Research projects
General overview: We study twenty-two communities of the bacterium Desulfovibrio vulgaris and the methanogen Methanococcus maripaludis. These communities evolved for over 2000 generations in conditions requiring their cooperation. The way D. vulgaris can gain energy in this environment, is by fermenting lactate, producing acetate, hydrogen and carbon dioxide as byproducts. This fermentation does not provide enough energy for growth under standard conditions. However, if the concentration of the products of this reaction is kept very low, the reaction provides more energy for growth. The methanogen consumes one of the reaction products - hydrogen - gaining energy by using it to reduce carbon dioxide to methane. The particular strains we use were originally isolated decades ago from very different environments and likely never cooperated with each other in their recent evolutionary history. Thus, these 22 communities and the samples frozen over time can show us how mutualists adapt in the first 5000 generations of reliance on a new interaction. The results of the first 300 generations was published in 2010. The original paper can be accessed here: Hillesland and Stahl, 2010. Commentaries on the work are here: Microbe magazine and Nature journal club. Further research can be found on our publications page.
Project area 1: Investigating origins of the Eukaryotic cell. This project is funded by the Moore Foundation.
One of the early stages of evolution of life on earth was the formation and evolution of cells. At some point, there were three major lineages, or domains of single-celled life forms - bacteria, archaea, and eukaryotes. Bacteria and archaea are very diverse single-celled species that can be found practically everywhere as long as you have a microscope or genetic tools to 'see' them. Multicellularity eventually evolved in eukaryotes and they represent pretty much every species you can see with the naked eye and some you cannot- plants, animals, insects, mold, fungi, algae, protists, amoebae, and humans. A current hypothesis is that eukaryotes evolved from an archaeal clade called the 'Aasgard archaea'. A key step in this evolution was the origin of the mitochondria. The mitochondria is the powerhouse of the eukaryotic cell, generating energy for all of its cellular functions. It is therefore very important to the functioning of eukaryotes. We know that the mitochondria's ancestor was a free-living bacteria that was eventually engulfed by a descendent of the First Eukaryotic Common Ancestor (FECA), an essential step in the evolution of the Last Eukaryotic Common Ancestor (LECA). There are several theories about how this happened. All of them seem to include the following two elements: The ancestor of the mitochondria and FECA became dependent on each other for survival because of a metabolic interaction, which could (but may not) include hydrogen exchange ; second, they developed a symbiosis, which is a physically intimate association for all or most of their life cycles.
Our research is focused on using experimental evolution to 'see' these events occur. We want to know how and how quickly the two species could become dependent on each other as they evolve together, and how symbiosis might affect the outcomes of evolution. To address these questions, we are studying the cocultures shown above at the phenotypic and genomic levels. In cooperation with the Kerr lab at UW Seattle, we are developing a mathematical model to determine how physical proximity might affect evolution and plan to test the model results in the lab.
Project area 2: Has coevolution affected the evolution of D. vulgaris and M. maripaludis in conditions that require them to depend on one another for survival?
If two species coevolve, then evolutionary changes in one species affects the others fitness, causing it to adapt to its partner's adaptation. The partner may then adapt in response. We have been exploring coevolution from a variety of angles. These include testing whether coevolution has occurred at the phenotypic level using timeshift experiments, testing whether D. vulgaris and M. maripaludis became locally-adapted to the specific partner they evolved with such that their fitness is lower with partners from other lines, and using genomics to look for potential signatures of coevolution at the molecular level. In a time-shift experiment, we pair an evolved population, say D. vulgaris that evolved for 1000 generations, with M. maripaludis partners from its evolutionary past and future. If there is coevolution, 1000-generation D. vulgaris will have different fitness with partners from different timepoints of evolution. If there is no coevolution, its fitness will be the same with all of their M. maripaludis partners. If populations have coevolved then they may have acquired adaptations that are unique to their partner's evolved phenotype, and thus may be most fit (locally adapted) to their evolved partner, in comparison to others that evolved in the same conditions but independently.
In addition to these phenotypic tests, we are also looking at how the genomes have changed over time. We have mini-metagenome sequences for several of these evolved communities at many timepoints in evolution. This shows us all of the alleles that became common over time for both species, allowing us to see the molecular dynamics of evolution. As controls, D. vulgaris and M. maripaludis were each propagated alone in near-identical conditions to the coculture evolution experiment. The genomes of these populations were also sequenced over time. By comparing the results of these controls with cocultures, we can determine which results represent generic evolutionary dynamics or adaptations that result from regular transfers, the temperature, media, etc. and which may be specific to evolution of mutualism. We are using this data to determine which mutations and population-genetic parameters may be specific to cooperative fermentation.
Why are we studying this? Despite the fact that mutually beneficial interactions (each species has a positive effect on the survival and reproduction of the other) are pervasive, rigorous tests of coevolution in these interactions have been rare. We seek to test this idea thoroughly to help provide insight on when coevolution happens, and when it does not. This work can help us to understand the process of evolution and how it has resulted in the incredible beauty and diversity of the biological world by telling us how much of that can be explained by species evolving in response to one another. Genomic analysis of the evolutionary dynamics of mutualisms is also rare.
Project area 3: Testing whether and why there is a tradeoff for D. vulgaris between maintaining sulfate respiration and flourishing in cooperative fermentation.
In the first 1000 generations of evolution in conditions that did not include sulfate but required cooperative fermentation with M. maripaludis, multiple independently-evolved populations acquired mutations that eliminated the function of genes required for sulfate respiration. At the same time, a very small subpopulation maintained this capability in these evolving mini-communities. Why was sulfate respiration lost? The fact that sulfate respiration was lost multiple times, and fairly quickly <1000 generations suggest that losing it may have a beneficial effect on fitness. We have been testing this hypothesis by competing sulfate-respiration mutants against wild-type cells. In addition, we have propagated D. vulgaris alone, without sulfate for 5000 generations to see if sulfate respiration will be lost when it is not involved in cooperative fermentation. In the future, we hope to learn more about why maintaining sulfate-respiration genes is favorable.