ERDDAP > info > bcodmo_dataset_739077

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	[Community 16S rRNA gene sequences] - Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016 (Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters)		I   M	background			BCO-DMO	bcodmo_dataset_739077

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	Samples were collected as part of collections and experiments conducted at Looe Key reef microcosm experiments (2015 and 2016) and field collections (2016) in the Florida Keys National Marine Sanctuary (as described in other datasets with this project). Samples (1 L) were prefiltered (2 um), concentrated on to 0.22 um filters, DNA extracted, and 16S rRNA in the V4 region amplified using 515F/806R primers with barcodes on both ends. Sequencing was conducted using Illumina MiSeq paired-end 250 chemistry.
attribute	NC_GLOBAL	awards_0_award_nid	String	553932
attribute	NC_GLOBAL	awards_0_award_number	String	OCE-1357423
attribute	NC_GLOBAL	awards_0_data_url	String	http://www.nsf.gov/awardsearch/showAward.do?AwardNumber=1357423
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	Community 16S rRNA gene sequences Accession numbers for raw sequences associated with field collections & microcosms (2015 and 2016) Saharan dust deposition and bacterioplankton in marine surface water PI's: E. Lipp, E. Ottesen (UGA) version: 2018-06-19
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	dataset_current_state	String	Final and no updates
attribute	NC_GLOBAL	date_created	String	2018-06-20T14:00:52Z
attribute	NC_GLOBAL	date_modified	String	2020-06-03T14:21:28Z
attribute	NC_GLOBAL	defaultDataQuery	String	&time<now
attribute	NC_GLOBAL	doi	String	10.26008/1912/bco-dmo.739077.1
attribute	NC_GLOBAL	infoUrl	String	https://www.bco-dmo.org/dataset/739077
attribute	NC_GLOBAL	institution	String	BCO-DMO
attribute	NC_GLOBAL	instruments_0_acronym	String	Automated Sequencer
attribute	NC_GLOBAL	instruments_0_dataset_instrument_nid	String	739091
attribute	NC_GLOBAL	instruments_0_description	String	General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.
attribute	NC_GLOBAL	instruments_0_instrument_name	String	Automated DNA Sequencer
attribute	NC_GLOBAL	instruments_0_instrument_nid	String	649
attribute	NC_GLOBAL	instruments_0_supplied_name	String	Illumina MiSeq
attribute	NC_GLOBAL	instruments_1_acronym	String	Thermal Cycler
attribute	NC_GLOBAL	instruments_1_dataset_instrument_nid	String	739090
attribute	NC_GLOBAL	instruments_1_description	String	General term for a laboratory apparatus commonly used for performing polymerase chain reaction (PCR). The device has a thermal block with holes where tubes with the PCR reaction mixtures can be inserted. The cycler then raises and lowers the temperature of the block in discrete, pre-programmed steps. (adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
attribute	NC_GLOBAL	instruments_1_instrument_name	String	PCR Thermal Cycler
attribute	NC_GLOBAL	instruments_1_instrument_nid	String	471582
attribute	NC_GLOBAL	keywords	String	bco, bco-dmo, bio, biological, BioProject, chemical, data, dataset, description, dmo, erddap, link, management, ncbi, NCBI_link, num, num_sequences, oceanography, office, preliminary, project, sample, sample_description, sequences, study, year
attribute	NC_GLOBAL	license	String	https://www.bco-dmo.org/dataset/739077/license
attribute	NC_GLOBAL	metadata_source	String	https://www.bco-dmo.org/api/dataset/739077
attribute	NC_GLOBAL	param_mapping	String	{'739077': {}}
attribute	NC_GLOBAL	parameter_source	String	https://www.bco-dmo.org/mapserver/dataset/739077/parameters
attribute	NC_GLOBAL	people_0_affiliation	String	University of Georgia
attribute	NC_GLOBAL	people_0_affiliation_acronym	String	UGA
attribute	NC_GLOBAL	people_0_person_name	String	Erin K. Lipp
attribute	NC_GLOBAL	people_0_person_nid	String	553935
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	University of Georgia
attribute	NC_GLOBAL	people_1_affiliation_acronym	String	UGA
attribute	NC_GLOBAL	people_1_person_name	String	Elizabeth Ottesen
attribute	NC_GLOBAL	people_1_person_nid	String	553937
attribute	NC_GLOBAL	people_1_role	String	Co-Principal Investigator
attribute	NC_GLOBAL	people_1_role_type	String	originator
attribute	NC_GLOBAL	people_2_affiliation	String	Woods Hole Oceanographic Institution
attribute	NC_GLOBAL	people_2_affiliation_acronym	String	WHOI BCO-DMO
attribute	NC_GLOBAL	people_2_person_name	String	Nancy Copley
attribute	NC_GLOBAL	people_2_person_nid	String	50396
attribute	NC_GLOBAL	people_2_role	String	BCO-DMO Data Manager
attribute	NC_GLOBAL	people_2_role_type	String	related
attribute	NC_GLOBAL	project	String	Vibrio-dust deposition
attribute	NC_GLOBAL	projects_0_acronym	String	Vibrio-dust deposition
