scholarly journals Exclusion of the fittest predicts microbial community diversity in fluctuating environments

2021 ◽  
Vol 18 (183) ◽  
Author(s):  
Shota Shibasaki ◽  
Mauro Mobilia ◽  
Sara Mitri
Keyword(s):  
Beta Diversity ◽  
Community Diversity ◽  
Harsh Environment ◽  
Interacting Species ◽  
Species Pairs ◽  
Fluctuating Environments ◽  
Environmental Fluctuations ◽  
Demographic Noise ◽  
Parameter Ranges ◽  
Harsh Conditions

Microorganisms live in environments that inevitably fluctuate between mild and harsh conditions. As harsh conditions may cause extinctions, the rate at which fluctuations occur can shape microbial communities and their diversity, but we still lack an intuition on how. Here, we build a mathematical model describing two microbial species living in an environment where substrate supplies randomly switch between abundant and scarce. We then vary the rate of switching as well as different properties of the interacting species, and measure the probability of the weaker species driving the stronger one extinct. We find that this probability increases with the strength of demographic noise under harsh conditions and peaks at either low, high, or intermediate switching rates depending on both species’ ability to withstand the harsh environment. This complex relationship shows why finding patterns between environmental fluctuations and diversity has historically been difficult. In parameter ranges where the fittest species was most likely to be excluded, however, the beta diversity in larger communities also peaked. In sum, how environmental fluctuations affect interactions between a few species pairs predicts their effect on the beta diversity of the whole community.

scholarly journals Microbial species interactions determine community diversity in fluctuating environments

2020 ◽  
Author(s):  
Shota Shibasaki ◽  
Mauro Mobilia ◽  
Sara Mitri
Keyword(s):  
Species Interactions ◽  
Intermediate Disturbance Hypothesis ◽  
Community Diversity ◽  
Intermediate Disturbance ◽  
Microbial Species ◽  
As Species ◽  
Species Pairs ◽  
Local Extinctions ◽  
Harsh Conditions ◽  
Strength Of Competition

AbstractMicroorganisms 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.

scholarly journals Make and break the alarmone: regulation of (p)ppGpp synthetase/hydrolase enzymes in bacteria

2019 ◽  
Vol 43 (4) ◽  
pp. 389-400 ◽  
Author(s):  
Séverin Ronneau ◽  
Régis Hallez
Keyword(s):  
Cell Cycle ◽  
Stress Response ◽  
Stress Responses ◽  
Biofilm Formation ◽  
Pathogenic Bacteria ◽  
Second Messengers ◽  
Molecular Devices ◽  
Environmental Cues ◽  
Fluctuating Environments ◽  
Harsh Conditions

ABSTRACTBacteria use dedicated mechanisms to respond adequately to fluctuating environments and to optimize their chances of survival in harsh conditions. One of the major stress responses used by virtually all bacteria relies on the sharp accumulation of an alarmone, the guanosine penta- or tetra-phosphate commonly referred to as (p)ppGpp. Under stressful conditions, essentially nutrient starvation, these second messengers completely reshape the metabolism and physiology by coordinately modulating growth, transcription, translation and cell cycle. As a central regulator of bacterial stress response, the alarmone is also involved in biofilm formation, virulence, antibiotics tolerance and resistance in many pathogenic bacteria. Intracellular concentrations of (p)ppGpp are determined by a highly conserved and widely distributed family of proteins called RelA-SpoT Homologs (RSH). Recently, several studies uncovering mechanisms that regulate RSH activities have renewed a strong interest in this field. In this review, we outline the diversity of the RSH protein family as well as the molecular devices used by bacteria to integrate and transform environmental cues into intracellular (p)ppGpp levels.

scholarly journals From environmental fluctuations and energy availability to evolutionary change and speciation

1992 ◽  
Vol 6 ◽  
pp. 230-230 ◽  
Author(s):  
Peter A. Parsons
Keyword(s):  
Stress Intensity ◽  
Metabolic Cost ◽  
Evolutionary Change ◽  
Metabolic Energy ◽  
Energy Availability ◽  
Tropical Rain Forests ◽  
Relict Species ◽  
Generalist Species ◽  
Fluctuating Environments ◽  
Environmental Fluctuations

