Publications

Agricultural plastic film mulch (PFM) covers ca. 50 million hectares of the Earth’s surface and has revolutionized agriculture, particularly in arid and semi-arid regions, by improving crop yields, water use efficiency, farmer incomes and feeding an extra 85 million people in China alone. However, concerns are growing about the impact of PFM-derived microplastics (MP) on soil quality, the food chain, and the environment. Here we show that current research on the effects of MP in agricultural soils is limited by inconsistent methodologies and unrealistic experimental concentrations, leading to major uncertainty in assessing the true risks associated with PFM use. Furthermore, we highlight the need for standardized protocols, experiments using realistic MP concentrations, and a better understanding of the relative contribution of PFM to MP pollution to develop informed policies. Furthermore, while biodegradable alternatives show promise, their significantly higher costs (2–3 times that of conventional LDPE PFM) and variable performance across different agricultural environments present economic and practical challenges that must be addressed through targeted policy incentives and continued technological innovation. Our findings suggest that while further research is conducted, managing PFM to reduce environmental impact, rather than imposing ill-informed bans on plastic use, is crucial to balance food security and sustainable development goals. Exploring “zero-leakage” instead of “zero-use” approaches to PFM should be the primary aim to help mitigate potential risks while preserving the substantial benefits of this agricultural technology.

Microplastic (MP) pollution can exert significant pressure on soil ecosystems, however, the interactive effects of MPs on soil bacterial, fungal and protist communities remains poorly understood. Soil macrofauna, such as earthworms, can be directly affected by MPs, potentially leading to a range of feedbacks on the soil microbial community. To address this, we conducted a microcosm experiment to examine the effects of conventional (i.e., polyethylene, polystyrene) and biodegradable MPs (i.e. PBAT, polylactic acid) on the structure of the soil bacterial, fungal, and protist communities in the presence or absence of earthworms. We found that MP contamination negatively affected the diversity and composition of soil microbial and protist communities, with smaller-sized conventional MPs having the most pronounced effects. For example, compared with the unamended control, small-sized polyethylene MPs both significantly reduced the Shannon diversity of soil bacteria, fungi, and protist by 4.3 %, 37.0 %, and 9.1 %, respectively. Biodegradable MPs increased negative correlations among bacteria, fungi, and protists. However, earthworms mitigated these effects, enhancing the diversity and altering the composition of these communities. They also increased the niche width and stability of the soil microbial food web network. Our study indicated that earthworms help attenuate the response of soil microorganisms to MPs stress by influencing the diversity and composition of soil microorganisms and soil physicochemical properties and underscores the importance of considering macrofauna in MPs research.

The rhizosphere is a key interface between plants, microbes and the soil which influences plant health and nutrition and modulates terrestrial biogeochemical cycling processes.Recently it has been shown that the rhizosphere environment is far more dynamic than previously recognized, with evidence emerging for diurnal rhythmicity in rhizosphere chemistry and in the composition of rhizosphere microbial communities.Rhythmicity of the rhizosphere microbiome is in part linked to the host plant's circadian rhythm, although evidence also points to some heterotrophic rhizosphere bacteria and fungi possessing rhythmicity.We review the evidence for diurnal rhythmicity in the composition and abundance of rhizosphere microbial communities, and its link to the plant circadian clock.Factors which may drive microbial rhythmicity in the rhizosphere are discussed, including diurnal change in the flux and composition of root exudates, rhizosphere physico-chemical properties and plant immunity mechanisms.The potential contributions of microbial processes to community rhythmicity are considered, including self-sustained microbial rhythms, bacterial movement into and out of the rhizosphere, and microbe-microbe interactions.We also consider evidence that changes in microbial composition mediated by the plant circadian clock may affect microbial function and its significance for plant health and broader soil biogeochemical cycling processes.We identify key knowledge gaps and approaches which could help to resolve the spatial and temporal variation and functional significance of rhizosphere microbial rhythmicity.This includes unravelling the factors which determine the oscillation of microbial activity, growth and death, and cross-talk with the host over diurnal time frames.We conclude that diurnal rhythmicity is an inherent characteristic of the rhizosphere environment and that temporal factors should be considered and reported in experimental studies conducted on the rhizosphere.

