BEACON Researchers at Work: Ecology of an evolving bacterium

This week’s BEACON Researchers at Work blog post is by MSU graduate student Caroline Turner.

Every day, human activities release a wide variety of chemical compounds into the environment, from fertilizers and pesticides to pharmaceuticals and industrial waste.  Many of these compounds are produced only by humans and not otherwise found in natural environments. While some chemicals are benign, others are harmful to human and ecosystem health. For example, over 200 industrial chemicals present in the environment have been identified as neurotoxins that may cause learning disorders, cerebral palsy, and delayed development. Naturally, there is strong interest in removing these harmful compounds from the environment.

Image from: epa.state.il.us

Readers of the BEACON Center blog, knowing the importance of “Evolution in Action,” will not be surprised to learn that microbes can evolve the capacity to consume novel compounds produced by humans. These compounds can often act as an energy source, providing a selective benefit to any organisms able to consume them. For example, in groundwater contaminated with chlorobenzene, a solvent that is used in the production of herbicides and does not occur naturally, bacteria have evolved that consume the contaminant (van der Meer et al. 1996).

Microbes evolving to remove our waste from the environment are an example of evolution working to our benefit. This capacity can potentially be further enhanced by active attempts at bioremediation. However, because evolution in natural systems occurs in complex assemblages, we know very little about the evolutionary and ecological processes by which these novel pathways for consuming new compounds emerge and achieve high abundance. How do these novel degradative pathways affect the ecology and evolution of coexisting organisms? How do coexisting organisms affect the evolution of organisms which consume novel compounds? My research addresses these questions using a model system in which a novel metabolic pathway has evolved in the laboratory, where it can be further studied in great detail from evolutionary and ecological standpoints.

In 1988, my adviser, Dr. Richard Lenski, began the “Long-Term Evolution Experiment” (LTEE) with 12 populations of initially identical* Escherichia coli. Every day since then, the populations have been transferred to fresh growth media, for a total of over 50,000 generations of evolution. The growth medium has a limited amount of carbon (food) in the form of glucose for the bacteria, so each day bacterial growth stops when the glucose runs out. In addition to glucose, the growth medium also contains substantial amounts of citrate, another carbon molecule. However, E. coli are not capable of consuming citrate in the presence of oxygen, and that inability has long been recognized as a defining feature of this species.

Courtesy Brian Baer

Thus for the first 30,000 generations of the LTEE, all the E. coli lived solely on glucose. As you may have guessed, however, after 30,000 generations, the capacity to consume citrate arose in one of the 12 populations. This population no longer stopped growing when it ran out of glucose. Instead, it continued to grow using the now available citrate (Blount et al 2008). As a result this population reached a density several times that of any of the other populations. Interestingly, the group of bacteria that consume citrate (Cit+) coexisted with a second group that still could not use citrate (Cit-). I am using the evolution of the Cit+ group and the coexistence of the Cit- group as a model system to study the ecology and evolution associated with consumption of novel compounds.

So far I have been investigating how it is that Cit- bacteria are able to survive when the Cit+ population has access to both citrate and glucose while the Cit- cells can only consume glucose.  One possibility is that the evolution of citrate consumption involves a decrease in the ability of Cit+ cells to consume glucose. Cit- cells could then survive by outcompeting the Cit+ population for glucose.  Another possibility is that during their growth the Cit+ bacteria release one or more additional carbon sources into the medium and the Cit- bacteria survive by consuming this addition resource. This type of interaction between microbes is known as cross-feeding.

How can I test which of these possibilities is occurring? Imagine taking some Cit- bacteria from before the evolution of the Cit+ lineage (“early Cit-”) and growing them in a flask together with Cit- bacteria from after the evolution of the Cit+ lineage (“late Cit-”). The bacteria from the LTEE are frozen at regular intervals and can be revived, so this is an experiment I can actually do. If the Cit- bacteria persisted solely by being better competitors for glucose, then I would expect that the “late Cit-” cells would be equally as good as or better then the “early Cit-” cells at growing in glucose. On the other hand, if the “late Cit-” cells have evolved to cross-feed, then they will have an advantage against the “early Cit-” cells in the presence of the Cit+ population but not in their absence.

Thinking back to the evolution of microorganisms to consume novel compounds produced by humans, it may be important to consider the possibility for cross-feeding interactions to evolve. The consumption of novel compounds could affect not only the specific bacteria doing the consumption, but also the ecology and evolution of coexisting bacteria.

*Or rather nearly identical. They differed only in a neutral marker, a genetic change which does not affect competitive ability in the experiment, but which allows the populations with different marker states to be distinguished from each other.

References:

Blount, Z. D., C. Z. Borland, and R. E. Lenski. 2008. Historical contingency and the evolution of a key innovation in an experimental population of Escherichia coli. Proceedings of the National Academy of Sciences of the United States of America 105:7899-7906.

van der Meer et al. 1996. Evolution of a pathway for chlorobenzene metabolism leads to natural attenuation in contaminated groundwater. Applied and Environmental Microbiology 64(11): 4185-93

This research was developed under STAR Fellowship Assistance Agreement no. FP917112 awarded by the U.S. Environmental Protection Agency (EPA). It has not been formally reviewed by EPA and the views expressed are solely those of Caroline Turner. For more information, please contact Caroline at cturner at msu dot edu.

About Danielle Whittaker

Danielle J. Whittaker, Ph.D. Managing Director of BEACON
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