scholarly journals Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia

2021 ◽  
Vol 17 (9) ◽  
pp. e1009381
Author(s):  
James J. Winkle ◽  
Bhargav R. Karamched ◽  
Matthew R. Bennett ◽  
William Ott ◽  
Krešimir Josić
Keyword(s):  
Population Dynamics ◽  
Population Control ◽  
Dynamic Control ◽  
Cell Length ◽  
Microbial Consortia ◽  
Cell Alignment ◽  
Rotational Parameter ◽  
Single Strain ◽  
Bacterial Consortia ◽  
Spatiotemporal Population Dynamics

The increased complexity of synthetic microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases in metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics using cell-length control in monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strain’s division length, nematic cell alignment in close-packed monolayers can be destabilized. We find that this destabilization confers an emergent, competitive advantage to smaller-length strains—but by mechanisms that differ depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains, and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.

scholarly journals Emergent spatiotemporal population dynamics with cell-length control of synthetic microbial consortia

2021 ◽  
Author(s):  
James J Winkle ◽  
Bhargav R Karamched ◽  
Matthew R Bennett ◽  
William Ott ◽  
Kresimir Josić
Keyword(s):  
Population Dynamics ◽  
Population Control ◽  
Dynamic Control ◽  
Cell Length ◽  
Microbial Consortia ◽  
Cell Alignment ◽  
Rotational Parameter ◽  
Single Strain ◽  
Bacterial Consortia ◽  
Spatiotemporal Population Dynamics

Increased complexity of engineered microbial biocircuits highlights the need for distributed cell functionality due to concomitant increases of metabolic and regulatory burdens imposed on single-strain topologies. Distributed systems, however, introduce additional challenges since consortium composition and spatiotemporal dynamics of constituent strains must be robustly controlled to achieve desired circuit behaviors. Here, we address these challenges with a modeling-based investigation of emergent spatiotemporal population dynamics that result from cell-length control of monolayer, two-strain bacterial consortia. We demonstrate that with dynamic control of a strain's division length, nematic cell alignment in close-packed monolayers can be destabilized. We found this destabilization conferred an emergent, competitive advantage on smaller-length strains---but by mechanisms that differed depending on the spatial patterns of the population. We used complementary modeling approaches to elucidate underlying mechanisms: an agent-based model to simulate detailed mechanical and signaling interactions between the competing strains and a reductive, stochastic lattice model to represent cell-cell interactions with a single rotational parameter. Our modeling suggests that spatial strain-fraction oscillations can be generated when cell-length control is coupled to quorum-sensing signaling in negative feedback topologies. Our research employs novel methods of population control and points the way to programming strain fraction dynamics in consortial synthetic biology.

scholarly journals A light tunable differentiation system for the creation and control of consortia in yeast

2021 ◽  
Author(s):  
Chetan Aditya ◽  
François Bertaux ◽  
Gregory Batt ◽  
Jakob Ruess
Keyword(s):  
Dynamic Control ◽  
Division Of Labour ◽  
Microbial Consortia ◽  
Continuous Cultures ◽  
Straightforward Manner ◽  
Single Strain ◽  
Differentiation Strategy ◽  
The Creation ◽  
And Control ◽  
Immense Potential

Artificial microbial consortia seek to leverage division-of-labour to optimize function and possess immense potential for bioproduction. Co-culturing approaches, the preferred mode of generating a consortium, remain limited in their ability to give rise to stable consortia having finely tuned compositions. Here, we present an artificial differentiation system in budding yeast capable of generating stable microbial consortia with custom functionalities from a single strain at user-defined composition in space and in time based on optogenetically-driven genetic rewiring. Owing to fast, reproducible, and light-tunable dynamics, our system enables dynamic control of consortia composition in continuous cultures for extended periods. We further demonstrate that our system can be extended in a straightforward manner to give rise to consortia with multiple subpopulations. Our artificial differentiation strategy establishes a novel paradigm for the creation of complex microbial consortia that are simple to implement, precisely controllable, and versatile to use.

scholarly journals A light tunable differentiation system for the creation and control of consortia in yeast

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Chetan Aditya ◽  
François Bertaux ◽  
Gregory Batt ◽  
Jakob Ruess
Keyword(s):  
Dynamic Control ◽  
Division Of Labour ◽  
Microbial Consortia ◽  
Continuous Cultures ◽  
Straightforward Manner ◽  
Single Strain ◽  
Differentiation Strategy ◽  
The Creation ◽  
And Control ◽  
Immense Potential

AbstractArtificial microbial consortia seek to leverage division-of-labour to optimize function and possess immense potential for bioproduction. Co-culturing approaches, the preferred mode of generating a consortium, remain limited in their ability to give rise to stable consortia having finely tuned compositions. Here, we present an artificial differentiation system in budding yeast capable of generating stable microbial consortia with custom functionalities from a single strain at user-defined composition in space and in time based on optogenetically-driven genetic rewiring. Owing to fast, reproducible, and light-tunable dynamics, our system enables dynamic control of consortia composition in continuous cultures for extended periods. We further demonstrate that our system can be extended in a straightforward manner to give rise to consortia with multiple subpopulations. Our artificial differentiation strategy establishes a novel paradigm for the creation of complex microbial consortia that are simple to implement, precisely controllable, and versatile to use.

