Browsing by Author "Jones, Davey L."
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Item Open Access Abundance and distribution of enteric bacteria and viruses in coastal and estuarine sediments - A review(Frontiers Media, 2016-11-01) Hassard, Francis; Gwyther, Ceri L.; Farkas, Kata; Andrews, Anthony; Jones, Vera; Cox, Brian; Howard, Brett; Jones, Davey L.; McDonald, James E.; Malham, Shelagh K.The long term survival of fecal indicator organisms (FIOs) and human pathogenic microorganisms in sediments is important from a water quality, human health and ecological perspective. Typically, both bacteria and viruses strongly associate with particulate matter present in freshwater, estuarine and marine environments. This association tends to be stronger in finer textured sediments and is strongly influenced by the type and quantity of clay minerals and organic matter present. Binding to particle surfaces promotes the persistence of bacteria in the environment by offering physical and chemical protection from biotic and abiotic stresses. How bacterial and viral viability and pathogenicity is influenced by surface attachment requires further study. Typically, long-term association with surfaces including sediments induces bacteria to enter a viable-but-non-culturable (VBNC) state. Inherent methodological challenges of quantifying VBNC bacteria may lead to the frequent under-reporting of their abundance in sediments. The implications of this in a quantitative risk assessment context remain unclear. Similarly, sediments can harbor significant amounts of enteric viruses, however, the factors regulating their persistence remains poorly understood. Quantification of viruses in sediment remains problematic due to our poor ability to recover intact viral particles from sediment surfaces (typically < 10%), our inability to distinguish between infective and damaged (non-infective) viral particles, aggregation of viral particles, and inhibition during qPCR. This suggests that the true viral titre in sediments may be being vastly underestimated. In turn, this is limiting our ability to understand the fate and transport of viruses in sediments. Model systems (e.g., human cell culture) are also lacking for some key viruses, preventing our ability to evaluate the infectivity of viruses recovered from sediments (e.g., norovirus). The release of particle-bound bacteria and viruses into the water column during sediment resuspension also represents a risk to water quality. In conclusion, our poor process level understanding of viral/bacterial-sediment interactions combined with methodological challenges is limiting the accurate source apportionment and quantitative microbial risk assessment for pathogenic organisms associated with sediments in aquatic environments.Item Open Access Establishment of local wastewater-based surveillance programmes in response to the spread and infection of COVID-19 – case studies from South Africa, the Netherlands, Turkey and England(IWA, 2022-02-07) Tlhagale, M.; Liphadzi, S.; Bhagwan, J.; Naidoo, V.; Jonas, K.; van Vuuren, L.; Medema, Gertjan; Andrews, L.; Béen, F.; Lousada-Ferreira, Maria; Saatci, Ahmet Mete; Alpaslan Kocamemi, B.; Hassard, Francis; Singer, Andrew C.; Bunce, J. T.; Grimsley, J. M. S.; Brown, M.; Jones, Davey L.The COVID-19 pandemic has resulted in over 340 million infection cases (as of 21 January 2022) and more than 5.57 million deaths globally. In reaction, science, technology and innovation communities across the globe have organised themselves to contribute to national responses to COVID-19 disease. A significant contribution has been from the establishment of wastewater-based epidemiological (WBE) surveillance interventions and programmes for monitoring the spread of COVID-19 in at least 55 countries. Here, we examine and share experiences and lessons learnt in establishing such surveillance programmes. We use case studies to highlight testing methods and logistics considerations associated in scaling the implementing of such programmes in South Africa, the Netherlands, Turkey and England. The four countries were selected to represent different regions of the world and the perspective based on the considerable progress made in establishing and implementing their national WBE programmes. The selected countries also represent different climatic zones, economies, and development stages, which influence the implementation of national programmes of this nature and magnitude. In addition, the four countries' programmes offer good experiences and lessons learnt since they are systematic, and cover extensive areas, disseminate knowledge locally and internationally and partnered with authorities (government). The programmes also strengthened working relations and partnerships between and among local and global organisations. This paper shares these experiences and lessons to encourage others in the water and public health sectors on the benefits and value of WBE in tackling SARS-CoV-2 and related future circumstances.Item Open Access On pedagogy of a Soil Science Centre for Doctoral Training(Wiley, 2021-10-13) Haygarth, Philip M.; Lawrenson, Olivia; Mezeli, Malika; Sayer, Emma J.; McCloskey, Christopher S.; Evans, Daniel L.; Kirk, Guy J. D.; Tye, Andrew M.; Chadwick, David R.; McGrath, Steve P.; Mooney, Sacha J.; Paterson, Eric; Robinson, David A.; Jones, Davey L.Here we describe and evaluate the success of a multi-institutional Centre for Doctoral Training (CDT), which was established to address a UK skills shortage in Soil Science. The government-funded ‘STARS’ (Soils Training And Research