Abstract
A few major discoveries have influenced how ecologists and evolutionists study microbes. Here, in the format of an interview, we answer questions that directly relate to how these discoveries are perceived in these two branches of microbiology, and how they have impacted on both scientific thinking and methodology.The first question is "What has been the influence of the 'Universal Tree of Life' based on molecular markers?" For evolutionists, the tree was a tool to understand the past of known (cultured) organisms, mapping the invention of various physiologies on the evolutionary history of microbes. For ecologists the tree was a guide to discover the current diversity of unknown (uncultured) organisms, without much knowledge of their physiology.The second question we ask is "What was the impact of discovering frequent lateral gene transfer among microbes?" In evolutionary microbiology, frequent lateral gene transfer (LGT) made a simple description of relationships between organisms impossible, and for microbial ecologists, functions could not be easily linked to specific genotypes. Both fields initially resisted LGT, but methods or topics of inquiry were eventually changed in one to incorporate LGT in its theoretical models (evolution) and in the other to achieve its goals despite that phenomenon (ecology).The third and last question we ask is "What are the implications of the unexpected extent of diversity?" The variation in the extent of diversity between organisms invalidated the universality of species definitions based on molecular criteria, a major obstacle to the adaptation of models developed for the study of macroscopic eukaryotes to evolutionary microbiology. This issue has not overtly affected microbial ecology, as it had already abandoned species in favor of the more flexible operational taxonomic units. This field is nonetheless moving away from traditional methods to measure diversity, as they do not provide enough resolution to uncover what lies below the species level.The answers of the evolutionary microbiologist and microbial ecologist to these three questions illustrate differences in their theoretical frameworks. These differences mean that both fields can react quite distinctly to the same discovery, incorporating it with more or less difficulty in their scientific practice.ReviewersThis article was reviewed by W. Ford Doolittle, Eugene V. Koonin and Maureen A. O'Malley.
Highlights
We often think of how certain major scientific discoveries have affected our own scientific field
Both evolutionary microbiology and microbial ecology initially resisted the discovery that lateral gene transfer (LGT) is frequent in microbes, as it made their respective ‘holy grails’ inaccessible
There would never be a simple and unique depiction of relationships between organisms, and for microbial ecologists, functions could not be linked to specific genotypes
Summary
We often think of how certain major scientific discoveries have affected our own scientific field. The first of three major discoveries we will discuss as having had an impact on these two branches of microbiology is that molecular markers can be used to reconstruct a phylogeny of all organisms (a ‘Universal Tree of Life’). This tree, regardless of its theoretical validity, has served as a framework to scientific inquiry in microbiology for decades. The third discovery is that the extent of genetic diversity in microbes is much greater than expected and can vary between species [5,6], which brings into question the universality of species as a unit of diversity or evolution. We ask a question pertaining to each discovery in an interview format and present the answer from both evolutionary and ecological perspectives
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