E. E. Nuccio

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.

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.

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.

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.

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.

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.

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.

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.

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.

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.