http://lod.bco-dmo.org/id/dataset/949777
eng; USA
utf8
dataset
Highest level of data collection, from a common set of sensors or instrumentation, usually within the same research project
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
2025-01-28
ISO 19115-2 Geographic Information - Metadata - Part 2: Extensions for Imagery and Gridded Data
ISO 19115-2:2009(E)
Transcriptomics of phytoplankton cultures grown on various phosphorus sources in a laboratory experiment
2025-02-17
publication
2025-02-17
revision
Marine Biological Laboratory/Woods Hole Oceanographic Institution Library (MBLWHOI DLA)
2025-02-17
publication
https://doi.org/10.26008/1912/bco-dmo.949777.1
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
principalInvestigator
LeAnn P. Whitney
Maine Maritime Academy
principalInvestigator
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
publisher
Cite this dataset as: Whitney, L. P., Sterling, H., Lomas, M. W. (2025) Transcriptomics of phytoplankton cultures grown on various phosphorus sources in a laboratory experiment. Biological and Chemical Oceanography Data Management Office (BCO-DMO). (Version 1) Version Date 2025-02-17 [if applicable, indicate subset used]. doi:10.26008/1912/bco-dmo.949777.1 [access date]
Transcriptomics of Phytoplankton Cultures Grown on Various Phosphorus Sources Dataset Description: Methods and Sampling: <p>Three species of marine phytoplankton – <em>Micromonas pusilla</em>, <em>Emiliania huxleyi</em>, and <em>Isochrysis galbana</em> - were grown under four phosphorus (P) conditions. These include phosphate (Pi) replete and deplete conditions and the phosphonate conditions where cultures received either methylphosphonate (MPN) or 2-aminoethylphosphonate (2-AEPN) as the sole source of phosphorus at replete levels.</p>
<p>Axenic cultures of the pico-prasinophyte <em>Micromonas pusilla</em> (CCMP1545), the coccolithophore <em>Emiliania huxleyi</em> (CCMP2090), and the pico-prymnesiophyte <em>Isochrysis galbana</em> (CCMP1323) were obtained from the National Center for Marine Algae and Microbiota (Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine). The cultures remained axenic throughout the experiments as determined by SYTO-staining and flow cytometric counting on a BD FACSJazz cell sorter; all cultures were free of bacteria during these experiments. Phytoplankton were grown in artificial sea water amended with L1 media silica. The P source was added separately to achieve the desired growth conditions; Pi-replete media contained 36 µM PO43-, the Pi-deficient condition received 0.1 µM PO43-, and the phosphonate treatments received either 36 µM MPN or 2-AEPN. The Pi-deficient treatment (0.1 µM) represents a control for the low level of contaminating Pi measured in the phosphonate media; thus, an increase in growth in the MPN and 2-AEPN conditions above that measured in the Pi-deficient condition is due to phosphonate utilization. The potential for abiotic breakdown of phosphonate to Pi was previously investigated in media-only tubes exposed to the experimental temperature and light conditions for 10 days. Pi levels did not change throughout the experimental period (MPN average Pi = 0.11 µM ± 0.02; 2-AEPN average Pi = 0.10 µM ± 0.02), strongly supporting the notion of active enzymatic breakdown of phosphonates for growth. Cultures were acclimated to the four growth conditions described above as they had been maintained in each P treatment for a minimum of two transfers (20 days). Cultures were grown at 20°C in a 14-hour light/10-hour dark cycle at ~100 µE m-2 s-1 with a starting concentration of ~1x104 cells per mL in 25 mL culture volumes. Phytoplankton growth was monitored by fluorescence measurements using a Turner TD-700 fluorometer and cell counts analyzed by flow cytometry. Triplicate cultures were setup for each treatment and were harvested in the late exponential phase of growth for transcriptomic analysis.</p>
Funding provided by NSF Division of Ocean Sciences (NSF OCE) Award Number: OCE-1756271 Award URL: https://www.nsf.gov/awardsearch/show-award?AWD_ID=1756271
completed
Michael W. Lomas
Bigelow Laboratory for Ocean Sciences
207-315-2567 ext 311
60 Bigelow Drive PO Box 380
East Boothbay
ME
04544
United States
mlomas@bigelow.org
pointOfContact
LeAnn P. Whitney
Maine Maritime Academy
207-326-2396
1 Pleasant Street
Castine
ME
04420
USA
leann.whitney@mma.edu
pointOfContact
asNeeded
Dataset Version: 1
Unknown
BioProject
Biosample
Treatment
Replicate
Organism
Tax_ID
Strain
URL
BD FACSJazz cell sorter
Illumina NovaSeq 6000
flow cytometry
Turner TD-700 fluorometer
theme
None, User defined
NCBI BioProject accession
NCBI BioSample accession
treatment
replicate
taxon
external_link
featureType
BCO-DMO Standard Parameters
Automated Cell Counter
Automated DNA Sequencer
Flow Cytometer
Turner Designs 700 Laboratory Fluorometer
instrument
BCO-DMO Standard Instruments
otherRestrictions
otherRestrictions
Access Constraints: none. Use Constraints: Please follow guidelines at: http://www.bco-dmo.org/terms-use Distribution liability: Under no circumstances shall BCO-DMO be liable for any direct, incidental, special, consequential, indirect, or punitive damages that result from the use of, or the inability to use, the materials in this data submission. If you are dissatisfied with any materials in this data submission your sole and exclusive remedy is to discontinue use.
