Multiple stable states in microbial communities explained by the stable marriage problem

Goyal, Akshit; Dubinkina, Veronika; Maslov, Sergei

doi:10.1038/s41396-018-0222-x

Cited by 83 publications

(74 citation statements)

References 70 publications

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“…Analyzing both theoretically and experimentally a minimal bistable community, we have shown that feedback between microbial 30 growth and environmental conditions (specifically, the pH) can mechanistically drive these transitions. While our results enhance the relevance of environmentally mediated interactions [46]-[49] in the microbial world, phenomenological models such as the generalized Lotka-Volterra model [50] and the stable marriage problem [51] indicate that analogous community dynamics could unfold from different microbial interactions. Analogous boom-and-bust invasions [52] have 35 also been reported as a main cause of macroecosystem disruption.…”

Section: Discussionsupporting

confidence: 55%

Transient invaders can induce shifts between alternative stable states of microbial communities

Amor

Ratzke

Gore

2019

Preprint

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Microbial dispersal often leads to the arrival of outsider organisms into ecosystems. When their arrival give rise to successful invasions, outsider species establish within the resident 10 community, which can dramatically alter the ecosystem. Seemingly less influential, the potential impact of unsuccessful invaders that interact only transiently with the community has remained largely ignored. Here, we experimentally demonstrate that such transient invasions can perturb the stability of microbial ecosystems and induce a lasting transition to an alternative stable state, even when the invader species itself does not survive the transition. First, we develop a 15 mechanistic understanding of how environmental changes caused by such transient invaders can drive a community shift in a simple, bistable model system. Beyond this, we show that transient invaders can also induce switches between stable states in more complex communities isolated from natural soil samples. Our results demonstrate that short-term interactions with an invader species can induce lasting shifts in community composition and function. 20 One Sentence Summary: Transient invaders can cause lasting shifts in community composition and function.

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Section: Discussionsupporting

confidence: 55%

Transient invaders can induce shifts between alternative stable states of microbial communities

Amor

Ratzke

Gore

2019

Preprint

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“…It is usually understood as the result of transparently cooperative processes, such as production of a public good [32], and modeled via an explicit cooperative term. In resourcecompetition models, multistability has been observed when species consume nutrients one at a time [33] or with unequal stoichiometries [34]. Here, both the Allee effect and multistability emerge naturally from the ability of a population to render its resource environment more favorable to itself.…”

Section: Discussionmentioning

confidence: 99%

Spatial Ecology of Territorial Populations

Weiner

Posfai

Wingreen

2019

Preprint

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Many ecosystems, from vegetation to biofilms, are composed of territorial populations that compete for both nutrients and physical space. What are the implications of such spatial organization for biodiversity? To address this question, we developed and analyzed a model of territorial resource competition. In the model, all species obey trade-offs inspired by biophysical constraints on metabolism; the species occupy non-overlapping territories while nutrients diffuse in space. We find that the nutrient diffusion time is an important control parameter for both biodiversity and the timescale of population dynamics. Interestingly, fast nutrient diffusion allows the populations of some species to fluctuate to zero, leading to extinctions. Moreover, territorial competition spontaneously gives rise to both multistability and the Allee effect (in which a minimum population is required for survival), so that small perturbations can have major ecological effects. While the assumption of trade-offs allows for the coexistence of more species than the number of nutrients -thus violating the principle of competitive exclusion -overall biodiversity is curbed by the domination of "oligotroph" species. Importantly, in contrast to well-mixed models, spatial structure renders diversity robust to inequalities in metabolic trade-offs. Our results suggest that territorial ecosystems can display high biodiversity and rich dynamics simply due to competition for resources in a spatial community.

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“…(2) for a review), which have been previously modelled 92 in the context of competition for nutrients (5,4) and without phages. In order for a 93 phage-bacterial ecosystem to be in principle capable of bistability, the slow-growing 94 bacterial species needs to produce disproportionately more phages per each unit 95 of consumed nutrient than the fast-growing one:…”

Section: Conditions For Bistability and Regime Shiftsmentioning

confidence: 99%

“…In microbial ecosystems (2) these 41 ms Submission Template mSystems Submission Template mSystems Submission Template mSystems Submission Template mSystems Submission Template mSystems Submission Tem transitions are known to be possible when a bacterial species directly produces some 42 metabolic waste products or antibiotics (3) that inhibit the growth of other bacteria. 43 They may also occur when bacterial species compete for several food sources, which 44 they use either in different stoichiometric ratios (4) or in different preferential orders 45 (5). Here we explore a new type of regime shifts caused by interactions between 46 bacteria and phages.…”

Section: Introductionmentioning

confidence: 99%

Regime shifts in a phage-bacterial ecosystem and strategies for its control

Maslov

Sneppen

2019

Preprint

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The competition between bacteria often involves both nutrients and phage 7 predators and may give rise to abrupt regime shifts between the alternative stable 8 states characterized by different species compositions. While such transitions have 9 been previously studied in the context of competition for nutrients, the case of phage-10 induced bistability between competing bacterial species has not been considered 11 yet. Here we demonstrate a possibility of regime shifts in well-mixed phage-bacterial 12 ecosystems. In one of the bistable states the fast-growing bacteria competitively 13 exclude the slow-growing ones by depleting their common nutrient. Conversely, in 14 the second state the slow-growing bacteria with a large burst size generate such a 15 large phage population that the other species cannot survive. This type of bistability 16 can be realized as the competition between a strain of bacteria protected from phage 17 by abortive infection and another strain with partial resistance to phage. It is often 18 desirable to reliably control the state of microbial ecosystems, yet bistability significantly 19 complicates this task. We discuss successes and limitations of one control strategy in 20 which one adds short pulses to populations of individual species. Our study proposes 21 a new type of phage therapy, where introduction of the phage is supplemented by 22 addition of a partially resistant host bacteria. 23 IMPORTANCE Phage-microbial communities play an important role in human health 24as well as natural and industrial environments. Here we show that these communities 25 can assume several alternative species compositions separated by abrupt regime shifts. 26 Our model predicts these regime shifts in the competition between bacterial strains 27 protected by two different phage defense mechanisms: abortive infection/CRISPR and 28 partial resistance. The history dependence caused by regime shifts greatly complicates 29 the task of manipulation and control of a community. We propose and study a success-30 ful control strategy via short population pulses aimed at inducing the desired regime 31 shifts. In particular, we predict that a fast-growing pathogen could be eliminated by a 32 combination of its phage and a slower-growing susceptible host. 33 KEYWORDS: keyword 1, keyword 2, keyword 3. 34 P lease read the Instructions to Authors carefully, or browse the FAQs for further 35 details. 36 131 phages can survive and the system stays abiotic B 1 = B 2 = P = 0. The fast-growing 132 bacteria B 1 first appears for φ ≥ 0.04 and prevents the appearance of the slow-growing 133 ms Submission Template mSystems Submission Template mSystems Submission Template mSystems Submission Template mSystems Submission Template mSystems Submission Tem

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Multiple stable states in microbial communities explained by the stable marriage problem

Cited by 83 publications

References 70 publications

Transient invaders can induce shifts between alternative stable states of microbial communities

Transient invaders can induce shifts between alternative stable states of microbial communities

Spatial Ecology of Territorial Populations

Regime shifts in a phage-bacterial ecosystem and strategies for its control

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