Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation

  title={Genome divergence in two Prochlorococcus ecotypes reflects oceanic niche differentiation},
  author={Gabrielle Rocap and Frank W. Larimer and Jane E. Lamerdin and Stephanie Malfatti and Patrick S. G. Chain and Nathan A. Ahlgren and and M. Carmen Ramirez de Arellano and Maureen L. Coleman and Loren J. Hauser and Wolfgang R. Hess and Zackary I. Johnson and Miriam L. Land and Debbie Lindell and Anton F. Post and Warren Regala and Manesh Shah and Stephanie L. Shaw and Claudia Steglich and Matthew B. Sullivan and Claire S. Ting and Andrew C. Tolonen and Eric A. Webb and Erik R. Zinser and Sallie W. Chisholm},
The marine unicellular cyanobacterium Prochlorococcus is the smallest-known oxygen-evolving autotroph. It numerically dominates the phytoplankton in the tropical and subtropical oceans, and is responsible for a significant fraction of global photosynthesis. Here we compare the genomes of two Prochlorococcus strains that span the largest evolutionary distance within the Prochlorococcus lineage and that have different minimum, maximum and optimal light intensities for growth. The high-light… 

Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus

Reconstruction of past gene gains and losses shows that much of the variability exists at the “leaves of the tree,” between the most closely related strains, which is largely consistent with the relative frequency of Prochlorococcus genes found in global ocean metagenomic databases, further closing the gap between understanding of these organisms in the lab and the wild.

Phosphate acquisition genes in Prochlorococcus ecotypes: Evidence for genome-wide adaptation

Analysis of a metagenomic library from the Sargasso Sea supports the hypothesis that most Prochlorococcus cells in this low-P environment contain the P-acquisition genes seen in MED4, although a number of previously undescribed gene combinations were observed.

Widespread metabolic potential for nitrite and nitrate assimilation among Prochlorococcus ecotypes

The data suggest that the ability to assimilate nitrite and nitrate is associated with microdiverse lineages within high- and low-light (LL) adapted Prochlorococcus ecotypes, and challenges 2 long-held assumptions that Pro chlorococcus cannot assimilate Nitrite and only LL adapted ecotypes can use nitrite.

Ecological Genomics of Marine Picocyanobacteria

This review puts the current knowledge of marine picocyanobacterial genomics into an environmental context and presents previously unpublished genomic information arising from extensive genomic comparisons in order to provide insights into the adaptations of these marine microbes to their environment and how they are reflected at the genomic level.

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria

It is proposed that while members of a given marine Synechococcus lineage may have the same broad geographical distribution, local niche occupancy is facilitated by lateral gene transfers, a process in which genomic islands play a key role as a repository for transferred genes.

Three Prochlorococcus Cyanophage Genomes: Signature Features and Ecological Interpretations

These marine cyanophages appear to be variations of two well-known phages—T7 and T4—but contain genes that, if functional, reflect adaptations for infection of photosynthetic hosts in low-nutrient oceanic environments.

Evolutionary Mechanisms of Long-Term Genome Diversification Associated With Niche Partitioning in Marine Picocyanobacteria

Comparison of core protein sequences highlighted variants specific to cold thermotypes, notably involved in carotenoid biosynthesis and the oxidative stress response, revealing that long-term adaptation to thermal niches relies on amino acid substitutions rather than on gene content variation.

Survey of the green picoalga Bathycoccus genomes in the global ocean

Analysis of 122 global ocean whole DNA metagenome samples from the Tara-Oceans expedition reveals that populations of Bathycoccus that were previously identified by 18S rRNA V9 metabarcodes are only composed of these two genomes.

Characterization of Prochlorococcus clades from iron-depleted oceanic regions

Detailed genomic analysis indicates that these clades comprise organisms that are adapted to iron-depleted environments by reducing their iron quota through the loss of several iron-containing proteins that likely function as electron sinks in the photosynthetic pathway in other Prochlorococcus clades from high-light environments.

