P. B. Rainey

Eco-evolutionary dynamics of massive, parallel bacteriophage outbreaks in compost communities

The paper studies bacteriophage outbreaks in compost communities, finding that viral migration accelerates evolution through recombination and mutation spread.

Rapid dissemination of host-metabolism-manipulating transposon-like entities via integrative and conjugative elements

The paper identifies a transposon-like entity in Pseudomonas syringae ICEs that manipulates bacterial metabolism, with a key regulator affecting gene expression and fitness.

Identifying and tracking mobile elements in evolving compost communities yields insights into the nanobiome

The paper develops a bioinformatic pipeline to detect horizontal gene transfer in compost communities, revealing new mobile genetic elements and their ecological roles.

The Effect of Bottleneck Size on Evolution in Nested Darwinian Populations

This paper investigates how varying bottleneck sizes in nested Darwinian populations affect evolutionary dynamics, showing that larger bottlenecks can reverse evolutionary direction under certain conditions.

Interaction among bacterial cells triggers exit from lag phase

The paper measures how bacterial population size affects lag phase duration and finds that lag time decreases with inoculum size due to cell-cell interactions.

Tradeoff breaking as model of evolutionary transitions in individuality and the limits of the fitness decoupling metaphor

The paper shows that fitness decoupling in evolutionary transitions is impossible and proposes tradeoff-breaking as a better marker for these transitions.

Polar accumulation of pyoverdin and exit from stationary phase

The paper shows pyoverdin accumulates at cell poles during stationary phase in Pseudomonas species and provides fitness advantages upon resuming growth.

Ancient Darwinian replicators nested within eubacterial genomes

The paper identifies REPINs as non-autonomous mobile genetic elements that form long-term beneficial associations with bacterial genomes, showing evidence of mutualistic relationships through population dynamics and conservation patterns.

Transposable elements drive the evolution of genome streamlining

The paper shows that transposable elements can drive genome streamlining in prokaryotes through horizontal gene transfer and rock-paper-scissors dynamics, despite being maladaptive to individual cells.

In vivo transcriptome analysis provides insights into host-dependent expression of virulence factors by Yersinia entomophaga MH96, during infection of Galleria mellonella

This study analyzes the in vivo transcriptome of Yersinia entomophaga MH96 during infection of Galleria mellonella, identifying genes upregulated at different stages and their roles in virulence.

Meta-population structure and the evolutionary transition to multicellularity

The paper shows that structured environments favor the evolution of multicellularity by maintaining group and dispersal phase discreteness in bacterial populations.

Eco-evolutionary dynamics of nested Darwinian populations and the emergence of community-level heredity

The paper shows how manipulating population structure can impose Darwinian properties on microbial communities, enabling them to reliably reproduce parental phenotypes through developmental correction.

Experimental evolution of nascent multicellularity: Recognizing a Darwinian transition in individuality

The paper examines an experimental evolution study of multicellularity in Pseudomonas fluorescens, arguing that bacterial groups developed Darwinian properties enabling group-level adaptation.

Experimental manipulation of selfish genetic elements links genes to microbial community function

The paper manipulates selfish genetic elements in microbial communities to study gene function, finding enrichment of nitrogen metabolism genes and measurable impacts on community function.

Ecological scaffolding and the evolution of individuality: the transition from cells to multicellular life

This paper uses mathematical models to show how ecological structures can scaffold evolutionary processes in cell collectives, leading to multicellular traits and reproductive division of labour.

Causes and biophysical consequences of cellulose production by Pseudomonas fluorescens SBW25 at the air-liquid interface

The paper investigates cellulose production by Pseudomonas fluorescens SBW25 at the air-liquid interface, revealing environmental signals that activate cellulose synthesis and resulting biophysical consequences.

Predicting mutational routes to new adaptive phenotypes

The paper predicts mutational routes to adaptive phenotypes in Pseudomonas fluorescens using mathematical models and experimental validation, finding discrepancies between predictions and observations due to undetected mutations.

Repeated phenotypic evolution by different genetic routes: the evolution of colony switching in Pseudomonas fluorescens SBW25

This study shows that two independent lineages of Pseudomonas fluorescens SBW25 evolved colony switching through different genetic mutations, with Line 6 relying on an rpoD mutation affecting ribosome expression.

Ribosome provisioning activates a bistable switch coupled to fast exit from stationary phase

The paper shows that pyrimidine limitation triggers ribosome biosynthesis, leading to a bistable switch in Pseudomonas fluorescens that enables rapid exit from stationary phase.

The ecological genetics of Pseudomonas syringae from kiwifruit leaves

The paper studies the population structure and genetic diversity of Pseudomonas syringae from kiwifruit leaves during an outbreak, revealing ecological interactions between pathogenic and commensal strains.

Adaptive evolution by spontaneous domain fusion and protein relocalisation

The paper describes how a new gene emerged through domain fusion and relocalization in Pseudomonas fluorescens, resulting in an adaptive phenotype.

Identification And Characterization Of Domesticated Bacterial Transposases

The paper identifies and characterizes RAYTs, a class of bacterial transposases, showing they are domesticated and functionally integrated into host genomes.