Dataset: Northern California Current Microorganisms

Name: 16S rRNA gene of microorganisms sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA in 2018 and 2019
Published: 2024-05-06
Keywords: microorganisms, upwelling, Northern California Current, oceans

View Data: Data not available yet

Cite This Dataset

Spatial Extent: N:44.6607 E:-124.00338333 S:41.05433333 W:-125.18113333

Northern California Current, off the coast of Oregon and Northern California.

Temporal Extent: 2018-02-16 - 2019-07-25

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:

2024-05-06

Restricted:

Validated:

Current State:

Data not available

16S rRNA gene of microorganisms sampled along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA in 2018 and 2019

Abstract:

The Northern California Current ecosystem is a productive system which supports major fisheries. To determine how the microbial community responds to variable upwelling, we examined the 16S rRNA gene of microorganisms from two size fractions, 0.2-1.6µm and greater than 1.6µm along the Newport Hydrographic (NH) and Trinidad Head (TR) lines, in OR and CA.

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Methods & Sampling

Transects ranged from 24 to 86 km in length were sampled along the Newport Hydrographic (NH) line as well as the Trinidad Head (TR) line during the winters (February-March) and summers (July-August) of 2018 and 2019 (winter 2018 transect sample size was n=2 per location due to weather days while summer 2018 – summer 2019, n=4-5). Located off Newport, Oregon, the NH Line has been sampled since 1961 (Peterson and Miller, 1975), while the TR line off northern California has been sampled since 2007.

DNA sampling for microbes was carried out from surface (5-10 meters depth) seawater samples (500-1000 mL, n=2 per station, 6 stations per transect), collected by CTD, that were size fractionated on 47 mm 1.6 µm GF/A filters (Whatman) followed by 47 mm 0.2 µm Supor polyethersulfone filters (Pall Corporation) using a peristaltic pump. Filter membranes were moved to bead-beater tubes and frozen immediately at -20 ˚C and stored at -80 ˚C. DNA extraction was done using the DNeasy Plant Tissue Mini Kit (Qiagen) with the following modifications. 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. PCR was performed in triplicate on 1 ng of DNA with the primer pair 515F‐Y/806R amplified the 16S rRNA V4 hypervariable region with conditions as published (Parada et al. 2016) using golay barcodes on the forward primers as in the EMP protocols. Reactions were performed with the QuantaBio 5Prime HotMasterMix (Qiagen Beverly, MA, USA). The Agilent High Sensitivity Kit in the Bioanalyzer (Agilent Technologies, Waldbronn, Germany) confirmed amplicon size. Triplicate PCR reactions from each sample were pooled then purified by magnetic beads. Each final pooled sample was paired-end sequenced with Illumina MiSeq v.3 (Illumina, San Diego, USA).

Data Processing Description

Amplicon sequence variants (ASVs) of seawater samples were identified based on 16S rRNA gene sequence reads that were processed using dada2 and phyloseq. Sequences were quality controlled using filterAndTrim() with truncLen set to 190 (forward reads) and 160 (reverse reads), maxEE was set to 3, and maxN set to 0 to eliminate low quality base calls. Forward and reverse primers were trimmed from all reads. Error learning, sample inference, and merging of paired-end reads were done with dada2 default settings to yield unique amplicon sequence variants (ASVs). Chimeric ASVs were removed with the "consensus" method. The reference database "RefSeq-RDP16S_v2_May2018" was used to assign taxonomy to the ASVs. phyloseq was used to connect ASV sequence counts per sample to taxonomic data and metadata. Sequence abundances were standardized to the median sequencing depth of all samples (“standardized relative abundance”) without rarefying. Raw sequence data can be accessed from the NCBI Sequence Read Archive at https://www.ncbi.nlm.nih.gov/bioproject/PRJNA999694/.

More Information about this dataset

Funding Sources

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

Deployments

None available yet

Instruments

CTD Sea-Bird

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: CTD Sea-Bird

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

Generic Description:

Conductivity, Temperature, Depth (CTD) sensor package from SeaBird Electronics, no specific unit identified. This instrument designation is used when specific make and model are not known. See also other SeaBird instruments listed under CTD. More information from Sea-Bird Electronics.

Niskin bottle

Supplied Name:

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
message	NCBI message	unitless	no_bcodmo_term
sample_name	Submitter sample name	unitless	sample
organism	Organism name by submitter	unitless	taxon
collection_date	Collection date of organism Format: %Y-%m-%d	unitless	date
depth	Sampling depth	meter (m)	depth
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
sampling_lat	Latitude of sampling location, south is negative	decimal degrees	lat
sampling_lon	Longitude of sampling location, west is negative	decimal degrees	lon
size_frac	Selected size fraction	unitless	samp_fraction
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_filename	Forward reads file name	unitless	file_name
fasta_filename2	Reverse reads file name	unitless	file_name

Database

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Dataset: Northern California Current Microorganisms