Extreme flood events are predicted to have a negative impact on soil quality. Currently, there is a lack of information about the effect of agricultural practices on soil functioning and microbial processes under these events. We hypothesized that the impact of flooding on soil quality will be exacerbated when crop residues are present in the soil as they will induce more extreme anaerobicity. A spring extreme flood event (10 °C, 9 weeks) was simulated in mesocosms containing an arable sandy-loam soil low in nutrients. The main treatments were (1) with and without flooding and (2) with and without maize residue addition (8 Mg ha−1). We monitored changes in soil chemical quality indicators (e.g. pH, salinity, Fe3+, P, C, NH4 +, NO3 − and organic N), greenhouse gas (GHG) emissions (CO2, CH4, N2O) and soil microbial community composition (PLFAs) during a prolonged flood period (9 weeks) and an 8-week "recovery" period after flooding. In comparison to the other treatments, flooding in the presence of crop residues resulted in a dramatic drop in soil redox potential. This was associated with the enhanced release of Fe and C into solution and an increase in CH4 emissions. In contrast, maize residues reduced potential nitrate losses and N2O emissions, possibly due to complete denitrification and microbial N immobilization. Both flooding and maize residues stimulated microbial growth and promoted a shift in microbial community composition. Following floodwater removal, most of the soil quality indicators returned to the levels of the control treatment within 5 weeks. After this short recovery phase, no major impact of flooding could be observed on plant growth (maize pot-grown). Overall, we conclude that both extreme flooding and management regime negatively impact upon a range of soil quality indicators (e.g. redox, GHG emissions); however, the soil showed high resilience and recovered quickly after floodwater removal. Further work is required to investigate the impact of repeated extreme flood events on soil quality and function over longer timescales.

Typically, half of the nitrogen (N) fertiliser applied to agricultural fields is lost to the wider environment. This inefficiency is driven by soil processes such as denitrification, volatilisation, surface run-off and leaching. Rainfall plays an important role in regulating these processes, ultimately governing when and where N fertiliser moves in soil and its susceptibility to gaseous loss. The interaction between rainfall, plant N uptake and N losses, however, remains poorly understood. In this study we use numerical modelling to predict the optimal N fertilisation strategy with respect to rainfall patterns and offer mechanistic explanations to the resultant differences in optimal times of fertiliser application. We developed a modelling framework that describes water and N transport in soil over a growing season and assesses nitrogen use efficiency (NUE) of split fertilisations within the context of different rainfall patterns. We used ninety rainfall patterns to determine their impact on optimal N fertilisation times. We considered the effects of root growth, root N uptake, microbial transformation of N and the effect of soil water saturation and flow on N movement in the soil profile. On average, we show that weather-optimised fertilisation strategies could improve crop N uptake by 20% compared to the mean uptake. In drier years, weather-optimising N applications improved the efficiency of crop N recovery by 35%. Further analysis shows that maximum plant N uptake is greatest under drier conditions due to reduced leaching, but it is harder to find the maximum due to low N mobility. The model could capture contrasting trends in NUE seen in previous arable cropping field trials. Furthermore, the model predicted that the variability in NUE seen in the field could be associated with precipitation-driven differences in N leaching and mobility. In conclusion, our results show that NUE in cropping systems could be significantly enhanced by synchronising fertiliser timings with both crop N demand and local weather patterns.

Survival and movement of Escherichia coli O157:H7 in both soil and vermicompost is of concern with regards to human health. Whilst it is accepted that E. coli O157:H7 can persist for considerable periods in soils, it is not expected to survive thermophilic composting processes. However, the natural behavior of earthworms is increasingly utilized for composting (vermicomposting), and the extent to which earthworms promote the survival and dispersal of the bacterium within such systems is unknown. The faecal material produced by earthworms provides a ready supply of labile organic substrates to surrounding microbes within soil and compost, thus promoting microbial activity. Earthworms can also cause significant movement of organisms through the channels they form. Survival and dispersal of E. coli O157:H7 were monitored in contaminated soil and farmyard manure subjected to earthworm digestion over 21 days. Our findings lead to the conclusion that anecic earthworms such as Lumbricus terrestris may significantly aid vertical movement of E. coli O157 in soil, whereas epigeic earthworms such as Dendrobaena veneta significantly aid lateral movement within compost. Although the presence of earthworms in soil and compost may aid proliferation of E. coli O157 in early stages of contamination, long-term persistence of the pathogen appears to be unaffected.

