Dr Thulani Makhalanyane


[email protected]

Tel: 012 420 6976


BSc (Hons) Microbiology (North-West University);

MSc (Biotechnology) Cum Laude (University of the Western Cape);

PhD Biotechnology (University of the Western Cape)


Teaching course involvement

GTS 354: Genome Evolution and Phylogenetics

MLB 721: Molecular and Cellular Biology

GTK 704: Advanced Discussion Topics

GTK 703: Research project

Short Biography:

I received my undergraduate education at the North West University (Mafikeng Campus), where I completed a BSc (Hons) degree in Microbiology. My honours degree project involved assessing ground water quality in the North West province, and represented my first foray into research. I absolutely enjoyed my research experience and became motivated to pursue further research experience. I then moved to the University of the Western Cape, Department of Biotechnology, for further studies, earning both an MSc (granted Cum laude, 2009) and PhD (2012).

I moved to the University of Pretoria in 2012, working briefly as a technical officer at the Centre for Microbial Ecology and Genomics, Department of Genetics. I began a postdoctoral fellowship in 2013, continuing to study the microbial ecology of desert systems with some expansion into projects focused on microbial genomics. I am currently a lecturer in the Department of Genetics, where I teach metagenomics. The broad focus of my research remains within the field of microbial ecology and specifically the ecology of niche communities associated with desert terrestrial systems. I currently serve as a young ambassador for the International Society for Microbial Ecology.


Description of Research Interest/Focus

  1. Marine Microbial Ecology of the Southern Ocean

The Southern Ocean is a crucial ecosystem as it has been shown to connect the world’s ocean. There is considerable evidence showing that this ecosystem harbors a high diversity of macro fauna, which is paralleled by even higher levels of microbial diversity. We will use the existing monitoring lines (e.g. GOODHOPE Transects) to profile microbial communities (bacteria, archaea, fungi and Protista) along three depths (i.e. surface, middle, deep), during summer and winter, over a three-year period. Through microbial community structure and gene content (metagenomics), functional analysis (metaproteomics), and profiling the diverse secondary metabolites and bioactive compounds (metabolomics). This study aims to profile microbial response at a variety of levels to changing environmental conditions. These findings will allow us to better the relationship between microbial diversity and functional processes.


  1. Understanding the effect of lifestyle, diet and geography on the gut microbiome

Microbial communities and their genes (the “human microbiome”) are recognized to significantly affect health. However, crucial aspects on the structure, function and diversity of healthy human microbiota remain poorly understood, especially in understudied populations such as in South Africa. This study aims to reduce this knowledge deficit regarding the state of the gut microbiota of South African populations through application of “omic-based’ methods. Specifically, the study aims to apply metagenomics, metaproteomics and metabolomics to assess the effect of lifestyle, diet and geographic location on the human gut microbiome.


  1. The impacts of global climate change on biodiversity and carbon functionality in areas subject to increased aridity

Soils store a third of total terrestrial carbon (C). Soil organic carbon (SOC) is the core of ecosystems functioning and therefore essential for soil fertility and health, which in turn sustain agriculture. Global change has led to alterations in temperatures and decreased more variable rainfall regimes. These factors have led to an increased proportion of areas, which are now under threat due to desertification (the transition of lands towards greater aridity). This study proposes a wide survey of microbial communities along an aridity gradient (bacteria, archaea, fungi, and protista). We will assess the diversity of microbial communities in South African soils along an aridity gradient. We will further measure soil carbon levels along this transect, and relate these to microbial diversity, through functional analyses, using carbon fixation assays, which will allow us to determine the contribution of microbial guilds to these processes.



