How does surface soil geomorphology and land-use influence the soil microbial ecosystems in south eastern Australia? Insights gained from DNA sequencing of the soil metagenome.

Soils are a vital resource in Australian agricultural production systems. The sustained health of this resource is dependent on how land-use and management practices impact on the underlying soil microbial community that delivers vital ecosystem goods and services. Collaborative research between Department of Primary Industries Victoria (Melbourne, Australia) and the J.Craig Venter Institute in Rockville (Maryland, USA) research has applied a stepwise DNA-based approached to resolve the influence of contrasting soils (calcarosol and ferrosol) and land-use (managed and remnant vegetation) on the soil bacterial communities. This approach generated small insert clone libraries based on 16S ribosomal RNA (rRNA) sequences for three samples; calcarosol; managed (cropped) and remnant samples and a ferrosol, managed (grazed dairy pasture) sample. A deeper, whole genome shotgun sequencing approach based on Titanium 454 pyrosequencing technology yielded detailed information on the structural and functional elements of the microbial community in two samples (calcarosol; managed and remnant). All samples yielded unique microbial communities with <1% shared sequences overall. Samples collected from the same regional soils (e.g. highly alkaline calcarosol soil) but with contrasting land-use patterns (e.g. cropped and remnant) were more similar with 13% shared sequences. Samples collected from different regional soils but with similar management shared 4% sequences. The greatest differences in communities were those with contrasting soil, and land-use characteristics with <3% shared sequences. Of the known taxa, Acidobacteria, Cyanobacteria and Planctomycetes were relatively prevalent in the acid soil and Actinobacteria, alpha and delta Proteobacteria prevail in the alkaline, remnant soils. In the alkaline managed soil, Bacteroidetes/chlorobi taxa prevail. We chose the calcarosol samples for additional Sanger and 454 FLX sequencing to evaluate functional genes, with specific emphasis on nutrient cycling and disease suppression pathways. The results provide insight for ecosystem function and management decisions in the context of climate change and resource sustainability.