Publications

Plant cell wall polysaccharides are the most abundant form of organic carbon in soils and their degradation by microorganisms represents a major link in the global carbon cycle. Soil carbon storage is a valuable ecosystem service, buffering against increasingly rapid climatic change, and underpinning services such as food production and flood prevention. Despite the importance of this link, little is known about the relative contributions of different microorganisms and their genes to lignocellulose degradation in soils. Here, we used a 10-year old plant-exclusion experiment on grasslands to study how reduced plant carbon inputs affects the microbial community, and genes which are putatively associated with lignocellulolysis. We show that 10-year plant exclusion consistently favours genera within the Bacillales, Thaumarchaeota, and diverse lineages of Proteobacteria, alters the repertoire of lignocellulolytic genes present, and that taxonomic and genetic changes are not clearly linked. Plant-exclusion was linked to increased hemicellulose breakdown product abundance and increased xylanase gene diversity after a single year, whereas 10 years of plant exclusion reduced xylanase gene diversity and altered lignocellulase gene composition. Additionally, this study investigates the fundamental and realised niches of specific soil microorganisms, and shows the temporal scale at which the microbial community responds to changing carbon inputs in grasslands.

Waste management is an increasingly important problem in many developed countries and much effort is currently being expended into identifying novel uses for waste products. We consider the effects of substituting proportions of earthworm-digested composted green waste (vermicompost) into commercial peat based growing media on the germination, growth, and productivity of Helianthus annuus, Cosmos bipinnatus and Eschscholzia californica. The percentage germination, time to flowering, seed production, overall heights and biomass were measured for all three species in treatments of commercial peat based growing media where the growth medium was substituted with vermicompost at rates of 0%, 20%, 40%, 60% and 100%. In addition, the total numbers of inflorescences was recorded in multiple flowering species. Results for Helianthus suggest that while vermicompost additions induced small species specific growth responses in germination rate, growth rate, overall height and total biomass, none were statistically significant. For Cosmos there was a significant increase in early plant growth rate and in the final flower numbers at substitution rates of 20% and 40% vermicompost. The total biomass and numbers of flowers produced by Eschscholzia was decreased significantly by substitution of 20% and 40% vermicompost. We conclude that the plant growth enhancement properties of this vermicompost seem more species specific than previously reported. Further, in order to preserve consumer confidence in waste-derived horticulture products, vermicompost marketing strategies should acknowledge these findings.

Summary Reliable modelling of above‐ground net primary production ( aNPP ) at fine resolution is a significant challenge. A promising avenue for improving process models is to include response and effect trait relationships. However, uncertainties remain over which leaf traits are correlated most strongly with aNPP . We compared abundance‐weighted values of two of the most widely used traits from the leaf economics spectrum (specific leaf area and leaf dry matter content) with measured aNPP across a temperate ecosystem gradient. We found that leaf dry matter content ( LDMC ) as opposed to specific leaf area ( SLA ) was the superior predictor of aNPP ( R 2 = 0·55). Directly measured in situ trait values for the dominant species improved estimation of aNPP significantly. Introducing intraspecific trait variation by including the effect of replicated trait values from published databases did not improve the estimation of aNPP . Our results support the prospect of greater scientific understanding for less cost because LDMC is much easier to measure than SLA . A lay summary is available for this article.

