Using soil metatranscriptomics to understand fungal functioning in a changing climate
Fungi are ubiquitous in terrestrial ecosystems and play an important role in biogeochemical cycling because of their function as litter decomposers. Nitrogen (N) deposition and soil warming decrease fungal biomass and change the relative abundance of particular groups and species. In addition, increased soil N availability can slow litter decomposition and reduce lignolytic enzyme activity. To understand the functioning of soil fungi in response to soil N enrichment and elevated soil temperatures, we performed a metatranscriptomic study on soil samples collected from the Soil Warming × Nitrogen Addition Study at the Harvard Forest Long-term Ecological Research (LTER) site in Petersham, MA, USA. We extracted total RNA, followed by reverse transcription of poly-A tailed mRNA to target the eukaryotic community, and sequenced cDNA using Illumina HiSeq. To complement the transcriptomics analysis we analyzed fungal community composition in the same soil samples using amplicon sequencing of the ITS2 region from DNA extracts.
Bioinformatic analysis of the transcriptomics data confirmed that, with poly-A selection, the majority of expressed genes were of eukaryotic origin, with fungi representing on average one third of the sequences. However, 40% of expressed genes, on average, had no match in current databases. Further annotation of expressed genes revealed multiple genes involved in the decomposition process: e.g., cellobiohydrolase genes (breakdown of cellulose) and Class II peroxidases (breakdown of lignin). Nitrogen addition and soil warming affected the expression of several decomposition genes; however, after performing multiple comparison corrections (e.g., False discovery rate (FDR)) few treatment differences were significant. Amplicon sequencing revealed that Ascomycota dominated the fungal community in the organic horizon, while Basidiomycota increased in relative abundance in the mineral horizon. However, fungal community composition overall was not affected by five years of soil warming. Comparison of the transcriptomics and amplicon data will be discussed, including how these modern molecular techniques can aid our quest to disentangle the links between fungal communities and their feedbacks to climate.