Diazotroph community structure and abundance in wheat–fallow and wheat–pea crop rotations

Biological input of nitrogen (N) from the atmosphere by free-living diazotrophs can help alleviate fertilizer use in agricultural systems. In this study, we investigated the effect of N fertilizer and winter pea (Pisum sativum L.) crop on the community structure and abundance of free-living diazotrophs in a two year study of dryland winter wheat (Triticum aestivum L.) no-till production system in Eastern Oregon, USA. Based on quantification of the nifH gene, diazotroph abundance was strongly influenced by plant species and the crop year in which the soil samples were collected. A greater amount of nifH copies was recovered in 2012 compared to 2011 either as copies per gram soil or normalized to the abundance of bacterial 16S rRNA genes. The quantity of genes was greater under pea than wheat in 2012 although no difference was observed in the preceding year. The nifH gene abundance was positively correlated to ammonium concentration in 2011 and bacterial abundance in 2012. Nitrogen application did not influence diazotroph abundance in the top 0–5 cm; however the abundance was reduced by application at the lower 5–10 cm depth under wheat crop. The diazotroph community structure appeared to be influenced more by N fertilization rather than plant species with the exception of wheat in 2012. Changes in the community structure over the two years were greater for fertilized than unfertilized soil. Collectively, these data suggest that year-to-year variability had a greater influence on diazotroph communities rather than specific parameters of plant species, fertilization, total N, total organic C, or soil pH. Multi-year studies are necessary to define the specific drivers of diazotroph abundance, community structure and function.     

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.