scholarly journals A macroecological description of alternative stable states reproduces intra- and inter-host variability of gut microbiome

2021 ◽  
Author(s):  
Silvia Zaoli ◽  
Jacopo Grilli
Keyword(s):  
Gut Microbiome ◽  
Community Dynamics ◽  
Temporal Dynamics ◽  
Alternative Stable States ◽  
Individual Variability ◽  
Statistical Properties ◽  
Stable States ◽  
Environmental Fluctuations ◽  
The Rich ◽  
Community Variability

The most fundamental questions in microbial ecology concern the diversity and variability of communities. Their composition varies widely across space and time, as it is determined by a non-trivial combination of stochastic and deterministic processes. The interplay between non-linear community dynamics and environmental fluctuations determines the rich statistical structure of community variability, with both rapid temporal dynamics fluctuations and non-trivial correlations across habitats. Here we analyze long time-series of gut microbiome and compare intra- and inter-community dissimilarity. Under a macroecological framework we characterize their statistical properties. We show that most taxa have large but stationary fluctuations over time, while a minority is characterized by quick changes of average abundance which cluster in time, suggesting the presence of alternative stable states. We disentangle inter-individual variability in a major stochastic component and a deterministic one, the latter recapitulated by differences in the carrying capacities of taxa. Finally, we develop a model which includes environmental fluctuations and alternative stable states. This model quantitatively predicts the statistical properties of both intra- and inter-individual community variability, therefore summarizing variation in a unique macroecological framework.

scholarly journals Regime shifts in exploited marine food webs: detecting mechanisms underlying alternative stable states using size-structured community dynamics theory

2015 ◽  
Vol 370 (1659) ◽  
pp. 20130262 ◽  
Author(s):  
Anna Gårdmark ◽  
Michele Casini ◽  
Magnus Huss ◽  
Anieke van Leeuwen ◽  
Joakim Hjelm ◽  
...  
Keyword(s):  
Community Dynamics ◽  
Prey Availability ◽  
Alternative Stable States ◽  
Individual Performance ◽  
Regime Shifts ◽  
Trophic Levels ◽  
Stable States ◽  
Ecosystem Recovery ◽  
Piscivorous Fish ◽  
Combining Data

Many marine ecosystems have undergone ‘regime shifts’, i.e. abrupt reorganizations across trophic levels. Establishing whether these constitute shifts between alternative stable states is of key importance for the prospects of ecosystem recovery and for management. We show how mechanisms underlying alternative stable states caused by predator–prey interactions can be revealed in field data, using analyses guided by theory on size-structured community dynamics. This is done by combining data on individual performance (such as growth and fecundity) with information on population size and prey availability. We use Atlantic cod ( Gadus morhua ) and their prey in the Baltic Sea as an example to discuss and distinguish two types of mechanisms, ‘cultivation-depensation’ and ‘overcompensation’, that can cause alternative stable states preventing the recovery of overexploited piscivorous fish populations. Importantly, the type of mechanism can be inferred already from changes in the predators' body growth in different life stages. Our approach can thus be readily applied to monitored stocks of piscivorous fish species, for which this information often can be assembled. Using this tool can help resolve the causes of catastrophic collapses in marine predatory–prey systems and guide fisheries managers on how to successfully restore collapsed piscivorous fish stocks.

scholarly journals Press disturbance unveils different community structure, function and assembly of bacterial taxa and functional genes in mesocosm-scale bioreactors

2019 ◽  
Author(s):  
E. Santillan ◽  
F. Constancias ◽  
S. Wuertz
Keyword(s):  
Organic Carbon ◽  
Community Assembly ◽  
Temporal Dynamics ◽  
Alternative Stable States ◽  
Treatment Plant ◽  
Functional Genes ◽  
Rrna Gene ◽  
Stable States ◽  
Organic Carbon Loading ◽  
Carbon Loading

