Soil metatranscriptomics of a temperate forest under increased nitrogen deposition; expression of transcripts encoding lignocellulolytic enzymes

Fungi are ubiquitous in terrestrial ecosystems and play an important role in biogeochemical cycling because of their function as litter decomposers. It has been demonstrated that increased nitrogen (N) deposition decreases fungal biomass and changes the relative abundance of particular groups and species. In addition, increased N can slow litter decomposition, increase carbon (C) storage and reduce lignolytic enzyme activity. To understand the functioning of fungi under increased N addition in more detail, we performed a soil metatranscriptomic analysis on samples from the organic and mineral soil horizon from a chronic N-addition experiment at the Harvard Forest LTER. We extracted total RNA, followed by reverse transcription of poly-A tailed mRNA and Illumina paired-end sequencing of the cDNA. In both horizons of control and N amended plots, a total of ~1.8 million genes were expressed at the time of sampling, of which ~70,000 and ~110,000 were uniquely expressed in the N addition and control plots, respectively. Using fungal enzyme databases, we matched our transcripts with lignocellulolytic enzymes involved in lignocellulose degradation. Even though N addition did not affect the community level expression of several lignocellulolytic enzymes, we did observe a significant decrease in the gene richness of class II peroxidases, which are a group of enzymes involved in lignin breakdown. Furthermore we found changes in the fungal community composition expressing cellobiohydrolase, which is an enzyme involved in the breakdown of cellulose. These results suggest that under N addition, fewer taxa and/or different taxa are expressing lignocellulolytic genes, which could partly explain the decrease in litter decomposition we have observed under N addition.