http://lod.bco-dmo.org/id/dataset/739077
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2018-06-20
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016
2018-06-19
publication
2018-06-19
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-06-03
publication
https://doi.org/10.26008/1912/bco-dmo.739077.1
Erin K. Lipp
University of Georgia
principalInvestigator
Elizabeth Ottesen
University of Georgia
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Lipp, E., Ottesen, E. (2020) Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-06-19 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.739077.1 [access date]
16S rRNA accessions Dataset Description: <p>This dataset includes NCBI GenBank accession from 2015 and 2016 field collections and experiments using Saharan source material and water from the lower Florida Keys to create microcosms for natural seawater communities. For full details, see (Westrich et al., 2016).</p> Methods and Sampling: <p>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).</p>
<p>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.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1357423 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1357423
completed
Erin K. Lipp
University of Georgia
706-583-8138
150 East Green St.
Athens
GA
30605
United States
elipp@uga.edu
pointOfContact
Elizabeth Ottesen
University of Georgia
706-542-9582
120 Cedar St.
Athens
GA
30605
United States
ottesen@uga.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject
study
sample_description
year
num_sequences
NCBI_link
Illumina MiSeq
theme
None, User defined
accession number
experiment type
sample description
year
count
external_link
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
instrument
BCO-DMO Standard Instruments
Lipp_2014-16
service
Deployment Activity
Florida Keys National Marine Sanctuary
place
Locations
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters
https://osprey.bco-dmo.org/project/553933
Vibrio as a model microbe for opportunistic heterotrophic response to Saharan dust deposition events in marine waters
<p><em>Description from NSF award abstract:</em><br />
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.</p>
<p>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.</p>
Vibrio-dust deposition
largerWorkCitation
project
eng; USA
biota
oceans
Florida Keys National Marine Sanctuary
-81.3547
-81.3547
24.634
24.634
2015-01-01
2016-12-31
Florida Keys, FL, USA
0
BCO-DMO catalogue of parameters from Accession numbers for raw sequences associated with field collections & microcosms, 2015 and 2016
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/739092.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI GenBank BioProject accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/739093.rdf
Name: study
Units: unitless
Description: <p>type of study</p>
http://lod.bco-dmo.org/id/dataset-parameter/739094.rdf
Name: sample_description
Units: unitless
Description: <p>description of samples</p>
http://lod.bco-dmo.org/id/dataset-parameter/739095.rdf
Name: year
Units: unitless
Description: <p>year of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/739096.rdf
Name: num_sequences
Units: unitless
Description: <p>number of sequences</p>
http://lod.bco-dmo.org/id/dataset-parameter/739097.rdf
Name: NCBI_link
Units: unitless
Description: <p>link to BioProject page at NCBI GenBank</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
382
https://darchive.mblwhoilibrary.org/bitstream/1912/25818/1/dataset-739077_community-16s-rrna-gene-sequences__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.739077.1
download
onLine
dataset
<p>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).</p>
<p>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.</p>
Specified by the Principal Investigator(s)
<p><strong>BCO-DMO Processing Notes:</strong><br />
- added conventional header with dataset name, PI name, version date<br />
- modified parameter names to conform with BCO-DMO naming conventions<br />
- added links to NCBI BioProject pages</p>
Specified by the Principal Investigator(s)
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
PI Supplied Instrument Name: Instrument Name: Thermal Cycler Instrument Short Name:Thermal Cycler Instrument Description: A thermal cycler or "thermocycler" is a general term for a type of laboratory apparatus, commonly used for performing polymerase chain reaction (PCR), that is capable of repeatedly altering and maintaining specific temperatures for defined periods of time. 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. They can also be used to facilitate other temperature-sensitive reactions, including restriction enzyme digestion or rapid diagnostics.
(adapted from http://serc.carleton.edu/microbelife/research_methods/genomics/pcr.html)
Deployment: Lipp_2014-16
Lipp_2014-16
Florida Keys National Marine Sanctuary
shoreside
Lipp_2014-16
Erin K. Lipp
University of Georgia
Florida Keys National Marine Sanctuary
shoreside