AbstractSustained perturbations, or press disturbances, are of interest in microbial ecology as they can drive systems to alternative stable states. Here, we tested the effect of a sustained doubling of organic carbon loading on structure, assembly and function of bacterial communities. Two sets of replicate 5-liter sequencing batch reactors were operated at two different organic carbon loading levels (323 and 629 mg COD L-1) for a period of 74 days, following 53 days of acclimation after inoculation with sludge from a full-scale treatment plant. Temporal dynamics of community taxonomic and functional gene structure were derived from metagenomics and 16S rRNA gene metabarcoding data. Assembly mechanisms were assessed through a mathematical null model on the effective bacterial turnover expressed as a proportion of total bacterial diversity. Disturbed reactors exhibited different community function, structure and assembly compared to the undisturbed reactors. Bacterial taxa and functional genes showed dissimilar alpha-diversity and community assembly patterns. Deterministic assembly mechanisms were generally stronger in disturbed reactors, associated with common taxa. Stochastic assembly was more important for functional genes and was driven by rare genes. We urge caution when assessing microbial community assembly mechanisms, as results can vary depending on the approach.

scholarly journals Quantifying the impact of ecological memory on the dynamics of interacting communities

2021 ◽  
Author(s):  
Moein Khalighi ◽  
Didier Gonze ◽  
Karoline Faust ◽  
Guilhem Sommeria-Klein ◽  
Leo Lahti
Keyword(s):  
Community Dynamics ◽  
Initial Conditions ◽  
Alternative Stable States ◽  
Interaction Model ◽  
Ecological Communities ◽  
Stable States ◽  
Ecological Memory ◽  
Recovery Times ◽  
Key Aspects ◽  
The Impact

Ecological memory refers to the influence of past events on the response of an ecosystem to exogenous or endogenous changes. Memory has been widely recognized as a key contributor to the dynamics of ecosystems and other complex systems, yet quantitative community models often ignore memory and its implications. Recent studies have shown how interactions between community members can lead to the emergence of resilience and multistability under environmental perturbations. We demonstrate how memory can complement such models. We use the framework of fractional calculus to study how the outcomes of a well-characterized interaction model are affected by gradual increases in ecological memory under varying initial conditions, perturbations, and stochasticity. Our results highlight the implications of memory on several key aspects of community dynamics. In general, memory slows down the overall dynamics and recovery times after perturbation, thus reducing the system's resilience. However, it simultaneously mitigates hysteresis and enhances the system's capacity to resist state shifts. Memory promotes long transient dynamics, such as long-standing oscillations and delayed regime shifts, and contributes to the emergence and persistence of alternative stable states. Collectively, these results highlight the fundamental role of memory on ecological communities and provide new quantitative tools to analyse its impact under varying conditions.

scholarly journals Environmental fluctuations restrict eco-evolutionary dynamics in predator–prey system

2015 ◽  
Vol 282 (1808) ◽  
pp. 20150013 ◽  
Author(s):  
Teppo Hiltunen ◽  
Gökçe B. Ayan ◽  
Lutz Becks
Keyword(s):  
Species Interactions ◽  
Community Dynamics ◽  
Evolutionary Dynamics ◽  
Temporal Dynamics ◽  
Rapid Evolution ◽  
Interactive Effects ◽  
Top Down ◽  
Bottom Up ◽  
Evolutionary Response ◽  
Environmental Fluctuations

Environmental fluctuations, species interactions and rapid evolution are all predicted to affect community structure and their temporal dynamics. Although the effects of the abiotic environment and prey evolution on ecological community dynamics have been studied separately, these factors can also have interactive effects. Here we used bacteria–ciliate microcosm experiments to test for eco-evolutionary dynamics in fluctuating environments. Specifically, we followed population dynamics and a prey defence trait over time when populations were exposed to regular changes of bottom-up or top-down stressors, or combinations of these. We found that the rate of evolution of a defence trait was significantly lower in fluctuating compared with stable environments, and that the defence trait evolved to lower levels when two environmental stressors changed recurrently. The latter suggests that top-down and bottom-up changes can have additive effects constraining evolutionary response within populations. The differences in evolutionary trajectories are explained by fluctuations in population sizes of the prey and the predator, which continuously alter the supply of mutations in the prey and strength of selection through predation. Thus, it may be necessary to adopt an eco-evolutionary perspective on studies concerning the evolution of traits mediating species interactions.

