List of works - Ashley Shade

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil

scientific article published on 01 March 2019

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

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

scientific article

A communal catalogue reveals Earth's multiscale microbial diversity

scientific article published in November 2017

A global survey of arsenic-related genes in soil microbiomes.

scientific article published on 30 May 2019

A meta-analysis of changes in bacterial and archaeal communities with time

scientific article published on 11 April 2013

A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class

scientific article published on 23 April 2018

Abundance-occupancy distributions to prioritize plant core microbiome membership

scientific article published on 01 June 2019

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

scientific article published in 2024

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

scientific article published on 12 September 2019

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes.

scientific article

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

article

Beyond the Venn diagram: the hunt for a core microbiome

scientific article

Broadening Participation in Scientific Conferences during the Era of Social Distancing

scientific article published on 22 September 2020

Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies

scientific article

Characterizing microbial communities through space and time

scientific article published on 7 December 2011

Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

scientific article published in February 2018

Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

scholarly article published 22 December 2017

Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

article

Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members

scientific article published on 16 November 2021

Comparison of primer sets for use in automated ribosomal intergenic spacer analysis of aquatic bacterial communities: an ecological perspective

scientific article published on 22 November 2006

Computing Workflows for Biologists: A Roadmap

scientific article published on 24 November 2015

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity

scientific article

Controls on soil microbial community stability under climate change

scientific article

Corrigendum: Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau

scientific article published on 18 April 2017

Culturing captures members of the soil rare biosphere

scientific article published on 13 July 2012

Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment

article

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

scientific article

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire

Diversity is the question, not the answer

scientific article

Diversity is the question, not the answer

Dormancy dynamics and dispersal contribute to soil microbiome resilience

scientific article published on 23 March 2020

Ecological patterns of seed microbiome diversity, transmission, and assembly

scientific article

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

scholarly article by Jackson W. Sorensen et al published 5 November 2018 in Nature Microbiology

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

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau

scientific article

Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes".

scientific article published on 19 July 2017

Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

scientific article published in 2020

Frontiers and Opportunities in Bioenergy Crop Microbiome Research Networks

scientific article published in 2022

Fundamentals of microbial community resistance and resilience

scientific article

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.).

scientific article published on 6 June 2018

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

scientific article published on 08 January 2016

Interannual dynamics and phenology of bacterial communities in a eutrophic lake

article

Lake microbial communities are resilient after a whole-ecosystem disturbance

scientific article published on 28 June 2012

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere

scientific article published in 2016

Lineage-specific responses of microbial communities to environmental change

scientific article

Locally Adapted <i>Mimulus</i> Ecotypes Differentially Impact Rhizosphere Bacterial and Archaeal Communities in an Environment-Dependent Manner

scientific article published in 2020

Macroecology to Unite All Life, Large and Small

scientific article published in 2018

Managing Plant Microbiomes for Sustainable Biofuel Production

Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

scientific article

Microbial metabolites in the marine carbon cycle

scientific article published in 2022

NITROGEN CHANGES AND DOMAIN BACTERIA RIBOTYPE DIVERSITY IN SOILS OVERLYING THE CENTRALIA, PENNSYLVANIA UNDERGROUND COAL MINE FIRE

No Evidence of Increased Chronic Traumatic Encephalopathy Pathology or Neurodegenerative Proteinopathy in Former Military Service Members: A Preliminary Study

scientific article published on 01 January 2019

Our microbial selves: what ecology can teach us

scientific article

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

scientific article published on 26 March 2021

RefSoil+: A reference for antimicrobial resistance genes on soil plasmids

article

RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

article

Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance

scientific article published on 30 August 2011

Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics

scientific article published on 18 September 2009

Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop

scientific article published on 20 August 2019

Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil

scientific article

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

article

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

scientific article

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

Temporal dynamics of South End tidal creek (Sapelo Island, Georgia) bacterial communities

scientific article

Temporal dynamics of bacterial communities during seed development and maturation

scientific article published on 23 September 2020

Temporal patterns of rarity provide a more complete view of microbial diversity

scientific article published on 6 February 2015

Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities

scientific article published in 2023

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

scientific article published on 23 January 2008

The microbial ecology of flowers: an emerging frontier in phyllosphere research

scientific article published in 2014

The under-ice microbiome of seasonally frozen lakes

article

Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science

scientific article

Trait-based community assembly and succession of the infant gut microbiome

scientific article published in Nature Communications

Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession

article published in 2018

Trait-based patterns of microbial dynamics in dormancy potential and heterotrophic strategy: case studies of resource-based and post-press succession

article published in 2017

Typhoons initiate predictable change in aquatic bacterial communities

article by Stuart E. Jones et al published July 2008 in Limnology and Oceanography

Understanding Microbiome Stability in a Changing World

scientific article published on 20 March 2018

Unexpected diversity during community succession in the apple flower microbiome

scientific article published on 26 February 2013

When, where and how does microbial community composition matter?

scientific article

“Gradual Entrainment Lake Inverter” (GELI): A novel device for experimental lake mixing

article

List of works by Ashley Shade

16S rRNA/rRNA Gene Ratios and Cell Activity Staining Reveal Consistent Patterns of Microbial Activity in Plant-Associated Soil

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

A Synthetic Community System for Probing Microbial Interactions Driven by Exometabolites

A communal catalogue reveals Earth's multiscale microbial diversity

A global survey of arsenic-related genes in soil microbiomes.

