- Email: [email protected]
Bacterial Adaptation in Structured Environments: Lessons from Darwin’s Finches
TIMI 1892 No. of Pages 2
Trends in
Microbiology Spotlight include quorum sensing and c-di-GMP signaling. Quorum sensing involves intercellular communication involving extracellular signals, while c-di-GMP is an important cytoplasmic secondary messenger. In this organism, these regulatory mechanisms are closely intertwined at the molecular 1 Joe J. Harrison, level. The quorum sensing signal synthase, 2, Matthew R. Parsek , * and RpfF, is capable of interacting with a pivotal Boo Shan Tseng3,* c-di-GMP signaling protein RpfR. In addition, the quorum sensing signal itself interIntricate gene regulatory networks acts with RpfR and these interactions control the transition between the determine whether RpfR either makes or planktonic and biofilm lifestyles in degrades c-di-GMP [3]. This is important bacteria. New evidence from Mhatre as high levels of intracellular c-di-GMP proet al. uncovers how various adaptive mote biofilm growth, while low levels favor mutations that arose in a key gene at biofilm dispersion and motility [4].
Bacterial Adaptation in Structured Environments: Lessons from Darwin’s Finches
the nexus of signaling networks in Burkholderia cenocepacia led to the emergence of lineages with different ecological roles, enabling stable coexistence of multiple genotypes and increasing productivity of the community. How bacteria integrate external signals that ultimately lead to the transition from the planktonic to the biofilm lifestyle is a major question in the biofilm field. Since switching between sessile and motile states is important for overall fitness, which genes are used by bacteria to control this transition? An article recently published in PNAS by Mhatre and colleagues [1], entitled ‘One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity’, shines light on this process by evaluating the functional outcomes of adaptive mutations that arise over time during biofilm evolution experiments with Burkholderia cenocepacia. B. cenocepacia, an opportunistic pathogen that is known to cause chronic infections in compromised individuals, engages in a variety of community-level behaviors that impact its pathogenicity [2]. The two global regulatory mechanisms by which this pathogen controls community-level behavior
The central question addressed by Mhatre et al. [1] is which adaptive mutations occur during prolonged in vitro biofilm growth of B. cenocepacia. The authors used a convenient and clever plastic bead model for biofilm culturing, where beads harboring biofilms were serially passaged daily over the course of weeks. DNA sequencing revealed that rpfR was the focal point of adaptive mutation. In separate, parallelly performed evolution experiments, common point mutations at different positions were observed in rpfR that led to altered activity in different ways. That adaptive mutations would occur over the course of repeated culture passage is not surprising. What was interesting is that: (i) different adaptive mutations in rpfR produced different functional outcomes for the microorganism; and (ii) genetic diversification that occurs through rpfR resulted in the generation of variants that could not only coexist, but together also increase the biofilm growth yield beyond that which any single rpfR allele could produce.
long been recognized [5]. Single mutations in global regulatory genes can impart pleiotropic phenotypic changes that could be beneficial in stable environments. For example, in Pseudomonas aeruginosa, the gene encoding the global quorum sensing regulator, lasR has been commonly reported to undergo inactivating mutations during chronic infections [6]. The fitness benefits conferred by such mutations are unclear. In B. cenocepacia, the global regulator rpfR lies at the nexus of two global regulatory systems that can influence a range of physiological properties. This makes it a logical target for adaptive mutation, as the authors have clearly shown [1]. A prediction moving forward would be that for any organism with defined global regulatory networks that intersect, regulators at these intersection points might be ideal candidates for maximizing the payoff for adaptive mutation.
Studying adaptive mutation in bacteria traditionally involves subjecting planktonic cultures to conditions of interest and identifying mutations that occur over time. This approach has been used effectively by Lenski and others to gain insight into the nature of selective pressures in different environments [7]. Perhaps one of the most fascinating aspects of this paper is that in structured systems, not only do different adaptive mutations that occur within rpfR coexist, but they also increase the carrying capacity of biomass in the system [1]. This finding implies that these mutants occupy different niches in the system. Indeed, they found that one consequence of coexistence is a profound impact on biofilm structure. Coexisting mutants were able to occupy more 3D space than any single mutant. Although the authors cannot be certain as to the mechaThe paper’s findings raise some interesting nism behind this genotypic synergy, they points. One pertains to an organism’s ability make some tantalizing speculations. They to maximize its phenotypic diversity through observed that different mutants produced adaptive mutation. Along these lines, the different levels/types of exopolysaccharides idea that global regulatory genes serve as (EPS), suggesting that EPS contributions great targets for adaptive mutation has by coexisting mutants might involve both Trends in Microbiology, Month 2020, Vol. xx, No. xx
1
Trends in Microbiology
adaptive point mutations are observed. Finally, trying to pinpoint the mechanisms that underlie the coexistence of adaptive mutant strains will be both challenging and important. This obviously will require further in vitro experimentation. The reward could be to help reveal some of the basic principles of biofilm community assembly and genotypic synergy/antagonism that undoubtedly govern natural systems.