  1. Bezuidt, O.K.I., Pierneef, R., Gomri, A.M., Adesioye, F., Makhalanyane, T.P., Kharroub, K., Cowan, D.A. 2016. The Geobacillus pan-genome: implications for the evolution of the genus. Frontiers in Microbiology 7:723.
  2. Miyambo, T., Makhalanyane, T.P., Cowan, D.A., Valverde, A. 2016. Plants of the Fynbos biome harbour host species-specific bacterial communities. FEMS Microbiology Letters. In press
  3. Adesioye, F.A., Makhalanyane, T.P., Biely, P., Cowan, D.A. 2016. Phylogeny, classification and function of acetyl xylan esterases. Enzyme and Microbial Technology
  4. Van Goethem, M.W., Makhalanyane, T.P., Valverde, A., Cary, S.C., Cowan, D.A. 2016. Characterization of bacterial communities in lithobionts and soil niches from Victoria Valley, Antarctica. FEMS Microbiology Ecology. In press.
  5. Vikram, S., Guerrero, L., Makhalanyane, T.P., Le, P., Seely, M., Cowan, D.A. 2016. Metagenomic analysis provides insights into functional capacity in a hyperarid desert soil niche community. Environmental Microbiology. In press.
  6. Makhalanyane, T.P., Van Goethem, M.W., Cowan, D.A. 2016. Microbial diversity and functional capacity in polar soils. Current Opinion in Biotechnology, 38, 159-166.
  7. Bezuidt, O., Makhalanyane, T.P., Mohammed, A., Karima, K., Cowan, D.A. 2015. Draft genome sequence of thermophilic Geobacillus sp. strain Sah69, isolated from Saharan soil, South-East Algeria, 3(6), e01447-15.
  8. Cowan, D.A., Ramond, J-B., Makhalanyane, T.P., De Maayer, P. 2015. Metagenomics of extreme environments. Current Opinion in Microbiology. Accepted
  9. Makhalanyane, T.P., Valverde, A., Velázquez, D., Gunnigle, E., Van Goethem, M.W., Quesada, A., Cowan, D.A. 2015. Ecology and biogeochemistry of cyanobacteria in soils, permafrost, aquatic and cryptic polar habitats. Biodiversity and Conservation. Accepted
  10. Gunnigle, E., Ramond, J-B., Guerrero, L., Makhalanyane, T.P., Cowan, D.A. 2015. Draft genomic DNA sequence of the multi-resistant Sphingomonas sp. strain AntH11 isolated from an Antarctic hypolith. FEMS Microbiology Letters. Accepted
  11. Makhalanyane, T.P., Valverde, A., Gunnigle, E., Frossard, A., Ramond, J-B., Cowan D.A. Microbial Ecology of hot desert edaphic systems. FEMS Microbiology Reviews (In press).
  12. Valverde, A, Makhalanyane, T.P., Seely, M., Cowan, D.A. Cyanobacteria drive community composition and functionality in rock-soil interface communities. Molecular Ecology (In press).
  13. Ronca, S., Frossard, A., Guerrero, L.D., Makhalanyane, T.P., Aislabie, J.M. Cowan, D.A. Draft genome Sequence of Sphingomonas sp. strain Ant20, isolated from oil-contaminated soil on Ross Island, Antarctica. Genome Announcements (In press)
  14. Ramond, J-B, Makhalanyane, T.P., Tuffin, M.I., Cowan, D.A. Normalization of environmental metagenomic DNA enhances the discovery of under-represented microbial community members. Letters in Applied Microbiology
  15. Valverde, A, Makhalanyane, T.P., Cowan, DA. 2014. Contrasting assembly processes in a bacterial metacommunity along a desiccation gradient. Frontiers in Microbiology doi: 10.3389/fmicb.2014.00668
  16. Ferreras, E.R., De Maayer, P., Makhalanyane, T.P., Guerrero, L.D., Aislabie, J.M. Cowan, D.A. 2014. The draft genome sequence of Microbacterium sp. CH12i, isolated from shallow groundwater in Cape Hallet, Antarctica. Genome Announcements 2(4):e00789-14. doi:10.1128/genomeA.00789-14.
  17. Adriaenssens, E.M., Guerrero, LD., Makhalanyane, T.P., Aislabie, J.M., Cowan, D.A. 2014. Draft genome sequence of the aromatic hydrocarbon-degrading bacterium Sphingobium sp. strain Ant17 isolated from Antarctic soil. Genome Announcements. 2(1) e00212-14. doi: 10.1125/genomeA.00212-14.
  18. Cowan, D.A., Makhalanyane, T.P., Dennis, P.G., and D.W, Hopkins. 2014. Microbial Ecology and biogeochemistry of continental Antarctic soils. Frontiers in Microbiology: 5:154 doi: 10.3389/fmicb.2014.00154
  19. Guerrero L.D., Makhalanyane T.P., Aislabie, J.M., Cowan, D.A. 2014. Draft genome sequence of Williamsia sp. strain D3, isolated from the Darwin Mountains, Antarctica. Genome Announcements 2(1):e01230-13.
  20. Makhalanyane, T.P., Valverde, A., Birkeland, N-K., Cary, S.C., Tuffin, I.M., and D.A. Cowan. 2013. Evidence for successional development in Antarctic hypolithic bacterial communities. The ISME Journal. 7, 2080-2090
  21. Makhalanyane, T.P., Valverde, A., Lacap, D.C., Pointing, S.B., Tuffin, I.M., D.A Cowan. 2013. Evidence of species recruitment and development of hot desert hypolithic communities. Environmental Microbiology Reports. 5 (2), 219-224.
  22. Stomeo, F., Makhalanyane T.P., Pointing, S.B., Stevens, M., Cary S.C., Tuffin, I.M., D.A Cowan. 2012. Abiotic drivers influence the microbial diversity in permanently cold soil horizons of a maritime-associated Antarctic Dry Valley. FEMS Microbiology Ecology. 82 (2), 326-340.
  23. Cowan, D.A., Sohm, J.A., Makhalanyane T.P., Capone, D.G, Green, T.G.A., Cary S.C, I.M Tuffin. 2011. Hypolithic communities: important nitrogen sources in Antarctic desert soils. Environmental Microbiology Reports, 3, 581-586.

Book Chapter:

Makhalanyane, T.P., Pointing, S.B., Cowan, D.A (2014). Chapter 13: Lithobionts: Cryptic and Refuge niches. In Antarctic Terrestrial Microbiology. Editor. D.A. Cowan. Springer-Verlag Berlin Heidelberg. ISBN: 978-3-642-45212-3


Published Conference Proceedings:

Cowan, DA, Khan, N, Makhalanyane, T.P., and A. Valverde. 2011. Antarctic hypolithic communities – model systems for a cryptic astrobiological lifestyle. Proceedings of the International Astronomical Congress. Cape Town, October 2011 4pp.

Last edited by Kishen Mahesh

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