Mechanism Across Scales: A Holistic Modeling Framework Integrating Laboratory and Field Studies for Microbial Ecology

Sulfur Metabolites Play Key System-Level Roles in Modulating Denitrification

(2021) Anne E. Otwell et al.   mSystems

Niche differentiation is spatially and temporally regulated in the rhizosphere

(2020) Erin E. Nuccio et al.   ISME Journal

Quantitative Framework for Model Evaluation in Microbiology Research Using Pseudomonas aeruginosa and Cystic Fibrosis Infection as a Test Case

(2020) Daniel M. Cornforth et al.   mBio

Selective carbon sources influence the end products of microbial nitrate respiration

(2020) Hans K. Carlson et al.   ISME Journal

Taxon-specific microbial growth and mortality patterns reveal distinct temporal population responses to rewetting in a California grassland soil

(2020) Steven J. Blazewicz et al.   ISME Journal

The National Microbiome Data Collaborative: enabling microbiome science

(2020) Elisha M. Wood-Charlson et al.   NATURE REVIEWS MICROBIOLOGY

Predictive biology: modelling, understanding and harnessing microbial complexity

(2020) Allison J. Lopatkin et al.   NATURE REVIEWS MICROBIOLOGY

Putting science back into microbial ecology: a question of approach

(2020) James I. Prosser   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Conceptual challenges in microbial community ecology

(2020) James I. Prosser et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

(2020) Yonatan Sher et al.   SOIL BIOLOGY & BIOCHEMISTRY

Small and mighty: adaptation of superphylum Patescibacteria to groundwater environment drives their genome simplicity

(2020) Renmao Tian et al.   Microbiome

GapMind: Automated Annotation of Amino Acid Biosynthesis

(2020) Morgan N. Price et al.   mSystems

Characterization of subsurface media from locations up- and down-gradient of a uranium-contaminated aquifer

(2020) Ji-Won Moon et al.   CHEMOSPHERE

Experimental evolution reveals nitrate tolerance mechanisms in Desulfovibrio vulgaris

(2020) Bo Wu et al.   ISME Journal

METLIN MS2 molecular standards database: a broad chemical and biological resource

(2020) Jingchuan Xue et al.   NATURE METHODS

In-field bioreactors demonstrate dynamic shifts in microbial communities in response to geochemical perturbations

(2020) Regina L. Wilpiszeski et al.   PLoS One

Gene-informed decomposition model predicts lower soil carbon loss due to persistent microbial adaptation to warming

(2020) Xue Guo et al.   Nature Communications

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

(2020) Daliang Ning et al.   Nature Communications

Characterization of a Metal-Resistant Bacillus Strain With a High Molybdate Affinity ModA From Contaminated Sediments at the Oak Ridge Reservation

(2020) Xiaoxuan Ge et al.   Frontiers in Microbiology

Stimulation of soil respiration by elevated CO2 is enhanced under nitrogen limitation in a decade-long grassland study

(2020) Qun Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Dual-barcoded shotgun expression library sequencing for high-throughput characterization of functional traits in bacteria

(2019) Vivek K. Mutalik et al.   Nature Communications

Resource Concentration Modulates the Fate of Dissimilated Nitrogen in a Dual-Pathway Actinobacterium

(2019) David C. Vuono et al.   Frontiers in Microbiology

Redirecting Metabolic Flux via Combinatorial Multiplex CRISPRi-Mediated Repression for Isopentenol Production in Escherichia coli

(2019) Tian Tian et al.   ACS Synthetic Biology

Adaptation of Desulfovibrio alaskensis G20 to perchlorate, a specific inhibitor of sulfate reduction

(2019) Misha G. Mehta‐Kolte et al.   ENVIRONMENTAL MICROBIOLOGY

Molecular Dynamics Simulations of Membrane Permeability

(2019) Richard M. Venable et al.   CHEMICAL REVIEWS

The Art of Reactive Transport Model Building

(2019) Kate Maher et al.   Elements

Reactive Transport Modeling of Microbial Dynamics

(2019) Christof Meile et al.   Elements

Affinity informs environmental cooperation between ammonia-oxidizing archaea (AOA) and anaerobic ammonia-oxidizing (Anammox) bacteria

(2019) Levi L. Straka et al.   ISME Journal

Curated BLAST for Genomes

(2019) Morgan N. Price et al.   mSystems

Nitrate-Utilizing Microorganisms Resistant to Multiple Metals from the Heavily Contaminated Oak Ridge Reservation

(2019) Michael P. Thorgersen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

EcoFABs: advancing microbiome science through standardized fabricated ecosystems

(2019) Karsten Zengler et al.   NATURE METHODS

Anion transport as a target of adaption to perchlorate in sulfate-reducing communities

(2019) Magdalena K. Stoeva et al.   ISME Journal

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

(2019) Evan P. Starr et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

High spatiotemporal variability of bacterial diversity over short time scales with unique hydrochemical associations within a shallow aquifer

