16s ribosomal RNA analysis to detect soil microbial community shifts in response to changing agricultural practices from row crops to short rotation woody crops

To monitoring soil microbial community dynamics at an Ames Plantation study in which agricultural management practices were changed from growing row crops to short rotation woody biomass crops, 16s rRNA was directly extracted from soil and without further amplification the RNA was blotted onto a membrane and hybridized with a hierarchical array of rRNA probes. The RNA was quantified by comparison to standard concentrations of RNA. The relative proportions of RNA from the three major domains; Eubacteria, Eukaryotic and Archaeal were compared. The relative proportions of Proteobacteria (Alpha, Beta, Gamma, and Delta subgroups). High G+C and Low G+C content bacteria and the Cytophaga/Flavobacterium/ Bacteriodes bacteria were also assessed. The microbial community composition in each test plot was compared using a Fisher's least significant difference test to see which components of the microbial community changed significantly with the changing agricultural practices.

The results showed that the techniques could be used to obtain quantifiable amounts of RNA and the hierarchical probe approach could be used to detect community shifts which occurred due to changing agricultural practices from row crop management to woody biomass production. Community shifts were detected between the test sites. Perhaps most interesting was the amount of unexplained diversity present at the sites that could be detected with the Universal probe, but was not detected using the individual group probes.