http://lod.bco-dmo.org/id/dataset/855320
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
2021-07-08
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Images corresponding to some of the samples that underwent 16S and 18S V4 amplicon sequencing of microbial communities in sinking particles collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda
2021-07-08
publication
2021-07-08
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-11-02
publication
https://doi.org/10.26008/1912/bco-dmo.855320.1
Susanne Neuer
Arizona State University
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: Neuer, S. (2021) Images corresponding to some of the samples that underwent 16S and 18S V4 amplicon sequencing of microbial communities in sinking particles collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2021-07-08 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.855320.1 [access date]
Methods and Sampling: <p><strong>Methodology:</strong><br />
Particles to be subjected to prokaryotic and eukaryotic microbial community analyses were imaged whilst embedded within polyacrylamide gels. Images were taken at various magnifications and calibrated using a 1.0 mm object micrometer slide. Particles were subsequently picked, pooled, and subjected to DNA extraction and microbial community analyses as outlined in the Methods text in&nbsp;Neuer et al. (2021).<br />
<br />
Although 8 particles were pooled per sample, a limited number of particles were imaged. Magnification metadata is not available for sample PA_150m_Fall.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1658527 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1658527
completed
Susanne Neuer
Arizona State University
480-727-7254
College of Liberal Arts and Sciences School of Life Sciences 427 East Tyler Mall
Tempe
AZ
85287-4501
USA
susanne.neuer@asu.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
media
sample_name
depth
latitude
longitude
particle_trap_deployment_date
particle_trap_recovery_date
Microscope color camera: OMAX Microscopy 3.2MP
Stereomicroscope: Zeiss Stemi 2000-C (Carl Zeiss Microscopy, LLC)
theme
None, User defined
file_name
sample identification
depth
latitude
longitude
date
featureType
BCO-DMO Standard Parameters
Camera
Microscope - Optical
instrument
BCO-DMO Standard Instruments
AE1718
AE1809
service
Deployment Activity
Bermuda
Sargasso Sea, Bermuda Atlantic Time-series Study site: 31 N 64 W
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.
Aggregation of Marine Picoplankton
https://osprey.bco-dmo.org/project/710239
Aggregation of Marine Picoplankton
<p>NSF abstract:</p>
<p>Marine phytoplankton are microscopic algae that live in the sunlit zone of the ocean. They play an important role in the uptake of carbon dioxide from the atmosphere through photosynthesis, similar to what plants do on land, and are the basis of the marine food web. However, instead of storing this organic carbon in leaf tissue and roots, marine phytoplankton are grazed by planktonic animals, or die and subsequently sink out of the sunlit zone in the form of aggregates, also called "Marine Snow". These particles not only export the organic carbon contained in their cells to the deep ocean, but also serve as food for animals and bacteria that live in the deep. A considerable portion of these phytoplankton are extremely small, among the tiniest of all organisms known. These extremely small cells have not been thought to play an important role in the formation and sinking of marine snow; however, recent findings challenge this view. This project will investigate how the smallest of these phytoplankton contribute to the rain of sinking particles from the sunlit surface to the deep ocean. This research is important because, in some of the largest expanses of the open oceans, these minute cells dominate the phytoplankton community, and larger plankton organisms are very sparse. The project, through a combination of work in the laboratory and at a field station, will shed light on how these tiny phytoplankton cells make aggregates, which ultimately enable them to sink as "Marine Snow". The project also provides unique opportunities for undergraduate students at Arizona State University, a land-locked public university, to gain experience in working with marine research. The project will serve to educate one PhD student, one MS student in an accelerated BS-MS program, and 8-10 undergraduate students/semester in a unique, inquiry based learning effort termed Microbial EducatioN Training and OutReach (MENTOR). The undergraduate students will also participate in Arizona State University (ASU)'s School of Life Sciences, Undergraduate Research Program (SOLUR), which seeks to increase the participation of minorities in science. They will also contribute towards developing web and classroom materials, based on this project, which will then be distributed through a partnership with the award-winning ASU-sponsored Ask A Biologist K-12 web site.</p>
