Soil survival and re-emergence, the continued threat of plague

Hypothesis, Rationale and Significance.
As the causative agent of plague, Yersinia pestis occupies a prominent place in human history as one of the most destructive infectious human diseases. Fleas and rats have been associated with the spread of the disease with research dating back as far as 1914 ensuring that this model of transmission has become scientific dogma. The general acceptance being that within an inveterate rodent population, enzootic plague episodes ensure Y. pestis is passed through a partially resistant host population by fleas and upon transmission into epizootic hosts plague rapidly spreads. Y. pestis is therefore circulating in associated hosts prior to re-emergence in the human population. Although the elegance of this model of transmission has endured, it is hugely oversimplified. For example, in locations where there have been no human cases or mass rodent die-offs, plague often re-emerges decades after an outbreak such as in Algeria, Libya, Madagascar and India 57, 25, 60 and 30 years later respectively. Given that Y. pestis evolved from a near identical (approx. 98% DNA identity) free-living soil borne gastrointestinal pathogen ancestor, Yersinia pseudotuberculosis, it is highly likely that apparently random plague resurgence events are actually due to the bacteria surviving under highly diverse ecological conditions by adopting a 'sit and wait' lifestyle in soil. However, soil samples used for laboratory Y. pestis survival experiments are almost always sterilized and such experiments generally assume that Y. pestis would survive independently and overlook survival strategies such as biofilm formation in soils or in association with other bacteria, fungi, protozoa or nematodes. It is already known that Y. pestis is resistant to trophozoite predation and can survive and replicate intracellularly in Dictyostelium discoideum and Acanthamoeba castellani and both Y. pestis and Y. pseudotuberculosis can also colonise the soil-dwelling nematode worm Caenorhabditis elegans, which has been exploited as an infection model for biotic surface biofilm formation.
Objectives.
Fundamental biological questions underlying the biology and molecular mechanisms controlling the soil-dwelling Y. pestis lifestyle have not been investigated and as a WHO classified re-emerging pathogen which is still endemic in some parts of the world, this significant gap in our understanding of plague biology is of grave concern.
This PhD project therefore aims to conduct an in-depth study to understand how the soil environment, and associated amoebae and nematodes act as significant reservoirs for Y. pestis during inter-epizootic episodes by addressing the following research questions. 1. How do soil environments impact on Y. pestis survival? 2. Does the presence of nematodes and amoeba enhance Y. pestis survival in soil? 3. What are the key genes and molecular mechanisms involved in Y. pestis survival in soil? These questions will be addressed using a variety of approaches including biofilm persistence assays in soils, amoebae and nematodes infection assays along with genomic and transcriptomic studies, transposon insertion sequencing technologies and targeted gene mutations. The project will be suitable for a student who has a keen interest in molecular genetics and infectious disease and is happy to train to work under containment level 3 conditions. Recent substantial NERC funding through to 2026 means that the student will embed into a team working on complementary aspects of this project and will therefore be fully supported throughout.