Effects of Community Versus Single Strain Inoculants on the Biocontrol of Salmonella and Microbial Community Dynamics in Alfalfa Sprouts†

2005 ◽  
Vol 68 (1) ◽  
pp. 40-48 ◽  
Author(s):  
ANABELLE MATOS ◽  
JAY L. GARLAND
Keyword(s):  
Microbial Community ◽  
Microbial Communities ◽  
Community Dynamics ◽  
Community Level ◽  
Microbial Consortia ◽  
Single Strain ◽  
Acridine Orange Staining ◽  
Physiological Profiles ◽  
Alfalfa Sprouts ◽  
Alfalfa Seeds

Potential biological control inoculants, Pseudomonas fluorescens 2-79 and microbial communities derived from market sprouts or laboratory-grown alfalfa sprouts, were introduced into alfalfa seeds with and without a Salmonella inoculum. We examined their ability to inhibit the growth of this foodborne pathogen and assess the relative effects of the inoculants on the alfalfa microbial community structure and function. Alfalfa seeds contaminated with a Salmonella cocktail were soaked for 2 h in bacterial suspensions from each inoculant tested. Inoculated alfalfa seeds were grown for 7 days and sampled during days 1, 3, and 7. At each sampling, alfalfa sprouts were sonicated for 7 min to recover microflora from the surface, and the resulting suspensions were diluted and plated on selective and nonselective media. Total bacterial counts were obtained using acridine orange staining, and the percentage culturability was calculated. Phenotypic potential of sprout-associated microbial communities inoculated with biocontrol treatments was assessed using community-level physiological profiles based on patterns of use of 95 separate carbon sources in Biolog plates. Community-level physiological profiles were also determined using oxygen-sensitive fluorophore in BD microtiter plates to examine functional patterns in these communities. No significant differences in total and mesophilic aerobe microbial cell density or microbial richness resulting from the introduction of inoculants on alfalfa seeds with and without Salmonella were observed. P. fluorescens 2-79 exhibited the greatest reduction in the growth of Salmonella early during alfalfa growth (4.22 log at day 1), while the market sprout inoculum had the reverse effect, resulting in a maximum log reduction (5.48) of Salmonella on day 7. Community-level physiological profiles analyses revealed that market sprout communities peaked higher and faster compared with the other inoculants tested. These results suggest that different modes of actions of single versus microbial consortia biocontrol treatments may be involved.

Population dynamics of large and small mammals: Graeme Caughley's grand vision

2009 ◽  
Vol 36 (1) ◽  
pp. 1 ◽  
Author(s):  
Charles J. Krebs
Keyword(s):  
Population Dynamics ◽  
Population Control ◽  
Population Increase ◽  
Control Mechanisms ◽  
Relative Role ◽  
Top Down ◽  
Large Herbivores ◽  
Disturbed Systems ◽  
Herbivorous Mammals ◽  
Grand Vision

Ecologists that study the population dynamics of large and small herbivorous mammals operate in two worlds that overlap only partly, and in this paper I address whether the conjecture that these worlds represent two distinct and valid paradigms is currently justified. I argue that large mammals fall into three groups depending on whether they have effective predators or not, and whether they are harvested by humans. Because of human persecution of large predators, more and more large herbivorous mammals are effectively predator-free and are controlled bottom-up by food. But in less disturbed systems, large herbivorous mammals should be controlled top-down by effective predators, and this can lead to a trophic cascade. Small herbivorous mammals have been suggested to be controlled top-down by predators but some experimental evidence has challenged this idea and replaced it with the notion that predation is one of several factors that may affect rates of population increase. Intrinsic control (territoriality, infanticide, social inhibition of breeding) appears to be common in small herbivorous mammals with altricial young but is absent in species with precocial young, in ecosystems with strong stochastic weather variation (deserts) and in areas of human-induced habitat fragmentation in agricultural monocultures. The extrinsic control of large herbivores with precocial young validates part of Graeme Caughley’s Grand Vision, but the relative role of intrinsic and extrinsic mechanisms for small herbivores with altricial young is still controversial. An improved knowledge of population control mechanisms for large and small herbivores is essential for natural resource management.

scholarly journals Population dynamics modify urban residents’ exposure to extreme temperatures across the United States

2019 ◽  
Vol 5 (12) ◽  
pp. eaay3452 ◽  
Author(s):  
Jiachuan Yang ◽  
Leiqiu Hu ◽  
Chenghao Wang
Keyword(s):  
Population Dynamics ◽  
Climate Adaptation ◽  
Heat Waves ◽  
Global Climate ◽  
The United States ◽  
Urban Residents ◽  
Extreme Temperatures ◽  
Mortality And Morbidity ◽  
Spatiotemporal Population Dynamics