The flux of nutrients into rivers is rising due largely to inputs from the expansion and intensification of agriculture along with inputs from treatment of human waste. This trend is set to continue due to changing climate and increasing population while we attempt to balance food security and environmental impact. While water quality legislation focuses on inorganic nutrients due to their bioavailability, the proportion of the total nitrogen (N) flux, which is organic in its molecular composition is important in many riverine systems. Despite this, the impact of organic N on ecosystem function is currently poorly understood. Here we address part of this knowledge gap using compound-specific stable isotope probing to investigate the extent to which dissolved organic matter substrates are bioavailable to stream biota and if they can be directly assimilated.Stable isotope probing was used to identify and quantify the routes of biotic uptake of organic N and carbon (C) into stream biota. Here, we added 15N labelled (nitrate, ammonium, glucosamine, sheep urine) and doubly labelled (15N/13C) substrates (glutamic acid, urea, glycine) to in-stream mesocosms containing water and epilithon, and bryophyte communities from the River Conwy North Wales, UK. Samples of epilithon and bryophyte were removed from the incubations after 2, 6, 12, 24 and 48 h and rates of assimilation of the labelled substrate were determined using bulk 15N/13C, followed by compound-specific 15N/13C analysis of extracted amino acids. This method allowed us to demonstrate the assimilation of labelled organic substrates into newly biosynthesised proteinaceous amino acids and to determine if they were utilised as intact organic molecules.The findings showed that the majority of the organic N substrates tested were directly bioavailable for utilisation as intact molecules by the stream biota, except for urea where transformation occurred before uptake. The data also showed that there were differences in the rates of assimilation both between the organic substrates added and between the epilithon and bryophyte communities. This work illustrates the analytical power of using doubly labelled 13C, 15N compounds in a stable isotope probing experiment, as the ability to trace the utilisation of both the N and C simultaneously had provided significant new insights in the biotic assimilation of organic-N substrates. Our findings confirm the importance of organic nutrients in ecosystem function and the need for changes to water quality legislation to reflect this.

The hyper-arid core of the Atacama Desert represents one of the oldest and driest regions of the world and is characterized by high aridity (precipitation <2 mm y^-1), hypersaline soil conditions, extremes in temperature (-5 °C to 50 °C), intense UV irradiation and low organic matter content. Despite this, the Yungay area within the hyper-arid core is capable of supporting vegetation adapted to these extreme environmental conditions, including <i>Distichlis spicata</i> and <i>Suaeda foliosa</i>, which access deep groundwater resources. Little is known, however, about the below-ground microbial community that these plants support. To understand plant-microbe interactions in this environment, we investigated the physicochemical properties in the rhizosphere soils of <i>D. spicata</i> and <i>S. foliosa</i>. In addition, DNA was extracted from the rhizosphere soil and 16S rRNA gene amplicon sequencing performed to describe the taxonomic composition of the bacterial community. Our results revealed significant differences in the physicochemical properties between the rhizosphere soils of the two native plants. <i>D. spicata</i> showed higher Electrical Conductivity (EC), while <i>S. foliosa</i> had elevated ammonium concentrations. The microbial composition also varied between the plant species: Firmicutes (Bacillota), Proteobacteria (Pseudomonadota), Halobacteria, and Actinobacteriota (Actinomycetota) were dominant in both plant rhizosphere samples, but their relative abundance differed. In this context, Halobacteria were highly represented in the soils of <i>D. spicata</i> and Firmicutes (Bacillota) in those from <i>S. foliosa</i>. Furthermore, bacterial genera such as <i>Enterococcus</i> were only present in the <i>S. foliosa</i> rhizosphere, while <i>Natrinema</i> was highly represented in soil from under <i>D. spicata</i> (33.4%) in comparison to <i>S. foliosa</i> (1.5%). The microbial community of <i>D. spicata</i> was strongly influenced by EC, whereas that of <i>S. foliosa</i> correlated more with ammonium levels. These findings advance our understanding of microbial community adaptation in one of Earth's most extreme environments and provide new insights into plant-microbe interaction in hyper-arid soils.

