In situ transcriptomic analysis of the globally important keystone N2-fixing taxon Crocosphaera watsonii

Department of Ocean Sciences, University of California Santa Cruz, Santa Cruz, CA, USA.
The ISME Journal (Impact Factor: 9.3). 03/2009; 3(5):618-31. DOI: 10.1038/ismej.2009.8
Source: PubMed


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.

14 Reads
  • Source
    • "Synechococcus are known to release siderophores which may also be strong ligands for Co(III) as demonstrated with the siderophore desferrioxamine B (DFOB, log K CoHDFOB = 37.5) (Duckworth et al., 2009). The N 2 -fixing marine cyanobacterium Crocosphaera watsonii is also found in our study region (Hewson et al., 2009) and may have the potential to produce siderophores (Hopkinson and Morel, 2009) though none have been detected yet. In the case of ligand production, it could be expected that excess unbound organic Co ligands may be found. "
    [Show abstract] [Hide abstract]
    ABSTRACT: Recent studies highlight the role of cobalt (Co) as an important micro-nutrient with a complex scavenged type oceanic distribution. To better understand the biogeochemical cycle of Co we investigate the distribution, speciation and reactivity of dissolved Co in the eastern tropical North Atlantic in the upper 800 m of the water column. For this purpose, we complement classical Co ligand titrations that require a thermodynamic equilibrium with evaluations of ligand-exchange kinetics and reducibility of potential Co(III) species. The experiments include additions of the artificial Co binding ligands dimethylglyoxime or Nioxime and detection by cathodic stripping voltammetry. We find two pools of Co compounds: a labile fraction that exchanges Co within minutes and a strong/inert fraction that does not react within a 24-h period. No intermediate, slowly exchanging fraction is observed. Detection window experiments to determine complex stability constants show that the labile Co fraction is weak and likely consists of Co(II) complexes with no detectable free Co(II) ligands. The fraction of inert Co is always highest at the depth of the chlorophyll-a maximum. Addition of the reductant ascorbate increases the fraction of Co with rapid ligand-exchange kinetics and indicates the presence of dissolved reducible Co(III). The apparent Co(III) reducibility is highest at the chlorophyll-a maximum and decreases in deeper waters. Our results are in agreement with phytoplankton and associated bacteria being a source of Co(III) species, such as vitamin B12. The presented results have important implications for our understanding of the biological availability and the marine cycle of Co.
    Full-text · Article · Oct 2014 · Marine Chemistry
  • Source
    • "Similarly, though the 16S-23S rRNA ITS region is variable among the picocyanobacteria Prochlorococcus and Synechococcus (Rocap et al. 2002), Crocosphaera 16S-23S ITS sequences from phenotypically distinct cultures were highly similar (Webb et al. 2009). Initial genomic studies found that cultivated and wild Crocosphaera genomes had unusually high numbers of transposases, suggesting a mechanism for adaptation to changing environmental conditions and establishment of the variety of phenotypic differences between strains (Mes and Doeleman 2006, Zehr et al. 2007a, Hewson et al. 2009a, Bench et al. 2011, 2013). However, sequencing of additional genomes does not support these conclusions as five of six sequenced genomes did not have unusually high numbers of transposons (Bench et al. 2013). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Marine nitrogen-fixing cyanobacteria play a central role in the open-ocean microbial community by providing fixed nitrogen (N) to the ocean from atmospheric dinitrogen (N2) gas. Once thought to be dominated by one genus of cyanobacteria, Trichodesmium, it is now clear that marine N2-fixing cyanobacteria in the open ocean are more diverse, include several previously unknown symbionts, and are geographically more widespread than expected. The next challenge is to understand the ecological implications of this genetic and phenotypic diversity for global oceanic N cycling. One intriguing aspect of the cyanobacterial N2 fixers ecology is the range of cellular interactions they engage in, either with cells of their own species or with photosynthetic protists. From organelle-like integration with the host cell to a free-living existence, N2-fixing cyanobacteria represent the range of types of interactions that occur among microbes in the open ocean. Here, we review what is known about the cellular interactions carried out by marine N2-fixing cyanobacteria and where future work can help. Discoveries related to the functional roles of these specialized cells in food webs and the microbial community will improve how we interpret their distribution and abundance patterns and contributions to global N and carbon (C) cycles.
    Preview · Article · Dec 2013 · Journal of Phycology
  • Source
    • "Physiological studies of cultivated and natural populations of C. watsonii have identified a number of genetic strategies which appear to be adaptations to the oligotrophic environment. These include regulation of gene expression, nitrogen fixation rates, and cellular protein content in response to changes in nutrient (e.g., iron and phosphorus) levels and other environmental variables (Webb et al. 2001, Tuit et al. 2004, Falcon et al. 2005, Dyhrman and Haley 2006, Fu et al. 2008, Hewson et al. 2009, Compaor e and Stal 2010, Shi et al. 2010, Saito et al. 2011). Currently, cultivated C. watsonii strains can be divided into two broad phenotypic categories: (i) those that produce large amounts of exopolysaccharide (EPS) and have larger cell diameters (over 4 lm), and (ii) those that do not produce noticeable EPS, and have cell diameters less than 4 lm (Webb et al. 2009, Sohm et al. 2011). "
    [Show abstract] [Hide abstract]
    ABSTRACT: Crocosphaera watsonii, a unicellular nitrogen-fixing cyanobacterium found in oligotrophic oceans, is important in marine carbon and nitrogen cycles. Isolates of C. watsonii can be separated into at least two phenotypes with environmentally important differences, indicating possibly distinct ecological roles and niches. To better understand the evolutionary history and variation in metabolic capabilities among strains and phenotypes, this study compared the genomes of six C. watsonii strains, three from each phenotypic group, which had been isolated over several decades from multiple ocean basins. While a substantial portion of each genome was nearly identical to sequences in the other strains, a few regions were identified as specific to each strain and phenotype, some of which help explain observed phenotypic features. Overall, the small-cell type strains had smaller genomes and a relative loss of genetic capabilities, while the large-cell type strains were characterized by larger genomes, some genetic redundancy, and potentially increased adaptations to iron and phosphorus limitation. As such, strains with shared phenotypes were evolutionarily more closely related than those with the opposite phenotype, regardless of isolation location or date. Unexpectedly, the genome of the type-strain for the species, C. watsonii WH8501, was quite unusual even among strains with a shared phenotype, indicating it may not be an ideal representative of the species. The genome sequences and analyses reported in this study will be important for future investigations of the proposed differences in adaptation of the two phenotypes to nutrient limitation, and to identify phenotype-specific distributions in natural Crocosphaera populations.
    Full-text · Article · Aug 2013 · Journal of Phycology
Show more