Publications

Norovirus (NoV) is a highly contagious enteric virus that causes widespread outbreaks and a substantial number of deaths across communities. As clinical surveillance is often insufficient, wastewater-based epidemiology (WBE) may provide novel pathways of tracking outbreaks. To utilise WBE, it is important to use accurate and sensitive methods for viral quantification. In this study, we developed a one-step duplex RT-qPCR assay to simultaneously test the two main human pathogenic NoV genogroups, GI and GII, in wastewater samples. The assay had low limits of detection (LOD), namely 0.52 genome copies (gc)/µl for NoVGI and 1.37 gc/µl for NoVGII. No significant concentration-dependent interactions were noted for both NoVGI and for NoVGII when the two targets were mixed at different concentrations in the samples. When tested on wastewater-derived RNA eluents, no significant difference between duplex and singleplex concentrations were found for either target. Low levels of inhibition (up to 32 %) were noted due to organic matter present in the wastewater extracts. From these results we argue that the duplex RT-qPCR assay developed enables the sensitive detection of both NoVGI and NoVGII in wastewater-derived RNA eluents, in a time and cost-effective way and may be used for surveillance to monitor public and environmental health.

Herbal leys (multispecies swards) can potentially deliver greater agronomic and environmental benefits than conventional grass-clover swards in grazed agroecosystems. However, despite their popularity in agri-environment schemes, little is known about the effect of herbal leys on soil physical (e.g., porosity), chemical (e.g., carbon), and biological (e.g., soil fauna) characteristics. In the UK, a 2-ha replicated-field experiment utilising a herbal or grass-clover ley (n = 3 per sward) aimed to investigate the effect of sward type on soil quality. Each sward was rotationally grazed by weaned lambs (3.2 LU ha−1) over two grazing seasons, with soil physiochemical and biological characteristics assessed after 2-years using techniques such as X-ray micro-Computed Tomography (µCT) and microbial shallow shotgun sequencing. Soil chemical characteristics (e.g., pH) were unaffected by sward type. Similarly, topsoil (0–10 cm) organic carbon stocks measured after 2-years did not differ between the herbal (26.1 ± 1.1 t C ha−1) and grass-clover ley (25.7 ± 1.1 t C ha−1). X-ray µCT analysis revealed greater pore connectivity (Euler number) in grass-clover ley intact soil cores (0–10 cm depth, 7.5 cm width) than herbal ley cores dominated by Plantago lanceolata (p = 0.008). However, there was no sward-type difference in aggregate stability or general pore characteristics, determined using X-ray µCT, in air-dried 4 mm aggregates obtained from 0–5 or 5–10 cm depth, nor did sward type affect earthworm abundance, microbial community composition or the functional gene profile. This study is the first to explore the effects of a commercial herbal ley on physical, chemical, and biological soil quality indicators in a rotationally grazed sheep pasture. While no improvements in soil quality indicators were observed after 2-years, these findings have significant implications for agri-environment schemes promoting herbal leys to achieve soil quality and sustainability, with further research needed to optimise the seed mixture and management regime to deliver greater long-term below-ground ecosystem service benefits.

Soils in the riparian zone, the interface between terrestrial and aquatic ecosystems, may decrease anthropogenic nitrogen (N) loads to streams through microbial transformations (e.g., denitrification). However, the ecological functioning of riparian zones is often compromised due to degraded conditions (e.g., vegetation clearing). Here we compare the efficacy of an urban remnant and a cleared riparian zone for supporting a putative denitrifying microbial community using 16S rRNA sequencing and quantitative polymerase chain reaction of archaeal and bacterial nitrogen cycling genes. Although we had no direct measure of denitrification rates, we found clear patterns in the microbial communities between the sites. Greater abundance of N-cycling genes was predicted by greater soil ammonium (N-NH4 ), organic phosphorus, and C:N. At the remnant site, we found positive correlations between microbial community composition, which was dominated by putative N oxidisers (Nitrosomonadaceae, Nitrospiraceae and Nitrosotaleaceae), and abundance of ammonia-oxidizing archaea (AOA), nirS, nirK and nosZ, whereas the cleared site had lower abundance of N-oxidisers and N cycling genes. These results were especially profound for the remnant riparian fringe, which suggests that this region maintains suitable soil conditions (via diverse vegetation structure and periodic saturation) to support putative N cyclers, which could amount to higher potential for N removal.