Evolutionary patterns can be considered in terms of two interacting continuums (a) the magnitude of environmental fluctuations of physical variables especially climatic, and (b) the availability of metabolic energy beyond basic needs for maintenance and survival (Parsons, 1991) so giving four extreme combinations:(1) widely fluctuating environments, low metabolic energy availability. This situation is a feature of species borders where the energetic costs of environmental perturbations restrict normal physiological processes so that ecological range expansions are precluded. Provided extinctions do not occur, species would alter their ranges to track longer term climatic changes as described in the historical and fossil records.(2) widely fluctuating environments, high metabolic energy availability. This combination favors opportunists and colonists. Furthermore, following a relaxation of stress intensity after a mass extinction there could be a burst of speciation in such generalist species.(3) stable environments, low metabolic energy availabilty. This combination represents deep sea and cave environments where low metabolic rate is an adaptation to accomodate stresses such as anoxia and low resource availability. Consequently the capacity for evolutionary change is low in these habitats which tend to contain relict species.(4) stable environments, high metabolic energy availability. On energetic grounds speciation is theoretically possible, but high vulnerability to any stressful perturbation would be restrictive in practice since some stress is the norm in natural populations.The potential for evolutionary change and speciation is low in these four extremes, however in intermediate habitats the potential is higher as implied in (2) when stress intensity is relaxed. The intermediate habitats would be characterized by moderately fluctuating environments where the metabolic cost of stress would not preclude adaptive change. Furthermore, the stress levels in such habitats should lead to sufficient underlying genetic variability to be permissive of adaptive responses to environmental change (Parsons, 1991). This paradigm may apply to speciation in tropical rain forests. A fossil analogy would be marine invertebrates in frequently disturbed onshore habitats.

scholarly journals Bacterial Community Diversity Harboured by Interacting Species

PLoS ONE ◽  
2016 ◽  
Vol 11 (6) ◽  
pp. e0155392 ◽  
Author(s):  
Mikaël Bili ◽  
Anne Marie Cortesero ◽  
Christophe Mougel ◽  
Jean Pierre Gauthier ◽  
Gwennola Ermel ◽  
...  
Keyword(s):  
Bacterial Community ◽  
Community Diversity ◽  
Interacting Species ◽  
Bacterial Community Diversity

scholarly journals Horizontal gene transfer becomes disadvantageous in rapidly fluctuating environments

2020 ◽  
Author(s):  
Akshit Goyal ◽  
David Gelbwaser-Klimovsky ◽  
Jeff Gore
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Geometric Model ◽  
Genetic Material ◽  
Natural Populations ◽  
Evolutionary Constraints ◽  
Trade Off ◽  
Fluctuating Environments ◽  
Environmental Fluctuations ◽  
Evolving Populations

Horizontal gene transfer (HGT) allows organisms to share genetic material with non-offspring, and is typically considered beneficial for evolving populations. Recent unexplained observations suggest that HGT rates in nature are linked with environmental dynamics, being high in static environments but surprisingly low in fluctuating environments. Here, using a geometric model of adaptation, we show that this trend might arise from evolutionary constraints. During adaptation in our model, a population of phenotype vectors aligns with a potentially fluctuating environmental vector while experiencing mutation, selection, drift and HGT. Simulations and theory reveal that HGT shapes a trade-off between the adaptation speed of populations and their fitness. This trade-off gives rise to an optimal HGT rate which decreases sharply with the rate of environmental fluctuations. Our results are consistent with data from natural populations, and strikingly suggest that HGT may sometimes carry a significant disadvantage for populations.

scholarly journals Symbiont community diversity is more constrained in holobionts that tolerate diverse stressors

2019 ◽  
Author(s):  
Lauren I. Howe-Kerr ◽  
Benedicte Bachelot ◽  
Rachel M. Wright ◽  
Carly D. Kenkel ◽  
Line K. Bay ◽  
...  
Keyword(s):  
Beta Diversity ◽  
Experimental Period ◽  
Community Diversity ◽  
Acropora Millepora ◽  
Alpha And Beta Diversity ◽  
Species Analysis ◽  
Total Community ◽  
Attribute Model ◽  
Microbial Symbionts ◽  
Diversity Metrics

