Behavioral heterogeneity in quorum sensing can stabilize social cooperation in microbial populations

Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition

The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.

Evolution of lasR mutants in polymorphic Pseudomonas aeruginosa populations facilitates chronic infection of the lung

Chronic infection with the bacterial pathogen Pseudomonas aeruginosa often leads to coexistence of heterogeneous populations carrying diverse mutations. In particular, loss-of-function mutations affecting the quorum-sensing regulator LasR are often found in bacteria isolated from patients with lung chronic infection and cystic fibrosis. Here, we study the evolutionary dynamics of polymorphic P. aeruginosa populations using isolates longitudinally collected from patients with chronic obstructive pulmonary disease (COPD). We find that isolates deficient in production of different sharable extracellular products are sequentially selected in COPD airways, and lasR mutants appear to be selected first due to their quorum-sensing defects. Polymorphic populations including lasR mutants display survival advantages in animal models of infection and modulate immune responses. Our study sheds light on the multistage evolution of P. aeruginosa populations during their adaptation to host lungs.

Impacts of exogenous quorum sensing signal molecule-acylated homoserine lactones (AHLs) with different addition modes on Anammox process

Anammox was proved having the quorum sensing ability, and several acylated homoserine lactones (AHLs) signal molecules were detected in the system. In this study, the impact of exogenous N-dodecanoyl homoserine lactone (C12-HSL) with different addition modes on the nitrogen removal, key enzymes' activity, and microbial revolution were investigated in Anammox system. Results showed that once-addition of C12-HSL had no obvious impact on Anammox. Daily-addition with 40 nM slightly improved the TN removal from 71.1 % to 74.5 %, while 80 and 200 nM significantly decreased it to 62.7 % and 61.8 %, respectively. The enzyme activity of ammonia monooxygenase increased from 0.015 to 0.068, nitrite reductase increased from 0.25 to 1.23, and nitrate reductase increased from 0.05 to 0.11 μg NO₂^--N mg^-1 Protein min^-1. Arenimonas abundance showed positive correlation with TN removal while Candidatus Kuenenia was continuously suppressed. C12-HSL was beneficial for partial nitrification, and it could be adopted for regulating the nitrite production.

Potential roles of acyl homoserine lactones (AHLs) in nitrifying bacteria survival under certain adverse circumstances

Potential roles of quorum sensing (QS) in nitrifying bacteria activity and ecology, particularly under adverse circumstances have been rarely reported. Herein, eight lab-scale nitrification sequencing batch reactors, with or without adding acyl homoserine lactones (AHLs) were operated under adverse circumstances respectively. The results indicated that the introduction of AHLs significantly enhanced the nitrogen removal efficiency in the presence of nitrification inhibitors (dicyandiamide, DCD), accelerated the low temperature (10 °C) group into stable stage, and improved the utilization efficiency of AHLs in these two groups. Community analysis and qPCR further confirmed that AHLs significantly increased the abundance of nitrifying bacteria in low temperature group and DCD group, especially AOB. For normal condition (28 °C, pH = 8) or low pH level (5.5), however, the AHLs had no significant effect. Canonical correspondence analysis showed that nitrifying bacteria positively responded to AHLs, indicating that adding AHLs was an effective strategy to regulate nitrification process. However, under acid conditions, the effect of this regulatory mechanism was not significant, indicating that the influence of pH on the system was greater than that of AHLs. This study demonstrated that exogenous AHLs could enhance the competitiveness of nitrifying bacteria to utilize more resource and occupy space under some adverse environmental conditions.

Shifts in evolutionary balance of phenotypes under environmental changes

Environments shape communities by driving individual interactions and the evolutionary outcome of competition. In static, homogeneous environments a robust, evolutionary stable, outcome is sometimes reachable. However, inherently stochastic, this evolutionary process need not stabilize, resulting in a dynamic ecological state, often observed in microbial communities. We use evolutionary games to study the evolution of phenotypic competition in dynamic environments. Under the assumption that phenotypic expression depends on the environmental shifts, existing periodic relationships may break or result in formation of new periodicity in phenotypic interactions. The exact outcome depends on the environmental shift itself, indicating the importance of understanding how environments influence affected systems. Under periodic environmental fluctuations, a stable state preserving dominant phenotypes may exist. However, rapid environmental shifts can lead to critical shifts in the phenotypic evolutionary balance. This might lead to environmentally favoured phenotypes dominating making the system vulnerable. We suggest that understanding of the robustness of the system's current state is necessary to anticipate when it will shift to a new equilibrium via understanding what level of perturbations the system can take before its equilibrium changes. Our results provide insights in how microbial communities can be steered to states where they are dominated by desired phenotypes.