Green manuring and crop straw returning are widely used to increase soil organic carbon (SOC) sequestration, while the pathways and drivers in native SOC mineralization and new SOC formation after implementing these practices remain unclear. Here, through a 10-locations' network field experiment in southern China, the effects of green manuring (Mv), rice straw returning (Rs), and their combination (MR) on soil C sequestration efficiency (CSE) were evaluated. A microcosmic experiment was performed to trace the components and participants of SOC mineralization and formation under the three practices. The network experiment showed that Mv, Rs, and MR annually improved SOC stock by 119.7, 477.0, and 830.2 kg C ha-1, respectively, with MR having the highest CSE of 23.1%, followed by Rs (17.7%) and Mv (13.3%). The microcosmic experiment further revealed that the highest CSE in MR most likely resulted from the low mineralization of native SOC (positive priming effects, PE) and great formation of new SOC through microbial C pump (MCP). Therein, MR mainly downregulated the K-strategists of the microbial community (e.g., Gaiellales) to yield negative PE on recalcitrant native SOC, such as protein/amino sugar- and lignin-like molecules; meanwhile, MR had the highest bacterial and fungal MCPs, which were, respectively, led by r-strategists (e.g., Sporobacter) and molds (e.g., Cladosporium). The study highlights the advantages of mixing low- (Rs) and high-quality (Mv) residues for efficiently increasing SOC sequestration and firstly discovers the core microbes that dominate the mineralization and formation of SOC in paddy fields.

1 Exchange of carbon dioxide (CO2) from soils can contribute significantly to the global warming potential (GWP) of agro-ecosystems. Due to variations in soil type, climatic conditions and land management practices, exchange of CO2 can differ markedly in different geographical locations. The food industry is developing carbon footprints for their products necessitating integration of CO2 exchange from soils with other CO2 emissions along the food chain. It may be advantageous to grow certain crops in different geographical locations to minimize CO2 emissions from the soil, and this may provide potential to offset other emissions in the food chain, such as transport. 2 Values are derived for the C balance of soils growing horticultural crops in the UK, Spain and Uganda. Net ecosystem production (NEP) is firstly calculated from the difference in net primary production (NPP) and heterotrophic soil respiration (Rh). Both NPP and Rh were estimated from intensive direct field measurements. Secondly, net biome production (NBP) is calculated by subtracting the crop biomass from NEP to give an indication of C balance. The importance of soil exchange is discussed in the light of recent discussions on carbon footprints and within the context of food life-cycle assessment (LCA). 3 The amount of crop relative to the biomass and the Rh prevailing in the different countries were the dominant factors influencing the magnitude of NEP and NBP. The majority of the biomass for lettuce Lactuca sativa and vining peas Pisum sativum, was removed from the field as crop; therefore, NEP and NBP were mainly negative. This was amplified for lettuces grown in Uganda (−16·5 and −17 t C ha−1 year−1 compared to UK and Spain −4·8 to 7·4 and −5·1 to 6·3 t C ha−1 year−1 for NEP and NBP, respectively) where the climate elevated Rh. 4 Synthesis and applications. This study demonstrates the importance of soil emissions in the overall life cycle of vegetables. Variability in such emissions suggests that assigning a single value to food carbon footprints may not be adequate, even within a country. Locations with high heterotrophic soil respiration, such as Spain and Uganda (21·9 and 21·6 t C ha−1 year−1, respectively), could mitigate the negative effects of climate on the C costs of crop production by growth of crops with greater returns of residue to the soil. This would minimize net CO2 emissions from these agricultural ecosystems.

Traditional microbiological techniques have been used for well over a century as the basis for contamination testing of pharmaceutical products and processes. With more recent focus on faster product release and concerns around the integrity of the test data, new technologies have been implemented to detect and enumerate organisms faster and provide paperless processes to minimize data integrity issues. Manual colony counting technologies, where incubation is performed in a standard incubator, and the plate is manually transferred to the colony counter for a single read at the end of incubation, have been used for many years to reduce the potential for human error; however, they pose validation challenges due to poor counting accuracy. Colony counters that automatically perform both the incubation and enumeration functions (multiple enumeration calculations through the incubation phase) have recently been implemented for quality control (QC) laboratory analytical processes, supporting a cGMP environment. This article summarizes the findings of eight companies demonstrating the qualification of an automated colony counter technology to perform the majority of microbial tests required for QC, environmental monitoring, and bioburden for in-process, bulk drug substance, and water system testing. Comparable analytical performance and time to result data generated during individual studies at all companies allows the system to be qualified and implemented for cGMP processes while reducing data integrity risks.

No abstract is provided for this article.

