by Roberto
Fig. 1. Typical colorful bar graph showing microbial community composition in different samples. Source
Many present-day microbial ecology studies involve some sort of sequencing effort to determine which microbes are present in a sample. Almost invariably, such analyses of microbial communities involve determining the relative abundance of the different types of microbes present – from phyla to strains, depending on the study. The figure shows an example of such an analysis; I suspect most STC readers are quite familiar with these colorful bar graphs. (This one I selected randomly, thus the lack of any further description; just enjoy viewing if you will.)
It seems that during the last three decades, every conceivable ecosystem of Earth and its inhabitants has been thus explored. In a few instances, research is beginning to make inroads in understanding the functional significance of the composition of some communities. But for the most part, much of the information obtained only answers the question of who is there. There's precious little in terms of understanding how come a community has its particular composition; we still do not know much about the mechanistic details underlying microbial community ecology. In contrast, we know much – sometimes in exceedingly fine detail – about how some microbes, when analyzed in pure culture, function. How can we bridge this large gap in understanding? What will it take to understand (at least some) microbial communities the way we understand some model microbes? In a recent Journal of Bacteriology editorial, entitled "We have a community problem," George O'Toole points us in the direction of model synthetic microbial communities as a way forward. I could not agree more. I strongly believe that if several research groups rally behind a few model synthetic communities it is likely that fundamental and maybe even universal principles will emerge.
I also believe that as investigators dive deeply into the study of a few model microbial communities, they should be guided by a general theory of what drives the co-existence of different microbial types. Naively, one might think that for a given microbe to be maintained in a community at a characteristic abundance, it must be due to its having some selective advantages that allow it to be there and reach those numbers. But it clearly cannot be that simple; there are so many interactions to consider even in simplified communities! If fact, the mechanistic understanding of community ecology can at first sight appear mind-boggling and unattainable.
Fig. 2. The Theory of Community Ecology.
Selection, drift, speciation, and dispersal interact to determine community dynamics across spatial scales. The delineation of discrete spatial scales is arbitrary. Source
But does community ecology necessarily have to be seen from the lens of remarkable and thus impenetrable complexity? I say no. I came to recognize the possibility of simplification after reading the 2010 essay by Mark Vellend "Conceptual Synthesis in Community Ecology." The author proposes that, despite all the complex interactions, the patterns of community composition are driven by only four classes of processes: selection, drift, speciation and dispersal. (Given that we still debate what is a microbial species, think of the word speciation here as diversification or variation.) How elegant a theory, reducing apparent chaos to the interplay of four processes. In the author's words: "Selection represents deterministic fitness differences among species, drift represents stochastic changes in species abundance, speciation creates new species, and dispersal is the movement of organisms across space." Moreover, this framework allows "for the articulation of a very general theory of community dynamics: species are added to communities via speciation and dispersal, and the relative abundances of these species are then shaped by drift and selection, as well as ongoing dispersal, to drive community dynamics." I am all for starting from simple principles. And I am particularly attracted to this theory because it applies across spatial scales. Maybe this simple conceptual synthesis will guide future detailed studies of a few model microbial communities around the world. I, for one, would be thrilled to see that happen.
Do you want to comment on this post? We would be happy about it! Please comment on Mastodon, Bluesky, or on 𝕏 (formerly Twitter).
Comments