Accelerated evolution associated with genome reduction in a free-living prokaryote

BACKGROUND: Three complete genomes of Prochlorococcus species, the smallest and most abundant photosynthetic organism in the ocean, have recently been published. Comparative genome analyses reveal that genome shrinkage has occurred within this genus, associated with a sharp reduction in G+C content. As all examples of genome reduction characterized so far have been restricted to endosymbionts or pathogens, with a host-dependent lifestyle, the observed genome reduction in Prochlorococcus is the first documented example of such a process in a free-living organism. RESULTS: Our results clearly indicate that genome reduction has been accompanied by an increased rate of protein evolution in P. marinus SS120 that is even more pronounced in P. marinus MED4. This acceleration has affected every functional category of protein-coding genes. In contrast, the 16S rRNA gene seems to have evolved clock-like in this genus. We observed that MED4 and SS120 have lost several DNA-repair genes, the absence of which could be related to the mutational bias and the acceleration of amino-acid substitution. CONCLUSIONS: We have examined the evolutionary mechanisms involved in this process, which are different from those known from host-dependent organisms. Indeed, most substitutions that have occurred in Prochlorococcus have to be selectively neutral, as the large size of populations imposes low genetic drift and strong purifying selection. We assume that the major driving force behind genome reduction within the Prochlorococcus radiation has been a selective process favoring the adaptation of this organism to its environment. A scenario is proposed for genome evolution in this genus

Why climate sensitivity may not be so unpredictable ?

International audienceDifferent explanations have been proposed as to why the range of climate sensitivity predicted by GCMs have not lessened substantially in the last decades, and subsequently if it can be reduced. One such study (\textit{Why is climate sensitivity so unpredictable?}, \cite{RB07}) adressed these questions using rather simple theoretical considerations and reached the conclusion that reducing uncertainties on climate feedbacks and underlying climate processes will not yield a large reduction in the envelope of climate sensitivity. In this letter, we revisit the premises of this conclusion. We show that it results from a mathematical artefact caused by peculiar definitions of uncertainty used by these authors. Applying standard concepts and definitions of descriptive statistics to the exact same framework of analysis as Roe and Baker, we show that within this simple framework, reducing inter-model spread on feedbacks does in fact induce a reduction of uncertainty on climate sensitivity, almost proportionally. Therefore, following Roe and Baker assumptions, climate sensitivity is actually not so unpredictable. %We then briefly focus on ongoing advances in cloud physics that may narrow the spread on feedbacks, thus reducing the uncertainty on climate sensitivity

Diversity and evolution of phycobilisomes in marine Synechococcus spp.: a comparative genomics study

Background Marine Synechococcus owe their specific vivid color (ranging from blue-green to orange) to their large extrinsic antenna complexes called phycobilisomes, comprising a central allophycocyanin core and rods of variable phycobiliprotein composition. Three major pigment types can be defined depending on the major phycobiliprotein found in the rods (phycocyanin, phycoerythrin I or phycoerythrin II). Among strains containing both phycoerythrins I and II, four subtypes can be distinguished based on the ratio of the two chromophores bound to these phycobiliproteins. Genomes of eleven marine Synechococcus strains recently became available with one to four strains per pigment type or subtype, allowing an unprecedented comparative genomics study of genes involved in phycobilisome metabolism. Results By carefully comparing the Synechococcus genomes, we have retrieved candidate genes potentially required for the synthesis of phycobiliproteins in each pigment type. This includes linker polypeptides, phycobilin lyases and a number of novel genes of uncharacterized function. Interestingly, strains belonging to a given pigment type have similar phycobilisome gene complements and organization, independent of the core genome phylogeny (as assessed using concatenated ribosomal proteins). While phylogenetic trees based on concatenated allophycocyanin protein sequences are congruent with the latter, those based on phycocyanin and phycoerythrin notably differ and match the Synechococcus pigment types. Conclusion We conclude that the phycobilisome core has likely evolved together with the core genome, while rods must have evolved independently, possibly by lateral transfer of phycobilisome rod genes or gene clusters between Synechococcus strains, either via viruses or by natural transformation, allowing rapid adaptation to a variety of light niches

Unraveling the Stratification of an Iron-Oxidizing Microbial Mat by Metatranscriptomics

International audienceA metatranscriptomic approach was used to study community gene expression in a naturally occurring iron-rich microbial mat. Total microbial community RNA was reversely transcribed and sequenced by pyrosequencing. Characterization of expressed gene sequences provided accurate and detailed information of the composition of the transcriptionally active community and revealed phylogenetic and functional stratifications within the mat. Comparison of 16S rRNA reads and delineation of OTUs showed significantly lower values of metatranscriptomic-based richness and diversity in the upper parts of the mat than in the deeper regions. Taxonomic affiliation of rRNA sequences and mRNA genome recruitments indicated that iron-oxidizing bacteria affiliated to the genus Leptothrix, dominated the community in the upper layers of the mat. Surprisingly, type I methanotrophs contributed to the majority of the sequences in the deep layers of the mat. Analysis of mRNA expression patterns showed that genes encoding the three subunits of the particulate methane monooxygenase (pmoCAB) were the most highly expressed in our dataset. These results provide strong hints that iron-oxidation and methane-oxidation occur simultaneously in microbial mats and that both groups of microorganisms are major players in the functioning of this ecosystem

