http://lod.bco-dmo.org/id/dataset/855750
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
2021-07-15
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Analysis protocols, sample information, code, and datasets associated with the manuscript Structure and long-term stability of the microbiome in diverse diatom cultures from samples collected in Guam, California, and Gulf of Mexico between 2008 and 2016
2021-07-15
publication
2021-07-15
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-08-02
publication
https://doi.org/10.26008/1912/bco-dmo.855750.1
James Jeffrey Morris
University of Alabama at Birmingham
principalInvestigator
Matt Ashworth
University of Texas at Austin
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: Morris, J. J., Ashworth, M. (2021) Analysis protocols, sample information, code, and datasets associated with the manuscript Structure and long-term stability of the microbiome in diverse diatom cultures from samples collected in Guam, California, and Gulf of Mexico between 2008 and 2016. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-07-15 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.855750.1 [access date]
Dataset Description: <p>See "Data&nbsp;Files" section for access to download the data and analysis code&nbsp;"Ashworth_data_and_analysis.zip".&nbsp; The sample information and genetic&nbsp;accession identifiers are&nbsp;available as a data table from this page.</p> Methods and Sampling: <p><strong>Location:&nbsp;</strong><br />
<br />
Lab work performed at University of Alabama at Birmingham and University of Texas at Austin; Samples collected from Guam, California, and Gulf of Mexico.</p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong></p>
<p>
Cultures were obtained from sites in Guam, California, and the Gulf of Mexico near Florida. Cells were isolated from collections made primarily by plankton net with 20 m mesh or by collection of the top millimeters of sediment from the benthos. Individual cells were isolated by glass Pasteur pipet (Andersen) into 15x100 mm glass test tubes in approximately 12 mL of liquid f/2 medium with double the normal concentration of silica (Guillard, Andersen) at a salinity of 32-35 ppt. The f/2 base was seawater collected from the Texas coast of the Gulf of Mexico and passed through a 0.22 um filter. Isolates were maintained under natural light from a north facing window between 20-24oC, or in a Percival growth chamber on a 12:12 light:dark cycle at 27oC in the case of the isolates from Guam. Once unialgal growth was confirmed by microscopy, strains were maintained in triplicate with cells (approximately 0.25 mL) from one tube transferred to three fresh media tubes every 3-4 months.</p>
<p>During the strain transfer cycle, one replicate tube was harvested by Pasteur pipet into a 1.5 mL microcentrifuge tube and centrifuged in an Eppendorf 5414 C microcentrifuge at 8,000 rpm for 10 minutes. Liquid media was decanted off the pellet, and the pellet was stored at -80oC until DNA extraction. DNA was extracted from the pellets using a MoBio Powersoil DNA kit, following the manufacturers protocol.</p>
<p>The V4 region of the bacterial 16S rRNA gene was amplified using bar-coded PCR primers (Caporaso), purified by gel electrophoresis, and then sequenced using the Illumina MiSeq platform. &nbsp;Quality control and sequence analysis was performed in mothur according to the mothur MiSeq SOP protocol (Schlosss, Kozich).</p>
<p>Sequence data is available from the NCBI SRA archive, BioProject PRJNA706454.</p>
<p><br />
<strong>Species List (ScientificName,AphiaID)</strong><br />
<br />
Astrosyne radiata,837899<br />
Roundia cardiophora,627356<br />
Florella pascuensis,646734<br />
Triceratium dubium,418600<br />
Striatella unipunctata,149177<br />
Hanicella moenia,842549<br />
Paralia longispina,708079<br />
Astrosyne radiata,837899<br />
Neosynedra provincialis,175369<br />
Leptocylindrus danicus,149106</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1851085 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1851085
completed
James Jeffrey Morris
University of Alabama at Birmingham
205-934-9498
1300 University Blvd CH253
Birmingham
AL
35294
USA
evolve@uab.edu
pointOfContact
Matt Ashworth
University of Texas at Austin
512-475-7741
mashworth@utexas.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject
BioSample
SRA_Study
Run
collection_date
lat
lon
env_biome
env_feature
env_material
geo_loc_name_country
geo_loc_name_country_continent
geo_loc_name
Organism
Sample_Name
sample_title
Description
Illumina MiSeq platform
Eppendorf 5414 C microcentrifuge
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA study accession (SRP)
NCBI SRA run accession (SRR)
date
latitude
longitude
site description
sample description
sample identification
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Centrifuge
instrument
BCO-DMO Standard Instruments
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.
