Taxon Biosciences

Concept

The environment harbors immense numbers of microbes. A single gram of soil may contain 10¹² bacterial cells representing thousands of distinct species. Soil is probably the single most significant repository for genetic information on Earth.

The distribution of bacteria in the environment is non-random. Like all living organisms, each bacterial species has a set of growth requirements that must be met in order to proliferate. Bacteria whose growth requirements can be satisfied in diverse habitats are likely to exhibit a cosmopolitan distribution. Conversely, bacteria that have adapted to unusual or distinct habitats are likely to be found in significant numbers only in those specific habitats. By learning the rules that govern the distribution of microbes in the environment, a large amount of information can be inferred just by the knowing the abundance of different organisms present at a given location.

Challenges

While soil harbors a significant diversity of bacteria, only a small fraction (<1%) can be grown in culture. Culture-independent methods must be used to detect the presence of these microbes. Direct detection of microbial DNA sequences enables microbial surveys of organisms to be performed irrespective of their ability to grow in culture.

Another challenge to conducting microbial surveys relates to microbial community structure itself. Often bacterial communities are comprised of a small number of abundant species and a large number of species present at low abundance. Survey strategies based upon sampling are burdened by the re-isolation of dominant members of the community. While the abundant members of the community are easily identified with minimal sampling effort, detection of the species present at lower abundance requires a significant sample size and effort. For this reason, an effective survey strategy must be capable of collecting a large sample set.

Approach

Taxon utilizes a combination of molecular approaches for surveying microbial communities. These methods include SARD (for Serial Analysis of Ribosomal DNA), a patented high throughput surveying method developed at Taxon, and DNA sequence analysis of 16S rRNA gene clone libraries.

Taxon’s strategy is to create profiles of microbial diversity from geochemically well-characterized samples. Comparison of these profiles from several samples reveals groups of sequences (organisms) that tend to be found together under certain geochemical settings. These communities can therefore be classified into functional units and tentatively assigned to biogeochemical processes. This approach enables the empirical construction of microbial community structure-function models and provides specific testable hypotheses as to the ecological roles of the taxa present.