AbstractCoral reefs are experiencing global declines as climate change and other stressors cause environmental conditions to exceed the physiological tolerances of host organisms and their microbial symbionts (collectively termed the holobiont). To assess the role of symbiont community composition in holobiont stress tolerance, diversity metrics and abundances of obligate dinoflagellate endosymbionts (Family: Symbiodiniaceae) were quantified from eight Acropora millepora coral colonies (hereafter called genets) that thrived under or responded poorly to various stressors. Four ‘best performer’ coral genets were selected for analysis because they survived 10 days of high temperature, high pCO2, bacterial addition, or combined stressors, whereas four ‘worst performer’ coral genets were analyzed because they experienced significant mortality under these stressors. At the end of the experimental period, seven of eight coral genets mainly hosted Cladocopium symbionts, but also contained Brevolium, Durusdinium, and/or Gerakladinium symbionts at lower abundances (<0.1% of the total community). After 10 days of stress, symbiont communities varied significantly among host genets, but not stress treatments, based on alpha and beta diversity metrics. A generalized joint attribute model (GJAM) also predicted that symbiont communities were primarily sensitive to host genet at regional scales. Indicator species analysis and the regional GJAM model identified significant associations among particular symbionts and host genet performance. Specifically, Cladocopium 3k contributed to the success of best performer host genets under various stressful conditions, whereas Durusdinium glynnii and Durusdinium trenchii were significantly associated with one worst performer genet. Cladocopium 3k dominance should be more broadly investigated as a potential predictor of stress resistance in Acropora millepora populations across their geographic range. Symbiodiniaceae communities exhibited higher richness and variance (beta diversity) in the worst performing genets. These findings highlight that symbiont community diversity metrics may be important indicators of resilience in hosts central to diverse disciplines, from agriculture to medicine.

scholarly journals Predicting population genetic change in an autocorrelated random environment: Insights from a large automated experiment

PLoS Genetics ◽  
2021 ◽  
Vol 17 (6) ◽  
pp. e1009611
Author(s):  
Marie Rescan ◽  
Daphné Grulois ◽  
Enrique Ortega Aboud ◽  
Pierre de Villemereuil ◽  
Luis-Miguel Chevin
Keyword(s):  
Population Genetics ◽  
Amplicon Sequencing ◽  
Reaction Norm ◽  
Frequency Change ◽  
Natural Environments ◽  
Selection Coefficient ◽  
Empirical Estimation ◽  
Fluctuating Environment ◽  
Fluctuating Environments ◽  
Environmental Fluctuations

Most natural environments exhibit a substantial component of random variation, with a degree of temporal autocorrelation that defines the color of environmental noise. Such environmental fluctuations cause random fluctuations in natural selection, affecting the predictability of evolution. But despite long-standing theoretical interest in population genetics in stochastic environments, there is a dearth of empirical estimation of underlying parameters of this theory. More importantly, it is still an open question whether evolution in fluctuating environments can be predicted indirectly using simpler measures, which combine environmental time series with population estimates in constant environments. Here we address these questions by using an automated experimental evolution approach. We used a liquid-handling robot to expose over a hundred lines of the micro-alga Dunaliella salina to randomly fluctuating salinity over a continuous range, with controlled mean, variance, and autocorrelation. We then tracked the frequencies of two competing strains through amplicon sequencing of nuclear and choloroplastic barcode sequences. We show that the magnitude of environmental fluctuations (determined by their variance), but also their predictability (determined by their autocorrelation), had large impacts on the average selection coefficient. The variance in frequency change, which quantifies randomness in population genetics, was substantially higher in a fluctuating environment. The reaction norm of selection coefficients against constant salinity yielded accurate predictions for the mean selection coefficient in a fluctuating environment. This selection reaction norm was in turn well predicted by environmental tolerance curves, with population growth rate against salinity. However, both the selection reaction norm and tolerance curves underestimated the variance in selection caused by random environmental fluctuations. Overall, our results provide exceptional insights into the prospects for understanding and predicting genetic evolution in randomly fluctuating environments.

scholarly journals Heat transfer analysis of insulation materials with flexible multilayers

2013 ◽  
Vol 17 (5) ◽  
pp. 1415-1420 ◽  
Author(s):  
Jin-Jing Chen ◽  
Zheng Guo ◽  
Wei-Dong Yu
Keyword(s):  
Heat Transfer ◽  
Thermal Analysis ◽  
Temperature Distribution ◽  
Optimal Design ◽  
Heat Transfer Analysis ◽  
Harsh Environment ◽  
Transfer Model ◽  
Insulation Material ◽  
Study Heat Transfer ◽  
Harsh Conditions

A new flexible multilayer thermal insulation material is presented for applications at harsh environment as high as 433 K or as low as 123 K. A heat transfer model is established and solved to study heat transfer through the material, including radiation, solid heat transfer and gas heat transfer. Comparison between the experimental results and the theoretical prediction shows that the model is feasible to be applied in engineering. The temperature distribution of samples with 10, 15, 20, 25, 30 layers, respectively, the radiation, solid and gas heat transfer of a sample with 10 layers are analyzed at harsh conditions (123 K and 433 K) and the normal condition as well. The theoretical thermal analysis provides an active instruction to an optimal design of such protective materials.

