Findings and Recommendations

From a total of > 4.5 million sequence reads, only 0.6 % of the reads overlapped between RNA and DNA samples. Marked differences were seen between the distribution of Phyla from RNA and DNA.

The community structure showed a few OTUs having high relative abundance and many OTUs being detected in low or single numbers, representing a ‘rare biosphere’ community composition. Taxonomy of RNA was further described at Phyla and family level. Only 30% of OTUs could be assigned taxonomy at Phyla level and, of those, only 46% at family or genus level (bootstrap support >70).

At Phyla level the RNA samples were homogeneous across all soil types, dominated by β/γ–Proteobacteria, α–Proteobacteria and Acidobacteria. 7 Phyla were detected in all samples and rarely detected Phyla showed high diversity between samples.

At family level the samples were much more heterogeneous, different Phyla showed different family taxonomic distribution patterns, with Firmicutes and Actinobacteria the most diverse.

We used principal component analysis comparing 27 environmental variables against the Shannon–Weaver diversity index of each soil sample. Each soil type was seen to have its own unique fingerprint of diversity. pH was observed as the most influential parameter to diversity, and C:N ratio, zirconium and zinc levels also considered important. 24 of the 27 parameters explained the majority of the variation in the diversity of the soil samples, concluding that prokaryote diversity in these soils is determined by complex interactions between a wide range of environmental conditions.

Together this demonstrates that the prokaryote soil community are extremely diverse and dynamic.