Collaborative Research: Ecology and Evolution of Microbial Interactions in a Changing Ocean
https://osprey.bco-dmo.org/project/752763
Collaborative Research: Ecology and Evolution of Microbial Interactions in a Changing Ocean
<p><em>NSF Award Abstract:</em><br />
Carbon dioxide released from fossil fuels is causing the ocean to become more acidic. Much attention has been given to how this will affect shelled animals like corals, but acidification also affects the algae that form the base of the ocean food chain. It is possible that future algal communities will look very different than they do today, with potentially negative consequences for fisheries, recreation, and climate. Alternatively, it is possible that these algae will be able to adapt rapidly enough to avoid the worst of it. This study looks at algae adapting to acidification in real time in the lab, focusing on "marketplace" interactions between the algae and the bacteria they live alongside. The researchers also go to sea to learn whether adaptations from the lab experiments are beneficial under real-world conditions. Ultimately, this project is helping scientists better understand how the ocean's most important and most overlooked organisms will respond to the changes humans are causing in their habitat. The researchers also use their scientific work to create fun educational opportunities from grade school to college, including agar art classes where students learn about microbial ecology by "painting" with freshly-isolated ocean bacteria.</p>
<p>The effect of ocean acidification on calcifying organisms has been well-studied, but less is known about how changing pH will affect phytoplankton. Previous work showed that the mutualistic interaction between the globally abundant cyanobacterium Prochlorococcus and its "helper" bacterium Alteromonas broke down under projected future CO2 conditions, leading to a strong decrease in the fitness of Prochlorococcus. It is possible that such interspecies interactions between microbes are important for many ecological processes, but a lack of understanding of how these interactions evolve makes it difficult to predict how important they are. This project is using laboratory evolution experiments to discover how evolution shapes the interactions between bacteria and algae like Prochlorococcus, and how these co-evolutionary dynamics might influence the biogeochemical processes that shape Earth's climate. Four research cruises to the Bermuda Atlantic Time Series are also planned to study how natural algal/bacterial communities respond to acidification, and whether evolved microbes from laboratory experiments have a competitive advantage in complex, natural communities exposed to elevated CO2. The ultimate goal of this project is to gain a mechanistic understanding of microbial interactions that can be used to inform models of Earth's oceans and biological feedbacks on global climate.</p>
LTPE
largerWorkCitation
project
eng; USA
oceans
144.7
-80.78
13.25
33.71
2008-08-18
2015-11-19
Lab work: Birmingham, Alabama and New York, New York. Field Work: Bermuda Atlantic Time Series.
0
BCO-DMO catalogue of parameters from Analysis protocols, sample information, code, and datasets associated with the manuscript Structure and long-term stability of the microbiome in diverse diatom cultures from samples collected in Guam, California, and Gulf of Mexico between 2008 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/856993.rdf
Name: BioProject
Units: unitless
Description: <p>NCBI BioProject</p>
http://lod.bco-dmo.org/id/dataset-parameter/856994.rdf
Name: BioSample
Units: unitless
Description: <p>NCBI BioSample</p>
http://lod.bco-dmo.org/id/dataset-parameter/856995.rdf
Name: SRA_Study
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) Study identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/856996.rdf
Name: Run
Units: unitless
Description: <p>NCBI Sequence Read Archive (SRA) Run identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/856997.rdf
Name: collection_date
Units: unitless
Description: <p>Sample collection date in format yyyy-mm-dd</p>
http://lod.bco-dmo.org/id/dataset-parameter/856998.rdf
Name: lat
Units: decimal degrees
Description: <p>Sample collection latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/856999.rdf
Name: lon
Units: decimal degrees
Description: <p>Sample collection longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/857000.rdf
Name: env_biome
Units: unitless
Description: <p>Collection location environmental biome (e.g. kelp bed)</p>
http://lod.bco-dmo.org/id/dataset-parameter/857001.rdf
Name: env_feature
Units: unitless
Description: <p>Collection location environment feature (e.g. open water)</p>
http://lod.bco-dmo.org/id/dataset-parameter/857002.rdf
Name: env_material
Units: unitless
Description: <p>Collection location material (e.g. water)</p>
http://lod.bco-dmo.org/id/dataset-parameter/857003.rdf
Name: geo_loc_name_country
Units: unitless
Description: <p>Collection location country</p>
http://lod.bco-dmo.org/id/dataset-parameter/857004.rdf
Name: geo_loc_name_country_continent
Units: unitless
