http://lod.bco-dmo.org/id/dataset/816367
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
2020-06-22
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial 16S OTU annotation information from staghorn coral health experiments with treatment with and without antibiotics
2020-06-26
publication
2020-06-26
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-02-01
publication
https://doi.org/10.26008/1912/bco-dmo.816367.1
Tarik C. Gouhier
Northeastern University
principalInvestigator
Steven V. Vollmer
Northeastern University
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: Gouhier, T. C., Vollmer, S. V. (2021) Microbial 16S OTU annotation information from staghorn coral health experiments with treatment with and without antibiotics. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2020-06-26 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.816367.1 [access date]
Microbes priority annotations (OTU taxonomy) Dataset Description: <p>This dataset reports assigned taxonomy of microbial 16S OTU's from a priority experiment with staghorn coral treated with and without antibiotics.</p> Methods and Sampling: <p>A priority experiment was conducted in 24 recirculating tanks at the Smithsonian stations in Bocas del Toro, Panama. Replicate staghorn corals fragments from 10 genotypes were placed into the tanks containing 12 liters of UV sterilized seawater. Twelve tanks were then exposed to an antibiotic cocktail of Kanamycin, Ampicillan, Tetracycline and Choloramphenicol (100mg/ml each) twice over a 48hr period, and the corals from the antibiotic treated and untreated tanks were sampled for DNA (T0 sample point) and lesioned with an airbrush. Half of the antibiotic- treated and untreated tanks were then exposed to 30ml of disease slurry (D) or healthy slurry (H) for the first exposure. 24hrs later a second dose of disease or healthy slurry was applied to complete the priority experiment treatments of healthy_healthy (h_h), disease_disease (d_d), healthy_disease (h_d), and disease_healthy (d_h). DNA for the microbial analyses were sampled 18hrs later (T2) and then disease was monitored over the course of the experiment. Corals that developed disease were sampled (T3) and sacrificed. All of the corals were sampled (T3 timepoint) on day 7.</p>
<p>DNA from preserved coral samples were extracted using an Agencourt DNAdvance kit, in order to prepare 16S rDNA profiling libraries. 16s libraries of the hypervariable V3_v4 region were then prepared using a two-step PCR protocol and combinatorial barcodes, resulting in amplicon lengths from ~300-400 bp paired-end joined sequences from Illumina 250 bp sequencing on an Illumina HiSeq 2500.</p>
<p>16s sequencing data were clustered into operational taxonomic units (OTUs) using a 97% identity threshold in QIIME. Default QIIME settings were used to align reads, to remove chimera sequences, and to assign taxonomy.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1458158 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1458158
completed
Tarik C. Gouhier
Northeastern University
781-581-7370 ext. 302
Marine Science Center 430 Nahant Road
Nahant
MA
01908
USA
t.gouhier@northeastern.edu
pointOfContact
Steven V. Vollmer
Northeastern University
781-581-7370 ext. 312
Marine Science Center 430 Nahant Road
Nahant
MA
01908
USA
steve.vollmer@gmail.com
pointOfContact
asNeeded
Dataset Version: 1
Unknown
OTUname
size
domain
phylum
class
order
family
genus
Illumina HiSeq 2500
theme
None, User defined
sample identification
length
kingdom
phylum
taxonomic class
order
family
genus
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Thermal Cycler
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.
Coral-microbial interactions as determinants of disease dynamics
https://osprey.bco-dmo.org/project/541019
Coral-microbial interactions as determinants of disease dynamics
<p><em>Description from NSF award abstract:</em><br />
The health of numerous animal and plant hosts depends on the composition of their microbiome. Although the health of hosts is often linked to environmental factors that favor the growth of pathogenic microbes, the diversity of animal and plant microbiomes suggests that competition plays an important role in determining the frequency and severity of disease outbreaks. This project uses the endangered Caribbean staghorn coral as a model system to understand how the environment and microbial interactions controls the spread of White Band Disease (WBD), a bacterial disease that has decimated nearly 95% of Caribbean staghorn coral populations. A combination of manipulative experiments, field surveys and mathematical modeling will be used to determine how water temperature, microbial movement between- and microbial competition within coral hosts influence WBD incidence. By identifying the environmental and microbial drivers of WBD, this project will allow managers to (i) predict hotspots of vulnerability to WBD in space and time, and (ii) identify optimal strategies for restoring these once prominent members of Caribbean coral reef communities. This research will address important societal needs by cross-training graduate students in coral biology, microbial genetics, bioinformatics, mathematical modeling, computer programming and statistics. Results of this project will be integrated into undergraduate courses in genetics, ecological modeling and biostatistics in order to emphasize the importance of quantitative and interdisciplinary STEM training for addressing important questions in biology. Finally, a series of interactive web modules will be created to disseminate the results of this project beyond academic circles, including to Northeastern University's Marine Science Center K-12 outreach programs and the Smithsonian Tropical Research Institute's outreach programs in Panama.</p>
