A metagenomic study of soil microbial communities under various vegetation types and soil depths

Background/Question/Methods
Carbon emissions are a major contributor to global climate change, and soils are the largest terrestrial sink for carbon. Soils hold twice as much carbon as vegetation and soil organic carbon is primarily cycled by microbial decomposition. The microbial communities involved in decomposition and the mechanisms used for carbon processing are poorly understood. We sought to determine whether the structure and carbon metabolic functions of soil communities are affected by different kinds of organic carbon that are derived from plants and how that changes with soil depth. We investigated the structures and enzymatic activities of soil microbial communities under three different vegetation types and at five soil depths. Soils were collected in June 2011 at Sedgwick Reserve, in Santa Barbara County, California. We collected 90 samples from five depths along the soil profile of Shedd silty clay loam soils under three vegetation types: grassland, oak woodland, and coastal sage. These vegetation types have distinct carbon chemistry, and differ in the abundance of labile and chemically complex carbon. These samples were assayed for carbon, nitrogen, and phosphorus metabolic enzyme activities, and 16S ribosomal DNA hyper variable region V4 was sequenced using Illumina MiSeq.

Results/Conclusions
We found significant differences in enzyme activities among vegetation types and soil depths. Under a random forest classification model, enzyme activity variables correctly classified 98.8% of the samples as belonging to one of the three habitat types. Alpha Diversity decreased with soil depth, and tended to be highest in coastal sage and lowest in grassland. We also found significant correlations between enzyme activities and beta diversity among vegetation types and at different soil depths for all enzymes but phosphatase. We conclude that vegetation type and soil depth play roles in shaping the microbial community structure and metabolic function as determined by 16S and extracellular enzyme production. This data suggests that further investigation of the molecular mechanisms of carbon metabolism in these communities and the identification of specific classes of organic carbon compounds in these soils could provide important insights into microbial decomposition in the soil.