K. D. McMahon

Bacterial ecology and evolution converge on seasonal and decadal scales

The paper analyzes a two-decade freshwater lake metagenome dataset to show that ecological and evolutionary processes in microbial communities operate on seasonal and decadal scales.

Expanded diversity of tfdA harboring bacteria across the natural and built environment

This study evaluates the accuracy of tfdA qPCR primers and expands the known diversity of 2,4-D degrading bacteria using genomic and molecular approaches.

A two-decade microbial time series from a freshwater lake, introducing the limony and TYMEFLIES datasets

The paper introduces two microbial time series datasets from Lake Mendota, providing long-term microbial and environmental data for ecological and evolutionary research.

Species invasions shift microbial phenology in a two-decade freshwater time series

The paper examines how invasive species alter microbial phenology over two decades in freshwater ecosystems, finding shifts in Cyanobacteria, cyanotoxins, and heterotrophic bacteria patterns following invasions.

Diversity, distribution, and expression of opsin genes in freshwater lakes

This study investigates opsin gene diversity, distribution, and expression in freshwater lakes, finding that opsin abundance correlates with lake optical properties and DOC levels, and highlights the role of rhodopsin-based phototrophy in clearwater lakes.

Environmental predictors of electroactive bacterioplankton in small boreal lakes.

The paper identifies environmental predictors of electroactive bacterioplankton in small boreal lakes by analyzing EET genes and their correlation with DOM.

Re-evaluation of the phylogenetic diversity and global distribution of the genus Candidatus Accumulibacter

This paper re-evaluates the phylogeny and taxonomy of Candidatus Accumulibacter using genome, ppk1, and 16S rRNA gene data, identifying 15 new species and confirming PAO metabolism across all species.

Microbial cysteine degradation is a source of hydrogen sulfide in oxic freshwater lakes

This study identifies bacteria in oxic freshwater lakes that produce hydrogen sulfide through cysteine degradation, revealing a new pathway for sulfur cycling in oxygenated environments.

Depth-discrete metagenomics reveals the roles of microbes in biogeochemical cycling in the tropical freshwater Lake Tanganyika

This study uses depth-discrete metagenomics to reveal microbial roles in biogeochemical cycling in Lake Tanganyika's anoxic waters.

Autotrophic and mixotrophic metabolism of an anammox bacterium revealed by in vivo 13C and 2H metabolic network mapping

This study uses isotope tracing and metabolomics to resolve the central carbon metabolism of an anammox bacterium, revealing discrepancies between genomic predictions and in vivo metabolic fluxes.

Host population diversity as a driver of viral infection cycle in wild populations of green sulfur bacteria with long standing virus-host interactions

This study examines viral infection dynamics in green sulfur bacteria, finding that multiple viruses, including lysogenic ones, co-infect host populations and that host diversity may influence the lytic/lysogenic switch.

Large Freshwater Phages with the Potential to Augment Aerobic Methane Oxidation

The paper identifies large freshwater phages encoding the pmoC gene, which may enhance bacterial methane oxidation and influence greenhouse gas emissions.

Wide distribution of phage that infect freshwater SAR11 bacteria

The paper identifies and characterizes phages infecting Fonsibacter, showing their global distribution and ecological impact on freshwater microbial communities.

Extracellular electron transfer may be an overlooked contribution to pelagic respiration in humic-rich freshwater lakes

The paper compares metagenomes from humic and clearwater lakes to show higher extracellular electron transfer gene abundance in humic bogs, suggesting HS as an overlooked electron acceptor in pelagic respiration.

Integrated ‘omic’ analyses provide evidence that a Ca. Accumulibacter phosphatis strain performs denitrification under micro-aerobic conditions

This study uses integrated omics analysis to show that an Accumulibacter strain can simultaneously respire oxygen and nitrate under micro-aerobic conditions, supporting denitrification.

Connections between freshwater carbon and nutrient cycles revealed through reconstructed population genomes

The paper links freshwater carbon and nutrient cycles by analyzing microbial population genomes and marker genes from two aquatic environments, showing co-occurrence of metabolic pathways and taxonomic patterns.

Contrasting patterns of genome-level diversity across distinct co-occurring bacterial populations

The paper examines genetic and ecological differentiation in freshwater bacterial populations using single-cell genomes and metagenomic data, finding ecologically distinct populations within some lineages but not others.

Metabolic Network Analysis and Metatranscriptomics Reveals Auxotrophies and Nutrient Sources of the Cosmopolitan Freshwater Microbial Lineage acI

Small subsets of highly connected taxa predict compositional change in microbial communities

The paper shows that highly connected taxa in microbial communities predict compositional changes better than all taxa, and that community connectivity reduces compositional turnover.

Genome-Enabled Insights Into The Ecophysiology Of The Comammox Bacterium Candidatus Nitrospira nitrosa

This study identifies and compares genomic traits of comammox and nitrite-oxidizing Nitrospira strains to understand their ecological and physiological adaptations.