Professional summary

Dan obtained a B.Sc. in Biology from Cardiff University, in 2002. Following this, he stayed at Cardiff University to pursue doctoral studies, where he developed molecular approaches to investigate food webs in soil ecosystems. For this work, he obtained his PhD in Molecular Ecology from Cardiff University in 2007.

Following a short postdoctoral position at Cardiff University, in 2008, Dan joined the Centre for Ecology & Hydrology (CEH) in Oxford as a Scientific Officer (band 6), focussing his research on the application of biospectroscopy and DNA sequencing to determine single-cell and strain level microbial ecophysiology. In 2015 he was promoted to Higher Scientific Officer (band 5) and in 2018 he took over as Group Leader for the UKCEH Molecular Ecology group. In 2021 he was promoted to a principal scientific (band 4) role, and from January 2024 is taking on the role of acting deputy Science Area Head (SAH) for the Soils & Land Use department.

Brief CV

2024 - Deputy Science Area Head - Soils and Land use Science Area.

2020 - Present: Secretariat Lead, UK Environmental Observation Framework (UKEOF) DNA working group.

2020 - Present: Visiting lecturer, Reading University - Molecular Methods for Species Identification and Survey.

2018 - Present: Group leader - Molecular Ecology research group

2014 - Present: Senior Scientific Officer, Centre for Ecology & Hydrology, Wallingford.

2008 - 2014: Higher Scientific Officer, Centre for Ecology & Hydrology, Wallingford. 

2007 to 2008: PDRA, Cardiff University.

 

Research Interests:

Freshwater microbiology

Microbes in freshwater ecosystems play a crucial role in major global biogeochemical cycles, including carbon cycling, the cycling of essential macronutrients such as nitrogen and phosphorous, and the breakdown of organic pollutants. Despite their importance, we lack an understanding of the processes that determine community composition, and the role that community composition plays in controlling nutrient cycling. Dr Read's research explores these issues by examining spatial and temporal changes in lotic microbial communities. Much of this work has been done on the river Thames, using the Thames Initiative as a platform for sample collection and contextual data, and well as overseas, under UKCEH's National Capability SUNRISE research programme.

Example publications:

  1. Ward, J., et al. (2020). Large-scale survey of seasonal drinking water quality in Malawi using in situ tryptophan-like fluorescence and conventional water quality indicators. Science of The Total Environment.
  2. Sorensen, J., et al. (2020). In-situ fluorescence spectroscopy indicates total bacterial abundance and dissolved organic carbon. Science of The Total Environment.
  3. Read, D., et al. (2015). Catchment-scale biogeography of riverine bacterioplankton. The ISME Journal 9(2)
  4. Read, D., et al. (2014). Weekly flow cytometric analysis of riverine phytoplankton to determine seasonal bloom dynamics. Environmental Science: Processes & Impacts 16(3)

Anthropogenic impacts on freshwater ecosystems, including antimicrobial resistance (AMR) in the environment

Freshwaters are some of the most highly impacted environments due to our reliance on them for water abstraction and waste removal. I am interested in the impact of chemicals (organic pollutants, pharmaceuticals) and nutrients on the structure and function of microbial ecosystems. One aspect of this is the impact of farm and human effluent waste on the prevalence and composition of pathogenic microbes and in particular, antimicrobial-resistant bacteria. This work is supported by the NERC funded REHAB project, in collaboration with the University of Oxford and the Animal and Plant Health Agency.

Example publications:

  1. Shaw, L., et al. (2020). Niche and local geography shape the pangenome of wastewater- and livestock-associated Enterobacteriaceae. bioRxiv
  2. Gweon, H., et al. (2019). The impact of sequencing depth on the inferred taxonomic composition and AMR gene content of metagenomic samples. Environmental Microbiome 14(1)
  3. Maio, N., et al. (2019). Comparison of long-read sequencing technologies in the hybrid assembly of complex bacterial genomes. Microbial genomics 5(9)

The application of environmental DNA (eDNA) for assessing biodiversity

Understanding how biodiversity is changing over time is critical to determine how human activity is changing ecosystems and the services they provide. However, conventional approaches using morpho-taxonomy, whilst often providing a gold standard, are often time-consuming and rely on a dwindling pool of expertise. DNA based approaches for assessing community composition have great potential to reduce costs, both through reductions in sampling and identification time, as well as the ability to identify cryptic genetic diversity. My research focussed on developing new approaches for assessing biodiversity based on high throughput sequencing and applying this to metabarcoding of bulk invertebrate samples as well as metabarcoding of environmental DNA (eDNA). I am involved in the National Honey Monitoring Scheme with uses DNA metabarcoding to describe honey bee floral resource utilisation, as well as examining relationships with bacterial communities and eDNA traces of bee pathogens in honey.

Example publications:

  1. Harper, L., et al. (2019). Environmental DNA (eDNA) metabarcoding of pond water as a tool to survey conservation and management priority mammals. Biological Conservation 238(), 108225.]
  2. Handley, L., et al. (2019). Temporal and spatial variation in distribution of fish environmental DNA in England’s largest lake. Environmental DNA 1(1), 26-39.
  3. Hänfling, B., et al. (2016). Environmental DNA metabarcoding of lake fish communities reflects long-term data from established survey methods. Molecular Ecology 25(13)

 

PhD students

Lead supervisor:

Claire Robertson (2019 - ). Supervised with Steve Ormerod (Cardiff University) and Jeremy Biggs (Freshwater Habitats Trust). Project: Using environmental DNA to understand the role of connectivity in pond ecosystems

Katharine Moss (2020 - ). Supervised with Richard Evershed (University of Bristol) and Penny Johnes (University of Bristol). Project: Understanding the ecological role of organic matter (OM) in urban freshwaters

Meriel Anderson (2023 - ). Supervised with Soon Gweon (University of Reading) and Kerry Walsh (Environment Agency). Project: Understanding freshwater ecosystem health from a microbial perspective

 

Completed PhDs:

Jade Ward (2016-2020). Co-supervised with Dan Lapworth (BGS) and Steve Pedley (University of Surrey). Project: Application of novel field sensors for tracking pathogens in drinking water supplies in Africa.

Liz Davidson (2018- 2022). Co-supervised with Steve Thackeray (UKCEH Lancaster) and Steve Ormerod (Cardiff University). Project: Molecular resolution of historic and contemporary food web interactions in lake ecosystems.

Kevin Chau (2018 - 2022). Co-supervised with Nicole Stoesser (University of Oxford) and Sarah Walker (University of Oxford). Project: Applying sewage epidemiology to understand AMR dynamics in non-clinical settings

Amy Thorpe (2019 - 2023). Supervised with James Bendle (University of Birmingham). Project: Unlocking the Toolbox of Soil Bacterial Biomarkers

 

Panels, committees and memberships

Steering committee member for the NERC Environmental Omics Facility (NEOF)

Member of the NERC Peer Review College

Co-director of the NERC GW4 FRESH CDT PhD training programme.

Co-director of the NERC Environmental Omics Synthesis (EOS) programme.

Secretariat lead for the UK DNA working group of the Environmental Observation Framework (UKEOF).

Associate editor for the journal Microbiome.

Associate editor for the journal Environmental Microbiome.

Selected publications