A meta-analysis of changes in bacterial and archaeal communities with time

A town on fire! Integrating 16S rRNA gene amplicon analyses into an undergraduate microbiology lecture class

Abundance-occupancy distributions to prioritize plant core microbiome membership

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

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

Assembly and seasonality of core phyllosphere microbiota on perennial biofuel crops

Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes.

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

Beyond the Venn diagram: the hunt for a core microbiome

Broadening Participation in Scientific Conferences during the Era of Social Distancing

Can the black box be cracked? The augmentation of microbial ecology by high-resolution, automated sensing technologies

Characterizing microbial communities through space and time

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

Community structure explains antibiotic resistance gene dynamics over a temperature gradient in soil

Comparing gut resistome composition among patients with acute Campylobacter infections and healthy family members

Comparison of primer sets for use in automated ribosomal intergenic spacer analysis of aquatic bacterial communities: an ecological perspective

Computing Workflows for Biologists: A Roadmap

Conditionally rare taxa disproportionately contribute to temporal changes in microbial diversity

Controls on soil microbial community stability under climate change

Corrigendum: Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau

Culturing captures members of the soil rare biosphere

Differential bacterial dynamics promote emergent community robustness to lake mixing: an epilimnion to hypolimnion transplant experiment

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

Divergent extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

Diversity and mechanisms of arsenic resistance among soil bacteria impacted by the ongoing Centralia coal mine fire

Diversity is the question, not the answer

Diversity is the question, not the answer

Diversity is the question, not the answer

Dormancy dynamics and dispersal contribute to soil microbiome resilience

Ecological patterns of seed microbiome diversity, transmission, and assembly

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

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

Effects of Short-Term Warming and Altered Precipitation on Soil Microbial Communities in Alpine Grassland of the Tibetan Plateau

Erratum for Linz et al., "Bacterial Community Composition and Dynamics Spanning Five Years in Freshwater Bog Lakes".

Exometabolite Dynamics over Stationary Phase Reveal Strain-Specific Responses

Frontiers and Opportunities in Bioenergy Crop Microbiome Research Networks

Fundamentals of microbial community resistance and resilience

Genetic Analysis of Flooding Tolerance in an Andean Diversity Panel of Dry Bean (Phaseolus vulgaris L.).

Genome-wide selective sweeps and gene-specific sweeps in natural bacterial populations

Interannual dynamics and phenology of bacterial communities in a eutrophic lake

Lake microbial communities are resilient after a whole-ecosystem disturbance

Lifestyles of rarity: understanding heterotrophic strategies to inform the ecology of the microbial rare biosphere

Lineage-specific responses of microbial communities to environmental change

Locally Adapted <i>Mimulus</i> Ecotypes Differentially Impact Rhizosphere Bacterial and Archaeal Communities in an Environment-Dependent Manner

Macroecology to Unite All Life, Large and Small

Managing Plant Microbiomes for Sustainable Biofuel Production

Manipulating Wild and Tamed Phytobiomes: Challenges and Opportunities

Meeting report: the terabase metagenomics workshop and the vision of an Earth microbiome project

Microbial metabolites in the marine carbon cycle

NITROGEN CHANGES AND DOMAIN BACTERIA RIBOTYPE DIVERSITY IN SOILS OVERLYING THE CENTRALIA, PENNSYLVANIA UNDERGROUND COAL MINE FIRE

No Evidence of Increased Chronic Traumatic Encephalopathy Pathology or Neurodegenerative Proteinopathy in Former Military Service Members: A Preliminary Study

Our microbial selves: what ecology can teach us

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

RefSoil+: A reference for antimicrobial resistance genes on soil plasmids

RefSoil+: a Reference Database for Genes and Traits of Soil Plasmids

Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance

Seasonal and episodic lake mixing stimulate differential planktonic bacterial dynamics

Stochastic extremes but convergent recovery of bacterial and archaeal soil communities to an ongoing subterranean coal mine fire

Strategies for Building Computing Skills To Support Microbiome Analysis: a Five-Year Perspective from the EDAMAME Workshop

Streptomycin application has no detectable effect on bacterial community structure in apple orchard soil

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

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

Taxonomically-linked growth phenotypes during arsenic stress among arsenic resistant bacteria isolated from soils overlying the Centralia coal seam fire

Temporal dynamics of South End tidal creek (Sapelo Island, Georgia) bacterial communities

Temporal dynamics of bacterial communities during seed development and maturation

Temporal patterns of rarity provide a more complete view of microbial diversity

Terpenes modulate bacterial and fungal growth and sorghum rhizobiome communities

The influence of habitat heterogeneity on freshwater bacterial community composition and dynamics

The microbial ecology of flowers: an emerging frontier in phyllosphere research

The under-ice microbiome of seasonally frozen lakes

Toward a Generalizable Framework of Disturbance Ecology Through Crowdsourced Science