Changes in microbial functional genes within the soil metagenome during forest ecosystem restoration

As important mediators of numerous ecological processes, soil microorganisms play essential roles in the recovery of ecosystems after disturbance. Using next-generation sequencing techniques, microbial taxonomic changes during ecosystem restoration have been widely studied, but data describing microbial community structure alone can be difficult to link to ecosystem processes mediated by microorganisms. Shotgun metagenome sequencing provides a chance to examine changes among thousands of functional genes during the recovery of microbial communities and ecological function. We analyzed 15 soil metagenomes from a chronosequence of mine soils spanning 6–31 years since reforestation along with unmined reference soils. Taxonomic and functional changes indicate a shift from copiotrophic to oligotrophic groups, increasing metabolism of recalcitrant carbon sources and the influence of vegetation. Increases in genes involved in transposable elements, virulence, defense, and stress response suggest more cooperative and competitive interactions among microorganisms with chronosequence age. Within N cycling groups, ammonia and nitrite oxidizing bacteria increased significantly during restoration, but few significant changes were observed in key N-cycle functional genes. The low relative abundances of methanotrophs and methane monooxygenase genes in all reforested soils explains previous observations that methane consumption has not recovered at these sites 31 years after reforestation. This work helps identify possible mechanisms linking the soil microbiome to ecosystem recovery, with a specific focus on N cycling and greenhouse gas emission, to better understand the roles soil microorganisms play in the restoration of ecosystem functions.