Robustness of a model microbial community emerges from population structure among single cells of a clonal population
Abstract
Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community. We investigated the mechanistic basis for loss of robustness by examining whether conditional gene regulation altered heterogeneity in gene expression across individual DvH cells. We discovered that robustness of a microbial population across environmental transitions was attributable to the retention of cells in two states that exhibited different condition-specific gene expression patterns. In our experiments, a population with disrupted conditional regulation successfully alternated between cell states. Meanwhile, a population with intact conditional regulation successfully switched between cell states initially, but collapsed after repeated transitions, possibly due to the high energy requirements of regulation. These results demonstrate that the survival of this entire model microbial community is dependent on the regulatory system's influence on the distribution of distinct cell states among individual cells within a clonal population.
- Authors:
-
- Institute for Systems Biology, Seattle, WA (United States)
- Univ. of Washington, Seattle, WA (United States)
- Publication Date:
- Research Org.:
- Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)
- Sponsoring Org.:
- USDOE Office of Science (SC), Biological and Environmental Research (BER)
- OSTI Identifier:
- 1777942
- Alternate Identifier(s):
- OSTI ID: 1375466
- Grant/Contract Number:
- AC02-05CH11231
- Resource Type:
- Accepted Manuscript
- Journal Name:
- Environmental Microbiology
- Additional Journal Information:
- Journal Volume: 19; Journal Issue: 8; Journal ID: ISSN 1462-2912
- Publisher:
- Wiley
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES; single cell; robustness; gene expression; Desulfovibrio; syntrophy; sulfate respiration
Citation Formats
Thompson, Anne W., Turkarslan, Serdar, Arens, Christina E., López García de Lomana, Adrián, Raman, Arjun V., Stahl, David A., and Baliga, Nitin S. Robustness of a model microbial community emerges from population structure among single cells of a clonal population. United States: N. p., 2017.
Web. doi:10.1111/1462-2920.13764.
Thompson, Anne W., Turkarslan, Serdar, Arens, Christina E., López García de Lomana, Adrián, Raman, Arjun V., Stahl, David A., & Baliga, Nitin S. Robustness of a model microbial community emerges from population structure among single cells of a clonal population. United States. https://doi.org/10.1111/1462-2920.13764
Thompson, Anne W., Turkarslan, Serdar, Arens, Christina E., López García de Lomana, Adrián, Raman, Arjun V., Stahl, David A., and Baliga, Nitin S. Mon .
"Robustness of a model microbial community emerges from population structure among single cells of a clonal population". United States. https://doi.org/10.1111/1462-2920.13764. https://www.osti.gov/servlets/purl/1777942.
@article{osti_1777942,
title = {Robustness of a model microbial community emerges from population structure among single cells of a clonal population},
author = {Thompson, Anne W. and Turkarslan, Serdar and Arens, Christina E. and López García de Lomana, Adrián and Raman, Arjun V. and Stahl, David A. and Baliga, Nitin S.},
abstractNote = {Microbial populations can withstand, overcome and persist in the face of environmental fluctuation. Previously, we demonstrated how conditional gene regulation in a fluctuating environment drives dilution of condition-specific transcripts, causing a population of Desulfovibrio vulgaris Hildenborough (DvH) to collapse after repeatedly transitioning from sulfate respiration to syntrophic conditions with the methanogen Methanococcus maripaludis. Failure of the DvH to successfully transition contributed to the collapse of this model community. We investigated the mechanistic basis for loss of robustness by examining whether conditional gene regulation altered heterogeneity in gene expression across individual DvH cells. We discovered that robustness of a microbial population across environmental transitions was attributable to the retention of cells in two states that exhibited different condition-specific gene expression patterns. In our experiments, a population with disrupted conditional regulation successfully alternated between cell states. Meanwhile, a population with intact conditional regulation successfully switched between cell states initially, but collapsed after repeated transitions, possibly due to the high energy requirements of regulation. These results demonstrate that the survival of this entire model microbial community is dependent on the regulatory system's influence on the distribution of distinct cell states among individual cells within a clonal population.},
doi = {10.1111/1462-2920.13764},
journal = {Environmental Microbiology},
number = 8,
volume = 19,
place = {United States},
year = {Mon Apr 17 00:00:00 EDT 2017},
month = {Mon Apr 17 00:00:00 EDT 2017}
}
Web of Science
Works referenced in this record:
Stochastic protein expression in individual cells at the single molecule level
journal, March 2006
- Cai, Long; Friedman, Nir; Xie, X. Sunney
- Nature, Vol. 440, Issue 7082
Metabolic Flexibility of Sulfate-Reducing Bacteria
journal, January 2011
- Plugge, Caroline M.; Zhang, Weiwen; Scholten, Johannes C. M.
- Frontiers in Microbiology, Vol. 2
The Plate Debate: Cultivable communities have no utility in contemporary environmental microbial ecology: The plate debate
journal, June 2007
- Ritz, Karl
- FEMS Microbiology Ecology, Vol. 60, Issue 3
Stochastic Gene Expression in a Single Cell
journal, August 2002
- Elowitz, M. B.
