ERDDAP > info > bcodmo_dataset_700773

Grid DAP Data	Sub- set	Table DAP Data	Make A Graph	W M S	Source Data Files	Acces- sible	Title	Sum- mary	FGDC, ISO, Metadata	Back- ground Info	RSS	E mail	Institution	Dataset ID
		data	graph		files	public	[13C incubation cell counts] - 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 (Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal?)		I   M	background			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
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/
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
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/
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/
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/
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
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/700773
attribute	NC_GLOBAL	param_mapping	String	{'700773': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/700773/parameters
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	[13C incubation cell counts] - 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 (Microbial ecology of coexisting ecotypes: Are all Prochlorococcus equal?)
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/
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.