D. K. Newman

Annotation-free prediction of microbial dioxygen utilization

This paper predicts microbial dioxygen utilization from genome sequences without gene annotation, achieving >70% accuracy and demonstrating environmental correlations.

Investigating 3D microbial community dynamics in the rhizosphere using complex-field and fluorescence microscopy

This paper introduces CFAST, a novel imaging technique for 3D microbial community dynamics in the rhizosphere, enabling non-invasive tracking of bacterial behavior and gene expression without genetic labeling.

The proteome is a terminal electron acceptor

The paper develops a mathematical model showing microbial proteins adapt to maintain redox balance, improving growth by aligning biomass redox state with nutrients.

Genetically dissecting the electron transport chain of a soil bacterium reveals a generalizable mechanism for biological phenazine-1-carboxylic acid oxidation

This paper identifies a generalizable mechanism for biological oxidation of phenazine-1-carboxylic acid (PCA) by studying the electron transport chain in Citrobacter portucalensis MBL.

Uncultivated DPANN archaea are ubiquitous inhabitants of global oxygen deficient zones with diverse metabolic potential

This study reports 33 new metagenome-assembled genomes of DPANN archaea from marine oxygen deficient zones, revealing their abundance, distribution, and potential roles in biogeochemical cycles.

Widespread detoxifying NO reductases impart a distinct isotopic fingerprint on N2O under anoxia

The paper identifies flavohemoglobin as a detoxifying NO reductase that imparts a distinct isotopic fingerprint on N2O under anoxia, suggesting a new framework for attributing N2O sources.

Intracellular Pseudomonas aeruginosa within the airway epithelium of Cystic Fibrosis lung tissues

The paper detects intracellular Pseudomonas aeruginosa in CF lung tissues using microscopy and culture, showing its presence in 3 out of 7 analyzed lungs.

Electrochemical disruption of extracellular electron transfer inhibits Pseudomonas aeruginosa cell survival within biofilms and is synergistic with antibiotic treatment

The paper shows electrochemical disruption of pyocyanin redox cycling in Pseudomonas aeruginosa biofilms reduces cell survival and synergizes with antibiotics like gentamicin.

Optical O2 sensors also respond to redox active molecules commonly secreted by bacteria

The paper shows that bacterial secretions, particularly redox-active molecules, can interfere with optical O2 sensors, complicating O2 measurements in bacterial cultures and biofilms.

Hopanoids confer robustness to physicochemical variability in the niche of the plant symbiont Bradyrhizobium diazoefficiens

This study shows that hopanoids in Bradyrhizobium diazoefficiens provide robustness to environmental variability in soil, explaining discrepancies between in vitro and in planta results.

Visualization of mRNA Expression in Pseudomonas aeruginosa Aggregates Reveals Spatial Patterns of Fermentative and Denitrifying Metabolism

This paper uses HCR to visualize gene expression in Pseudomonas aeruginosa aggregates, revealing spatial patterns of fermentative and denitrifying metabolism across oxygen gradients.

Polyphosphate affects cytoplasmic and chromosomal dynamics in nitrogen-starved Pseudomonas aeruginosa

This study shows that polyphosphate reduces cytoplasmic mobility and chromosomal accessibility in nitrogen-starved Pseudomonas aeruginosa, potentially explaining its pleiotropic effects.

The contrasting roles of nitric oxide drive microbial community organization as a function of oxygen presence

The paper shows that oxygen levels determine whether nitric oxide cross-feeding is harmful or beneficial in microbial communities.

Redox-active secondary metabolites act as interspecies modulators of antibiotic resilience

The paper investigates how redox-active secondary metabolites like pyocyanin and toxoflavin modulate antibiotic resilience across bacterial species, showing they can antagonize or potentiate antibiotic effects.

Prevalence and correlates of phenazine resistance in culturable bacteria from a dryland wheat field

The paper assesses phenazine resistance in bacteria from a wheat field, finding Gram-positive bacteria are more sensitive to phenazines and resistance correlates with rhizosphere presence and pH.

Paraburkholderia edwinii protects Aspergillus sp. from phenazines by acting as a toxin sponge

The paper identifies Paraburkholderia edwinii as a bacterium that protects Aspergillus sp. from phenazines by sequestering them, and shows this interaction is mediated by HrcA and environmental conditions.

In situ single-cell activities of microbial populations revealed by spatial transcriptomics

This study uses spatial transcriptomics to analyze microbial populations, revealing spatially resolved metabolic and virulence states in Pseudomonas aeruginosa.

Global landscape of phenazine biosynthesis and biodegradation reveals species-specific colonization patterns in agricultural soils and crop microbiomes

The paper uses metagenomics to study phenazine biosynthesis and biodegradation in soils and crop microbiomes, revealing species-specific associations and ecological roles.

Bacterial defenses against a natural antibiotic promote collateral resilience to clinical antibiotics

This study shows that bacterial production of natural antibiotics like pyocyanin increases tolerance to clinical antibiotics and accelerates resistance mutation rates in multispecies infections.

Extracellular DNA promotes efficient extracellular electron transfer by pyocyanin in Pseudomonas aeruginosa biofilms

This study shows extracellular DNA enhances electron transfer efficiency in Pseudomonas aeruginosa biofilms by facilitating phenazine retention and redox reactions.

Quantitative visualization of gene expression in Pseudomonas aeruginosa aggregates reveals peak expression of alginate in the hypoxic zone

This paper uses HCR v3.0 to visualize and quantify gene expression in Pseudomonas aeruginosa biofilms, revealing hypoxic zone-specific alginate gene expression.

Aggregation of nontuberculous mycobacteria is regulated by carbon:nitrogen balance

This study shows that nontuberculous mycobacteria aggregate in response to carbon:nitrogen balance, not their mycolic acid-rich cell wall.

Extended hopanoid loss reduces bacterial motility and surface attachment and leads to heterogeneity in root nodule kinetics in a Bradyrhizobium-Aeschynomene symbiosis

This study shows that loss of extended hopanoids in Bradyrhizobium reduces bacterial motility and surface attachment, leading to heterogeneous root nodule development in Aeschynomene afraspera.

Refining the application of microbial lipids as tracers of Staphylococcus aureus growth rates in cystic fibrosis sputum

This study refines the use of microbial lipids as growth rate tracers for Staphylococcus aureus in CF sputum by identifying alternative microbial sources of fatty acids and recommending best practices for stable isotope probing.

Towards measuring growth rates of pathogens during infections by D2O-labeling lipidomics

This paper develops a D2O-labeling lipidomics approach to measure microbial growth rates in infections, finding that deuterium incorporation in lipids can estimate generation times of pathogens like S. aureus.