Dataset Information

Seismic refraction tracks porosity generation and possible CO₂ production at depth under a headwater catchment.

ABSTRACT: In weathered bedrock aquifers, groundwater is stored in pores and fractures that open as rocks are exhumed and minerals interact with meteoric fluids. Little is known about this storage because geochemical and geophysical observations are limited to pits, boreholes, or outcrops or to inferences based on indirect measurements between these sites. We trained a rock physics model to borehole observations in a well-constrained ridge and valley landscape and then interpreted spatial variations in seismic refraction velocities. We discovered that P-wave velocities track where a porosity-generating reaction initiates in shale in three boreholes across the landscape. Specifically, velocities of 2.7 ± 0.2 km/s correspond with growth of porosity from dissolution of chlorite, the most reactive of the abundant minerals in the shale. In addition, sonic velocities are consistent with the presence of gas bubbles beneath the water table under valley and ridge. We attribute this gas largely to CO₂ produced by 1) microbial respiration in soils as meteoric waters recharge into the subsurface and 2) the coupled carbonate dissolution and pyrite oxidation at depth in the rock. Bubbles may nucleate below the water table because waters depressurize as they flow from ridge to valley and because pores have dilated as the deep rock has been exhumed by erosion. Many of these observations are likely to also describe the weathering and flow path patterns in other headwater landscapes. Such combined geophysical and geochemical observations will help constrain models predicting flow, storage, and reaction of groundwater in bedrock systems.

SUBMITTER: Gu X

PROVIDER: S-EPMC7431088 | biostudies-literature | 2020 Aug

REPOSITORIES: biostudies-literature

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Seismic refraction tracks porosity generation and possible CO<sub>2</sub> production at depth under a headwater catchment.

Gu Xin X Mavko Gary G Ma Lisa L Oakley David D Accardo Natalie N Carr Bradley J BJ Nyblade Andrew A AA Brantley Susan L SL

Proceedings of the National Academy of Sciences of the United States of America 20200727 32

In weathered bedrock aquifers, groundwater is stored in pores and fractures that open as rocks are exhumed and minerals interact with meteoric fluids. Little is known about this storage because geochemical and geophysical observations are limited to pits, boreholes, or outcrops or to inferences based on indirect measurements between these sites. We trained a rock physics model to borehole observations in a well-constrained ridge and valley landscape and then interpreted spatial variations in sei ...[more]

PMID: 32719121

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Project description:BackgroundNext-generation sequencing allows genome-wide analysis of changes in chromatin states and gene expression. Data analysis of these increasingly used methods either requires multiple analysis steps, or extensive computational time. We sought to develop a tool for rapid quantification of sequencing peaks from diverse experimental sources and an efficient method to produce coverage tracks for accurate visualization that can be intuitively displayed and interpreted by experimentalists with minimal bioinformatics background. We demonstrate its strength and usability by integrating data from several types of sequencing approaches.ResultsWe have developed BAMscale, a one-step tool that processes a wide set of sequencing datasets. To demonstrate the usefulness of BAMscale, we analyzed multiple sequencing datasets from chromatin immunoprecipitation sequencing data (ChIP-seq), chromatin state change data (assay for transposase-accessible chromatin using sequencing: ATAC-seq, DNA double-strand break mapping sequencing: END-seq), DNA replication data (Okazaki fragments sequencing: OK-seq, nascent-strand sequencing: NS-seq, single-cell replication timing sequencing: scRepli-seq) and RNA-seq data. The outputs consist of raw and normalized peak scores (multiple normalizations) in text format and scaled bigWig coverage tracks that are directly accessible to data visualization programs. BAMScale also includes a visualization module facilitating direct, on-demand quantitative peak comparisons that can be used by experimentalists. Our tool can effectively analyze large sequencing datasets (~?100 Gb size) in minutes, outperforming currently available tools.ConclusionsBAMscale accurately quantifies and normalizes identified peaks directly from BAM files, and creates coverage tracks for visualization in genome browsers. BAMScale can be implemented for a wide set of methods for calculating coverage tracks, including ChIP-seq and ATAC-seq, as well as methods that currently require specialized, separate tools for analyses, such as splice-aware RNA-seq, END-seq and OK-seq for which no dedicated software is available. BAMscale is freely available on github (https://github.com/ncbi/BAMscale).

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Seismic refraction tracks porosity generation and possible CO₂ production at depth under a headwater catchment.

Publications

Seismic refraction tracks porosity generation and possible CO<sub>2</sub> production at depth under a headwater catchment.

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Seismic refraction tracks porosity generation and possible CO2 production at depth under a headwater catchment.

Publications

Seismic refraction tracks porosity generation and possible CO<sub>2</sub> production at depth under a headwater catchment.

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OmicsDI is part of the ELIXIR infrastructure

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Seismic refraction tracks porosity generation and possible CO₂ production at depth under a headwater catchment.