Publications

Grass species may acquire different forms of nitrogen (N) to reduce competition for the same resources. Climate change influences the availability of soil N and is therefore likely to cause shifts in N forms acquired by plants, thereby affecting their competitive interactions. We investigated the effects of warming on the uptake of different N forms and competitive interactions of Festuca ovina and Anthoxanthum odoratum in a pot experiment. The plants were grown either in monocultures or mixture, and at ambient or elevated temperature (+10 °C), and supplied with 13C and 15N isotopes to test for treatment effects on the relative uptake of ammonium, alanine or tri-alanine. Both grass species took up relatively more N supplied as ammonium than as alanine or tri-alanine when grown under ambient conditions in monoculture. In contrast, when grown in mixtures, F. ovina took up the three supplied N forms in equal amounts, whereas A. odoratum switched to tri-alanine as the main N form. Under warmed conditions, both species took up the N forms equally, irrespective of competition treatments. We have shown that grass species grown in mixture and under ambient conditions reduce competition by acquiring different N forms. Warming increased the availability of inorganic N in the soil and therefore deregulated the need for differential uptake of N forms.

Ruminants, and to a lesser extent monogastric farm animals, are known to be natural reservoirs of Escherichia coli O157:H7, and contact with contaminated faeces has been linked to human infection. This study used a nontoxigenic, chromosomally marked, lux reporter strain to compare the persistence and activity (bioluminescence) of E. coli O157:H7 over 21 days in the faecal liquor of five farm animals: horse, sheep, cow, pig and piglet. Samples were inoculated with the lux E. coli O157:H7 (7.82 log CFU mL−1) and stored at 20 ± 1 °C. The organism was recovered from all samples throughout the experimental period, although lower numbers were recovered from horse faecal liquor relative to all other types (P<0.001). The organisms' activity declined in all samples over time and no luminescence could be detected in any sample 21 days postinoculation. However, activity did increase greatly within pig and piglet faeces during initial stages of monitoring and overall luminescence was greater in piglet samples compared with all other samples (P<0.001). This is the first study to demonstrate how both the persistence and metabolic activity of E. coli O157:H7 notably varies within a range of ruminant and nonruminant animal faeces. Further research is needed to elucidate the factors that govern differential persistence and metabolic activity of E. coli O157:H7 within such matrices.

Soil microbial community is essential for maintaining and improving ecosystem functioning in ecological restoration practice and is intimately linked with the plant community. However, little is known on how soil microbial communities respond to the functional characteristics of plant communities. Here we investigated the changes in plant community functional attributes, soil properties, and soil microbial community characteristics of four land restoration (vegetation) types in a subtropical plateau region. The relative contributions of soil abiotic properties and plant community functional attributes to variation in microbial community composition and function were then assessed. We found that plant community attributes, soil properties, and the soil microbial communities differed significantly among land restoration types, and the plant functional traits of dominant species and soil properties jointly determined soil microbial community structure and functions. Specifically, soil microbial community structure was significantly linked to the community-weighted mean (CWM) of plant functional traits, soil water content, and soil organic carbon. Soil microbial carbon-metabolic functions were tightly correlated with the CWM of leaf dry matter content, specific leaf area, and specific root length. Variance partitioning also revealed that the CWM of plant functional traits and soil variables cooperatively explained 67% and 64% variation in soil microbial community structure and carbon-metabolic functions. Meanwhile, significant correlations were found between variation in microbial community composition and carbon-metabolic functions. In conclusion, our observations demonstrate that soil microbial community characteristics were governed by dominant species in plant communities across land restoration types, mainly due to differences in plant functional traits and soil resource driven by plant traits.

The discharge of human-derived wastewater represents a major threat to water quality with the potential for waterborne disease outbreaks mainly associated with enteric viruses. To prevent illnesses, indicators associated with fecal contamination are monitored in polluted areas, however, their prevalence often does not correlate well with viral pathogens. In this study, we used crAssphage, a recently discovered human-specific gut-associated bacteriophage, for the surveillance of wastewater-derived viral contamination. Untreated and treated wastewater, surface water, sediment and mussel samples were collected monthly over 1 year from the Conwy River and estuary (UK) and were analyzed for crAssphage marker by quantitative PCR. This is the first long-term catchment-to-coast scale study of environmental crAssphage concentrations. CrAssphage was detected in all sample types and showed no distinct seasonal pattern. CrAssphage concentrations were 2 × 105-109 genome copies (gc)/L in all untreated wastewater influent and 107-108 gc/L in secondary treated effluent samples, 3 × 103 gc/L-3 × 107 gc/L in surface water samples (94% positive) and 2 × 102-104 gc/g sediment (68% positive) and mussel digestive tissue (79% positive). CrAssphage concentrations were 1-5 log10 higher than human enteric virus titers (norovirus, sapovirus, adenovirus, polyomavirus). Our results indicate that crAssphage is well suited to tracking human wastewater contamination and pollution risk assessment in aquatic environments.

