An evolutionary mechanism for diversity in siderophore-producing bacteria

Bacteria produce a great diversity of siderophores to scavenge for iron in their environment. We suggest that this diversity results from the interplay between siderophore producers (cooperators) and non-producers (cheaters): when there are many cheaters exploiting a siderophore type it is beneficial for a mutant to produce a siderophore unusable by the dominant population. We formulated and analysed a mathematical model for tagged public goods to investigate the potential for the emergence of diversity. We found that, although they are rare most of the time, cheaters play a key role in maintaining diversity by regulating the different populations of cooperators. This threshold-triggered feedback prevents any stain of cooperators from dominating the others. Our study provides a novel general mechanism for the evolution of diversity that may apply to many forms of social behaviour.     

Cooperation as a volunteer’s dilemma and the strategy of conflict in public goods games

Conflict and cooperation for the exploitation of public goods are usually modelled as an N‐person prisoner’s dilemma. Many social dilemmas, however, would be described more properly as a volunteer’s dilemma, in which a certain number of individuals are necessary to produce a public good. If volunteering is costly, but so is failure to produce the public good, cheaters can invade and form a stable mixed equilibrium with cooperators. The dilemma is that the benefit for the group decreases with group size because the larger the group is, the less likely it is that someone volunteers. This problem persists even in the presence of a high degree of relatedness between group members. This model provides precise, testable predictions for the stability of cooperation. It also suggests a counterintuitive but practical solution for this kind of social dilemmas: increasing the damage resulting from the failure to produce the public good increases the probability that the public good is actually produced. Adopting a strategy that entails a deliberate risk (brinkmanship), therefore, can lead to a benefit for the society without being detrimental for the individual.     

Cheating on Cheaters Stabilizes Cooperation in Pseudomonas aeruginosa

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Rewards and the evolution of cooperation in public good games

Properly coordinating cooperation is relevant for resolving public good problems, such as clean energy and environmental protection. However, little is known about how individuals can coordinate themselves for a certain level of cooperation in large populations of strangers. In a typical situation, a consensus-building process rarely succeeds, owing to a lack of face and standing. The evolution of cooperation in this type of situation is studied here using threshold public good games, in which cooperation prevails when it is initially sufficient, or otherwise it perishes. While punishment is a powerful tool for shaping human behaviours, institutional punishment is often too costly to start with only a few contributors, which is another coordination problem. Here, we show that whatever the initial conditions, reward funds based on voluntary contribution can evolve. The voluntary reward paves the way for effectively overcoming the coordination problem and efficiently transforms freeloaders into cooperators with a perceived small risk of collective failure.     

Evolutionary assembly of cooperating cell types in an animal chemical defense system

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入侵植物替代控制中土著种选择机制的研究

生物入侵对入侵地生态系统的稳定性及社会经济造成严重危害,成为全球三大环境问题之一。为有效治理入侵植物,结合常采用的物理、化学和生物防治等方法,从防治机制方面分析土著种替代控制入侵植物的有效性。通常土著种替代控制入侵植物是由于土著植物向环境中分泌化感物质,使得土壤中的微生物、动物以及化学成分相互作用,从而改变了入侵植物的生存环境。同时,土著植物利用自身的优势条件与入侵植物进行养分和光能等资源竞争,使入侵植物处于不利地位。通过对替代控制机理的概述,提出了替代植物的选择方法,讨论了需要进一步加强的领域,以期拓展替代控制这一领域的广度和深度,为入侵植物的生态防治提供理论依据。     

The evolution of siderophore production as a competitive trait

Microbes have the potential to be highly cooperative organisms. The archetype of microbial cooperation is often considered to be the secretion of siderophores, molecules scavenging iron, where cooperation is threatened by “cheater” genotypes that use siderophores without making them. Here, we show that this view neglects a key piece of biology: siderophores are imported by specific receptors that constrain their use by competing strains. We study the effect of this specificity in an ecoevolutionary model, in which we vary siderophore sharing among strains, and compare fully shared siderophores with private siderophores. We show that privatizing siderophores fundamentally alters their evolution. Rather than a canonical cooperative good, siderophores become a competitive trait used to pillage iron from other strains. We also study the physiological regulation of siderophores using in silico long‐term evolution. Although shared siderophores evolve to be downregulated in the presence of a competitor, as expected for a cooperative trait, privatized siderophores evolve to be upregulated. We evaluate these predictions using published experimental work, which suggests that some siderophores are upregulated in response to competition akin to competitive traits like antibiotics. Although siderophores can act as a cooperative good for single genotypes, we argue that their role in competition is fundamental to understanding their biology.     