(2019) Anna J. Zelaya et al.   WATER RESEARCH

Review and perspective on mathematical modeling of microbial ecosystems

(2018) Antonella Succurro et al.   BIOCHEMICAL SOCIETY TRANSACTIONS

KBase: The United States Department of Energy Systems Biology Knowledgebase

(2018) Adam P Arkin et al.   NATURE BIOTECHNOLOGY

Use of in-field bioreactors demonstrate groundwater filtration influences planktonic bacterial community assembly, but not biofilm composition

(2018) Geoff A. Christensen et al.   PLoS One

Microbial Functional Gene Diversity Predicts Groundwater Contamination and Ecosystem Functioning

(2018) Zhili He et al.   mBio

Need for Laboratory Ecosystems To Unravel the Structures and Functions of Soil Microbial Communities Mediated by Chemistry

(2018) Kateryna Zhalnina et al.   mBio

Microbial Interactions With Dissolved Organic Matter Drive Carbon Dynamics and Community Succession

(2018) Xiaoqin Wu et al.   Frontiers in Microbiology

Abundance determines the functional role of bacterial phylotypes in complex communities

(2018) Damian W. Rivett et al.   Nature Microbiology

Magic Pools: Parallel Assessment of Transposon Delivery Vectors in Bacteria

(2018) Hualan Liu et al.   mSystems

Web of microbes (WoM): a curated microbial exometabolomics database for linking chemistry and microbes

(2018) Suzanne M. Kosina et al.   BMC MICROBIOLOGY

Systems biology approaches towards predictive microbial ecology

(2018) Anne E. Otwell et al.   ENVIRONMENTAL MICROBIOLOGY

Mutant phenotypes for thousands of bacterial genes of unknown function

(2018) Morgan N. Price et al.   NATURE

Emergent simplicity in microbial community assembly

(2018) Joshua E. Goldford et al.   SCIENCE

Climate warming leads to divergent succession of grassland microbial communities

(2018) Xue Guo et al.   Nature Climate Change

Iron- and aluminium-induced depletion of molybdenum in acidic environments impedes the nitrogen cycle

(2018) Xiaoxuan Ge et al.   ENVIRONMENTAL MICROBIOLOGY

The selective pressures on the microbial community in a metal-contaminated aquifer

(2018) Hans K. Carlson et al.   ISME Journal

Mitigating Sulfidogenesis With Simultaneous Perchlorate and Nitrate Treatments

(2018) Anna Engelbrektson et al.   Frontiers in Microbiology

Robustness of a model microbial community emerges from population structure among single cells of a clonal population

(2017) Anne W. Thompson et al.   ENVIRONMENTAL MICROBIOLOGY

Temporal Dynamics of In-Field Bioreactor Populations Reflect the Groundwater System and Respond Predictably to Perturbation

(2017) Andrew J. King et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Dynamic Succession of Groundwater Sulfate-Reducing Communities during Prolonged Reduction of Uranium in a Contaminated Aquifer

(2017) Ping Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

A dual nitrite isotopic investigation of chemodenitrification by mineral-associated Fe(II) and its production of nitrous oxide

(2017) Kalina C. Grabb et al.   GEOCHIMICA ET COSMOCHIMICA ACTA

Push-pull tests for estimating effective porosity: expanded analytical solution and in situ application

(2017) Charles J. Paradis et al.   HYDROGEOLOGY JOURNAL

Stochastic Community Assembly: Does It Matter in Microbial Ecology?

(2017) Jizhong Zhou et al.   MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS

A communal catalogue reveals Earth’s multiscale microbial diversity

(2017) Luke R. Thompson et al.   NATURE

Parallelized, Aerobic, Single Carbon-Source Enrichments from Different Natural Environments Contain Divergent Microbial Communities

(2017) Theodore M. Flynn et al.   Frontiers in Microbiology

Global Isotope Metabolomics Reveals Adaptive Strategies for Nitrogen Assimilation

(2016) Michael E. Kurczy et al.   ACS Chemical Biology

Rapid detection of microbial cell abundance in aquatic systems

(2016) Andrea M. Rocha et al.   BIOSENSORS & BIOELECTRONICS

Challenges in microbial ecology: building predictive understanding of community function and dynamics

(2016) Stefanie Widder et al.   ISME Journal

Perchlorate Reductase Is Distinguished by Active Site Aromatic Gate Residues

(2016) Matthew D. Youngblut et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

In situ mobility of uranium in the presence of nitrate following sulfate-reducing conditions

(2016) Charles J. Paradis et al.   JOURNAL OF CONTAMINANT HYDROLOGY

A modeling study on mitigation of N 2 O emissions and NO 3 leaching at different agricultural sites across Europe using LandscapeDNDC

(2016) Saúl Molina-Herrera et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Lateral Gene Transfer in a Heavy Metal-Contaminated-Groundwater Microbial Community

(2016) Christopher L. Hemme et al.   mBio

Microbial interactions lead to rapid micro-scale successions on model marine particles

