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Dr Daniel Padfield

Dr Daniel Padfield

NERC Independent Research Fellow

 Environment and Sustainability Institute 

 

Environment and Sustainability Institute, University of Exeter, Penryn Campus, Penryn, Cornwall, TR10 9FE, UK

Overview

I am a NERC Independent Research fellow and my research is broadly interested in understanding how microbial communities respond to environmental change. Specifically, my fellowship is exploring whether climate change will worsen the problem of antibiotic resistance. To do this, I use a variety of sequencing, experimental, and modelling approaches.

I am also committed to reproducible and open science. All of the code and data from my projects are freely available online through GitHub and archived on Zenodo.

I have been using R for >10 years and authored and maintain the R packages nls.multstart and rTPC and specialise in the wrangling and manipulation of large datasets and statistical analyses. I am also a bioinformatician, processing and analysing everything from 16S sequencing to de novo genome assembly, the latter using bash. Basically a bit of jack-of-all-trades master of none!

Qualifications

PhD., Biological Sciences 2013-2017 Environment & Sustainability Institute, University of Exeter, Cornwall, UK.

The direct and indirect effects of warming on aquatic metabolism

Combined ideas from metabolic theory with a variety of experimental approaches to further our understanding of how warming will impact photosynthesis and respiration across different temporal and organisational scales.

MBiolSci., Zoology 2008-2012 Animal & Plant Sciences Department, University of Sheffield, UK.

First class degree honours. Bergmann’s rule in fish in the North Sea: a snapshot from a single year and a temporal perspective

Career

2023 - present: NERC IRF fellow, University of Exeter, Cornwall Campus.

2021 - 2022: Postdoctoral Research Fellow with Michiel Vos, University of Exeter, Cornwall Campus.

2017 - 2020: Postdoctoral Research Fellow with Angus Buckling, University of Exeter, Cornwall Campus.

2012 - 2017: PhD in Biological Sciences with Gabriel Yvon-Durocher, University of Exeter, Cornwall Campus.

Throughout my research career, I have balanced work with caring for my partner.

Links

Research group links

Research

Research interests

Climate change

Community ecology

Microbial ecology

Experimental evolution

Thermal adaptation

Open science

Research projects

My current research project

Understanding the effect of temperature on the ecology and evolution of antimicrobial resistance.

The evolution and spread of antimicrobial resistance (AMR) are major threats to global health. Recent correlational studies have shown that levels of AMR increase at higher temperatures in environmental and pathogenic bacteria. However, an almost complete lack of empirical evidence to explain the mechanisms of these broad scale-patterns limits our ability to quantify, understand, and ultimately control potential synergistic impacts of climate change and AMR. 

One of the major ways AMR spreads is through horizontal gene transfer (HGT), which allows bacteria to acquire DNA from individuals other than their immediate ancestors and is driven by mobile genetic elements, such as plasmids. This project’s key research question is whether the spread of plasmids and antimicrobial resistance increases at higher temperatures. If this is the case, then climate change may increase environmental reservoirs of AMR that can then spread into clinically relevant bacteria.

This project is made of 4 main objectives:

1. Explore variation in the response of environmental and human-associated bacteria to temperature.

Theory predicts that human-associated bacteria should have higher optimal temperatures and a narrower tolerance range than environmental bacteria.

2. Understand how plasmid transfer rate changes across temperatures in environmental and human-associated bacteria.

Plasmid transfer rate is linked to the growth rates of the donor and recipient bacteria. We therefore expect plasmid transfer across different bacteria to be highest close to their optimal temperatures. 

3. Understand how selection for resistance changes across temperatures.

We will measure the cost of plasmid carriage and the impact of environmentally-relevant antibiotic concentrations on susceptible bacteria across their full temperature range to understand how the selection for resistance changes with warming.

4. Understand how plasmid spread and dynamics of environmental and human-associated bacteria change across temperatures in natural sewage communities

We will use sequencing to test whether plasmids spread more at higher environmental temperatures in natural communities, and investigate whether human associated bacteria survive better in a warmer world.

Other things I have done and retain interest in!

Macroevolutionary dynamics in micro-organisms

Understanding the ecological and evolutionary forces that structure prokaryote diversity is a central objective in microbial ecology. In macro-organisms, a common approach to do this is to use comparative phylogenetics to look back through macroevolutionary time, but this approach is difficult to do bacteria due a lack of a fossil record and difficulties in actually sampling extant diversity! To tackle this in my most recent postdoc with Mick Vos, we used targeted deep sequencing of the protein coding gene rpoB to sample the phylum Myxococcota across >70 sites in Cornwall. I then did a lot of comparative phylogenetics - and I mean A LOT - and revealed that biome specialists very rarely transitioned to specialise in another biome. Instead, generalists mediated transitions between biome specialists.

