
Professor Penny Johnes
BSc, D.Phil (Oxon.)
Current positions
Professor of Biogeochemistry
School of Geographical Sciences
Contact
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Research interests
Penny is an environmental scientist by background who has worked on the biogeochemistry of aquatic systems, and the impacts of food production and environmental change on the quality of inland and coastal waters for the past 30 years. She has provided advice to a range of UK Government, intergovernmental organisations and international agencies on the nature and scale of nutrient enrichment in waters, the consequences of this enrichment for ecosystem health, and the most effective strategies for the control of nutrient flux from land basd sources to waters. She is currently a member of the UNECE Task Force for Reactive Nitrogen and its Expert Panel on Nitrogen Budgets, advises the Wessex Water Catchment Panel, sat on the Defra Biodiversity Targets Advisory Group and Defra Nutrient Management Expert Group, and was Chair of the Defra Water Expert Advisory Group.
Penny has particular interests in the role of dissolved organic matter as a driver of biodiversity loss in freshwater ecosystems, the potential to develop holistic management strategies which tackle multiple stressors in freshwaters and their catchments, and in ensuring that environmental management policy is underpinned by robust science evidence. She works with researchers across a range of disciplines to meet these challenges, from chemical to biological, environmental, earth, agricultural, social, economic and political sciences.
Her research to date has highlighted the quantitative importance of organic and particulate nitrogen and phosphorus fractions in the total nutrient load transported to and within water bodies; the importance of short-term, extreme flow conditions in controlling the nutrient source/sink function in soils, wetlands and freshwaters; and the necessity when upscaling findings from local to national scale, of defining quasi-homogenous geoclimatic units exerting broadly similar controls on nutrient flux from land to water, as the base unit for modelling. Her work has revealed the finite capacity of both natural and constructed wetlands to store nutrients in transit from land to stream. Her most recent work has revealed the diversity of nutrient, organic, pathogen and ecotoxin contaminants flushed from livestock farming to streams. This research has been critical in helping us to better understand the sources of pollutants within the landscape, the pathways by which material moves from land to stream under differing environmental conditions, the rates at which this material is cycled, transported and transformed instream and the impacts of multiple contaminant stressors on stream ecosystem health.
Penny's ongoing research focus is on characterising the role of dissolved organic matter (DOM) in freshwater ecosystems. Originally she was funded to study its character and flux to freshwaters in relation to nutrient enrichment and climatic controls under the NERC Large Grant DOMAINE programme (2014-2019). More recently her attention has focused on exploring livestock farming as a source of DOM in UK rivers under her NERC QUANTUM project (2023-2026) as part of the NERC and Defra-funded National Freshwater Quality Programme, and in exploring the processing of DOM, focusing on both carbon and nitrogen, by the riverine bacterioplankton community under the NERC MICRO-CYCLE (2025-2028) programme. Her most recent work is funded under the ERC REFRESH Advanced Grant (2024-2029) where she is combining newly developed field experimental approaches using isotope tracers with environmental genomics approaches to reveal the relative rates and mechanisms governing biotic uptake of DOM as nutrient resource by the freshwater biota, and its food web scale and biodiversity impacts. These programmes capitalise on recent novel analytical and in situ monitoring technologies to elucidate the fine scale variability in nutrient flux behaviours and source character in catchments, and the ways in which the hydrochemical signature of nutrient flux from catchments, defined at high resolution, may be used to diagnose the stresses on that system and their likely responses to proposed on-farm mitigation efforts.
Projects and supervisions
Research projects
Reservoir Operations and Nutrient Cycling: managing freshwater nutrients for ecological health and sustainable water supply (AMP8 WINEP Investigation 08BW100005).
Principal Investigator
Description
This project is funded under the Asset Management Planning (AMP) cycle as Water Industry National Environment Programme (WINEP) Investigation 08BW100005. It is a major regulatory research project funded by Bristol…Managing organisational unit
Dates
03/11/2025 to 02/11/2029
Researching the role of dissolved organic matter as a nutrient resource in freshwater ecosystems
Principal Investigator
Managing organisational unit
School of Geographical SciencesDates
19/05/2025 to 30/09/2029
MICRO-CYCLE: Unravelling the role of microbial genomic traits in organic matter cycling and molecular composition along the river continuum
Principal Investigator
Managing organisational unit
School of Geographical SciencesDates
01/01/2025 to 31/12/2027
MICRO-CYCLE: Unravelling the role of microbial genomic traits in organic matter cycling and molecular composition along the river continuum
Principal Investigator
Managing organisational unit
School of Geographical SciencesDates
01/01/2025 to 31/12/2027
Researching the role of dissolved organic matter as a nutrient resource in freshwater ecosystems
Principal Investigator
Description
Freshwaters are losing biodiversity at a higher rate than any other planetary domain. A wide range of stressors are driving this trend, of which climate change and increasing nutrient delivery…Managing organisational unit
Dates
01/08/2024 to 31/07/2029
Thesis supervisions
Is photodegradation the critical pathway in the transformation of DOM in aquatic systems during autumn and winter
Supervisors
Determining nutrient fluxes and sources driving lowland drinking water reservoir ecosystem response
Supervisors
Investigating the bioavailability of dissolved organic nitrogen using freshwater algae
Supervisors
Molecular investigations of the nature, occurrence and behaviour of myo-inositol hexakisphosphate in soils using ion chromatography and high-resolution mass spectrometry
Supervisors
Anthropogenic and lithological controls on production and bioavailability of mineral nutrients in agricultural karst critical zones
Supervisors
Do oxalic acid exudates from mycorrhizal fungi influence the uptake of phosphorus by primary producers in the karst critical zone of south west China?
Supervisors
Investigating Nutrient Cycling, Retention and Bioavailability of Effluents Discharged from Constructed Wetlands
Supervisors
Freshwater Picocyanobacteria and their Organic Diet
Supervisors
Molecular insights into the role of particulate organic matter in biogeochemical cycling in freshwater ecosystems
Supervisors
Direct vs indirect microplastic consumption
Supervisors
Determination of the nature and origins of phosphorus in catchments underlain by Upper Greensand
Supervisors
Understanding the ecological impact of sewage effluent on freshwater environments
Supervisors
Untargeted Chemometric Characterisation of High Resolution Orbitrap Mass Spectra of Riverine and Point Source Dissolved Organic Matter
Supervisors
Microbial responses to physico-chemical alterations during peatland restoration
Supervisors
Publications
Selected publications
01/05/2023Exploring the nature, origins and ecological significance of dissolved organic matter in freshwaters: state of the science and new directions
Biogeochemistry
Microbial uptake kinetics of dissolved organic carbon (DOC) compound groups from river water and sediments
Scientific Reports
Dissolved organic nutrient uptake by riverine phytoplankton varies along a gradient of nutrient enrichment
Science of the Total Environment
Determining patterns in the composition of dissolved organic matter in fresh waters according to land use and management
Biogeochemistry
What do macroinvertebrate indices measure?
Freshwater Biology
Recent publications
16/05/2026Investigating the impact of environmental character on dissolved organic nutrient uptake by freshwater biota using mesocosm experiments
Are laboratory-based stable isotope dosing experiments representative of field-based experiment outcomes when exploring the role of dissolved organic matter in freshwater ecosystems?
Determining the role of DOM as a nutrient resource in freshwater ecosystems using dual-labelled stable isotope probing
Seasonal patterns in preferential uptake of inorganic versus dual-labelled organic compounds by freshwater biota under eutrophic conditions
Legacy of peatland erosion shapes microbial communities during recovery
Communications Earth & Environment


