http://lod.bco-dmo.org/id/dataset/554055
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
2015-03-24
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Oceanus and R/V Urania (OC454-02) in the eastern Mediterranean Sea in 2009 (Pickled Protists project)
2015-03-19
publication
2015-03-19
revision
BCO-DMO Linked Data URI
2015-03-19
creation
http://lod.bco-dmo.org/id/dataset/554055
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
principalInvestigator
Joan M. Bernhard
Woods Hole Oceanographic Institution
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. (2015) Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Oceanus and R/V Urania (OC454-02) in the eastern Mediterranean Sea in 2009 (Pickled Protists project). Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 2015-03-19) Version Date 2015-03-19 [if applicable, indicate subset used]. http://lod.bco-dmo.org/id/dataset/554055 [access date]
Microbial metatranscriptomics: upper and lower halocline water column Dataset Description: <p>Cloned SSU rRNA sequences of kinetoplastids detected in Discovery, Urania and Kryos Basin haloclines and brines.</p>
<p><strong>Related Reference:</strong></p>
<p>Edgcomb, V.P., W. Orsi, H.-W. Breiner, A. Stock, S. Filker, M.M. Yakimov, and T. Stoeck. 2011, Novel kinetoplastids associated with hypersaline anoxic lakes in the Eastern Mediterranean deep-sea. Deep-Sea Research I 58(10):1040-1048.</p> Methods and Sampling: <p>The position of the halocline was determined during the R/V Oceanus cruise using a SBE9 CTD (Sea-Bird Electronics, USA) equipped with an SBE43 oxygen sensor (Sea-Bird Electronics, USA). Samples were collected from the halocline and brine of Discovery basin using a rosette equipped with Niskin bottles (12&nbsp;L) on R/V Oceanus.</p>
<p>RNA was extracted as described in detail previously (Alexander et al., 2009) using bead beating of filters in an extraction buffer and E-Matrix tubes (QBiogene, MP Biomedicals, USA), followed by the RNA/DNA Allprep kit (Qiagen, Hildesheim, Germany) according to the manufacturer's instructions. Total RNA was transcribed into cDNA using the Two-Step Omniscript Reverse Transcription kit (Qiagen) according to the manufacturer's instructions. Subsequently, the small subunit ribosomal RNA gene (18S rRNA) was amplified using the kinetoplastid-specific primers 14F (5′-CTGCCAGTAGTCATATATGCTTGTTTCAAGGA-3′) and 2026R (5′-GATCCTCTGCAGGTTCACCTACAGCT-3′) (von der Heyden et al., 2004).</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-0849578 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=0849578
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
asNeeded
Dataset Version: 2015-03-19
Unknown
cruise_id
lat
lon
sample_location
sample_descrip
depth
sal
O2
cond
accession_number
url
Sequencer
Niskin bottle
MS_SID
PCR
theme
None, User defined
Cruise identfier
latitude
longitude
site description
sample description
depth
salinity
dissolved Oxygen
conductivity
accession number
No BCO-DMO term
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
Submersible Incubation Device-In Situ Microbial Sampler
Thermal Cycler
instrument
BCO-DMO Standard Instruments
OC454-02
Urania-2009-09
service
Deployment Activity
Mediterranean Sea
eastern Mediterranean Sea
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.
Pickled Protists or Community Uniquely Adapted to Hypersalinity?
https://osprey.bco-dmo.org/project/2134
Pickled Protists or Community Uniquely Adapted to Hypersalinity?
