Accessing BCO-DMO data
log in    
Brought to you by BCO-DMO    

ERDDAP > info > bcodmo_dataset_700773

Title Sum-
Institution Dataset ID
     data   graph     files  public Counts of Prochlorococcus from on-deck incubations with 13C-bicarbonate as part of DNA-SIP
experiments conducted on Hawaii Ocean Time-series (HOT) cruises, HOT283 and HOT288 in 2016
   ?     I   M   background (external link) RSS Subscribe BCO-DMO bcodmo_dataset_700773

The Dataset's Variables and Attributes

Row Type Variable Name Attribute Name Data Type Value
attribute NC_GLOBAL access_formats String .htmlTable,.csv,.json,.mat,.nc,.tsv
attribute NC_GLOBAL acquisition_description String Water was sampled from the CTD under trace metal clean conditions into 2 L
polycarbonate bottles (acid-washed) and amended with 13C-bicarbonate. Flow
cytometry samples were collected from triplicate bottles at several time
points between 0 hours (unlabeled control) and 36 hours after the initiation
of incubation. Flow cytometry samples were collected in 1 mL volumes and fixed
immediately with 25% TEM-grade glutaraldehyde to a final concentrations of
0.125%. Samples were inverted 10 times to mix, incubated at room temperature
in the dark for 10 minutes, then flash frozen in liquid nitrogen to archive.
Samples were stored at -80C until analysis. For analysis, each sample was
thawed at room temperature then analyzed by flow cytometry.\u00a0