Indirect exclusion can promote cooperation in repeated group interactions

Social exclusion has been regarded as one of the most effective measures to promote the evolution of cooperation. In real society, the way in which social exclusion works can be direct or indirect. However, thus far there is no related work to explore how indirect exclusion influences the evolution of cooperation from a theoretical perspective. Here, we introduce indirect exclusion into the repeated public goods game where the game organizer probabilistically selects cooperators after the first game round to participate in the following possible game interactions. We then investigate the evolutionary dynamics of cooperation both in infinite and finite well-mixed populations. Through theoretical analysis and numerical calculations, we find that the introduction of indirect exclusion can induce the stable coexistence of cooperators and defectors or the dominance of cooperators, which thus effectively promotes the evolution of cooperation. Besides, we show that the identifying probability of the organizer has a nonlinear effect on public cooperation when its value is lower than an intermediate value, while the higher identifying probability can maintain a high level of cooperation. Furthermore, our results show that increasing the average rounds of game interactions can effectively promote the evolution of cooperation.

Intertemporal trade-off between population growth rate and carrying capacity during public good production

Public goods are biomolecules that benefit cellular populations, such as by providing access to previously unutilized resources. Public good production is energetically costly. To reduce this cost, populations control public good biosynthesis, for example using density-dependent regulation accomplished by quorum sensing. Fitness costs and benefits of public good production must be balanced, similar to optimal investment decisions used in economics. We explore the regulation of a public good that increases the carrying capacity, through experimental measurements of growth in Escherichia coli and analysis using a modified logistic growth model. The timing of public good production showed a sharply peaked optimum in population fitness. The cell density associated with maximum public good benefits was determined by the trade-off between the cost of public good production, in terms of reduced growth rate, and benefits received from public goods, in the form of increased carrying capacity.

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Public good production creates trade-off between growth rate and carrying capacity

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Cell density-dependent regulation times the production to optimize this trade-off

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At this time, benefits of public good are maximum and received instantaneously

Early exclusion leads to cyclical cooperation in repeated group interactions

Explaining the emergence and maintenance of cooperation among selfish individuals from an evolutionary perspective remains a grand challenge in biology, economy and social sciences. Social exclusion is believed to be an answer to this conundrum. However, previously related studies often assume one-shot interactions and ignore how free-riding is identified, which seem to be too idealistic. In this work, we consider repeated interactions where excluders need to pay a monitoring cost to identify free-riders for exclusion and free-riders cannot participate in the following possible game interactions once they are identified and excluded by excluders in the repeated interaction process. We reveal that the introduction of such exclusion can prevent the breakdown of cooperation in repeated group interactions. In particular, we demonstrate that an evolutionary oscillation among cooperators, defectors and excluders can appear in infinitely large populations when early exclusion is implemented. In addition, we find that the population spends most of the time in states where cooperators dominate for early exclusion when stochastic mutation-selection is considered in finite populations. Our results highlight that early exclusion is successful in solving the mentioned enigma of cooperation in repeated group interactions.

Kin discrimination drives territorial exclusion during Bacillus subtilis swarming and restrains exploitation of surfactin

Swarming is the collective movement of bacteria across a surface. It requires the production of surfactants (public goods) to overcome surface tension and provides an excellent model to investigate bacterial cooperation. Previously, we correlated swarm interaction phenotypes with kin discrimination between B. subtilis soil isolates, by showing that less related strains form boundaries between swarms and highly related strains merge. However, how kin discrimination affects cooperation and territoriality in swarming bacteria remains little explored. Here we show that the pattern of surface colonization by swarming mixtures is influenced by kin types. Closely related strain mixtures colonize the surface in a mixed swarm, while mixtures of less related strains show competitive exclusion as only one strain colonizes the surface. The outcome of nonkin swarm expansion depends on the initial ratio of the competing strains, indicating positive frequency-dependent competition. We find that addition of surfactin (a public good excreted from cells) can complement the swarming defect of nonkin mutants, whereas close encounters in nonkin mixtures lead to territorial exclusion, which limits the exploitation of surfactin by nonkin nonproducers. The work suggests that kin discrimination driven competitive territorial exclusion may be an important determinant for the success of cooperative surface colonization.

Bacterial cooperation through horizontal gene transfer

Cooperation exists across all scales of biological organization, from genetic elements to complex human societies. Bacteria cooperate by secreting molecules that benefit all individuals in the population (i.e., public goods). Genes associated with cooperation can spread among strains through horizontal gene transfer (HGT). We discuss recent findings on how HGT mediated by mobile genetic elements promotes bacterial cooperation, how cooperation in turn can facilitate more frequent HGT, and how the act of HGT itself may be considered as a form of cooperation. We propose that HGT is an important enforcement mechanism in bacterial populations, thus creating a positive feedback loop that further maintains cooperation. To enforce cooperation, HGT serves as a homogenizing force by transferring the cooperative trait, effectively eliminating cheaters.

