Browsing by Author "Whitby, Corinne"
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Item Open Access Air quality and mental illness: role of bioaerosols, causal mechanisms and research priorities(Royal College of Psychiatrists, 2024-09-19) Bhui, Kamaldeep; Ucci, Marcella; Kumar, Prashant; Jackson, Simon K; Whitby, Corinne; Colbeck, Ian; Pfrang, Christian; Nasir, Zaheer A; Coulon, FredericBackground: Poor air quality can both trigger and aggravate lung and heart conditions, as well as affecting child development. It can even lead to neurological and mental health problems. However, the precise mechanisms by which air pollution affect human health are not well understood. Aims: To promote interdisciplinary dialogue and better research based on a critical summary of evidence on air quality and health, with an emphasis on mental health, and to do so with a special focus on bioaerosols as a common but neglected air constituent. Method: A rapid narrative review and interdisciplinary expert consultation, as is recommended for a complex and rapidly changing field of research. Results: The research methods used to assess exposures and outcomes vary across different fields of study, resulting in a disconnect in bioaerosol and health research. We make recommendations to enhance the evidence base by standardising measures of exposure to both particulate matter in general and bioaerosols specifically. We present methods for assessing mental health and ideal designs. There is less research on bioaerosols, and we provide specific ways of measuring exposure to these. We suggest research designs for investigating causal mechanisms as important intermediate steps before undertaking larger-scale and definitive studies. Conclusions: We propose methods for exposure and outcome measurement, as well as optimal research designs to inform the development of standards for undertaking and reporting research and for future policy.Item Open Access Bacterial community legacy effects following the Agia Zoni II oil-spill, Greece(Frontiers Media, 2020-07-17) Thomas, Gareth E.; Cameron, Tom C.; Campo, Pablo; Clark, Dave R.; Coulon, Frederic; Gregson, Benjamin H.; Hepburn, Leanne J.; McGenity, Terry J.; Miliou, Anastasia; Whitby, Corinne; McKew, Boyd A.In September 2017 the Agia Zoni II sank in the Saronic Gulf, Greece, releasing approximately 500 tonnes of heavy fuel oil, contaminating the Salamina and Athens coastlines. Effects of the spill, and remediation efforts, on sediment microbial communities were quantified over the following 7 months. Five days post-spill, the concentration of measured hydrocarbons within surface sediments of contaminated beaches was 1,093–3,773 μg g–1 dry sediment (91% alkanes and 9% polycyclic aromatic hydrocarbons), but measured hydrocarbons decreased rapidly after extensive clean-up operations. Bacterial genera known to contain oil-degrading species increased in abundance, including Alcanivorax, Cycloclasticus, Oleibacter, Oleiphilus, and Thalassolituus, and the species Marinobacter hydrocarbonoclasticus from approximately 0.02 to >32% (collectively) of the total bacterial community. Abundance of genera with known hydrocarbon-degraders then decreased 1 month after clean-up. However, a legacy effect was observed within the bacterial community, whereby Alcanivorax and Cycloclasticus persisted for several months after the oil spill in formerly contaminated sites. This study is the first to evaluate the effect of the Agia Zoni II oil-spill on microbial communities in an oligotrophic sea, where in situ oil-spill studies are rare. The results aid the advancement of post-spill monitoring models, which can predict the capability of environments to naturally attenuate oilItem Open Access Bioaerosol biomonitoring: sampling optimisation for molecular microbial ecology(Wiley, 2019-02-08) Ferguson, Robert M. W.; Garcia Alcega, Sonia; Coulon, Frederic; Dumbrell, Alex J.; Whitby, Corinne; Colbeck, IanBioerosols (or biogenic aerosols) have largely been overlooked by molecular ecologists. However, this is rapidly changing as bioaerosols play key roles in public health, environmental chemistry and the dispersal ecology of microbes. Due to the low environmental concentrations of bioaerosols, collecting sufficient biomass for molecular methods is challenging. Currently, no standardized methods for bioaerosol collection for molecular ecology research exist. Each study requires a process of optimization, which greatly slows the advance of bioaerosol science. Here, we evaluated air filtration and liquid impingement for bioaerosol sampling across a range of environmental conditions. We