In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii
ABSTRACT The diazotrophic cyanobacterium Crocosphaera watsonii supplies fixed nitrogen (N) to N-depleted surface waters of the tropical oceans, but the factors that determine its distribution and contribution to global N(2) fixation are not well constrained for natural populations. Despite the heterogeneity of the marine environment, the genome of C. watsonii is highly conserved in nucleotide sequence in contrast to sympatric planktonic cyanobacteria. We applied a whole assemblage shotgun transcript sequencing approach to samples collected from a bloom of C. watsonii observed in the South Pacific to understand the genomic mechanisms that may lead to high population densities. We obtained 999 C. watsonii transcript reads from two metatranscriptomes prepared from mixed assemblage RNA collected in the day and at night. The C. watsonii population had unexpectedly high transcription of hypothetical protein genes (31% of protein-encoding genes) and transposases (12%). Furthermore, genes were expressed that are necessary for living in the oligotrophic ocean, including the nitrogenase cluster and the iron-stress-induced protein A (isiA) that functions to protect photosystem I from high-light-induced damage. C. watsonii transcripts retrieved from metatranscriptomes at other locations in the southwest Pacific Ocean, station ALOHA and the equatorial Atlantic Ocean were similar in composition to those recovered in the enriched population. Quantitative PCR and quantitative reverse transcriptase PCR were used to confirm the high expression of these genes within the bloom, but transcription patterns varied at shallower and deeper horizons. These data represent the first transcript study of a rare individual microorganism in situ and provide insight into the mechanisms of genome diversification and the ecophysiology of natural populations of keystone organisms that are important in global nitrogen cycling.
SourceAvailable from: Caroline Belser[Show abstract] [Hide abstract]
ABSTRACT: Metatranscriptomics is rapidly expanding our knowledge of gene expression patterns and pathway dynamics in natural microbial communities. However, to cope with the challenges of environmental sampling, various rRNA removal and cDNA synthesis methods have been applied in published microbial metatranscriptomic studies, making comparisons arduous. Whereas efficiency and biases introduced by rRNA removal methods have been relatively well explored, the impact of cDNA synthesis and library preparation on transcript abundance remains poorly characterized. The evaluation of potential biases introduced at this step is challenging for metatranscriptomic samples, where data analyses are complex, for example because of the lack of reference genomes.BMC Genomics 10/2014; 15(1):912. DOI:10.1186/1471-2164-15-912 · 4.04 Impact Factor
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ABSTRACT: Understanding the evolution of the free-living, cyanobacterial, diazotroph Trichodesmium is of great importance because of its critical role in oceanic biogeochemistry and primary production. Unlike the other >150 available genomes of free-living cyanobacteria, only 63.8% of the Trichodesmium erythraeum (strain IMS101) genome is predicted to encode protein, which is 20-25% less than the average for other cyanobacteria and nonpathogenic, free-living bacteria. We use distinctive isolates and metagenomic data to show that low coding density observed in IMS101 is a common feature of the Trichodesmium genus, both in culture and in situ. Transcriptome analysis indicates that 86% of the noncoding space is expressed, although the function of these transcripts is unclear. The density of noncoding, possible regulatory elements predicted in Trichodesmium, when normalized per intergenic kilobase, was comparable and twofold higher than that found in the gene-dense genomes of the sympatric cyanobacterial genera Synechococcus and Prochlorococcus, respectively. Conserved Trichodesmium noncoding RNA secondary structures were predicted between most culture and metagenomic sequences, lending support to the structural conservation. Conservation of these intergenic regions in spatiotemporally separated Trichodesmium populations suggests possible genus-wide selection for their maintenance. These large intergenic spacers may have developed during intervals of strong genetic drift caused by periodic blooms of a subset of genotypes, which may have reduced effective population size. Our data suggest that transposition of selfish DNA, low effective population size, and high-fidelity replication allowed the unusual "inflation" of noncoding sequence observed in Trichodesmium despite its oligotrophic lifestyle.Proceedings of the National Academy of Sciences 03/2015; 112(14). DOI:10.1073/pnas.1422332112 · 9.81 Impact Factor
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ABSTRACT: A dynamical model is proposed that describes the daily dynamics of diazotrophy in a unicellular cyanobacterium, Crocosphaera watsonii WH8501, in regard to light limitation and obligate diazotrophy. In this model, intracellular carbon and nitrogen are both divided into a functional pool and a storage pool. An internal pool that explicitly describes the nitrogenase enzyme is also added. The various intracellular carbon and nitrogen flows between these pools lead to a complex dynamics driven by the light regime. The model is successfully validated with continuous cultures experiments of C. watsonii under three light regimes, indicating that proposed mechanisms accurately reproduce the growth dynamics of this organism under various light environments. Then, a series of model simulations is run for a range of light regimes with different photoperiods and daily light doses. Results reveal how nitrogen and carbon are coupled, through the diel cycle, along with nitrogenase dynamics whose activity is constrained by the light regime. In an ecological perspective, we picture the effect of such irradiance condition on growth and on the carbon to nitrogen stoichiometry on cells. This model could prove useful to understand the latitudinal distribution of this cyanobacterium in the global ocean.Ecological Modelling 10/2014; Accepted. DOI:10.1016/j.ecolmodel.2014.07.016 · 2.33 Impact Factor