(2016) Manoshi S. Datta et al.   Nature Communications

Exometabolomics Assisted Design and Validation of Synthetic Obligate Mutualism

(2016) Suzanne M. Kosina et al.   ACS Synthetic Biology

The FAIR Guiding Principles for scientific data management and stewardship

(2016) Mark D. Wilkinson et al.   Scientific Data

Dynamic Succession of Groundwater Functional Microbial Communities in Response to Emulsified Vegetable Oil Amendment during SustainedIn SituU(VI) Reduction

(2015) Ping Zhang et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Molybdenum Availability Is Key to Nitrate Removal in Contaminated Groundwater Environments

(2015) Michael P. Thorgersen et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

Determining Roles of Accessory Genes in Denitrification by Mutant Fitness Analyses

(2015) Brian J. Vaccaro et al.   APPLIED AND ENVIRONMENTAL MICROBIOLOGY

A Slow-Release Substrate Stimulates Groundwater Microbial Communities for Long-Term in Situ Cr(VI) Reduction

(2015) Ping Zhang et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Monofluorophosphate Is a Selective Inhibitor of Respiratory Sulfate-Reducing Microorganisms

(2015) Hans K. Carlson et al.   ENVIRONMENTAL SCIENCE & TECHNOLOGY

Aquifer environment selects for microbial species cohorts in sediment and groundwater

(2015) Laura A Hug et al.   ISME Journal

Conductive consortia

(2015) Michael Wagner   NATURE

Natural Bacterial Communities Serve as Quantitative Geochemical Biosensors

(2015) Mark B. Smith et al.   mBio

The Earth Microbiome project: successes and aspirations

(2014) Jack A Gilbert et al.   BMC BIOLOGY

Disturbed subsurface microbial communities follow equivalent trajectories despite different structural starting points

(2014) Kim M. Handley et al.   ENVIRONMENTAL MICROBIOLOGY

Mechanisms of direct inhibition of the respiratory sulfate-reduction pathway by (per)chlorate and nitrate

(2014) Hans K Carlson et al.   ISME Journal

Stochasticity, succession, and environmental perturbations in a fluidic ecosystem

(2014) Jizhong Zhou et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sulfur-mediated electron shuttling during bacterial iron reduction

(2014) T. M. Flynn et al.   SCIENCE

Inhibition of microbial sulfate reduction in a flow-through column system by (per)chlorate treatment

(2014) Anna Engelbrektson et al.   Frontiers in Microbiology

Hydrogeophysical investigations of the former S-3 ponds contaminant plumes, Oak Ridge Integrated Field Research Challenge site, Tennessee

(2013) A. Revil et al.   GEOPHYSICS

Stochastic Assembly Leads to Alternative Communities with Distinct Functions in a Bioreactor Microbial Community

(2013) J. Zhou et al.   mBio

High throughput nanostructure-initiator mass spectrometry screening of microbial growth conditions for maximal β-glucosidase production

(2013) Xiaoliang Cheng et al.   Frontiers in Microbiology

Physiology and Diversity of Ammonia-Oxidizing Archaea

(2012) David A. Stahl et al.   Annual Review of Microbiology

Models, validation, and applied geochemistry: Issues in science, communication, and philosophy

(2012) D. Kirk Nordstrom   APPLIED GEOCHEMISTRY

Growing Unculturable Bacteria

(2012) E. J. Stewart   JOURNAL OF BACTERIOLOGY

Toward a Mechanistic Understanding of Anaerobic Nitrate-Dependent Iron Oxidation: Balancing Electron Uptake and Detoxification

(2012) Hans K. Carlson et al.   Frontiers in Microbiology

Network News: Innovations in 21st Century Systems Biology

(2011) Adam P. Arkin et al.   CELL

Differential Growth Responses of Soil Bacterial Taxa to Carbon Substrates of Varying Chemical Recalcitrance

(2011) Katherine C. Goldfarb et al.   Frontiers in Microbiology

Genome-scale dynamic modeling of the competition between Rhodoferax and Geobacter in anoxic subsurface environments

(2010) Kai Zhuang et al.   ISME Journal

Soil amoebae rapidly change bacterial community composition in the rhizosphere of Arabidopsis thaliana

(2009) Katja Rosenberg et al.   ISME Journal

Ammonia oxidation kinetics determine niche separation of nitrifying Archaea and Bacteria

(2009) Willm Martens-Habbena et al.   NATURE

Predictive microbial ecology

(2009) Jizhong Zhou   Microbial Biotechnology

Coupling a genome-scale metabolic model with a reactive transport model to describein situuranium bioremediation

(2009) Timothy D. Scheibe et al.   Microbial Biotechnology

Microbial biodiversity in groundwater ecosystems

(2008) C. GRIEBLER et al.   FRESHWATER BIOLOGY

Bacterial community succession during in situ uranium bioremediation: spatial similarities along controlled flow paths

(2008) Chiachi Hwang et al.   ISME Journal