Timothy Klein

Timothy Klein


Academic qualifications

2009-2011​:​ BSc (Biotechnology) University of the Western Cape (Cape Town,South Africa)
2012​:​ BSc (Med) (Honours) Medical Biochemistry University of Cape Town
Thesis title​: The role of sexually transmitted bacterial infections in regulating HIV susceptibility in women
2013-2015​:​ MSc (Biotechnology) University of the Western Cape
Thesis title​: The isolation and characterisation of novel natural products from marine bacterial symbionts.


Research Interests

My primary research centres around environmental microbiology. I am particularly interested in the discovery of novel microorganisms and subsequent biodiscovery of relevant microbial products (enzymes, chemicals) and processes with relevant industrial, medical or environmental applications​.

Timothy Klein

Environmental Genomics and Microbiology

University of East Anglia, School of Biological Sciences

PhD title: Developing CRISPR genome engineering tools to understand nitrogen cycling by novel archaea


Nitrification is a key step in the global nitrogen biogeochemical cycle that facilitates the bioavailability of nitrogen. It is a two-step reaction involving the initial oxidation of ammonia to nitrite and the subsequent conversion of nitrites to nitrates. The release of nitrates and nitrous oxide, key players in eutrophication and greenhouse gas emissions respectively, highlight the role of nitrification in environmental change.

The oxidation of ammonia, the rate limiting step in nitrification, is performed by two distinct groups of organisms; ammonia oxidizing bacteria (AOB) and the ammonia oxidizing archaea (AOA). AOA have only recently been discovered and consequently there is limited information available on their ecology, physiology hindering comprehensive comparative studies with AOB. Studies to-date have identified evidence for niche differentiation between these two distinct groups of microorganisms. For example, AOA frequently favour low pH and low ammonia environments although the underlying mechanisms to this adaptation is yet unclear. Therefore, to ensure effective use of agricultural land and mitigate nitrogen losses, it is critical to understand the basis for niche selection in AOA.



This project aims to isolate and characterise a novel AOA strain, characterise the ammonia uptake pathway (absent in AOB) and make a correlation between archaeal cell physiology and their ecological niche.


Research methodology

The project will make use of a powerful CRISPR-Cas9 genetic engineering approach to knockout genes associated with ammonia uptake in archaeal strains.


    Regulation of HIV receptor expression in cervical epithelial cells by Gram-negative bacterial lipopolysaccharide

    Draft Genome Sequences of Three Bacillus Species from South African Marine Sponges


  • Co-awarded a travel grant by the National Research Foundation (South Africa)

Other Information

Practical Demonstrator – Life sciences undergraduate training laboratories (University of the Western Cape).