Synechococcus was used to distinguish this group from Prochlorococcus and picoalgae.

To visualize non-pigmented picoplankton (bacteria) and heterotrophic protists, samples were stained with SYBR Green I DNA dye (SG, 1:10000 final concentration, for 10 min at 4C in the dark) (Zubkov et al. 2007, Christaki et al. 2011). Because bacteria and Prochlorococcus groups exhibit overlapping signal characteristics in surface samples after SG staining, the abundances of bacteria in surface samples were calculated by subtracting the Prochlorococcus abundance, determined in the unstained aliquot, from the total SG-stained group abundance. An internal standard of 1-um diameter fluorescent microspheres (Fluoresbrite, Polysciences) was added to each sample.

Sampling and Analytical Methodology:

Seawater samples were acquired from bottle samples collected by a CTD rosette during the OUTPACE cruise. 1.8 ml water samples were collected in duplicate, fixed with 0.25% (w/v) paraformaldehyde, flash frozen, and preserved at -80C. One of the duplicate samples was used to count phytoplankton (Prochlorococcus, Synechococcus, picoalgae), and the other was used to count bacteria and protists.

For pigmented groups (Prochlorococcus, Synechococcus, and picoalgae), cells were excited using a combination of two lasers (488+456 nm) focused into one pinhole; while for non-pigmented groups (bacteria and heterotrophic protists), cells were excited using the 488 nm laser only. For calibration, a solution of 1-um diameter fluorescent microspheres (Fluoresbrite, Polysciences) was used.

References:

Christaki U, Courties C, Massana R, Catala P, Lebaron P, Gasol JM, Zubkov MV (2011) Optimized routine flow cytometric enumeration of heterotrophic flagellates using SYBR Green I. Limnology and Oceanography-Methods 9:329-339. https://doi.org/10.4319/lom.2011.9.329

Marie D, Partensky F, Vaulot D, Brussaard C (1999) Enumeration of Phytoplankton, Bacteria, and Viruses in Marine Samples. Current Protocols in Cytometry:11.11.11-11.11.15. https://doi.org/10.1002/0471142956.cy1111s10

Zubkov M, Burkill PH, Topping JN (2007) Flow cytometric enumeration of DNA-stained oceanic planktonic protists. Journal of Plankton Research 29:79-86. https://doi.org/10.1093/plankt/fbl059

1b:T5c2,Description from NSF award abstract: Unicellular cyanobacteria are major contributors to primary production and carbon export in the open ocean. They also play an important role in the control of nutrient availability. The ability of these microbes to harvest light energy benefits a range of physiological functions, but the effect of light on their metabolism (other than for photosynthesis) is poorly known and controversial. This project will investigate the role of light in uptake of organic substrates (carbon and nutrients) by unicellular cyanobacteria and elucidate the importance of photoheterotrophy. The ability of these organisms to assimilate organic compounds and its modulation by light and nutrients will provide additional hints about the ecological success of unicellular cyanobacteria in the ocean. The proposed work will involve field experiments in the southwest Pacific Ocean, complemented by laboratory experiments in controlled cultures of ecologically relevant cyanobacteria. The study will employ innovative methods, including single cell assays and molecular tools that target individual cyanobacteria and evaluate their response to light for the assimilation of organic substrates. This research project will lead to an increased understanding of the microbial adaptations to light and nutrient gradients and the role these adaptations play in elemental cycling in oceanic habitats. Unicellular cyanobacteria inhabit the surface ocean (generally6:["$","$L19",null,{"dataset":{"_id":"663918","description":"

This dataset contains abundances of cyanobacteria (Synechococcus, and Prochlorococcus), picoalgae, non-pigmented picoplankton (bacteria), and heterotrophic protists acquired through flow cytometry. Latitude, longitude, timestamp, and sample depth are also included in this dataset.

Water samples were acquired during the Oligotrophy to UlTra-oligotrophy PACific Experiment (OUTPACE) cruise between New Caledonia and Tahiti from February to April 2015.

\n","problem":"","acquisition":"$1a","processing":"

Flow cytometry data were analyzed using FCS Express Pro (De Novo Software).

BCO-DMO Processing Notes:

* added ISO timestamp from OUTPACE cruise CTD logs
\n* stripped out_c_ from station column for matching with bottle data
\n* column station renamed cast to be consistent with CTD log
\n* added a conventional header with dataset name, PI name, version date
\n* modified parameter names to conform with BCO-DMO naming conventions

