Ashley L. Shade

MATRIX: Rapid Quantification of Total and Active Microbial Cells with Single Cell Phenotypes for Environmental Microbiomes

MATRIX quantifies total and redox-active microbial cells in environmental samples using imaging and Bayesian inference, providing direct measurements of population size and activity.

Biotic versus environmental controls on microbial degradation of permafrost organic matter

This study investigates how biotic and environmental factors influence microbial degradation of permafrost organic matter using an in situ thaw experiment.

Evaluating the legacy of drought exposure on root and rhizosphere bacterial microbiomes over two plant generations

This study examines drought's legacy effects on root and rhizosphere bacterial microbiomes across two plant generations in common bean, finding no significant microbiome response in one genotype but a minor legacy effect in another.

Activation dynamics and assembly of root zone soil bacterial communities in response to stress-associated phytohormones

The paper examines how root zone soil bacteria reactivate in response to stress phytohormones, identifying specific taxa activated by abscisic acid and salicylic acid in different crops.

Disturbance increases soil microbiome functional redundancy but decreases capacity for insurance via winnowed environmental responsiveness

The paper examines how disturbance affects soil microbiome functional redundancy and insurance potential using metagenome sequencing from heated and reference sites.

Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress

This study tracks how drought or nutrient excess affects the transmission of bacterial communities in bean seeds across generations, finding stable transmission of 22 bacterial members regardless of parental treatment.

Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils

The paper examines soil viral community dynamics over seven years in heated and unheated soils, finding greater spatial variation than temporal changes in viral communities.

A five-fold expansion of the global RNA virome reveals multiple new clades of RNA bacteriophages

The paper expands the global RNA virome by five-fold, identifying new clades of RNA bacteriophages and revealing novel virus-host interactions.

RefSoil+: A reference for antimicrobial resistance genes on soil plasmids

RefSoil+ is a database of soil plasmids that reveals their size, diversity, and antibiotic resistance gene content, suggesting limited potential for plasmid-mediated transfer of resistance genes to clinical strains.