Optimisation of RNA extraction methods to identify active microbes involved in Microbially Induced Carbonate Precipitation in soils
Supervisor: Dr Carla Comadran Casas
Industry Partner: Environmental Reclamation Services
School: Engineering
Description:
Microbial-Induced Calcite Precipitation is an emerging field of research with applications in environmental remediation of soil pollutants, geotechnics, and structural engineering. Identification of autochthonous soil bacteria driving the process is key towards engineering systems. Efforts in bacteria isolation and characterisation have used culture plates, known to represent a very low percentage of overall bacterial community, and holistic characterization of bacterial communities through DNA extraction plus sequencing. DNA sequencing provides information on bacterial community composition but cannot infer active bacteria. Isolation of RNA is critical for the identification of active bacteria driving MICP.
MICP involves applying significant quantify of salts (CaCl2 and NH4) and the biological process induces soil solution pH of 9. Literature shows both pH and salt content affect RNA and DNA partitioning to the aqueous phase during phenol extraction. The goal of this internship will be to advance the understanding of abiotic effects of high salt content and alkaline pH on RNA and DNA partition into the aqueous phase in the context of MICP as a first step towards optimising the extraction method.
The student will conduct a series of experiments in a laboratory setting. A factorial experiment design will be used to determine the effect of salts on DNA and RNA extraction. Soil samples (~4 g) will be treated with solutions of increasing concentrations of salts (i.e., 50 to 1000 mM) and adjusted pH (6 to 10). This covers MICP applications in bioremediation and geotechnical engineering. RNeasy PowerSoil Total RNA commercial kit will be used to co-extract DNA and RNA. PCR will be used to test the presence of DNA and RNA in the extracted sample. Results of this experiment will be used to determine salt content and pH thresholds and inform future development of a rapid assay.
Through this internship the student will learn how microorganisms, specifically bacteria, affect soil physicochemical properties, and how civil engineers and microbiologists are working together to engineer bacterial processes for environmental (e.g., pollution remediation) and geotechnical (e.g., prevent liquefaction) applications. The ideal candidate should be a highly motivated and independent person with interest in laboratory research, soil engineering and microbiology. As an intern you will work in the Water and Environment research laboratory of the Advanced Research Centre conducting laboratory work using chemistry and microbiology analytical techniques under the supervision of Dr Carla Comadran Casas.