Roadmap on biology in time varying environments.

Biological organisms experience constantly changing environments, from sudden changes in physiology brought about by feeding, to the regular rising and setting of the Sun, to ecological changes over evolutionary timescales. Living organisms have evolved to thrive in this changing world but the general principles by which organisms shape and are shaped by time varying environments remain elusive. Our understanding is particularly poor in the intermediate regime with no separation of timescales, where the environment changes on the same timescale as the physiological or evolutionary response. Experiments to systematically characterize the response to dynamic environments are challenging since such environments are inherently high dimensional. This roadmap deals with the unique role played by time varying environments in biological phenomena across scales, from physiology to evolution, seeking to emphasize the commonalities and the challenges faced in this emerging area of research.

Evolutionary Phase Transitions in Random Environments.

We present analytical results for long-term growth rates of structured populations in randomly fluctuating environments, which we apply to predict how cellular response networks evolve. We show that networks which respond rapidly to a stimulus will evolve phenotypic memory exclusively under random (i.e., nonperiodic) environments. We identify the evolutionary phase diagram for simple response networks, which we show can exhibit both continuous and discontinuous transitions. Our approach enables exact analysis of diverse evolutionary systems, from viral epidemics to emergence of drug resistance.

Humidity Reduces Rapid and Distant Airborne Dispersal of Viable Viral Particles in Classroom Settings.

The transmission of airborne pathogens is considered to be the main route through which a number of known and emerging respiratory diseases infect their hosts. While physical distancing and mask wearing may help mitigate short-range transmission, the extent of long-range transmission in closed spaces where a pathogen remains suspended in the air remains unknown. We have developed a method to detect viable virus particles by using an aerosolized bacteriophage Phi6 in combination with its host Pseudomonas phaseolicola, which when seeded on agar plates acts as a virus detector that can be placed at a range of distances away from an aerosol-generating source. By applying this method, we consistently detected viable phage particles at distances of up to 18 feet away from the source within 15 min of exposure in a classroom equipped with a state of the art HVAC system and determined that increasing the relative humidity beyond 40% significantly reduces dispersal. Our method, which can be further modified for use with other virus/host combinations, quantifies airborne transmission in the built environment and can thus be used to set safety standards for room capacity and to ascertain the efficacy of interventions in closed spaces of specified sizes and intended uses.

Ecological memory preserves phage resistance mechanisms in bacteria.

Bacterial defenses against phage, which include CRISPR-mediated immunity and other mechanisms, can carry substantial growth rate costs and can be rapidly lost when pathogens are eliminated. How bacteria preserve their molecular defenses despite their costs, in the face of variable pathogen levels and inter-strain competition, remains a major unsolved problem in evolutionary biology. Here, we present a multilevel model that incorporates biophysics of molecular binding, host-pathogen population dynamics, and ecological dynamics across a large number of independent territories. Using techniques of game theory and non-linear dynamical systems, we show that by maintaining a non-zero failure rate of defenses, hosts sustain sufficient levels of pathogen within an ecology to select against loss of the defense. This resistance switching strategy is evolutionarily stable, and provides a powerful evolutionary mechanism that maintains host-pathogen interactions, selects against cheater strains that avoid the costs of immunity, and enables co-evolutionary dynamics in a wide range of systems.