Wood represents the single most important source of renewable energy worldwide and depending on the mechanism of energy production can lead to the production of by-products with vastly different properties (i.e. wood ash (WA) from incineration and biochar (BC) from pyrolysis). These are typically applied to land, however, a critical comparison of their impact on soil quality and carbon (C) cycling is lacking. To address this, we generated biochar (450 °C) and wood ash (870 °C) from the same mixed hardwood feedstock and added it to an agricultural grassland at comparable rates under both laboratory and field conditions (10 t ha−1 and 571 kg ha−1 for BC and WA, respectively). We hypothesized that alkaline, nutrient-rich wood ash would stimulate microbial activity, resulting in the loss of soil organic matter (SOM), while biochar which is recalcitrant to microbial attack would promote the stabilization of native SOM. The effects on the soil microbial community and soil C and N cycling were determined over 1 year. Overall, biochar promoted soil quality by enhancing nutrient availability (P and K), moisture retention and increasing soil C content. However, it was also associated with an increase in below-ground CO2 loss. As plant productivity was unaffected and laboratory incubations of biochar with 14C-labelled SOM showed no indication of priming, we deduce that this CO2 originates from the biochar itself. This is supported by the lack of effect of biochar on soil N cycling, microbial biomass and community structure. Wood ash had almost no effect on either soil quality or vegetation quality (yield and foliar nutrient content) under field conditions but did induce negative SOM priming under both laboratory and field conditions. We conclude that when applied at field-relevant rates, neither amendment had a detrimental effect on native SOM cycling. While wood ash promotes the retention of native SOM, biochar may be a better strategy for enhancing SOM levels because of its intrinsic recalcitrant character, however, this needs to be offset against the reduced amount of energy derived from pyrolysis in comparison to incineration.

Urban wastewater treatment plants (WWTP) represent key point-source discharges of microplastics (MP) into the environment, however, little is known about the microbial carrying capacity of plastics travelling through them. The purpose of this study was to quantify the number of cells that become associated with MP at different locations within a WWTP, and to assess differences in microbiome communities. We conducted a field experiment incubating low density polyethylene (LDPE) MP beads in WWTP influent and effluent, as well as tracking free floating beads during passage in wastewater from a large municipal hospital to an urban WWTP, where they were subsequently recovered. Using two cell counting methods - automated flow cytometric true absolute cell counts and indirect cell quantification via protein content based on a model E. coli cell - we quantified cell attachment to LDPE beads. LDPE associated counts ranged from 350 × 103 cells cm−2 after incubation in wastewater effluent, and 990 × 103 cells cm−2 after incubation in wastewater influent. 16S rRNA gene amplicon sequencing was used to determine the bacterial community structure of the plastic-associated microbiomes. Our results showed that distinct bacterial communities developed on the LDPE MP following exposure to each wastewater type. Influent (untreated) wastewater LDPE-associated microbiomes were dominated by Bacillota whereas the microbes that attached in wastewater effluent (tertiary treated) were dominated by Pseudomonadota. In conclusion, this study provides clear evidence that microplastics migrating through the sewer network and WWTP rapidly accumulate microbiomes with unique microbial community structures varying from sewage influent to effluent. These findings demonstrate the differential microbiological risk from MP associated with routine wastewater discharges to those released from intermittent combined sewer overflows (CSOs) during storm events.

Wastewater-based epidemiology is emerging as a powerful early-warning public health surveillance tool. However, gold-standard PCR necessitates transporting samples to laboratories, with significant reporting delays (24-72 h), prompting growing interest in rapid, near-source tests for resource-limited settings. Research has focused on gold nanoparticle dipsticks, but these typically lack sensitivity in wastewater. Herein, we explore two complementary nanomaterial based approaches, using SARS-CoV-2 as an exemplar: 1) visually-read carbon black dipsticks; 2) spin-enhanced fluorescent nanodiamond dipsticks, exploiting selective separation from background autofluorescence. The assay provides a 2-hour turnaround from sample preparation to result with minimal equipment and achieves a limit of detection down to 7 copies per assay. A pilot study with samples from the Welsh National WBE programme finds 80% sensitivity and 100% specificity for carbon black, and 100% sensitivity, specificity for nanodiamonds. A proof-of-concept lab-in-a-suitcase nanodiamond assay tests raw, unprocessed wastewater samples. These findings lay the foundations for near-source WBE early-warning quantum sensors in the environment.