Phosphonate Utilization by Eukaryotic Phytoplankton: Who, How, and Where?
https://osprey.bco-dmo.org/project/720969
Phosphonate Utilization by Eukaryotic Phytoplankton: Who, How, and Where?
<p><em>NSF Award Abstract:</em><br />
Phosphorus (P) is an essential nutrient for all living cells. It is a central component of genetic material and cellular membranes and is integral to energy production and regulating enzyme activity. In the marine environment, P occurs as inorganic (Pi) and dissolved organic (DOP) forms; the availability and concentration of these different forms of P is an important control on marine phytoplankton growth. Marine phytoplankton are single-celled photosynthetic organisms and can be both prokaryotic bacteria and eukaryotic plants. While Pi is the preferred form of P for marine phytoplankton, in large regions of the oceans it is at such low levels that it restricts phytoplankton growth. In these regions, DOP is the most important P source. The composition of the DOP pool can generally be divided into two major groups: P esters and phosphonates. All marine phytoplankton are capable of using P esters to support growth; in contrast, phosphonates have only been shown to be an important source of P in the nutrition of bacteria to date. This project will determine the ability of marine eukaryotic phytoplankton to use phosphonates as a source of P for growth. Genomic analyses will determine the metabolic response of eukaryotic phytoplankton species to growth on phosphonates as well as the relevance of phosphonate use by natural populations. It is critical to understand the metabolic capabilities of phytoplankton which control marine nutrient cycling. In addition, the project is of great value in understanding the potential impacts of a changing ocean on phytoplankton growth. The project supports reseach opportunities for undergraduates from a local community college as well as hands-on enrichment programs for an afterschool program that serves a diverse student population.</p>
<p>Comprising up to 10% of the marine DOP pool, phosphonates have been shown to be a dynamic P pool both being assimilated and produced by marine photosynthetic bacteria. The ability of eukaryotic phytoplankton to supplement their growth with phosphonates remains vastly unexplored. Several eukaryotic phytoplankton species have been shown to use glyphosate, a chemically synthesized herbicidal phosphonate, as a P source; it remains unknown if open ocean eukaryotic phytoplankton can utilize phosphonates found naturally in the marine environment. Preliminary experiments suggest at least some eukaryotic phytoplankton are able to directly utilize extracellular phosphonates. This project characterizes the pervasiveness of phosphonate utilization within eukaryotic phytoplankton lineages and identifies the cellular underpinnings that support the acquisition of and growth on naturally occuring phosphonates. The project uses whole-cell transcriptomics and functional gene complementation assays, in addition to phylogenetic analyses, to understand the bioavailability of phosphonates and relevance of phosphonate utilization by natural eukaryotic phytoplankton populations. It is critical to understand the metabolic capabilities of phytoplankton which control marine biogeochemical cycles. This is especially important given the prediction that future oceans may become more stratified which could increase the importance of DOP, including phosphonates, in supporting phytoplankton growth.</p>
Euk Phn Utilization
largerWorkCitation
project
eng; USA
oceans
2022-05-01
2024-05-31
Laboratory culture studies
0
BCO-DMO catalogue of parameters from Transcriptomics of phytoplankton cultures grown on various phosphorus sources in a laboratory experiment
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
http://lod.bco-dmo.org/id/dataset-parameter/952997.rdf
Name: BioProject
Units: unitless
Description: <p>BioProject ID in NCBI (<a href="https://www.ncbi.nlm.nih.gov/">https://www.ncbi.nlm.nih.gov/</a>)</p>