The impact of soil parent material on soil chemical conditions, needle composition and tree growth

Amino acids and peptides are important regulators of ecosystem functioning due to their potential role as direct nutrient sources for plants and soil microbes. However, the turnover and driving factors of these compounds in agricultural soils remain poorly understood. This study aimed to reveal the short-term fate of 14C-labeled alanine and tri-alanine derived C under flooding conditions of the top (0–20 cm) and sub-horizons (20–40 cm) of subtropical paddy soils taken from four long-term (31 years since treatment) nitrogen (N) fertilization regimes (i.e., without fertilization, NPK, NPK with straw return (NPKS) or with manure (NPKM)). Amino acid mineralization was strongly affected by the N fertilization regime and soil depth, while peptide mineralization was only distinct between soil layers. The average half-life of amino acid and peptide in the topsoil was 8 h across all treatments, which was higher than previously reported in uplands. The microbial turnover of amino acid and peptide was 7–10 times slower in the subsoil than in the topsoil, with a half-life of about 2–3 days. The half-life of amino acid and peptide for the respired pool was strongly associated with soil physicochemical characteristics, the total biomass, and the structure of soil microbial communities. The N fertilization regime and soil depth affected the substrate uptake rate by microorganisms, with greater uptake observed in the NPKS and NPKM treatments and the topsoil. Microbial amino acid uptake was correlated with the biomass of total and individual microbial groups, whereas microbial peptide uptake was associated with the soil microbial community structure and physicochemical characteristics. This suggests that there are various pathways of amino acid and peptide use by microorganisms under flooding conditions. We conclude that microbial mineralization of amino acid and its peptide in paddy soils under flooding conditions is slower than in upland soils, and that microbial uptake of these substrates is related to soil abiotic factors and the biomass and structure of soil microbial community. These findings have important implications for understanding nutrient cycling and ecosystem functioning in agricultural soils.

Viral pathogens including SARS-CoV-2 RNA have been detected in wastewater treatment effluent, and untreated sewage overflows, that pose an exposure hazard to humans. We assessed whether SARS-CoV-2 RNA was likely to have been present in detectable quantities in UK rivers and estuaries during the first wave of the Covid-19 pandemic. We simulated realistic viral concentrations parameterised on the Camel and Conwy catchments (UK) and their populations, showing detectable SARS-CoV-2 RNA concentrations for untreated but not for treated loading, but also being contingent on viral decay, hydrology, catchment type/shape, and location. Under mean or low river flow conditions, viral RNA concentrated within the estuaries allowing for viral build-up and caused a lag by up to several weeks between the peak in community infections and the viral peak in the environment. There was an increased hazard posed by SARS-CoV-2 RNA with a

Global peatlands store more carbon than is naturally present in the atmosphere1,2. However, many peatlands are under pressure from drainage-based agriculture, plantation development and fire, with the equivalent of around 3 per cent of all anthropogenic greenhouse gases emitted from drained peatland3–5. Efforts to curb such emissions are intensifying through the conservation of undrained peatlands and re-wetting of drained systems6. Here we report eddy covariance data for carbon dioxide from 16 locations and static chamber measurements for methane from 41 locations in the UK and Ireland. We combine these with published data from sites across all major peatland biomes. We find that the mean annual effective water table depth (WTDe; that is, the average depth of the aerated peat layer) overrides all other ecosystem- and management-related controls on greenhouse gas fluxes. We estimate that every 10&nbsp;centimetres of reduction in WTDe could reduce the net warming impact of CO2 and CH4 emissions (100-year global warming potentials) by the equivalent of at least 3&nbsp;tonnes of CO2 per hectare per year, until WTDe is less than 30&nbsp;centimetres. Raising water levels further would continue to have a net cooling effect until WTDe is within 10&nbsp;centimetres of the surface. Our results suggest that greenhouse gas emissions from peatlands drained for agriculture could be greatly reduced without necessarily halting their productive use. Halving WTDe in all drained agricultural peatlands, for example, could reduce emissions by the equivalent of over 1 per cent of global anthropogenic emissions. Halving average drainage depths&nbsp;in agricultural peatlands could reduce greenhouse gas emissions by the equivalent of 1 per cent of all anthropogenic emissions.

