http://lod.bco-dmo.org/id/dataset/749412
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
2018-11-07
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017
2018-11-07
publication
2018-11-07
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2020-07-15
publication
https://doi.org/10.26008/1912/bco-dmo.749412.1
Colleen Durkin
Moss Landing Marine Laboratories
principalInvestigator
Margaret L. Estapa
Skidmore College
principalInvestigator
Melissa Omand
University of Rhode Island
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: Durkin, C., Estapa, M., Omand, M. (2020) Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2018-11-07 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.749412.1 [access date]
Images of particles collected in sediment traps for quantitative analysis Dataset Description: <p>Samples were collected at the New England shelf break aboard the R/V Endeavor on 3-7 November 2017 (EN572) and 13-18 June 2016 (EN581) and on a transit between Honolulu, Hawaii and Portland, Oregon aboard the R/V Falkor between 24 January-20 February, 2017 (FK170124).&nbsp; Sediment trap collector tubes were deployed on various platform designs, including a neutrally-buoyant sediment trap (NBST), a surface tethered sediment trap (STST), and a Wire Walker (WW) trap.&nbsp; &nbsp;The location, time, duration, depth, and collection types from each trap deployment are listed in Trap Deployment Log.</p> Methods and Sampling: <p>The NBST carried 4 collection tubes with a diameter of 12 cm (Valdes and Price 2000). The STST included 5 frames (KC Denmark) clipped onto a surface-tethered, free drifting array line at increasing depths and each frame carried 4, 7 cm diameter collection tubes. The WW trap consisted of one, 4-tube trap frame (KC Denmark) tethered by a bungee below the profiling component of the WW array.&nbsp; To prepare tubes for deployment, seawater was collected from a depth of 150 m using a CTD rosette and pumped through a 1 μm filter cartridge. Trap tubes were filled with filtered water overlying a jar containing a polyacrylamide gel layer (Durkin et al. 2015). Trap platforms were deployed for between 1 day and 3.5 days (see Trap Deployment Log).&nbsp; Identically prepared tubes were incubated in parallel onboard the ship to serve as process blanks.</p>
<p>Upon recovery, collection tubes were allowed to settle for at least 1 hour before the overlying water was siphoned off.&nbsp; Jars containing polyacrylamide gel were removed from trap tubes and the remaining overlying water was carefully pipetted off the gel.&nbsp; Gels were stored at 4 degrees C and imaged within the following 2 days before being stored at -80 degrees C.&nbsp;</p>
<p>Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment.&nbsp; Particles collected in gel layers during EN572 and EN581 were imaged under brightfield illumination.&nbsp; Particles collected in gel layers during FK170124 were imaged under both brightfield and oblique illumination, producing two separate sets of images for each sample.&nbsp; EN572 gel layers were imaged with a transparent grid to assist in tracking gel location during imaging. The grid was not used when imaging samples collected during subsequent cruises because the pronounced grid lines complicated image analysis. All gel layers were imaged at 4 increasing magnifications, though the combination of magnifications varied by cruise: at 7x, 20x, 40x, and 115x for EN572 samples, at 7x, 20x, 40x, and 80x for EN581 samples, and at 7x, 20x, 50x, and 115x for FK170124 samples. At magnifications greater than 7x, multiple focal planes within a field of view were imaged to capture particles embedded in different depths of the gel layer.&nbsp; The number of focal planes imaged was consistent across all fields of view for a given magnification but varied across cruises due to variation in gel thickness and particle types present. To determine whether measured particle properties changed if gel layers are frozen, samples collected during FK170124 were thawed after being stored for approximately 1 year at -80&nbsp; degrees C and imaged again under both brightfield and oblique illumination.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1703664 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1703664
completed
Colleen Durkin
Moss Landing Marine Laboratories
831-771-4431
8272 Moss Landing Road
Moss Landing
CA
95039-9647
USA
cdurkin@mbari.org
pointOfContact
Margaret L. Estapa
Skidmore College
207-581-5176
193 Clarks Cove Road
Walpole
ME
04573
United States
margaret.estapa@maine.edu
pointOfContact
Melissa Omand
University of Rhode Island
401-874-6610
215 S Ferry Rd
Narrangsett
RI
02882-1197
USA
momand@uri.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
Cruise
Trap_Platform
Additional_Trap_Label
Depth
Deployment_Duration_days
Deploy_Latitude
Deploy_Longitude
Deploy_Date_UTC
Deploy_Time_UTC
Recover_Latitude
Recover_Longitude
Recover_Date_UTC
Recover_Time_UTC
deploy_date_time
recover_date_time
Luminera Infinity 2 microscope camera
Olympus SZX16 Stereomicroscope
theme
None, User defined
Cruise identfier
platform
No BCO-DMO term
depth trap
duration
latitude
longitude
date
time of day
ISO_DateTime_UTC
featureType
BCO-DMO Standard Parameters
Camera
Microscope - Optical
Sediment Trap
instrument
BCO-DMO Standard Instruments
FK170124
EN572
EN581
service
Deployment Activity
North Pacific Ocean
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.
Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump
https://osprey.bco-dmo.org/project/675296
Collaborative Research: EAGER: Particle-specific DNA sequencing to directly observe ecological mechanisms of the biological pump
<p><em>NSF Award Abstract:</em><br />
Carbon is fixed into organic matter by phytoplankton growing in the surface ocean, and is naturally sequestered in the ocean interior when particles and organisms sink: a process called the "biological pump." Because of its recognized influence on the global carbon cycle, ocean scientists have studied the biological pump for decades. However, we still do not have a sufficient understanding of the underlying processes to accurately quantify and predict carbon cycling. Much of this uncertainty stems from an inability to directly link specific plankton in the surface ocean with the types of particles sinking out of the surface ocean. To address this missing link in biological pump research, this work will directly observe how plankton are transported out of the surface ocean using novel, particle-specific observational approaches embedded within an interdisciplinary field program that will finely resolve upper ocean plankton groups and the resulting amount of sinking carbon across space and in time. The genetic identity of organisms within different types of sinking particles will be determined by sequencing the genetic contents of individually collected particles. This new application of a molecular method will definitively link surface plankton with sinking particles at five locations across the Pacific Ocean. This work has the potential to transform our understanding of the biological pump by identifying previously unknown links between surface ecosystems and sinking carbon particles. Because this work is embedded within an interdisciplinary field program, including biogeochemical modelers and remote sensing scientists, these data will feed directly into new models of the biological pump, improving our ability to quantify and predict carbon uptake by the ocean. This project will train 1 graduate student and at least 2 undergraduate researchers. Findings will be communicated to the non-scientific public through blogs, videos, and the public communication channels of participating institutions.</p>
<p>Accurate prediction of the global carbon cycle requires an understanding of the specific processes that link surface plankton communities and sinking particulate carbon flux (export) out of the surface ocean, but current methodological paradigms in biological pump research do not directly observe these processes. This project will comprehensively determine who is exported from the surface ocean and how using new, particle-resolving optical and molecular techniques embedded within a sampling scheme that characterizes export events at high time and space resolution. The investigation suggests that different plankton types in the surface waters are transported out of the surface ocean by distinct export pathways, and that an understanding of these connections is critical knowledge for global carbon cycle modeling. If successful, this work has the potential to transform our conceptual understanding of the biological pump by directly identifying mechanisms that link surface plankton with particle export, without relying on bulk sampling schemes and large-scale correlation analysis. Particle export environments will be studied at five open ocean locations during a cruise from Hawaii to Seattle in January-February 2017. The surface plankton communities will be characterized by a combination of satellite observations, sensors attached to a free-drifting, continuously profiling WireWalker, an in situ holographic camera, microscopy, and by sequencing 18S and 16S rRNA gene fragments. Exported particles will simultaneously be captured by various specialized sediment traps and their characteristics will be directly related to their sources in the surface community by identifying the genetic contents of individual particle types. Individual particles will be isolated from gel layers and the 16S and 18S rRNA gene fragments will be amplified and sequenced. This work would, for the first time, combine molecular approaches with particle-specific observations to enable simultaneous identification of both which organisms are exported and the processes responsible for their export.</p>
EAGER DNA BioPump
largerWorkCitation
project
eng; USA
oceans
North Pacific Ocean
-151.779
-70.8119