http://lod.bco-dmo.org/id/dataset-parameter/952998.rdf
Name: Biosample
Units: unitless
Description: <p>BioSample accession number</p>
http://lod.bco-dmo.org/id/dataset-parameter/952999.rdf
Name: Treatment
Units: unitless
Description: <p>Source of phosphorus in the growth media (+P: phosphate replete; -P: phosphate deplete; +MPN: methylphosphonate replete; +AEPN: aminoethylphosphonate</p>
http://lod.bco-dmo.org/id/dataset-parameter/953000.rdf
Name: Replicate
Units: unitless
Description: <p>Biological replicate sequenced</p>
http://lod.bco-dmo.org/id/dataset-parameter/953001.rdf
Name: Organism
Units: unitless
Description: <p>Taxonomic name of phytoplankton strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/953002.rdf
Name: Tax_ID
Units: unitless
Description: <p>Genus species identification of strain</p>
http://lod.bco-dmo.org/id/dataset-parameter/953003.rdf
Name: Strain
Units: unitless
Description: <p>National Center for Marine Algae and Microbiota numerical designation (CCMPxxxx)</p>
http://lod.bco-dmo.org/id/dataset-parameter/953004.rdf
Name: URL
Units: unitless
Description: <p>URL of the BioSample</p>
GB/NERC/BODC > British Oceanographic Data Centre, Natural Environment Research Council, United Kingdom
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
4373
https://darchive.mblwhoilibrary.org/server/api/core/bitstreams/8adbce3b-d0ba-4cee-bbaa-b955c61e201c/content
download
https://doi.org/10.26008/1912/bco-dmo.949777.1
download
onLine
dataset
<p>Three species of marine phytoplankton – <em>Micromonas pusilla</em>, <em>Emiliania huxleyi</em>, and <em>Isochrysis galbana</em> - were grown under four phosphorus (P) conditions. These include phosphate (Pi) replete and deplete conditions and the phosphonate conditions where cultures received either methylphosphonate (MPN) or 2-aminoethylphosphonate (2-AEPN) as the sole source of phosphorus at replete levels.</p>
<p>Axenic cultures of the pico-prasinophyte <em>Micromonas pusilla</em> (CCMP1545), the coccolithophore <em>Emiliania huxleyi</em> (CCMP2090), and the pico-prymnesiophyte <em>Isochrysis galbana</em> (CCMP1323) were obtained from the National Center for Marine Algae and Microbiota (Bigelow Laboratory for Ocean Sciences, East Boothbay, Maine). The cultures remained axenic throughout the experiments as determined by SYTO-staining and flow cytometric counting on a BD FACSJazz cell sorter; all cultures were free of bacteria during these experiments. Phytoplankton were grown in artificial sea water amended with L1 media silica. The P source was added separately to achieve the desired growth conditions; Pi-replete media contained 36 µM PO43-, the Pi-deficient condition received 0.1 µM PO43-, and the phosphonate treatments received either 36 µM MPN or 2-AEPN. The Pi-deficient treatment (0.1 µM) represents a control for the low level of contaminating Pi measured in the phosphonate media; thus, an increase in growth in the MPN and 2-AEPN conditions above that measured in the Pi-deficient condition is due to phosphonate utilization. The potential for abiotic breakdown of phosphonate to Pi was previously investigated in media-only tubes exposed to the experimental temperature and light conditions for 10 days. Pi levels did not change throughout the experimental period (MPN average Pi = 0.11 µM ± 0.02; 2-AEPN average Pi = 0.10 µM ± 0.02), strongly supporting the notion of active enzymatic breakdown of phosphonates for growth. Cultures were acclimated to the four growth conditions described above as they had been maintained in each P treatment for a minimum of two transfers (20 days). Cultures were grown at 20°C in a 14-hour light/10-hour dark cycle at ~100 µE m-2 s-1 with a starting concentration of ~1x104 cells per mL in 25 mL culture volumes. Phytoplankton growth was monitored by fluorescence measurements using a Turner TD-700 fluorometer and cell counts analyzed by flow cytometry. Triplicate cultures were setup for each treatment and were harvested in the late exponential phase of growth for transcriptomic analysis.</p>
