Open Access Highly Accessed Research article

Using pyrosequencing to shed light on deep mine microbial ecology

Robert A Edwards1234*, Beltran Rodriguez-Brito13, Linda Wegley1, Matthew Haynes1, Mya Breitbart1, Dean M Peterson5, Martin O Saar6, Scott Alexander6, E Calvin Alexander6 and Forest Rohwer12

Author affiliations

1 Department of Biology, San Diego State University, San Diego, USA.

2 Center for Microbial Sciences, San Diego State University, San Diego, USA.

3 Computational Science Research Center, San Diego State University, San Diego, USA.

4 Fellowship for Interpretation of Genomes, Burr Ridge, USA.

5 Natural Resources Research Institute, Department of Geological Sciences, University of Minnesota, Duluth, USA.

6 Department of Geology and Geophysics, University of Minnesota, Minneapolis, USA.

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Citation and License

BMC Genomics 2006, 7:57  doi:10.1186/1471-2164-7-57

Published: 20 March 2006



Contrasting biological, chemical and hydrogeological analyses highlights the fundamental processes that shape different environments. Generating and interpreting the biological sequence data was a costly and time-consuming process in defining an environment. Here we have used pyrosequencing, a rapid and relatively inexpensive sequencing technology, to generate environmental genome sequences from two sites in the Soudan Mine, Minnesota, USA. These sites were adjacent to each other, but differed significantly in chemistry and hydrogeology.


Comparisons of the microbes and the subsystems identified in the two samples highlighted important differences in metabolic potential in each environment. The microbes were performing distinct biochemistry on the available substrates, and subsystems such as carbon utilization, iron acquisition mechanisms, nitrogen assimilation, and respiratory pathways separated the two communities. Although the correlation between much of the microbial metabolism occurring and the geochemical conditions from which the samples were isolated could be explained, the reason for the presence of many pathways in these environments remains to be determined. Despite being physically close, these two communities were markedly different from each other. In addition, the communities were also completely different from other microbial communities sequenced to date.


We anticipate that pyrosequencing will be widely used to sequence environmental samples because of the speed, cost, and technical advantages. Furthermore, subsystem comparisons rapidly identify the important metabolisms employed by the microbes in different environments.