Research

My research combines a variety of techniques, from laboratory experiments to bioinformatics and mathematical modelling, to understand how organisms, populations and communities respond and adapt to changing environments. Much of my work also uses these data as a basis for predictions of how ecosystem functioning and carbon storage may vary due to global climate change. In particular my research has been focused on the effects of stressors on the functioning and dynamics of microbial populations, however recently I have also investigated the effects of climate on COVID-19 transmission rates. Some highlights from past and ongoing projects are shown below.

Main Research Areas

Effects of Multiple Chemical Stressors on Microbial Populations

Freshwater ecosystems are under an increasing array of threats, especially from a wide range of new and emerging chemical stressors. These ecosystems are underpinned by microbes, which perform key ecosystem functions and services. Therefore, understanding the impacts of chemical stressors on freshwater microbes is key to understanding their impacts at the ecosystem level. We are testing the impacts of chemical stressors in freshwater mesocosms, however this is labour intensive and limited in the number of chemical combinations that can be tested.

By contrast, the limits of chemical testing in the lab can be orders of magnitude higher than in the field. Here in the lab, we are testing the effects of a large array of replicated mixtures of chemicals on microbes and microbial communities, to provide a vast database of first responses to chemicals to answer fundamental questions about interactions among chemical stressors.

This work is with Prof. Tom Bell and Prof. Guy Woodward.

Microbial Thermal Ecology and Evolution

Bacteria and archaea (collectively "prokaryotes") are globally ubiquitous and may comprise in the region of half of the Earth's total biomass. Understanding how these diverse micro-organisms are affected by temperature is therefore key to our understanding of the impacts of climate change on ecosystem functioning.

My work on this broad topic can be roughly divided into two main aspects. Firstly, investigating how the evolution and adaptation of microbial metabolic rates is constrained by temperature, within the framework of Ecological Metabolic Theory. Secondly, understanding how changes in temperature may affect the composition of microbial communities and the impacts that these changes may have on ecosystem functioning.

This work is with Dr. Samraat Pawar and Prof. Tom Bell.

Relevant papers:

  • "Community-level respiration of prokaryotic microbes may rise with global warming" (2019), Smith et. al. | link | press release
  • "Adaptive evolution explains the present-day distribution of the thermal sensitivity of population growth rate" (2020), Kontopoulos et. al. | link
  • "Systematic variation in the temperature dependence of bacterial carbon use efficiency" (2021), Smith et. al. | link
  • [preprint] "Latent functional diversity may accelerate microbial community responses to environmental fluctuations" (2021), Smith et. al. | link

Other Projects (click for details)

Climate as a driver of SARS-CoV-2 transmission rates

Given its similar structure to other viruses that display seasonal dynamics, it has been suggested that SARS-CoV-2 (the causative agent of COVID-19) should display similar responses to environmental factors, with transmission rates peaking in winter. We investigated this potential seasonality, by incorporating environmental parameters into epidemiological models of viral transmission. Our findings suggest a role for the environment, but only when human mobility is not restricted through policy or behaviour.

This work was with Dr. Will Pearse and funded by a NERC grant.

Papers:

  • "Temperature and population density influence SARS-CoV-2 transmission in the absence of non-pharmaceutical interventions" (2021) Smith et. al. | link | press release | Guardian article
  • [Preprint] "Environmental drivers of SARS-CoV-2 lineage B.1.1.7 transmission intensity" (2021) Smith et. al. | link
Evolution in the Absence of Sex

Bdelloid rotifers are a bizarre group of anciently asexual microscopic animals, dubbed an evolutionary "scandal". In order to be successful over an evolutionary time-scale in the absence of sexual recombination, bdelloid rotifers appear to have incorporated an unusually high number of foreign genes into their genomes, via horizontal gene transfer (HGT). My involvement in understanding this process began with working to produce a genome for one rotifer species, Rotaria magnacalcarata, and then mapping putative HGT genes (previously identified via transcriptomics) to the genome assembly in order to confirm their presence.

This was with Prof. Tim Barraclough's group - barralab.

Relevant papers:

  • "Comparative genomics of bdelloid rotifers: Insights from desiccating and nondesiccating species" (2018), Nowell et. al. | link | press release
  • "Horizontal gene transfer in bdelloid rotifers is ancient, ongoing and more frequent in species from desiccating habitats" (2015), Eyres et. al. | link