<p>There is growing recognition that the processes that structure microbial communities may scale up to explain disease outbreaks in their hosts. Despite the complexity of microbial communities, most studies to date have focused on resolving the direct relationship between the environment, the occurrence of pathogenic microbes, and the incidence of disease. However, the effects of microbial species interactions and dispersal on the emergence of host diseases remain largely unknown. This project will combine microbial genetics and mathematical modeling to understand the relative influence of the environment, species interactions and dispersal on the structure of microbial communities and the dynamics of disease in their coral hosts. This research uses the endangered Caribbean staghorn coral (Acropora cervicornis) and White Band Disease (WBD) as a model host-pathogen system. This once dominant, reef-building coral was decimated by WBD, prompting its listing as an endangered species. Recent work in this system suggests that (i) bacteria are the cause of WBD, (ii) the microbial community living within the host can produce antibiotic compounds that suppress pathogenic bacteria, and (iii) temperature increase promotes infection and reduces the production of antibiotic compounds. These findings suggest that the interplay between the environment and host-associated microbial species determines the structure of the microbial community and the health of the coral host. To disentangle these processes, a multi-factorial transmission experiment will be conducted to understand the direct and indirect effects of temperature, pathogen exposure, and microbial community complexity on disease dynamics. To determine how these results scale up to natural coral reefs, a spatial coral-microbial model will be fitted to field survey data. This fitted model will elucidate how seasonal temperature variation and microbial dispersal jointly influence coral disease outbreaks and the structure of coral-microbial communities across spatial scales. The proposed research will integrate research with teaching and training of undergraduate students.</p>
Coral-microbial interactions
largerWorkCitation
project
eng; USA
biota
oceans
-82.2565
-82.2565
9.3513
9.3513
2015-06-01
2015-06-30
Panama, Bocas del Toro Archipelago
0
BCO-DMO catalogue of parameters from Microbial 16S OTU annotation information from staghorn coral health experiments with treatment with and without antibiotics
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/816386.rdf
Name: OTUname
Units: unitless
Description: <p>Operational Taxonomic Unit (OUT) identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/816387.rdf
Name: size
Units: unitless
Description: <p>size of OTU (base pairs)</p>
http://lod.bco-dmo.org/id/dataset-parameter/816388.rdf
Name: domain
Units: unitless
Description: <p>OTU domain name</p>
http://lod.bco-dmo.org/id/dataset-parameter/816389.rdf
Name: phylum
Units: unitless
Description: <p>OTU phylum name</p>
http://lod.bco-dmo.org/id/dataset-parameter/816390.rdf
Name: class
Units: unitless
Description: <p>OTU class name</p>
http://lod.bco-dmo.org/id/dataset-parameter/816391.rdf
Name: order
Units: unitless
Description: <p>OTU order name</p>
http://lod.bco-dmo.org/id/dataset-parameter/816392.rdf
Name: family
Units: unitless
Description: <p>OTU family name</p>
http://lod.bco-dmo.org/id/dataset-parameter/816393.rdf
Name: genus
Units: unitless
Description: <p>OTU genus name</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
612784
https://darchive.mblwhoilibrary.org/bitstream/1912/26635/1/dataset-816367_microbes-priority-annotations-otu-taxonomy__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.816367.1
download
onLine
dataset
<p>A priority experiment was conducted in 24 recirculating tanks at the Smithsonian stations in Bocas del Toro, Panama. Replicate staghorn corals fragments from 10 genotypes were placed into the tanks containing 12 liters of UV sterilized seawater. Twelve tanks were then exposed to an antibiotic cocktail of Kanamycin, Ampicillan, Tetracycline and Choloramphenicol (100mg/ml each) twice over a 48hr period, and the corals from the antibiotic treated and untreated tanks were sampled for DNA (T0 sample point) and lesioned with an airbrush. Half of the antibiotic- treated and untreated tanks were then exposed to 30ml of disease slurry (D) or healthy slurry (H) for the first exposure. 24hrs later a second dose of disease or healthy slurry was applied to complete the priority experiment treatments of healthy_healthy (h_h), disease_disease (d_d), healthy_disease (h_d), and disease_healthy (d_h). DNA for the microbial analyses were sampled 18hrs later (T2) and then disease was monitored over the course of the experiment. Corals that developed disease were sampled (T3) and sacrificed. All of the corals were sampled (T3 timepoint) on day 7.</p>
<p>DNA from preserved coral samples were extracted using an Agencourt DNAdvance kit, in order to prepare 16S rDNA profiling libraries. 16s libraries of the hypervariable V3_v4 region were then prepared using a two-step PCR protocol and combinatorial barcodes, resulting in amplicon lengths from ~300-400 bp paired-end joined sequences from Illumina 250 bp sequencing on an Illumina HiSeq 2500.</p>
<p>16s sequencing data were clustered into operational taxonomic units (OTUs) using a 97% identity threshold in QIIME. Default QIIME settings were used to align reads, to remove chimera sequences, and to assign taxonomy.</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 />
- removed 'size=' preceding number from the size column<br />
- replaced no data symbols *, +, - with 'nd'</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 HiSeq 2500
Illumina HiSeq 2500
PI Supplied Instrument Name: Illumina HiSeq 2500 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)