http://lod.bco-dmo.org/id/dataset/554005
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)
Data on microbial metatranscriptomics: Niskin vs. in situ sampler from the R/V Urania cruise in the Mediterranean Sea during 2012 (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/554005
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) Data on microbial metatranscriptomics: Niskin vs. in situ sampler from the R/V Urania cruise in the Mediterranean Sea during 2012 (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/554005 [access date]
Microbial metatranscriptomics: Niskin vs. in situ sampler Dataset Description: <p>Metatranscriptome of whole microbial community from a deep Mediterranean normal salinity site comparing results for a Niskin sample vs. an in situ sampler</p>
<p><strong>Related Reference:</strong></p>
<p>Edgcomb, V.P., Taylor, C., Pachiadaki, M., Engstrom, I., Yakimov, M. 2014. Comparison of Niskin vs. <em>in situ </em>approaches for analysis of gene expression in deep Mediterranean Sea water samples. Deep Sea Res II, doi: 10.1016/j.dsr2.2014.10.020</p> Methods and Sampling: <p>Water was collected using 12L Niskin bottles mounted on a General Oceanics rosette sampler equipped with conductivity-temperature and depth (CTD) and pressure sensors. After transferring water from Niskin bottles to a large sterile carboy, 30 liters of water were pumped through a 0.22µm Sterivex filter cartridge using a peristaltic pump operating around 125 ml/min containing a Durapore filter (Millipore, Millford, MA, USA), which was immediately filled with RNAlater (Life Technologies Inc., Grand Island, NY, USA) and frozen at -80°C until extraction. Water samples from the same depth and on the same day were also collected and preserved <em>in situ</em> using the MS-SID in situ microbial sampler equipped with a CTD, two turbidity sensors, and an oxygen optode. Three MS-SID samples were filtered <em>in situ</em> at 125 ml/min through a 47mm 0.2 µm Durapore (Millipore, USA) filter that, upon cessation of filtration was within 10-20 seconds flooded with the preservative RNAlater following filtration. The three filters collected 4L, 3L and 3.4L of water, respectively. Upon retrieval of the instrument to the ship’s deck, the Fixation Filter Units were disassembled, and the filters and associated RNAlater solutions were transferred aseptically to three separate sterile cryovials, and frozen at -80°C until extraction. The Sterivex capsule (from Niskin bottle collection) was also stored at -80°C until extraction. RNA preps performed as in Edgcomb et al. 2014 DSR II.&nbsp;</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
site
lat
lon
sampling_method
project_id
accession_number
sample
tax_id
filename
Sequencer
Niskin bottle
MS_SID
theme
None, User defined
Cruise identfier
site
latitude
longitude
sampling_method
No BCO-DMO term
accession number
sample identification
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
Niskin bottle
Submersible Incubation Device-In Situ Microbial Sampler
instrument
BCO-DMO Standard Instruments
Urania-2012-09
service
Deployment Activity
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
eastern Mediterranean Sea
2015-03-19
Mediterranean Sea
0
BCO-DMO catalogue of parameters from Data on microbial metatranscriptomics: Niskin vs. in situ sampler from the R/V Urania cruise in the Mediterranean Sea during 2012 (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/554018.rdf
Name: cruise_id
Units: unitless
Description: <p>cruise identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/554019.rdf
Name: site
Units: unitless
Description: <p>sampling location</p>
http://lod.bco-dmo.org/id/dataset-parameter/554020.rdf
Name: lat
Units: decimal degrees
Description: <p>latitude; north is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/554021.rdf
Name: lon
Units: decimal degrees
Description: <p>longitude; east is positive</p>
http://lod.bco-dmo.org/id/dataset-parameter/554022.rdf
Name: sampling_method
Units: unitless
Description: <p>sampling method</p>
http://lod.bco-dmo.org/id/dataset-parameter/554023.rdf
Name: project_id
Units: unitless
Description: <p>GenBank Bioproject number</p>
http://lod.bco-dmo.org/id/dataset-parameter/554024.rdf
Name: accession_number
Units: unitless
Description: <p>GenBank accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/554025.rdf
Name: sample
Units: unitless
Description: <p>sample identification</p>
http://lod.bco-dmo.org/id/dataset-parameter/554026.rdf
Name: tax_id
Units: unitless
Description: <p>GenBank Taxonomy ID number</p>
http://lod.bco-dmo.org/id/dataset-parameter/554027.rdf
Name: filename
Units: unitless
Description: <p>sequence result file 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
1041
https://datadocs.bco-dmo.org/file/zqqA81rs8DngZj/KM3_metatranscriptomics.csv
KM3_metatranscriptomics.csv
Primary data file for dataset ID 554005
download
https://osprey.bco-dmo.org/dataset/554005/data/download
download
onLine
dataset
<p>Water was collected using 12L Niskin bottles mounted on a General Oceanics rosette sampler equipped with conductivity-temperature and depth (CTD) and pressure sensors. After transferring water from Niskin bottles to a large sterile carboy, 30 liters of water were pumped through a 0.22µm Sterivex filter cartridge using a peristaltic pump operating around 125 ml/min containing a Durapore filter (Millipore, Millford, MA, USA), which was immediately filled with RNAlater (Life Technologies Inc., Grand Island, NY, USA) and frozen at -80°C until extraction. Water samples from the same depth and on the same day were also collected and preserved <em>in situ</em> using the MS-SID in situ microbial sampler equipped with a CTD, two turbidity sensors, and an oxygen optode. Three MS-SID samples were filtered <em>in situ</em> at 125 ml/min through a 47mm 0.2 µm Durapore (Millipore, USA) filter that, upon cessation of filtration was within 10-20 seconds flooded with the preservative RNAlater following filtration. The three filters collected 4L, 3L and 3.4L of water, respectively. Upon retrieval of the instrument to the ship’s deck, the Fixation Filter Units were disassembled, and the filters and associated RNAlater solutions were transferred aseptically to three separate sterile cryovials, and frozen at -80°C until extraction. The Sterivex capsule (from Niskin bottle collection) was also stored at -80°C until extraction. RNA preps performed as in Edgcomb et al. 2014 DSR II.&nbsp;</p>
Specified by the Principal Investigator(s)
<p>Quality trimming of the reads (minimum quality score 28, minimum read length 94 bp and no ambiguous nucleotides) as well as read assembly into contigs and mapping of reads to contigs were performed using CLC Genomics Workbench 6.0, CLCBio, Cambridge, MA, USA). The Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline (RAMMCAP) was used to assign contigs to clusters of orthologous gene (COG) families, gene ontologies (GO), and protein families (Pfam). Taxonomic assignments of contigs were made using PhymmBL, incorporating all available fungal and protist genomes in public databases. The total number of annotated reads assigned to different COG families for each dataset was expressed as a percentage of the total annotated reads for each dataset.</p>
<p><strong>BCO-DMO Processing:</strong><br />
original file: EdgcombKM3MetatranscriptomeData.xlsx<br />
- added conventional header with dataset name, PI name, version date<br />
- renamed parameters to BCO-DMO standard<br />
- added cruise id, lat, lon<br />
- added html links to GenBank BioProject</p>
<p>&nbsp;</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:Illumina HiSeq system 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 conductivity-temperature and depth (CTD) and pressure sensors. 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/
Cruise: Urania-2012-09
Urania-2012-09
R/V Urania
vessel
Urania-2012-09
Dr Michail M Yakimov
Italian National Research Council
R/V Urania
vessel