Ashley Shade ShadeLab

Publications

• Prioritizing persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype
• Seasonal activities of the phyllosphere microbiome of perennial crops
• Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil
• Endophytic Microbiome Variation Among Single Plant Seeds
• A coevolution experiment reveals parallel mutations in the AcrA-AcrB-TolC efflux pump that contributes to bacterial antibiotic resistance
• A coevolution experiment between Flavobacterium johnsoniae and Burkholderia thailandensis reveals parallel mutations that reduce antibiotic susceptibility
• Microbiome rescue: directing resilience of environmental microbial communities
• A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class
• Trait-based community assembly and succession of the infant gut microbiome
• Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops
• Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient
• Strategies for building computing skills to support microbiome analysis: a five-year perspective from the EDAMAME workshop
• Dormancy dynamics and dispersal contribute to soil microbiome resilience
• Macroecology to Unite All Life, Large and Small
• Disentangling plant- and environment-mediated drivers of active rhizosphere bacterial community dynamics during short-term drought
• Bioactive exometabolites drive maintenance competition in simple bacterial communities
• Accounting for active populations provides a new perspective on the degree and mechanisms of soil microbiome resilience
• Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities
• Phyllosphere Exudates Select for Distinct Microbiome Members in Sorghum Epicuticular Wax and Aerial Root Mucilage
• Deciphering the Microbiome: Integrating Theory, New Technologies, and Inclusive Science
• Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members
• Abiotic Treatment to Common Bean Plants Results in an Altered Endophytic Seed Microbiome
• Phyllosphere exudates select for distinct microbiome members in sorghum epicuticular wax and aerial root mucilage
• A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites
• Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession
• Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession
• Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire
• Ecological selection for small microbial genomes along a temperate-to-thermal soil gradient
• Understanding Microbiome Stability in a Changing World
• Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession
• RefSoil+: A reference for antimicrobial resistance genes on soil plasmids
• 16S rRNA:rDNA ratios and cell activity staining reveal consistent patterns of soil microbial activity
• A global survey of arsenic related genes in soil microbiomes
• Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops
• RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids
• 16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil
• A global survey of arsenic-related genes in soil microbiomes
• Locally-adapted Mimulus ecotypes differentially impact rhizosphere bacterial and archaeal communities in an environment-dependent manner
• Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop
• Locally Adapted Mimulus Ecotypes Differentially Impact Rhizosphere Bacterial and Archaeal Communities in an Environment-Dependent Manner
• Discovery of a spatially and temporally persistent core microbiome of the common bean rhizosphere
• Dormancy dynamics and dispersal contribute to soil microbiome resilience
• Biogeography and Diversity of Multi-Trophic Root Zone Microbiomes in Michigan Apple Orchards: Analysis of Rootstock, Scion, and Local Growing Region
• Abiotic treatment to common bean plants results in an altered endophytic seed microbiome
• Seasonal Dynamics of Core Fungi in the Switchgrass Phyllosphere, and Co-Occurrence with Leaf Bacteria
• Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses
• Persistent microbiome members in the common bean rhizosphere: an integrated analysis of space, time, and plant genotype
• Life on the leaf: Seasonal activities of the phyllosphere microbiome of perennial crops
• Endophytic microbiome variation at the level of a single plant seed
• Managing Plant Microbiomes for Sustainable Biofuel Production
• "Gradual Entrainment Lake Inverter" (GELI): A novel device for experimental lake mixing
• Ecological patterns of seed microbiome diversity, transmission, and assembly
• Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire
• Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire
• Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations
• Corrigendum: "Effects of short-term warming and altered precipitation on soil microbial communities in Alpine Grassland of the Tibetan Plateau" [Front. Microbiol., 7, (2017):(1032)]. Doi: 10.3389/fmicb.2016.01032
• Our microbial selves: what ecology can teach us.
• Typhoons initiate predictable change in aquatic bacterial communities
• Lineage-specific responses of microbial communities to environmental change
• Temporal dynamics of South End tidal creek (Sapelo Island, Georgia) bacterial communities
• Lifestyles of rarity: Understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere
• Comparison of primer sets for use in automated ribosomal intergenic spacer analysis of aquatic bacterial communities: An ecological perspective
• Differential bacterial dynamics promote emergent community robustness to lake mixing: An epilimnion to hypolimnion transplant experiment
• Effects of short-term warming and altered precipitation on soil microbial communities in alpine grassland of the tibetan plateau
• "Gradual entrainment lake inverter" (GELI): A novel device for experimental lake mixing
• Diversity is the question, not the answer
• Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil
• Computing Workflows for Biologists: A Roadmap
• The causes and consequences of microbial community structure
• Controls on soil microbial community stability under climate change
• When, where and how does microbial community composition matter?
