W. W. Fischer

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.

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.

Metabolic evolution of pyranopterin-dependent biochemistry

The paper models metabolic evolution and finds that Mo-dependent biochemistry emerged after oxygen rise, supported by genomic and machine learning analyses.

An evolutionary timescale for Bacteria calibrated using the Great Oxidation Event

This paper uses machine learning and phylogenetic reconciliation to estimate the evolutionary timeline of Bacteria, linking transitions to aerobic lifestyles to the Great Oxidation Event.

Bacterial Form I' rubisco has smaller carbon isotope fractionation than its Form I counterpart

The paper measures the kinetic isotope effects (KIEs) of two Form I rubiscos and finds that the L8 variant has a smaller KIE than the L8S8 variant.

Carbon isotope fractionation by an ancestral rubisco suggests biological proxies for CO2 through geologic time should be re-evaluated

The paper measures carbon isotope fractionation of an ancestral rubisco in cyanobacteria, showing that evolutionary changes in photosynthesis physiology, not just atmospheric CO2, affect the carbon isotope record.

Trajectories for the evolution of bacterial CO2-concentrating mechanisms

This paper studies the evolution of bacterial CO2-concentrating mechanisms by engineering E. coli to express ancestral forms of these systems and testing their growth under varying CO2 concentrations.

Diversity and evolution of nitric oxide reduction

This study identifies new nitric oxide reductase families and shows they evolved independently from oxygen reductases, expanding known denitrifying microbes.

Genomic Evidence for Phototrophic Oxidation of Small Alkanes in a Member of the Chloroflexi Phylum

The paper describes a new bacterial genome from the Chloroflexi phylum that exhibits both methanotrophy and phototrophy, suggesting a novel metabolic pathway for photomethanotrophy.

Geochemical and metagenomic characterization of Jinata Onsen, a Proterozoic-analog hot spring, reveals novel microbial diversity including iron-tolerant phototrophs and thermophilic lithotrophs

The paper characterizes the geochemistry and microbial communities of Jinata Onsen, revealing novel microbial diversity and insights into Proterozoic-like ecosystems.