R. Stepanauskas

Flotillin-Associated rhodopsin (FArhodopsin), a widespread paralog of proteorhodopsin in aquatic bacteria with streamlined genomes

The paper identifies a new class of rhodopsins, FArhodopsins, found in marine and freshwater microbes, associated with membrane microdomains and potentially retinal-less function.

Single cell genome sequencing of laboratory mouse microbiota improves taxonomic and functional resolution of this model microbial community

The paper uses single-cell genome sequencing of mouse stool to improve taxonomic and functional resolution of the mouse gut microbiome by identifying novel species and enhancing metagenomic analysis.

Strain-level variation influences Methanothermococcus fitness in marine hydrothermal systems

The paper examines strain-level variation in Methanothermococcus across hydrothermal vents, finding that some strains outcompete others and that accessory genes like nitrogen fixation and CRISPR/Cas do not always confer a fitness advantage.

Novel integrative elements and genomic plasticity in ocean ecosystems

The paper identifies tycheposons, mobile genetic elements in Prochlorococcus, that drive genomic plasticity through gene exchange and contribute to microbial adaptation in ocean ecosystems.

Methylotrophy, alkane-degradation, and pigment production as defining features of the globally distributed yet-uncultured phylum Binatota

This study analyzes genomes from the uncultured bacterial phylum Binatota, revealing their methylotrophic, alkane-degrading, and pigment-producing capabilities, along with ecological preferences.

Gene exchange networks define species-like units in marine prokaryotes

The paper identifies gene exchange networks in marine prokaryotes, showing they form broader evolutionary units than traditional species definitions.

Ancestral absence of electron transport chains in Patescibacteria and DPANN

The paper investigates Patescibacteria and DPANN, finding they lack electron transport chains and rely on fermentation, suggesting ancestral adaptations to symbiotic lifestyles.

Emergence of trait variability through the lens of nitrogen assimilation in Prochlorococcus

The paper examines nitrate assimilation gene distribution across Prochlorococcus genomes to understand evolutionary mechanisms shaping trait variability in microbial species.

Hydrogen-based metabolism - An ancestral trait in lineages sibling to the Cyanobacteria

This paper predicts the metabolisms of Margulisbacteria and Saganbacteria using genomic data and compares them to their phylogenetic neighbors, supporting the hypothesis that their ancestor used hydrogen metabolism and fermentation.

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.