Cell counts were determined by flow cytometry using a BD Biosciences Influx
high speed cell sorter. A 488 nm laser was used in addition to chlorophyll and
phycoerythrin filters, forward scatter relative to 1 um beads, and side
scattered light.\u00a0
attribute NC_GLOBAL awards_0_award_nid String 658942
attribute NC_GLOBAL awards_0_award_number String OCE-1646709
attribute NC_GLOBAL awards_0_data_url String https://www.nsf.gov/awardsearch/showAward?AWD_ID=1646709 (external link)
attribute NC_GLOBAL awards_0_funder_name String NSF Division of Ocean Sciences
attribute NC_GLOBAL awards_0_funding_acronym String NSF OCE
attribute NC_GLOBAL awards_0_funding_source_nid String 355
attribute NC_GLOBAL awards_0_program_manager String Michael E. Sieracki
attribute NC_GLOBAL awards_0_program_manager_nid String 50446
attribute NC_GLOBAL cdm_data_type String Other
attribute NC_GLOBAL comment String 13C incubation cell counts
PI: Anne Thompson (Portland State University)
Version: 23 May 2017
attribute NC_GLOBAL Conventions String COARDS, CF-1.6, ACDD-1.3
attribute NC_GLOBAL creator_email String info at bco-dmo.org
attribute NC_GLOBAL creator_name String BCO-DMO
attribute NC_GLOBAL creator_type String institution
attribute NC_GLOBAL creator_url String https://www.bco-dmo.org/ (external link)
attribute NC_GLOBAL data_source String extract_data_as_tsv version 2.3 19 Dec 2019
attribute NC_GLOBAL date_created String 2017-05-23T19:34:18Z
attribute NC_GLOBAL date_modified String 2019-08-02T18:52:30Z
attribute NC_GLOBAL defaultDataQuery String &time<now
attribute NC_GLOBAL doi String 10.1575/1912/bco-dmo.700773.1
attribute NC_GLOBAL infoUrl String https://www.bco-dmo.org/dataset/700773 (external link)
attribute NC_GLOBAL institution String BCO-DMO
attribute NC_GLOBAL instruments_0_acronym String CTD
attribute NC_GLOBAL instruments_0_dataset_instrument_description String Water was sampled from the CTD under trace metal clean conditions into 2L polycarbonate bottles (acid-washed) and amended with 13C-bicarbonate.
attribute NC_GLOBAL instruments_0_dataset_instrument_nid String 700785
attribute NC_GLOBAL instruments_0_description String The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column and permits scientists observe the physical properties in real time via a conducting cable connecting the CTD to a deck unit and computer on the ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast. This instrument designation is used when specific make and model are not known.
attribute NC_GLOBAL instruments_0_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/130/ (external link)
attribute NC_GLOBAL instruments_0_instrument_name String CTD profiler
attribute NC_GLOBAL instruments_0_instrument_nid String 417
attribute NC_GLOBAL instruments_0_supplied_name String CTD
attribute NC_GLOBAL instruments_1_acronym String TM Bottle
attribute NC_GLOBAL instruments_1_dataset_instrument_description String Water was sampled from the CTD under trace metal clean conditions into 2L polycarbonate bottles (acid-washed) and amended with 13C-bicarbonate.
attribute NC_GLOBAL instruments_1_dataset_instrument_nid String 700784
attribute NC_GLOBAL instruments_1_description String Trace metal (TM) clean rosette bottle used for collecting trace metal clean seawater samples.
attribute NC_GLOBAL instruments_1_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/30/ (external link)
attribute NC_GLOBAL instruments_1_instrument_name String Trace Metal Bottle
attribute NC_GLOBAL instruments_1_instrument_nid String 493
attribute NC_GLOBAL instruments_2_acronym String Flow Cytometer
attribute NC_GLOBAL instruments_2_dataset_instrument_description String Cell counts were determined by flow cytometry using a BD Biosciences Influx high speed cell sorter.
attribute NC_GLOBAL instruments_2_dataset_instrument_nid String 700786
attribute NC_GLOBAL instruments_2_description String 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)
attribute NC_GLOBAL instruments_2_instrument_external_identifier String https://vocab.nerc.ac.uk/collection/L05/current/LAB37/ (external link)
attribute NC_GLOBAL instruments_2_instrument_name String Flow Cytometer
attribute NC_GLOBAL instruments_2_instrument_nid String 660
attribute NC_GLOBAL instruments_2_supplied_name String BD Biosciences Influx high speed cell sorter
attribute NC_GLOBAL keywords String bco, bco-dmo, biological, chemical, cruise, data, dataset, depth, depth2, dmo, erddap, incubation, management, oceanography, office, preliminary, prochlorococcus, replicate, timepoint
attribute NC_GLOBAL license String https://www.bco-dmo.org/dataset/700773/license (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/700773 (external link)
attribute NC_GLOBAL param_mapping String {'700773': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/700773/parameters (external link)
attribute NC_GLOBAL people_0_affiliation String Portland State University
attribute NC_GLOBAL people_0_affiliation_acronym String PSU
attribute NC_GLOBAL people_0_person_name String Anne Thompson
attribute NC_GLOBAL people_0_person_nid String 632764
attribute NC_GLOBAL people_0_role String Principal Investigator
attribute NC_GLOBAL people_0_role_type String originator
attribute NC_GLOBAL people_1_affiliation String Woods Hole Oceanographic Institution
attribute NC_GLOBAL people_1_affiliation_acronym String WHOI BCO-DMO
attribute NC_GLOBAL people_1_person_name String Shannon Rauch
attribute NC_GLOBAL people_1_person_nid String 51498
attribute NC_GLOBAL people_1_role String BCO-DMO Data Manager
attribute NC_GLOBAL people_1_role_type String related
attribute NC_GLOBAL project String ProEco
attribute NC_GLOBAL projects_0_acronym String ProEco
attribute NC_GLOBAL projects_0_description String Description from the NSF award abstract:
