Team profile by Ze-Yi Han

Microbial communities (i.e., collections of microbes and their interactions) play a crucial role in the global carbon cycle that sets the pace of global climate change. These communities can also evolve rapidly in response to a changing environment. However, we still lack the understanding of the mechanisms through which rapid evolution in complex microbial food webs mediates their responses to global warming. The challenges to the field rise from simultaneously keeping track of rapid evolution at genetic level and ecological processes at community level.

The Gibert lab has been using protists (unicellular eukaryotes) to compose food webs in microcosms to understand how changes in climate, such as warming and eutrophication, affect microbial food webs. To address the challenge of linking genes to community-level interactions, the Gibert lab is collaborating with the Onishi lab, a cell biology lab, and the Ciocanel lab, a mathematical biology lab, to 1) study the rapid evolution and cell-mechanism underpinning it using the model organism Chlamydomonas reinhardtii; and 2) use math modeling to predict the effects of rapid evolution on microbial food webs under warming conditions. 

Our project team is composed of math, ecology and cell biology subteams that work both collaboratively and independently. Together, our project team uses math models to generate testable predictions. We also set up trackable microcosms to understand how rapid evolution and warming affects microbial food web dynamics using DNA sequencing data as well as ecological data. Specifically, we aim to address the following questions:

• How do microbial food web structure (e.g., number of species and trophic levels) and genetic diversity affect rapid evolution in the algae prey C. reinhardtii?
• What are the effects of rapid evolution of prey on microbial food webs and what traits mediate these effects?
• How does temperature influence these processes? 

The Math Team designed models with differential equations and individual-based models to model the interaction between predators and algal prey. The math team worked with the Cell Biology Team to design models that are biologically sound. Their models tracked population growth and account for rapid evolution of traits that mediate interactions between C. reinhardtii and its predators across temperatures. Their key results show that changes in temperature can lead to different evolutionary outcomes when the prey genotypes have different thermal performance. 

The Ecology Team set up microcosm experiments to address the project’s goals empirically. They worked with the Math Team so that their manipulations matched theoretical assumptions. They also worked with the Cell Biology Team to sample experimental microcosms for DNA extraction. They also generated time series data of population dynamics and changes in cell traits (cell shape, size, and optical properties). 

Then, the Ecology Team used a combination of statistical approaches to analyze these data. Students on this team also ran an independent experiment looking at how different protist predators affect C. reinhardtii plastic response. They key results showed that higher genetic diversity increases prey population, especially in the absence of predators. Higher predator diversity led to decreased variation in population size of the prey. 

The Cell Biology Team worked closely with the Ecology Team to extract DNA from experimental samples and prepare it for next-generation sequencing. They also are the main force addressing any technical issues with DNA extraction and PCR. One of the biggest challenges we had arose from differences between the experimental methods of cell biology and ecology, which are the differences we aim to bridge. The density of our focal species C. reinhardtii in standard culture conditions of the cell biology lab and the experimental microcosm that mimics natural food webs of the ecology lab differed by multiple magnitudes. Inevitably, this made existing DNA extraction and PCR protocols unsuitable for our experiments. Despite the difficulties, the Cell Biology team designed robust methods and generated excellent DNA sequencing results. 

In the future, our project team will continue data analysis on the existing data. We will also set up a large-scale microcosm composed of 300+ microcosms to collect more data about warming effects on microbial food web dynamics and on the underlying rapid evolution. 

Warming Effects on Microbial Food Webs — From Genes to Ecosystems

Poster by Ze-Yi Han, Daniel J. Wieczynski, Yaning Yuan, Enzo Bruscato, Matilde M. Giglietti, Anushka Goel, Nick Sortisio, Luca Tjossem, Haipei Yao, Andrea Yammine, Veronica Ciocanel, Masayuki Onishi and Jean Philippe Gibert