• Beyond the Venn diagram: the hunt for a core microbiome
• The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics
• Culturing captures members of the soil rare biosphere
• Seasonal and Episodic Lake Mixing Stimulate Differential Planktonic Bacterial Dynamics
• A meta-analysis of changes in bacterial and archaeal communities with time
• The microbial ecology of flowers: an emerging frontier in phyllosphere research 1
• Interannual dynamics and phenology of bacterial communities in a eutrophic lake
• Our microbial selves: what ecology can teach us
• Typhoons initiate predictable change in aquatic bacterial communities
• The under-ice microbiome of seasonally frozen lakes
• Characterizing microbial communities through space and time
• Lake microbial communities are resilient after a whole-ecosystem disturbance
• Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies
• Fundamentals of Microbial Community Resistance and Resilience
• Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance
• Temporal patterns of rarity provide a more complete view of microbial diversity
• Meeting Report: The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project
• Unexpected Diversity during Community Succession in the Apple Flower Microbiome
• Conditionally Rare Taxa Disproportionately Contribute to Temporal Changes in Microbial Diversity
• Bacterial community composition and dynamics spanning five years in freshwater bog lakes
• Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil
• Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil
• Diversity is the question, not the answer
• Diversity is the question, not the answer
• Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire
• Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire
• Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire
• Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire
• Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire
• NITROGEN CHANGES AND DOMAIN BACTERIA RIBOTYPE DIVERSITY IN SOILS OVERLYING THE CENTRALIA, PENNSYLVANIA UNDERGROUND COAL MINE FIRE
• Interannual dynamics and phenology of bacterial communities in a eutrophic lake
• Nitrogen changes and domain bacteria ribotype diversity in soils overlying the Centralia, Pennsylvania underground coal mine fire
• Bridging the gap between micro - and macro-scale perspectives on the role of microbial communities in global change ecology
• Genome-sequenced bacterial collection from sorghum aerial root mucilage
• Genome-sequenced bacterial collection from sorghum epicuticular wax
• Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.)
• Abundance-occupancy distributions to prioritize plant core microbiome membership
• Temporal dynamics of bacterial communities during seed development and maturation
• Resource Competition and Host Feedbacks Underlie Regime Shifts in Gut Microbiota
• Standardized multi-omics of Earth's microbiomes reveals microbial and metabolite diversity
• Frontiers and Opportunities in Bioenergy Crop Microbiome Research Networks
• Scientific Life Broadening Participation in Scientific Conferences during the Era of Social Distancing
• Microbial metabolites in the marine carbon cycle
• Manipulating Wild and Tamed Phlytobiomes: Challenges and Opportunities
• Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science
• Assembly of seed-associated microbial communities within and across successive plant generations
• Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes (vol 2, e00169-17, 2017)
• Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes
• A communal catalogue reveals Earth's multiscale microbial diversity
• Isolation of Bio Energy Crop Phyllosphere Bacteria from Switchgrass
• Arrive and wait: inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance
• Arrive and wait: Inactive bacterial taxa contribute to perceived soil microbiome resilience after a multidecadal press disturbance
• Stable, multigenerational transmission of the bean seed microbiome despite abiotic stress
• Is everything everywhere? A hands-on activity to engage undergraduates with key concepts in quantitative microbial biogeography
• Seven years of microbial community metagenomes from temperate soils affected by an ongoing coal seam fire
• Soil viral community dynamics over seven years of heat disturbance: spatial variation exceeds temporal in annually sampled soils
• Bacterial isolate collection from switchgrass rhizosphere
• Correction for Mechan-Llontop et al., “Genome-sequenced bacterial collection from sorghum aerial root mucilage”
• Correction for Mechan-Llontop et al., “Genome-sequenced bacterial collection from sorghum epicuticular wax”
• Announcing the mSystems special collection on microbial dormancy
• Complete genome sequence of Sporosarcina pasteurii type strain DSM33
• Embracing the systems complexity of microbial ecology and evolution: call for papers
• Activation dynamics and assembly of root zone soil bacterial communities in response to stress-associated phytohormones