Dataset: North Pacific Bathycoccus Culture Experiment

Name: Response of Bathycoccus sp. to iron-limitation sampled aboard R/V Roger Revelle RR1813 in the Subarctic North Pacific near Station PAPA (50 N, 144.8 W) from August to September 2018
Published: 2024-12-05
Keywords: Picoeukaryotes, Nitrogen, Iron, Phytoplankton cultures, oceans

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Spatial Extent: N:50 E:-145 S:50 W:-145

Ocean Station Papa, Subarctic North Pacific Ocean, approximate location lat:50, lon:-145

Temporal Extent: 2018-08-16 - 2018-09-07

Project:

Collaborative Research: Evaluating the contribution of small eukaryotes to nitrate-based new production in the North Pacific Subtropical Gyre (Small Euks)

Principal Investigator:

Adrian Marchetti (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

Student:

Meredith G Meyer (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

Contact:

Meredith G Meyer (University of North Carolina at Chapel Hill, UNC-Chapel Hill)

BCO-DMO Data Manager:

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

Version:

Version Date:

2024-12-05

Restricted:

Validated:

Current State:

Data not available

Response of Bathycoccus sp. to iron-limitation sampled aboard R/V Roger Revelle RR1813 in the Subarctic North Pacific near Station PAPA (50 N, 144.8 W) from August to September 2018

Abstract:

Small eukaryotic phytoplankton can account for considerable amounts of biomass and primary production in high nutrient, low chlorophyll (HNLC) regions of the ocean where iron-limitation is pronounced. However, the strategies these cells invoke to cope under low iron conditions and the extent to which they are responsible for new production (i.e., the fraction of primary production supported by nutrients from outside of the euphotic zone) is unclear. Here, we examine how a representative picoeukaryote, the chlorophyte Bathycoccus sp., recently isolated from the iron-limited subarctic North Pacific Ocean, responds to iron-limitation and quantify its potential contribution to new production. Iron-limited Bathycoccus exhibits reductions in cellular growth rate, volume, and carbon and nitrogen quotas along with a restructuring of cellular metabolism as inferred through gene expression. Gene expression and pathway analyses show evidence of cellular strategies to mitigate iron limitation but conservation of genes related to nitrogen uptake and utilization. Additionally, when grown on nitrate, cellular carbon and nitrogen quotas ranged from 0.02 – 0.17 pmol C cell-1 and 3.3 x 10-3 – 2.2 x 10-2 pmol N cell-1 as a function of iron status.

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Methods & Sampling

Samples were taken at Ocean Station Papa, Subarctic North Pacific Ocean. Sampling depth during cruise RR1813 was 3 m. The culture was isolated from a sample taken at approximate location (lat:50, lon:-145). Bathycoccus cells were isolated using a 10 mL pipette after whole seawater sampling from a trace metal clean rosette aboard the R/V Revelle. Cultures were transported back to the University of North Carolina at Chapel Hill and stored in Aquil media under constant 120-150 µmol photons m-2 d-1 light in a 12ºC incubator.

Cultures were grown with either 1.37x10-6 M total Fe ("Fe+") or 3.10x10-9 M total Fe ("Fe-") media. Upon reaching exponential phase growth (based on trends in relative fluorescence units as measured by a Turner fluorometer), cultures were filtered for chlorophyll a concentration, particulate carbon/particulate nitrogen, and RNA. Additional samples for cell count were collected and fixed with a 10% addition of paraformaldehyde. Measurements of the maximum quantum yield of photochemistry in photosystem II (Fv/Fm) and the functional absorption cross section of photosystem II (sigma) were collected. Filters used in chlorophyll and carbon/nitrogen sampling were uncombusted and combusted Whatman 0.7µm glass fiber filters, respectively.

For RNA sampling, Isopore 0.4 µm 47 mm polycarbonate filters were used. A RNAqueous-4PCR kit and RNeasy MinElute Clean-up kit were used for RNA extraction and clean-up.

Problems/Issues

Sample NO3- Fe+ A had low Fv/Fm and high sigma, suggesting it was no longer in exponential phase and thus scientifically different from NO3- Fe+ B and C. Therefore, NO3- Fe+ A was removed from average analyses.