also investigated the effect of sampling matrices, sample concentration strategies and sampling duration on DNA yield. Air filtration using polycarbonate filters gave the highest recovery, but due to the faster sampling rates possible with impingement, we recommend this method for fine ‐scale temporal/spatial ecological studies. To prevent bias for the recovery of Gram‐positive bacteria, we found that the matrix for impingement should be phosphate‐buffered saline. The optimal method for bioaerosol concentration from the liquid matrix was centrifugation. However, we also present a method using syringe filters for rapid in‐field recovery of bioaerosols from impingement samples, without compromising microbial diversity for high ‐throughput sequencing approaches. Finally, we provide a resource that enables molecular ecologists to select the most appropriate sampling strategy for their specific research question.Item Open Access Can chemical and molecular biomarkers help discriminate between industrial, rural and urban environments?(Elsevier, 2018-03-16) Garcia Alcega, Sonia; Nasir, Zaheer A.; Ferguson, Robert M. W.; Noël, Cyril; Cravo-Laureau, Cristiana; Whitby, Corinne; Dumbrell, Alex J.; Colbeck, Ian; Tyrrel, Sean; Coulon, FredericAir samples from four contrasting outdoor environments including a park, an arable farm, a waste water treatment plant and a composting facility were analysed during the summer and winter months. The aim of the research was to study the feasibility of differentiating microbial communities from urban, rural and industrial areas between seasons with chemical and molecular markers such as microbial volatile organic compounds (MVOCs) and phospholipid fatty acids (PLFAs). Air samples (3 l) were collected every 2 h for a total of 6 h in order to assess the temporal variations of MVOCs and PLFAs along the day. MVOCs and VOCs concentrations varied over the day, especially in the composting facility which was the site where more human activities were carried out. At this site, total VOC concentration varied between 80 and 170 μg m−3 in summer and 20–250 μg m−3 in winter. The composition of MVOCs varied between sites due to the different biological substrates including crops, waste water, green waste or grass. MVOCs composition also differed between seasons as in summer they are more likely to get modified by oxidation processes in the atmosphere and in winter by reduction processes. The composition of microbial communities identified by the analysis of PLFAs also varied among the different locations and between seasons. The location with higher concentrations of PLFAs in summer was the farm (7297 ng m−3) and in winter the park (11,724 ng m−3). A specific set of MVOCs and PLFAs that most represent each one of the locations was identified by principal component analyses (PCA) and canonical analyses. Further to this, concentrations of both total VOCs and PLFAs were at least three times higher in winter than in summer. The difference in concentrations between summer and winter suggest that seasonal variations should be considered when assessing the risk of exposure to these compounds.Item Open Access Fingerprinting ambient air to understand bioaerosol profiles in three different environments in the South East of England(Elsevier, 2020-02-24) Garcia Alcega, Sonia; Nasir, Zaheer A.; Cipullo, Sabrina; Ferguson, Robert M. W.; Yan, Cheng; Whitby, Corinne; Dumbrell, Alex J.; Drew, Gillian; Colbeck, Ian; Tyrrel, Sean F.Molecular and chemical fingerprints from 10 contrasting outdoor air environments, including three agricultural farms, three urban parks and four industrial sites were investigated to advance our understanding of bioaerosol distribution and emissions. Both phospholipid fatty acids (PLFA) and microbial volatile organic compounds (MVOC) profiles showed a different distribution in summer compared to winter. Further to this, a strong positive correlation was found between the total concentration of MVOCs and PLFAs (r = 0.670, p = 0.004 in winter and r = 0.767, p = 0.001 in summer) demonstrating that either chemical or molecular fingerprints of outdoor environments can provide good insights into the sources and distribution of bioaerosols. Environment specific variables and most representative MVOCs were identified and linked to microbial species emissions via a MVOC database and PLFAs taxonomical classification. While similar MVOCs and PLFAs were identified across all the environments suggesting common microbial communities, specific MVOCs were identified for each contrasting environment. Specifically, 3,4-dimethylpent-1-yn-3-ol, ethoxyethane