Functional and molecular responses of soil microbial communities under differing soil management practices

The effects of soil management on some microbiological properties and soil bacterial community structure were evaluated. Two field sites with the same soil type, located on the same geographic area adjacent to one other, have received different soil management practices and cultivation. One site has been subjected for 20 years to intensive horticulture under conventional tillage and irrigation with low quality salt-rich water; the second field site has been uncultivated for a long period and was turned to organic farming practices over the last 5 years and is currently cultivated with fruit orchard. Total bacterial counts, microbial ATP, microbial community metabolic (BIOLOG^®) profiles, and DNA fingerprinting by PCR-DGGE were determined. Two-way ANOVA revealed that total bacterial counts were not significantly (P>0.3) affected by the two different management practices; ATP content was consistently and significantly (P<0.001) lower in salt-water irrigated soil than in organic soil at the three sampling times. The cluster analysis of community level physiological profiles indicated that microbial communities were much more uniform in organic soil than in irrigated one, suggesting that salt-water irrigation could have affected the size of the microbial population, its metabolic activities, as well as its composition. Molecular patterns fitted the BIOLOG^® profile diversity. In particular, at any sampling time, PCR-DGGE patterns of bacterial DNA, extracted by an indirect method, significantly discriminated irrigated from organic soil samples. The PCR-DGGE patterns of total soil DNA, extracted by a direct method, showed a moderate to significant variation among irrigated and organic soil samples. Biochemical, microbiological and molecular data contributed to evidence a significantly different response of indigenous microflora to soil management by using saline water or organic farming.