Metagenomic reconstruction of nitrogen cycling pathways in a CO2-enriched grassland ecosystem

The nitrogen (N) cycle is a collection of important biogeochemical pathways mediated by microbial communities and is an important constraint in response to elevated CO2 in many terrestrial ecosystems. Previous studies attempting to relate soil N cycling to microbial genetic data mainly focused on a few gene families by PCR, protein assays and functional gene arrays, leaving the taxonomic and functional composition of soil microorganisms involved in the whole N cycle less understood. In this study, 24 soil samples were collected from the long-term experimental site, BioCON, in 2009. A shotgun metagenome sequencing approach was employed to survey the microbial gene families involved in soil N cycle in the grassland that had been exposed to elevated CO2 (eCO2) for >12 years. In addition to evaluating the responses of major N cycling gene families to long-term eCO2, we also aimed to characterize the taxonomic and functional composition of these gene families involved in soil N transformations. At the taxonomic level, organic N metabolism and nitrate reduction had the most diverse microbial species involved. The distinct taxonomic composition of different N cycling processes suggested that the complex N cycle in natural ecosystems was a result of multiple processes by many different microorganisms. Belowground microbial communities that mediate N cycling responded to eCO2 in several different ways, including through stimulated abundances of the gene families related with organic decomposition, dissimilatory nitrate reduction, and N2 fixation, and suppressed abundances of the gene families in glutamine synthesis and anammox. This study provides a genetic basis of the microorganisms involved in key processes in the N cycle in complex ecosystems, and shows that long-term eCO2 selectively affects N cycling pathways instead of tuning up every process. © 2016 Elsevier Ltd. All rights reserved.