| Contributors | Affiliation | Role |
|---|---|---|
| Dyhrman, Sonya T. | Lamont-Doherty Earth Observatory (LDEO) | Principal Investigator |
| Morris, James Jeffrey | University of Alabama at Birmingham (UA/Birmingham) | Co-Principal Investigator |
| Copley, Nancy | Woods Hole Oceanographic Institution (WHOI BCO-DMO) | BCO-DMO Data Manager |
This dataset includes a link to Prochlorococcus clone NCBI BioProject and associated metadata.
PRJNA377729: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA377729
Six clones of high light II Prochlorococcus VOL4, a streptomycin-resistant derivative of strain MIT9312 were isolated by dilution to extinction in Pro99 media pretreated with the helper bacterium Alteromonas sp. strain EZ55. Prochlorococcus clones were made axenic by addition of streptomycin. For co-culture experiments, Alteromonas bacteria were introduced to Prochlorococcus cultures prior to growth experiments. Alteromonas was diluted onto YTSS agar plates and each Prochlorococcus culture was inoculated with a single separate colony. Alteromonas stock cultures were grown in YTSS liquid medium and cryopreserved in 20% glycerol at -80 C.
Each of the six Prochlorococcus clones was grown in ambient or elevated CO2 in co-culture with Alteromonas, in PEv media.
The mRNA libraries were prepared for Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY).
RNA extractions were performed with the RNeasy Mini Kit.
Sequence reads were de-multiplexed and trimmed to remove sequencing barcodes. Trimmed reads were aligned to both the MIT9312 gene models (accession: NC_007577.1) and the draft EZ55 genome (Genbank accession TBD) using bowtie2 with sensitive end-to-end mode. Reads aligning to coding sequences in the MIT9312 gene models were counted with samtools idxstats. Reads aligning to the EZ55 draft genome were counted with HT-seq count.
BCO-DMO Processing Notes:
- added conventional header with dataset name, PI name, version date
- modified parameter names to conform with BCO-DMO naming conventions
- added links to NCBI BioProject page
- replaced blanks with nd (no data)
| File |
|---|
Pro_ancestor.csv (Comma Separated Values (.csv), 8.38 KB) MD5:dbc2079cbd98a30a17ad4b2ef5721685 Primary data file for dataset ID 688162 |
| Parameter | Description | Units |
| sample | sequencing facility sample identifier | unitless |
| sample_title | laboratory sample identifier | unitless |
| NCBI_BioProject | collection of biological data related to a single initiative | unitless |
| BioProject_link | url for collection of biological data related to a single initiative | unitless |
| organism | bacterium used in this study | unitless |
| strain | population of organism that descends from a single organism or pure culture isolate | unitless |
| isolate | specific individual from which this sample was obtained | unitless |
| isolation_source | physical/ environmental/ geographic source of the sample | unitless |
| collection_date | date sample was obtained | date |
| geo_loc_name | geographical origin of the sample | unitless |
| sample_type | sample type such as whole organism, mixed culture, cell culture, metagenomic assembly | unitless |
| biomaterial_provider | laboratory and principal investigator where sample came from | unitless |
| collected_by | laboratory and principal investigator where organism was isolated | unitless |
| lat_lon | geographical coordinates of the location where the sample was collected; north and east are positive | decimal degrees |
| depth | vertical distance below the surface where sample was collected | meters |
| env_biome | descriptor of the broad ecological context of sample | unitless |
| genotype | observed genotype | unitless |
| passage_history | number of sample generations | generations |
| samp_size | amount of sample collected | number of cells |
| temp_C | temperature at which sample was collected | degrees Celsius |
| light_level | light level at which sample was collected | micromol photons m-2 s-1 |
| light_dark_hr | number of hours of light:dark for a 24 hour period | hours:hours |
| CO2 | carbon dioxide concentration | ppm |
| Alkalinity | buffering capacity of water | umoles/kg |
| pH | scale of acidity | unitless |
| DIC | dissolved inorganic carbon concentration | umoles/kg |
| co_cultured_with | additional organisms grown with the primary organism | unitless |
| Media | type of water or broth organism was grown in | unitless |
| Dataset-specific Instrument Name | Illumina Hi-seq 2500 paired-end sequencing (PE100) with TruSeq RNA sample Prep Kit v2 (Illumina, San Diego, CA) |
| Generic Instrument Name | Automated DNA Sequencer |
| Dataset-specific Description | Used to prepare the mRNA libraries. Samples were barcoded for multiplex sequencing and run on in a single lane by the Columbia University Genome Center (CUGC) (New York, NY). |
| Generic Instrument 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. |
| Website | |
| Platform | LDEO |
| Start Date | 2013-01-01 |
| End Date | 2017-03-31 |
| Description | Phytoplankton studies |
Note: This project is also affiliated with the NSF BEACON Center for the Study of Evolution in Action.
