Project Highlights:

  • Pollution causes millions of premature deaths worldwide, particularly in urban centres
  • The project will assess how microbes deliver specific ecosystem services in cities and explore their potential for increasing sustainability of cities
  • You will characterise urban microbiomes using using environmental genomics approaches

Air pollution causes millions of premature deaths worldwide (1) and is a particular problem in metropolitan areas of developing countries such as Beijing. Alleviating air pollution is an important cornerstone of the UN’s Sustainable Development Goals (Goal 3: Ensure healthy lives and promote well-being for all at all ages; Goal 11: Make cities inclusive, safe, resilient & sustainable). Air pollution is likely to increase further with continuing economic progress in developing countries. Focussing on reduction of pollutant sources such as traffic emissions alone for improving air quality will therefore not be a viable strategy; improving air quality will benefit from enhancing the trapping and removal of pollutants from the atmosphere. The role of vegetation in maintaining and improving air quality is undisputed, but the underlying mechanisms are poorly understood. Pollutant-degrading microorganisms associated with trees and inanimate surfaces have considerable potential as major contributors to improving air quality. For instance, our research shows that tree leaves are colonised by bacteria which can degrade para-nitrophenol (PNP; Palmer et al unpublished), the dominant atmospheric nitrophenol (2), which affects plant and human health and is a component of particulate matter from diesel engines (3) and biomass burning (4). Preliminary evidence suggests that airborne pollutants such as carbon monoxide (Kröber & Schäfer, unpublished) and polycyclic aromatic hydrocarbons are also degraded by bacteria present on plants (5).

Besides air pollution, urban environments also produce pollutants that end up in soils, lakes and rivers. Microorganisms are the key biological agents driving biogeochemical cycles on Earth. The traditional focus of biogeochemistry has been on studying natural environments, although environmental microbiology has sought to characterise and exploit microorganisms involved in bioremediation of pollutants. Despite their pivotal role in mitigation of pollution, the diversity and role of microbiota in our built environment, in particular in heavily urbanised areas has not been studied in much detail and their adaptation to the characteristics of urban environments remains largely unexplored.

This project will assess the diversity and functional potential of urban microbiota using a range of molecular environmental omics approaches and characterise microbial ecosystem services that may mitigate pollution in cities.

Air pollution in Beijing (China) under the Creative Commons Attribution 2.0 Generic license. https://en.wikipedia.org/wiki/Road_space_rationing).


You will use a combination of environmental sampling and laboratory experiments to assess diversity and activity of tree phyllosphere microbial populations. Samples will be obtained from local sites initially and further afield as required. You will use a variety of molecular approaches to characterise microbial community organisation and its ecological function. This will include DNA and RNA extraction and purification, PCR, sequencing using next generation platforms and bioinformatic analysis. You will also measure the rate of environmental processes such as trace gas/pollutant degradation using gas chromatography and liquid chromatography/mass spectrometry, as required.

Training and Skills

CENTA students are required to complete 45 days training throughout their PhD including a 10 day placement. In the first year, students will be trained as a single cohort on environmental science, research methods and core skills. Throughout the PhD, training will progress from core skills sets to master classes specific to CENTA research themes.


Year 1 and 2: Measure degradative activities of microorganisms associated with different samples (vegetation, building materials, soils, waters) in urban areas, focusing on priority air and groundwater pollutants. Characterise urban microbiomes of such samples using high throughput amplicon sequencing of ribosomal marker genes and compare with similar samples from non-urban environments. Apply a metagenomics approach to reveal the identity and metabolic properties of microorganisms carrying out the measured activities. Carry out bioinformatics analyses to identify the potential for degradation of a wide range of pollutants by searching datasets for key genes of relevant pollutant degradation pathways.

Year 3: Assess diversity of microbial communities along transects across an urban centre with adjoining green belt. Analyse patterns of diversity for correlation with environmental factors and assess the potential for ‘managing’ or exploiting urban microbiomes for increasing the future sustainability of cities.

Partners and collaboration (including CASE)

We have already identified key project partners within the CENTA partnership and elsewhere in the UK with whom we will seek opportunities to formalise collaborations during this project.

Further Details

Further details of research in each of the supervisors labs can be obtained from

Dr Hendrik Schäfer

School of Life sciences, University of Warwick

Coventry, CV4 7AL


Prof Gary Bending

School of Life sciences, University of Warwick

Coventry, CV4 7AL