Jonathan Mercier

MicroScope in 2017: an expanding and evolving integrated resource for community expertise of microbial genomes

The annotation of genomes from NGS platforms needs to be automated and fully integrated. However, maintaining consistency and accuracy in genome annotation is a challenging problem because millions of protein database entries are not assigned reliable functions. This shortcoming limits the knowledge that can be extracted from genomes and metabolic models. Launched in 2005, the MicroScope platform (http://www.genoscope.cns.fr/agc/microscope) is an integrative resource that supports systematic and efficient revision of microbial genome annotation, data management and comparative analysis. Effective comparative analysis requires a consistent and complete view of biological data, and therefore, support for reviewing the quality of functional annotation is critical. MicroScope allows users to analyze microbial (meta)genomes together with post-genomic experiment results if any (i.e. transcriptomics, re-sequencing of evolved strains, mutant collections, phenotype data). It combines tools and graphical interfaces to analyze genomes and to perform the expert curation of gene functions in a comparative context. Starting with a short overview of the MicroScope system, this paper focuses on some major improvements of the Web interface, mainly for the submission of genomic data and on original tools and pipelines that have been developed and integrated in the platform: computation of pan-genomes and prediction of biosynthetic gene clusters. Today the resource contains data for more than 6000 microbial genomes, and among the 2700 personal accounts (65% of which are now from foreign countries), 14% of the users are performing expert annotations, on at least a weekly basis, contributing to improve the quality of microbial genome annotations.

Contrasting tectonically driven exhumation and incision patterns, western versus central Nepal Himalaya

Although the Himalayan range is classically presented as cylindrical along strike, segmentation of the range in terms of structure, topography, precipitation, and erosion patterns is becoming widely recognized. The potential climatic or tectonic controls on these lateral variations remain controversial. Thermokinematic models predict that the geometry of the main Himalayan detachment controls the kinematics, exhumation, and topography of the orogen: where the detachment includes a major crustal ramp, the topography shows a steep gradient that focuses orographic precipitation and exhumation, whereas the topography is gentler and exhumation less focused above a flatter detachment. We test this prediction by comparing the patterns of river incision (specific stream power) and long-term exhumation (from apatite fission track thermochronology) in central Nepal, where a major crustal ramp has been imaged by geophysical methods, with new exploratory data from the remote Karnali River transect in western Nepal, where a ramp is predicted to be absent or minor. Our results show that both exhumation rates and river incision capacity are significantly higher and focused on the crustal ramp in central Nepal, whereas they are lower and the pattern is more diffuse in western Nepal. These differences support a model in which lateral variations in topography and exhumation are controlled by variations in the geometry of the detachment, and imply that along-strike climatic variations in the Himalaya respond to tectonics rather than driving it.

A simple model for regolith formation by chemical weathering

We present here a new model for the formation of regolith on geological time scales by chemical weathering based on the assumption that the rate of chemical weathering is primarily controlled by the ability of groundwater to transport solute away from the reacting solid-fluid interface and keep the system from reaching equilibrium (saturation). This allows us to specify the rate of propagation of the weathering front as linearly proportional to the pore fluid velocity which we obtain by computing the water table geometry in the regolith layer. The surface of the regolith layer is affected by mass transport and erosion. The main prediction of the model is that the geometry of the regolith, i.e. whether it is thickest beneath topographic highs or topographic lows, is controlled by the value of a dimensionless number, which depends on the square of the surface slope, the hydraulic conductivity and local precipitation rate, but is independent of the chemical weathering rate. In orogenic environments, where regolith formation by chemical weathering competes with surface erosion, the model predicts that the existence and thickness of the regolith layer are controlled by the value of another dimensionless number which is the ratio between the time scale for erosion and the time scale for weathering. The model also predicts that in anorogenic areas, regolith thickness increases as the square root of time, whereas in orogenic environments, a steady-state regolith thickness can be achieved, when the propagation of the weathering front equals erosion rate.

Fore arc tectonothermal evolution of the El Oro metamorphic province (Ecuador) during the Mesozoic

The El Oro metamorphic province of SW Ecuador is a composite massif made of juxtaposed terranes of both continental and oceanic affinity that has been located in a fore-arc position since Late Paleozoic times. Various geochemical, geochronological, and metamorphic studies have been undertaken on the El Oro metamorphic province, providing an understanding of the origin and age of the distinct units. However, the internal structures and geodynamic evolution of this area remain poorly understood. Our structural analysis and thermal modeling in the El Oro metamorphic province show that this fore-arc zone underwent four main geological events. (1) During Triassic times (230–225 Ma), the emplacement of the Piedras gabbroic unit at crustal-root level (~9 kbar) triggered partial melting of the metasedimentary sequence under an E-W extensional regime at pressure-temperature conditions ranging from 4.5 to 8.5 kbar and from 650 to 900°C for the migmatitic unit. (2) At 226 Ma, the tectonic underplating of the Arenillas-Panupali oceanic unit (9 kbar and 300°C) thermally sealed the fore-arc region. (3) Around the Jurassic-Cretaceous boundary, the shift from trench-normal to trench-parallel subduction triggered the exhumation and underplating of the high-pressure, oceanic Raspas Ophiolitic Complex (18 kbar and 600°C) beneath the El Oro Group (130–120 Ma). This was followed by the opening of a NE-SW pull-apart basin, which tilted the massif along an E-W subhorizontal axis (110 Ma). (4) In Late Cretaceous times, an N-S compressional event generated heterogeneous deformation due to the presence of the Cretaceous Celica volcanic arc, which acted as a buttress and predominantly affected the central and eastern part of the massif.

Convection in a partially molten metasedimentary crust? Insights from the El Oro complex (Ecuador)

The El Oro complex, southwestern Ecuador, is a tilted section of the metasedimentary Ecuadorian forearc, which was partially molten during Triassic time due to gabbroic magma emplacement. Pressure and maximum temperature estimates show that the metamorphic gradient during anatexis was 45 °C/km in the upper crust and 10 °C/km in the 7–8 km garnet-bearing migmatitic lower crust, controlled by biotite-breakdown melting reactions. Our petrological and geochemical studies indicate that melts produced during biotite-breakdown (5–15 vol%) were trapped and pervasively distributed in the garnet-bearing migmatite. Based on these results we carried out one-dimensional thermal modeling to characterize the heat transfer processes that led to the establishment of such a low thermal gradient during partial melting. Our results show that neither diffusive nor upward melt transfer models account for the low metamorphic gradient in the garnet-bearing migmatite. We demonstrate that in the El Oro complex, convection of the garnet-bearing migmatitic layer is the most likely heat transfer process that explains all the petrological, geochemical, and metamorphic data.