Frequency- and Amplitude-Dependent Microbial Population Dynamics during Cycles of Feast and Famine

The proteome is a terminal electron acceptor

Microbial metabolism is impressively flexible, enabling growth even when available nutrients differ greatly from biomass in redox state. E. coli, for example, rearranges its physiology to grow on reduced and oxidized carbon sources through several forms of fermentation and respiration. To understand the limits on and evolutionary consequences of metabolic flexibility, we developed a mathematical model coupling redox chemistry with principles of cellular resource allocation. Our integrated model clarifies key phenomena, including demonstrating that autotrophs grow slower than heterotrophs because of constraints imposed by intracellular production of reduced carbon. Our model further indicates that growth is improved by adapting the redox state of biomass to nutrients, revealing an unexpected mode of evolution where proteins accumulate mutations benefiting organismal redox balance.

Coupled environmental and demographic fluctuations shape the evolution of cooperative antimicrobial resistance

There is a pressing need to better understand how microbial populations respond to antimicrobial drugs, and to find mechanisms to possibly eradicate antimicrobial-resistant cells. The inactivation of antimicrobials by resistant microbes can often be viewed as a cooperative behaviour leading to the coexistence of resistant and sensitive cells in large populations and static environments. This picture is, however, greatly altered by the fluctuations arising in volatile environments, in which microbial communities commonly evolve. Here, we study the eco-evolutionary dynamics of a population consisting of an antimicrobial-resistant strain and microbes sensitive to antimicrobial drugs in a time-fluctuating environment, modelled by a carrying capacity randomly switching between states of abundance and scarcity. We assume that antimicrobial resistance (AMR) is a shared public good when the number of resistant cells exceeds a certain threshold. Eco-evolutionary dynamics is thus characterised by demographic noise (birth and death events) coupled to environmental fluctuations which can cause population bottlenecks. By combining analytical and computational means, we determine the environmental conditions for the long-lived coexistence and fixation of both strains, and characterise a fluctuation-driven AMR eradication mechanism, where resistant microbes experience bottlenecks leading to extinction. We also discuss the possible applications of our findings to laboratory-controlled experiments.

Complementary resource preferences spontaneously emerge in diauxic microbial communities

Many microbes grow diauxically, utilizing the available resources one at a time rather than simultaneously. The properties of communities of microbes growing diauxically remain poorly understood, largely due to a lack of theory and models of such communities. Here, we develop and study a minimal model of diauxic microbial communities assembling in a serially diluted culture. We find that unlike co-utilizing communities, diauxic community assembly repeatably and spontaneously leads to communities with complementary resource preferences, namely communities where species prefer different resources as their top choice. Simulations and theory explain that the emergence of complementarity is driven by the disproportionate contribution of the top choice resource to the growth of a diauxic species. Additionally, we develop a geometric approach for analyzing serially diluted communities, with or without diauxie, which intuitively explains several additional emergent community properties, such as the apparent lack of species which grow fastest on a resource other than their most preferred resource. Overall, our work provides testable predictions for the assembly of natural as well as synthetic communities of diauxically shifting microbes.

Exclusion of the fittest predicts microbial community diversity in fluctuating environments

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species' ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.

Feast/famine ratio determined continuous flow aerobic granulation

Plug flow reactors (PFRs) made of multiple completely stirred tank reactors (CSTRs) in series were used to cultivate aerobic granules in real domestic wastewater. Theoretically, changing the number of CSTR chambers in series will change the nature of plug flow, and thus alter the pattern of the feast/famine condition and impact the aerobic granulation progress. Therefore, PFRs were operated in 4-, 6-, and 8-chamber mode under the same gravity selection pressure (a critical settling velocity of 9.75 m h^-1) and hydraulic retention time (6.5 h) until steady states were reached to evaluate the effect of the feast/famine condition on continuous flow aerobic granulation. The sludge particle size, circularity, settleability, specific gravity, zone settling velocity, and extracellular polymeric substance contents were analyzed to evaluate the role that a feast/famine regime plays in aerobic granulation. It was found that aerobic granulation failed whenever the feast/famine ratio was greater than 0.5. The results support a conclusion that the feast/famine condition is likely a prerequisite for continuous flow aerobic granulation.

Higher-Order Interaction between Species Inhibits Bacterial Invasion of a Phototroph-Predator Microbial Community

The composition of an ecosystem is thought to be important for determining its resistance to invasion. Studies of natural ecosystems, from plant to microbial communities, have found that more diverse communities are more resistant to invasion. In some cases, more diverse communities resist invasion by more completely consuming the resources necessary for the invader. We show that Escherichia coli can successfully invade cultures of the alga Chlamydomonas reinhardtii (phototroph) or the ciliate Tetrahymena thermophila (predator) but cannot invade a community where both are present. The invasion resistance of the algae-ciliate community arises from a higher-order interaction between species (interaction modification) that is unrelated to resource consumption. We show that the mode of this interaction is the algal inhibition of bacterial aggregation, which leaves bacteria vulnerable to predation. This mode requires both the algae and the ciliate to be present and provides an example of invasion resistance through an interaction modification.

Cooperation in Microbial Populations: Theory and Experimental Model Systems

Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where ensembles of local communities (subpopulations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. As a specific but generic biological example, we consider populations of Pseudomonas putida and its regulation and use of pyoverdines, iron scavenging molecules, as public goods. The review closes with an overview on cooperation in spatially extended systems and also provides a critical assessment of the insights gained from the experimental and theoretical studies discussed. Current challenges and important new research opportunities are discussed, including the biochemical regulation of public goods, more realistic ecological scenarios resembling native environments, cell-to-cell signaling, and multispecies communities.