\n","bcodmoProcessing":"","title":"Flow cytometry cell counts obtained during the R/V L'Atalante OUTPACE cruise between New Caledonia and Tahiti from February to April 2015","nickname":"OUTPACE - flow cytometry cell counts","dataUrl":"","currentState":"Final no updates expected","currentStateId":"7","validated":true,"restricted":false,"version":"","version_date":"2016-11-03T04:00:00.000Z","abstract":"","citation":"Duhamel, S. (2016) Flow cytometry cell counts obtained during the R/V L'Atalante OUTPACE cruise between New Caledonia and Tahiti from February to April 2015. Biological and Chemical Oceanography Data Management Office (BCO-DMO). Version Date 2016-11-03 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/663918 [access date]","citationParts":{"identifier":"http://lod.bco-dmo.org/id/dataset/663918","versionDate":"2016-11-03","versionId":"","year":"2016","title":"Flow cytometry cell counts obtained during the R/V L'Atalante OUTPACE cruise between New Caledonia and Tahiti from February to April 2015","authors":"Duhamel, S.","publisher":"Biological and Chemical Oceanography Data Management Office (BCO-DMO)."},"doi":"","release_date":null,"field_dataset_location":"","temporal_extent":{"start":null,"end":null},"temporal":{"resolution":"","type":"","start":{"value":"","label":""},"end":{"value":"","label":""}},"spatial_extent":{"shape":"multipolygon","center":{"latitude":-19.9989,"longitude":179.8266},"wkt":"POLYGON ((-200.3568 -22.0008, -159.99 -22.0008, -159.99 -17.997, -200.3568 -17.997, -200.3568 -22.0008))","north":-17.997,"east":-159.99,"south":-22.0008,"west":159.6432},"dataset_type":["Cruise Results"],"keywords":["oceans"],"data_files":[{"id":"901273","title":"flowCyto.csv","url":"https://datadocs.bco-dmo.org/dataset/663918/file/N77GgDZcNKxq2E/flowCyto.csv","showTableUrl":"https://www.bco-dmo.org/dataset/663918/data/view/901273","description":"Primary data file for dataset ID 663918","filename":"flowCyto.csv","bytesize":32503,"checksum":{"value":"67794f743014e520ebb4e52abb5dee17","Algorithm":{"_id":"190","name":"MD5"}},"mimetype":"text/csv","fileType":{"_id":"192","name":"Comma Separated Values (.csv)"},"isErddap":"","date":"","isPublicDuringEmbargo":false,"primaryDataFile":true,"showTable":true,"restricted":false}],"supplemental_files":[],"roles":[{"role":{"_id":"138","name":"Principal Investigator"},"performedBy":{"_id":"542287","name":"Solange Duhamel"},"performedAtOrganization":{"_id":"68","name":"Lamont-Doherty Earth Observatory"}},{"role":{"_id":"133","name":"Contact"},"performedBy":{"_id":"542287","name":"Solange Duhamel"},"performedAtOrganization":{"_id":"68","name":"Lamont-Doherty Earth Observatory"}},{"role":{"_id":"145","name":"BCO-DMO Data Manager"},"performedBy":{"_id":"643627","name":"Amber D. York"},"performedAtOrganization":{"_id":"191","name":"Woods Hole Oceanographic Institution"}}],"deployments":[{"_id":"663891","name":"OUTPACE","synonyms":[],"dates":{"start":"2015-02-18T00:00:00.000Z","end":"2015-04-03T00:00:00.000Z"},"platform":{"_id":"663890","name":"R/V L'Atalante"},"chiefScientists":[{"id":"663893","name":"Thierry Moutin","role":"Chief Scientist"},{"id":"663895","name":"Sophie Bonnet","role":"Co-Chief Scientist"}]}],"funding":[{"_id":"542284","name":"OCE-1434916","fundingSource":{"_id":"355","name":"NSF Division of Ocean Sciences"},"url":"https://www.nsf.gov/awardsearch/show-award?AWD_ID=1434916"}],"instruments":[{"_id":"663981","name":"Sea-Bird CTD 9+","description":"This CTD-Rosette was called \"classique\" to differentiate it from the trace metal CTD-Rosette.\nFor more information on the CTD configuration see the OUTPACE site.\n ","type_id":"447","type_name":"CTD Sea-Bird","type_desc":"A Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics. This instrument designation is used when specific make and model are not known or when a more specific term is not available in the BCO-DMO vocabulary. Refer to the dataset-specific metadata for more information about the specific CTD used. More information from: http://www.seabird.com/","type_acronym":"CTD Sea-Bird"},{"_id":"663922","name":"Influx Flow cytometer","description":"Instrument Type: Flow cytometer (Manufacturer: BD) Model: Influx","type_id":"660","type_name":"Flow Cytometer","type_desc":"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. Description from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm","type_acronym":"Flow Cytometer"}],"parameters":[{"_id":"663923","name":"cast","format":"","frictionlessType":"","description":"

CTD cast number that acquired sample

","units":{"_id":"","name":"unitless"},"type":{"_id":"761","name":"cast","description":"

cast or profile number

"}},{"_id":"663924","name":"bottle","format":"","frictionlessType":"","description":"

bottle number

","units":{"_id":"","name":"unitless"},"type":{"_id":"757","name":"bottle","description":"

water bottle number, generally assigned to a position on a CTD rosette, identifies all samples drawn from a given bottle

"}},{"_id":"663925","name":"depth_w","format":"","frictionlessType":"","description":"

depth of sample

","units":{"_id":"","name":"meters"},"type":{"_id":"808","name":"depth","description":"

Observation/sample depth below the sea surface. Units often reported as: meters, feet.

\nWhen used in a JGOFS/GLOBEC dataset the depth is a best estimate; usually but not always calculated from pressure; calculated either from CTD pressure using Fofonoff and Millard (1982; UNESCO Tech Paper #44) algorithm adjusted for 1980 equation of state for seawater (EOS80) or simply equivalent to nominal depth as recorded during sampling if CTD pressure was unavailable.

"}},{"_id":"663926","name":"lat","format":"","frictionlessType":"","description":"

latitude of cast

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"730","name":"latitude","description":"

latitude, in decimal degrees, North is positive, negative denotes South; Reported in some datasets as degrees, minutes

"}},{"_id":"663927","name":"lon","format":"","frictionlessType":"","description":"

longitude of cast; west is negative

","units":{"_id":"","name":"decimal degrees"},"type":{"_id":"731","name":"longitude","description":"

longitude, in decimal degrees, East is positive, negative denotes West; Reported in some datasets as degrees, minutes

"}},{"_id":"663928","name":"pro","format":"","frictionlessType":"","description":"

Prochlorococcus cell abundance

","units":{"_id":"","name":"cells per milliliter"},"type":{"_id":"735","name":"abundance","description":"