Life has been busy, very busy. And life has been good! But the busy-ness has made it hard for me to keep up with this blog. In the next few weeks, I hope to share some of the things that have kept me so occupied this past month.
For starters, I’d like to discuss some recent teaching where I tried to emphasize the interplay between theory and experiments in ecology.
I recently taught part of our graduate-level course called “Integrative Microbial Biology.” Some years ago this course replaced several other graduate courses (microbial ecology, microbial physiology, microbial diversity, etc.) that each had a low enrollment. The idea is that we now offer a single, annual, intensive, team-taught course that covers all these topics, albeit more superficially but with the hope that it encourages students and faculty alike to develop a more integrated perspective of microorganisms as organisms. More specialized courses, with a focus on reading and discussion, are offered as occasional seminar-style courses.
I teach two parts of the course – one on aspects of microbial ecology, the other on microbial evolution. Many of the students have not had an undergraduate course in general ecology or evolutionary biology, and so I try to bring them up to speed, albeit with examples that focus on microorganisms.
So, for the ecology portion I begin with population growth and competition. I’m a fan of resource-based competition theory, as opposed to the more familiar logistic growth and Lotka-Volterra competition models. The key strength of resource-based competition theory is that one can predict the outcome of competition based on parameters that can be measured separately for each species or strain, without requiring that one compete them in order to understand their competition. Of course, there are many reasons the predictions might fail, but the resource-based model (and extensions to it) provide a mechanistic framework for understanding competition.
I then present predator-prey interactions, surveying the extraordinary diversity of microbe-on-microbe predation and parasitism, and then providing again a dynamical framework for understanding those interactions. Here, Lotka-Volterra predator-prey models do provide a reasonable starting point because one can measure key parameters that have mechanistic interpretations (e.g., attack rates, conversion efficiencies) and use them to make new predictions about the dynamics of the system as a whole.
Besides presenting the general theory, I also present empirical studies from the primary literature. In some cases, I summarize the papers in my lectures, while in other cases the students read the papers and we then discuss them. Here are four of the papers with summaries; I hope to blog someday in greater depth on at least the Hansen & Hubbell and Rainey & Travisano papers, which I view as “must-read” papers in the field of ecology.
This paper presented an early, concise, and compelling demonstration of the utility of resource-based competition theory. By choosing three pairs of competitors that differed in various parameters, and then competing them in chemostats, the authors showed that the outcome depended on the two competitors’ relative “break-even” (equilibrium) concentrations of the growth-limiting resource. For any student who wants more information on this approach – and every year at least some students ask for more – I recommend they read David Tilman’s outstanding book, Resource Competition and Community Structure (1982, Princeton University Press).
This paper is a beauty. The authors showed that the evolutionary emergence of diversity can sometimes depend on something as simple as whether a flask is shaken or not. In the absence of shaking, an initially monotypic population of Pseudomonas fluorescens evolved into a community of three distinct ecotypes that differentially exploit the environmental gradients that arise without constant mixing; that diversity is stably maintained, as was shown by analyzing pairwise interactions. By contrast, simply shaking the flask, with all else being equal, homogenizes the environment and the ecotypic diversity does not evolve; and if the diversity had already evolved, then it was eliminated as a single type came to dominate the well-mixed system.
Lenski, R. E., and B. R. Levin. 1985. Constraints on the coevolution of bacteria and virulent phage: a model, some experiments, and predictions for natural communities. American Naturalist 125:585-602.
Virulent phage infect bacteria, and they have life-cycles like those of insect parasitoids; that is, a successful infection is lethal to the host, and many phage are produced from a single infection. In this paper, we examined the ecological and evolutionary dynamics of the interactions between E. coli and four different virulent phages. First, the Lotka-Volterra predator-prey model – modified to include resource-based growth for the prey (bacteria) and a time-lag associated with predator reproduction (phage replicating inside bacteria) – predicted reasonably well the short-term dynamics of the interaction between E. coli and one of the phages, called T4. Second, the model was extended to include the evolution of bacteria that are resistant to phage attack. Resistance mutations changed the equilibrium density of the bacteria by several orders of magnitude, as the bacterial population went from top-down predator limitation to bottom-up resource limitation. Yet despite complete resistance, the phage population persisted because there was a “cost of resistance” – in the absence of phage, the sensitive bacteria out-competed the resistant mutants. In essence, the system becomes one of predator-mediated coexistence of sensitive and resistant prey populations. Third, the interactions between E. coli and three other phages were examined. Each interaction had somewhat different dynamics depending on whether resistance was costly or not, whether resistance was partial or complete, and whether the phage population produced host-range mutants that could infect the mutant bacteria that had become resistant to the progenitor phage. [This paper built on related work that Lin Chao had done a few years earlier with Bruce Levin, and which inspired me to contact Bruce about joining his lab.]
This paper reviews the research that Brendan Bohannan did for his dissertation in my lab. His work examined the same four bacteria-phage interactions studied in the Lenski and Levin paper above, but the work was extended to include some elegant new manipulations and analyses. In particular, by changing the levels of resource available to the bacteria, the classic “paradox of enrichment” predicted by Lotka-Volterra predator-prey models was confirmed, with respect to the effects of enrichment on both equilibrium densities and the temporal fluctuations in population densities. These experiments also provided compelling evidence for predator-prey cycles and the effects of bacterial resistance on the dynamics of the interaction between the remaining sensitive bacteria and phage populations.