<p>Protists are an essential component of microbial food webs and play a central role in global biogeochemical cycles, and thus are key players in sustaining the healthy functioning of any ecosystem. Over the past few years a rich diversity of protists has been revealed in a range of extreme environments, indicating that the frontiers of eukaryotic life are still being explored. Only recently, one of the most extreme marine environments known to science was discovered in the eastern Mediterranean Sea at a depth of ~3500m, namely deep hypersaline anoxic basins (DHABs). These basins are characterized by extremely high salt concentrations (up to saturation) that have been considered anathema to life. Instead, highly diverse communities of bacteria exist in the waters of these basins. With the exception of a preliminary study to this proposal that indicated a diverse and active assemblage of protists in the water column along the halocline and below the halocline, these DHABs remain largely unexplored regarding eukaryotic life forms. The sediments of the DHABs have not been explored for protists at all. </p>
<p>The investigators will collect water column and sediment samples on a short cruise to two basins with different brine chemistries. An exciting combination of molecular, cultivation-independent and culture-based approaches will be used to study the microbial communities of two basins. Investigators will use those approaches to determine adaptive strategies of marine protist communities to hypersaline, anoxic environments and the degree of their potential impact on biogeochemical cycling as a result of their predation activities, the degree to which the dominant protists maintain bacterial or archaeal symbionts, and the identity of those symbionts. The original research proposal identified Bannock and Discovery Basins as the field study areas, however the 2009 cruise collected samples at Discovery and Urania Basin. Methods to be employed include RNA-based sequence analysis of diversity based on 18S rDNA genes, statistical analyses of community composition and phylotype richness, geochemical documentation of the water column and sediments using classical and microelectrode approaches, expression profiling using 3'-UTR fragments of mRNAs, sequencing of complete gene transcripts for proteins appearing to confer adaptation to hypersalinity, analysis of the proteome signatures, FISH-SEM to characterize novel extremophiles, CARD-FISH to identify eukaryote prey and putative symbionts, and TEM to assess morphology and endobiont presence in common benthic morphotypes. </p>
<p>Hypersaline environments rank highly in the list of extreme systems that have attracted increasing notice in science as well as by the lay public. For example, considering predictions of increasing temperatures and drought in certain regions of our planet, the number of hypersaline habitats may increase dramatically causing this ecosystem to gain importance on a global scale. Thus, an understanding of the ecosystem in these habitats will help predict future ecosystem functioning due to global change. From a different perspective, revealing the mechanisms of adaptation to high salinity has become a major objective, both for biological science and for potential commercial exploitation of natural products associated with those adaptations. </p>
Pickled Protists
largerWorkCitation
project
eng; USA
biota
oceans
Mediterranean Sea; eastern Mediterranean Sea
2015-03-19
Mediterranean Sea
0
BCO-DMO catalogue of parameters from Microbial metatranscriptomics: upper and lower halocline water column data from the R/V Oceanus and R/V Urania (OC454-02) in the eastern Mediterranean Sea in 2009 (Pickled Protists 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/554092.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/554093.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/554094.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/554095.rdf
Name: sample_location
Units: unitless
Description: <p>sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/554096.rdf
Name: sample_descrip
Units: unitless
Description: <p>description of sample</p>
http://lod.bco-dmo.org/id/dataset-parameter/554097.rdf
Name: depth
Units: meters
Description: <p>depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/554098.rdf
Name: sal
Units: unitless
Description: <p>total salinity</p>
http://lod.bco-dmo.org/id/dataset-parameter/554099.rdf
Name: O2
Units: ml/L
Description: <p>dissolved oxygen</p>
http://lod.bco-dmo.org/id/dataset-parameter/554100.rdf
Name: cond
Units: S/m
Description: <p>conductivity</p>
http://lod.bco-dmo.org/id/dataset-parameter/554101.rdf
