The Applied and Environmental Microbiology Group at UFS bioprospects extreme environments (e.g., acid mine drainage and subsurface) and medicinal plants aiming to understand their microbial community structure and composition and explore their biotechnological potential by combining omics, bioinformatics, and biogeochemical techniques. The knowledge gathered from the bioprospecting studies is then used to develop biotechnologies focused on the bioremediation of industrial wastewater contaminated with organic or inorganic compounds and recovering precious metals. In addition, the genomic characterization of endophytes of medicinal plants may lead to the discovery of novel drugs or drugs also biosynthesized by the plants. The discovery could contribute to avoiding overharvesting and, thus, conserving medicinal plants. In recent years, phytoremediation and soil microbiome have also been part of our research.

Principal Investigators
  • Industry Funding. Northwest Metals Group. "Biorecovery of Platinoids using the co-culturing technique at bench-scale." Budget €45 000. Period: March – October 2023. International.
  • Horizon Europe-ERAMIN-DSI (South Africa). The University of the Free State, University of Huelva, University of Aveiro, Central Univ. of Tech., BCMaterials and the National University of Altiplano Puno. "Mine tailings reprocessing, revalorization and risk reduction through sequential innovations in metal recovery, geopolymerization, ceramics and sealing processes (TailingR32Green)." South Africa will carry out the bioleaching of rare earth and cobalt. Budget: €834 524.80 (South Africa-UFS: €199 386). Period: July 2022- July 2025. International.
  • TIA funding "Developing a bacterial consortium to improve mining-contaminated water quality." Budget: €133 678.30. Period: March 2020- December 2023. National.
  • The University of the Free State. "Endophytes in African potato as an alternative source of bioactive compounds: a single genomic approach." Budget: €16 470. Period: July 2022- July 2023. National.
  • BIOGRIP Seed funding. Centre of Mineral Biogeochemistry – CMBG and Applied and Environmental Microbiology Group. “Cyanide biodegradation.” Budget €5 000. Period: November 2021- November 2022. National.
  • Agencia Andaluza del Conocimiento. “Bioprecipitation of metallic copper from acid mine drainage in the Iberian Pyrite Belt." Budget: €98 600.00. PI: Alfonso Corzo. Period: July 2021- July 2023. International.
  • Enriqueta C. Barrera Funding - National Science Foundation-USA. Princeton University - Applied and Environmental Microbiology Group. Collaborative Research "Biogeochemical processes in a subsurface hypersaline environment near the Abiotic Fringe Zone." Budget: € 95 890.00. Period: August 2020- July 2023. International.
  • Collaborative Research: ICDP Drilling into Seismogenic Zones of M2.0-5.5 Earthquakes in South African Gold Mines (DSeis)- Moab Mine: "Bioprospection of Deep Biosphere". In this project, the funding is managed by Ritsumeikan Univ (PI: Hiroshi Ogasawara). Co-Investigator. Universities participants: Ritsumeikan Univ., Kusatsu, Japan; Tohoku Univ., Sendai, Japan; Kyoto Univ., Uji, Japan; Osaka Univ., Toyonaka, Japan; Kochi Core Center, Kochi Univ., Nankoku, Japan; Princeton Univ., Princeton, US; New Mexico Inst. of Technology, Socorro, US; Univ. Witwatersrand, Johannesburg, South Africa; ETH, Zurich, Switzerland; GFZ, Potsdam, Germany; Berlin Free Univ., Berlin, Germany; Indian Inst. Technology, Hyderabad, India; iWater, Bloemfontein, South Africa; Univ. of the Free State (Co-PI: Dr Julio Castillo), South Africa;  Western Australia Univ., Perth, Australia. Period: July 2017- Present. International.

System and AMD

The Applied Environmental Microbiology Group (AEMG) in the Department of Microbiology and Biochemistry. The projects developed in AEMG seek to have a social impact with a positive benefit for the community. From the left are Avela Mqambalala; Alba Gomez; Dinewo Dlalisa; Jameel Alom; Julio Castillo; Aoate Tsimatsima; Andisiwe Matu; Karabello Moloantoa; and Martha Mogale.


Principal Investigator

Dr Julio Castillo. Environmental Microbiology is a multidisciplinary (metagenomics, metatranscriptomics and bio/geochemistry) research area that has defined my career and research interests over the past 12 years. Specifically, I have been focused on the interaction between bacterial and in-/organic compounds (metals and emerging contaminants), addressing water bioremediation (acid and alkaline mine drainage and industrial wastewater) and bio-recovery of precious metals (Cu, Au and rare earth elements), as well as, biofilm formation and syntrophic interactions in extreme environments (acid mine drainage and deep subsurface).


Elfrieda van den Berg (Marketing Manager)
T: +27 51 401 2531

Dilahlwane Mohono (Faculty Officer)
T: +27 58 718 5284

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