Dataset: Microorganisms associated with pyrosomes

Name: High-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry of pyrosome-associated microorganisms compared to seawater sampled during a Pyrosoma atlanticum bloom in the Northern California Current System in July 2018.
Published: 2024-04-26
Keywords: pyrosomes, microorganisms, Synechococcus, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:44.652141 E:-124.589313 S:44.651756 W:-125.117573

Northern California Current System

Temporal Extent: 2018-07-09 - 2018-07-11

Project:

Collaborative Research: Comparative feeding by gelatinous grazers on microbial prey (Gelatinous Grazer Feeding)

Co-Principal Investigator:

Anne W. Thompson (Portland State University, PSU)

Contact:

Anne W. Thompson (Portland State University, PSU)

BCO-DMO Data Manager:

Karen Soenen (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

Version Date:

2024-04-26

Restricted:

Validated:

Current State:

Data not available

High-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry of pyrosome-associated microorganisms compared to seawater sampled during a Pyrosoma atlanticum bloom in the Northern California Current System in July 2018.

Abstract:

Pyrosomes are widely distributed pelagic tunicates that have the potential to reshape marine food webs when they bloom. However, their grazing preferences and interactions with the background microbial community are poorly understood. The diversity, relative abundance, and taxonomy of pyrosome-associated microorganisms were compared to seawater during a Pyrosoma atlanticum bloom in the Northern California Current System using high-throughput sequencing of the 16S rRNA gene, microscopy, and flow cytometry.

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Methods & Sampling

Pyrosomes and seawater were collected from the NCC, off the Oregon Coast, in July 2018, near the peak of a multiyear bloom of P. atlanticum. Samples were collected from the R/V Sally Ride (SR1810) along the Newport Hydrographic Line. Station D5 (Cast 20, 44.652141N; 125.117573W) was sampled on July 9, 2018 in the presence of a strong temperature gradient in the top 20 meters and a chlorophyll peak at 17 meters. Station D3 (Cast 26, 44.651756N; 124.589313W) was sampled on July 11, 2018 in the presence of a mixed layer depth of 15 meters and a chlorophyll peak at the base of the mixed layer.

Data Processing Description

DNA extraction was done using the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. Pyrosome tissue was ground with a sterile pestle (Axygen, Tewksbury, USA) for 3 minutes prior to extraction. Seawater and pyrosome samples were lysed by bead beating with 0.55 mm and 0.25 mm sterile glass beads at 30 Hz for 2 minutes after addition of lysis buffer, freeze-fractured 3 times, incubated with Proteinase K (VWR Chemicals, Solon, OH, USA) at 20 mg/mL for 1 hour at 55 ˚C, and incubated with RNase A at 100 mg/mL for 10 minutes at 65 ˚C. To minimize amplification of eukaryotic host DNA, the primer pair 515F‐Y/806R was chosen to amplify the 16S rRNA V4 hypervariable region with conditions as published. Reactions were performed with 0.5-2 ng of DNA using the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA, USA). The Agilent High Sensitivity Kit in the Bioanalyzer (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate reactions from each sample were pooled and paired-end sequenced with Illumina MiSeq v.3 (Illumina, San Diego, USA).

BCO-DMO Processing

* Converted NCBI biosample file to flat file format
* Merged biosample and SRA run file
* Removed no data columns from files
* Adjusted parameters to comply with databaser requirements (spaces, characters, etc)
* Converted date to ISO format
* Split lat/lon column into their own columns

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1851412

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
SR1810	S18	2018-07-06	R/V Sally Ride	Robert K. Cowen (Chief Scientist)	data info

Instruments

CTD - profiler

Supplied Name: Niskin CTD Rosette for seawater

Supplied Description:

Instrument Type

Generic Name: CTD - profiler

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/130/

Generic Description:

The Conductivity, Temperature, Depth (CTD) unit is an integrated instrument package designed to measure the conductivity, temperature, and pressure (depth) of the water column. The instrument is lowered via cable through the water column. It permits scientists to observe the physical properties in real-time via a conducting cable, which is typically connected to a CTD to a deck unit and computer on a ship. The CTD is often configured with additional optional sensors including fluorometers, transmissometers and/or radiometers. It is often combined with a Rosette of water sampling bottles (e.g. Niskin, GO-FLO) for collecting discrete water samples during the cast.

