Page 37 - University of Pretoria RESEARCH REVIEW 2018

Professor Cowan first visited CHARS in August 2017, to design a new
joint research programme aimed at investigating the manner in which Arctic tundra microbiomes, in surface soils, intermediate active (seasonally thawing and re-freezing) layers,
and deeper permafrost, respond
to seasonal temperature changes. With Professor Hogg, he established a series of appropriate field sites, designed a comprehensive monthly sampling protocol for the ice-free duration of a full annual cycle,
and selected a series of advanced analytical methods designed to address microbial population and gene expression changes, and to investigate carbon exchange and the effect of bacteriophage on microbiome structure and function.
The project will test the hypotheses that seasonal warming (as a proxy for longer-term climate-related warming) triggers fixed-carbon mobilisation, and that there is a net loss of soil carbon through an annual cycle.
After assembly of the necessary equipment and facilities, the full research programme, in collaboration with emerging academic Eric Bottos, from Thompson Rivers University, Canada, will kick off during the next visit to CHARS, planned for July 2019.
Right: Angel Valverde in the Namib Desert.
Investigating antibiotic- resistance genes
Yashini Naidoo, a member of the Centre for Microbial Ecology and Genomics and jointly supervised by Professor Don Cowan and Dr Rian Pierneef, is mid-way through her PhD studies. Her topic is the environmental distribution of Antibiotic Resistance Genes (ARGs), focusing particularly on the ARGs in Namib Desert soils.
ARGs are a hot topic right now: these genes encode
proteins that are responsible for resistance to clinically
important antibiotics in human and animal pathogenic bacteria. ARGs are often plasmid- encoded, and can be passed from one microorganism to another by a process termed Lateral Gene Transfer.
One of the more important questions relating to ARGs is ‘where do they originally come from?’ It is an accepted concept that soils represent a reservoir of ARGs which, by processes of Lateral Gene Transfer and mutation, may ultimately end up in clinically important bacteria.
Yashini’s project addresses this issue. She is using advanced metagenomic sequence analysis to investigate the diversity of ARGs (there are some 160 different types already catalogued) in desert soils. The choice of desert soils is based on the fact that these soils have relatively little human or domestic animal impact, compared to agricultural soils, so that the ARGs present should better reflect the ancestral genotypes.
She has already made some fascinating discoveries: her desert soil metagenomes contain 75 different classes of ARGs, and she has already discovered one clinically relevant multidrug-resistant plasmid-encoded ARG. She has identified 15 different classes of metal- resistance genes with a few on mobile genetic elements (MGEs). MGEs encoding metal- resistance genes play an important role in the Lateral Gene Transfer of ARGs and the spread of multidrug resistance, increasing the risk to environmental and public health systems.
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