Research Agenda

Technical overview of biological research

The effects of anthropogenic forces such as climate change and urbanization on higher-order structures and functions of biological systems is a major focus of research in ecology and evolution. However, one emerging anthropogenic force is the development and release of bioengineered organisms into the environment. Tools such as metabolic engineering, gene editing, and synthetic cells are being used to create novel bioindustrial, biomedical, and agricultural products for release into natural systems. Yet, the environmental effects of such organisms on ecological processes such as community assembly and ecosystem function has been largely unexplored. Introduced genetic variation through bioengineering has the potential to alter species’ traits far beyond what might otherwise be constrained by eco-evolutionary processes, yet we lack a theoretical basis to predict their long-term effects on ecological communities and ecosystems. 

As both an ecologist and bioengineer, my research describes how the introduction of bioengineered organisms influences community and ecosystem processes in naturally-occurring microbial systems. I use two approaches: 

1. Genetic engineering: I use reverse genetics (gene editing) and forward genetics (experimental evolution) to generate bioengineered microbes that exhibit a phenotypic range of functional traits. 

2. Community ecology: I then use methods in ecology to study the community and ecosystem effects of these bioengineered traits.

Prior Research

In my PhD, I studied the assembly of both ecological and social communities in the life sciences. My dissertation research included typical ecological research as well as community-engaged art and activism. 

First, I aimed to reimagine the current scientific enterprise within its own terms. By publishing scientific papers that center scientific art,  intergenerational mentorship, and celebration of diverse lived experiences within academic science, I showed that science can flourish from diverse, equitable, and interdisciplinary groups. The topic of my research primarily focused on the assembly of microbial communities in the nectar of a California wildflower, Diplacus aurantiacus. By applying population genetics, functional genomics, and experimental evolution to this wild microbiome, I identified mechanisms that connect genetic variation to community-level processes such as priority effects and show that population-level variation can alter molecular traits associated with community assembly. 

Second, I questioned the academic structure as the central nexus for scientific discovery. By dissolving the duality between science and art, creating new science spaces that center culture and lived experience, and reimagining entire educational ecosystems outside of "traditional" scientific venues, I proposed new frameworks for how science can be conducted and perhaps, what we consider science to be. 

Publications

1.     C.R. Chappell, R.C. Perez, C. Takara*, Growing biodesign ecosystems: Community exchange spaces advance biotechnology innovation. Research Directions: Biotechnology Design. 1, e13 (2023).

2. C.R. Chappell, L.J. Muglia, Fostering science-art collaborations: A toolbox of resources. PLOS Biology, 21, 2, e3001992 (2023).

3.     C. R. Chappell, M.K. Dhami, M.C. Bitter, L.C. Czech, S.H. Parades, F.B. BarrieX, Y. CalderónX, K. EritanoX, L-A. GoldenX, D. Hekmat-Scafe, V. HsuX, C. KieschnickX, S. Malladi, N. Rush, T. Fukami, Wide-ranging consequences of priority effects governed by an overarching factor. eLife 11, e79647 (2022).

4.     C.R. Chappell, R.C. Perez, C. Takara*, Bioengineering everywhere, for everyone Issues in Science and Technology. 38, 3, 88-90 (2022).

5.     S. Li, S. A. Newmister, A. N. Lowell, J. Zi, C. R. Chappell, F. Yu, R. M. Hohlman, J. Orjala, R. M. Williams, D. H. Sherman, Control of Stereoselectivity in Diverse Hapalindole Metabolites is Mediated by Cofactor-Induced Combinatorial Pairing of Stig Cyclases. Angewandte Chemie International Edition. 59, 8166–8172 (2020).

6.     C. R. Chappell, T. Fukami, Nectar yeasts: a natural microcosm for ecology.Yeast. 35, 417–423 (2018).

X = Undergraduate mentee

* = Non-academic community collaborator

Research mentorship and service

As a graduate student, I led a team of 15+ undergraduate researchers from both Stanford and minority-serving institutions. This collaborative team, which operated like a lab-within-a-lab, centered researcher autonomy, transformative justice, and wellness. 

Read a blog post we collaboratively wrote about our mentorship program published on Dynamic Ecology here. 

