J. Pett-Ridge

Arbuscular mycorrhiza convey significant plant carbon to a diverse hyphosphere microbial food web and mineral-associated organic matter

This study quantifies how arbuscular mycorrhizal fungi transfer plant carbon to soil microbial communities and mineral-associated organic matter.

Soil microbial community response to corrinoids is shaped by a natural reservoir of vitamin B12.

The paper investigates how corrinoid structure affects soil microbial community composition and stability through experimental and genomic analysis.

Exploring viral particle, soil, and extraction buffer physicochemical characteristics and their impacts on extractable viral communities

This study examines how extraction buffer chemistry affects extractable viral communities in different soil types, finding that spatial distance is the primary driver of community composition.

Rhizosphere and detritusphere habitats modulate expression of soil N-cycling genes during plant development

The paper analyzes soil metatranscriptomes across different habitats to show how root presence and litter affect nitrogen cycling gene expression during plant growth.

Improved characterization of soil organic matter by integrating FTICR-MS, liquid chromatography tandem mass spectrometry and molecular networking: a case study of root litter decay under drought conditions

The paper integrates FTICR-MS, LC-MS/MS, and molecular networking to characterize soil organic matter under drought and normal conditions, revealing changes in composition and decomposition patterns.

Viral but not bacterial community succession is characterized by extreme turnover shortly after rewetting dry soils

The paper examines viral and bacterial community dynamics in dry soils after rewetting, finding that viral communities show extreme turnover while bacterial communities remain more stable.

A standardized quantitative analysis strategy for stable isotope probing metagenomics

This paper introduces a standardized analysis framework and R package for quantifying isotopic enrichment in SIP metagenomics to identify active microbial genomes.

A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil

The paper investigates virus-host dynamics in soil following rewetting, finding that a subset of viruses thrive and drive microbial lysis, contributing to CO2 efflux.

Divergent microbial traits influence the transformation of living versus dead root inputs to soil carbon

The paper investigates how microbial traits affect soil carbon transformation from living and dead root inputs under different moisture conditions.

HT-SIP: A semi-automated Stable Isotope Probing pipeline identifies interactions in the hyphosphere of arbuscular mycorrhizal fungi

The paper introduces a semi-automated DNA-SIP pipeline to improve efficiency and reproducibility in microbial community studies, demonstrating its application in analyzing the hyphosphere of arbuscular mycorrhizal fungi.

Life history strategies and niches of soil bacteria emerge from interacting thermodynamic, biophysical, and metabolic traits

The paper predicts life history traits of soil bacteria based on thermodynamic, biophysical, and metabolic traits, showing growth efficiency becomes more important later in plant growth.

Functional succession of actively growing soil microorganisms during rewetting is shaped by precipitation history

The paper investigates how precipitation history affects microbial succession in rewetted soils by analyzing functional traits and gene abundance over time.

Metabolic traits and the niche of bulk soil bacteria in a Mediterranean grassland

This study compares metabolic traits of bulk soil and rhizosphere bacteria in a Mediterranean grassland, finding bulk soil bacteria better adapted to degrade plant polymers.

Nutrient and moisture limitation reveal keystone metabolites that link switchgrass rhizosphere metabolome and microbiome dynamics

This study identifies keystone metabolites linking switchgrass rhizosphere metabolome and microbiome dynamics under nutrient and moisture stress.

Quantitative stable-isotope probing (qSIP) with metagenomics links microbial physiology and activity to soil moisture in Mediterranean-climate grassland ecosystems

This study uses qSIP with metagenomics to link microbial activity and physiology to soil moisture in Mediterranean grasslands, finding that precipitation levels influence microbial growth and phage dynamics.

Spatial turnover of soil viral populations and genotypes overlain by cohesive responses to moisture in grasslands

The paper analyzes soil viromes in a Mediterranean grassland to show spatial turnover and moisture-driven responses in viral communities.

Plant-associated fungi support bacterial resilience following water limitation

This study shows that plant-associated fungi enhance bacterial resilience to water limitation by protecting their growth and diversity in hyphospheres.

Belowground allocation and dynamics of recently fixed plant carbon in a California annual grassland soil

This study tracks the fate of plant-fixed carbon in a California grassland soil over two years, showing rapid mineral association and long-term persistence of carbon in heavy soil fractions.

Active communities and growth of soil microorganisms are framed by mean annual precipitation in three California annual grasslands

The paper examines how mean annual precipitation affects microbial community growth and soil carbon cycling in three California grasslands, finding that growth rates and community composition vary with precipitation.

Soil depth gradients in microbial growth kinetics under deeply- vs. shallow-rooted plants

This study examines how microbial growth kinetics vary with soil depth under different plant root systems and finds that depth, not vegetation type, primarily influences microbial parameters in deep soils.

Differential effects of redox conditions on the decomposition of litter and soil organic matter

This study investigates how different redox conditions affect the decomposition of litter and soil organic matter, finding that substrate source influences redox sensitivity of decomposition.

Root carbon interaction with soil minerals is dynamic, leaving a legacy of microbially-derived residues

The paper investigates how plant-derived carbon interacts with soil minerals and microbial activity, finding that rhizosphere conditions shape the chemistry of mineral-associated organic matter.

The Functional Significance of Bacterial Predators

This study quantifies the growth and carbon assimilation rates of predatory bacteria across 15 sites, showing obligate predators grow faster and assimilate more carbon than non-predatory bacteria.

Ecology of active viruses and their bacterial hosts in frozen Arctic peat soil revealed with H218O stable isotope probing metagenomics

This study identifies active viral and bacterial populations in frozen Arctic peat soil using H218O SIP metagenomics, showing significant microbial activity and viral influence on carbon cycling during winter.

Community RNA-Seq: Multi-kingdom responses to living versus decaying root inputs in soil

The paper uses community RNA-Seq to analyze multi-kingdom microbial responses to living and decaying root inputs in soil, finding shifts in microbial community composition and substrate preferences.

Minnesota peat viromes reveal terrestrial and aquatic niche partitioning for local and global viral populations

The paper analyzes viromes from a boreal peatland to reveal niche partitioning of viruses between terrestrial and aquatic environments, showing distinct viral community patterns.

Expression of macromolecular organic nitrogen degrading enzymes identifies potential mediators of soil organic N availability to an annual grass

The paper identifies microbial taxa associated with organic nitrogen degradation in soil and suggests potential candidates for bioaugmentation to improve plant nitrogen availability.

VirION2: a short- and long-read sequencing and informatics workflow to study the genomic diversity of viruses in nature

VirION2 improves viral metagenomics by integrating short- and long-read sequencing, enhancing genome recovery and microdiversity detection in low-biomass samples.

Routes to Roots: Direct Evidence of Water Transport by Arbuscular Mycorrhizal Fungi to Host Plants

The paper directly tracks and quantifies water transport by arbuscular mycorrhizal fungi to host plants using isotopically-labeled water and a fluorescent dye in a greenhouse experiment.

Stable isotope informed genome-resolved metagenomics uncovers potential trophic interactions in rhizosphere soil

This study uses stable isotope-informed genome-resolved metagenomics to trace carbon flow in rhizosphere soil and identify microbial interactions with plants and phages.