Species are fundamental units in plant and animal communities, but is this true in the microbial world? There is considerable debate as to whether bacteria evolve in fundamentally different ways than eukaryotes due to their rapid reproduction, rare (and promiscuous) sexuality, and evolutionarily significant gene exchange. Modern genetic and genomic analyses make  “named” bacterial species (traditionally demarcated by phenotypic properties) appear to be diverse, chaotic assemblages of rapidly exchanged genes. However, modern population genetics analysis challenges the concept that these named species are really biologically meaningful entities. Furthermore, natural patterning of genetic diversity and evolutionary theory suggest a more orderly concept of species as discrete ecologically adapted populations (ecotypes). Our conceptual framework is that ecotypes are the fundamental units of microbial communities that play a central role in linking genetic diversity to microbial community composition, structure and function. We will investigate a well-studied hot spring microbial mat community in Yellowstone National Park with ideal properties for employing sophisticated molecular methods. To understand how genetic diversity is organized in the mat community, we will compare (i) direct genomic sequencing of predominant mat populations (to objectively assay genomic diversity and determine how it is organized according to genetic criteria) with (ii) theory-driven population genetics analysis and evolutionary simulation designed to test for putative ecotypes. Genomic sequencing will enable development of microarray technology and high-throughput analysis of variant alleles that will be used to evaluate whether, as expected, putative ecotypes occupy unique niches and order gene distribution and expression within the mat community. The discovery of genetically separable ecotypes will broadly impact thinking in microbial evolution, systematics, ecology and physiology and will unify evolutionary principles across the breadth of size and complexity among organisms. 

Green hot spring microbial mats occur below ca. 74°C (a). The top green layer (b) is comprised of filamentous green nonsulfur-like bacteria and unicellular cyanobacteria, Synecho-coccus (c) that form distinct layers of different autofluorescence intensity in the top 1 mm. (d)

Figure 1. Green hot spring microbial mats occur below ca. 74°C (a).  The top green layer (b) is comprised of filamentous green nonsulfur-like bacteria and unicellular cyanobacteria, Synecho-coccus (c) that form distinct layers of different autofluorescence intensity in the top 1 mm. (d).

Broader Impacts:

Our team is a balance of young and established, male and female investigators from geographically and demographically diverse institutions.  The research integrates principles from general biology with microbiology and molecular biology, providing a cross-training opportunity that will help fill the chasm separating these fields.  Participants will share their disciplinary perspectives (microbial ecology, evolutionary biology, genomics and microbial physiology) with each other and the scientific community through a workshop series that will lead to web-based learning modules.  The microbial community is in Yellowstone Park, providing numerous opportunities for interaction with the park’s trained informal educators.  Preparation of new educational resources (e.g., resource manual for educating seasonal rangers and park managers, signage, trail guides, websites and exhibits for a new Visitor Education Center) will help millions of annual visitors, young and old, change the way they think about microorganisms. Five linked websites will broadly disseminate our databases and interpret the interdisciplinary importance of our work for nonscientists. Genomic websites will present sequences from direct mat analysis as well as two closely related, ecologically distinct pure-cultured thermophilic cyanobacteria (Synechococcus). Another website will describe the microarray in detail and report comparisons of gene expression in situ and in relevant Synechococcus isolates grown in laboratory culture.  A project website will collect all data, report tests of our main hypotheses, and serve as a conduit for dissemination of educational products.