Influence of pore-scale disorder on viscous fingering during drainage

We study viscous fingering during drainage experiments in linear Hele-Shaw cells filled with a random porous medium. The central zone of the cell is found to be statistically more occupied than the average, and to have a lateral width of 40% of the system width, irrespectively of the capillary number $Ca$. A crossover length $w_f \propto Ca^{-1}$ separates lower scales where the invader's fractal dimension $D\simeq1.83$ is identical to capillary fingering, and larger scales where the dimension is found to be $D\simeq1.53$. The lateral width and the large scale dimension are lower than the results for Diffusion Limited Aggregation, but can be explained in terms of Dielectric Breakdown Model. Indeed, we show that when averaging over the quenched disorder in capillary thresholds, an effective law $v\propto (\nabla P)^2$ relates the average interface growth rate and the local pressure gradient.Comment: 4 pages, 4 figures, submitted to Phys Rev Letter

Global genomic analysis of microbial biotransformation of arsenic highlights the importance of arsenic methylation in environmental and human microbiomes

Arsenic is a ubiquitous toxic element, the global cycle of which is highly affected by microbial redox reactions and assimilation into organoarsenic compounds through sequential methylation reactions. While microbial biotransformation of arsenic has been studied for decades, the past years have seen the discovery of multiple new genes related to arsenic metabolism. Still, most studies focus on a small set of key genes or a small set of cultured microorganisms. Here, we leveraged the recently greatly expanded availability of microbial genomes of diverse organisms from lineages lacking cultivated representatives, including those reconstructed from metagenomes, to investigate genetic repertoires of taxonomic and environmental controls on arsenic metabolic capacities. Based on the collection of arsenic-related genes, we identified thirteen distinct metabolic guilds, four of which combine the aio and ars operons. We found that the best studied phyla have very different combinations of capacities than less well-studied phyla, including phyla lacking isolated representatives. We identified a distinct arsenic gene signature in the microbiomes of humans exposed or likely exposed to drinking water contaminated by arsenic and that arsenic methylation is important in soil and in human microbiomes. Thus, the microbiomes of humans exposed to arsenic have the potential to exacerbate arsenic toxicity. Finally, we show that machine learning can predict bacterial arsenic metabolism capacities based on their taxonomy and the environment from which they were sampled

Transport in rough self-affine fractures

Transport properties of three-dimensional self-affine rough fractures are studied by means of an effective-medium analysis and numerical simulations using the Lattice-Boltzmann method. The numerical results show that the effective-medium approximation predicts the right scaling behavior of the permeability and of the velocity fluctuations, in terms of the aperture of the fracture, the roughness exponent and the characteristic length of the fracture surfaces, in the limit of small separation between surfaces. The permeability of the fractures is also investigated as a function of the normal and lateral relative displacements between surfaces, and is shown that it can be bounded by the permeability of two-dimensional fractures. The development of channel-like structures in the velocity field is also numerically investigated for different relative displacements between surfaces. Finally, the dispersion of tracer particles in the velocity field of the fractures is investigated by analytic and numerical methods. The asymptotic dominant role of the geometric dispersion, due to velocity fluctuations and their spatial correlations, is shown in the limit of very small separation between fracture surfaces.Comment: submitted to PR

Clades of huge phages from across Earth's ecosystems.

Bacteriophages typically have small genomes1 and depend on their bacterial hosts for replication2. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems

Influence of Viscous Fingering on Dynamic Saturation–Pressure Curves in Porous Media

We report on results from primary drainage experiments on quasi-two-dimensional porous models. The models are transparent, allowing the displacement process and structure to be monitored in space and time during primary drainage experiments carried out at various speeds. By combining detailed information on the displacement structure with global measurements of pressure, saturation and the capillary number Ca, we obtain a scaling relation relating pressure, saturation, system size and capillary number. This scaling relation allows pressure-saturation curves for a wide range of capillary numbers to be collapsed on the same master curve. We also show that in the case of primary drainage, the dynamic effect in the capillary pressure-saturation relationship observed on partially water saturated soil samples might be explained by the combined effect of capillary pressure along the invasion front of the gaseous phase, and pressure changes caused by viscous effects in the wetting fluid phase. © 2010 The Author(s)

Sea ice dynamics across the Mid-Pleistocene transition in the Bering Sea.

Sea ice and associated feedback mechanisms play an important role for both long- and short-term climate change. Our ability to predict future sea ice extent, however, hinges on a greater understanding of past sea ice dynamics. Here we investigate sea ice changes in the eastern Bering Sea prior to, across, and after the Mid-Pleistocene transition (MPT). The sea ice record, based on the Arctic sea ice biomarker IP25 and related open water proxies from the International Ocean Discovery Program Site U1343, shows a substantial increase in sea ice extent across the MPT. The occurrence of late-glacial/deglacial sea ice maxima are consistent with sea ice/land ice hysteresis and land-glacier retreat via the temperature-precipitation feedback. We also identify interactions of sea ice with phytoplankton growth and ocean circulation patterns, which have important implications for glacial North Pacific Intermediate Water formation and potentially North Pacific abyssal carbon storage

Clades of huge phages from across Earth's ecosystems

Bacteriophages typically have small genomes and depend on their bacterial hosts for replication. Here we sequenced DNA from diverse ecosystems and found hundreds of phage genomes with lengths of more than 200 kilobases (kb), including a genome of 735 kb, which is-to our knowledge-the largest phage genome to be described to date. Thirty-five genomes were manually curated to completion (circular and no gaps). Expanded genetic repertoires include diverse and previously undescribed CRISPR-Cas systems, transfer RNAs (tRNAs), tRNA synthetases, tRNA-modification enzymes, translation-initiation and elongation factors, and ribosomal proteins. The CRISPR-Cas systems of phages have the capacity to silence host transcription factors and translational genes, potentially as part of a larger interaction network that intercepts translation to redirect biosynthesis to phage-encoded functions. In addition, some phages may repurpose bacterial CRISPR-Cas systems to eliminate competing phages. We phylogenetically define the major clades of huge phages from human and other animal microbiomes, as well as from oceans, lakes, sediments, soils and the built environment. We conclude that the large gene inventories of huge phages reflect a conserved biological strategy, and that the phages are distributed across a broad bacterial host range and across Earth's ecosystems

A global ocean atlas of eukaryotic genes

While our knowledge about the roles of microbes and viruses in the ocean has increased tremendously due to recent advances in genomics and metagenomics, research on marine microbial eukaryotes and zooplankton has benefited much less from these new technologies because of their larger genomes, their enormous diversity, and largely unexplored physiologies. Here, we use a metatranscriptomics approach to capture expressed genes in open ocean Tara Oceans stations across four organismal size fractions. The individual sequence reads cluster into 116 million unigenes representing the largest reference collection of eukaryotic transcripts from any single biome. The catalog is used to unveil functions expressed by eukaryotic marine plankton, and to assess their functional biogeography. Almost half of the sequences have no similarity with known proteins, and a great number belong to new gene families with a restricted distribution in the ocean. Overall, the resource provides the foundations for exploring the roles of marine eukaryotes in ocean ecology and biogeochemistry