http://lod.bco-dmo.org/id/dataset/724355
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
2018-01-19
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources (Coral Microbial Relationships project)
2021-06-10
publication
2021-06-10
revision
BCO-DMO Linked Data URI
2021-06-10
creation
http://lod.bco-dmo.org/id/dataset/724355
Amy Apprill
Woods Hole Oceanographic Institution
principalInvestigator
Megan Huggett
University of Newcastle
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: Apprill, A., Huggett, M. (2021) A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources (Coral Microbial Relationships project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2) Version Date 2021-06-10 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/724355 [access date]
Coral SSU rRNA gene database Dataset Description: <p>A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources. These data are described in Huggett and Apprill (in press).</p>
<p>Metadata for the database is available in the primary dataset file coral_microb_suppl.csv.&nbsp; The database is also available for download as an ARB file&nbsp;coralmicrobiome_database.arb.</p>
<p>ARB software (version arb-6.06) is available from&nbsp;<a href="http://www.arb-home.de/downloads.html" target="_blank">http://www.arb-home.de/downloads.html</a></p> Methods and Sampling: <p>The coral-microbial database was built over time using the ARB software (Ludwig et al., 2004). Initially, the All-Species Living Tree Project (LTP) s95 database containing SSU rRNA gene sequences for type strains of bacteria, archaea and eukarya was used as the database backbone (Yarza et al., 2008). In 2009, we used the search criteria ‘coral + bacteria’ and ‘coral + archaea’ within BLAST (Altschul et al., 1990) to obtain coral-associated SSU rRNA gene sequences from studies that applied cultivation-dependent or independent approaches from the GenBank database (Benson et al., 2008). These sequences were aligned using SINA (Pruesse et al., 2007) and imported into ARB. This database was then revised by first searching for all sequences coded as ‘coral*’ in any field. From these, sequences that matched ‘eukaryot*’ in the field tax_slv were removed, and all others were marked. An initial search of these marked sequences for those that had *coral* in the field isolation_source was done and these were manually checked. For those that were isolated from a coral (soft or hard, tropical or deep sea, etc.) were assigned ‘coral’ in the remark field. For those that were not isolated from a coral all were assigned ‘checked’ in the remark field. At this stage, there were 1333 sequences remaining with the term *coral* in any field. These were manually checked for their description and isolation details and marked either ‘coral’ or ‘checked’ in the remark field. From these, a database was created that contained just the sequences marked ‘coral’ from our in-house (2009) database. This small curated database was then merged with the SSU_Ref111_SILVA_NR (Pruesse et al., 2007) database (released 19 July 2012) which created new names for the living tree sequences. All sequences that were brought in from the small living tree database were marked with an identifier and the SSU_Ref database was searched as above to locate sequences in the SSU_Ref database that were bacteria or archaea sequences derived from corals. Information was added to these sequences in the location, author, journal and host species fields and all were given the term ‘coral’ in the remark field.</p>
<p>Next, the ISI web of science electronic database was searched for any publications that contained the search term 'coral*' and 'bacteria*' or ‘coral*’ and ‘archaea* in ‘topic’ from 2010 to present. From these, the publications were manually checked and any manuscript that mentioned sequence data or appeared likely to contain Sanger sequence data was obtained. If sequence data was associated with a manuscript, the corresponding sequences were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) in fasta format, aligned using the online SINA aligner (Pruesse et al., 2007) and imported into arb. If replicates were located they were removed from arb. Newly imported sequences were manually curated to include as much metadata as possible. These included the location (in country field), host (in host field), author names (in author field) and any other accessible data (e.g. Journal).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1233612 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1233612
completed
Amy Apprill
Woods Hole Oceanographic Institution
508-289-2649
Marine Chemistry and Geochemistry Department 266 Woods Hole Road, MS# 4
Woods Hole
MA
02543
USA
aapprill@whoi.edu
pointOfContact
Megan Huggett
University of Newcastle
pointOfContact
asNeeded
Dataset Version: 2
Unknown
Sequence_Identifier
gi_number
Accession_source
Accession_number
Accession_link
Length_bp
Taxonomy
Organism_details
Host
Location
Accession_Number
Isolate_Clone
theme
None, User defined
accession number
sample description
external_link
taxon
site description
featureType
BCO-DMO Standard Parameters
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.