Description: <p>Collection location continent</p>
http://lod.bco-dmo.org/id/dataset-parameter/857005.rdf
Name: geo_loc_name
Units: unitless
Description: <p>Collection geolocation name (e.g."Guam: Achang Reef")</p>
http://lod.bco-dmo.org/id/dataset-parameter/857006.rdf
Name: Organism
Units: unitless
Description: <p>Organism sampled (e.g. algae metagenome)</p>
http://lod.bco-dmo.org/id/dataset-parameter/857007.rdf
Name: Sample_Name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/857008.rdf
Name: sample_title
Units: unitless
Description: <p>Sample title</p>
http://lod.bco-dmo.org/id/dataset-parameter/857009.rdf
Name: Description
Units: unitless
Description: <p>Sample description</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
18955
https://darchive.mblwhoilibrary.org/bitstream/1912/27398/1/Ashworth_data_and_analysis.zip
download
3531
https://darchive.mblwhoilibrary.org/bitstream/1912/27398/2/dataset-855750_long-term-diatom-microbiome-data-and-analysis-package__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.855750.1
download
onLine
dataset
<p><strong>Location:&nbsp;</strong><br />
<br />
Lab work performed at University of Alabama at Birmingham and University of Texas at Austin; Samples collected from Guam, California, and Gulf of Mexico.</p>
<p><strong>Sampling and analytical procedures:&nbsp;</strong></p>
<p>
Cultures were obtained from sites in Guam, California, and the Gulf of Mexico near Florida. Cells were isolated from collections made primarily by plankton net with 20 m mesh or by collection of the top millimeters of sediment from the benthos. Individual cells were isolated by glass Pasteur pipet (Andersen) into 15x100 mm glass test tubes in approximately 12 mL of liquid f/2 medium with double the normal concentration of silica (Guillard, Andersen) at a salinity of 32-35 ppt. The f/2 base was seawater collected from the Texas coast of the Gulf of Mexico and passed through a 0.22 um filter. Isolates were maintained under natural light from a north facing window between 20-24oC, or in a Percival growth chamber on a 12:12 light:dark cycle at 27oC in the case of the isolates from Guam. Once unialgal growth was confirmed by microscopy, strains were maintained in triplicate with cells (approximately 0.25 mL) from one tube transferred to three fresh media tubes every 3-4 months.</p>
<p>During the strain transfer cycle, one replicate tube was harvested by Pasteur pipet into a 1.5 mL microcentrifuge tube and centrifuged in an Eppendorf 5414 C microcentrifuge at 8,000 rpm for 10 minutes. Liquid media was decanted off the pellet, and the pellet was stored at -80oC until DNA extraction. DNA was extracted from the pellets using a MoBio Powersoil DNA kit, following the manufacturers protocol.</p>
<p>The V4 region of the bacterial 16S rRNA gene was amplified using bar-coded PCR primers (Caporaso), purified by gel electrophoresis, and then sequenced using the Illumina MiSeq platform. &nbsp;Quality control and sequence analysis was performed in mothur according to the mothur MiSeq SOP protocol (Schlosss, Kozich).</p>
<p>Sequence data is available from the NCBI SRA archive, BioProject PRJNA706454.</p>
<p><br />
<strong>Species List (ScientificName,AphiaID)</strong><br />
<br />
Astrosyne radiata,837899<br />
Roundia cardiophora,627356<br />
Florella pascuensis,646734<br />
Triceratium dubium,418600<br />
Striatella unipunctata,149177<br />
Hanicella moenia,842549<br />
Paralia longispina,708079<br />
Astrosyne radiata,837899<br />
Neosynedra provincialis,175369<br />
Leptocylindrus danicus,149106</p>
Specified by the Principal Investigator(s)
<p>R version 4.0.3</p>
<p>mothur version &nbsp;1.42.3<br />
<br />
BCO-DMO Data Manager processing notes:<br />
* Species names in file axes.csv run through the World Register of Marine Species (WoRMS) taxa match tool to check taxonomic names.&nbsp; All names matched accepted names exactly as of 2021-07-15.&nbsp; Unique species list with associated AphiaIDs added to the metadata.<br />
* Sample collection information and accession numbers at NCBI extracted using the NCBI Run Selector.&nbsp; Sample information imported into the BCO-DMO data system.&nbsp;<br />
* Latitude and longitude split into individual columns and converted to decimal degrees.&nbsp; e.g. lat_lon "24.84 N 80.78 W" -&gt; lat: 24.84, lon: -80.78<br />
* After email correspondence about a coordinate outlier, the latitude for "USA: San Pedro California, kelp bed" was changed from 38.71 to&nbsp;33.71 after the submitters double-checked their notes.</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 platform
Illumina MiSeq platform
PI Supplied Instrument Name: Illumina MiSeq platform 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.
Eppendorf 5414 C microcentrifuge
Eppendorf 5414 C microcentrifuge
PI Supplied Instrument Name: Eppendorf 5414 C microcentrifuge Instrument Name: Centrifuge Instrument Short Name: Instrument Description: A machine with a rapidly rotating container that applies centrifugal force to its contents, typically to separate fluids of different densities (e.g., cream from milk) or liquids from solids.