scholarly journals Emergence of alternative stable states in microbial communities in a fluctuating environment

2019 ◽  
Author(s):  
Vilhelm L. Andersen Woltz ◽  
Clare I. Abreu ◽  
Jonathan Friedman ◽  
Jeff Gore
Keyword(s):  
Dilution Rate ◽  
Competitive Exclusion ◽  
Bacterial Species ◽  
Alternative Stable States ◽  
Volterra Model ◽  
Time Averaging ◽  
Stable States ◽  
Major Question ◽  
Fluctuating Environment ◽  
Environmental Fluctuations

AbstractThe effect of environmental fluctuations is a major question in ecology. While it is widely accepted that fluctuations and other types of disturbances can increase biodiversity, we have only a limited understanding of the circumstances in which other types of outcomes can occur in a fluctuating environment. Here we explore this question with laboratory microcosms, using cocultures of two bacterial species, P. putida and P. veronii. At low dilution rates we observe competitive exclusion of P. veronii, whereas at high dilution rates we observe competitive exclusion of P. putida. When the dilution rate alternates between high and low, we do not observe coexistence between the species, but rather alternative stable states, in which only one species survives and initial species’ fractions determine the identity of the surviving species. The Lotka-Volterra model with a fluctuating mortality rate predicts that this outcome is independent of the timing of the fluctuations, and that the time-averaged mortality would also lead to alternative stable states, a prediction that we confirm experimentally. Other pairs of species can coexist in a fluctuating environment, and again consistent with the model we observe coexistence in the time-averaged dilution rate. We find a similar time-averaging result holds in a three-species community, highlighting that simple linear models can in some cases provide powerful insight into how communities will respond to environmental fluctuations.

scholarly journals Resources, mortality, and disease ecology: importance of positive feedbacks between host growth rate and pathogen dynamics

2015 ◽  
Vol 61 (1) ◽  
pp. 37-49 ◽  
Author(s):  
Val H. Smith ◽  
Robert D. Holt ◽  
Marilyn S. Smith ◽  
Yafen Niu ◽  
Michael Barfield
Keyword(s):  
Growth Rate ◽  
Disease Ecology ◽  
Community Dynamics ◽  
Physiological State ◽  
Alternative Stable States ◽  
Stable States ◽  
Metabolic Scaling ◽  
Pathogen Dynamics ◽  
Host Growth ◽  
Resource Effects

Resource theory and metabolic scaling theory suggest that the dynamics of a pathogen within a host should strongly depend upon the rate of host cell metabolism. Once an infection occurs, key ecological interactions occur on or within the host organism that determine whether the pathogen dies out, persists as a chronic infection, or grows to densities that lead to host death. We hypothesize that, in general, conditions favoring rapid host growth rates should amplify the replication and proliferation of both fungal and viral pathogens. If a host population experiences an increase in mortality, to persist it must have a higher growth rate, per host, often reflecting greater resource availability per capita. We hypothesize that this could indirectly foster the pathogen, which also benefits from increased within-host resource turnover. We first bring together in a short review a number of key prior studies which illustrate resource effects on viral and fungal pathogen dynamics. We then report new results from a semi-continuous cell culture experiment with SHIV, demonstrating that higher mortality rates indeed can promote viral proliferation. We develop a simple model that illustrates dynamical consequences of these resource effects, including interesting effects such as alternative stable states and oscillatory dynamics. Our paper contributes to a growing body of literature at the interface of ecology and infectious disease epidemiology, emphasizing that host abundances alone do not drive community dynamics: the physiological state and resource content of infected hosts also strongly influence host–pathogen interactions.

Fire Feedbacks with Vegetation and Alternative Stable States

2009 ◽  
Vol 18 (1) ◽  
pp. 159-173 ◽  
Author(s):  
Brian Beckage ◽  
Chris Ellingwood ◽  
Keyword(s):  
Alternative Stable States ◽  
Stable States ◽  
Fire Feedbacks
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