Project Description from NSF Award:
Human activities are driving up atmospheric carbon dioxide concentrations at an unprecedented rate, perturbing the ocean's carbonate buffering system, lowering oceanic pH, and changing the concentration and composition of dissolved inorganic carbon. Recent studies have shown that this ocean acidification has many short-term effects on phytoplankton, including changes in carbon fixation among others. These physiological changes could have profound effects on phytoplankton metabolism and community structure, with concomitant effects on Earth's carbon cycle and, hence, global climate. However, extrapolation of present understanding to the field are complicated by the possibility that natural populations might evolve in response to their changing environments, leading to different outcomes than those predicted from short-term studies. Indeed, evolution experiments demonstrate that microbes are often able to rapidly adapt to changes in the environment, and that beneficial mutations are capable of sweeping large populations on time scales relevant to predictions of environmental dynamics in the coming decades. This project addresses two major areas of uncertainty for phytoplankton populations with the following questions:
1) What adaptive mutations to elevated CO2 are easily accessible to extant species, how often do they arise, and how large are their effects on fitness?
2) How will physical and ecological interactions affect the expansion of those mutations into standing populations?
This study will address these questions by coupling experimental evolution with computational modeling of ocean biogeochemical cycles. First, cultured unicellular phytoplankton, representative of major functional groups (e.g. cyanobacteria, diatoms, coccolithophores), will be evolved under simulated year 2100 CO2 concentrations. From these experiments, estimates will be made of a) the rate of beneficial mutations, b) the magnitude of fitness gains conferred by these mutations, and c) secondary phenotypes (i.e., trade-offs) associated with these mutations, assayed using both physiological and genetic approaches. Second, an existing numerical model of the global ocean system will be modified to a) simulate the effects of changing atmospheric CO2 concentrations on ocean chemistry, and b) allow the introduction of CO2-specific adaptive mutants into the extant populations of virtual phytoplankton. The model will be used to explore the ecological and biogeochemical impacts of beneficial mutations in realistic environmental situations (e.g. resource availability, predation, etc.). Initially, the model will be applied to idealized sensitivity studies; then, as experimental results become available, the implications of the specific beneficial mutations observed in our experiments will be explored.
This interdisciplinary study will provide novel, transformative understanding of the extent to which evolutionary processes influence phytoplankton diversity, physiological ecology, and carbon cycling in the near-future ocean. One of many important outcomes will be the development and testing of nearly-neutral genetic markers useful for competition studies in major phytoplankton functional groups, which has applications well beyond the current proposal.
NSF Climate Research Investment (CRI) activities that were initiated in 2010 are now included under Science, Engineering and Education for Sustainability NSF-Wide Investment (SEES). SEES is a portfolio of activities that highlights NSF's unique role in helping society address the challenge(s) of achieving sustainability. Detailed information about the SEES program is available from NSF (https://www.nsf.gov/funding/pgm_summ.jsp?pims_id=504707).
In recognition of the need for basic research concerning the nature, extent and impact of ocean acidification on oceanic environments in the past, present and future, the goal of the SEES: OA program is to understand (a) the chemistry and physical chemistry of ocean acidification; (b) how ocean acidification interacts with processes at the organismal level; and (c) how the earth system history informs our understanding of the effects of ocean acidification on the present day and future ocean.
Solicitations issued under this program:
NSF 10-530, FY 2010-FY2011
NSF 12-500, FY 2012
NSF 12-600, FY 2013
NSF 13-586, FY 2014
NSF 13-586 was the final solicitation that will be released for this program.
PI Meetings:
1st U.S. Ocean Acidification PI Meeting(March 22-24, 2011, Woods Hole, MA)
2nd U.S. Ocean Acidification PI Meeting(Sept. 18-20, 2013, Washington, DC)
3rd U.S. Ocean Acidification PI Meeting (June 9-11, 2015, Woods Hole, MA – Tentative)
NSF media releases for the Ocean Acidification Program:
Press Release 10-186 NSF Awards Grants to Study Effects of Ocean Acidification
Discovery Blue Mussels "Hang On" Along Rocky Shores: For How Long?
Press Release 13-102 World Oceans Month Brings Mixed News for Oysters
| Funding Source | Award |
|---|---|
| NSF Division of Ocean Sciences (NSF OCE) |