Capturing the Spatial Variability of Microbial Communities within Agricultural Soils.

Understanding patterns in microbial community spatial variability can provide important insights into the mechanisms that control ecosystem function. The level of replication required to adequately characterize the variability of soil communities across both small and large geographic and edaphic gradients, however, is not well understood. Here we asked: How extensive does sampling need to be to capture variability across different spatial scales? Furthermore, how much information is lost by decreasing field-sampling effort?

To address this, we utilized an agricultural research network in three geographically and edaphically distinct sites across Minnesota, USA. At each site, we identified five 24 x 24 meter plots and collected surface soil from six individual locations per plot. Illumina sequencing of the bacterial 16S rRNA genes (V4 region) was used to characterize sensitivity of community data to physical sample pooling. Individual samples and physical composites were rarefied to a depth of 100,000.

Community richness and diversity of physical pools was the same, if not greater, than individual samples, suggesting that a single physical composite provides a sufficient assessment of both richness and diversity. Further, results suggest that the between-sample variability of physical pools and individual samples may be similar. Effort and expense associated with extracting and sequencing replicate soil samples is often a motivation for physically pooling spatially explicit samples. We recommend that researchers consider the effectiveness of pooling may vary by soil type.