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SEEDS INTERNSHIP: Isolation of anaerobic acidophiles with metal bioremediation potential
Project Description
Acidic pit lakes are extreme environments containing high concentrations of metals and sulphate. Recent studies highlight the potential of the microbial communities present in these lakes to immobilise metals as sulphides through sulphate reduction, which is particularly relevant for bioremediation. Our project aims to determine the sources of organic carbon consumed by sulphate reducing microorganisms in acidic waters; this internship will focus on the cultivation, enrichment and isolation of sulphate-reducing microorganisms from acidic waters. The student will work in the laboratory, setting up anoxic bacterial cultures in sulphate-containing media and testing different organic substrates (electron donors) to assess which conditions support the growth of sulphate reducers. The student will monitor culture development and use the most promising conditions to progress towards isolation and identification of acid-tolerant sulphate reducers. This internship will also provide the opportunity to develop skills in bioinformatics, by working with 16S rRNA sequencing data to characterise the microbial community present in acidic pit lakes. The outcomes of this internship will help to improve our understanding of microbial communities present in acidic pit lakes and will provide key knowledge for future experiments aimed to determine the main organic carbon sources for sulphate reduction.
Research themes
Project Specific Training
Internship project work plan: Full-time
The intern will be supported by the supervisory team and will work closely with a PhD student day-to-day. Training will be provided throughout the internship, with weekly check-ins and clear objectives.
Weeks 1-2: Laboratory training and culture set-up
The training will focus on the isolation of acidophilic organisms using different culturing approaches. This will serve to set the first cultures of anaerobic acidophiles for the coming weeks. This will have as objective to familiarise the inter with the cultivation of anaerobic acidophiles.
Week 3: Molecular methods
The student will continue working with culture to obtain isolates of anaerobic acidophiles. This will be complemented by DNA extraction of isolates and/or environmental samples, and subsequent PCR amplification.
Weeks 4 – 6: Sequence analysis and community profiling
The student will be trained in the processing and interpretation of Sanger sequencing results for isolate identification, and will be trained in metagenomics and amplicon concepts, analysing 16S datasets from pit lakes samples to characterise the microbial community.
Week 7: Synthesis and communication
The student will be able to synthesise the results and will have the opportunity to prepare and present the results to the research group and other members of the department.
Internship project work plan: Part-time
The intern will be supported by the supervisory team and will work closely with the PhD student day-to-day. Training will be provided throughout the internship, with weekly check-ins and clear objectives. Weeks 1-3: Laboratory training and culture set-up The training will focus on the isolation of acidophilic organisms using different culturing approaches. This will serve to set the first cultures of anaerobic acidophiles for the coming weeks. This will have as objective to familiarise the inter with the cultivation of anaerobic acidophiles. Week 4: Molecular methods The student will continue working with culture to obtain isolates of anaerobic acidophiles. This will be complemented by DNA extraction of isolates and/or environmental samples, and subsequent PCR amplification. Weeks 5-7: Sequence analysis and community profiling The student will be trained in the processing and interpretation of Sanger sequencing results for isolate identification. The student will be able to synthesise the results and will have the opportunity to prepare and present the results to the research group and other members of the department.
Project supervisor/s
Carmen Falagan
School of the Environment and Life Sciences
University of Portsmouth
carmen.falagan@port.ac.uk
Kenneth Wasmund
School of the Environment and Life Sciences
University of Portsmouth
kenneth.wasmund@port.ac.uk