Evolution of mate choice and the so‐called magic traits in ecological speciation

Non‐random mating provides multiple evolutionary benefits and can result in speciation. Biological organisms are characterised by a myriad of different traits, many of which can serve as mating cues. We consider multiple mechanisms of non‐random mating simultaneously within a unified modelling framework in an attempt to understand better which are more likely to evolve in natural populations going through the process of local adaptation and ecological speciation. We show that certain traits that are under direct natural selection are more likely to be co‐opted as mating cues, leading to the appearance of magic traits (i.e. phenotypic traits involved in both local adaptation and mating decisions). Multiple mechanisms of non‐random mating can interact so that trait co‐evolution enables the evolution of non‐random mating mechanisms that would not evolve alone. The presence of magic traits may suggest that ecological selection was acting during the origin of new species.     

Horizontal gene transfer (HGT) as a mechanism of disseminating RDX-degrading activity among Actinomycete bacteria

Aims: Hexahydro‐1,3,5‐trinitro‐1,3,5,‐triazine (RDX) is a cyclic nitramine explosive that is a major component in many high‐explosive formulations and has been found as a contaminant of soil and groundwater. The RDX‐degrading gene locus xplAB, located on pGKT2 in Gordonia sp. KTR9, is highly conserved among isolates from disparate geographical locations suggesting a horizontal gene transfer (HGT) event. It was our goal to determine whether Gordonia sp. KTR9 is capable of transferring pGKT2 and the associated RDX degradation ability to other bacteria. Methods and Results: We demonstrate the successful conjugal transfer of pGKT2 from Gordonia sp. KTR9 to Gordonia polyisoprenivorans, Rhodococcus jostii RHA1 and Nocardia sp. TW2. Through growth and RDX degradation studies, it was demonstrated that pGKT2 conferred to transconjugants the ability to degrade and utilize RDX as a nitrogen source. The inhibitory effect of exogenous inorganic nitrogen sources on RDX degradation in transconjugant strains was found to be strain specific. Conclusions: Plasmid pGKT2 can be transferred by conjugation, along with the ability to degrade RDX, to related bacteria, providing evidence of at least one mechanism for the dissemination and persistence of xplAB in the environment. Significance and Impact of Study: These results provide evidence of one mechanism for the environmental dissemination of xplAB and provide a framework for future field relevant bioremediation practices.     

Interaction effects of cell diffusion,cell density and public goods properties on the evolution of cooperation in digital microbes

Microbial cooperation typically consists in the sharing of secreted metabolites (referred to as public goods) within the community. Although public goods generally promote population growth, they are also vulnerable to exploitation by cheating mutants, which no longer contribute, but still benefit from the public goods produced by others. Although previous studies have identified a number of key factors that prevent the spreading of cheaters, little is known about how these factors interact and jointly shape the evolution of microbial cooperation. Here, we address this issue by investigating the interaction effects of cell diffusion, cell density, public good diffusion and durability (factors known to individually influence costs and benefits of public goods production) on selection for cooperation. To be able to quantify these effects across a wide parameter space, we developed an individual‐based simulation platform, consisting of digital cooperator and cheater bacteria inhabiting a finite two‐dimensional continuous toroidal surface. Our simulations, which closely mimic microbial microcolony growth, revealed that: (i) either reduced cell diffusion (which keeps cooperators together) or reduced public good diffusion (which keeps the public goods closer to the producer) is not only essential but also sufficient for cooperation to be promoted; (ii) the sign of selection for or against cooperation can change as a function of cell density and in interaction with diffusion parameters; and (iii) increased public goods durability has opposing effects on the evolution of cooperation depending on the level of cell and public good diffusion. Our work highlights that interactions between key parameters of public goods cooperation give rise to complex fitness landscapes, a finding that calls for multifactorial approaches when studying microbial cooperation in natural systems.     

