In the light of evolution V: Cooperation and conflict

Strassmann, Joan E.; Queller, David C.; Avise, John C.; Ayala, Francisco J.

doi:10.1073/pnas.1100289108

Cited by 17 publications

(12 citation statements)

References 39 publications

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“…Such a meta-species network allows for an analogue mathematical representation as described for classical FBA. The choice of an appropriate objective function, however, is even less obvious on the community level than it is for monocultures as there has been a long-standing debate on which level natural selection actually occurs [90][91][92][93][94][95][96][97].…”

Section: Steady-state Community Flux Balance Analysismentioning

confidence: 99%

Constraint-based stoichiometric modelling from single organisms to microbial communities

Gottstein

Olivier²,

Bruggeman³

et al. 2016

J. R. Soc. Interface.

108

103

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Microbial communities are ubiquitously found in Nature and have direct implications for the environment, human health and biotechnology. The species composition and overall function of microbial communities are largely shaped by metabolic interactions such as competition for resources and cross-feeding. Although considerable scientific progress has been made towards mapping and modelling species-level metabolism, elucidating the metabolic exchanges between microorganisms and steering the community dynamics remain an enormous scientific challenge. In view of the complexity, computational models of microbial communities are essential to obtain systems-level understanding of ecosystem functioning. This review discusses the applications and limitations of constraint-based stoichiometric modelling tools, and in particular flux balance analysis (FBA). We explain this approach from first principles and identify the challenges one faces when extending it to communities, and discuss the approaches used in the field in view of these challenges. We distinguish between steady-state and dynamic FBA approaches extended to communities. We conclude that much progress has been made, but many of the challenges are still open.

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Section: Steady-state Community Flux Balance Analysismentioning

confidence: 99%

Constraint-based stoichiometric modelling from single organisms to microbial communities

Gottstein

Olivier²,

Bruggeman³

et al. 2016

J. R. Soc. Interface.

108

103

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“…Bistable expression of the T3SS may promote social cheating. Social cheating occurs when certain members of a population produce a beneficial trait, such as T3SS-mediated killing of immune cells, and other members (cheaters) take advantage without incurring the costs associated with producing the benefit (205). A recent study found that ϳ80% of P. aeruginosa cells express the T3SS in an acute murine infection model (206).…”

Section: Discussionmentioning

confidence: 99%

Fitting Pieces into the Puzzle of Pseudomonas aeruginosa Type III Secretion System Gene Expression

et al. 2019

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Type III secretion systems (T3SS) are widely distributed in Gram-negative microorganisms and critical for host-pathogen and host-symbiont interactions with plants and animals. Central features of the T3SS are a highly conserved set of secretion and translocation genes and contact dependence wherein host-pathogen interactions trigger effector protein delivery and serve as an inducing signal for T3SS gene expression. In addition to these conserved features, there are pathogen-specific properties that include a unique repertoire of effector genes and mechanisms to control T3SS gene expression. The Pseudomonas aeruginosa T3SS serves as a model system to understand transcriptional and posttranscriptional mechanisms involved in the control of T3SS gene expression. The central regulatory feature is a partner-switching system that controls the DNA-binding activity of ExsA, the primary regulator of T3SS gene expression. Superimposed upon the partner-switching mechanism are cyclic AMP and cyclic di-GMP signaling systems, two-component systems, global regulators, and RNA-binding proteins that have positive and negative effects on ExsA transcription and/or synthesis. In the present review, we discuss advances in our understanding of how these regulatory systems orchestrate the activation of T3SS gene expression in the context of acute infections and repression of the T3SS as P. aeruginosa adapts to and colonizes the cystic fibrosis airways.

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“…Similarly but at the deeper level of function, coherent processes in plants underpin the capacity for photosynthesis [48] and possibly sound production [42]. Moreover, a closer look into the nature of all things reveals that such collective 'in tune' behaviour is in fact an essential aspect of life in general and so ubiquitous that it is found at all levels of biological organization from the assembly of eukaryotic cell that relies on the symbiotic cooperation of its internal organelles [63] to the evolution of multicellular organisms [64] and ultimately organismal colonies and societies as we know them for many animal species including humans [65]. Interestingly, the best insights into the process of how single-celled organisms may have evolved into simple (e.g., colonial) and then later more complex multicellular forms through communication and collaborative effort amongst cells have, in fact, been offered by plant phylogenies, where the emergence of multicellularity in the three major clades has occurred, at least, six separate times [66].…”

Section: Taking Plants Seriously: Lessons On the Nature Of All Thingsmentioning

confidence: 99%

“…So it seems that cooperation, the process of acting and working together in a coherent mode, is far from being a rare trait and despite the general idea that biological evolution is the outcome of fierce competition among selfish parties, the evidence indicates that, paradoxically, the very competitive evolutionary process of natural selection involves cooperation [67]. It is becoming clearer that the complex web of life is a system built on minimal conflict and instead substantial cooperation among lower-level units to evolve into higher-level units; in fact, it is through the evolution of new levels of organization, when the competing units at the lower level begin to work together, that cooperation allows specialization and promotes biological diversity [65].…”

Section: Taking Plants Seriously: Lessons On the Nature Of All Thingsmentioning

confidence: 99%

Seeing Green: The Re-discovery of Plants and Nature’s Wisdom

Gagliano

2013

Societies

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Abstract:In this article, I endeavor to recount the odd history of how we have come to perceive plants like we do, and illustrate how plants themselves perceive and sense the world and, most importantly, what they can tell us about Nature. Through examples of the ingenious ways plants have evolved to thrive, I engage the idea that our modern society is afflicted by a severe disorder known as plant blindness, a pervasive condition inherited from our forefather Aristotle and accountable for the current state of vegetal disregard and hence environmental dilapidation. I propose that the solution to this state of affairs rests in a radical change of perspective, one that brings the prevailing, yet defective, Aristotelian paradigm together with its expectations on how Nature should behave to an end. Enacted, such change releases us into a new experience of reality, where the coherent nature of Nature is revealed.Keywords: plant blindness; coherence; cooperation; facilitation; competition; plant behavior; sensing Sensing the World through Historical DeviationsWe have to remember that what we observe is not nature in itself, but nature exposed to our method of questioning.-Theoretical physicist and philosopher Werner Heisenberg [1] Everything any living organism knows about the world comes to it through its senses. Such a deceptively simple task bears the most crucial challenge all living organisms are confronted with-the requirement to evolve and use numerous signal-transduction systems (i.e., stimulus-response pathways; [2]) to sense the surrounding environment and ensure the most appropriate adaptive responses in order to survive and proliferate in a range of biological niches. By definition then, all OPEN ACCESS

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In the light of evolution V: Cooperation and conflict

Cited by 17 publications

References 39 publications

Constraint-based stoichiometric modelling from single organisms to microbial communities

Constraint-based stoichiometric modelling from single organisms to microbial communities

Fitting Pieces into the Puzzle of Pseudomonas aeruginosa Type III Secretion System Gene Expression

Seeing Green: The Re-discovery of Plants and Nature’s Wisdom

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