M. K. Firestone

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.

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.

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.

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.

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.

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.

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.

Methane-derived carbon flow through host-virus trophic networks in soil

This study identifies active host-virus interactions in methane-fueled soil microbial networks by tracing carbon transfer from hosts to viruses.

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.

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.

Unexpected diversity of CPR bacteria and nanoarchaea in the rare biosphere of rhizosphere-associated grassland soil

The paper identifies unexpected diversity of CPR bacteria and nanoarchaea in grassland soil by analyzing particles less than 0.2 m, revealing new taxa and potential adaptations to aerobic conditions.

Measurement error and resolution in quantitative stable isotope probing: implications for experimental design

This paper evaluates measurement error and resolution in qSIP, finding that variance decreases with taxon abundance and that nine density fractions balance cost and precision.

A quantitative framework reveals the ecological drivers of grassland soil microbial community assembly in response to warming

The paper introduces a framework to quantify microbial community assembly mechanisms in grassland soils under warming, finding homogeneous selection and drift dominate, with warming altering their relative contributions.

Microbial extracellular polysaccharide production and aggregate stability controlled by Switchgrass (Panicum virgatum) root biomass and soil water potential

This study shows switchgrass cultivation increases microbial extracellular polysaccharide (EPS) production and water-stable soil aggregates in marginal soils, driven by root biomass and soil water potential.

Niche differentiation is spatially and temporally regulated in the rhizosphere

This study identifies four microbial guilds in the rhizosphere and detritusphere of Avena fatua, showing niche differentiation drives carbohydrate depolymerization and soil carbon cycling.

Metatranscriptomic reconstruction reveals RNA viruses with the potential to shape carbon cycling in soil

This study reconstructs RNA viruses in soil metatranscriptomes, revealing their diversity, activity, and role in carbon cycling through host cell death.