This term applies to profiling CTDs. For fixed CTDs, see https://www.bco-dmo.org/instrument/869934.

MOCNESS

Supplied Name: MOCNESS for animals

Supplied Description:

Instrument Type

Generic Name: MOCNESS

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/NETT0097/

Generic Description:

The Multiple Opening/Closing Net and Environmental Sensing System or MOCNESS is a family of net systems based on the Tucker Trawl principle. There are currently 8 different sizes of MOCNESS in existence which are designed for capture of different size ranges of zooplankton and micro-nekton Each system is designated according to the size of the net mouth opening and in two cases, the number of nets it carries. The original MOCNESS (Wiebe et al, 1976) was a redesigned and improved version of a system described by Frost and McCrone (1974).(from MOCNESS manual) This designation is used when the specific type of MOCNESS (number and size of nets) was not specified by the contributing investigator.

Niskin bottle

Supplied Name: Niskin CTD Rosette for seawater

Supplied Description:

Instrument Type

Generic Name: Niskin bottle

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0412/

Generic 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.

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
bioproject_accession	NCBI Bioproject accession ID	unitless	BioProject
biosample_accession	NCBI Biosample accession ID	unitless	BioSample
sample_name	Submitter sample name	unitless	sample
sra_sample_accession	NCBI SRA sample accession ID	unitless	SRA_sample
sample_accession_title	Sample accession title	unitless	sample_descrip
organism_name	Organism name by submitter	unitless	taxon
organism_taxonomy_id	NCBI Taxonomy ID	unitless	taxon_code
organism_taxonomy_name	NCBI organism name related to taxonomy id	unitless	taxon_code
keywords	NCBI biosample keywords	unitless	sample_descrip
biosample_package	NCBI biosample attribute package and package version	unitless	sample_descrip
collection_date	Collection date of organism Format: %Y-%m-%d	unitless	date
env_broad_scale	Broad-scale environmental context	unitless	sample_descrip
env_local_scale	Local-scale environmental context	unitless	sample_descrip
env_medium	Material displaced by the entity at time of sampling	unitless	sample_descrip
geo_loc_name	Geographic location of the origin of the sample	unitless	region
host	Host name	unitless	taxon
sampling_lat	Latitude of sampling location, south is negative	decimal degrees	lat
sampling_lon	Longitude of sampling location, west is negative	decimal degrees	lon
depth	Sampling depth	meter (m)	depth
host_length	Length of the subject	centimeter (cm)	length
source_material_id	Unique identifier assigned to a material sample used for extracting nucleic acids, and subsequent sequencing.	unitless	sample
status	Sample NCBI status (live)	unitless	no_bcodmo_term
when	When status set Format: %Y-%m-%dT%H:%M:%S.%f	unitless	no_bcodmo_term
access	Accessibility: public	unitless	no_bcodmo_term
date_publication	Date of publication at NCBI Format: %Y-%m-%dT%H:%M:%S.%f	unitless	ISO_DateTime_UTC
date_last_update	Data of last update at NCBI Format: %Y-%m-%dT%H:%M:%S.%f	unitless	ISO_DateTime_UTC
date_submission_date	Date of submisison at NCBI Format: %Y-%m-%dT%H:%M:%S.%f	unitless	ISO_DateTime_UTC
sra_run_accession	NCBI SRA run accession ID	unitless	SRA_run
sra_study_accession	NCBI study accession ID	unitless	SRA_study
object_status	Status of object	unitless	no_bcodmo_term
library_ID	Unique identifier for the sequencing library (can be the sample name repeated).	unitless	sample
title	Library title	unitless	seq_descrip
library_strategy	Sequencing library strategy	unitless	seq_descrip
library_source	Source of sequencing library	unitless	seq_descrip
library_selection	Selection used for sequencing library	unitless	seq_descrip
library_layout	single or paired end sequencing reads	unitless	seq_descrip
platform	Sequencing platform manufacturer	unitless	instrument
instrument_model	Sequencer model	unitless	inst_model
design_description	Description explaining how this library was prepared and sequenced	unitless	seq_descrip
filetype	File type	unitless	datatype
fasta_filename1	Forward reads file name	unitless	file_name
fasta_filename2	Reverse reads file name	unitless	file_name

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Database

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Dataset: Microorganisms associated with pyrosomes