Exposure to extreme temperatures is one primary cause of weather-related human mortality and morbidity. Global climate change raises the concern of public health under future extreme events, yet spatiotemporal population dynamics have been long overlooked in health risk assessments. Here, we show that the diurnal intra-urban movement alters residents’ exposure to extreme temperatures during cold and heat waves. To do so, we incorporate weather simulations with commute-adjusted population profiles over 16 major U.S. metropolitan areas. Urban residents’ exposure to heat waves is intensified by 1.9° ± 0.7°C (mean ± SD among cities), and their exposure to cold waves is attenuated by 0.6° ± 0.8°C. The higher than expected exposure to heat waves significantly correlates with the spatial temperature variability and requires serious attention. The essential role of population dynamics should be emphasized in temperature-related climate adaptation strategies for effective and successful interventions.

scholarly journals Understanding the Evolutionary Ecology of host–pathogen Interactions Provides Insights into the Outcomes of Insect Pest Biocontrol

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 141
Author(s):  
David J. Páez ◽  
Arietta E. Fleming-Davies
Keyword(s):  
Population Dynamics ◽  
Life History ◽  
Transmission Rate ◽  
Insect Pest ◽  
Pathogen Transmission ◽  
Single Strain ◽  
Classical Biocontrol ◽  
Life History Tradeoffs ◽  
Pathogen Strains

The use of viral pathogens to control the population size of pest insects has produced both successful and unsuccessful outcomes. Here, we investigate whether those biocontrol successes and failures can be explained by key ecological and evolutionary processes between hosts and pathogens. Specifically, we examine how heterogeneity in pathogen transmission, ecological and evolutionary tradeoffs, and pathogen diversity affect insect population density and thus successful control. We first review the existing literature and then use numerical simulations of mathematical models to further explore these processes. Our results show that the control of insect densities using viruses depends strongly on the heterogeneity of virus transmission among insects. Overall, increased heterogeneity of transmission reduces the effect of viruses on insect densities and increases the long-term stability of insect populations. Lower equilibrium insect densities occur when transmission is heritable and when there is a tradeoff between mean transmission and insect fecundity compared to when the heterogeneity of transmission arises from non-genetic sources. Thus, the heterogeneity of transmission is a key parameter that regulates the long-term population dynamics of insects and their pathogens. We also show that both heterogeneity of transmission and life-history tradeoffs modulate characteristics of population dynamics such as the frequency and intensity of “boom–bust" population cycles. Furthermore, we show that because of life-history tradeoffs affecting the transmission rate, the use of multiple pathogen strains is more effective than the use of a single strain to control insect densities only when the pathogen strains differ considerably in their transmission characteristics. By quantifying the effects of ecology and evolution on population densities, we are able to offer recommendations to assess the long-term effects of classical biocontrol.

scholarly journals Cell alignment is induced by cyclic changes in cell length: studies of cells grown in cyclically stretched substrates

2001 ◽  
Vol 19 (2) ◽  
pp. 286-293 ◽  
Author(s):  
C. Neidlinger-Wilke ◽  
E. S. Grood ◽  
J. H.-C. Wang ◽  
R. A. Brand ◽  
L. Claes
Keyword(s):  
Cell Length ◽  
Cell Alignment ◽  
Cyclic Changes

Isolation and Genetic Identification of Dibenzothiophene Degrading Bacteria from Contaminated Soil

2012 ◽  
Vol 610-613 ◽  
pp. 292-295 ◽  
Author(s):  
Lin Li ◽  
Chao Cheng Zhao ◽  
Qi You Liu ◽  
Yun Bo Zhang
Keyword(s):  
Phylogenetic Analysis ◽  
Species Identification ◽  
Contaminated Soil ◽  
Bacterial Strain ◽  
Degradation Efficiency ◽  
Genetic Identification ◽  
Microbial Consortia ◽  
Bacterial Strains ◽  
Bacterial Consortia ◽  
Degrading Bacteria

The biodegradation abilities of 10 dibenzothiophene degrading microbial consortia isolated from contaminated soil were investigated. 5 highly efficient dibenzothiophene degrading bacterial strains were obtained from the consortium LKY10 by screening on LB-agar plates.The bacterial strain LKY10-5 reduced more than 90% of dibenzothiophene with 40 mg•L-1concentration, and had higher degradation efficiency than enriched bacterial consortia in 7 days of cultivation. According to species identification and phylogenetic analysis, strain LKY10-1 and LKY10-3 belonged to Actinobacteria and could be included in Rhodococcus and Cellulosimicrobium genus, LKY10-5 and LKY10-6 belonged to Proteobacteria and could be included in Pseudomonas and Devosia genus, and LKY10-13 could be included in Lysinibacillus genus and belonged to Firmicutes.

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