It is well established that air travel plays a key role in the global spread of many enteric and respiratory diseases, including COVID-19. Even with travel restrictions (e.g. mask wearing, negative COVID-19 test prior to departure), SARS-CoV-2 may be transmitted by asymptomatic or pre-symptomatic individuals carrying the virus. Due to the limitation of current clinical surveillance approaches, complementary methods need to be developed to allow estimation of the frequency of SARS-CoV-2 entry across international borders. Wastewater-based epidemiology (WBE) represents one such approach, allowing the unbiased sampling of SARS-CoV-2 carriage by passenger cohorts entering via airports. In this study, we monitored sewage in samples from terminals (n = 150) and aircraft (n = 32) at three major international airports in the UK for 1–3 weeks in March 2022. As the raw samples were more turbid than typical municipal wastewater, we used beef extract treatment followed by polyethylene glycol (PEG) precipitation to concentrate viruses, followed by reverse transcription quantitative PCR (RT-qPCR) for the detection of SARS-CoV-2 and a faecal indicator virus, crAssphage. All samples taken from sewers at the arrival terminals of Heathrow and Bristol airports, and 85% of samples taken from sites at Edinburgh airport, were positive for SARS-CoV-2. This suggests a high COVID-19 prevalence among passengers and/or airport staff members. Samples derived from aircraft also showed 93% SARS-CoV-2 positivity. No difference in viral prevalence was found before and after COVID-19 travel restrictions were lifted. Our results suggest that WBE is a useful tool for monitoring the global transfer rate of human pathogens and other disease-causing agents across international borders and should form part of wider international efforts to monitor and contain the spread of future disease outbreaks.

The fecal indicator organism (FIO) Escherichia coli is frequently used as a general indicator of sewage contamination and for evaluating the success of shellfish cleaning (depuration) processes. To evaluate the robustness of this approach, the accumulation, retention, and depuration of non-pathogenic E. coli , pathogenic E. coli O157:H7 and norovirus GII (NoV GII) RNA were evaluated using a combination of culture-based ( E. coli ) and molecular methods ( E. coli , NoV GII) after exposure of mussels ( Mytilus edulis ) to water contaminated with human feces. We simulated water contamination after a point-source release from a combined sewer overflow (CSO) where untreated wastewater is released directly into the coastal zone. All three microbiological indicators accumulated rapidly in the mussels, reaching close to maximum concentration within 3 h of exposure, demonstrating that short CSO discharges pose an immediate threat to shellfish harvesting areas. Depuration (72 h) in clean water proved partially successful at removing both pathogenic and non-pathogenic E. coli from shellfish tissue, but failed to eradicate NoV GII RNA. We conclude that current EU standards for evaluating microbiological risk in shellfish are inadequate for protecting consumers against exposure to human norovirus GII found in polluted marine waters.

There is a growing body of evidence that suggests that both biodegradable and conventional (non-degradable) microplastics (MP) are hazardous to soil health by affecting the delivery of key ecological functions such as litter decomposition, nutrient cycling and water retention. Specifically, soil fauna may be harmed by the presence of MPs while also being involved in their disintegration, degradation, migration and transfer in soil. Therefore, a comprehensive understanding of the interactions between MPs and soil fauna is essential. Here, we conducted a 120-day soil microcosm experiment applying polyethylene (PE) and polylactic acid (PLA), in the absence/presence of the earthworm Eisenia nordenskioldi to estimate the relative singular and combined impact of MPs and earthworms on the soil bacterial community. Our findings revealed contrasting effects of PE and PLA on the composition and diversity of soil bacteria. All treatments affected the community and network structure of the soil bacterial community. Compared to the control (no MPs or earthworms), PE decreased bacterial alpha diversity, while PLA increased it. Patescibacteria were found to be significantly abundant in the PE group whereas Actinobacteria and Gemmatimonadetes were more abundant in PE, and PLA and earthworms groups. The presence of earthworms appeared to mediate the impact of PE/PLA on soil bacteria, potentially through bacterial consumption or by altering soil properties (e.g., pH, aeration, C availability). Earthworm presence also appeared to promote the chemical aging of PLA. Collectively, our results provide novel insights into the soil-fauna-driven impact of degradable/nondegradable MPs exposure on the long-term environmental risks associated with soil microorganisms.

Cross-sectional survey results from a toileting behaviour survey conducted between the 27th to the 28th of June 2022. Participants (<em>n</em> = 2109) were aged 18 years or older and were living in the UK. The survey consisted of 17 closed-ended questions, with 7 of the questions addressing specific demographic topics and 10 questions addressed toileting behaviour. The questionnaire was designed by a team consisting of environmental microbiologists, public health specialists, wastewater-based epidemiologists, and social scientists, based on the study objectives and incorporating information from previous studies on the same topic. First, self-report questions were asked on typical frequency of urination and defecation, followed by self-reports of frequency of urination and defecation at a variety of locations including at home, at work, educational buildings, transport hubs, and in public toilets. The comfort in urination/defecation at these locations for defecation and urination was also measured. Other questions about toileting behaviour and health monitoring were measured by statements with a 5-point Likert scale (e.g., strongly disagree to strongly agree).