Biochar incorporation into soil has been advocated as a potential large scale solution to offset global greenhouse gas emissions. However, the application of biochar to agricultural land must have few if any negative economic and environmental consequences if farmers are to readily adopt biochar as soil amendment. Biochar use as an organic amendment has been recently rising due to its positive effect on soil fertility, but there is still limited information available about longer-term effects, especially with regard to the effects on soil pollutant content and distribution. In a field-scale trial we investigated the effect of single doses of biochar (25 and 50tha−1) and repeat-applications (two years later) of biochar (25+25 and 50+50tha−1) on heavy metal (As, Cu, Zn, Cd, Ni) content and distribution in soil, together with metal concentrations in plants (barley, beans) over repeated cropping cycles. Here we demonstrate that biochar produced from forest residues is of a low risk due to its inherently low metal content and the lack of observed negative effects on crop or soil quality. Although biochar did cause small changes in metal fractionation in soil, it did not alter total metal concentrations in soil or plants. We conclude that the application of wood-derived biochar does not increase the concentrations of metals in this soil, even after repeated applications, and could be safely used for agriculture

Soil organic nitrogen (SON) decomposition is a fundamental process in the nitrogen (N) cycle that influences N availability for plant uptake and soil health. However, the long-term effects of nutrient fertilisation on SON decomposition and its microbial drivers remain poorly understood. Here, we used the 180-year-old Broadbalk Winter Wheat Experiment to investigate how farmyard manure (FYM), mineral fertiliser (NPK), and no fertilisation input (NIL) affect crop yield, SON turnover, microbial community composition, and functional genes. Our findings showed that distinct and complementary microbial mechanisms regulate SON decomposition under different nutrient fertilisation treatments. FYM application increased gross N mineralisation to 43.1 mg N kg−1 soil d−1, by doubling microbial biomass and promoting bacterial-dominated protein and peptide decomposition. During the early stage of decomposition, CO2 release from protein and peptide turnover under FYM increased by 96 % and 44 %, respectively, compared to NIL. NPK fertilisation enhanced the decomposition of complex N compounds and promoted the turnover of high-molecular-weight N to support microbial growth by upregulating N-cycling genes and extracellular enzyme production. The carbon use efficiency of protein was increased to 0.68. NPK fertilisation also stimulated fungal and Actinobacteria populations, accelerating the turnover rate of peptides and amino acids to 22.7 and 2.4 mg N kg−1 soil d−1, respectively. These results provide new insights into how nutrient fertilisation practices affect microbialy-mediated N dynamics and crop productivity, emphasising the importance of microbial functional diversity in supporting soil N cycling and fertility.

Organic-rich, eutrophic peat soils (Histosols) represent a major store of carbon (C) within the terrestrial biosphere. However, these soils are also highly susceptible to damage, particularly when used for intensive agricultural production. Sustainable management of such soils is contingent upon improved understanding of the impact of their management on the environment. In this context, we report the first annual budget of greenhouse gas emissions from temperate peat soils under intensive horticultural production. Fluxes of CO2, N2O and CH4 were measured using static chambers on three farms along an organic matter loss gradient (∼20%, ∼35%, and ∼70% soil organic matter (SOM) content respectively), under a number of commercially important crops in similar rotations. Cumulative annual fluxes of CO2 in fallow and cropped soils were large and ranged from 13.0±2.4 to 30.9±2.5t CO2-eha−1 y−1, showing a general increase with SOM, and on cropped compared to bare soils. Annual emissions of N2O varied from 5.0±0.7 to 13.9±1.9t CO2-eha−1 y−1, and CH4 from −0.02±0.08 to 0.04±0.02t CO2-eha−1 y−1; neither showed a significant relationship with either SOM content or cropping. Distinct seasonal patterns of CO2 and N2O fluxes were observed, corresponding to significant correlations between emissions and soil and air temperature, soil moisture content, water table depth, and soil nitrate on some soil types. No discernible seasonal pattern in CH4 fluxes was observed, and very few significant correlations with soil environmental variables were found. Compared to emissions estimates suggested in IPCC inventory guidelines for cultivated peat soils, the observed emissions in this study were relatively high, and net annual fluxes of CO2 and CH4 are equivalent to a loss of soil depth of 0.33–0.75cmy−1. We conclude that arable farming is promoting extreme mineralization of the soil’s organic carbon reserves and that a change in land use or management regime is needed to protect and preserve this natural capital.

Free amino acids (FAAs) and peptides, and dissolved organic nitrogen (DON) comprise key pools in terrestrial soil carbon (C) and nitrogen (N) cycles. A com