scholarly journals Extent of adaptation is not limited by unpredictability of the environment in laboratory populations of Escherichia coli

2017 ◽  
Author(s):  
Shraddha Karve ◽  
Devika Bhave ◽  
Sutirth Dey
Keyword(s):  
Escherichia Coli ◽  
Environmental Variability ◽  
Acidic Ph ◽  
Simultaneous Presence ◽  
Environmental Stressor ◽  
The Earth ◽  
Fluctuating Environments ◽  
Environmental Fluctuations ◽  
Laboratory Populations ◽  
Different Parts

AbstractEnvironmental variability is on the rise in different parts of the earth and the survival of many species depend on how well they cope with these fluctuations. Our current understanding of how organisms adapt to unpredictably fluctuating environments is almost entirely based on studies that investigate fluctuations among different values of a single environmental stressor like temperature or pH. However, in nature multiple stresses often exist simultaneously. How would unpredictability in environmental fluctuations affect adaptation under such a scenario? To answer this question, we subjected laboratory populations of Escherichia coli to selection over ~260 generations. The populations faced predictable and unpredictable environmental fluctuations across qualitatively different selection environments, namely, salt and acidic pH. We show that predictability of environmental fluctuations does not play a role in determining the extent of adaptation. Interestingly, the extent of ancestral adaptation, to the chosen selection environments, is of key importance. Integrating the insights from two previous studies, our results suggest that it is the simultaneous presence of multiple environmental factors that poses a bigger constraint on extent of adaptation, rather than unpredictability of the fluctuations.

scholarly journals Evolutionary contingency’s impact on laboratory evolution ofEscherichia coliunder fluctuating environments

2019 ◽  
Author(s):  
Ximo Pechuan ◽  
Daniel Biro ◽  
Maryl Lambros ◽  
Aviv Bergman
Keyword(s):  
Escherichia Coli ◽  
Environmental Conditions ◽  
Phenotypic Characterization ◽  
General Tendency ◽  
Environmental Fluctuation ◽  
Laboratory Evolution ◽  
Phenotypic Response ◽  
Final Population ◽  
Fluctuating Environments ◽  
Environmental Fluctuations

1AbstractThe adaptation of biological organisms to fluctuating environments is one major determinant of their structural and dynamical complexity. Organisms have evolved devoted adaptations to ensure the robust performance of physiological functions under environmental fluctuations. To further our understanding of particular adaptation strategies to different environmental fluctuations, we perform laboratory evolution experiments ofEscherichia coliunder three temperature fluctuation regimes alternating between 15°C and 43°C. Two of these regimes are determined by the population’s growth, while the third regime switches stochastically. To address evolutionary contingencies, the experiments are performed on two lineages departing from different genetic backgrounds. The two lineages display distinct evolutionary trajectories, demonstrating dependency on the starting strain’s genetic background. Several genes exhibit a high degree of parallelism, suggesting their potential adaptive nature. The growth increase of the representative clones from each final population relative to their ancestor at 15°C and 43°C demonstrated no correlation between both temperatures, insinuating an absence of a strong trade-off between these two temperatures. Some had a growth rate decrease at 15°C unless exposed to a 43°C epoch, indicating some degree of internalization of the structure of the environment fluctuations. The phenotypic response of the evolved clones at 15°C and 43°C was assessed by a phenotype array method. The resulting responses reveal a general tendency to move closer to the phenotypic response of our starting strains at the optimum of 37°C. This observation expands the documented restorative responses, even when facing complex environmental conditions.2Author SummaryLaboratory evolution experiments have been widely employed to test hypotheses from evolutionary theory. To assess the dynamics of adaptation under environmental fluctuations, we evolved 24Escherichia colipopulations under different regimes of temperature switching between 15°C and 43°C for about 600 generations. At the final point of the evolution experiment, the evolved populations were genome sequenced and clones were isolated and sequenced for phenotypic characterization. Fitness measurements revealed adaptation to both environmental conditions and some strains internalized the environmental fluctuation. Array phenotypic measurements showed that the majority of evolved strains tended to restore the phenotypic signature of the perturbed environments to that of the optimal temperature condition. This observation expands the documented restorative responses, even when facing complex environmental conditions.

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