Name: accession_number
Units: unitless
Description: <p>GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/554102.rdf
Name: url
Units: unitless
Description: <p>link to GenBank accession data</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
1489
https://datadocs.bco-dmo.org/file/nGGlALLuX1LDGx/kinetoplastid.csv
kinetoplastid.csv
Primary data file for dataset ID 554055
download
https://osprey.bco-dmo.org/dataset/554055/data/download
download
onLine
dataset
<p>The position of the halocline was determined during the R/V Oceanus cruise using a SBE9 CTD (Sea-Bird Electronics, USA) equipped with an SBE43 oxygen sensor (Sea-Bird Electronics, USA). Samples were collected from the halocline and brine of Discovery basin using a rosette equipped with Niskin bottles (12&nbsp;L) on R/V Oceanus.</p>
<p>RNA was extracted as described in detail previously (Alexander et al., 2009) using bead beating of filters in an extraction buffer and E-Matrix tubes (QBiogene, MP Biomedicals, USA), followed by the RNA/DNA Allprep kit (Qiagen, Hildesheim, Germany) according to the manufacturer's instructions. Total RNA was transcribed into cDNA using the Two-Step Omniscript Reverse Transcription kit (Qiagen) according to the manufacturer's instructions. Subsequently, the small subunit ribosomal RNA gene (18S rRNA) was amplified using the kinetoplastid-specific primers 14F (5′-CTGCCAGTAGTCATATATGCTTGTTTCAAGGA-3′) and 2026R (5′-GATCCTCTGCAGGTTCACCTACAGCT-3′) (von der Heyden et al., 2004).</p>
Specified by the Principal Investigator(s)
<p>PCR products were cloned and Sanger sequenced (bidirectionally)</p>
<p><strong>BCO-DMO Processing:</strong><br />
original file: EdgcombKinetoplastid.xlsx<br />
- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- converted lat/lon to decimal degrees from degrees-decimal minutes<br />
- added cruise id's<br />
- added html links to GenBank Popset</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
Sequencer
Sequencer
PI Supplied Instrument Name: Sequencer PI Supplied Instrument Description:Roche 454 FLX Titanium 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.
Niskin bottle
Niskin bottle
PI Supplied Instrument Name: Niskin bottle PI Supplied Instrument Description:12L Niskin bottles mounted on a General Oceanics rosette sampler equipped with a SBE- 911plus conductivity-temperature-depth (CTD) sensor (Sea- Bird Electronics) Instrument Name: Niskin bottle Instrument Short Name:Niskin bottle Instrument Description: A Niskin bottle (a next generation water sampler based on the Nansen bottle) is a cylindrical, non-metallic water collection device with stoppers at both ends. The bottles can be attached individually on a hydrowire or deployed in 12, 24, or 36 bottle Rosette systems mounted on a frame and combined with a CTD. Niskin bottles are used to collect discrete water samples for a range of measurements including pigments, nutrients, plankton, etc. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/
MS_SID
MS_SID
PI Supplied Instrument Name: MS_SID PI Supplied Instrument Description:Microbial Sampler - In Situ Incubation Device (MS-SID) Instrument Name: Submersible Incubation Device-In Situ Microbial Sampler Instrument Short Name:SID-ISMS Instrument Description: The Submersible Incubation Device-In Situ Microbial Sampler (SID-ISMS) system was developed for the 2011 NSF funded DHAB Metazoans Mediterranean Brine research project and first used on cruise AT18-14. The system includes several integrated components including: a 2 liter incubation chamber; fixation filters and water sample bottles; a High Range CTD (Neil Brown Ocean Sensors, Inc., USA) equipped with two turbidity sensors (Wet Labs ECOView); an Aanderra 2808F oxygen optode; an SDSL-data link; and a sonardyne beacon, a pinger and a 24 volt deep-sea battery. The sensors and sampling devices are mounted on a frame that is attached to the hydro-wire. Lowering rate and recovery speed are controlled by a winch mounted on the surface vessel. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/82/
PCR
PCR
PI Supplied Instrument Name: PCR 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)
Cruise: OC454-02
OC454-02
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
OC454-02
Virginia P. Edgcomb
Woods Hole Oceanographic Institution
http://data.bco-dmo.org/Protists_2009/OC454-02_cruise_report.pdf
Report describing OC454-02
Cruise: Urania-2009-09
Urania-2009-09
R/V Urania
vessel
Urania-2009-09
Dr Michail M Yakimov
Italian National Research Council
R/V Oceanus
Community Standard Description
International Council for the Exploration of the Sea
R/V Oceanus
vessel
R/V Urania
vessel