attribute	NC_GLOBAL	projects_0_description	String	Description from NSF award abstract: Dust and mineral aerosols are a significant source of micro and macronutrients to oligotrophic ocean surface waters. Evidence is growing that heterotrophic microbes may play key roles in processing deposited minerals and nutrients. Yet it is not known which components of dust stimulate the heterotrophic bacteria, which cellular mechanisms are responsible for the utilization of those components and how the activity of these bacteria affect the availability and utilization of dust-derived minerals and nutrients by marine autotrophs. Knowledge of these factors is key to understanding how dust deposition impacts carbon cycles and for predicting the response of tropical oceans to future changes in the frequency and intensity of dust deposition events. The objective of this project is to examine the specific effects of aeolian dust on heterotrophic microbes in a tropical marine system under controlled conditions. The central hypothesis is that in oligotrophic tropical systems numerically minor opportunistic bacteria are the first responders to influx of dust constituents and respond primarily by rapidly accessing soluble trace metals and limiting nutrients that are deposited with Saharan dust. The project will focus on two specific aims: 1) Quantify changes in community structure, composition and transcriptional activity among marine microbial populations upon exposure to dust, and 2) Identify key components in Saharan dust aerosols that stimulate or repress growth and/or activity in Vibrio, a model opportunistic marine heterotrophic group. The study will use a series of controlled experiments designed to identify and quantify heterotrophic microbial response to dust deposition events using both natural communities and model bacteria (Vibrio) through metagenomics, transcriptomics and atmospheric and marine biogeochemical techniques. This innovative approach will identify the most critical (reactive) components leached from dust aerosols on the microbial community as well as elucidate potential mechanisms of response. There is great interest in the biological response to dust aerosols given its potentially large influence on biogeochemical cycling, but there has been relatively little work that has addressed the mechanisms of response (especially among the heterotrophic microbial fraction) or identified the relative importance of specific constituents of dust aerosols. A detailed framework for microbial response (focusing on opportunistic heterotrophs) will facilitate efforts to link autotrophic and heterotrophic processing. This contribution is significant because it will provide one of the first end-to-end (chemistry to physiology to ecology) mechanistic pathways for marine biological response to desert dust aerosols.
attribute	NC_GLOBAL	projects_0_end_date	String	2017-03
attribute	NC_GLOBAL	projects_0_geolocation	String	Florida Keys, FL, USA
attribute	NC_GLOBAL	projects_0_name	String	Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters
attribute	NC_GLOBAL	projects_0_project_nid	String	553933
attribute	NC_GLOBAL	projects_0_start_date	String	2014-04
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	Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016
attribute	NC_GLOBAL	title	String	[Community 16S rRNA gene sequences] - Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016 (Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters)
attribute	NC_GLOBAL	version	String	1
attribute	NC_GLOBAL	xml_source	String	osprey2erddap.update_xml() v1.5
variable	BioProject		String
attribute	BioProject	bcodmo_name	String	accession number
attribute	BioProject	description	String	NCBI GenBank BioProject accession number
attribute	BioProject	long_name	String	Bio Project
attribute	BioProject	units	String	unitless
variable	study		String
attribute	study	bcodmo_name	String	exp_type
attribute	study	description	String	type of study
attribute	study	long_name	String	Study
attribute	study	units	String	unitless
variable	sample_description		String
attribute	sample_description	bcodmo_name	String	sample_descrip
attribute	sample_description	description	String	description of samples
attribute	sample_description	long_name	String	Sample Description
attribute	sample_description	units	String	unitless
variable	year		short
attribute	year	_FillValue	short	32767
attribute	year	actual_range	short	2015, 2016
attribute	year	bcodmo_name	String	year
attribute	year	description	String	year of sample collection
attribute	year	long_name	String	Year
attribute	year	nerc_identifier	String	https://vocab.nerc.ac.uk/collection/P01/current/YEARXXXX/
attribute	year	units	String	unitless
variable	num_sequences		byte
attribute	num_sequences	_FillValue	byte	127
attribute	num_sequences	actual_range	byte	57, 125
attribute	num_sequences	bcodmo_name	String	count
attribute	num_sequences	description	String	number of sequences
attribute	num_sequences	long_name	String	Num Sequences
attribute	num_sequences	units	String	unitless
variable	NCBI_link		String
attribute	NCBI_link	bcodmo_name	String	external_link
attribute	NCBI_link	description	String	link to BioProject page at NCBI GenBank
attribute	NCBI_link	long_name	String	NCBI Link
attribute	NCBI_link	units	String	unitless

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.