GC-Content evolution in bacterial genomes: The biased gene conversion hypothesis expands

The characterization of functional elements in genomes relies on the identification of the footprints of natural selection. In this quest, taking into account neutral evolutionary processes such as mutation and genetic drift is crucial because these forces can generate patterns that may obscure or mimic signatures of selection. In mammals, and probably in many eukaryotes, another such confounding factor called GC-Biased Gene Conversion (gBGC) has been documented. This mechanism generates patterns identical to what is expected under selection for higher GC-content, specifically in highly recombining genomic regions. Recent results have suggested that a mysterious selective force favouring higher GC-content exists in Bacteria but the possibility that it could be gBGC has been excluded. Here, we show that gBGC is probably at work in most if not all bacterial species. First we find a consistent positive relationship between the GC-content of a gene and evidence of intra-genic recombination throughout a broad spectrum of bacterial clades. Second, we show that the evolutionary force responsible for this pattern is acting independently from selection on codon usage, and could potentially interfere with selection in favor of optimal AU-ending codons. A comparison with data from human populations shows that the intensity of gBGC in Bacteria is comparable to what has been reported in mammals. We propose that gBGC is not restricted to sexual Eukaryotes but also widespread among Bacteria and could therefore be an ancestral feature of cellular organisms. We argue that if gBGC occurs in bacteria, it can account for previously unexplained observations, such as the apparent non-equilibrium of base substitution patterns and the heterogeneity of gene composition within bacterial genomes. Because gBGC produces patterns similar to positive selection, it is essential to take this process into account when studying the evolutionary forces at work in bacterial genomes

Ancestral genome estimation reveals the history of ecological diversification in Agrobacterium

Horizontal gene transfer (HGT) is considered as a major source of innovation in bacteria, and as such is expected to drive adaptation to new ecological niches. However, among the many genes acquired through HGT along the diversification history of genomes, only a fraction may have actively contributed to sustained ecological adaptation. We used a phylogenetic approach accounting for the transfer of genes (or groups of genes) to estimate the history of genomes in Agrobacterium biovar 1, a diverse group of soil and plant-dwelling bacterial species. We identified clade-specific blocks of cotransferred genes encoding coherent biochemical pathways that may have contributed to the evolutionary success of key Agrobacterium clades. This pattern of gene coevolution rejects a neutral model of transfer, in which neighboring genes would be transferred independently of their function and rather suggests purifying selection on collectively coded acquired pathways. The acquisition of these synapomorphic blocks of cofunctioning genes probably drove the ecological diversification of Agrobacterium and defined features of ancestral ecological niches, which consistently hint at a strong selective role of host plant rhizospheres

Differential rotation and meridional flow in the solar supergranulation layer: Measuring the eddy viscosity

We measure the eddy viscosity in the outermost layers of the solar convection zone by comparing the rotation law computed with the Reynolds stress resulting from f-plane simulations of the angular momentum transport in rotating convection with the observed differential rotation pattern. The simulations lead to a negative vertical and a positive horizontal angular momentum transport. The consequence is a subrotation of the outermost layers, as it is indeed indicated both by helioseismology and the observed rotation rates of sunspots. In order to reproduce the observed gradient of the rotation rate a value of about 1.5 x 10^{13} cm/s for the eddy viscosity is necessary. Comparison with the magnetic eddy diffusivity derived from the sunspot decay yields a surprisingly large magnetic Prandtl number of 150 for the supergranulation layer. The negative gradient of the rotation rate also drives a surface meridional flow towards the poles, in agreement with the results from Doppler measurements. The successful reproduction of the abnormally positive horizontal cross correlation (on the northern hemisphere) observed for bipolar groups then provides an independent test for the resulting eddy viscosity.Comment: 6 pages, 8 figures, Astronomy and Astrophysics (subm.

Efficient and feasible state tomography of quantum many-body systems

We present a novel method to perform quantum state tomography for many-particle systems which are particularly suitable for estimating states in lattice systems such as of ultra-cold atoms in optical lattices. We show that the need for measuring a tomographically complete set of observables can be overcome by letting the state evolve under some suitably chosen random circuits followed by the measurement of a single observable. We generalize known results about the approximation of unitary 2-designs, i.e., certain classes of random unitary matrices, by random quantum circuits and connect our findings to the theory of quantum compressed sensing. We show that for ultra-cold atoms in optical lattices established techniques like optical super-lattices, laser speckles, and time-of-flight measurements are sufficient to perform fully certified, assumption-free tomography. Combining our approach with tensor network methods - in particular the theory of matrix-product states - we identify situations where the effort of reconstruction is even constant in the number of lattice sites, allowing in principle to perform tomography on large-scale systems readily available in present experiments.Comment: 10 pages, 3 figures, minor corrections, discussion added, emphasizing that no single-site addressing is needed at any stage of the scheme when implemented in optical lattice system

Fate of CMY-2-encoding plasmids introduced into the human fecal microbiota by exogenous Escherichia coli

The gut is a hot spot for transfer of antibiotic resistance genes from ingested exogenous bacteria to the indigenous microbiota. The objective of this study was to determine the fate of two nearly identical blaCMY-2-harboring plasmids introduced into the human fecal microbiota by two Escherichia coli strains isolated from human and poultry meat, respectively. The chromosome and the CMY-2-encoding plasmid of both strains were labeled with distinct fluorescent markers (mCherry and GFP), allowing Fluorescence Activated Cell Sorting (FACS)-based tracking of the strain and the resident bacteria that have acquired its plasmid. Each strain was introduced into an established in vitro gut model (CoMiniGut) inoculated with individual feces from ten healthy volunteers. Fecal samples collected 2, 6 and 24 h after strain inoculation were analyzed by FACS and plate counts. Although the human strain survived better than the poultry meat strain, both strains transferred their plasmids to the fecal microbiota at concentrations as low as 102 CFU/mL. Strain survival and plasmid transfer varied significantly depending on inoculum concentration and individual fecal microbiota. Identification of transconjugants by 16S rRNA gene sequencing and MALDI-TOF mass spectrometry revealed that the plasmids were predominantly acquired by Enterobacteriaceae such as E. coli and Hafnia alvei. Our experimental data demonstrate that exogenous E. coli of human or animal origin can readily transfer CMY-2-encoding IncI1 plasmids to the human fecal microbiota. Low amounts of exogenous strain are sufficient to ensure plasmid transfer if the strain is able to survive the gastric environment