Protocols

Systematic collection of sediment samples from floodplain sites at regular depth intervals followed by DNA extraction and metagenomic sequencing to characterize microbial communities.

Integrates multiple spatial data layers including lidar, airborne geophysics, hyperspectral remote sensing, and satellite data to characterize hillslope properties. Computes average values and percent...

Systematic collection of snowpack samples across elevation gradients using snow pits dug at 10 cm increments to obtain SWE-weighted composite isotopic signatures representative of accumulated snowpack...

Uses stable isotope ratios (δ²H and δ¹⁸O) of precipitation and streamflow to quantify the relative contributions of snow versus rain to streamflow and evapotranspiration through endmember mixing and s...

Standard Illumina library preparation using Nextera XT kit followed by paired-end sequencing on HiSeq 2500 platform to generate comprehensive metagenomic datasets from phylloplane microbial communitie...

Random Forest regression to predict ecosystem drought sensitivity from hydrological and topographic variables. Uses bootstrapped subsampling with multiple regression trees to identify key predictive v...

Standard metagenomics pipeline involving assembly with MEGAHIT, binning with multiple tools, dereplication, and taxonomic classification using GTDB-tk.

Combined use of major ion chemistry and Sr isotope signatures to identify distinct groundwater end members and quantify their contributions to stream flow using PCA-based end member mixing analysis.

Processing of Landsat NDVI time series to quantify foresummer drought sensitivity as the slope of peak NDVI versus June Palmer Drought Severity Index. Represents plant productivity responses to early ...

Comprehensive Hidden Markov Model analysis of metagenomic sequences to identify and quantify metabolic functions across biogeochemical pathways. Uses both standardized TIGR-FAM and custom HMM database...

A comprehensive statistical framework for quality assurance and quality control of meteorological time series data involving preliminary data exploration, quality assessment with outlier detection, an...

Sulfur K-edge X-ray Absorption Near Edge Structure spectroscopy was used to determine sulfur speciation in solid samples including bedrock, soils, and sediments. Linear combination fitting was used to...

Computational pipeline using VirSorter2 and CheckV for viral sequence identification, followed by clustering into viral operational taxonomic units and taxonomic/host prediction.

Taxonomic classification of microbial communities using ribosomal protein S3 (rpS3) marker genes identified through Hidden Markov Models and phylogenetic analysis.

Processing of sediment samples in anaerobic chamber with nitrogen-hydrogen gas mixture to preserve field conditions.

Sediment samples collected in 15-cm increments using 5 cm diameter soil core sampler with slide hammer, then 8.3 cm diameter bucket auger after reaching coarse alluvium.