Table of Contents

• Dataset Description
  • Methods & Sampling
  • Data Processing Description
• Data Files
• Related Publications
• Related Datasets
• Parameters
• Instruments
• Deployments
• Project Information
• Funding

Trichodesmium erythraeum was grown in biological triplicate under two CO2 regimes (380 and 750 uatm pCO2) and four different nutrient regimes (replete, phosphorus-limited,iron-limited, iron/phosphorus colimited).  

Raw sequence reads from the Trichodesmium erythraeum used in this experiment can be accessed at The National Center for Biotechnology Information (NCBI) under the BioProject PRJNA312342. 

Protein sequences can be accessed through NCBI BioProject PRJNA318.

The fasta file IMG_Trichodesmium_IMS101_genes.fasta (5.4 MB) contains all of the Integrated Microbial Genomes (IMG)-annotated genes in the Trichodesmium erythraeum IMS101 genome.  More information can be found at the IMG Trichodesmium genome portal, "genes page" and IMG Genome ID 637000329 page.

Related dataset: Trichodesmium physiology and cell growth

The following are excerpts from Walworth et al. 2016a. Please refer to this reference for more details of the methodology used to generate these data.

"Protein spectral counts are generated by extracting proteins from cells, digesting into smaller peptides, separating them on HPLC (high-performance liquid chromatography), and measuring peptide masses on a mass spectrometer to ascertain mass-to-charge ratio. Peptide fragment ratios are then compared to a reference genome and spectral counts per protein are enumerated."

"Nitrogen fixation by cyanobacteria supplies critical bioavailable nitrogen to marine ecosystems worldwide; however, field and lab data have demonstrated it to be limited by iron, phosphorus and/or CO2. To address unknown future interactions among these factors, we grew the nitrogen-fixing cyanobacterium Trichodesmium for 1 year under Fe/P co-limitation following 7 years of both low and high CO2 selection. Fe/P co-limited cell lines demonstrated a complex cellular response including increased growth rates, broad proteome restructuring and cell size reductions relative to steady-state growth limited by either Fe or P alone. Fe/P co-limitation increased abundance of a protein containing a conserved domain previously implicated in cell size regulation, suggesting a similar role in Trichodesmium. Increased CO2 further induced nutrient-limited proteome shifts in widespread core metabolisms. Our results thus suggest that N2-fixing microbes may be significantly impacted by interactions between elevated CO2 and nutrient limitation, with broad implications for global biogeochemical cycles in the future ocean."

"Spectral counts compare a specific protein’s abundance between treatments, rather than against other proteins, because the sensitivity of spectral counts can vary between proteins depending on the number of tryptic peptides within the sequence and their chemical characteristics." 

BCO-DMO data manager notes:
* Data version 2: 2018-03-15 replaces version 1: 2016-06-22. Data version 2 removed column "accession_numbers" containing protein sequence accession numbers at NCBI which were no loger valid due to an annotation remapping effort.  The appropriate protein accessions can instead be found through the NCBI BioProject page:  PRJNA318.  The data parameter "Gene ID" was changed to name "Locus Tag" to be consistent with terminology at IMG and NCBI.

Description from NSF award abstract:
This study will employ a novel combination of experimental evolution techniques and state-of-the-art molecular methods to yield unique insights into adaptive changes in the keystone marine cyanobacteria Trichodesmium and Crocosphaera in response to selection by high CO2. Several studies have suggested that N2-fixation rates of the biogeochemically-critical cyanobacteria Trichodesmium and Crocosphaera may increase dramatically in the future high CO2 ocean, but these have all used the same limited set of cultured isolates and considered cells only briefly acclimated to elevated CO2. The investigator's new results, however, demonstrate that a broad diversity of high- and low-CO2 adapted ecotypes exists within each diazotroph genus. Furthermore, in a preliminary four year experimental evolution study with Trichodesmium, the PIs observed large adaptive responses following 500-700 generations of selection by high CO2- but in a completely unexpected way. All of the six replicate high CO2-adapted cell lines exhibited strong constitutive up-regulation of N2 fixation rates. These very elevated N2 fixation rates continued, even though the cultures have were switched back to low-CO2 conditions for many months. Expression of the nif operon and N assimilatory genes was also up-regulated in these cell lines, as is expression of many intergenic regions of the genome.

The investigators hypothesize that constitutive up-regulation of cellular N2 fixation systems may be a common adaptive response of both Trichodesmium and Crocosphaera under extended selection by elevated CO2. This project will test this hypothesis in a four-year experimental evolution study to determine the adaptive responses of both high- and low-CO2 specialized ecotypes of these two diazotrophs to increased CO2.

The investigators will grow representative high- and low-CO2 adapted ecotypes from each genus in well-replicated cell lines at 380 ppm and 750 ppm CO2 for up to 1000 generations. Periodically, they will perform "switch" experiments to measure N2 and CO2 fixation rates and growth rates of high CO2-selected cell lines grown briefly (one week) at low CO2, and vice versa. These switch experiments will allow screening for cell lines which exhibit adaptive changes in phenotypically-expressed rate parameters, such as those observed in the preliminary Trichodesmium study. Evolutionary mechanisms in the CO2-selected cell lines will be examined by comparison of changes in their genomes, transcriptomes, and proteomes over time relative to reference genomes, using frozen samples archived monthly during the preceding selection period. Examination of these molecular and biochemical changes will be coordinated with an in-depth array of physiological and biogeochemical analyses. This combined approach will allow an evaluation of potential adaptive mechanisms in diazotrophic cyanobacteria ranging from indel, duplication, single nucleotide polymorphism, and transposition mutations to altered putative non-coding RNA expression, protein expression, and post-translational protein modifications, and then allow the investigators to link these mechanisms directly with their potential impacts on ecosystem-level biogeochemical processes like N2 and CO2 fixation. Finally, the research team will determine how long term selection by high CO2 affects the iron and phosphorus requirements of Trichodesmium and Crocosphaera, since constitutive up-regulation of N2 fixation would also have major implications for limitation of diazotrophs by these two critical nutrients in the future high CO2 ocean.