Ecological suicide in microbes

Ratzke, Christoph; Denk, Jonas; Gore, Jeff

doi:10.1038/s41559-018-0535-1

Cited by 81 publications

(63 citation statements)

References 44 publications

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“…At low nutrient concentrations, there was a high amount of coexistence in pairwise co-culture. For the same interaction partners at high nutrient concentrations we observed a striking loss of coexistence, where either one species out-competed the other or, in many cases, both went extinct by ecological suicide as we described recently 21 . Intermediate nutrient concentrations lead to intermediate loss of coexistence ( Supplementary Fig.…”

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confidence: 78%

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Strength of species interactions determines biodiversity and stability in microbial communities

Ratzke

Barrere

Gore

2019

Preprint

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Organisms -especially microbes -tend to live in complex communities. While some of these ecosystems are very bio-diverse, others aren't 1-3 , and while some are very stable over time others undergo strong temporal fluctuations 4,5 . Despite a long history of research and a plethora of data it is not fully understood what sets biodiversity and stability of ecosystems 6,7 . Theory as well as experiments suggest a connection between species interaction, biodiversity, and stability of ecosystems [8][9][10][11][12][13] , where an increase of ecosystem stability with biodiversity could be observed in several cases 7,9,14 . However, what causes these connections remains unclear. Here we show in microbial ecosystems in the lab that the concentrations of available nutrients can set the strength of interactions between bacteria. At high nutrient concentrations, extensive microbial growth leads to strong chemical modifications of the environment, causing more negative interactions between species. These stronger interactions exclude more species from the community -resulting in a loss of biodiversity. At the same time, these stronger interactions also decrease the stability of the microbial communities, providing a mechanistic link between species interaction, biodiversity and stability.

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confidence: 78%

“…modify and react to their environment [19][20][21][22][23] . The higher the nutrient concentrations the microbes have access to the stronger they can metabolize and hence the stronger they can modify the environment.…”

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confidence: 99%

Strength of species interactions determines biodiversity and stability in microbial communities

Ratzke

Barrere

Gore

2019

Preprint

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“…In E. faecalis , the reverse IE arises from density-dependent changes in local pH (11), which are associated with increased activity of ampicillin and related drugs (58). Similar growth-driven changes in pH (in antibioticfree environments) have been shown to modulate intercellular interactions (59) and even promote ecological suicide in other microbial species (60). In addition to these in vitro studies, recent work shows that E. faecalis infections started from high-and low-dose inocula lead to different levels of immune response and colonization in a mouse model (61).…”

Section: Introductionmentioning

confidence: 99%

Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations

Hallinen

Karslake

Wood

2019

Preprint

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Bacteria exploit a diverse set of defenses to survive exposure to antibiotics.While the molecular and genetic underpinnings of antibiotic resistance are increasingly understood, less is known about how these molecular events influence microbial dynamics on the population scale. In this work, we show that the dynamics of E. faecalis communities exposed to antibiotics can be surprisingly rich, revealing scenarios where-for example-increasing population size or delaying drug exposure can promote population collapse. Specifically, we combine experiments in computer-controlled bioreactors with simple mathematical models to reveal density-dependent feedback loops that couple population growth and antibiotic efficacy when communities include drug-resistant (β-lactamase producing) subpopulations. The resulting communities exhibit a wide range of behavior, including population survival, population collapse, or one of two qualitatively distinct bistable behaviors where survival is favored in either small or large populations. These dynamics reflect competing density-dependent effects of different subpopulations, with growth of drug-sensitive cells increasing but growth of drug-resistant cells decreasing effective drug inhibition. Guided by these results, we experimentally demonstrate how populations receiving immediate drug influx may sometimes thrive, while identical populations exposed to delayed drug influx (and lower average drug concentrations) collapse. These results illustrate that the spread of drug resistant determinants-even in a simplified single-species communities-may be governed by potentially counterintuitive dynamics driven by population-level interactions.

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“…Often, microbes themselves are triggering such shifts. Consider for example the lysogenic and lytic spreading of phages [352,239,318], or the fall of local pH values, caused by acidic fermentation products [57,11,288,289]. Conversely, such sudden environmental changes can drastically effect the fitness landscape, strongly selecting for genes increasing viability and survival.…”

Section: Future Challengesmentioning

confidence: 99%

Cooperation in Microbial Populations: Theory and Experimental Model Systems

Cremer

Melbinger

Wienand

et al. 2019

Journal of Molecular Biology

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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 an ensemble of local communities (sub populations) 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 utilization of pyoverdines, iron scavenging molecules. 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 signalling, and multi-species communities.

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Ecological suicide in microbes

Cited by 81 publications

References 44 publications

Strength of species interactions determines biodiversity and stability in microbial communities

Strength of species interactions determines biodiversity and stability in microbial communities

Delayed antibiotic exposure induces population collapse in enterococcal communities with drug-resistant subpopulations

Cooperation in Microbial Populations: Theory and Experimental Model Systems

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