Environmental fluctuations and their effects on microbial communities, populations and individuals

Nguyen, Jen; Lara-Gutiérrez, Juanita; Stocker, Roman

doi:10.1093/femsre/fuaa068

Cited by 118 publications

(102 citation statements)

References 121 publications

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“…Our work has begun to bridge this gap demonstrating how important the dynamics of CRISPR-Cas systems are to their functioning and the outcome of populations facing a threat. Further investigation into different CRISPR- Cas types and classes, fluctuating environments 70 , and conditions supporting the formation of subpopulations 71 will enhance the understanding of CRISPR-Cas dynamics on both the molecular and population scale.…”

Section: Discussionmentioning

confidence: 99%

Single Cell Variability of CRISPR-Cas Interference and Adaptation

McKenzie

Keizer

Vink

et al. 2021

Preprint

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CRISPR-Cas defence is a combination of adaptation to new invaders by spacer acquisition, and interference by targeted nuclease activity. While these processes have been studied on a population level, the individual cellular variability has remained unknown. Here, using a microfluidic device combined with time-lapse microscopy, we monitor invader clearance in a population of Escherichia coli across multiple generations. We observed that CRISPR interference is fast with a narrow distribution of clearance times. In contrast, for invaders with escaping PAM mutations we show large cell-to-cell variability of clearance times, which originates from primed CRISPR adaptation. Faster growth and cell division, as well as higher levels of Cascade, increase the chance of clearance by interference. In contrast, faster growth is associated with decreased chances of clearance by priming. A mathematical model explains the experimental findings, and identifies Cascade binding to the mutated invader DNA, rather than spacer integration, as the main source of priming heterogeneity. The highly stochastic nature of primed CRISPR adaptation implies that only subpopulations of bacteria are able to respond to invading threats in a timely manner. We conjecture that CRISPR-Cas dynamics and heterogeneity at the cellular level are crucial to understanding the strategy of bacteria in their competition with other species and phages.

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Section: Discussionmentioning

confidence: 99%

Single Cell Variability of CRISPR-Cas Interference and Adaptation

McKenzie

Keizer

Vink

et al. 2021

Preprint

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“…For example, individual size is under physiological regulatory control (Davidowitz, Roff & Nijhout 2005;Chelini, Delong & Hebets 2019) and therefore responds to changes in resource levels (Marañón et al 2013). While resource levels can vary independently of population abundance (Holt 2008;Fey, Gibert & Siepielski 2019;Nguyen, Lara-Gutiérrez & Stocker 2020), high abundance leads to crowding and increasing intra-specific competition (Gavina et al 2018). Stronger competition in turn effectively reduces resource availability at the individual level, which often results in stunted growth and smaller body sizes (e.g., (Vanni et al 2009)).…”

Section: Introductionmentioning

confidence: 99%

Feedbacks between size and density determine rapid eco-phenotypic dynamics

Gibert

Han

Wieczynski

et al. 2021

Preprint

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1. Body size is a fundamental trait linked to many ecological processes-from individuals to ecosystems. Although the effects of body size on metabolism are well-known, how body size influences, and is influenced by, population growth and density is less clear. Specifically, 1) whether body size, or population dynamics, more strongly influences the other, and, 2) whether observed changes in body size are due to plasticity or rapid evolutionary change, are not well understood. 2. Here, we address these two issues by experimentally tracking population density and mean body size in the protist Tetrahymena pyriformis as it grows from low density to carrying capacity. We then use state-of-the-art time-series analyses to infer the direction, magnitude, and causality of the link between body size and ecological dynamics. Last, we fit two alternative dynamical models to our empirical time series to assess whether plasticity or rapid evolution better explains changes in mean body size. 3. Our results clearly indicate that changes in body size precede and determine changes in population density, not the other way around. We also show that a model assuming that size changes via plasticity more parsimoniously explains these observed coupled phenotypic and ecological dynamics than one that assumes rapid evolution drives changes in size. 4. Together these results suggest that rapid, plastic phenotypic change not only occurs well within ecological timescales but may even precede -and causally influence- ecological dynamics. Furthermore, large individuals may be favored and fuel high population growth rates when population density is low, but smaller individuals may be favored once populations reach carrying capacity and resources become scarcer. Thus, rapid plastic changes in functional traits may play a fundamental and currently unrecognized role in familiar ecological processes like logistic population growth.

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“…There could be a trade-off between growth rate in the exponential phase of fermentation and survival rate in the stationary phase that is following the fermentation which will result in a balance of organisms that have a different strategy [110,111]. While predicted in theory, these microbial experiments have demonstrated that such a trade-off exists [112,113].…”

Section: Fluctuating Environmental Factorsmentioning

confidence: 99%

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

Alekseeva

Groenenboom

Smid

et al. 2021

IJERPH

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Eco-evolutionary forces are the key drivers of ecosystem biodiversity dynamics. This resulted in a large body of theory, which has partially been experimentally tested by mimicking evolutionary processes in the laboratory. In the first part of this perspective, we outline what model systems are used for experimental testing of eco-evolutionary processes, ranging from simple microbial combinations and, more recently, to complex natural communities. Microbial communities of spontaneous fermented foods are a promising model system to study eco-evolutionary dynamics. They combine the complexity of a natural community with extensive knowledge about community members and the ease of manipulating the system in a laboratory setup. Due to rapidly developing sequencing techniques and meta-omics approaches incorporating data in building ecosystem models, the diversity in these communities can be analysed with relative ease while hypotheses developed in simple systems can be tested. Here, we highlight several eco-evolutionary questions that are addressed using microbial communities from fermented foods. These questions relate to analysing species frequencies in space and time, the diversity-stability relationship, niche space and community coalescence. We provide several hypotheses of the influence of these factors on community evolution specifying the experimental setup of studies where microbial communities of spontaneous fermented food are used.

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Environmental fluctuations and their effects on microbial communities, populations and individuals

Cited by 118 publications

References 121 publications

Single Cell Variability of CRISPR-Cas Interference and Adaptation

Single Cell Variability of CRISPR-Cas Interference and Adaptation

Feedbacks between size and density determine rapid eco-phenotypic dynamics

Eco-Evolutionary Dynamics in Microbial Communities from Spontaneous Fermented Foods

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