Long-term coexistence of a model microbial community

Using microbes in experiments to test theory from community ecology requires having a highly stable community with species that coexist with each other. However, most synthetic communities do not actually test for long-term coexistence, or even check whether the species can coexist together. Together with Elze Hesse, Angus Buckling, Meaghan Castledine, and others, we created a model microbial community consisting of 5 species that (dis)assembled and have coexisted for hundreds (if not thousands) of generations.

These species have been sequenced using long and short-read technology and we have high quality reference genomes of each one. This community is now being utilised across many projects being used to understand how species interactions change through evolutionary time, how plasmids spread and are maintained in communities, and how species interactions change under environmental stress.

Temperature-dependent changes to host–parasite interactions 

Thermal performance curves (TPCs) are used to predict changes in species interactions, and hence, range shifts, disease dynamics and community composition, under forecasted climate change. Species interactions might in turn affect TPCs. We investigated how temperature-dependent changes in a microbial host–parasite interaction (the bacterium Pseudomonas fluorescens, and its lytic bacteriophage, SBWΦ2Φ2) changed the host TPC and uncovered the ecological and evolutionary mechanisms underlying these changes.

Publications

Journal articles

Lear L, Padfield D, Hesse E, Kay S, Buckling A, Vos M (In Press). Copper Reduces the Virulence of Bacterial Communities at Environmentally Relevant Concentrations.
Bagra K, Kneis D, Padfield D, Szekeres E, Teban-Man A, Coman C, Singh G, Berendonk TU, Klümper U (2024). Contrary effects of increasing temperatures on the spread of antimicrobial resistance in river biofilms. mSphere Abstract.  Author URL.
Vos M, Padfield D, Quince C, Vos R (2023). Adaptive radiations in natural populations of prokaryotes: innovation is key. FEMS Microbiol Ecol, 99(12). Abstract.  Author URL.
Barton S, Padfield D, Masterson A, Buckling A, Smirnoff N, Yvon‐Durocher G (2023). Comparative experimental evolution reveals species‐specific idiosyncrasies in marine phytoplankton adaptation to warming. Global Change Biology, 29(18), 5261-5275. Abstract.
Sierocinski P, Stilwell P, Padfield D, Bayer F, Buckling A (2023). The ecology of scale: impact of volume on coalescence and function in methanogenic communities. Interface Focus, 13(4). Abstract.  Author URL.
Bartlett A, Padfield D, Lear L, Bendall R, Vos M (2022). A comprehensive list of bacterial pathogens infecting humans. Microbiology, 168(12).
Swan GJF, Bearhop S, Redpath SM, Silk MJ, Padfield D, Goodwin CED, McDonald RA (2022). Associations between abundances of free-roaming gamebirds and common buzzards <i>Buteo buteo</i> are not driven by consumption of gamebirds in the buzzard breeding season. ECOLOGY AND EVOLUTION, 12(5). Author URL.
Lear L, Padfield D, Dowsett T, Jones M, Kay S, Hayward A, Vos M (2022). Bacterial colonisation dynamics of household plastics in a coastal environment. Sci Total Environ, 838(Pt 4). Abstract.  Author URL.
Lear L, Padfield D, Inamine H, Shea K, Buckling A (2022). Disturbance-mediated invasions are dependent on community resource abundance. Ecology, 103(8). Abstract.  Author URL.
Castledine M, Sierocinski P, Inglis M, Kay S, Hayward A, Buckling A, Padfield D (2022). Greater Phage Genotypic Diversity Constrains Arms-Race Coevolution. Frontiers in Cellular and Infection Microbiology, 12
Castledine M, Padfield D, Sierocinski P, Soria Pascual J, Hughes A, Mäkinen L, Friman V-P, Pirnay J-P, Merabishvili M, de Vos D, et al (2022). Parallel evolution of Pseudomonas aeruginosa phage resistance and virulence loss in response to phage treatment in vivo and in vitro. eLife, 11 Abstract.
Castledine M, Padfield D, Sierocinski P, Pascual JS, Hughes A, Mäkinen L, Friman V-P, Pirnay J-P, Vos DD, Buckling A, et al (2022). Parallel phage resistance - virulence trade - offs during clinical phage therapy and in vitro. Access Microbiology, 4(5).
Padfield D, O'Sullivan H, Pawar S (2021). <i>rTPC</i> and <i>nls.multstart</i>: a new pipeline to fit thermal performance curves in r. METHODS IN ECOLOGY AND EVOLUTION, 12(6), 1138-1143. Author URL.
van Houte S, Padfield D, Gómez P, Luján AM, Brockhurst MA, Paterson S, Buckling A (2021). Compost spatial heterogeneity promotes evolutionary diversification of a bacterium. J Evol Biol, 34(2), 246-255. Abstract.  Author URL.
Sierocinski P, Soria Pascual J, Padfield D, Salter M, Buckling A (2021). The impact of propagule pressure on whole community invasions in biomethane-producing communities. iScience, 24(6). Abstract.
