Characterising the soil ecosystem phenotype associated with relatively low nitrate-N concentrations

Abstract

In agricultural systems, elevated concentrations of soil nitrate (NO3−-N) pose an environmental risk. Nitrate is highly mobile, and can be transported through soil into aquatic ecosystems resulting in eutrophication. Furthermore, under anaerobic conditions nitrate-N can undergo microbial denitrification. This latter process is a significant source of N2O, a potent greenhouse gas. The goal of this research is to determine (1) if there are soils, from under live-stock grazed (pastoral) land use, that contain lower than expected (anomalous) nitrate-N per total N content, and (2) characterise the phenotypes of these soils based on physicochemical and microbial attributes. Using a set of 50 soils that have been fully characterised based on edaphic properties, and for which GeoChip environmental functional microarray data is available, the ratio of nitrate-N to total N, an expected value was determined for the 50 soils. Using a ‘leave one out’ prediction strategy, soils anomalously high (n = 13) or low (n = 14) in nitrate-N were determined. The phenotypes of these two groups were characterised based on the edaphic and molecular (functional gene and associated phylogenetic association) data. Significant (permutation p < 0.05) variation in mid-level carbon (C) and nitrogen (N) cycling gene categories were evident between groups of soil with relatively low or high nitrate N levels. Low nitrate-N soils were characterised by increased abundance of genes involved in reductive acetyl CoA pathway, acetyl-CoA carboxylase, glyoxylate cycling, starch and chitin degradation, and nitrogen reduction (denitrification). Furthermore, the increased occurrence of these metabolic pathways was associated with increased abundance of Classes of Firmicute, Actinobacteria, and some groups of Proteobacteria and fungal taxa. In the group of soils with anomalously low nitrate-N, changes in the function and composition of the microbial community occurred with increased ratios of C:P, C:N, and C:S., and lower sulphate-S contents. These results indicate that a general widening of the stoichiometry of C with other nutrients maybe an important driver, or associative factor, linked with changes in the microbial community function. Opportunities to shift soil ecosystems to a low nitrate-N phenotype may be best achieved through alteration of C inputs to soil or changing C-cycling ecophysiology. This maybe achieved through selection of plants for specific (quantitative and qualitative) rhizosphere C allocation profiles.