Fundamental Coral-Microbial Associations
https://osprey.bco-dmo.org/project/564442
Fundamental Coral-Microbial Associations
<p><em>Description from NSF award abstract:</em><br />
Reef-building corals are in decline worldwide due in part to climate change and other human activities, and it is becoming increasingly important to understand what aspects of coral biology are degraded by environmental stress which then leads to coral mortality. It is now widely known that corals harbor communities of bacteria and archaea that are believed to play important roles in maintaining the health of their hosts, but we lack any appreciable understanding about the identity of the microbial associates regularly residing within healthy, reef-building corals. This project asks the central question: do reef-building corals harbor fundamental or persistent microbial associates that are symbiotic within their tissues? In order to address this hypothesis, the investigator will assess the identity of the bacterial and archaeal microbes using a variety of molecular and microscopy approaches that includes the identification and localization of a widespread group of coral bacterial associates belonging to the genus Endozoicomonas. The results of this study will then be used to develop additional questions about the role of these microbial associates in nutrient cycling and how they contribute to the health and survival of corals.</p>
Coral Microbial Relationships
largerWorkCitation
project
eng; USA
biota
oceans
2021-06-10
Florida Keys, Federated States of Micronesia, Red Sea, & Bermuda
0
BCO-DMO catalogue of parameters from A custom ARB database of SSU rRNA gene sequences from corals, as well representative cultivated and environmental sequences from public sources (Coral Microbial Relationships 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
http://lod.bco-dmo.org/id/dataset-parameter/736027.rdf
Name: Sequence_Identifier
Units: unitless
Description: <p>Sequence identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/736028.rdf
Name: gi_number
Units: unitless
Description: <p>gi number; A series of digits that are assigned consecutively to each sequence record processed by NCBI.</p>
http://lod.bco-dmo.org/id/dataset-parameter/736029.rdf
Name: Accession_source
Units: unitless
Description: <p>Source of genetic accession; Database containing accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/736030.rdf
Name: Accession_number
Units: unitless
Description: <p>Genetic accession number for the database supplied in Accession_source</p>
http://lod.bco-dmo.org/id/dataset-parameter/736031.rdf
Name: Accession_link
Units: unitless
Description: <p>Link to the genetic accession in the database specified in Accession_source</p>
http://lod.bco-dmo.org/id/dataset-parameter/736032.rdf
Name: Length_bp
Units: count
Description: <p>Length of base pairs (bp) in the genetic accession</p>
http://lod.bco-dmo.org/id/dataset-parameter/736033.rdf
Name: Taxonomy
Units: unitless
Description: <p>Taxonomic heirarchy of the sampled organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/736034.rdf
Name: Organism_details
Units: unitless
Description: <p>Description of sequence and organism source</p>
http://lod.bco-dmo.org/id/dataset-parameter/736035.rdf
Name: Host
Units: unitless
Description: <p>Scientific name of organism sampled or description of organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/736036.rdf
Name: Location
Units: various
Description: <p>Latitude and longitude of sampled organism</p>
http://lod.bco-dmo.org/id/dataset-parameter/736037.rdf
Name: Accession_Number
Units: unitless
Description: <p>Accession number (either relative to NCBI or ARB)</p>
http://lod.bco-dmo.org/id/dataset-parameter/736038.rdf
Name: Isolate_Clone
Units: unitless
Description: <p>Indication of whether clone" or "isolate"</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
5355360
https://datadocs.bco-dmo.org/file/ZZZgx8gSP1NDV6/coral_microb_suppl.csv
coral_microb_suppl.csv
Primary data file for dataset ID 724355
download
38182485
https://datadocs.bco-dmo.org/file/nGyPQRoTlpML1M/coralmicrobiome_database.arb
coralmicrobiome_database.arb
The database is also available for download as an ARB file: coralmicrobiome_database.arb
download
https://osprey.bco-dmo.org/dataset/724355/data/download
download
onLine
dataset
<p>The coral-microbial database was built over time using the ARB software (Ludwig et al., 2004). Initially, the All-Species Living Tree Project (LTP) s95 database containing SSU rRNA gene sequences for type strains of bacteria, archaea and eukarya was used as the database backbone (Yarza et al., 2008). In 2009, we used the search criteria ‘coral + bacteria’ and ‘coral + archaea’ within BLAST (Altschul et al., 1990) to obtain coral-associated SSU rRNA gene sequences from studies that applied cultivation-dependent or independent approaches from the GenBank database (Benson et al., 2008). These sequences were aligned using SINA (Pruesse et al., 2007) and imported into ARB. This database was then revised by first searching for all sequences coded as ‘coral*’ in any field. From these, sequences that matched ‘eukaryot*’ in the field tax_slv were removed, and all others were marked. An initial search of these marked sequences for those that had *coral* in the field isolation_source was done and these were manually checked. For those that were isolated from a coral (soft or hard, tropical or deep sea, etc.) were assigned ‘coral’ in the remark field. For those that were not isolated from a coral all were assigned ‘checked’ in the remark field. At this stage, there were 1333 sequences remaining with the term *coral* in any field. These were manually checked for their description and isolation details and marked either ‘coral’ or ‘checked’ in the remark field. From these, a database was created that contained just the sequences marked ‘coral’ from our in-house (2009) database. This small curated database was then merged with the SSU_Ref111_SILVA_NR (Pruesse et al., 2007) database (released 19 July 2012) which created new names for the living tree sequences. All sequences that were brought in from the small living tree database were marked with an identifier and the SSU_Ref database was searched as above to locate sequences in the SSU_Ref database that were bacteria or archaea sequences derived from corals. Information was added to these sequences in the location, author, journal and host species fields and all were given the term ‘coral’ in the remark field.</p>
<p>Next, the ISI web of science electronic database was searched for any publications that contained the search term 'coral*' and 'bacteria*' or ‘coral*’ and ‘archaea* in ‘topic’ from 2010 to present. From these, the publications were manually checked and any manuscript that mentioned sequence data or appeared likely to contain Sanger sequence data was obtained. If sequence data was associated with a manuscript, the corresponding sequences were downloaded from NCBI (http://www.ncbi.nlm.nih.gov/) in fasta format, aligned using the online SINA aligner (Pruesse et al., 2007) and imported into arb. If replicates were located they were removed from arb. Newly imported sequences were manually curated to include as much metadata as possible. These included the location (in country field), host (in host field), author names (in author field) and any other accessible data (e.g. Journal).</p>
Specified by the Principal Investigator(s)
BCO-DMO Data Manager Processing Notes:
* added a conventional header with dataset name, PI name, version date
* modified parameter names to conform with BCO-DMO naming conventions
* blank values in this dataset are displayed as "nd" for "no data."&nbsp; nd is the default missing data identifier in the BCO-DMO system.
* converted non-delimiter commas to semicolons to support export as csv
* removed duplicate column of lengths
* data version 2: 2018-08-06 is an update of data version 1: 2018-05-11 with the following change. In the file coralmicrobiome_database.arb, phylogenetic trees were updated to include those available in Huggett and Apprill (in press) which describes this dataset.
Dataset version 2 (2021-06-10) replaces version 1(2018-08-06):
* Converted file to UTF-8
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