Ecotype diversity in the marine picoeukaryote Ostreococcus (Chlorophyta, Prasinophyceae).

Different growth rates and features strongly suggest distinct adaptation to environmental conditions encountered at surface and the bottom of the oceanic euphotic zone, reminiscent of that described in prokaryotes.



Physiology and molecular phylogeny of coexisting Prochlorococcus ecotypes

Direct evidence supporting the coexistence and distribution of multiple ecotypes permits the survival of the population as a whole over a broader range of environmental conditions than would be possible for a homogeneous population is reported.

The photosynthetic apparatus of Prochlorococcus: Insights through comparative genomics

Intriguing features found in both Prochlorococcus strains include a gene cluster for Rubisco and carboxysomal proteins that is likely of non-cyanobacterial origin and two genes for a putative $$\varepsilon$$ and β lycopene cyclase, respectively, explaining how Pro chlorococcus may synthesize the α branch of carotenoids that is common in green organisms but not in other cyanobacteria.

Photophysiology of the marine cyanobacterium Prochlorococcus: Ecotypic differences among cultured isolates

The photophysiology of 10 different Prochlorococcus isolates from diverse oceanographic regimes is compared and it is found that the 10 isolates could be grouped into two loose clusters based on their growth response to varying light intensity and their chlorophyll b/a2 (Chl b/ a2) ratios.

Cyanophages infecting the oceanic cyanobacterium Prochlorococcus

The isolation of cyanophages that infect Prochlorococcus is reported, and it is hypothesized that gradients in cyanobacterial population diversity, growth rates, and/or the incidence of lysogeny underlie these trends.

Genome sequence of the cyanobacterium Prochlorococcus marinus SS120, a nearly minimal oxyphototrophic genome

  • A. DufresneM. Salanoubat W. Hess
  • Biology, Environmental Science
    Proceedings of the National Academy of Sciences of the United States of America
  • 2003
The genome of P. marinus SS120 is one of the two smallest genomes of a photosynthetic organism known to date and lacks many genes that are involved in photosynthesis, DNA repair, solute uptake, intermediary metabolism, motility, phototaxis, and other functions that are conserved among other cyanobacteria.

Phycobiliprotein genes of the marine photosynthetic prokaryote Prochlorococcus: evidence for rapid evolution of genetic heterogeneity.

Differences in phycoerythrin gene sequences between Prochlorococcus and Synechococcus appear to be consistent with a model of elevated mutation rates rather than relaxed selection, which suggests that although phycobiliproteins is not a major constituent of the light-harvesting apparatus in Pro chlorococcus, the cpeB and cpeA genes are still under selection, albeit a different type of selection than in SyneChococcus.

Resolution of Prochlorococcus and Synechococcus Ecotypes by Using 16S-23S Ribosomal DNA Internal Transcribed Spacer Sequences

The results provide further evidence that natural populations of Prochlorococcus and Synechococcus consist of multiple coexisting ecotypes, genetically closely related but physiologically distinct, which may vary in relative abundance with changing environmental conditions.

Expression and phylogeny of the multiple antenna genes of the low-light-adapted strain Prochlorococcus marinus SS120 (Oxyphotobacteria)

Pcb genes likely evolved at a different rate in the two Prochlorococcus ecotypes and their early multiplication and diversification is likely a key factor in the successful adaptation of some genotypes to very-low-light conditions.

A genetic manipulation system for oceanic cyanobacteria of the genus Synechococcus

  • B. Brahamsha
  • Biology
    Applied and environmental microbiology
  • 1996
A number of molecular tools for the genetic manipulation of Synechococcus sp.

A novel free-living prochlorophyte abundant in the oceanic euphotic zone

The recent discovery of photosynthetic picoplankton has changed our understanding of marine food webs1. Both prokaryotic2,3 and eukaryotic4,5 species occur in most of the world's oceans and account