The public and private benefit of an impure public good determines the sensitivity of bacteria to population collapse in a snowdrift game

Purine and pyrimidine synthesis differently affect the strength of the inoculum effect for aminoglycoside and β-lactam antibiotics

The inoculum effect has been observed for nearly all antibiotics and bacterial species. However, explanations accounting for its occurrence and strength are lacking. We previously found that growth productivity, which captures the relationship between [ATP] and growth, can account for the strength of the inoculum effect for bactericidal antibiotics. However, the molecular pathway(s) underlying this relationship, and therefore determining the inoculum effect, remain undiscovered. We show that nucleotide synthesis can determine the relationship between [ATP] and growth, and thus the strength of inoculum effect in an antibiotic class-dependent manner. Specifically, and separate from activity through the tricarboxylic acid cycle, we find that transcriptional activity of genes involved in purine and pyrimidine synthesis can predict the strength of the inoculum effect for β-lactam and aminoglycosides antibiotics, respectively. Our work highlights the antibiotic class-specific effect of purine and pyrimidine synthesis on the severity of the inoculum effect and paves the way for intervention strategies to reduce the inoculum effect in the clinic.

Growth productivity as a determinant of the inoculum effect for bactericidal antibiotics

Understanding the mechanisms by which populations of bacteria resist antibiotics has implications in evolution, microbial ecology, and public health. The inoculum effect (IE), where antibiotic efficacy declines as the density of a bacterial population increases, has been observed for multiple bacterial species and antibiotics. Several mechanisms to account for IE have been proposed, but most lack experimental evidence or cannot explain IE for multiple antibiotics. We show that growth productivity, the combined effect of growth and metabolism, can account for IE for multiple bactericidal antibiotics and bacterial species. Guided by flux balance analysis and whole-genome modeling, we show that the carbon source supplied in the growth medium determines growth productivity. If growth productivity is sufficiently high, IE is eliminated. Our results may lead to approaches to reduce IE in the clinic, help standardize the analysis of antibiotics, and further our understanding of how bacteria evolve resistance.

A Salvaging Strategy Enables Stable Metabolite Provisioning among Free-Living Bacteria

All organisms rely on complex metabolites such as amino acids, nucleotides, and cofactors for essential metabolic processes. Some microbes synthesize these fundamental ingredients of life de novo, while others rely on uptake to fulfill their metabolic needs. Although certain metabolic processes are inherently "leaky," the mechanisms enabling stable metabolite provisioning among microbes in the absence of a host remain largely unclear. In particular, how can metabolite provisioning among free-living bacteria be maintained under the evolutionary pressure to economize resources? Salvaging, the process of "recycling and reusing," can be a metabolically efficient route to obtain access to required resources. Here, we show experimentally how precursor salvaging in engineered Escherichia coli populations can lead to stable, long-term metabolite provisioning. We find that salvaged cobamides (vitamin B₁₂ and related enzyme cofactors) are readily made available to nonproducing population members, yet salvagers are strongly protected from overexploitation. We also describe a previously unnoted benefit of precursor salvaging, namely, the removal of the nonfunctional, proliferation-inhibiting precursor. As long as compatible precursors are present, any microbe possessing the terminal steps of a biosynthetic process can, in principle, forgo de novo biosynthesis in favor of salvaging. Consequently, precursor salvaging likely represents a potent, yet overlooked, alternative to de novo biosynthesis for the acquisition and provisioning of metabolites in free-living bacterial populations. IMPORTANCE Recycling gives new life to old things. Bacteria have the ability to recycle and reuse complex molecules they encounter in their environment to fulfill their basic metabolic needs in a resource-efficient way. By studying the salvaging (recycling and reusing) of vitamin B₁₂ precursors, we found that metabolite salvaging can benefit others and provide stability to a bacterial community at the same time. Salvagers of vitamin B₁₂ precursors freely share the result of their labor yet cannot be outcompeted by freeloaders, likely because salvagers retain preferential access to the salvaging products. Thus, salvaging may represent an effective, yet overlooked, mechanism of acquiring and provisioning nutrients in microbial populations.

Social Learning Strategies and Cooperative Behaviour: Evidence of Payoff Bias, but Not Prestige or Conformity, in a Social Dilemma Game

Human cooperation, occurring without reciprocation and between unrelated individuals in large populations, represents an evolutionary puzzle. One potential explanation is that cooperative behaviour may be transmitted between individuals via social learning. Using an online social dilemma experiment, we find evidence that participants’ contributions were more consistent with payoff-biased transmission than prestige-biased transmission or conformity. We also found some evidence for lower cooperation (i) when exposed to social information about peer cooperation levels than without such information, and (ii) in the prisoners’ dilemma game compared to the snowdrift game. A simulation model established that the observed cooperation was more likely to be caused by participants’ general propensity to cooperate than by the effect of social learning strategies employed within the experiment, but that this cooperative propensity could be reduced through selection. Overall, our results support previous experimental evidence indicating the role of payoff-biased transmission in explaining cooperative behaviour, but we find that this effect was small and was overwhelmed by participants’ general propensity for cooperation.

Density-dependent private benefit leads to bacterial mutualism

Microorganisms produce and secrete materials that are beneficial for themselves and their neighbors. We modeled the situation when cells can produce different costly secretions which increase the carrying capacity of the population. Strains that lose the function of producing one or more secretions avoid the cost of production and can exhaust the producers. However, secreting substances provides a private benefit for the producers in a density-dependent way. We developed a model to examine the outcome of the selection among different types of producer strains from the nonproducer strain to the partial producers, to the full producer strain. We were interested in circumstances under which selection maintains partners that produce complementary secreted materials thus forming an interdependent mutualistic interaction. We show that interdependent mutualism is selected under a broad range of conditions if private benefit decreases with density. Selection frequently causes the coexistence of more and less generalist cooperative strains, thus cooperation and exploitation co-occur. Interdependent mutualism is evolved under more specific circumstances if private benefit increases with density and these general observations are valid in a well-mixed and a structured deme model. We show that the applied population structure allows the invasion of rare cooperators and supports cooperation in general.