Wastewater-based epidemiology (WBE) has emerged as a valuable surveillance tool for SARS-CoV-2 and other pathogens globally, providing insights into community-level infections, including asymptomatic and pre-symptomatic cases. While most WBE programmes focus on quantitative pathogen assessment, next-generation sequencing (NGS) approaches have enabled more detailed analyses, including variant and recombinant genotype identification for viruses like SARS-CoV-2 and poliovirus. Despite recent NGS advancements allowing for the detection of known and novel viruses in wastewater, many of these tools remain underutilised in routine WBE. This short review critically evaluates the applicability of common NGS tools in routine WBE programmes, assessing their capability for identifying emerging threats with epidemic or pandemic potential. Here, we provide evidence-based recommendations for integrating NGS techniques into WBE and the use of results for informed decision-making within a One Health framework, aiming to enhance global infectious disease surveillance and pandemic preparedness.

Sheep wool can be used as an eco–friendly type of packaging that, due to its complex physical and chemical composition, can also help control humidity and reduce condensation. Given these properties, the potential of wool to be used as packaging liners for the transport of food products is of interest. The present study assessed the microbiological quality of meat packaged and stored at room temperature for 40 h in conventional EPS (expanded polystyrene) boxes and cardboard boxes lined with wool using standard, approved culturing techniques. The findings suggest that the wool may have potential market value as packaging liners for transporting meat, and possibly other food products. Further research is needed to allow better characterization to real-world conditions, and understanding of how wool used as a packaging liner could help maintain food quality on a larger scale.

SARS-CoV-2 and the resulting COVID-19 pandemic represents one of the greatest recent threats to human health, wellbeing and economic growth. Wastewater-based epidemiology (WBE) of human viruses can be a useful tool for population-scale monitoring of SARS-CoV-2 prevalence and epidemiology to help prevent further spread of the disease, particularly within urban centres. Here, we present a longitudinal analysis (March–July 2020) of SARS-CoV-2 RNA prevalence in sewage across six major urban centres in the UK (total population equivalent 3 million) by q(RT-)PCR and viral genome sequencing. Our results demonstrate that levels of SARS-CoV-2 RNA generally correlated with the abundance of clinical cases recorded within the community in large urban centres, with a marked decline in SARS-CoV-2 RNA abundance following the implementation of lockdown measures. The strength of this association was weaker in areas with lower confirmed COVID-19 case numbers. Further, sequence analysis of SARS-CoV-2 from wastewater suggested that multiple genetically distinct clusters were co-circulating in the local populations covered by our sample sites, and that the genetic variants observed in wastewater reflected similar SNPs observed in contemporaneous samples from cases tested in clinical diagnostic laboratories. We demonstrate how WBE can be used for both community-level detection and tracking of SARS-CoV-2 and other virus’ prevalence, and can inform public health policy decisions. Although, greater understanding of the factors that affect SARS-CoV-2 RNA concentration in wastewater are needed for the full integration of WBE data into outbreak surveillance. In conclusion, our results lend support to the use of routine WBE for monitoring of SARS-CoV-2 and other human pathogenic viruses circulating in the population and assessment of the effectiveness of disease control measures.

Understanding the abundance and fate of human viral pathogens in wastewater is essential when assessing the public health risks associated with wastewater discharge to the environment. Typically, however, the microbiological monitoring of wastewater is undertaken on an infrequent basis and peak discharge events may be missed leading to the misrepresentation of risk levels. To evaluate diurnal patterns in wastewater viral loading, we undertook 3-day sampling campaigns with bi-hourly sample collection over three seasons at three wastewater treatment plants. Untreated influent was collected at Ganol and secondary-treated effluent was sampled at Llanrwst and Betws-y-Coed (North Wales, UK). Our results confirmed the presence of human adenovirus (AdV), norovirus genotypes I and II (NoVGI and NoVGII) in both influent and effluent samples while sapovirus GI (SaVGI) was only detected in influent water. The AdV titre was high and relatively constant in all samples, whereas the NoVGI, NoVGII and SaVGI showed high concentrations during autumn and winter and low counts during the summer. Diurnal patterns were detected in pH and turbidity for some sampling periods; however, no such changes in viral titres were observed apart from slight fluctuations in the influent samples. Our findings suggest that viral particle number in wastewater is not affected by daily chemical fluctuations. Hence, a grab sample taken at any point during the day may be sufficient to enumerate the viral load of wastewater effluent within an order of magnitude while four samples a day are recommended for testing wastewater influent samples.