An interview with Professor Jim Prosser

Professor Jim Prosser FRS Chair of Molecular and Cell Biology at the University of Aberdeen and a member of the Microbiology Society, tells us more about how soil microbes play an essential role in creating and maintaining soil fertility, and therefore crop production.

© Jim Prosser

Why are soil microbes important to microbiology?

Soil microbes play essential roles in creating and maintaining soil fertility and therefore crop production. An important microbial group, the ammonia oxidisers gains energy by oxidising ammonia to nitrite, which is then oxidised to nitrate. This process, nitrification, leads to multimillion-pound losses of ammonia-based fertilisers and is responsible, directly and indirectly, for most terrestrial emissions of the greenhouse gas nitrous oxide.

Tell us more about your research.

We study the ecology of ammonia oxidiser communities, particularly the influence of soil pH on their diversity and activity. This presented us with a paradox, as cultivated ammonia oxidisers could not grow in acidic media, but nitrification occurs, often at high rates, in acidic soils.

In the early 1990s, it became possible to characterise natural microbial communities by sequencing genes amplified from DNA extracted directly from soil, eliminating the need for laboratory culture. When we applied this approach to bacterial ammonia oxidisers, we discovered unexpectedly high diversity of these organisms and abundant novel groups. Some of these were selected in acidic soils, suggesting adaptation of uncultivated ammonia oxidisers to acidic conditions.

A further revolution was the discovery of archaeal ammonia oxidisers. Bacteria and archaea comprise the two major domains of life and archaea were traditionally thought to exist only in extreme environments. Molecular techniques showed them to be abundant in soil and many soil archaea are ammonia oxidisers, frequently more abundant and active than bacterial ammonia oxidisers. We discovered that some archaeal ammonia oxidisers were selected in acidic soils. We then isolated the first acidophilic ammonia oxidiser, which only grows under acidic conditions and is found globally in acid soils. It therefore provides the best of explanation for nitrification in, and fertiliser loss from, these important soils.

Why is this research important?

Our research has shown that bacterial and archaeal ammonia oxidisers are selected by different fertiliser strategies and that nitrous oxide emissions from soil are much greater when ammonia oxidation is dominated by bacteria rather than archaea. This provides the potential to control and mitigate terrestrial greenhouse gas emissions by modifying fertiliser strategies and shows that a greater understanding of the activity and diversity of soil microbes can impact the economic and environmental costs of agriculture.


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