1
Trends in Microbiology
Figure 1. Adaptive Radiation in Finches and Bacteria Are Governed by Variation in Global Gene Regulators. (A) Niche partitioning in Darwin’s finches led to beak shape diversity, which has been associated with variation in gene regulators affecting craniofacial development (left to right, the gray warbler, common cactus, and large ground finches) [8,9]. (B) Colony morphology phenotypes of different rpfR mutations. Analogous niche partitioning enables coexisting adaptive diversity in biofilms; this radiation is linked to mutations in the gene regulator RpfR [1]. (Credit: Jesse Horne for original scientific illustration.)
Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada Department of Microbiology, University of Washington, Seattle, WA 98155 3 Department of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154 2
*Correspondence: [email protected] (M.R. Parsek) and [email protected] (B.S. Tseng). https://doi.org/10.1016/j.tim.2020.10.010
compensation for and augmentation of biofilm matrix production. This study reveals the importance of studying adaptive mutation in structured systems, as well as some of the limitations of similar studies conducted in well-mixed liquid culture.
tractability that can reveal the remarkable breadth of biochemical functional space that a gene regulator can occupy.
Moving forward, some of the challenges are clear. In chronic infections caused by B. cenocepacia, where the existence Observations of niche differentiation in of structured microbial communities has biofilms are analogous to an important been documented, do similar adaptations historical precedent in ecology and evolu- and evidence of their coexistence exist? tionary biology (Figure 1). Darwin’s finches This will require careful analyses of longitudiprovided fundamental insights into adaptive nal collections of B. cenocepacia strains radiation in heterogenous environments taken from people suffering from chronic inleading to ecological diversification and co- fections. It is also important to consider the existence. The beak shape diversity that fitness of B. cenocepacia adaptative mutaenables foraging for different food types tions in the context of multispecies chronic has been linked to allelic variation in gene infections, such as those observed in cystic regulators affecting craniofacial develop- fibrosis. Different coexisting adaptive mument, such as ALX1 and HMGA2 [8,9]. tant strains might have to compete with Although it can be more challenging to other species within different niches present observe behaviors that provide selective in the system. The fitness of individual adapbenefits to bacterial variants, a key advan- tive mutants relative to competing species tage of studying bacteria is the genetic could impact the frequency at which these
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Trends in Microbiology, Month 2020, Vol. xx, No. xx
© 2020 Elsevier Ltd. All rights reserved.
References 1. Mhatre, E. et al. (2020) One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity. Proc. Natl. Acad. Sci. U. S. A. 117, 21647–21657 2. Vial, L. et al. (2011) The various lifestyles of the Burkholderia cepacia complex species: a tribute to adaptation. Environ. Microbiol. 13, 1–12 3. Deng, Y. et al. (2012) Cis-2-dodecenoic acid receptor RpfR links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover. Proc. Natl. Acad. Sci. U. S. A. 109, 15479–15484 4. Srivastava, D. and Waters, C.M. (2012) A tangled web: regulatory connections between quorum sensing and cyclic Di-GMP. J. Bacteriol. 194, 4485–4493 5. Philippe, N. et al. (2007) Evolution of global regulatory networks during a long-term experiment with Escherichia coli. BioEssays 29, 846–860 6. Smith, E.E. et al. (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl. Acad. Sci. U. S. A. 103, 8487–8492 7. Lenski, R.E. and Travisano, M. (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Natl. Acad. Sci. U. S. A. 91, 6808–6814 8. Lamichhaney, S. et al. (2016) A beak size locus in Darwin’s finches facilitated character displacement during a drought. Science 352, 470–474 9. Lamichhaney, S. et al. (2015) Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518, 371–375
Trends in
Microbiology Spotlight include quorum sensing and c-di-GMP signaling. Quorum sensing involves intercellular communication involving extracellular signals, while c-di-GMP is an important cytoplasmic secondary messenger. In this organism, these regulatory mechanisms are closely intertwined at the molecular 1 Joe J. Harrison, level. The quorum sensing signal synthase, 2, Matthew R. Parsek , * and RpfF, is capable of interacting with a pivotal Boo Shan Tseng3,* c-di-GMP signaling protein RpfR. In addition, the quorum sensing signal itself interIntricate gene regulatory networks acts with RpfR and these interactions control the transition between the determine whether RpfR either makes or planktonic and biofilm lifestyles in degrades c-di-GMP [3]. This is important bacteria. New evidence from Mhatre as high levels of intracellular c-di-GMP proet al. uncovers how various adaptive mote biofilm growth, while low levels favor mutations that arose in a key gene at biofilm dispersion and motility [4].
