The aim here was to examine microbial community composition and the distribution of microbial functional genes across a soil pH gradient in northern hardwood forest. Studies in the literature suggest that soil pH is a dominant driver of differences in the diversity and richness of the soil bacterial community. However, most studies have been done at the continental scale and have focused on 16S rRNA gene analysis, and thus they lack geographical and physiological resolution. In this study, we ask whether the same idea applies across a kilometer-scale gradient, and how soil acidity influences microbial functional genes. Three sugar maple-dominated forests in the northeastern USA were sampled from, each containing a soil pH gradient from ~3.8 to 6.1 due to discontinuities in the chemistry of the underlying bedrock. A metagenomic approach was used for community analysis and to focus specifically on denitrification functional genes. Denitrification is a four-step process that converts nitrate to dinitrogen, and portions of the pathway are known to be sensitive to acidity.
Results/Conclusions
The difference in community composition at the phylum level was driven largely by the increased presence of Acidobacteria in the most acidic soil (pH = 3.8); however, members of this phylum were present in lesser abundance in the less acidic soils. There was evidence that Alphaproteobacteria abundance increased with increasing soil acidity, whereas acidity led to less of the Beta- and Deltaproteobacteria. However, overall we did not observe large differences in microbial community composition at the phyla level. On the other hand, principal component analysis of all microbial functional genes demonstrated distinct community separation with pH and not geography. Although the most acidic soil had the smallest amount of denitrification genes, it did show a large increase in the proportion of qNor (nitric oxide reductase) and a large decrease in proportion of Nos (nitrous oxide reductase) relative to the higher pH soils. The qNor gene will likely provide a competitive advantage for bacteria in the face of large amounts of toxic nitric oxide produced in acidic forest soils. Thus, the results suggest that soil acidity does serve as an environmental filter for microbial community composition even at more resolute geographic scales. The results also suggest that soil pH helps to determine the presence (or absence) of functional genes that give bacteria an advantage in ecological interactions.