Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

Zuñiga, Cristal; Li, Chien‐Ting; Yu, Guizhen; Al‐Bassam, Mahmoud M.; Li, Tingting; Jiang, Liqun; Zaramela, Livia S.; Guarnieri, Michael T.; Betenbaugh, Michael J; Zengler, Karsten

doi:10.1038/s41564-019-0567-6

Cited by 69 publications

(65 citation statements)

References 47 publications

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“…An opportunity awaits to define interspecies PPI lists with omics methods. Considering the avalanche of data generated in the microbiome field 146 – 149 and recent approaches for modelling microbial communities 150 , lists of interacting proteins or cross-species ligand–receptor pairs to enable CCI analyses would evidently yield novel discoveries. For example, a study mapped the interaction between inclusion membrane proteins secreted by Chlamydia trachomatis and cognate human proteins 145 , providing insights into the host machinery this pathogen uses to establish the intracellular niche needed for infection.…”

Section: Challenges and Future Directionsmentioning

confidence: 99%

Deciphering cell–cell interactions and communication from gene expression

et al. 2020

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Section: Challenges and Future Directionsmentioning

confidence: 99%

Deciphering cell–cell interactions and communication from gene expression

et al. 2020

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“…However, these results are subject to strong experimental biases, such as the use of a single environment-even though microbial interactions can differ dramatically across environmental conditions (16)(17)(18)-and the use of strains that each grow individually in the environmental conditions being tested. Metabolic modeling, which can simulate millions of interactions across myriad environments, as well as limited experimental evidence, suggest that positive interactions emerge via environment-dependent secretions and can facilitate otherwise non-growing species (18)(19)(20)(21). Additionally, evolutionary theories like the Black Queen Hypothesis argue that such secretion-mediated positive interactions are selected for (22).…”

Section: Main Textmentioning

confidence: 99%

Positive interactions are common among culturable bacteria

Kehe

Ortiz

Kulesa

et al. 2020

Preprint

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Interspecies interactions shape the structure and function of microbial communities. In particular, positive, growth-promoting interactions can significantly affect the diversity and productivity of natural and engineered communities. However, the prevalence of positive interactions and the conditions in which they occur are not well understood. To address this knowledge gap, we used kChip, an ultra-high throughput coculture platform, to measure 180,408 interactions among 20 soil bacteria across 40 carbon environments. We find that positive interactions, often described to be rare, occur commonly, primarily as parasitisms between strains that differ in their carbon consumption profiles. Notably, non-growing strains are almost always promoted by strongly growing strains (85%), suggesting a simple positive interaction-mediated approach for cultivation, microbiome engineering, and microbial consortium design.One Sentence Summary: Experimental measurement of >150,000 bacterial cocultures reveals that growth-promoting interactions occur commonly and depend on differences in nutrient consumption preferences.

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“…Resources and toxins have opposite effects on growth rates: consumption of resources by other species decreases the growth rate of a focal species (competition/exploitation) while absorption of toxin by others can increase its growth rate (facilitation). This implies that environmental conditions, especially amounts of resources and toxins, can affect the sign and/or magnitude of species interactions (Hoek et al, 2016; Piccardi et al, 2019; Zuñiga et al, 2019). In turn, how pairs of species in a community interact (i.e., competition or facilitation) affects species diversity and community stability (Mougi and Kondoh, 2012; Coyte et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

“…We start with a simple scenario with just two species in an environment that switches between scarce and abundant resource supplies. In addition to resources, our model includes the dynamics of toxins, as we expect them to affect inter-species interactions (Hoek et al, 2016; Piccardi et al, 2019; Zuñiga et al, 2019). Accordingly, the two species can both compete for resources and facilitate each other by absorbing toxic compounds.…”

Section: Introductionmentioning

confidence: 99%

Exclusion of the fittest predicts microbial community diversity in fluctuating environments

Shibasaki

Mobilia

Mitri

2020

Preprint

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Microorganisms often live in environments that fluctuate between mild and harsh conditions. Although such fluctuations are bound to cause local extinctions and affect species diversity, it is unknown how diversity changes at different fluctuation rates and how this relates to changes in species interactions. Here, we use a mathematical model describing the dynamics of resources, toxins, and microbial species in a chemostat where resource supplies switch. Over most of the explored parameter space, species competed, but the strength of competition peaked at either low, high or intermediate switching rates depending on the species’ sensitivity to toxins. Importantly, however, the strength of competition in species pairs was a good predictor for how community diversity changed over the switching rate. In sum, predicting the effect of environmental switching on competition and community diversity is difficult, as species’ properties matter. This may explain contradicting results of earlier studies on the intermediate disturbance hypothesis.

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Environmental stimuli drive a transition from cooperation to competition in synthetic phototrophic communities

Cited by 69 publications

References 47 publications

Deciphering cell–cell interactions and communication from gene expression

Deciphering cell–cell interactions and communication from gene expression

Positive interactions are common among culturable bacteria

Exclusion of the fittest predicts microbial community diversity in fluctuating environments

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