Shotgun sequencing of soil from a plant exclusion experiment

Plant cell wall polysaccharides are the most abundant form of organic carbon in soils; their degradation by microorganisms represents a major link in the global carbon cycle. Soil carbon storage is a valuable ecosystem service, buffering against increasingly rapid climatic change, and underpinning services such as food production and flood prevention. Despite the importance of this link, little is known about the relative contributions of different microorganisms and genes to lignocellulose degradation in soils. Here, we use a 10-year old plant-exclusion experiment on grasslands to study how reduced plant inputs affects the microbial community, and genes which are putatively associated with lignocellulolysis. We show that 10 years of plant exclusion reduces lignocellulolytic gene abundance and Actinobacteria, and increases Acidobacteria, Firmicutes, and several other phyla, due to changes in available carbon sources. Using the abundance of genes for different carbohydrate-active enzymes (CAZy), we classify Proteobacteria, Actinobacteria, Planctomycetes, Gemmatimonadetes, and Firmicutes as potential specialist degraders of lignocellulose, and Ascomycota, Acidobacteria, Euryarchaeota, and Bacteroidetes as potential generalist lignocellulose degraders. This study begins to classify microbial phyla into broad functional guilds with respect to lignocellulose decomposition, which may help to target future cultivation work on particular taxonomic groups, and parameterise global carbon-cycling models.