21.52
39.94
2016-06-13
2017-11-07
Eastern Pacific
0
BCO-DMO catalogue of parameters from Images of particles collected in sediment traps for quantitative analysis from multiple platforms from 2016-2017
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/818524.rdf
Name: Cruise
Units: unitless
Description: <p>Cruise identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/818525.rdf
Name: Trap_Platform
Units: unitless
Description: <p>trap identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/818526.rdf
Name: Additional_Trap_Label
Units: unitless
Description: <p>additional trap label</p>
http://lod.bco-dmo.org/id/dataset-parameter/818527.rdf
Name: Depth
Units: meters
Description: <p>depth of trap</p>
http://lod.bco-dmo.org/id/dataset-parameter/818528.rdf
Name: Deployment_Duration_days
Units: days
Description: <p>deployment duration</p>
http://lod.bco-dmo.org/id/dataset-parameter/818529.rdf
Name: Deploy_Latitude
Units: decimal degrees
Description: <p>deployment latitude with positive values indicating North</p>
http://lod.bco-dmo.org/id/dataset-parameter/818530.rdf
Name: Deploy_Longitude
Units: decimal degrees
Description: <p>deployment longitude with negative values indicating West</p>
http://lod.bco-dmo.org/id/dataset-parameter/818531.rdf
Name: Deploy_Date_UTC
Units: unitless
Description: <p>date of deployment in UTC following ISO-8601 convention</p>
http://lod.bco-dmo.org/id/dataset-parameter/818532.rdf
Name: Deploy_Time_UTC
Units: unitless
Description: <p>Time of deployment in UTC following ISO-8601 convention</p>
http://lod.bco-dmo.org/id/dataset-parameter/818533.rdf
Name: Recover_Latitude
Units: decimal degrees
Description: <p>recover latitude with positive values indicating North</p>
http://lod.bco-dmo.org/id/dataset-parameter/818534.rdf
Name: Recover_Longitude
Units: decimal degrees
Description: <p>recover longitude with negative values indicating West</p>
http://lod.bco-dmo.org/id/dataset-parameter/818535.rdf
Name: Recover_Date_UTC
Units: unitless
Description: <p>date of recover in UTC following ISO-8601 convention</p>
http://lod.bco-dmo.org/id/dataset-parameter/818536.rdf
Name: Recover_Time_UTC
Units: unitless
Description: <p>Time of recover in UTC following ISO-8601 convention</p>
http://lod.bco-dmo.org/id/dataset-parameter/818537.rdf
Name: deploy_date_time
Units: yyyy-MM-dd'T'HH:mm
Description: <p>deployment date and time following ISO-8901 convention</p>
http://lod.bco-dmo.org/id/dataset-parameter/818538.rdf
Name: recover_date_time
Units: unitless
Description: <p>recover date and time following ISO-8901 convention</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
23497472644
https://darchive.mblwhoilibrary.org/bitstream/1912/25971/1/FK170124_Gel_Images_after_freezing.tar.gz
download
35782978992
https://darchive.mblwhoilibrary.org/bitstream/1912/25971/2/FK170124_Gel_Images.tar.gz
download
79450472
https://darchive.mblwhoilibrary.org/bitstream/1912/25971/3/EN581_Gel_Images.tar.gz
download
144735727
https://darchive.mblwhoilibrary.org/bitstream/1912/25971/4/EN572_Gel_Images.tar.gz
download
2546
https://darchive.mblwhoilibrary.org/bitstream/1912/25971/5/dataset-749412_geltrap-micrographs__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.749412.1
download
onLine
dataset
<p>The NBST carried 4 collection tubes with a diameter of 12 cm (Valdes and Price 2000). The STST included 5 frames (KC Denmark) clipped onto a surface-tethered, free drifting array line at increasing depths and each frame carried 4, 7 cm diameter collection tubes. The WW trap consisted of one, 4-tube trap frame (KC Denmark) tethered by a bungee below the profiling component of the WW array.&nbsp; To prepare tubes for deployment, seawater was collected from a depth of 150 m using a CTD rosette and pumped through a 1 μm filter cartridge. Trap tubes were filled with filtered water overlying a jar containing a polyacrylamide gel layer (Durkin et al. 2015). Trap platforms were deployed for between 1 day and 3.5 days (see Trap Deployment Log).&nbsp; Identically prepared tubes were incubated in parallel onboard the ship to serve as process blanks.</p>
<p>Upon recovery, collection tubes were allowed to settle for at least 1 hour before the overlying water was siphoned off.&nbsp; Jars containing polyacrylamide gel were removed from trap tubes and the remaining overlying water was carefully pipetted off the gel.&nbsp; Gels were stored at 4 degrees C and imaged within the following 2 days before being stored at -80 degrees C.&nbsp;</p>
