Peter J. Yunker

Killing by Type VI secretion drives genetic phase separation and correlates with increased cooperation

By nature of their small size, dense growth and frequent need for extracellular metabolism, microbes face persistent public goods dilemmas. Genetic assortment is the only general solution stabilizing cooperation, but all known mechanisms structuring microbial populations depend on the availability of free space, an often unrealistic constraint. Here we describe a class of self-organization that operates within densely packed bacterial populations. Through mathematical modelling and experiments with Vibrio cholerae, we show how killing adjacent competitors via the Type VI secretion system (T6SS) precipitates phase separation via the ‘Model A universality class of order-disorder transition mediated by killing. We mathematically demonstrate that T6SS-mediated killing should favour the evolution of public goods cooperation, and empirically support this prediction using a phylogenetic comparative analysis. This work illustrates the twin role played by the T6SS, dealing death to local competitors while simultaneously creating conditions potentially favouring the evolution of cooperation with kin.

Record dynamics: Direct experimental evidence from jammed colloids

In a broad class of complex materials a quench leads to a multi-scaled relaxation process known as aging. To explain its commonality and the astounding insensitivity to most microscopic details, record dynamics (RD) posits that a small set of increasingly rare and irreversible events, so called quakes, controls the dynamics. While key predictions of RD are known to concur with a number of experimental and simulational results, its basic assumption on the nature of quake statistics has proven extremely difficult to verify experimentally. The careful distinction of rare (record) cage-breaking events from in-cage rattle accomplished in previous experiments on jammed colloids, enables us to extract the first direct experimental evidence for the fundamental hypothesis of RD that the rate of quakes decelerates with the inverse of the system age. The resulting description shows the predicted growth of the particle mean square displacement and of a mesoscopic lengthscale with the logarithm of time.

Transport and trapping of nanosheets via hydrodynamic forces and curvature-induced capillary quadrupolar interactions

HYPOTHESISnThe manipulation of nanosheets on a fluid-fluid interface remains a significant challenge. At this interface, hydrodynamic forces can be used for long-range transport (>1× capillary length) but are difficult to utilize for accurate and repeatable positioning. While capillary multipole interactions have been used for particle trapping, how these interactions manifest on large but thin objects, i.e., nanosheets, remains an open question. Hence, we posit hydrodynamic forces in conjunction with capillary multipole interactions can be used for nanosheet transport and trapping.nnnEXPERIMENTSnWe designed and characterized a fluidic device for transporting and trapping nanosheets on the water-air interface. Analytical models were compared against optical measurements of the nanosheet behavior to investigate capillary multipole interactions. Energy-based modeling and dimensional analysis were used to study trapping stability.nnnFINDINGSnHydrodynamic forces and capillary interactions successfully transported and trapped nanosheets at a designated trapping location with a repeatability of 10% of the nanosheets length and 12% of its width (lengthu202f=u202f1500u202fµm, widthu202f=u202f1000u202fµm) and an accuracy of 20% of their length and width. Additionally, this is the first report that surface tension forces acting upon nanoscale-thick objects manifest as capillary quadrupolar interactions and can be used for precision manipulation of nanosheets.

Cycles in Zero-Sum Differential Games and Biological Diversity

Negative frequency-dependent selection (i.e., declining fitness with increased frequency in the population) is thought to be one of the factors that maintains biological diversity. In this paper, we give a concrete mathematical argument supporting this. Our model is as follows: A collection of species derive their fitnesses via a rock-paper-scissors-type game whose precise payoffs are a function of the environment. The new aspect of our model lies in adding a feedback loop: the environment changes according to the relative fitnesses of the species (hence, payoffs change as a function of fitness, which in turn changes as a function of payoffs). The changes in the payoffs are in keeping with the principle of negative frequency-dependent selection, which is widespread in nature. In order to model our game as a continuous time dynamical system, we cast it in the setting of a differential game. We show that for certain parameters, this dynamics cycles, i.e., no species goes extinct and diversity is maintained. We believe that our techniques can be applied to optimization and machine learning to show that first order methods (e.g., gradient descent/ascent) do cycle even in online settings in which the loss function changes with time.

Ecological advantages and evolutionary limitations of aggregative multicellular development

All multicellular organisms develop through one of two basic routes: they either aggregate from free-living cells, creating potentially-chimeric multicellular collectives, or they develop clonally via mother-daughter cellular adhesion. While evolutionary theory makes clear predictions about trade-offs between these developmental modes, these have never been experimentally tested in otherwise genetically-identical organisms. We engineered unicellular baker’s yeast (Saccharomyces cerevisiae) to develop either clonally (‘snowflake’, Δace2), or aggregatively (‘floc’, GAL1p::FLO1), and examined their fitness in a fluctuating environment characterized by periods of growth and selection for rapid sedimentation. When cultured independently, aggregation was far superior to clonal development, providing a 35% advantage during growth, and a 2.5-fold advantage during settling selection. Yet when competed directly, clonally-developing snowflake yeast rapidly displaced aggregative floc. This was due to unexpected social exploitation: snowflake yeast, which do not produce adhesive FLO1, nonetheless become incorporated into flocs at a higher frequency than floc cells themselves. Populations of chimeric clusters settle much faster than floc alone, providing snowflake yeast with a fitness advantage during competition. Mathematical modeling suggests that such developmental cheating may be difficult to circumvent; hypothetical ‘choosy floc’ that avoid exploitation by maintaining clonality pay an ecological cost when rare, often leading to their extinction. Our results highlight the conflict at the heart of aggregative development: non-specific cellular binding provides a strong ecological advantage – the ability to quickly form groups – but this very feature leads to its exploitation.

Killing by Type VI secretion drives clonal phase separation and the evolution of cooperation

By nature of their small size, dense growth and frequent need for extracellular metabolism, microbes face persistent public goods dilemmas1–5. Spatial assortment can act as a general solution to social conflict by allowing extracellular goods to be utilized preferentially by productive genotypes1,6,7. Established mechanisms that generate microbial assortment depend on the availability of free space8–14; however, microbes often live in densely-packed environments, wherein these mechanisms are ineffective. Here, we describe a novel class of self-organized pattern formation that facilitates the development of spatial structure within densely-packed bacterial colonies. Contact-mediated killing through the Type VI secretion system (T6SS) drives high levels of assortment by precipitating phase separation, even in initially well-mixed populations that do not necessarily exhibit net growth. We examine these dynamics using three different classes of mathematical models and experiments with mutually antagonistic strains of Vibrio cholerae growing on solid media, and find that all appear to de-mix via the same ‘Model A’ universality class of order-disorder transition. We mathematically demonstrate that contact killing should favour the evolution of public goods cooperation, and empirically examine the relationship between T6SSs and potential cooperation through phylogenetic analysis. Across 26 genera of Proteobacteria and Bacteroidetes, the proportion of a strain’s genome that codes for potentially-exploitable secreted proteins increases significantly with boththe number of Type 6 secretion systems and the number of T6SS effectors that it possesses. This work demonstrates how antagonistic traits—likely evolved for the purpose of killing competitors—can indirectlylead to the evolution of cooperation by driving genetic phase separation.