A new route to the evolution of cooperation

The Prisoner's Dilemma (PD) constitutes a widely used metaphor to investigate problems related to the evolution of cooperation. Whenever evolution takes place in well-mixed populations engaged in single rounds of the PD, cooperators cannot resist invasion by defectors, a feature, which is somewhat alleviated whenever populations are spatially distributed. In both cases the populations are characterized by a homogeneous pattern of connectivity, in which every individual is equivalent, sharing the same number of neighbours. Recently, compelling evidence has been accumulated on the strong heterogeneous nature of the network of contacts between individuals in populations. Here we describe the networks of contacts in terms of graphs and show that heterogeneity provides a new mechanism for cooperation to survive. Specifically, we show that cooperators are capable of exploring the heterogeneity of the population structure to become evolutionary competitive. As a result, cooperation becomes the dominating trait in scale-free networks of contacts in which the few highly connected individuals are directly inter-connected, in this way contributing to self-sustain cooperation.     

A molecular ruler mechanism for length control of extended protein structures in bacteria

The lengths of the hook structure of flagellar motors and of the needle of the injectosome are both carefully controlled, by apparently similar mechanisms. In this paper we propose a novel mechanism for this length control and develop a mathematical model of this process which shows excellent agreement with published data on hook lengths.The proposed mechanism for length control (described using biochemical nomenclature appropriate for hooks) is as follows: Hook growth is terminated when the C-terminus of the length control molecule FliK interacts with FlhB, the secretion gatekeeper. The probability of this interaction is an increasing function of the length of the hook for two reasons. First, FliK is secreted through the hook intermittently during hook growth. Second, the probability of interaction with FlhB is a function of the amount of time the C-terminus of a secreted FliK spends in the vicinity of FlhB. This time is short when the hook is short because the folding of FliK exiting the distal end of the hook acts to pull the FliK molecule through the hook rapidly. In contrast, this time is much longer when the hook is longer than the unfolded FliK polymer since movement through the tube is not enhanced by folding. Thus, it is much more likely that interaction will occur when the hook is long than when the hook is short.     

Phenotypic plasticity of a cooperative behaviour in bacteria

There is strong evidence that natural selection can favour phenotypic plasticity as a mechanism to maximize fitness in animals. Here, we aim to investigate phenotypic plasticity of a cooperative trait in bacteria – the production of an iron‐scavenging molecule (pyoverdin) by Pseudomonas aeruginosa. Pyoverdin production is metabolically costly to the individual cell, but provides a benefit to the local group and can potentially be exploited by nonpyoverdin‐producing cheats. Here, we subject bacteria to changes in the social environment in media with different iron availabilities and test whether cells can adjust pyoverdin production in response to these changes. We found that pyoverdin production per cell significantly decreased at higher cell densities and increased in the presence of cheats. This phenotypic plasticity significantly influenced the costs and benefits of cooperation. Specifically, the investment of resources into pyoverdin production was reduced in iron‐rich environments and at high cell densities, but increased under iron limitation, and when pyoverdin was exploited by cheats. Our study demonstrates that phenotypic plasticity in a cooperative trait as a response to changes in the environment occurs in even the simplest of organisms, a bacterium.     

