http://lod.bco-dmo.org/id/dataset/4004
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
2013-07-25
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sequence accession numbers from microbialite mats sampled from R/V F.G. Walton Smith cruise WS1005 in the Bahamas and from Hamelin Pool, Australia from 2010-2011 (Protists_Stromatolites project)
2013-07-25
publication
2013-07-25
revision
BCO-DMO Linked Data URI
2013-07-25
creation
http://lod.bco-dmo.org/id/dataset/4004
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
principalInvestigator
Joan M. Bernhard
Woods Hole Oceanographic Institution
principalInvestigator
Dr Roger Summons
Massachusetts Institute of Technology
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: Edgcomb, V. P., Bernhard, J. M., Summons, R. (2013) Sequence accession numbers from microbialite mats sampled from R/V F.G. Walton Smith cruise WS1005 in the Bahamas and from Hamelin Pool, Australia from 2010-2011 (Protists_Stromatolites project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 25 July 2013) Version Date 2013-07-25 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/4004 [access date]
Sequence accession numbers from microbialite mats. Dataset Description: <p>This dataset contains GenBank and GenBank Short Read Archive (SRA) sequence accession numbers for samples from microbialite mats at Hamelin Pool, Australia and Highborne Cay, Bahamas.</p>
<p><b>References:</b><br />
<b>Bernhard et al. 2013</b>. Insights into foraminiferal influences on microfabrics of microbialites at Highborne Cay, Bahamas.<i> PNAS</i> 110(24); published ahead of print May 28, 2013. doi: <a href="http://dx.doi.org/10.1073/pnas.1221721110" target="_blank">10.1073/pnas.1221721110</a>.<br />
<b>Edgcomb et al. 2013</b>. Active eukaryotes in microbialites from Highborne Cay, Bahamas and Hamelin Pool (Shark Bay), Australia. In press,<i> ISME Journal</i>.<br />
<b>Edgcomb et al. 2013</b>. Molecular indicators of microbial diversity in oolitic sands of Highborne Cay, Bahamas. <i>Geobiology</i> 11: 234-251. doi: <a href="http://dx.doi.org/10.1111/gbi.12029" target="_blank">10.1111/gbi.12029</a>.</p> Methods and Sampling: <p>See the publications above (in the dataset description) for detailed methodology.</p>
<p>For accession numbers JX873274 - JX873955, refer to Bernhard et al. 2013 and Edgcomb et al. 2013, ISME Journal.<br />
For accession number KC790540, refer to Bernhard et al. 2013.<br />
For accession numbers JX872558 - JX873273, SRA061992 and SRA061825, refer to Edgcomb et al. 2013, ISME Journal.<br />
For accession numbers JX255738 - JX255917 and JX504252 - JX504530, refer to Edgcomb et al. 2013, Geobiology.</p>
<p>Brief summary of methods:<br />
Samples were collected from Highborne Cay, Bahamas in March 2010 and from Hamelin Pool, Australia in June 2011. Microbialite mat types at Highborne Cay were designated according to Reid et al. (2000) and Myshrall et al. (2010). Microbialites at Hamelin Pool were classified following Jahnert and Collins (2011) and Logan (1961). The water column in the vicinity of the microbialite mats was also sampled. Water column measurments included temperature, salinity, and ligh intensity. Microbialite samples were obtained using syringe cores (refer to publications for sizes and depths).</p>
<p>RNA was extracted from preserved samples, reverse transcribed, and PCR amplified. PCR products were purified and foraminiferal PCR products were cloned for Sanger sequencing. Sequences were clustered into operational taxonomic units (OTUs). JAguc (Nebel et al. 2011) was used to assign taxonomy of OTU representatives. Again, <b>refer to publications above for detailed methodology, statistical analyses, and results</b>.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0926421 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0926421
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0926372 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0926372
completed
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
508-289-3734
Department of Geology and Geophysics 220 McLean Lab, MS #8
Woods Hole
MA
02543
USA
vedgcomb@whoi.edu
pointOfContact
Joan M. Bernhard
Woods Hole Oceanographic Institution
508-289-3480
Department of Geology and Geophysics Woods Hole Oceanographic Institution, MS#52
Woods Hole
MA
02543
USA
jbernhard@whoi.edu
pointOfContact
Dr Roger Summons
Massachusetts Institute of Technology
617.452.2791
Department of Earth, Atmospheric and Planetary Sciences, MIT E25-633, 45 Carleton Street
Cambridge
MA
02139
USA
rsummons@mit.edu
pointOfContact
asNeeded
Dataset Version: 25 July 2013
Unknown
location
site
lat
lon
subject
description
accession_number_range
link
Light Meter
salinity sensor
theme
None, User defined
site description
site
latitude
longitude
taxon
brief description
accession number
featureType
BCO-DMO Standard Parameters
Light Meter
Salinity Sensor
instrument
BCO-DMO Standard Instruments
WS1005
Hamelin_Pool_Edgcomb
service
Deployment Activity
Miami to Bahamas
Hamelin Pool, Australia
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.