Mistakes can stabilise the dynamics of rock-paper-scissors games

A game of rock-paper-scissors is an interesting example of an interaction where none of the pure strategies strictly dominates all others, leading to a cyclic pattern. In this work, we consider an unstable version of rock-paper-scissors dynamics and allow individuals to make behavioural mistakes during the strategy execution. We show that such an assumption can break a cyclic relationship leading to a stable equilibrium emerging with only one strategy surviving. We consider two cases: completely random mistakes when individuals have no bias towards any strategy and a general form of mistakes. Then, we determine conditions for a strategy to dominate all other strategies. However, given that individuals who adopt a dominating strategy are still prone to behavioural mistakes in the observed behaviour, we may still observe extinct strategies. That is, behavioural mistakes in strategy execution stabilise evolutionary dynamics leading to an evolutionary stable and, potentially, mixed co-existence equilibrium.

Quorum sensing provides a molecular mechanism for evolution to tune and maintain investment in cooperation

As selection frequently favors noncooperating defectors in mixed populations with cooperators, mechanisms that promote cooperation stability clearly exist. One potential mechanism is bacterial cell-to-cell communication, quorum sensing (QS), which can allow cooperators to prevent invasion by defectors. However, the impact of QS on widespread maintenance of cooperation in well-mixed conditions has not been experimentally demonstrated over extended evolutionary timescales. Here, we use wild-type (WT) Vibrio campbellii that regulates cooperation with QS and an unconditional cooperating (UC) mutant to examine the evolutionary origins and dynamics of novel defectors during a long-term evolution experiment. We found that UC lineages were completely outcompeted by defectors, whereas functioning QS enabled the maintenance of cooperative variants in most WT populations. Sequencing evolved populations revealed multiple luxR mutations that swept the UC lineages. However, the evolution of mutant lineages with reduced levels of bioluminescence (dims) occurred in many WT lineages. These dim variants also decreased other cooperative phenotypes regulated by QS, including protease production, indicating they result from changes to QS regulation. This diminished investment phenotype optimizes a tradeoff between cooperative input and growth output and suggests that decreasing the cost of QS could be a favorable strategy for maintaining the cooperative behaviors it regulates.

Function of quorum sensing and cell signaling in wastewater treatment systems

Quorum sensing (QS) is a communication mode between microorganisms to regulate bacteria ecological relations and physiological behaviors, thus achieve the physiological function that single bacteria cannot complete. This phenomenon plays important roles in the formation of biofilm and granular sludge, and may be related to enhancement of some functional bacteria activity in wastewater treatment systems. There is a need to better understand bacterial QS in engineered reactors, and to assess how designs and operations might improve the removal efficiency. This article reviewed the recent advances of QS in several environmental systems and mainly analyzed the regulation mechanism of QS-based strategies for biofilm, granular sludge, functional bacteria, and biofouling control. The co-existences of multiple signal molecules in wastewater treatment (WWT) processes were also summarized, which provide basis for the future research on the QS mechanism of multiple signal molecules' interaction in WWT. This review would present some prospects and suggestions which are of practical significance for further application.

Nutrient factor-dependent performance of bacterial quorum sensing system during population evolution

Bacterial quorum sensing (QS) system regulates the production of most costly but sharable extracellular products (public goods) in a growth-phase-dependent manner, and the development of this energy-intensive process is susceptible to environmental changes. However, the role of nutrient factors in dominating the QS-mediated cooperative interaction and intracellular metabolism still remains less understood. Here we studied the performance of QS system by growing Pseudomonas aeruginosa under different nutrient and culture conditions. The results of comparative-transcriptomic analyses revealed that carbon source-limitation was the main factor suppressing the activation of QS system, and a substantial number of public-good-encoding genes were induced when phosphorus is limiting in short-term culture. By contrast, although the QS regulation of P. aeruginosa in all the cultures was generally decreased along with the enrichment of QS-deficient individuals during evolution, limitation of different nutrient factors had discrepant effects in directing the formation of population structure by coordinating the production of public goods and primary metabolism, especially the starch and sucrose metabolism. These findings demonstrate the pleiotropy of QS regulation in balancing the development of cooperative behavior and metabolism, and provide a reference for further understanding the role of QS system in causing persistent infections.

Investigating the dynamics of microbial consortia in spatially structured environments

The spatial organization of microbial communities arises from a complex interplay of biotic and abiotic interactions, and is a major determinant of ecosystem functions. Here we design a microfluidic platform to investigate how the spatial arrangement of microbes impacts gene expression and growth. We elucidate key biochemical parameters that dictate the mapping between spatial positioning and gene expression patterns. We show that distance can establish a low-pass filter to periodic inputs and can enhance the fidelity of information processing. Positive and negative feedback can play disparate roles in the synchronization and robustness of a genetic oscillator distributed between two strains to spatial separation. Quantification of growth and metabolite release in an amino-acid auxotroph community demonstrates that the interaction network and stability of the community are highly sensitive to temporal perturbations and spatial arrangements. In sum, our microfluidic platform can quantify spatiotemporal parameters influencing diffusion-mediated interactions in microbial consortia.

