Engineering topics

McCue, Lee Ann (ORCID:000000034456517X)

Publications and source records attributed to McCue, Lee Ann (ORCID:000000034456517X).

4 records

DOE OSTI2022

Soil Metabolomics Predict Microbial Taxa as Biomarkers of Moisture Status in Soils from a Tidal Wetland

We present observations from a laboratory-controlled study on the impacts of extreme wetting and drying on a wetland soil microbiome. Our approach was to experimentally challenge the soil microbiome to understand impacts on anaerobic carbon cycling processes as the system transitions from dryness to saturation and vice-versa. Specifically, we tested for impacts on stress responses related to shifts from wet to drought conditions. We used a combination of high-resolution data for small organic chemical compounds (metabolites) and biological (community structure based on 16S rRNA gene sequencing) features. Using a robust correlation-independent data approach, we further tested the predictive power of soil metabolites for the presence or absence of taxa. Here, we demonstrate that taking an untargeted, multidimensional data approach to the interpretation of metabolomics has the potential to indicate the causative pathways selecting for the observed bacterial community structure in soils.

16S rRNA gene↗

DOE OSTI2021

Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding

Abstract Climate change is intensifying the global water cycle, with increased frequency of drought and flood. Water is an important driver of soil carbon dynamics, and it is crucial to understand how moisture disturbances will affect carbon availability and fluxes in soils. Here we investigate the role of water in substrate-microbe connectivity and soil carbon cycling under extreme moisture conditions. We collected soils from Alaska, Florida, and Washington USA, and incubated them under Drought and Flood conditions. Drought had a stronger effect on soil respiration, pore-water carbon, and microbial community composition than flooding. Soil response was not consistent across sites, and was influenced by site-level pedological and environmental factors. Soil texture and porosity can influence microbial access to substrates through the pore network, driving the chemical response. Further, the microbial communities are adapted to the historic stress conditions at their sites and therefore show site-specific responses to drought and flood.

58 GEOSCIENCES↗

DOE OSTI2021

Data for "Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding"

This dataset contains data used for the paper "Soil texture and environmental conditions influence the biogeochemical responses of soils to drought and flooding". The Related References field will be updated with a full citation when available.Climate change is intensifying the global water cycle, with increased frequency of drought and flood. Water is an important driver of soil carbon dynamics, and it is crucial to understand how moisture disturbances will affect carbon availability and fluxes in soils. Here we investigate the role of water in substrate-microbe connectivity and soil carbon cycling under extreme moisture conditions. We collected soils from Alaska, Florida, and Washington USA, and incubated them under Drought and Flood conditions. Drought had a stronger effect on soil respiration, pore-water carbon, and microbial community composition than flooding. Soil response was not consistent across sites, and was influenced by site-level pedological and environmental factors. Soil texture and porosity can influence microbial access to substrates through the pore network, driving the chemical response. Further, the microbial communities are adapted to the historic stress conditions at their sites and therefore show site-specific responses to drought and flood.This dataset contains a compressed (.zip) archive of the data and R scripts used for this manuscript. The dataset includes files in .csv and .txt format, which can be accessed and processed using MS Excel or R. This archive can also be accessed on GitHub at https://github.com/kaizadp/TES_3Soils_2021 (DOI: 10.5281/zenodo.4792655).

54 ENVIRONMENTAL SCIENCES↗

DOE OSTI2020

ftmsRanalysis: An R package for exploratory data analysis and interactive visualization of FT-MS data

The high-resolution and mass accuracy of Fourier transform mass spectrometry (FT-MS) has made it an increasingly popular technique for discerning the composition of soil, plant and aquatic samples containing complex mixtures of proteins, carbohydrates, lipids, lignins, hydrocarbons, phytochemicals and other compounds. Thus, there is a growing demand for informatics tools to analyze FT-MS data that will aid investigators seeking to understand the availability of carbon compounds to biotic and abiotic oxidation and to compare fundamental chemical properties of complex samples across groups. We present ftmsRanalysis, an R package which provides an extensive collection of data formatting and processing, filtering, visualization, and sample and group comparison functionalities. The package provides a suite of plotting methods and enables expedient, flexible and interactive visualization of complex datasets through functions which link to a powerful and interactive visualization user interface, Trelliscope. Example analysis using FT-MS data from a soil microbiology study demonstrates the core functionality of the package and highlights the capabilities for producing interactive visualizations.

97 MATHEMATICS AND COMPUTING↗