Dataset: Prokaryotic and eukaryotic abundance in BATS microbial communities

Name: Prokaryote and eukaryote abundance in phytodetrital aggregates (PA), fecal aggregates (FA), and the ambient seawater from samples 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.855296.1

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

Prokaryote and eukaryote abundance in phytodetrital aggregates (PA), fecal aggregates (FA), and the ambient seawater from samples collected during R/V Atlantic Explorer cruises AE1718 and AE1809 in 2017 and 2018 at BATS in Bermuda

Abstract:

Abundances of prokaryotic classes and eukaryotic orders and species found in phytodetrital aggregates (PA), fecal aggregates (FA), and the ambient seawater in the fall and spring seasons, as well as of species in DNA extraction negative controls. Abundance values are prior to (raw) and following rarefaction. These data were published in Neuer et al. (2021).

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Archival Copy

Version Date	Archive	Persistent Identifier (PID)	Date PID Issued
2021-07-08	Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)	10.26008/1912/bco-dmo.855296.1	2021-11-02

Methods & Sampling

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). 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.

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 -80C. 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 -80C.

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.

Problem report:
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.

Supplemental file "16S_Control-Blanks_Species_Raw.csv" contains the taxa excluded from downstream analyses.

Data Processing Description

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.

BCO-DMO data manager processing notes:
* After correspondence with the submitter, the final format of this dataset was combined into one table with added columns for sample name, and transformed to have abundances for the samples in an additional "abundance" column instead of an abundance column per sample.
* Data originally submitted in excel sheets was combined into one data table. The originally named Sheet "16S_Control-Blanks_Species_Raw" with the description "Taxa excluded from downstream analyses" was not combined into the dataset and was instead served as an independent data table in the supplemental files section.

Data Files

File
Abundance of species in negative controls filename: 16S_Control-Blanks_Species_Raw.csv (Comma Separated Values (.csv), 1.05 KB) MD5:5b5225084eaa05ea852a843565ebc711 Abundance of prokaryotic species found in blank negative control samples, samples include empty microcentrifuge tubes and blank GF/F filters. These taxa were excluded from downstream bioinformatic and statistical analyses.
microbial_abundance.csv (Comma Separated Values (.csv), 16.36 MB) MD5:3c30482d293bc7155643bd44f2ae3021 Primary data file for dataset ID 855296

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

Automated DNA Sequencer

Supplied Name: Illumina MiSeq

Supplied Description:

Instrument Type

Generic Name: Automated DNA Sequencer

Acronym: Automated Sequencer

Generic Description:

General term for a laboratory instrument used for deciphering the order of bases in a strand of DNA. Sanger sequencers detect fluorescence from different dyes that are used to identify the A, C, G, and T extension reactions. Contemporary or Pyrosequencer methods are based on detecting the activity of DNA polymerase (a DNA synthesizing enzyme) with another chemoluminescent enzyme. Essentially, the method allows sequencing of a single strand of DNA by synthesizing the complementary strand along it, one base pair at a time, and detecting which base was actually added at each step.

CTD Sea-Bird SBE 911plus

Supplied Name:

Supplied 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 Type

Generic Name: CTD Sea-Bird SBE 911plus

Acronym: CTD SBE 911plus

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0058/

Generic 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

Microscope - Optical

Supplied Name: Stemi 2000-C, Carl Zeiss

Supplied Description:

Stemi 2000-C, Carl Zeiss

3.2MP Digital USB Microscope Camera, OMAX Microscope

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".

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
prokaryotic_or_eukaryotic	Prokaryotic or eukaryotic	unitless	sample_descrip
Taxonomy	Taxonomy	unitless	sample_descrip
abundance	Abundances of prokaryotic classes and eukaryotic orders and species. Abundance values are prior to (raw) and following rarefaction.	unitless	abundance
sample_name	Sample name	unitless	sample
sample_type	Sample type ("Seawater";"PA_Particles" = phytodetrital aggregate (PA) particles;"FA_Particles"= fecal aggregate (FA) particles)	unitless	sample_descrip
depth	Nominal depth of sample	meters (m)	depth
season	Season of the sample	unitless	sample_descrip
sample_group	Sample group (e.g. 16s classes raw)	unitless	sample_descrip

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Database

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Dataset: Prokaryotic and eukaryotic abundance in BATS microbial communities