- Science, Vol. 297, Issue 5584
New insights into bacterial adaptation through in vivo and in silico experimental evolution
journal, March 2012
- Hindré, Thomas; Knibbe, Carole; Beslon, Guillaume
- Nature Reviews Microbiology, Vol. 10, Issue 5
Non-genetic individuality: chance in the single cell
journal, August 1976
- Spudich, John L.; Koshland, D. E.
- Nature, Vol. 262, Issue 5568
Intrinsic and extrinsic contributions to stochasticity in gene expression
journal, September 2002
- Swain, P. S.; Elowitz, M. B.; Siggia, E. D.
- Proceedings of the National Academy of Sciences, Vol. 99, Issue 20
A method to analyze, sort, and retain viability of obligate anaerobic microorganisms from complex microbial communities
journal, October 2015
- Thompson, Anne W.; Crow, Matthew J.; Wadey, Brian
- Journal of Microbiological Methods, Vol. 117
Population robustness arising from cellular heterogeneity
journal, June 2010
- Paszek, P.; Ryan, S.; Ashall, L.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 25
Does replication-induced transcription regulate synthesis of the myriad low copy number proteins ofEscherichia coli?
journal, November 1995
- Guptasarma, Purnananda
- BioEssays, Vol. 17, Issue 11
Metabolic modeling of a mutualistic microbial community
journal, January 2007
- Stolyar, Sergey; Van Dien, Steve; Hillesland, Kristina Linnea
- Molecular Systems Biology, Vol. 3, Issue 1
Single-cell analysis reveals gene-expression heterogeneity in syntrophic dual-culture of Desulfovibrio vulgaris with Methanosarcina barkeri
journal, December 2014
- Qi, Zhenhua; Pei, Guangsheng; Chen, Lei
- Scientific Reports, Vol. 4, Issue 1
The Electron Transfer System of Syntrophically Grown Desulfovibrio vulgaris
journal, July 2009
- Walker, C. B.; He, Z.; Yang, Z. K.
- Journal of Bacteriology, Vol. 191, Issue 18
What Is the Allee Effect?
journal, October 1999
- Stephens, P. A.; Sutherland, W. J.; Freckleton, R. P.
- Oikos, Vol. 87, Issue 1
Evolutionary dynamics of bacteria in a human host environment
journal, April 2011
- Yang, L.; Jelsbak, L.; Marvig, R. L.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 18
Integrating Ecological and Engineering Concepts of Resilience in Microbial Communities
journal, December 2015
- Song, Hyun-Seob; Renslow, Ryan S.; Fredrickson, Jim K.
- Frontiers in Microbiology, Vol. 6
Bacterial Adaptation through Loss of Function
journal, July 2013
- Hottes, Alison K.; Freddolino, Peter L.; Khare, Anupama
- PLoS Genetics, Vol. 9, Issue 7
RT-qPCR work-flow for single-cell data analysis
journal, January 2013
- Ståhlberg, Anders; Rusnakova, Vendula; Forootan, Amin
- Methods, Vol. 59, Issue 1
Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli
journal, June 2008
- Blount, Z. D.; Borland, C. Z.; Lenski, R. E.
- Proceedings of the National Academy of Sciences, Vol. 105, Issue 23
Whole Genome Amplification and De novo Assembly of Single Bacterial Cells
journal, September 2009
- Rodrigue, Sébastien; Malmstrom, Rex R.; Berlin, Aaron M.
- PLoS ONE, Vol. 4, Issue 9
Microbial heterogeneity affects bioprocess robustness: Dynamic single-cell analysis contributes to understanding of microbial populations
journal, October 2013
- Delvigne, Frank; Goffin, Philippe
- Biotechnology Journal, Vol. 9, Issue 1
Biological robustness
journal, November 2004
- Kitano, Hiroaki
- Nature Reviews Genetics, Vol. 5, Issue 11
Global analysis of protein expression in yeast
journal, October 2003
- Ghaemmaghami, Sina; Huh, Won-Ki; Bower, Kiowa
- Nature, Vol. 425, Issue 6959
Competition and coexistence of sulfate-reducing and methanogenic populations in anaerobic biofilms.
journal, January 1996
- Raskin, L.; Rittmann, B. E.; Stahl, D. A.
- Applied and environmental microbiology, Vol. 62, Issue 10
Phenotypic Consequences of Promoter-Mediated Transcriptional Noise
journal, December 2006
- Blake, William J.; Balázsi, Gábor; Kohanski, Michael A.
- Molecular Cell, Vol. 24, Issue 6
Marine microbial community dynamics and their ecological interpretation
journal, February 2015
- Fuhrman, Jed A.; Cram, Jacob A.; Needham, David M.