Unraveling the genomic mosaic of a ubiquitous genus of marine cyanobacteria

Background: The picocyanobacterial genus Synechococcus occurs over wide oceanic expanses, having colonized most available niches in the photic zone. Large scale distribution patterns of the different Synechococcus clades (based on 16S rRNA gene markers) suggest the occurrence of two major lifestyles ('opportunists'/'specialists'), corresponding to two distinct broad habitats ('coastal'/'open ocean'). Yet, the genetic basis of niche partitioning is still poorly understood in this ecologically important group. Results: Here, we compare the genomes of 11 marine Synechococcus isolates, representing 10 distinct lineages. Phylogenies inferred from the core genome allowed us to refine the taxonomic relationships between clades by revealing a clear dichotomy within the main subcluster, reminiscent of the two aforementioned lifestyles. Genome size is strongly correlated with the cumulative lengths of hypervariable regions (or 'islands'). One of these, encompassing most genes encoding the light-harvesting phycobilisome rod complexes, is involved in adaptation to changes in light quality and has clearly been transferred between members of different Synechococcus lineages. Furthermore, we observed that two strains (RS9917 and WH5701) that have similar pigmentation and physiology have an unusually high number of genes in common, given their phylogenetic distance. Conclusion: We propose 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. Our work also highlights the need for developing picocyanobacterial systematics based on genome-derived parameters combined with ecological and physiological data

Groundwater Isolation Governs Chemistry and Microbial Community Structure along Hydrologic Flowpaths

International audienceThis study deals with the effects of hydrodynamic functioning of hard-rock aquifers on microbial communities. In hard-rock aquifers, the heterogeneous hydrologic circulation strongly constrains groundwater residence time, hydrochemistry, and nutrient supply. Here, residence time and a wide range of environmental factors were used to test the influence of groundwater circulation on active microbial community composition, assessed by high throughput sequencing of 16S rRNA. Groundwater of different ages was sampled along hydrogeologic paths or loops, in three contrasting hard-rock aquifers in Brittany (France). Microbial community composition was driven by groundwater residence time and hydrogeologic loop position. In recent groundwater, in the upper section of the aquifers or in their recharge zone, surface water inputs caused high nitrate concentration and the predominance of putative denitrifiers. Although denitrification does not seem to fully decrease nitrate concentrations due to low dissolved organic carbon concentrations, nitrate input has a major effect on microbial communities. The occurrence of taxa possibly associated with the application of organic fertilizers was also noticed. In ancient isolated groundwater, an ecosystem based on Fe(II)/Fe(III) and S/SO4 redox cycling was observed down to several 100 of meters below the surface. In this depth section, microbial communities were dominated by iron oxidizing bacteria belonging to Gallionellaceae. The latter were associated to old groundwater with high Fe concentrations mixed to a small but not null percentage of recent groundwater inducing oxygen concentrations below 2.5 mg/L. These two types of microbial community were observed in the three sites, independently of site geology and aquifer geometry, indicating hydrogeologic circulation exercises a major control on microbial communities

Génomique comparée des procaryotes synthétiques marins Prochlorococcus et Synechococcus

The Picocyanobacteria of genres Prochlorococcus and Synechococcus are the most abundant photosynthetic organisms in the ocean. Their ecological success seems to be related to the implementation of different strategies to adapt to different ecological niches. However, the molecular basis to explain the adaptation of these cyanobacteria remain largely unknown. Recently, the genomes of three strains of Prochlorococcus (MED4, SS120 and MIT9313) and two strains of Synechococcus (WH8102 and WH7803) were sequenced. The comparison of these five genomes reveals a low level of genomic differentiation. Nevertheless, the presence of certain genes can be related to characteristics of their ecological niches. Similarly, our work has shown a process of reductive evolution in Prochlorococcus, a phenomenon which was hitherto known only in pathogenic or symbiotic bacteria.Les picocyanobactéries des genres Prochlorococcus et Synechococcus sont les organismes photosynthétiques les plus abondants de l'océan. Leur succès écologique semble être lié à la mise en place de stratégies différentes leur permettant de s'adapter à des niches écologiques distinctes. Cependant, les bases moléculaires expliquant l'adaptation de ces cyanobactéries restent en grande partie inconnues. Récemment, les génomes de trois souches de Prochlorococcus (MED4, SS120 et MIT9313) et de deux souches de Synechococcus (WH8102 et WH7803) ont été séquencés. La comparaison de ces cinq génomes révèle un faible niveau de différenciation génomique. Néanmoins, la présence de certains gènes peut être reliée aux caractéristiques de leurs niches écologiques. De même, nos travaux ont montré un processus d'évolution réductive chez Prochlorococcus, un qui phénomène n'était jusqu'à présent connu que chez les bactéries pathogènes ou symbiotiques

Diversité microbienne et vitesse de renouvellement des eaux souterraines dans les aquifères

communication oral

Functional community analysis of a microbial mat involved in the oxydation of iron by metatranscriptomics

International audienc