Using SIP and MinION sequencing to uncover active microbial communities

Seda Mirzoyan (Rutgers University) began her talk by describing how blueberry production is a $700 million industry and that the United Sates is the world's largest producer. Blueberry plants grow in acidic, well-drained soils, which usually have high organic content.

The aim of this research was to uncover the differences between low- and high-productivity soils in terms of microbial composition. In order to identify active microbes, the team at Rutgers employed stable isotope probing (SIP) using carbon-13 (¹³C) with a negative carbon-12 (¹²C) control. Following DNA extraction from a caesium chloride gradient, full-length rRNA operons were amplified and screened against a comprehensive 16S database. In total, 19 major eukaryotic clades were detected. Virtually all of the active eukaryotic community and 70% of the resident community was identified as fungi. In forest soil controls it was observed that the resident and active community differed. High-productivity soils were enriched with Glomeromycotan species — beneficial fungi that help provide nutrients to plants. Low-productivity soils were found to be enriched with members of the fungal pathogen phylum Rozellomycota. Examining the bacterial composition of the soils revealed that, in low productivity soils, the active microbial community were enriched with members of the phylum Firmicutes.

In summary, Seda suggested that SIP combined with ribosomal operon profiling using the MinION can differentiate between resident and active microbial communities in agricultural and forest soil systems.