<p>Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment.&nbsp; Particles collected in gel layers during EN572 and EN581 were imaged under brightfield illumination.&nbsp; Particles collected in gel layers during FK170124 were imaged under both brightfield and oblique illumination, producing two separate sets of images for each sample.&nbsp; EN572 gel layers were imaged with a transparent grid to assist in tracking gel location during imaging. The grid was not used when imaging samples collected during subsequent cruises because the pronounced grid lines complicated image analysis. All gel layers were imaged at 4 increasing magnifications, though the combination of magnifications varied by cruise: at 7x, 20x, 40x, and 115x for EN572 samples, at 7x, 20x, 40x, and 80x for EN581 samples, and at 7x, 20x, 50x, and 115x for FK170124 samples. At magnifications greater than 7x, multiple focal planes within a field of view were imaged to capture particles embedded in different depths of the gel layer.&nbsp; The number of focal planes imaged was consistent across all fields of view for a given magnification but varied across cruises due to variation in gel thickness and particle types present. To determine whether measured particle properties changed if gel layers are frozen, samples collected during FK170124 were thawed after being stored for approximately 1 year at -80&nbsp; degrees C and imaged again under both brightfield and oblique illumination.</p>
Specified by the Principal Investigator(s)
<p>Infinity Capture for Mac</p>
<p>BCO-DMO Processing Notes:</p>
<ul>
<li>images have been zipped into packages.</li>
</ul>
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
Luminera Infinity 2 microscope camera
Luminera Infinity 2 microscope camera
PI Supplied Instrument Name: Luminera Infinity 2 microscope camera PI Supplied Instrument Description:Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) with either a Luminera Infinity 2 (FK170124) or an Allied Vision Technologies StingRay (EN572 and EN581) camera attachment. Instrument Name: Camera Instrument Short Name:camera Instrument Description: All types of photographic equipment including stills, video, film and digital systems. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/311/
Olympus SZX16 Stereomicroscope
Olympus SZX16 Stereomicroscope
PI Supplied Instrument Name: Olympus SZX16 Stereomicroscope PI Supplied Instrument Description:Polyacrylamide gel layers were imaged on a dissecting microscope (Olympus SZX16) Instrument Name: Microscope - Optical Instrument Short Name: Instrument Description: Instruments that generate enlarged images of samples using the phenomena of reflection and absorption of visible light. Includes conventional and inverted instruments. Also called a "light microscope". Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/
PI Supplied Instrument Name: PI Supplied Instrument Description:Sediment trap collector tubes were deployed on various platform designs, including a neutrally-buoyant sediment trap (NBST), a surface tethered sediment trap (STST), and a Wire Walker (WW) trap. Instrument Name: Sediment Trap Instrument Short Name:Sediment Trap Instrument Description: Sediment traps are specially designed containers deployed in the water column for periods of time to collect particles from the water column falling toward the sea floor. In general a sediment trap has a jar at the bottom to collect the sample and a broad funnel-shaped opening at the top with baffles to keep out very large objects and help prevent the funnel from clogging. This designation is used when the specific type of sediment trap was not specified by the contributing investigator. Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/33/
Cruise: FK170124
FK170124
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
FK170124
Ivona Cetinic
National Aeronautics and Space Administration
https://datadocs.bco-dmo.org/docs/302/EAGER_DNA_BioPump/data_docs/DurkinOmandEstapa_Cruise_report.pdf
Report describing FK170124
Cruise: EN572
EN572
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN572
Melissa Omand
University of Rhode Island
Cruise: EN581
EN581
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel
EN581
Susanne Menden-Deuer
University of Rhode Island
R/V Falkor
Community Standard Description
International Council for the Exploration of the Sea
R/V Falkor
vessel
R/V Endeavor
Community Standard Description
International Council for the Exploration of the Sea
R/V Endeavor
vessel