Dynamic aggregation and dispersal of Escherichia coli under cycles of feast and famine

Microbes in nature are constantly subject to environmental fluctuations on varying timescales, and have developed a host of strategies for dealing with environmental stress. In particular, variation in nutrient levels is believed to impact community function and drive a dynamic equilibrium between planktonic and aggregated microbial populations in liquid environments. Although models of population dynamics cannot be adequately designed or tested in the absence of precise quantitative data, experiments quantitatively documenting the dynamics of large microbial populations in response to fluctuating environments with high-frequency measurement over long timescales are rare, with most studies relying on non-quantitative measurement techniques, measurements with low temporal resolution, or small population sizes. We develop a custom continuous-culture device coupled to an epifluorescence microscope, permitting high-throughput (>10^7 objects per system per experiment) quantitative fluorescence measurements of macroscopic populations of bacteria at the single-cell level with measurements as frequent as once per minute. Our design is stable over many weeks of operation and has fully automated control allowing us to perturb bacterial communities and measure the resulting dynamics. We find that populations of Escherichia coli propagated at slow but non-zero growth form large, free-floating cell aggregates, and that subjecting these populations to cycles of nutrient abundance (feast) and scarcity (famine) results in history-dependent dynamics whereby the planktonic populations appear to achieve increasing resilience to perturbation, as measured by the maximum apparent growth rate during periods of feast. By varying the frequency and amplitude of feasts we find a strong dependence of the maximum planktonic growth rate on both variables. We find that these transiently high planktonic population growth rates do not result from cell division, but from patterns of aggregation and dispersal from aggregated populations of E. coli which exhibit both history-dependence and sensitivity to nutrient levels. We present a simple model that accurately describes the majority of our data in terms of these aggregation dynamics, and confirm the model with measurements of aggregate sizes and control experiments in conditions similar to batch culture, in which aggregates do not form. We present additional results demonstrating a history-dependent effect whereby the lag phase of individual cells decreases with increasing amplitude or frequency of feasts. Finally, we briefly present work involving modification of our custom continuous-culture devices to enable future experiments in our lab examining the dynamics of complex phototroph-heterotroph communities exhibiting fluorescence in multiple channels.

Name thesis:degree_name

Ph.D.

Level thesis:degree_level

Dissertation

Discipline thesis:degree_discipline

Physics

Grantor

University of Illinois at Urbana-Champaign

Year dc:date

2019

Author dc:creator

• Merritt, Jason

Contributors dc:contributor

• Kuehn, Seppe
• O'Dwyer, James
• Kuhlman, Thomas
• Goldenfeld, Nigel
• Whitaker, Rachel

• Escherichia coli
• E. coli
• Biophysics
• Physics
• Aggregation
• Dispersal
• Biofilm
• Population dynamics
• Microbial populations
• Chemostat
• Continuous-culture
• Fluorescence microscopy
• Image segmentation
• Lag phase
• History-dependence
• Feast and famine
• Starvation

Statement dc:rights

• Copyright 2018 Jason Merritt

Language dc:language

en

Handle dc:identifier

http://hdl.handle.net/2142/102414

OAI identifier oai:identifier

oai:www.ideals.illinois.edu:2142/102414