Were Protists the Beginning of the End for Stromatolites?
https://osprey.bco-dmo.org/project/2203
Were Protists the Beginning of the End for Stromatolites?
<p><span class="pageheadline"><span class="pageheadline"><strong>Collaborative Research: Were Protists the Beginning of the End for Stromatolites? </strong></span></span></p>
<p>This award is funded under the American Recovery and Reinvestment Act of 2009 (Public Law 111-5).</p>
<p>Microbial mats are conspicuous components of many benthic marine and aquatic settings. A subset of these microbial mats binds sediments to form potentially fossilizable structures, often called stromatolites or microbialites. While much is known about microbialite autotrophs, little is known about their heterotrophic eukaryotes. The lack of understanding is surprising given that stromatolites have an extensive geologic record spanning most of Earth's history. Stromatolites are layered sedimentary structures formed by a combination of microbial activities, abiotic carbonate precipitation, and sedimentary processes. Details of stromatolite formation and preservation are poorly understood, and a drastic decline in stromatolite occurrence and diversity in the late Precambrian has long been a conundrum. A popular hypothesis to explain this decline at ~1 billion years ago is that eukaryotic organisms evolved to become predators on stromatolites. To date, the most commonly proposed predatory culprit is an unidentified metazoan, although evidence of such an organism is lacking from the fossil record. Protists, most of which are not expected to leave an obvious fossil record, are additional possible stromatolitic predators, but they have been largely ignored in this context. The hypotheses of this project are: (1) Heterotrophic protist activity caused the textural change from stromatolites (layered sediment fabric) to thrombolites (clotted sediment fabric) and (2) Heterotrophic protists caused the decimation of Neoproterozoic stromatolites. Since it is impossible to recreate the Neoproterozoic, studies of modern analogs serve to indirectly test these hypotheses. The overall goal of this project is to describe the eukaryotic communities associated with modern stromatolites and thrombolites from the Bahamas and Australia, compare the communities from the two sites, and to relate the communities to stromatolitic / thrombolitic sediment fabric and biomarker signatures. </p>
<p>The overall goal will be achieved by addressing the following specific aims: (1) Identify, via morphologic and molecular approaches, the eukaryotic community of modern stromatolites and thrombolites; (2) Analyze modern and fossil stromatolites and thrombolites for their eukaryotic lipid biomarkers using solvent extraction, chromatographic and mass spectrometric methods; (3) Using the Fluorescently Labeled Embedded Core (FLEC) method, document the sub-millimeter distributions of the heterotrophic eukaryotic community inhabiting modern stromatolites and thrombolites in conjunction with fine-scale sediment fabric; (4) Using solvent extraction, chromatographic and mass spectrometric methods, analyze cultures of allogromiid foraminifers to survey for lipid biomarkers unique to them; (5) After incubation of modern stromatolites with heterotrophic protists, use FLEC methodology to determine how their activity affects sediment fabric and conduct preliminary comparisons of these modern fabrics to those of stromatolite fossils. </p>
<p>Intellectual Merit: The oldest fossil stromatolites are >3.4 billion years old and are the most visible manifestations of pervasive microbial life on the early Earth. The changes in stromatolite abundance and morphology document complex interplays between biological and geological processes. This project addresses multiple aspects of stromatolite genesis and pre-fossilization alteration but at its core, focuses on one of the greatest geological enigmas: the possible connection between stromatolite decline and the rise of complex life.</p>
Protists_Stromatolites
largerWorkCitation
project
eng; USA
oceans
Miami to Bahamas; Hamelin Pool, Australia
2013-07-25
Highborne Cay, Bahamas and Carbla Station (Shark Bay), Western Australia
0
BCO-DMO catalogue of parameters from Sequence accession numbers from microbialite mats sampled from R/V F.G. Walton Smith cruise WS1005 in the Bahamas and from Hamelin Pool, Australia from 2010-2011 (Protists_Stromatolites 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/35788.rdf