Barneche DR, Hulatt CJ, Dossena M, Padfield D, Woodward G, Trimmer M, Yvon-Durocher G (2021). Warming impairs trophic transfer efficiency in a long-term field experiment. Nature, 592(7852), 76-79.
Silk MJ, McDonald RA, Delahay RJ, Padfield D, Hodgson DJ (2020). CMR<scp>net</scp>: an <scp>r</scp> package to derive networks of social interactions and movement from mark–recapture data. Methods in Ecology and Evolution, 12(1), 70-75. Abstract.
Castledine M, Sierocinski P, Padfield D, Buckling A (2020). Community coalescence: an eco-evolutionary perspective. Philos Trans R Soc Lond B Biol Sci, 375(1798). Abstract.  Author URL.
Padfield D, Vujakovic A, Paterson S, Griffiths R, Buckling A, Hesse E (2020). Evolution of diversity explains the impact of pre-adaptation of a focal species on the structure of a natural microbial community. ISME J, 14(11), 2877-2889. Abstract.  Author URL.
Castledine M, Padfield D, Buckling A (2020). Experimental (co)evolution in a multi-species microbial community results in local maladaptation. Ecol Lett, 23(11), 1673-1681. Abstract.  Author URL.
McNicol CM, Bavin D, Bearhop S, Bridges J, Croose E, Gill R, Goodwin CED, Lewis J, MacPherson J, Padfield D, et al (2020). Postrelease movement and habitat selection of translocated pine martens <i>Martes martes</i>. ECOLOGY AND EVOLUTION, 10(11), 5106-5118. Author URL.
Padfield D, Castledine M, Pennycook J, Hesse E, Buckling A (2020). Short-term relative invader growth rate predicts long-term equilibrium proportion in a stable, coexisting microbial community.
Castledine M, Buckling A, Padfield D (2019). A shared coevolutionary history does not alter the outcome of coalescence in experimental populations of Pseudomonas fluorescens. J Evol Biol, 32(1), 58-65. Abstract.  Author URL.
Hesse E, Padfield D, Bayer F, van Veen EM, Bryan CG, Buckling A (2019). Anthropogenic remediation of heavy metals selects against natural microbial remediation. Proceedings of the Royal Society B: Biological Sciences, 286(1905), 20190804-20190804. Abstract.
Padfield D, Castledine M, Buckling A (2019). Temperature-dependent changes to host-parasite interactions alter the thermal performance of a bacterial host.
Padfield D, Buckling A, Warfield R, Lowe C, Yvon‐Durocher G (2018). Linking phytoplankton community metabolism to the individual size distribution. Ecology Letters, 21(8), 1152-1161. Abstract.
García-Carreras B, Sal S, Padfield D, Kontopoulos D-G, Bestion E, Schaum C-E, Yvon-Durocher G, Pawar S (2018). Role of carbon allocation efficiency in the temperature dependence of autotroph growth rates. Proc Natl Acad Sci U S A, 115(31), E7361-E7368. Abstract.  Author URL.
Schaum CE, Student Research Team, Ffrench-Constant R, Lowe C, Ólafsson JS, Padfield D, Yvon-Durocher G (2018). Temperature-driven selection on metabolic traits increases the strength of an algal-grazer interaction in naturally warmed streams. Glob Chang Biol, 24(4), 1793-1803. Abstract.  Author URL.
Padfield D, Lowe C, Buckling A, Ffrench-Constant R, Student Research Team, Jennings S, Shelley F, Ólafsson JS, Yvon-Durocher G (2017). Metabolic compensation constrains the temperature dependence of gross primary production. Ecology letters, 20(10), 1250-1260. Abstract.
Padfield D, Yvon-Durocher G, Buckling A, Jennings S, Yvon-Durocher G (2016). Rapid evolution of metabolic traits explains thermal adaptation in phytoplankton. Ecol Lett, 19(2), 133-142. Abstract.  Author URL.


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External Engagement and Impact

Administrative responsibilities

I am co-chair of the Cornwall Disability Network that aims to provide a support system for staff and students at the University of Exeter’s Penryn campus, to share experiences within a secure and confidential environment and to seek guidance and support regarding disability issues. We also aim to raise awareness of issues affecting those with disability and carers at the Penryn campus, and to help promote a culture that supports disabled and caring staff and students through all areas of campus life.


Other

Software

I developed and maintain two R packages that are useful to people fitting non-linear models and thermal performance curves.

nls.multstart is an R package that allows more robust and reproducible non-linear regression compared to nls() or nlsLM(). This package is designed to work with the tidyverse, harnessing the functions within broom, tidyr, dplyr and purrr to extract estimates and plot things easily with ggplot2.

rTPC is an R package that helps fit thermal performance curves (TPCs) in R. rTPC contains 26 model formulations previously used to fit TPCs and has helper functions to help set sensible start parameters, upper and lower parameter limits and estimate parameters useful in downstream analyses, such as cardinal temperatures, maximum rate and optimum temperature.

Teaching

Supervision / Group

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