Dataset: Images of sinking particles in BATS microbial communities

Name: 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
Published: 2021-07-08
Keywords: oceans

Cite This Dataset

DOI:10.26008/1912/bco-dmo.855320.1

Spatial Extent: N:31.97 E:-64.42 S:31.57 W:-64.57

Temporal Extent: 2017-09-12 - 2018-03-15

Project:

Aggregation of Marine Picoplankton (Marine Plankton Aggregation)

Principal Investigator:

Susanne Neuer (Arizona State University, ASU)

Contact:

Bianca N. Cruz (Arizona State University, ASU)

BCO-DMO Data Manager:

Amber D. York (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2021-07-08

Restricted:

Validated:

Yes

Current State:

Final no updates expected

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

Abstract:

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Archival Copy

Version Date	Archive	Persistent Identifier	Date Assigned
2021-07-08	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.855320.1	2021-11-02

Methods & Sampling

Methodology:
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 Neuer et al. (2021).

Although 8 particles were pooled per sample, a limited number of particles were imaged. Magnification metadata is not available for sample PA_150m_Fall.

Data Processing Description

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).

BCO-DMO data manager processing notes:
* converted lat and lon from degrees north and east to decimal degrees.
* replaced line returns separating image names within values for "media" column to semicolons. Replacement made to support interoperable file formats.

Data Files

File
image_metadata.csv (Comma Separated Values (.csv), 1.60 KB) MD5:3c5a9f04b4deb130d1addafb9d5a5a0f Primary data file for dataset ID 855320
Sinking Particle Images filename: sinking_particle_images.zip (ZIP Archive (ZIP), 262.46 MB) MD5:b42f05fb41bf69350020f41bae5c305d Images of sinking particles collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1658527

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
AE1718	BATS 10339 HS 61318	2017-09-11	R/V Atlantic Explorer	Rodney J. Johnson (Chief Scientist)	data info
AE1809	BATS20345	2018-03-12	R/V Atlantic Explorer	Rodney J. Johnson (Chief Scientist) Bianca N. Cruz (Contact)	data info

Instruments

Camera

Supplied Name: Microscope color camera: OMAX Microscopy 3.2MP

Supplied Description:

Instrument Type

Generic Name: Camera

Acronym: camera

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/311/

Generic Description:

All types of photographic equipment including stills, video, film and digital systems.

Microscope - Optical

Supplied Name: Stereomicroscope: Zeiss Stemi 2000-C (Carl Zeiss Microscopy, LLC)

Supplied Description:

Instrument Type

Generic Name: Microscope - Optical

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB05/

Generic 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".

Parameters

Date and time formats are described in python strftime() syntax.

Supplied Name	Supplied description	Supplied Units	Standard Name
media	Media. List of imagenames for the sample. List delimiter is a semicolon.	unitless	file_name
sample_name	Sample name	unitless	sample
depth	Sample depth	meters (m)	depth
latitude	latitude	decimal degrees	lat
longitude	longitude	decimal degrees	lon
particle_trap_deployment_date	Particle trap deployment date (ISO 8601 format YYYY-MM-DD) Format: %Y-%m-%d	unitless	date
particle_trap_recovery_date	Particle trap recovery date (ISO 8601 format YYYY-MM-DD) Format: %Y-%m-%d	unitless	date

Status message

Database

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Dataset: Images of sinking particles in BATS microbial communities