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A protocol that couples poly(A) polymerase with a multifunctional reverse transcriptase (RT) for targeted cloning of environmental prokaryotic cDNA is described. The reverse transcriptase PCR (RT-PCR) cDNA synthesis kit demonstrates the feasibility of directly accessing prokaryote RNA (rRNA and/or mRNA) in environmental samples, but the results also show potentially important problems.

Multiple soil samples were obtained from a nonradioactive model low-level-waste pit at the Idaho National Laboratory to understand the effect of the cellulosic waste products on the soil microbial community. The obtained results suggested that the presence of the cellulosic material significantly influenced the bacterial community structure in a stratified soil system.

Novel arsenite [As(III)] oxidase structural genes (aoxAB) are cloned from Hydrogenobaculum bacteria isolated from an acidic geothermal spring. Reverse transcriptase PCR has shown expression throughout the outflow channel and the aoxB cDNA clones have displayed distribution patterns relative to the physicochemical gradients in the spring.

The relative importance of [H.sub.2] and [H.sub.2]S as energy sources for supporting chemolothotrophic metabolism in an acidic geothermal spring in Yellowstone National Park is assessed. The studies have shown that phylogeny might not be reliable for predicting physiology and that [H.sub.2]S can dominate over [H.sub.2] as an energy source in terms of availability, apparent in situ consumption rates and growth-supporting energy.

As(III) oxidation in Dragon Spring is reexamined in order to assess the potential for As(III) chemolithotrophs to inhabit the geothermal feature. The findings have shown that [H.sub.2]S is a potent inhibitor of As(III) oxidation and will affect the opportunities and population distribution of As(III) chemolithotrophs.

An arsenite-oxidizing Hydrogenobaculum strain is isolated from a geothermal spring that was previously shown to contain microbial populations engaged in arsenite oxidation. The isolate is sensitive to both arsenite and arsenate and behaves as an obligate chemolithoautograph that uses H2 as its sole energy source and has an optimum temperature of 55 to 60 degrees and an optimum pH of 3.0.