CR2025_40 Life in mines: exploring and harnessing the hidden microbiology of mine tailings, a journey of discovery and restoration

Lead Supervisor: Anne Jungblut, Natural History Museum

Email: a.jungblut@nhm.ac.uk

Co-supervisors: Mark Tibbett, Department of Sustainable Land Management, University of Reading; Benjamin Warr, Phyla Earth

The climate emergency demands a fundamental shift in our energy supply but technologies achieving this require an increased demand in metals and consequent mining. Mineral extraction can often have a negative impact on ecosystems, biodiversity and stakeholder communities. There is a need to improve our understanding of how to rehabilitate post-mining landscapes, especially the waste materials from processing ore. Each year mining generates over 2.5 billion metric tons of processing waste. The wastes generated by copper mining are particularly difficult to manage. Ore bearing rocks are mined and crushed so that metals can be extracted by applying powerful acid solutions to separate the metals from the rock. This process generates a toxic highly erodible sludge called tailings, which are stored in large heaps, many hundred times the size of a football pitch. Across Zambia, the Philippines and many other major copper producing countries past mining activities have left vast tracts of contaminated ‘legacy’ land, while rapidly increasing global copper production creates new wastelands that require remediation. Efforts to rehabilitate these landscapes have failed and our knowledge of the biology and ecological potential of these tailings is very limited.

The Philippines and Zambia possess significant potential for critical minerals such as copper and are strategically positioned to contribute to the world’s green energy transition, yet their mining industry face several challenges including the rehabilitation of landscapes for biodiversity, agriculture and economies to support local communities. Therefore, multidisciplinary approaches are needed, incorporating biology, geology and environmental engineering to develop sustainable interventions with local communities that will mitigate environmental and societal issues.

The soil microbiome performs important ecosystem functions but receives limited attention in restoration. Microorganisms play a crucial role in biogeochemical cycles of soils as well as mineral and metal transformations. Molecular analyses have shown that diverse microbial communities including bacteria, archaea, fungi and protists are also abundant in mine tailings, but their taxonomic richness, diversity and biogeography remain poorly characterised. However, the few existing relevant studies indicate that there is significant genomic and functional novelty in these systems that demand further study to understand key ecological processes driven by microbes in mine tailings and elucidating their beneficial role in the growth of plants in degraded mined land. Certain bacteria and fungi interact with the roots of plants in ways that enhance plant growth, health and resistance to environmental stressors. Of particular interest are mycorrhiza, a symbiosis between fungi and plants. Fungi help the plants to avoid poisoning itself with toxic metals, while enhancing plant growth and nutrient uptake. The diazotrophic bacteria group rhizobia also form symbiotic relations with leguminous plants and these symbionts can fix atmospheric nitrogen but may be negatively affected by metals.

The legume tree Pongamia pinnata is tolerant of high copper concentrations and infertile soils. It supplies its own nitrogen through a symbiotic association with bacteria and forms mycorrhizal symbiosis. It is a drought, salinity, acidity and waterlogging tolerant tree and prime candidate for phytoremediation. Importantly it produces seeds that contain a non-edible oil that has as a low carbon alternative to fossil diesel. P. pinnata oil and leaves also contain biological compounds called karanjin and pongamol, that have been proven to be useful as biological alternatives to pesticides and have anticancer and antidiabetic properties.

The aims of the PhD project are to explore the (un)natural history of microbial communities in copper mine tailings. This will include microbiome community composition and their metabolic capacity that drive geochemical cycling in mine tailings in the Philippines and Zambia; and determine how microbiomes in particular bacteria and fungi interact with roots and their beneficial effects for the plants in overcoming extreme conditions of copper contamination and even contribute to mechanisms leading to phytoremediation.

This project will take an integrative approach, combining a unique fieldwork opportunity in Zambia and laboratory-based methodologies including state-of-the-art sequencing techniques in the UK. The PhD student will use DNA sequencing, bioinformatics, statistical and microbial community structure analysis and metagenomic techniques. The plant-microbe interactions will be studied and documented using laboratory-based experiments.

Training opportunities: 

• Molecular techniques: DNA extraction methodologies from environmental samples, PCR, amplicon and shotgun metagenomic high throughput sequencing.
• Bioinformatic and statistical analysis: Microbial community structure analysis, 16S rRNA and 18S rRNA gene and fungal ITS metabarcoding, metagenomics, phylogenetics, statistics, R.
• Fieldwork skills: Hands-on training in sampling techniques, recording protocols, plant health and fungal mycorrhiza assessment.
• International case partner: Opportunity of a minimum 3-month research stay with the CASE partner in Zambia.
• Science communication skills: Opportunities in participation in public talks and outreach activities at the NHM
• Personal and professional development delivered by University of Reading and the NHM postgraduate office.

Student profile: 

The project would suit a candidate interested in environmental microbiology and mycology, and bioinformatics. Basic molecular and sequence analysis skills would be beneficial for the project.

Please note: Due to the nature of this project and to comply with visa regulations, only Home students should apply.

Co-Sponsorship details: 

This project will receive a CASE award from Phyla Earth.

References:

• Degani E et al. A critical review of Pongamia pinnata multiple applications: From land remediation and carbon sequestration to socioeconomic benefits, Journal of Environmental Management, 2022, p. 116297, https://doi.org/10.1016/j.jenvman.2022.116297
• Herrington et al Development of a site-specific system for the rehabilitation of a former copper mine, Sto. Niño, Philippines, in B Abbasi, J Parshley, A Fourie & M Tibbett (eds), Mine Closure 2023: Proceedings of the 16th International Conference on Mine Closure, Australian Centre for Geomechanics, Perth, https://doi.org/10.36487/ACG_repo/2315_091
• Hooper M et al , Arctic cyanobacterial mat community diversity decreases with latitude across the Canadian Arctic, FEMS Microbiology Ecology, Volume 100, Issue 6, June 2024, fiae067, https://doi.org/10.1093/femsec/fiae067
• Peddle, S. D., Bissett, A., Borrett, R. J., Bullock, P., Gardner, M. G., Liddicoat, C., Tibbett, M., Breed, M. F., & Krauss, S. L. (2023). Soil DNA chronosequence analysis shows bacterial community re-assembly following post-mining forest rehabilitation. Restoration Ecology, 31(3), Article e13706. https://doi.org/10.1111/rec.13706
• Tibbett (2024) Post-mining ecosystem reconstruction, Current Biology, Volume 34, Issue 9, R387 – R393