Ecology and Evolution

Regulation, evolution and resilience of microbial communities

Managing tradeoffs through gene regulation is believed to confer resilience to a microbial community in a fluctuating resource environment. Microbial generalists are metabolically versatile and able to cope with periodically or randomly fluctuating natural environments by up- or down-regulating genes to optimize resource utilization. However, it is generally assumed and not demonstrated whether or how regulatory mutations foster adaptive evolution to new environments. We investigate these questions in an environmentally significant context in which a sulfate-reducing generalist (Desulfovibrio vulgaris) has to manage the tradeoff between retaining metabolic independence (active capacity for sulfate respiration) and becoming metabolically specialized to a mutualistic association with a methanogen (Methanococcus maripaludis) when sulfate is not available. During long term experimental evolution and even in anaerobic digesters, a microbial culture or community experiences frequent, iterative changes and bottlenecks due to growth and successive transfers to new media (Chen et al, 2008; Demirel & Yenigün, 2002). We have demonstrated how disrupted regulation stabilizes frequent transitions of a generalist between metabolic independence and mutualism, fostering its longer term adaptive evolution in a fluctuating resource environment. Further, we provide evidence that the population collapse occurs due to loss of relational resilience, i.e., progressive drift from the environmentally-relevant physiological state (Fuhrman et al, 2015). Our studies in this project led to manuscripts Turkarslan et al., 2017.



Brooks, Aaron N., Serdar Turkarslan, Karlyn D. Beer, Fang Yin Lo, and Nitin S. Baliga. “Adaptation of Cells to New Environments.” Wiley Interdisciplinary Reviews. Systems Biology and Medicine 3, no. 5 (October 2011): 544–61. Cite
Turkarslan, Serdar, David J. Reiss, Goodwin Gibbins, Wan Lin Su, Min Pan, J. Christopher Bare, Christopher L. Plaisier, and Nitin S. Baliga. “Niche Adaptation by Expansion and Reprogramming of General Transcription Factors.” Molecular Systems Biology 7 (2011): 554. Cite
Hillesland, Kristina L., Sujung Lim, Jason J. Flowers, Serdar Turkarslan, Nicolas Pinel, Grant M. Zane, Nicholas Elliott, et al. “Erosion of Functional Independence Early in the Evolution of a Microbial Mutualism.” Proceedings of the National Academy of Sciences of the United States of America 111, no. 41 (October 14, 2014): 14822–27. Cite
Thompson, Anne W., Matthew J. Crow, Brian Wadey, Christina Arens, Serdar Turkarslan, Sergey Stolyar, Nicholas Elliott, et al. “A Method to Analyze, Sort, and Retain Viability of Obligate Anaerobic Microorganisms from Complex Microbial Communities.” Journal of Microbiological Methods 117 (October 2015): 74–77. Cite
Beer, Karlyn D., Elisabeth J. Wurtmann, Nicolas Pinel, and Nitin S. Baliga. “Model Organisms Retain an ‘Ecological Memory’ of Complex Ecologically Relevant Environmental Variation.” Applied and Environmental Microbiology 80, no. 6 (March 2014): 1821–31. Cite