Analysis of the occurrence and activity of diazotrophic communities in organic and conventional horticultural soils

Nitrogen (N)-fixing microorganisms are an important soil component as they help replenish the pool of available N. Organic management can influence the N-fixing community; however, diazotroph community structure and activity in horticultural systems and the impacts of specific cultivation methods (i.e., greenhouse and open field) are unclear. Using the nifH gene, a marker gene for the microbial community involved in N fixation, we investigated the occurrence (DNA) and activity (RNA) of the diazotrophic community in organically and conventionally managed soils in a horticultural system over the course of 1 year. Ordination analysis of DGGE profiles revealed organic management affected the community structure in the greenhouse but not the open field; fertilization intensity may explain this divergent response, as indicated by the relevance of total C content to community structure. Quantitative PCR revealed that organic management increased the abundance and activity of diazotrophs. The soluble organic N concentration was higher in organically managed soils and during warmer months, and correlated with diazotroph abundance. Most identified sequences were from known diazotrophs, predominantly β-, γ- and α-proteobacteria. Twenty-four bands resembled Pseudomonas stutzeri and eight resembled Azoarcus sp. Our results show that the cultivation method controls the extent of the effects of season and organic management on diazotrophs, and that greenhouse cultivation can boost the effects of organic management on this community. Organic management intensified the positive effect of seasonal temperature on diazotroph abundance and activity, which may increase biological nitrogen fixation rates. In tandem, soil DNA and RNA analyses provide a comprehensive picture of the community.