Microbial Research: Progress and Potential

Toranzos of NSF provided guidance and logistical support for the workshop. We thank Myrna Watanabe for help with report preparation. Executive Summary Introduction The National Science Foundation (NSF) Microbial Observatory (MO) and Life in Extreme Environments (LExEn) programs have fostered significant advances in microbial ecosystems research in a wide variety of natural environments. The investigators funded by these programs have extended the frontiers of microbial diversity and microbial biogeochemistry research, discovering novel microbial lineages, describing the complexity of natural microbial communities, and linking microbial taxa to critical ecosystem functions. This workshop, the first of its kind, provided a platform for MO and LExEn researchers to discuss recent accomplishments and future directions in microbial ecosystem research. LExEn and MO projects have greatly benefited from the use of new molecular technologies to identify organisms and their activities in natural environments. Molecular methods have provided microbial ecologists with invaluable information about the enormous reservoir of uncultured microbes; 16S rRNA work alone has identified more than 13,000 new prokaryotes. These technologies have also allowed access to functional genes, providing a mechanism to assess both capability for and expression of ecologically important microbial processes in natural environments. The challenges now facing microbial-life researchers are to move beyond the limitations of 16S rRNA-based approaches and characterized functions to access the unknown organisms, functions, and activities of uncultured members of microbial communities. Metagenomics Genomic analysis, now used primarily to observe the structures of genomes of individual organisms, can also be used to study the genetic reservoir of entire communities , i.e., the metagenome (Vergin et al., 1998; Rondon et al., 2000; Béjà et al., 2000b). With this approach, genetic material from a natural community can be analyzed without first culturing all the organisms. Several MO projects are making use of this new technology to describe and discover microbes and microbial products from environments as diverse as soils, the ocean, and the guts of insects. Before metagenomics can take a leading position in microbial-life research, however, technological capabilities must be improved for obtaining sufficient DNA from natural environments ; for cloning, sequencing, and storing metagenomic DNA; and for capturing the dynamics of microbial communities over time and space through gene sequencing approaches. Environmental Microarrays Use of microarray technology represents another potentially valuable, yet challenging , prospect for microbial-life research. A reasonably complete set of functional genes collected from an environment or collection of environments provides a window into …