Specified by the Principal Investigator(s)
<p><em>I. galbana</em> RNA-seq data was trimmed of adapters using BBDuk v38.84 and quality controlled using FastQC v0.11.9. The transcriptome was assembled using Trinity v2.14.0 and quality controlled using TrinityStats.pl, BUSCO v5.4.3, Bowtie 2 v2.4.4. The transcriptome was filtered using Trinity and TransDecoder v5.5.0. The count matrix was generated using Bowtie2 and RSEM and differential expression determined using DESeq2 v1.38.1. Transcripts were functionally annotated using eggNOG-mapper v2.1.9, InterProScan v5.60-92.0, PANNZER2, KEGG, Blast2GO v6.0.3, and Diamond v2.0.14.</p>
<p><em>E. huxleyi</em> and <em>M. pusilla</em> transcriptomes were trimmed of adapters using BBDuk 38.84 and quality controlled using FastQC v0.11.9, as above. Unlike <em>I. galbana</em>, <em>E. huxleyi</em> and <em>M. pusilla</em> have existing genomes; the transcripts were mapped to the genomes and count matrices were generating using STAR v2.7.10b. The transcripts were functionally annotated using InterProScan v5.60-92.0, Blast2GO v6.0.3, and Diamond v2.0.14. DESeq2 v1.38.1 was used analyze transcripts counts for differential expression.</p>
Specified by the Principal Investigator(s)
- Imported original file "Phn_Transcriptomics metadata_2024 update.xlsx" into the BCO-DMO system.
- Renamed fields to comply with BCO-DMO naming conventions.
- Saved the final file as "949777_v1_phyto_transcriptomics.csv".
Specified by BCO-DMO Data Managers
asNeeded
7.x-1.1
Biological and Chemical Oceanography Data Management Office (BCO-DMO)
Unavailable
508-289-2009
WHOI MS#36
Woods Hole
MA
02543
USA
info@bco-dmo.org
http://www.bco-dmo.org
Monday - Friday 8:00am - 5:00pm
For questions regarding this resource, please contact BCO-DMO via the email address provided.
pointOfContact
BD FACSJazz cell sorter
BD FACSJazz cell sorter
PI Supplied Instrument Name: BD FACSJazz cell sorter Instrument Name: Automated Cell Counter Instrument Short Name:ACC Instrument Description: An instrument that determines the numbers, types or viability of cells present in a sample.
Illumina NovaSeq 6000
Illumina NovaSeq 6000
PI Supplied Instrument Name: Illumina NovaSeq 6000 PI Supplied Instrument Description:SAMN44278360 - SAMN44278371 (I. galbana) RNA-seq data were generated using the Illumina NovaSeq 6000 instrument at the University of New Hampshire.
SAMN44278372 - SAMN44278383 (E. huxleyi) RNA-seq data were generated using the Illumina NoveSeq Plus instrument at the University of Chicago.
SAMN44278384 - SAMN44278395 (M. pusilla) RNA-seq data were generated using the Illumina NoveSeq Plus instrument at the University of Chicago. Instrument Name: Automated DNA Sequencer Instrument Short Name:Automated Sequencer Instrument Description: A DNA sequencer is an instrument that determines the order of deoxynucleotides in deoxyribonucleic acid sequences.
flow cytometry
flow cytometry
PI Supplied Instrument Name: flow cytometry Instrument Name: Flow Cytometer Instrument Short Name:Flow Cytometer Instrument 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) Community Standard Description: http://vocab.nerc.ac.uk/collection/L05/current/LAB37/
Turner TD-700 fluorometer
Turner TD-700 fluorometer
PI Supplied Instrument Name: Turner TD-700 fluorometer Instrument Name: Turner Designs 700 Laboratory Fluorometer Instrument Short Name:TD-700 Instrument Description: The TD-700 Laboratory Fluorometer is a benchtop fluorometer designed to detect fluorescence over the UV to red range. The instrument can measure concentrations of a variety of compounds, including chlorophyll-a and fluorescent dyes, and is thus suitable for a range of applications, including chlorophyll, water quality monitoring and fluorescent tracer studies. Data can be output as concentrations or raw fluorescence measurements. Community Standard Description: http://vocab.nerc.ac.uk/collection/L22/current/TOOL0510/