Name: location
Units: text
Description: <p>General location of sampling.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35789.rdf
Name: site
Units: text
Description: <p>Name of specific site sampled.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35790.rdf
Name: lat
Units: decimal degrees
Description: <p>Latitude of sampling site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35791.rdf
Name: lon
Units: decimal degrees
Description: <p>Longitude of sampling site.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35792.rdf
Name: subject
Units: text
Description: <p>Name/description of the organism.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35793.rdf
Name: description
Units: text
Description: <p>Brief description of the type of sequence.</p>
http://lod.bco-dmo.org/id/dataset-parameter/35794.rdf
Name: accession_number_range
Units: alphanumeric
Description: <p>Accession number (or accession number range) at GenBank or the GenBank Short Read Archive (SRA).</p>
http://lod.bco-dmo.org/id/dataset-parameter/35795.rdf
Name: link
Units: alphanumeric
Description: <p>Link to the accession number (or range) at 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
1850
https://datadocs.bco-dmo.org/file/A88rL0mhlB9vVw/sequences.csv
sequences.csv
Primary data file for dataset ID 4004
download
https://osprey.bco-dmo.org/dataset/4004/data/download
download
onLine
dataset
<p>See the publications above (in the dataset description) for detailed methodology.</p>
<p>For accession numbers JX873274 - JX873955, refer to Bernhard et al. 2013 and Edgcomb et al. 2013, ISME Journal.<br />
For accession number KC790540, refer to Bernhard et al. 2013.<br />
For accession numbers JX872558 - JX873273, SRA061992 and SRA061825, refer to Edgcomb et al. 2013, ISME Journal.<br />
For accession numbers JX255738 - JX255917 and JX504252 - JX504530, refer to Edgcomb et al. 2013, Geobiology.</p>
<p>Brief summary of methods:<br />
Samples were collected from Highborne Cay, Bahamas in March 2010 and from Hamelin Pool, Australia in June 2011. Microbialite mat types at Highborne Cay were designated according to Reid et al. (2000) and Myshrall et al. (2010). Microbialites at Hamelin Pool were classified following Jahnert and Collins (2011) and Logan (1961). The water column in the vicinity of the microbialite mats was also sampled. Water column measurments included temperature, salinity, and ligh intensity. Microbialite samples were obtained using syringe cores (refer to publications for sizes and depths).</p>
<p>RNA was extracted from preserved samples, reverse transcribed, and PCR amplified. PCR products were purified and foraminiferal PCR products were cloned for Sanger sequencing. Sequences were clustered into operational taxonomic units (OTUs). JAguc (Nebel et al. 2011) was used to assign taxonomy of OTU representatives. Again, <b>refer to publications above for detailed methodology, statistical analyses, and results</b>.</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
Light Meter
Light Meter
PI Supplied Instrument Name: Light Meter PI Supplied Instrument Description:Light was measured using a LI-COR LI-250 meter equipped with a SA190A quantum sensor. Instrument Name: Light Meter Instrument Short Name:Light Meter Instrument Description: Light meters are instruments that measure light intensity. Common units of measure for light intensity are umol/m2/s or uE/m2/s (micromoles per meter squared per second or microEinsteins per meter squared per second). (example: LI-COR 250A)
salinity sensor
salinity sensor
PI Supplied Instrument Name: salinity sensor PI Supplied Instrument Description:Temperature and salinity were measured using an Accumet AP75 temperature/conductivity meter. Instrument Name: Salinity Sensor Instrument Short Name:Salinity Sensor Instrument Description: Category of instrument that simultaneously measures electrical conductivity and temperature in the water column to provide temperature and salinity data. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/350/
Cruise: WS1005
WS1005
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
WS1005
Joan M. Bernhard
Woods Hole Oceanographic Institution
Deployment: Hamelin_Pool_Edgcomb
Hamelin_Pool_Edgcomb
WHOI
laboratory
Hamelin_Pool_Edgcomb
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
R/V F.G. Walton Smith
Community Standard Description
International Council for the Exploration of the Sea
R/V F.G. Walton Smith
vessel
WHOI
laboratory