<p>The oceanic "biological carbon pump", the photosynthetically mediated transformation of dissolved inorganic carbon into particulate and dissolved organic carbon and its subsequent export to deep water, functions as a significant driver of atmospheric carbon uptake by the oceans. The traditional view of the biological carbon pump in the ocean is that of sinking of large aggregates (marine snow) or fecal pellets, which are made up of large, mineral ballasted cells of phytoplankton. However, recent evidence, stemming from in situ investigations of particulate matter, trap studies and modelling studies, have shown that micron-sized phytoplankton such as picocyanobacteria as well as picoeukaryotes can contribute significantly to the sinking of particulate matter. The specific mechanisms behind the sinking of these micrometer sized cells remain elusive as the cells are too small to sink on their own, and mesozooplankton is likely unable to ingest single cells. Intriguingly, recent research by the investigators has shown that the ubiquitous picocyanobacteria Synechococcus are able to form aggregates and sink at velocities comparable to those of marine snow. They found that the matrix of the Synechococcus aggregates was made of Transparent Exopolymeric Particles (TEP), and that TEP production was enhanced under nutrient limited culture conditions. Interaction with clays and presence of heterotrophic bacteria also enhanced aggregation and sinking velocity. This study aims to further investigate aggregation of other common picoplankton in the laboratory and aggregation occurring in natural settings at an oligotrophic open ocean site, the Bermuda Atlantic Time-series Site (BATS). Ultimately, this project will increase and refine our understanding of the role of the smallest phytoplankton in aggregation and sinking - information vital to understanding carbon cycling processes in the oceans.</p>
Marine Plankton Aggregation
largerWorkCitation
project
eng; USA
oceans
Bermuda; Sargasso Sea, Bermuda Atlantic Time-series Study site: 31 N 64 W
-64.57
-64.42
31.57
31.97
2017-09-12
2018-03-15
Bermuda Atlantic Time-Series station
0
BCO-DMO catalogue of parameters from Images corresponding to some of the samples that underwent 16S and 18S V4 amplicon sequencing of microbial communities in sinking particles collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda
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/859512.rdf
Name: media
Units: unitless
Description: <p>Media. List of imagenames for the sample. List delimiter is a semicolon.</p>
http://lod.bco-dmo.org/id/dataset-parameter/859513.rdf
Name: sample_name
Units: unitless
Description: <p>Sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/859514.rdf
Name: depth
Units: meters (m)
Description: <p>Sample depth</p>
http://lod.bco-dmo.org/id/dataset-parameter/859515.rdf
Name: latitude
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/859516.rdf
Name: longitude
Units: decimal degrees
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/859517.rdf
Name: particle_trap_deployment_date
Units: unitless
Description: <p>Particle trap deployment date (ISO 8601 format YYYY-MM-DD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859518.rdf
Name: particle_trap_recovery_date
Units: unitless
Description: <p>Particle trap recovery date (ISO 8601 format YYYY-MM-DD)</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
275212094
https://darchive.mblwhoilibrary.org/bitstream/1912/27681/1/sinking_particle_images.zip
download
1643
https://darchive.mblwhoilibrary.org/bitstream/1912/27681/2/dataset-855320_images-sinking-particles-bats-microbial-communities__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.855320.1
download
onLine
dataset
<p><strong>Methodology:</strong><br />
Particles to be subjected to prokaryotic and eukaryotic microbial community analyses were imaged whilst embedded within polyacrylamide gels. Images were taken at various magnifications and calibrated using a 1.0 mm object micrometer slide. Particles were subsequently picked, pooled, and subjected to DNA extraction and microbial community analyses as outlined in the Methods text in&nbsp;Neuer et al. (2021).<br />
<br />
Although 8 particles were pooled per sample, a limited number of particles were imaged. Magnification metadata is not available for sample PA_150m_Fall.</p>
Specified by the Principal Investigator(s)
<p>Images were taken using ToupView (version released 2020-12-21), as well as cropped and calibrated with the addition of a scale bar using ImageJ (version 153).<br />
<br />
BCO-DMO data manager processing notes:<br />
* converted lat and lon from degrees north and east to decimal degrees.<br />
* replaced line returns&nbsp;separating image names within values for "media" column to&nbsp;semicolons.&nbsp; Replacement made&nbsp;to support interoperable file formats.</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
Microscope color camera: OMAX Microscopy 3.2MP
Microscope color camera: OMAX Microscopy 3.2MP
PI Supplied Instrument Name: Microscope color camera: OMAX Microscopy 3.2MP 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/
Stereomicroscope: Zeiss Stemi 2000-C (Carl Zeiss Microscopy, LLC)
Stereomicroscope: Zeiss Stemi 2000-C (Carl Zeiss Microscopy, LLC)
PI Supplied Instrument Name: Stereomicroscope: Zeiss Stemi 2000-C (Carl Zeiss Microscopy, LLC) 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/
Cruise: AE1718
AE1718
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1718
Rodney J. Johnson
Cruise: AE1809
AE1809
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel
AE1809
Rodney J. Johnson
Bermuda Institute of Ocean Sciences
R/V Atlantic Explorer
Community Standard Description
International Council for the Exploration of the Sea
R/V Atlantic Explorer
vessel