http://lod.bco-dmo.org/id/dataset/828922
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
2020-11-16
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Sample information for 16S and 18S V4 amplicon sequencing of microbial communities in sinking particles and water column samples collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda
2020-11-16
publication
2020-11-16
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2021-11-02
publication
https://doi.org/10.26008/1912/bco-dmo.828922.1
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., Cruz, B. N. (2021) Sample information for 16S and 18S V4 amplicon sequencing of microbial communities in sinking particles and water column samples 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 2020-11-16 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.828922.1 [access date]
Methods and Sampling: <p>Particles were collected on the monthly sampling cruises affiliated with the Bermuda Atlantic Time-series Study (BATS) in fall 2017 (AE1718) and spring 2018 (AE1809) using surface-tethered Particle Interceptor Traps deployed at 150 m, 200 m, and 300 m depths for 72 h (Table 1, Neuer et al., 2021). To collect particles with minimal alteration to their structure, traps containing a polycarbonate jar with 100 mL of 12% polyacrylamide gel were deployed at each depth. Seawater was collected from the surface, deep chlorophyll maximum (DCM) or 20 m above the mixed layer depth (MLD), and at every trap deployment depth using 12 L Niskin bottles mounted on a CTD rosette.<br />
8 particles were categorized and manually picked based on their morphology using characteristics described in the literature (phytodetrital aggregates or fecal aggregates), washed three times using ultrapure nuclease-free distilled water (Invitrogen), and pooled in Eppendorf LoBind tubes stored at -80°C. For DNA analysis of the microbial community in the ambient seawater, 2 L from each sampling depth was filtered onto GF/F and stored in Eppendorf LoBind tubes at -80°C.&nbsp;<br />
DNA from the pooled particles and GF/F were extracted using a DNeasy Blood and Tissue extraction kit, and bacterial and eukaryotic paired-end V4 amplicon sequences were acquired via an Illumina MiSeq platform.</p>
<p>Issues:<br />
As a result of low DNA yield, five samples of pooled aggregates failed PCR amplification attempts using eukaryotic (18S, V4) primers: fall 200m and 300m phytodetrital aggregates, fall 200m fecal aggregates, spring 300m phytodetrital aggregates, and spring 300m fecal aggregates</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
sample_description
depth
particle_trap_deployment_date
particle_trap_recovery_date
seawater_collection_date
latitude
longitude
associated_media
sample_name
bioproject_accession
biosample_accession
SRA_run_ID
library_ID
SRA_study_ID
SRA_title
library_strategy
library_source
library_selection
library_layout
platform
instrument_model
design_description
filetype
filename
filetype2
filename2
Illumina MiSeq
Stemi 2000-C, Carl Zeiss
theme
None, User defined
sample description
depth
date
latitude
longitude
file_name
sample identification
NCBI BioProject accession
NCBI BioSample accession
NCBI SRA run accession (SRR)
NCBI SRA study accession (SRP)
instrument
brief description
datatype
featureType
BCO-DMO Standard Parameters
Automated DNA Sequencer
CTD Sea-Bird SBE 911plus
Microscope - Optical
Niskin bottle
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 Sample information for 16S and 18S V4 amplicon sequencing of microbial communities in sinking particles and water column samples 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/859553.rdf
Name: sample_description
Units: unitless
Description: <p>Sample description</p>
http://lod.bco-dmo.org/id/dataset-parameter/859554.rdf
Name: depth
Units: meters (m)
Description: <p>Nominal depth of sample collection</p>
http://lod.bco-dmo.org/id/dataset-parameter/859555.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/859556.rdf
Name: particle_trap_recovery_date
Units: unitless
Description: <p>Particle trap recovery date (ISO 8601 format YYYY-MM-DD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859557.rdf
Name: seawater_collection_date
Units: unitless
Description: <p>Seawater collection date (ISO 8601 format YYYY-MM-DD)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859558.rdf
Name: latitude
Units: decimal degrees
Description: <p>latitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/859559.rdf
Name: longitude
Units: decimal degrees
Description: <p>longitude</p>
http://lod.bco-dmo.org/id/dataset-parameter/859560.rdf
Name: associated_media
Units: unitless
Description: <p>Filenames of images of the particles pertaining to this sample (list of image names delimited with semicolons)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859561.rdf
Name: sample_name
Units: unitless
Description: <p>sample name</p>
http://lod.bco-dmo.org/id/dataset-parameter/859562.rdf
Name: bioproject_accession
Units: unitless
Description: <p>BioProject accession identifier at the National Center for Biotechnology Information (NCBI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859563.rdf
Name: biosample_accession
Units: unitless
Description: <p>BioSample accession identifier at the National Center for Biotechnology Information (NCBI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859564.rdf
Name: SRA_run_ID
Units: unitless
Description: <p>Sequence Read Archive (SRA) Run identifier at the National Center for Biotechnology Information (NCBI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859565.rdf
Name: library_ID
Units: unitless
Description: <p>library identifier</p>
http://lod.bco-dmo.org/id/dataset-parameter/859566.rdf
Name: SRA_study_ID
Units: unitless
Description: <p>Study identifier in the Sequence Read Archive (SRA) at the National Center for Biotechnology Information (NCBI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859567.rdf
Name: SRA_title
Units: unitless
