Using metagenomics to reveal landscape scale patterns of denitrifiers in a montane forest ecosystem

Abstract

Denitrificationis an important process in the nitrogen cycle of many soil ecosystems, but the relationships between process rates and the genotype of denitrifying microorganisms are poorly understood. Genotyping may identify denitrifiers with less than the full complement of nitrogen-oxide reductases, which might be crucial for denitrification in nitrogen-limited environments, such as in montane forest landscapes. Therefore, a metagenomics survey was undertaken using soils from the Hubbard Brook Experimental Forest (HBEF) in New Hampshire, USA where steep elevation, vegetation, and soil gradients provide a complex landscape matrix to assess occurrence patterns of the genes involved in denitrification. DNA was extracted from soils taken from three soil horizons, at three elevations, in two watersheds. Metagenomic analysis of reads showed that the relative abundance of denitrification genes within a community did not differ across soil depths but did vary among elevation zones, with total denitrification reads in High Hardwood > Spruce Fir > Low Hardwood. Reads from nirS were extremely rare, which suggests that complete denitrification is uncommon across this forest landscape. The gene with the largest proportion of denitrification specific reads was the quinol-oxidizing nitric oxide reductase, qnor, which reduces toxic nitric oxide to nitrous oxide. The relative enrichment of specialized denitrification genes involved in intermediate reactions may indicate that environmental factors are selecting for a partial denitrification process, rather than complete denitrification. High Hardwood soils had the highest denitrification gene abundance and the greatest potential rate of denitrification, indicating that metagenomic information was consistent with the process measurements. Although little energy is generated from complete denitrification, due to the acidic soil conditions and low nitrate availability in HBEF soils, the denitrifier community appears to compensate by producing particular denitrification genes. In particular, qnor may help the community cope with toxic nitric oxide produced via chemodenitrification, making it a public good.