Shape matters: Lifecycle of cooperative patches promotes cooperation in bulky populations

Natural cooperative systems take many forms, ranging from one‐dimensional cyanobacteria arrays to fractal‐like biofilms. We use in silico experimental systems to study a previously overlooked factor in the evolution of cooperation, physical shape of the population. We compare the emergence and maintenance of cooperation in populations of digital organisms that inhabit bulky (100 × 100 cells) or slender (4 × 2500) toroidal grids. Although more isolated subpopulations of secretors in a slender population could be expected to favor cooperation, we find the opposite: secretion evolves to higher levels in bulky populations. We identify the mechanistic explanation for the shape effect by analyzing the lifecycle and dynamics of cooperator patches, from their emergence and growth, to invasion by noncooperators and extinction. Because they are constrained by the population shape, the cooperator patches expand less in slender than in bulky populations, leading to fewer cooperators, less public good secretion, and generally lower cooperation. The patch dynamics and mechanisms of shape effect are robust across several digital cooperation systems and independent of the underlying basis for cooperation (public good secretion or a cooperation game). Our results urge for a greater consideration of population shape in the study of the evolution of cooperation across experimental and modeling systems.     

植物连作障碍的形成机制及其调控技术研究进展

针对植物连作障碍现象较为普遍且十分严重的现状,综述了连作障碍的具体表现。从土壤理化性状改变、土壤生物学环境恶化及化感自毒作用3个方面概述了近年来植物连作障碍形成机制的研究进展,总结了植物连作障碍的主要调控技术,包括实施轮作、合理施肥、土壤灭菌及选育抗性品种等。在此基础上,还对植物连作障碍相关研究中应进一步关注的热点问题进行了展望。     

Structure of aspartate racemase complexed with a dual substrate analogue, citric acid, and implications for the reaction mechanism

Pyrococcus horikoshii OT3 aspartate racemase (PhAspR) catalyzes the interconversion between L- and D-aspartate. The X-ray structure of PhAspR revealed a pseudo mirror-symmetric distribution of the residues around its active site, which is very reasonable for its chiral substrates, L-aspartate and D-aspartate. In this study, we have determined the crystal structure of an inactive mutant PhAspR complexed with a citric acid (Cit) at a resolution of 2.0 A. Cit contains the substrate analogue moieties of both L- and D-aspartate and exhibits a low competitive inhibition activity against PhAspR. In the structure, Cit binds to the catalytic site of PhAspR, which induced the conformational change to close the active site. The distance between the thiolates was estimated to be 7.4 A, representing a catalytic state and the substrate binding modes of PhAspR. Two conserved basic residues, Arg48 and Lys164, seem to be indispensable for PhAspR activity. Arg48 is thought to be responsible for recognizing carboxyl groups of the substrates L-/D-aspartates and stabilizing a reaction intermediate, and Lys164 is responsible for stabilizing a closed state structure. In this structure, the L-aspartate moiety of Cit is likely to take the substrate position of the PhAspR-substrate complex, which is very similar to that of Glutamate racemase. There is also another possibility that the two substrate analogue moieties of the bound Cit reflect the binding modes of both L- and D-aspartates. Based on the PhAspR-Cit complex structure, the reaction mechanism of aspartate racemase was elucidated.     

Molecular dynamics simulation of the processive endocellulase Cel48F from Clostridium cellulolyticum: a novel “water‐control mechanism” in enzymatic hydrolysis of cellulose

Glycoside hydrolase of Cel48F from Clostridium cellulolyticum is an important processive cellulose, which can hydrolyze cellulose into cellobiose. Molecular dynamics simulations were used to investigate the hydrolysis mechanism of cellulose. The two conformations of the Cel48F‐cellotetrose complex in which the cellotetroses are bound at different sites (known as the sliding conformation and the hydrolyzing conformation) were simulated. By comparing these two conformations, a water‐control mechanism is proposed, in which the hydrolysis proceeds by providing a water molecule for every other glucosidic linkage. The roles of certain key residues are determined: Glu55 and Asp230 are the most probable candidates for acid and base, respectively, in the mechanism of inverting anomeric carbon. Met414 and Trp417 constitute the water‐control system. Glu44 might keep the substrate at a certain location within the active site or help the substrate chain to move from the sliding conformation to the hydrolyzing conformation. The other hydrophobic residues around the substrate can decrease the sliding energy barrier or provide a hydrophobic environment to resist entry of the surrounding water molecules into the active site, except for those coming from a specific water channel. Copyright © 2014 John Wiley & Sons, Ltd.