Wastewater-based epidemiology (WBE) has been demonstrably successful as a relatively unbiased tool for monitoring levels of SARS-CoV-2 virus circulating in communities during the COVID-19 pandemic. Accumulated biobanks of wastewater samples allow retrospective exploration of spatial and temporal trends for public health indicators such as chemicals, viruses, antimicrobial resistance genes, and the possible emergence of novel human or zoonotic pathogens. We investigated virus resilience to time, temperature, and freeze-thaw cycles, plus the optimal storage conditions to maintain the stability of genetic material (RNA/DNA) of viral +ssRNA (Envelope - E, Nucleocapsid - N and Spike protein - S genes of SARS-CoV-2), dsRNA (Phi6 phage) and circular dsDNA (crAssphage) in wastewater. Samples consisted of (i) processed and extracted wastewater samples, (ii) processed and extracted distilled water samples, and (iii) raw, unprocessed wastewater samples. Samples were stored at -80 °C, -20 °C, 4 °C, or 20 °C for 10 days, going through up to 10 freeze-thaw cycles (once per day). Sample stability was measured using reverse transcription quantitative PCR, quantitative PCR, automated electrophoresis, and short-read whole genome sequencing. Exploring different areas of the SARS-CoV-2 genome demonstrated that the S gene in processed and extracted samples showed greater sensitivity to freeze-thaw cycles than the E or N genes. Investigating surrogate and normalisation viruses showed that Phi6 remains a stable comparison for SARS-CoV-2 in a laboratory setting and crAssphage was relatively resilient to temperature variation. Recovery of SARS-CoV-2 in raw unprocessed samples was significantly greater when stored at 4 °C, which was supported by the sequencing data for all viruses - both time and freeze-thaw cycles negatively impacted sequencing metrics. Historical extracts stored at -80 °C that were re-quantified 12, 14 and 16 months after original quantification showed no major changes. This study highlights the importance of the fast processing and extraction of wastewater samples, following which viruses are relatively robust to storage at a range of temperatures.

Soil exoenzymes released by microorganisms break down organic matter and are crucial in regulating C, N and P cycling. Soil pH is known to influence enzyme activity, and is also a strong driver of microbial community composition; but little is known about how alterations in soil pH affect enzymatic activity and how this is mediated by microbial communities. To assess long term enzymatic adaptation to soil pH, we conducted enzyme assays at buffered pH levels on two historically managed soils maintained at either pH 5 or 7 from the Rothamsted Park Grass Long-term experiment. The pH optima for a range of exoenzymes involved in C, N, P cycling, differed between the two soils, the direction of the shift being toward the source soil pH, indicating the production of pH adapted isoenzymes by the soil microbial community. Soil bacterial and fungal communities determined by amplicon sequencing were clearly distinct between pH 5 and soil pH 7 soils, possibly explaining differences in enzymatic responses. Furthermore, β-glucosidase gene sequences extracted from metagenomes revealed an increased abundance of Acidobacterial producers in the pH 5 soils, and Actinobacteria in pH 7 soils. Our findings demonstrate that the pH optimum of soil exoenzymes adapt to long term changes in soil pH, the direction being dependent on the soil pH shift; and we provide further evidence that changes in functional microbial communities may underpin this phenomena, though new research is now needed to directly link change in enzyme activity optima with microbial communities. More generally, our new findings have large implications for modelling the efficiency of different microbial enzymatic processes under changing environmental conditions.

Contamination of watercourses with fecal matter represents a significant risk to public health due to the associated risk from human pathogens (e.g. Escherichia coli O157, norovirus). In addition, water contamination may also perpetuate the re-infection cycle of human pathogens within domesticated and wild animal populations. While diffuse pollution from agricultural fields has been identified as a major source of these pathogens, the relationship between livestock grazing intensity and subsequent pathogen persistence in water is not well established. Our aim was to critically evaluate the importance of land use management on the activity of E. coli O157 in freshwaters collected from a livestock dominated catchment in the UK. We inoculated replicate batches of both filter-sterilised and non-sterile freshwaters with a chromosomally lux-marked E. coli O157 and monitored pathogen survival and activity over a 5 d period. Our results indicate that the greatest risk for pathogens entering freshwater is probably associated with high intensity livestock areas, although their subsequent survival is greatest in waters from low intensity livestock areas. We ascribe this enhanced persistence in the latter to reduced competition and predation within these aquatic environments. These results have serious implications for the reliability of pathogen risk exposure maps which are based on grazing intensity alone.