Bacterial Adaptation in Structured Environments: Lessons from Darwin’s Finches
the nexus of signaling networks in Burkholderia cenocepacia led to the emergence of lineages with different ecological roles, enabling stable coexistence of multiple genotypes and increasing productivity of the community. How bacteria integrate external signals that ultimately lead to the transition from the planktonic to the biofilm lifestyle is a major question in the biofilm field. Since switching between sessile and motile states is important for overall fitness, which genes are used by bacteria to control this transition? An article recently published in PNAS by Mhatre and colleagues [1], entitled ‘One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity’, shines light on this process by evaluating the functional outcomes of adaptive mutations that arise over time during biofilm evolution experiments with Burkholderia cenocepacia. B. cenocepacia, an opportunistic pathogen that is known to cause chronic infections in compromised individuals, engages in a variety of community-level behaviors that impact its pathogenicity [2]. The two global regulatory mechanisms by which this pathogen controls community-level behavior
The central question addressed by Mhatre et al. [1] is which adaptive mutations occur during prolonged in vitro biofilm growth of B. cenocepacia. The authors used a convenient and clever plastic bead model for biofilm culturing, where beads harboring biofilms were serially passaged daily over the course of weeks. DNA sequencing revealed that rpfR was the focal point of adaptive mutation. In separate, parallelly performed evolution experiments, common point mutations at different positions were observed in rpfR that led to altered activity in different ways. That adaptive mutations would occur over the course of repeated culture passage is not surprising. What was interesting is that: (i) different adaptive mutations in rpfR produced different functional outcomes for the microorganism; and (ii) genetic diversification that occurs through rpfR resulted in the generation of variants that could not only coexist, but together also increase the biofilm growth yield beyond that which any single rpfR allele could produce.
long been recognized [5]. Single mutations in global regulatory genes can impart pleiotropic phenotypic changes that could be beneficial in stable environments. For example, in Pseudomonas aeruginosa, the gene encoding the global quorum sensing regulator, lasR has been commonly reported to undergo inactivating mutations during chronic infections [6]. The fitness benefits conferred by such mutations are unclear. In B. cenocepacia, the global regulator rpfR lies at the nexus of two global regulatory systems that can influence a range of physiological properties. This makes it a logical target for adaptive mutation, as the authors have clearly shown [1]. A prediction moving forward would be that for any organism with defined global regulatory networks that intersect, regulators at these intersection points might be ideal candidates for maximizing the payoff for adaptive mutation.
Studying adaptive mutation in bacteria traditionally involves subjecting planktonic cultures to conditions of interest and identifying mutations that occur over time. This approach has been used effectively by Lenski and others to gain insight into the nature of selective pressures in different environments [7]. Perhaps one of the most fascinating aspects of this paper is that in structured systems, not only do different adaptive mutations that occur within rpfR coexist, but they also increase the carrying capacity of biomass in the system [1]. This finding implies that these mutants occupy different niches in the system. Indeed, they found that one consequence of coexistence is a profound impact on biofilm structure. Coexisting mutants were able to occupy more 3D space than any single mutant. Although the authors cannot be certain as to the mechaThe paper’s findings raise some interesting nism behind this genotypic synergy, they points. One pertains to an organism’s ability make some tantalizing speculations. They to maximize its phenotypic diversity through observed that different mutants produced adaptive mutation. Along these lines, the different levels/types of exopolysaccharides idea that global regulatory genes serve as (EPS), suggesting that EPS contributions great targets for adaptive mutation has by coexisting mutants might involve both Trends in Microbiology, Month 2020, Vol. xx, No. xx
1
Trends in Microbiology
adaptive point mutations are observed. Finally, trying to pinpoint the mechanisms that underlie the coexistence of adaptive mutant strains will be both challenging and important. This obviously will require further in vitro experimentation. The reward could be to help reveal some of the basic principles of biofilm community assembly and genotypic synergy/antagonism that undoubtedly govern natural systems.