- Nature Reviews Microbiology, Vol. 13, Issue 3
Noise Facilitates Transcriptional Control under Dynamic Inputs
journal, January 2015
- Kellogg, Ryan A.; Tay, Savaş
- Cell, Vol. 160, Issue 3
Erosion of functional independence early in the evolution of a microbial mutualism
journal, September 2014
- Hillesland, K. L.; Lim, S.; Flowers, J. J.
- Proceedings of the National Academy of Sciences, Vol. 111, Issue 41
Computational analysis of cell-to-cell heterogeneity in single-cell RNA-sequencing data reveals hidden subpopulations of cells
journal, January 2015
- Buettner, Florian; Natarajan, Kedar N.; Casale, F. Paolo
- Nature Biotechnology, Vol. 33, Issue 2
Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells
journal, July 2010
- Taniguchi, Y.; Choi, P. J.; Li, G. -W.
- Science, Vol. 329, Issue 5991
Mechanism for microbial population collapse in a fluctuating resource environment
journal, March 2017
- Turkarslan, Serdar; Raman, Arjun V.; Thompson, Anne W.
- Molecular Systems Biology, Vol. 13, Issue 3
Rapid Transposon Liquid Enrichment Sequencing (TnLE-seq) for Gene Fitness Evaluation in Underdeveloped Bacterial Systems
journal, September 2013
- Fels, Samuel R.; Zane, Grant M.; Blake, Sean M.
- Applied and Environmental Microbiology, Vol. 79, Issue 23
The Evolution of Ecological Specialization
journal, November 1988
- Futuyma, D. J.; Moreno, G.
- Annual Review of Ecology and Systematics, Vol. 19, Issue 1
Stochastic mechanisms in gene expression
journal, February 1997
- McAdams, H. H.; Arkin, A.
- Proceedings of the National Academy of Sciences, Vol. 94, Issue 3
Annual community patterns are driven by seasonal switching between closely related marine bacteria
journal, February 2017
- Ward, Christopher S.; Yung, Cheuk-Man; Davis, Katherine M.
- The ISME Journal, Vol. 11, Issue 6
Violin Plots: A Box Plot-Density Trace Synergism
journal, May 1998
- Hintze, Jerry L.; Nelson, Ray D.
- The American Statistician, Vol. 52, Issue 2
Knockout and pullout recombineering for naturally transformable Burkholderia thailandensis and Burkholderia pseudomallei
journal, July 2011
- Kang, Yun; Norris, Michael H.; Wilcox, Bruce A.
- Nature Protocols, Vol. 6, Issue 8
Generic Indicators for Loss of Resilience Before a Tipping Point Leading to Population Collapse
journal, May 2012
- Dai, L.; Vorselen, D.; Korolev, K. S.
- Science, Vol. 336, Issue 6085
ASYMMETRIC, BIMODAL TRADE-OFFS DURING ADAPTATION OF METHYLOBACTERIUM TO DISTINCT GROWTH SUBSTRATES
journal, November 2009
- Lee, Ming-Chun; Chou, Hsin-Hung; Marx, Christopher J.
- Evolution, Vol. 63, Issue 11
Rapid evolution of stability and productivity at the origin of a microbial mutualism
journal, January 2010
- Hillesland, K. L.; Stahl, D. A.
- Proceedings of the National Academy of Sciences, Vol. 107, Issue 5
Microorganisms with Novel Dissimilatory (Bi)Sulfite Reductase Genes Are Widespread and Part of the Core Microbiota in Low-Sulfate Peatlands
journal, December 2010
- Steger, Doris; Wentrup, Cecilia; Braunegger, Christina
- Applied and Environmental Microbiology, Vol. 77, Issue 4
Beanplot: A Boxplot Alternative for Visual Comparison of Distributions
journal, January 2008
- Kampstra, Peter
- Journal of Statistical Software, Vol. 28, Issue Code Snippet 1
Biogeochemical Hot Spots and Hot Moments at the Interface of Terrestrial and Aquatic Ecosystems
journal, June 2003
- McClain, Michael E.; Boyer, Elizabeth W.; Dent, C. Lisa
- Ecosystems, Vol. 6, Issue 4
The population genetics of ecological specialization in evolving Escherichia coli populations
journal, October 2000
- Cooper, Vaughn S.; Lenski, Richard E.
- Nature, Vol. 407, Issue 6805
Growth of Desulfovibrio in Lactate or Ethanol Media Low in Sulfate in Association with H2-Utilizing Methanogenic Bacteria
journal, January 1977
- Bryant, M. P.; Campbell, L. Leon; Reddy, C. A.
- Applied and Environmental Microbiology, Vol. 33, Issue 5
Works referencing / citing this record:
Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level
journal, September 2017
- Chen, Zixi; Chen, Lei; Zhang, Weiwen
- Frontiers in Microbiology, Vol. 8
Tools for Genomic and Transcriptomic Analysis of Microbes at Single-Cell Level
journal, September 2017
- Chen, Zixi; Chen, Lei; Zhang, Weiwen
- Frontiers in Microbiology, Vol. 8