Prochlorococcus is a photosynthetic organism that is tremendously abundant in the ocean and influences biogeochemical cycles on global scales. This project aims to link Prochlorococcus community structure to primary productivity in situ. The twelve known Prochlorococcus ecotypes exhibit extensive diversity. It is thought that this diversity allows the Prochlorococcus "collective" to maintain numerical dominance across gradients in light, nutrients, and temperature that accompany changes in depth, season, and latitude. A large gap in our understanding lies in whether we should assess the ecosystem value of Prochlorococcus by its abundance or by its community structure or both. Ecosystem models assign all ecotypes the same role. However, genomic and physiological evidence from cultivated isolates and wild populations suggests tentatively that distinct genotypes may contribute differently to the ecosystem through variation in light and nutrient physiologies and interactions with other microorganisms. The consequences of these molecular-level differences to primary productivity in situ are unknown. This project tests whether absolute abundance, or community structure, determines the contributions of Prochlorococcus to biogeochemical dynamics by measuring the contributions of different ecotypes to primary productivity. The results of this project will inform ecosystem models towards better representation of how shifts in climate and Prochlorococcus diversity will affect global nutrient cycles, trophic cascades, and interactions with other bacteria, viruses, and grazers. The insights and approaches delineated by this work will be generally applicable to the ecology of abundant microbial populations in the open ocean such as pigmented and non-pigmented eukaryotes, heterotrophic bacteria, and other cyanobacterial lineages. A basic understanding of differences between coexisting ecotypes will provide inroads into understanding mechanisms of cooperation, competition, and collaboration among ecotypes in all microbial ecosystems. The investigators will build a teaching module to expose high school students to microbial oceanography, big data, and systems biology through virtual ocean exploration. The primary objective will be to impress upon students the importance of an "invisible forest" of microorganisms in the ocean. Students will examine the distribution patterns of abundant microbial groups in the context of oceanographic data from large publically available databases. High school teachers and student interns, a graduate student, the investigators, and an educational specialist will design, implement, and test the module for classrooms nationwide. This effort will follow a successful education model (Systems Education Experience - SEE) developed previously.
The investigators will address an overarching hypothesis that Prochlorococcus ecotypes vary in their contribution to the ecosystem as primary producers. More specifically, the investigators hypothesize that patterns of cell division and carbon fixation vary between coexisting ecotypes, and these differences are a function of genome content, gene expression, environmental conditions, and community composition. The technical approach will involve two field-based experiments will be applied to three different depths, at the oceanographic Station ALOHA, that differ in Prochlorococcus community composition. Experiment 1 will examine whether coexisting ecotypes vary in cell division, using 16S rRNA sequencing to quantify ecotype abundance in G1, S, and G2 cells. Experiment 2 will examine how carbon fixation varies between coexisting ecotypes using RNA-stable isotope probing and 16S rRNA sequencing of RNA enriched in 13C after incubation with 13C-bicarbonate. These experiments will be performed with Prochlorococcus communities under native in situ conditions and shifts in conditions to mimic light and temperature of other depths. In both experiments, the temporal gene expression of a selected set of carbon fixation and cell division genes will be examined to link gene expression patterns to primary productivity. All data will be related to the oceanographic environment including its physical, chemical, and biological features.
attribute NC_GLOBAL projects_0_end_date String 2019-03
attribute NC_GLOBAL projects_0_geolocation String North Pacific Ocean, Station ALOHA
attribute NC_GLOBAL projects_0_name String Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal?
attribute NC_GLOBAL projects_0_project_nid String 632763
attribute NC_GLOBAL projects_0_start_date String 2016-06
attribute NC_GLOBAL publisher_name String Biological and Chemical Oceanographic Data Management Office (BCO-DMO)
attribute NC_GLOBAL publisher_type String institution
attribute NC_GLOBAL sourceUrl String (local files)
attribute NC_GLOBAL standard_name_vocabulary String CF Standard Name Table v55
attribute NC_GLOBAL summary String Counts of Prochlorococcus from on-deck incubations with 13C-bicarbonate as part of DNA-SIP experiments conducted on Hawaii Ocean Time-series (HOT) cruises, HOT283 and HOT288 in 2016.
attribute NC_GLOBAL title String Counts of Prochlorococcus from on-deck incubations with 13C-bicarbonate as part of DNA-SIP experiments conducted on Hawaii Ocean Time-series (HOT) cruises, HOT283 and HOT288 in 2016
attribute NC_GLOBAL version String 1
attribute NC_GLOBAL xml_source String osprey2erddap.update_xml() v1.3
variable cruise   String  
attribute cruise bcodmo_name String cruise_id
attribute cruise description String Cruise name/identifier
attribute cruise long_name String Cruise
attribute cruise units String unitless
variable incubation   byte  
attribute incubation _FillValue byte 127
attribute incubation actual_range byte 1, 2
attribute incubation bcodmo_name String exp_id
attribute incubation description String Incubation identifier
attribute incubation long_name String Incubation
attribute incubation units String unitless
variable depth2   String  
attribute depth2 bcodmo_name String depth_comment
attribute depth2 description String Sample depth; DCM = deep chlorophyll maxium
attribute depth2 long_name String Depth
attribute depth2 standard_name String depth
attribute depth2 units String unitless
variable timepoint   byte  
attribute timepoint _FillValue byte 127
attribute timepoint actual_range byte 0, 36
attribute timepoint bcodmo_name String time_sample
attribute timepoint description String Time point in the incubation
attribute timepoint long_name String Timepoint
attribute timepoint units String hours
variable replicate   byte  
attribute replicate _FillValue byte 127
attribute replicate actual_range byte 1, 3
attribute replicate bcodmo_name String replicate
attribute replicate description String Replicate identifier
attribute replicate long_name String Replicate
attribute replicate units String unitless
variable prochlorococcus   int  
attribute prochlorococcus _FillValue int 2147483647
attribute prochlorococcus actual_range int 48602, 272633
attribute prochlorococcus bcodmo_name String coccus_p
attribute prochlorococcus description String Count of Prochlorococcus cells
attribute prochlorococcus long_name String Prochlorococcus
attribute prochlorococcus nerc_identifier String https://vocab.nerc.ac.uk/collection/P01/current/P701A90Z/ (external link)
attribute prochlorococcus units String cells per milliliter (cells/mL)

The information in the table above is also available in other file formats (.csv, .htmlTable, .itx, .json, .jsonlCSV1, .jsonlCSV, .jsonlKVP, .mat, .nc, .nccsv, .tsv, .xhtml) via a RESTful web service.

ERDDAP, Version 2.02
Disclaimers | Privacy Policy | Contact