Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat

Balagadde, Frederick; Li, You; Hansen, Carl L.; Arnold, Frances H.; Quake, Stephen R.

doi:10.1126/science.1109173

Cited by 536 publications

(430 citation statements)

References 15 publications

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“…In general ecological science one often encounters terms such as within and between species competition, cooperation and density dependence (Turchin, 1995;Stenseth et al, 1998;Ciannelli et al, 2005;Moe et al, 2005). Such concepts are much less frequently explored in the context of microbes (Hagen et al, 1982;Bradshaw et al, 1994;Rainey and Rainey, 2003;You et al, 2004;Balagadde et al, 2005). This is partly due to a historical division between the fields of microbiology and general ecology, but the difficulty of quantitative population data collection from complex microbial systems has also been a major factor contributing to the paucity of information on population dynamics in microcosm.…”

Section: Introductionmentioning

confidence: 99%

Characterizing mixed microbial population dynamics using time-series analysis

Trosvik

Rudi²,

Næs

et al. 2008

The ISME Journal

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Due to a general shortage of temporal population data, dynamic structures in microbial communities remain largely unexplored. Knowledge of community dynamics is, however, essential for understanding the mechanisms by which microbes interact. Here, we have used a computational approach for quantification of bacteria in multispecies populations, generating data for time-series modeling. Moreover, we have used online FR-IR spectroscopy to monitor the main metabolic processes. The approach enabled us to provide a functional description of the parameters governing the population dynamics in a three-species model bacterial community, demonstrating density-dependent regulation, interspecies competition and even a case of cooperation between two species. Since the field of microbial ecology has yet to embrace many of the concepts and methods developed for the study of ecology of higher plants and animals, the realization that microbial systems can be analyzed within the same conceptual framework as other ecosystems is of fundamental importance.

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Section: Introductionmentioning

confidence: 99%

Characterizing mixed microbial population dynamics using time-series analysis

Trosvik

Rudi²,

Næs

et al. 2008

The ISME Journal

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“…The nanofabricated habitat landscapes we can construct afford a variability in habitat structure, allowing us to experimentally explore Wright's adaptive landscape. There have been microchemostat systems created recently (13,14), but the technology discussed here differs in a fundamental way. Microfabricated chemostats described so far (just as the macroscopic ones) do not allow for the emergence of a metapopulation [a spatially distributed network, of parallel populations adapted to different local conditions but weakly coupled with one another by dispersal (4)].…”

mentioning

confidence: 99%

Bacterial metapopulations in nanofabricated landscapes

Keymer

Galajda

Muldoon

et al. 2006

Proc. Natl. Acad. Sci. U.S.A.

153

180

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We have constructed a linear array of coupled, microscale patches of habitat. When bacteria are inoculated into this habitat landscape, a metapopulation emerges. Local bacterial populations in each patch coexist and weakly couple with neighbor populations in nearby patches. These spatially distributed bacterial populations interact through local extinction and colonization processes. We have further built heterogeneous habitat landscapes to study the adaptive dynamics of the bacterial metapopulations. By patterning habitat differences across the landscape, our device physically implements an adaptive landscape. In landscapes with higher niche diversity, we observe rapid adaptation to large-scale, low-quality (high-stress) areas. Our results illustrate the potential lying at the interface between nanoscale biophysics and landscape evolutionary ecology.biophysics ͉ microbiology ͉ landscape ecology ͉ metapopulation biology

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“…15 Since their introduction in 1950, 1,2 chemostat systems have been developed to function on a variety of scales ranging from liters to microliters and for a variety of applications. [16][17][18][19] These various designs, which range from commercially produced bioreactors to glassblown vessels to custom microfluidics platforms, share general design principles. A culture chamber is stirred and aerated (usually by bubbling air through it) and the microbes contained therein are kept homogeneously dispersed throughout the culture chamber at all times.…”

Section: Introductionmentioning

confidence: 99%

Design and Use of Multiplexed Chemostat Arrays

Miller

Befort

Kerr

et al. 2013

JoVE

105

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Chemostats are continuous culture systems in which cells are grown in a tightly controlled, chemically constant environment where culture density is constrained by limiting specific nutrients.1,2 Data from chemostats are highly reproducible for the measurement of quantitative phenotypes as they provide a constant growth rate and environment at steady state. For these reasons, chemostats have become useful tools for fine-scale characterization of physiology through analysis of gene expression [3][4][5][6] and other characteristics of cultures at steady-state equilibrium. 7 Long-term experiments in chemostats can highlight specific trajectories that microbial populations adopt during adaptive evolution in a controlled environment. In fact, chemostats have been used for experimental evolution since their invention. 8 A common result in evolution experiments is for each biological replicate to acquire a unique repertoire of mutations. 9-13 This diversity suggests that there is much left to be discovered by performing evolution experiments with far greater throughput.We present here the design and operation of a relatively simple, low cost array of miniature chemostats-or ministats-and validate their use in determination of physiology and in evolution experiments with yeast. This approach entails growth of tens of chemostats run off a single multiplexed peristaltic pump. The cultures are maintained at a 20 ml working volume, which is practical for a variety of applications. It is our hope that increasing throughput, decreasing expense, and providing detailed building and operation instructions may also motivate research and industrial application of this design as a general platform for functionally characterizing large numbers of strains, species, and growth parameters, as well as genetic or drug libraries.

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Long-Term Monitoring of Bacteria Undergoing Programmed Population Control in a Microchemostat

Cited by 536 publications

References 15 publications

Characterizing mixed microbial population dynamics using time-series analysis

Characterizing mixed microbial population dynamics using time-series analysis

Bacterial metapopulations in nanofabricated landscapes

Design and Use of Multiplexed Chemostat Arrays

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