Studentships) CDT was established in 2015 across a range of universities and research institutes in the UK. It recruited 41 PhD students equitably split across the institutions under four core research themes identified as being central to the national need, namely, (1) Understanding the soil–root interface, (2) Soils and the delivery of ecosystem services, (3) Resilience and response of functions in soil systems and (4) Modelling the soil ecosystem at different spatial and temporal scales. In addition, the STARS CDT provided a diverse skills programme, including: Holistic training in soils, the promotion of collegiality and joint working, strategies to promote science and generate impact, internships with end users (e.g., policymakers, industry), personal wellbeing, and ways to generate a lasting soils training legacy. Overall, both supervisors and students have reported a positive experience of the CDT in comparison to the conventional doctoral training programmes, which have less discipline focus and little chance for students to scientifically interact with their cohorts or to undertake joint training activities. The STARS CDT also allowed students to freely access research infrastructure across the partner institutions (e.g., long-term field trials, specialised analytical facilities, high-performance computing), breaking down traditional institutional barriers and thus maximising the students' potential to undertake high-quality research. The success and legacy of the STARS CDT can be evidenced in many ways; however, it is exemplified by the large number and diversity of journal papers produced, the lasting collaborations, final career destinations, and creation of a web-based legacy portal including new and reflective video material.Item Open Access Physicochemical factors influence the abundance and culturability of human enteric pathogens and fecal indicator organisms in estuarine water and sediment(Frontiers Media, 2017-10-17) Hassard, Francis; Andrews, Anthony; Jones, Davey L.; Parsons, Louise; Jones, Vera; Cox, Brian A.; Daldorph, Peter; Brett, Howard; McDonald, James E.; Malham, Shelagh K.To assess fecal pollution in coastal waters, current monitoring is reliant on culture-based enumeration of bacterial indicators, which does not account for the presence of viable but non-culturable or sediment-associated micro-organisms, preventing effective quantitative microbial risk assessment (QMRA). Seasonal variability in viable but non-culturable or sediment-associated bacteria challenge the use of fecal indicator organisms (FIOs) for water monitoring. We evaluated seasonal changes in FIOs and human enteric pathogen abundance in water and sediments from the Ribble and Conwy estuaries in the UK. Sediments possessed greater bacterial abundance than the overlying water column, however, key pathogenic species (Shigella spp., Campylobacter jejuni, Salmonella spp., hepatitis A virus, hepatitis E virus and norovirus GI and GII) were not detected in sediments. Salmonella was detected in low levels in the Conwy water in spring/summer and norovirus GII was detected in the Ribble water in winter. The abundance of E. coli and Enterococcus spp. quantified by culture-based methods, rarely matched the abundance of these species when measured by qPCR. The discrepancy between these methods was greatest in winter at both estuaries, due to low CFU's, coupled with higher gene copies (GC). Temperature accounted for 60% the variability in bacterial abundance in water in autumn, whilst in winter salinity explained 15% of the variance. Relationships between bacterial indicators/pathogens and physicochemical variables were inconsistent in sediments, no single indicator adequately described occurrence of all bacterial indicators/pathogens. However, important variables included grain size, porosity, clay content and concentrations of Zn, K, and Al. Sediments with greater organic matter content and lower porosity harbored a greater proportion of non-culturable bacteria (including dead cells and extracellular DNA) in winter. Here, we show the link between physicochemical variables and season which govern culturability of human enteric pathogens and FIOs. Therefore, knowledge of these factors is critical for accurate microbial risk assessment. Future water quality management strategies could be improved through monitoring sediment-associated bacteria and non-culturable bacteria. This could facilitate source apportionment of human enteric pathogens and FIOs and direct remedial action to improve water quality.Item Open Access Scaling-up engineering biology for enhanced environmental solutions(American Chemical Society (ACS), 2024-06-21) Hassard, Francis; Curtis, Thomas P.; Dotro, Gabriela C.; Golyshin, Peter; Gutierrez, Tony; Heaven, Sonia; Horsfall, Louise; Jefferson, Bruce; Jones, Davey L.; Krasnogor, Natalio; Kumar, Vinod; Lea-Smith, David J.; Le Corre Pidou, Kristell; Liu, Yongqiang; Lyu, Tao; McCarthy, Ronan R.; McKew, Boyd; Smith, Cindy; Yakunin, Alexander; Yang, Zhugen; Zhang, Yue; Coulon, FredericSynthetic biology (SynBio) offers transformative solutions for addressing environmental challenges by engineering organisms capable of degrading pollutants, enhancing carbon sequestration, and valorizing waste (Figure 1). These innovations hold the potential to revolutionize bioremediation strategies, ecosystem restoration, and sustainable environmental management.Item Open Access Soils training and research: Who's legacy?(EGU: European Geophysical Union, 2021-04-30) Mezeli, Malika; Evans, Daniel L.; Jones, Davey L.; Lawrenson, Olivia; Haygarth, Philip