Description: <p>Descriptive title of Sequence Read Archive (SRA) accession at the National Center for Biotechnology Information (NCBI)</p>
http://lod.bco-dmo.org/id/dataset-parameter/859568.rdf
Name: library_strategy
Units: unitless
Description: <p>Library strategy ("AMPLICON")</p>
http://lod.bco-dmo.org/id/dataset-parameter/859569.rdf
Name: library_source
Units: unitless
Description: <p>Library source ("GENOMIC")</p>
http://lod.bco-dmo.org/id/dataset-parameter/859570.rdf
Name: library_selection
Units: unitless
Description: <p>Library selection ("PCR")</p>
http://lod.bco-dmo.org/id/dataset-parameter/859571.rdf
Name: library_layout
Units: unitless
Description: <p>Library layout ("paired")</p>
http://lod.bco-dmo.org/id/dataset-parameter/859572.rdf
Name: platform
Units: unitless
Description: <p>Sequencing platform ("Illumina")</p>
http://lod.bco-dmo.org/id/dataset-parameter/859573.rdf
Name: instrument_model
Units: unitless
Description: <p>Sequencing instrument model ("Illumina MiSeq")</p>
http://lod.bco-dmo.org/id/dataset-parameter/859574.rdf
Name: design_description
Units: unitless
Description: <p>Sequencing design description</p>
http://lod.bco-dmo.org/id/dataset-parameter/859575.rdf
Name: filetype
Units: unitless
Description: <p>Type of file 1 at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/859576.rdf
Name: filename
Units: unitless
Description: <p>Name of file 1 at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/859577.rdf
Name: filetype2
Units: unitless
Description: <p>Type of file 2 at NCBI</p>
http://lod.bco-dmo.org/id/dataset-parameter/859578.rdf
Name: filename2
Units: unitless
Description: <p>Name of file 2 at NCBI</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
23591
https://darchive.mblwhoilibrary.org/bitstream/1912/27682/1/dataset-828922_sinking-particle-sample-information-bats-microbial-communities__v1.tsv
download
https://doi.org/10.26008/1912/bco-dmo.828922.1
download
onLine
dataset
<p>Particles were collected on the monthly sampling cruises affiliated with the Bermuda Atlantic Time-series Study (BATS) in fall 2017 (AE1718) and spring 2018 (AE1809) using surface-tethered Particle Interceptor Traps deployed at 150 m, 200 m, and 300 m depths for 72 h (Table 1, Neuer et al., 2021). To collect particles with minimal alteration to their structure, traps containing a polycarbonate jar with 100 mL of 12% polyacrylamide gel were deployed at each depth. Seawater was collected from the surface, deep chlorophyll maximum (DCM) or 20 m above the mixed layer depth (MLD), and at every trap deployment depth using 12 L Niskin bottles mounted on a CTD rosette.<br />
8 particles were categorized and manually picked based on their morphology using characteristics described in the literature (phytodetrital aggregates or fecal aggregates), washed three times using ultrapure nuclease-free distilled water (Invitrogen), and pooled in Eppendorf LoBind tubes stored at -80°C. For DNA analysis of the microbial community in the ambient seawater, 2 L from each sampling depth was filtered onto GF/F and stored in Eppendorf LoBind tubes at -80°C.&nbsp;<br />
DNA from the pooled particles and GF/F were extracted using a DNeasy Blood and Tissue extraction kit, and bacterial and eukaryotic paired-end V4 amplicon sequences were acquired via an Illumina MiSeq platform.</p>
<p>Issues:<br />
As a result of low DNA yield, five samples of pooled aggregates failed PCR amplification attempts using eukaryotic (18S, V4) primers: fall 200m and 300m phytodetrital aggregates, fall 200m fecal aggregates, spring 300m phytodetrital aggregates, and spring 300m fecal aggregates</p>
Specified by the Principal Investigator(s)
<p>Bioinformatic analyses were performed using QIIME2 v2019.1. PhiX reads and chimeric sequences were removed and remaining reads were assembled, demultiplexed, and trimmed to salvage reads with a median quality score above 25 using DADA2 within the QIIME2 pipeline.<br />
<br />
BCO-DMO data manager processing notes:</p>
<div>* converted lat and lon from degrees north and east to decimal degrees.</div>
<div>* replaced line returns separating image names within values for "associated_media" column to semicolons.&nbsp; Replacement made to support interoperable file formats.<br />
* removed direct HTML links to accession pages at NCBI, these are accessible with the accession numbers in the dataset.</div>
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
Illumina MiSeq
Illumina MiSeq
PI Supplied Instrument Name: Illumina MiSeq 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.
PI Supplied Instrument Name: PI Supplied Instrument Description:CTD Rosette with 12L Niskin bottles used to collect seawater samples:
12L Niskin bottles affixed to a SBE9/11+ CTD Rosette, Sea-Bird Electronics, Inc. Instrument Name: CTD Sea-Bird SBE 911plus Instrument Short Name:CTD SBE 911plus Instrument Description: The Sea-Bird SBE 911 plus is a type of CTD instrument package for continuous measurement of conductivity, temperature and pressure. The SBE 911 plus includes the SBE 9plus Underwater Unit and the SBE 11plus Deck Unit (for real-time readout using conductive wire) for deployment from a vessel. The combination of the SBE 9 plus and SBE 11 plus is called a SBE 911 plus. The SBE 9 plus uses Sea-Bird's standard modular temperature and conductivity sensors (SBE 3 plus and SBE 4). The SBE 9 plus CTD can be configured with up to eight auxiliary sensors to measure other parameters including dissolved oxygen, pH, turbidity, fluorescence, light (PAR), light transmission, etc.). more information from Sea-Bird Electronics Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/
Stemi 2000-C, Carl Zeiss
Stemi 2000-C, Carl Zeiss
PI Supplied Instrument Name: Stemi 2000-C, Carl Zeiss PI Supplied Instrument Description:Stemi 2000-C, Carl Zeiss
3.2MP Digital USB Microscope Camera, OMAX Microscope 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: 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/
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