Evaluation of Nitrogenase Genes as Markers in Soil Microbial Community Studies
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Molecular tools were developed to overcome some of the constraints to analyzing nitrogen-fixing bacteria in the environment. Two distinct plant-microbe systems were used to develop these tools, and to evaluate their utility and flexibility. The first system focused on nitrogen-fixing bacteria in the rhizosphere of salt-meadow grass (Spartina patens), a key plant species in high salt marshes. Members of the ɛ-subdivision of Proteobacteria were shown to be prominent nitrogen-fixers in this system, with specific populations changing seasonally and in response to the presence of arbuscular mycorrhizal fungi. The second system involved nitrogen-fixing bacteria of the genus Frankia that form root-nodules in symbiosis with certain woody plants. The diversity of nodule-forming frankiae was assessed in soils from 5 continents, and in natural populations in root nodules of alder trees growing on 3 different mountain tops in central and southern Arizona. Specific difficulties in the development of molecular tools in these two systems were discussed. These studies provided significant databases for specific target sequences, i.e., the nifH gene, for both uncultured nitrogen-fixing members of the ɛ-subdivision of Proteobacteria and cultured and uncultured frankiae, and baseline data that demonstrated the usefulness of the molecular tools for studies on the ecology of both nitrogen-fixing members of the ɛ-subdivision of Proteobacteria and Frankia populations.