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Title Sum-
Institution Dataset ID
     data   graph     files  public Accession numbers for raw sequences associated with field collections & microcosms, 2015 and
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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 (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 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/ (external link)
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 (external link)
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 (external link)
attribute NC_GLOBAL metadata_source String https://www.bco-dmo.org/api/dataset/739077 (external link)
attribute NC_GLOBAL param_mapping String {'739077': {}}
attribute NC_GLOBAL parameter_source String https://www.bco-dmo.org/mapserver/dataset/739077/parameters (external link)
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 Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016
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/ (external link)
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.

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