Data Processing Description

Chlorophyll was analyzed at the University of North Carolina on a Turner 10AU fluorometer following the protocol of Graff and Rynearson (2011). Particulate carbon/particulate nitrogen was analyzed on an elemental analyzer at the University of Maryland Center for Environmental Science Application Laboratory. Cell counts were measured at North Carolina State University on a Guava easyCyte flow cytometer equipped with a red laser. RNA was analyzed at the Azenta Genewiz Sequencing Facility via Illumina high throughput sequencing with 350M raw paired-end reads per lane and single index, 2 x 150 bp per lane.

RNA transcripts were processed according to the pipeline outlined in https://github.com/omtorano/Exports-Metatranscriptomics (Author: Olivia Torano). Programs for processing include Trim_galore (v.0.6.2), FastQC (v.0.11.9), Trinity (v.2.8.6), cdhit (v.4.8.1), Salmon (v.10.9.1), tximport, and the DESeq2 package in RStudio. Sequences were blasted to the Kyoto Encyclopedia of Genes and Genomes (Release 88.2).

BCO-DMO Processing

* Renamed parameters to comply with database requirements
* Added cruise ID and apporximate sampling location to data

More Information about this dataset

Funding Sources

Funding Source	Award Number
NSF Division of Ocean Sciences	OCE-2219973

Deployments

Deployment	Synonyms	Start Date	Platform	Investigator
RR1813	EXPORTS	2018-08-10	R/V Roger Revelle	Deborah K. Steinberg (Chief Scientist)	data info

Instruments

Elemental Analyzer

Supplied Name:

Supplied Description:

Instrument Type

Generic Name: Elemental Analyzer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB01/

Generic Description:

Instruments that quantify carbon, nitrogen and sometimes other elements by combusting the sample at very high temperature and assaying the resulting gaseous oxides. Usually used for samples including organic material.

Flow Cytometer

Supplied Name: Guava easyCyte flow cytometer

Supplied Description:

Instrument Type

Generic Name: Flow Cytometer

Community Identifier: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/

Generic Description:

Flow cytometers (FC or FCM) are automated instruments that quantitate properties of single cells, one cell at a time. They can measure cell size, cell granularity, the amounts of cell components such as total DNA, newly synthesized DNA, gene expression as the amount messenger RNA for a particular gene, amounts of specific surface receptors, amounts of intracellular proteins, or transient signalling events in living cells.
(from: http://www.bio.umass.edu/micro/immunology/facs542/facswhat.htm)

Turner Designs Fluorometer 10-AU

Supplied Name: Turner 10AU fluorometer

Supplied Description:

Instrument Type

Generic Name: Turner Designs Fluorometer 10-AU

Acronym: Turner Fluorometer 10-AU

Community Identifier: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0393/

Generic Description:

The Turner Designs 10-AU Field Fluorometer is used to measure Chlorophyll fluorescence. The 10AU Fluorometer can be set up for continuous-flow monitoring or discrete sample analyses. A variety of compounds can be measured using application-specific optical filters available from the manufacturer. (read more from Turner Designs, turnerdesigns.com, Sunnyvale, CA, USA)

Parameters

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

Supplied Name	Supplied description	Supplied Units	Standard Name
Cruise	Cruise ID	unitless	cruise_id
Latitude	Approximate sampling latitude	unitless	lat
Longitude	Approximat sampling longitude	unitless	lon
Treatment	Treatment (NO3- Fe-, NO3- Fe+) - iron treatment, Fe- refers to Aquil media concentrations of 1.37 x 10-6 M Fe and Fe+ refers to Aquil media concentrations of 3.10 x 10-6 M Fe	unitless	treatment
Replicate	Replicate (A, B, C) - culture replicate	unitless	replicate
Volume	Measured volume	liter (L)	volume
Cell_Count	Cell Count	cell per liter (cell L-1)	count
Carbon	Particulate carbon concentration	grams (g)	C
Nitrogen	Particulate nitrogen concentration	grams (g)	N
Fv_Fm	Estimates of maximum photochemical yield of photosystem II	unitless	Fv_Fm
Sigma	Cross-sectional absorption area of photosystem II	unitless	no_bcodmo_term
Growth_Rates	Growth rates (d-1)	per day (d-1)	growth

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Database

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Dataset: North Pacific Bathycoccus Culture Experiment