Comparison of nifH gene pools in soils and soil microenvironments with contrasting properties

The similarities and differences in the structures of the nifH gene pools o f six different soils (Montrond, LCSA-p, Vernon, Dombes, LCSA-c, and Thysse Kaymor) and five soil fractions extracted from LCSA-c were studied. Bacter ial DNA was directly extracted from the soils, and a region of the nifH gen e was amplified by PCR and analyzed by restriction. Soils were selected on the basis of differences in soil management, plant cover, and major physico chemical propel ties. Microenvironments differed on the basis of the sizes of the constituent particles and the organic carbon and clay contents. Rest riction profiles were subjected to principal-component analysis. We showed that the composition of the diazotrophic communities varied both on a large scale (among sells) and on a microscale (among microenvironments in LCSA-c soil). Soil management seemed to be the major parameter influencing differ ences in the nifH gene pool structure among soils by controlling inorganic nitrogen content and its variation. However, physicochemical parameters (te xture and total C and N contents) were found to correlate with differences among nifH gene pools on a microscale. We hypothesize that the observed nif H genetic structures resulted from the adaptation to fluctuating conditions (cultivated soil, forest soil, coarse fractions) or constant conditions (p ermanent pasture soil, fine fractions). We attempted to identify a specific band within the profile of the clay fraction by cloning and sequencing it and comparing it with the gene databases. Unexpectedly, the nifH sequences of the dominant bacteria were most similar to sequences of unidentified mar ine eubacteria.