Heterogeneous cell density and genetic structure of bacterial pools associated with various soil microenvironments as determined by enumeration and DNA fingerprinting approach (RISA)

The cell density and the genetic structure of bacterial subcommunities (fur ther named pools) present in the various microenvironments of a silt loam s oil were investigated. The microenvironments were isolated first using a pr ocedure of soil washes that separated bacteria located outside aggregates ( outer part) from those located inside aggregates (inner part). A nondestruc tive physical fractionation was then applied to the inner part in order to separate bacteria located inside stable aggregates of different size (size fractions, i.e., two macroaggregate fractions, two microaggregate fractions , and the dispersible day fraction). Bacterial densities measured by acridi ne orange direct counts (AODC) and viable heterotrophic (VH) cell enumerati ons showed the heterogeneous quantitative distribution of cells in soil. Ba cteria were preferentially located in the inner part with 87.6% and 95.4% o f the whole AODC and VH bacteria, respectively, and in the microaggregate a nd dispersible clay fractions of this part with more than 70% and 80% of th e whole AODC and VH bacteria, respectively. The rRNA intergenic spacer anal ysis (RISA) was used to study the genetic structure of the bacterial pools. Different fingerprints and consequently different genetic structures were observed between the unfractionated soil and the microenvironments, and als o among the various microenvironments, giving evidence that some population s were specific to a given location in addition to the common populations o f all the microenvironments. Cluster and multivariate analysis of RISA prof iles showed the weak contribution of the pools located in the macroaggregat e fractions to the whole soil community structure, as well as the clear dis tinction between the pool associated to the macroaggregate fractions and th e pools associated to the microaggregate ones. Furthermore, these statistic al analyses allowed us to ascertain the influence of the clay and organic m atter content of microenvironments on the genetic structure relatedness bet ween pools.