Spatial changes in the bacterial community structure along a vertical oxygen gradient in flooded paddy soil cores

Molecular ecology techniques were applied to assess changes in the bacteria l community structure along a vertical oxygen gradient in flooded paddy soi l cores. Microsensor measurements showed that oxygen was depleted from 140 mu M at the floodwater/soil interface to nondetectable amounts at a depth o f approximately 2.0 mm and below. Bacterial 16S rRNA gene (rDNA)-based comm unity fingerprint patterns were obtained from 200-mu m-thick soil slices of both the oxic and anoxic zones by using the T-RFLP (terminal restriction f ragment length polymorphism) technique. The fingerprints revealed a tremend ous shift in the community patterns in correlation to the oxygen depletion measured with depth. 16S rDNA clone sequences recovered from the oxic or an oxic zone directly corresponded to those terminal restriction fragments whi ch were highly characteristic of the respective zone. Comparative sequence analysis of these clones identified members of the alpha and beta subclasse s of Proteobacteria as the abundant populations in the oxic zone. In contra st, members of clostridial cluster I were determined to be the predominant bacterial group in the oxygen-depleted soil. The extraction of total RNA fo llowed by reverse transcription-PCR of the bacterial 16S rRNA and T-RFLP an alysis resulted for both oxic and anoxic zones of flooded soil cores in com munity fingerprint patterns similar to those obtained by the rDNA-based ana lysis. This finding suggests that the microbial groups detected on the rDNA level are the metabolically active populations within the oxic and anoxic soil slices examined.