A. Shade

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.

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.

Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought

This study investigates how drought affects the active bacterial communities in the rhizosphere of switchgrass and common bean, distinguishing between plant- and environment-mediated effects.

Arrive and wait: inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance

The study examines soil bacterial microbiome resilience after a long-term coal seam fire using 16S rRNA sequencing, finding that whole communities are more resilient than active subsets due to dormant taxa.

Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage

This study examines the microbiome of sorghum phyllosphere exudates, finding distinct bacterial and fungal communities in epicuticular wax and aerial root mucilage influenced by environmental factors.

A coevolution experiment reveals parallel mutations in the AcrA-AcrB-TolC efflux pump that contributes to bacterial antibiotic resistance

This study shows that coevolution between antibiotic-producing and antibiotic-sensitive bacteria leads to mutations in efflux pumps that enhance antibiotic resistance.

Bioactive exometabolites drive maintenance competition in simple bacterial communities

The paper shows that exometabolites from bacterial strains during stationary phase influence community outcomes through competitive interactions.

Multi-omics profiling of Earth's biomes reveals patterns of diversity and co-occurrence in microbial and metabolite composition across environments

The paper performs a multi-omics meta-analysis of microbial and metabolite data from diverse environments, revealing patterns of diversity and co-occurrence across biomes.

Endophytic microbiome variation at the level of a single plant seed

The paper develops a protocol to extract metagenomic DNA from individual seeds to assess microbiome variation at the seed level and finds higher variability at the plant level.

Life on the leaf: Seasonal activities of the phyllosphere microbiome of perennial crops

This study analyzes the seasonal activities of the phyllosphere microbiome in switchgrass and miscanthus using metagenome and metatranscriptome sequencing to identify key microbial functions and their responses to environmental cues.

Prioritizing persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype

The paper identifies core microbiome taxa in common bean rhizosphere across multiple agricultural dimensions using macroecology concepts.

Abiotic treatment to common bean plants results in an altered seed microbiome.

This study investigates how abiotic treatments affect the seed microbiome of common bean plants, finding that water withholding and nutrient addition alter bacterial/archaeal communities but not fungal communities.

Exometabolite dynamics over stationary phase reveal strain-specific responses to nutrient limitation

This study examines exometabolite dynamics in three environmental bacteria during stationary phase, revealing strain-specific responses to nutrient limitation and metabolic reprogramming.

Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere

The paper identifies a core microbiome in common bean rhizosphere that persists across space and time, suggesting deterministic selection and potential for translational plant-microbiome management.

Dormancy dynamics and dispersal contribute to soil microbiome resilience

This study quantifies how dormancy and dispersal contribute to soil microbiome resilience after thermal disturbance by comparing communities with and without dispersal.

Locally-adapted Mimulus ecotypes differentially impact rhizosphere bacterial and archaeal communities in an environment-dependent manner

This study shows that locally adapted Mimulus ecotypes influence rhizosphere microbial communities, but environmental factors have a stronger impact than host genetics.

Strategies for building computing skills to support microbiome analysis: a five-year perspective from the EDAMAME workshop

The paper describes an educational workshop series aimed at teaching microbiologists computing skills for microbiome analysis over five years.

Targeting microbial arsenic resistance genes: a new bioinformatic toolkit informs arsenic ecology and evolution in soil genomes and metagenomes

The paper develops a bioinformatic toolkit to analyze arsenic resistance and metabolism genes in soil genomes and metagenomes, revealing gene distribution patterns and their ecological implications.

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

The paper characterizes the origins and seasonal dynamics of core microbial communities on switchgrass and miscanthus leaves, finding soil-derived taxa adapted to the phyllosphere.

16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity

The paper compares 16S rRNA:rDNA ratios and CTC staining to assess microbial activity in soil, finding they provide complementary and robust estimates of community activity.

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.

Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient

The paper investigates microbial genome size along a soil temperature gradient, finding smaller genomes in hotter soils and linking this to ecological selection for thermotolerant microbes.

Bacterial community composition and dynamics spanning five years in freshwater bog lakes

This study tracks bacterial community composition and dynamics over five years in eight freshwater bog lakes, revealing annual and seasonal trends and a core community of ubiquitous taxa.