Bacterial Community Interactions During Chronic Respiratory Disease

Chronic respiratory diseases including chronic rhinosinusitis, otitis media, asthma, cystic fibrosis, non-CF bronchiectasis, and chronic obstructive pulmonary disease are a major public health burden. Patients suffering from chronic respiratory disease are prone to persistent, debilitating respiratory infections due to the decreased ability to clear pathogens from the respiratory tract. Such infections often develop into chronic, life-long complications that are difficult to treat with antibiotics due to the formation of recalcitrant biofilms. The microbial communities present in the upper and lower respiratory tracts change as these respiratory diseases progress, often becoming less diverse and dysbiotic, correlating with worsening patient morbidity. Those with chronic respiratory disease are commonly infected with a shared group of respiratory pathogens including Haemophilus influenzae, Streptococcus pneumoniae, Staphylococcus aureus, Pseudomonas aeruginosa, and Moraxella catarrhalis, among others. In order to understand the microbial landscape of the respiratory tract during chronic disease, we review the known inter-species interactions among these organisms and other common respiratory flora. We consider both the balance between cooperative and competitive interactions in relation to microbial community structure. By reviewing the major causes of chronic respiratory disease, we identify common features across disease states and signals that might contribute to community shifts. As microbiome shifts have been associated with respiratory disease progression, worsening morbidity, and increased mortality, these underlying community interactions likely have an impact on respiratory disease state.

Phenotypic and genetic characterization of Pseudomonas aeruginosa isolate COP2 from the lungs of COPD patients in China

Pseudomonas aeruginosa is an important opportunistic pathogen normally associated with increasing morbidity and mortality of immunocompromised hosts with respiratory infections. The phenotypic and genetic features of P. aeruginosa from patients with chronic obstructive pulmonary disease (COPD) remain poorly understood. By using the sputum samples of 25 hospitalized COPD patients from the affiliated hospital of Southwest Medical University (China), we identified a P. aeruginosa isolate, COP2, which showed multiple antibiotic resistance and enhanced Pseudomonas quinolone signal (PQS) production but decreased motility, biofilm formation and virulence compared with the model strain PAO1. Importantly, COP2 harbored a substantial amount of mutations that might influence the functions of 1771 genes in the genome and the evolutionary status of this isolate was clearly distinct from the PAO1 lineage. Accordingly, COP2 had a discrepant transcriptional pattern relating to flagellar assembly, antibiotic resistance, biofilm and PQS production, and can increase the capacities of compound degradation in response to resource/space stresses. Therefore, the identification of COP2 in this study provides preliminary information regarding the genetic features and survival strategy of P. aeruginosa in colonizing COPD lungs and lays the foundations for further understanding of the pathogenic mechanisms of pseudomonal infections.

Coexistence of Microbial Species in Structured Communities by Forming a Hawk-Dove Game Like Interactive Relationship

Microorganisms evolve kinds of elaborate interaction models that can form relatively stable communities in a wide range of ecosystems. It is recognized that the spatial genetic structure of microbes in surface-attached environments lays a good foundation for the persistence of polymicrobial communities in adverse conditions. However, the interacting dynamics of microbes in facilitating the formation and stabilization of community structure still remains elusive. In this study, we identify a hawk-dove game like interspecific relationship between the two Gram-negative opportunistic pathogens Pseudomonas aeruginosa and Klebsiella pneumoniae, which naturally coexist in insect gut and can cocolonize human tissues. Specifically, although P. aeruginosa had significant competitive advantage over cocultured K. pneumoniae on solid medium with rich nutrient factors, K. pneumoniae could resist the suppression of P. aeruginosa by enhancing the expression of membrane transporters induced by the extracellular metabolites of P. aeruginosa. By contrast, under the condition that K. pneumoniae had a growth advantage but P. aeruginosa met a metabolic burden in producing quorum-sensing-controlled extracellular products, the frequency of K. pneumoniae would be slightly higher than P. aeruginosa during the coexistence because K. pneumoniae was also capable of exploiting the extracellular metabolite from P. aeruginosa. In addition, P. aeruginosa quorum-sensing variant could reap benefits from K. pneumoniae in turn and reach a relatively stable two species equilibrium. These findings provide an explanation for the formation and maintenance of polymicrobial communities in different spatially structured environments, and thus may contribute to understanding the complex interspecific interactions of microbes in local communities and shed new light on the development of social microbiology.