Areas of interest

Microbial community ecology

Genetic variation influences individual phenotypes, but it is not fully understood how it affects processes above the level of the individual: species interactions, community assembly, and ecosystem processes. To address these gaps, in my dissertation I studied how genetic variation influences species' traits that govern ecological community assembly. Assembly history structures the diversity, richness, and functioning of ecosystems. In particular, priority effects, where the order and timing of species arrival influences communities, have often been overlooked. I used an established system, nectar-inhabiting microbes, to explore how intraspecific genetic variation influences community assembly across spatially-structured landscapes. By applying population genetics, multi-omics, and experimental evolution to this wild microbiome, I (a) showed that population-level variation can alter community assembly and (b) identifyed mechanisms that connect genetic variation to community-level processes such as priority effects. 

In the first part of my PhD, I studied the effects of intraspecific (population-level) variation on yeasts' molecular response to priority effects. Previously, 102 strains of nectar yeast, Metschnikowia reukaufii, were isolated and genotyped from Mimulus aurantiacus plants growing throughout the Greater Bay Area. I studied how population-level variation in these yeast influenced their response to competition from another yeast species, Metschnikowia rancensis. Using RNA-seq, I found that population structure strongly influences yeasts' transcriptomic response to priority effects. In the same experiment, I also conducted targeted and untargeted metabolomics to study how genetic variation affects the catabolism and production of secondary metabolites, a mechanism of priority effects. 

In the second part of my PhD, I examined how priority effects imposed by a bacterial competitor, Acinetobacter nectaris, might affect the evolution of the nectar yeast, M. reukaufii. This work was motivated by field and laboratory data that established that nectar bacteria negatively influence the growth of nectar yeast by reducing nectar pH. I experimentally evolved nectar yeast, and found that yeast evolved in low pH nectar indeed better resisted priority effects by bacteria than ancestral yeast or yeast evolved in a neutral nectar environment. After sequencing the evolved yeast, I was able to identify genomic variants underlying differential evolutionary strategies to resist priority effects. Specifically, yeast evolved resistance to nectar bacteria through loss of heterozygosity and accumulation of de novo mutations. 

My research suggests that intraspecific genetic variation not only determines how individuals respond to competition, but also has cascading impacts on how communities assemble. By integrating ecology and evolution across multiple scales--taxonomic, temporal, and spatial--I found that population structure influences individuals' molecular response to competition, and in turn, processes such as community assembly can drive rapid evolution. This work affirms that we must look across short and long timescales, individual patches and spatially-structured habitats, to understand processes that span levels of taxonomic organization.

Natural products bioengineering

As a master’s student in the Molecular, Cellular, and Developmental Biology (University of Michigan), I worked in the lab of David Sherman (Department of Chemistry, Department of Microbiology and Immunology) investigating the biosynthesis of indole alkaloid natural products in cyanobacteria. We  found that a cluster of non-heme Rieske oxygenases and/or cytochrome P450s catalyze critical diversification steps in the biosynthesis of hapalindoles, valuable natural products with known anti-cancer, antibacterial, and insecticidal qualities. I used heterologous expression in engineered E. coli, in vitro enzymatic assays, and analytical chemistry (LC-MS) to study the biochemistry of enzymes involved in hapalindole biosynthesis by cyanobacteria. 

Chemical ecology

As an undergraduate at the University of Michigan, I completed my Honors Thesis and a National Science Foundation Research Experience for Undergraduates (NSF REU) with Dr. Mark Hunter (Department of Ecology & Evolutionary Biology) at the University of Michigan Biological Station. In this research, I investigated the effects of elevated, atmospheric carbon dioxide on plant chemistry, specifically two milkweed species, Asclepias syriaca (common milkweed) and Asclepias speciosa (showy milkweed), and how this changing plant chemistry may mediate plant-herbivore interactions with a specialist herbivore, Aphis nerii (Oleander aphid).

For this work, I won the Marshall Nirenberg Life Science Award, which is awarded to the top graduating student in the life sciences at the University of Michigan, and the Christine Psujek Memorial Undergraduate Award, which is awarded to the top honors thesis in the University of Michigan's Program in Biology. 

Read this article written in for the Department of Ecology and Evolutionary Biology’s Natural Selections newsletter for more information about my research in the Hunter lab.