Dataset: Copepod Bacteria RNA transcriptome Sequences

Name: Bacteria assemblages associated with Eurytemora affinis in both salt and fresh water from shoreside Lee-DaSilva Lee-DaSilva_Collection in the USA; Netherlands; Canada; Belgium; various locations each from 2012-2014 (CopepodMicrobiome project)
Published: 2016-03-18
Keywords: biota, oceans

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Cite This Dataset

Project:

Dimensions: Uncovering the novel diversity of the copepod microbiome and its effect on habitat invasions by the copepod host (CopepodMicrobiome)

Program:

Dimensions of Biodiversity (Dimensions of Biodiversity)

Principal Investigator:

Dr Joana Carneiro da Silva (University of Maryland School of Medicine, UMaryland SOM)

Carol E. Lee (University of Wisconsin, UW-Madison)

Contact:

Martin Bontrager (University of Wisconsin, UW-Madison)

BCO-DMO Data Manager:

Ms Dicky Allison (Woods Hole Oceanographic Institution, WHOI BCO-DMO)

Version:

first

Version Date:

2016-03-18

Restricted:

Yes

Release Date:

2017-01-20

Validated:

Current State:

Final with updates expected

Bacteria assemblages associated with Eurytemora affinis in both salt and fresh water from shoreside Lee-DaSilva Lee-DaSilva_Collection in the USA; Netherlands; Canada; Belgium; various locations each from 2012-2014 (CopepodMicrobiome project)

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Description

Bacteria in the water and bacteria from the same location but directly associated (in the cuticle) with copepods were collected from several locations world-wide with pumps and nets from saline and fresh water. The acquired DNA was sequenced and sent to GenBank. The links are here.

These data will be available after January, 2017.

Methods & Sampling

The water samples were collected this way: Approximately 10 liters of water were collected from a depth of 1 meter near the shore and filtered through a 3.0 micron filter to exclude sediment, algae, and other large particles. Then the water was passed through a 0.1 micron filter to collect bacteria. DNA was extracted from the filter with a MoBio PowerWater DNA isolation kit.

The copepods and their associated bacteria were collected this way: 100 pooled adult male and female Eurytemora affinis were collected via plankton tow from depth of ~1-2 meters from near the shore. These animals were isolated from the zooplankton community under a microscope, and homogenized in a glass pestle tissue grinder. DNA was extracted with a MoBio UltraClean Microbial DNA isolation kit.

Data Processing Description

There was no way to isolate bacteria from their copepod hosts, so the entire sample was processed and the DNA from the whole thing was extracted.

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-1046371
NSF Division of Ocean Sciences	OCE-1046372

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
Lee-DaSilva_Collection		2012-10-15	shoreside Lee-DaSilva		data info

Instruments

Plankton Net

Supplied Name: Plankton net

Supplied Description:

Some of the samples were collected by small boat (Blue Hammock Bayou and Lake Pontchartrain) very near the shore. The rest of the net collection was from throwing the plankton net off the dock.

Instrument Type

Generic Name: Plankton Net

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/22/

Generic Description:

A Plankton Net is a generic term for a sampling net that is used to collect plankton. It is used only when detailed instrument documentation is not available.

Pump

Supplied Name: Water pump

Supplied Description:

Battery powered water pump dropped into the water to depth of 1 m and pumped into 25L Nalgene carboys.

Instrument Type

Generic Name: Pump

Generic Description:

A pump is a device that moves fluids (liquids or gases), or sometimes slurries, by mechanical action. Pumps can be classified into three major groups according to the method they use to move the fluid: direct lift, displacement, and gravity pumps

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
collection	how the sample was collected; water by a pump; copepods and associated bacteria by a net	text	brief_desc
sample_name	how the sample is identified; the first initials correspond to the location and the W(water) and E(Eurytemora) indicates the method	coded text	sample
date_start	date of start of collection	day-three letter month-four digit year	date_start
date_end	date of end of collection	day-three letter month-four digit year	date_end
site	sampling location	text	site
lat	latitude of the collection; N is positive	decimal degrees	lat
lon	longitude of the collection; W is negative	decimal degrees	lon
SRA_accession_number	Sequence Read Archive. This makes biological sequence data available to the research community to enhance reproducibility and allow for new discoveries. The identification number of the sequence submitted to GenBank.	link	accession_number

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Database

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Dataset: Copepod Bacteria RNA transcriptome Sequences