Exclusion of the fittest predicts microbial community diversity in fluctuating environments

Shibasaki, Shota; Mobilia, Mauro; Mitri, Sara

doi:10.1101/2020.07.22.216010

Cited by 4 publications

(4 citation statements)

References 87 publications

(163 reference statements)

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“…However, current understanding of resource competition predicts a "competitive exclusion principle" that there should not be more surviving species than resources to compete for 5 . Amongst mechanisms such as tradeoffs between growth at high and low resource availability and interactions other than resource competition, temporal dynamics were an early suggestion for resolving the paradox and are still widely assumed to be a central part of the puzzle 2,4,[6][7][8][9][10][11][12][13][14][15] , in additional to broader experimental and theoretical interest in how temporal dynamics alter community assembly [16][17][18][19][20][21] . However, how competitive exclusion violations become possible, whether these violations are biologically likely, and what niche structure arises remain largely unresolved.…”

Section: Introductionmentioning

confidence: 99%

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

Bloxham

Lee

Gore

2023

Preprint

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Natural communities are incredibly diverse, and explaining how this biodiversity is even possible remains a central question in ecology. Resource competition is thought to play an important role in community interactions, but understanding diverse communities using resource competition is limited by the competitive exclusion principle: the prediction that only as many species as resources should coexist. Here, we demonstrate that sequential resource utilization, also known as diauxie, under periodic growth and death cycles allows for many more coexisting species than resources, violating the competitive exclusion principle. These violations become possible when fluctuations produce variations in the resource depletion order on each growth cycle. The depletion order varying allows the community to experience different sequences of temporal niches on each growth cycle, with temporal niches being the increasingly depleted environments produced by sequential resource depletions. While community-driven fluctuations and competitive-exclusion violations are rare under constant environmental conditions, we find that with even small environmental fluctuations most communities violate competitive exclusion, with several times as many survivors as resources in some simulations. We explore the competitive interactions within these communities and show that survivors are accurately predicted by temporal niches. We thus demonstrate highly diverse communities as a likely outcome of resource competition with a competitive structure based on ordered resource preferences.

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Section: Introductionmentioning

confidence: 99%

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

Bloxham

Lee

Gore

2023

Preprint

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“…In conclusion, we show that contrasting results from previously published studies linking environmental variation to species interactions [4,10,17] can be viewed as special cases of a more general framework that we develop here (figure 5). By explicitly taking different temporal scales of environmental variation into account [51,52], simultaneously considering the mean environmental condition and modelling different types of stochastic environments, we develop a framework that can be used to explore rich patterns of species coexistence. This framework will be useful for developing testable predictions at a time when environmental fluctuations are increasing globally.…”

Section: Discussionmentioning

confidence: 99%

Antagonistic effects of long- and short-term environmental variation on species coexistence

et al. 2021

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Assessing the impact of environmental fluctuations on species coexistence is critical for understanding biodiversity loss and the ecological impacts of climate change. Yet determining how properties like the intensity, frequency or duration of environmental fluctuations influence species coexistence remains challenging, presumably because previous studies have focused on indefinite coexistence. Here, we model the impact of environmental fluctuations at different temporal scales on species coexistence over a finite time period by employing the concepts of time-windowed averaging and performance curves to incorporate temporal niche differences within a stochastic Lotka–Volterra model. We discover that short- and long-term environmental variability has contrasting effects on transient species coexistence, such that short-term variation favours species coexistence, whereas long-term variation promotes competitive exclusion. This dichotomy occurs because small samples (e.g. environmental changes over long time periods) are more likely to show large deviations from the expected mean and are more difficult to predict than large samples (e.g. environmental changes over short time periods), as described in the central limit theorem. Consequently, we show that the complex set of relationships among environmental fluctuations and species coexistence found in previous studies can all be synthesized within a general framework by explicitly considering both long- and short-term environmental variation.

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“…It is tantalizing to speculate, when examining other microbial communities, under what conditions this statement is valid. Recent work by Shibasaki et al (2020) shows that under a fluctuating environment species properties play an important role in community diversity. Our results corroborate their finding.…”

Section: Discussionmentioning

confidence: 99%

Impact of Temporal pH Fluctuations on the Coexistence of Nasal Bacteria in an in silico Community

et al. 2021

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To manipulate nasal microbiota for respiratory health, we need to better understand how this microbial community is assembled and maintained. Previous work has demonstrated that the pH in the nasal passage experiences temporal fluctuations. Yet, the impact of such pH fluctuations on nasal microbiota is not fully understood. Here, we examine how temporal fluctuations in pH might affect the coexistence of nasal bacteria in in silico communities. We take advantage of the cultivability of nasal bacteria to experimentally assess their responses to pH and the presence of other species. Based on experimentally observed responses, we formulate a mathematical model to numerically investigate the impact of temporal pH fluctuations on species coexistence. We assemble in silico nasal communities using up to 20 strains that resemble the isolates that we have experimentally characterized. We then subject these in silico communities to pH fluctuations and assess how the community composition and coexistence is impacted. Using this model, we then simulate pH fluctuations—varying in amplitude or frequency—to identify conditions that best support species coexistence. We find that the composition of nasal communities is generally robust against pH fluctuations within the expected range of amplitudes and frequencies. Our results also show that cooperative communities and communities with lower niche overlap have significantly lower composition deviations when exposed to temporal pH fluctuations. Overall, our data suggest that nasal microbiota could be robust against environmental fluctuations.

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Exclusion of the fittest predicts microbial community diversity in fluctuating environments

Cited by 4 publications

References 87 publications

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

Biodiversity is enhanced by sequential resource utilization and environmental fluctuations via emergent temporal niches

Antagonistic effects of long- and short-term environmental variation on species coexistence

Impact of Temporal pH Fluctuations on the Coexistence of Nasal Bacteria in an in silico Community

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