1
Trends in Microbiology
Figure 1. Adaptive Radiation in Finches and Bacteria Are Governed by Variation in Global Gene Regulators. (A) Niche partitioning in Darwin’s finches led to beak shape diversity, which has been associated with variation in gene regulators affecting craniofacial development (left to right, the gray warbler, common cactus, and large ground finches) [8,9]. (B) Colony morphology phenotypes of different rpfR mutations. Analogous niche partitioning enables coexisting adaptive diversity in biofilms; this radiation is linked to mutations in the gene regulator RpfR [1]. (Credit: Jesse Horne for original scientific illustration.)
Department of Biological Sciences, University of Calgary, Calgary, Alberta, Canada Department of Microbiology, University of Washington, Seattle, WA 98155 3 Department of Life Sciences, University of Nevada Las Vegas, Las Vegas, NV 89154 2
*Correspondence: [email protected] (M.R. Parsek) and [email protected] (B.S. Tseng). https://doi.org/10.1016/j.tim.2020.10.010
compensation for and augmentation of biofilm matrix production. This study reveals the importance of studying adaptive mutation in structured systems, as well as some of the limitations of similar studies conducted in well-mixed liquid culture.
tractability that can reveal the remarkable breadth of biochemical functional space that a gene regulator can occupy.
Moving forward, some of the challenges are clear. In chronic infections caused by B. cenocepacia, where the existence Observations of niche differentiation in of structured microbial communities has biofilms are analogous to an important been documented, do similar adaptations historical precedent in ecology and evolu- and evidence of their coexistence exist? tionary biology (Figure 1). Darwin’s finches This will require careful analyses of longitudiprovided fundamental insights into adaptive nal collections of B. cenocepacia strains radiation in heterogenous environments taken from people suffering from chronic inleading to ecological diversification and co- fections. It is also important to consider the existence. The beak shape diversity that fitness of B. cenocepacia adaptative mutaenables foraging for different food types tions in the context of multispecies chronic has been linked to allelic variation in gene infections, such as those observed in cystic regulators affecting craniofacial develop- fibrosis. Different coexisting adaptive mument, such as ALX1 and HMGA2 [8,9]. tant strains might have to compete with Although it can be more challenging to other species within different niches present observe behaviors that provide selective in the system. The fitness of individual adapbenefits to bacterial variants, a key advan- tive mutants relative to competing species tage of studying bacteria is the genetic could impact the frequency at which these
2
Trends in Microbiology, Month 2020, Vol. xx, No. xx
© 2020 Elsevier Ltd. All rights reserved.
References 1. Mhatre, E. et al. (2020) One gene, multiple ecological strategies: a biofilm regulator is a capacitor for sustainable diversity. Proc. Natl. Acad. Sci. U. S. A. 117, 21647–21657 2. Vial, L. et al. (2011) The various lifestyles of the Burkholderia cepacia complex species: a tribute to adaptation. Environ. Microbiol. 13, 1–12 3. Deng, Y. et al. (2012) Cis-2-dodecenoic acid receptor RpfR links quorum-sensing signal perception with regulation of virulence through cyclic dimeric guanosine monophosphate turnover. Proc. Natl. Acad. Sci. U. S. A. 109, 15479–15484 4. Srivastava, D. and Waters, C.M. (2012) A tangled web: regulatory connections between quorum sensing and cyclic Di-GMP. J. Bacteriol. 194, 4485–4493 5. Philippe, N. et al. (2007) Evolution of global regulatory networks during a long-term experiment with Escherichia coli. BioEssays 29, 846–860 6. Smith, E.E. et al. (2006) Genetic adaptation by Pseudomonas aeruginosa to the airways of cystic fibrosis patients. Proc. Natl. Acad. Sci. U. S. A. 103, 8487–8492 7. Lenski, R.E. and Travisano, M. (1994) Dynamics of adaptation and diversification: a 10,000-generation experiment with bacterial populations. Proc. Natl. Acad. Sci. U. S. A. 91, 6808–6814 8. Lamichhaney, S. et al. (2016) A beak size locus in Darwin’s finches facilitated character displacement during a drought. Science 352, 470–474 9. Lamichhaney, S. et al. (2015) Evolution of Darwin’s finches and their beaks revealed by genome sequencing. Nature 518, 371–375