Soil-Environment
Our lab focuses on molecular microbial biology and ecology in WA environments. Areas include soil amendment for agricultural use as well soil rehabilitation of land use sites. We search for novel microbes as well as analyse which microbes have critical roles in the ecology within the selected environments. From this we hope to increase the efficacy of restorative efforts on land use and polluted sites.
Area of science
Molecular microbiology and ecology
Systems used
Nimbus
Applications used
Megahit, BWA, Samtools, metabat2, checkmThe Challenge
The approach of microbial discovery requires molecular identification of microbes through genomic sequencing. When genomic investigation is applied en masse to an environmental sample, its is known as metagenomics. The technology which facilitates this is known as high throughput sequencing. The issue is data generated by high throughput sequencing is immense and beyond the computation power of standard computers
The Solution
The data that high throughput sequencing contains a lot of information that can be used to determine both phylogeny and function of microbial communities. This is critical as it allows researchers to discover what microbes are present and what metabolic functions they provide in the maintenance and running of the environmental processes. As newer programs develop and sequencing output increases more information can be alluded of the ecological properties of microbes.
The Outcome
The Pawsey Supercomputing Centre’s vast computing resources allow computation analyses to be done on the large datasets generated by high through sequencing. Post sequencing, data analysis is done mostly in silico and without Pawsey’s resources, minimal to no information would be gleamed from the data provided. For example, the assembly of novel genomes from metagenomic data would not be possible without supercomputing as it is an immensely computationally intense workload. Nimbus is the one of the major reasons why our research can even be undertaken in the first place.