and propanal were identified as key MVOCs for the industrial areas (and were correlated to fungi, Staphylococcus aureus (Gram positive bacteria) and Gram negative bacteria, R = 0.863, R = 0.618 and R = 0.676, respectively) while phthalic acid, propene and isobutane were key for urban environments (correlated to Gram negative bacteria, fungi and bacteria, R = 0.874, R = 0.962 and R = 0.969 respectively); and ethanol, 2-methyl-2-propanol, 2-methyl-1-pentene, butane, isoprene and methyl acetate were key for farms (correlated to fungi, Gram positive bacteria and bacteria, R = 0.690 and 0.783, R = 0.706 and R = 0.790, 0.761 and 0.768). The combination of MVOCs and PLFAs markers can assist in rapid microbial fingerprinting of distinct environmental influences on ambient air quality.Item Open Access Fingerprinting ambient air to understand bioaerosol profiles in three different environments in the South East of England(Cranfield University, 2020-02-24 08:10) Coulon, Frederic; Garcia Alcega, Sonia; Tyrrel, Sean; Nasar, Zaheer; Drew, Gill; Cipullo, Sabrina; colbeck, ian; ferguson, Robert; Whitby, Corinne; J. Dumbrell, Alex; Yan, ChengRaw data used and supporting the data and results presented in: "Fingerprinting ambient air to understand bioaerosol profiles in three different environments in the South East of England" Science of the Total EnvironmentItem Open Access Fingerprinting outdoor air environment using microbial volatile organic compounds (MVOCs) – A review(Elsevier, 2016-11-08) Garcia Alcega, Sonia; Nasir, Zaheer A.; Ferguson, Robert M. W.; Whitby, Corinne; Dumbrell, Alex J.; Colbeck, I.; Gomes, D. M.; Tyrrel, Sean F.; Coulon, FredericThe impact of bioaerosol emissions from urban, agricultural and industrial environments on local air quality is of growing policy concern. Yet the risk exposure from outdoor emissions is difficult to quantify in real-time as microbial concentration in air is low and varies depending on meteorological factors and land use types. While there is also a large number of sampling methods in use, there is yet no standardised protocol established. In this review, a critical insight into chemical fingerprint analysis of microbial volatile organic compounds (MVOC) is provided. The most suitable techniques for sampling and analysing MVOCs in outdoor environments are reviewed and the need for further studies on MVOCs from outdoor environments including background levels is highlighted. There is yet no rapid and portable technique that allows rapid detection and analysis of MVOCs on site. Further directions towards a portable GC–MS coupled with SPME or an electronic nose are discussed.Item Open Access Nitrogen oxidation consortia dynamics influence the performance of full-scale rotating biological contactors(Elsevier, 2019-12-19) Freeman, D.; Bajón Fernández, Yadira; Wilson, Andrea; McKew, Boyd A.; Whitby, Corinne; Clark, Dave R.; Jefferson, Bruce; Coulon, Frederic; Hassard, FrancisAmmonia oxidising microorganisms (AOM) play an important role in ammonia removal in wastewater treatment works (WWTW) including rotating biological contactors (RBCs). Environmental factors within RBCs are known to impact the performance of key AOM, such that only some operational RBCs have shown ability for elevated ammonia removal. In this work, long-term treatment performance of seven full-scale RBC systems along with the structure and abundance of the ammonia oxidising bacteria (AOB) and archaea (AOA) communities within microbial biofilms were examined. Long term data showed the dominance of AOB in most RBCs, although two RBCs had demonstrable shift toward an AOA dominated AOM community. Next Generation Sequencing of the 16S rRNA gene revealed diverse evolutionary ancestry of AOB from RBC biofilms while nitrite-oxidising bacteria (NOBs) were similar to reference databases. AOA were more abundant in the biofilms subject to lower organic loading and higher oxygen concentration found at the distal end of RBC systems. Modelling revealed a distinct nitrogen cycling community present within high performing RBCs, linked to efficient control of RBC process variables (retention time, organic loading and oxygen concentration). We present a novel template for enhancing the resilience of RBC systems through microbial community analysis which can guide future strategies for more effective ammonia removal. To best of the author’s knowledge, this is the first comparative study reporting the use of next generation sequencing data on microbial biofilms from RBCs to inform effluent quality of small WWTW.Item Open Access Rapid measurement tools or fast identification of bioaerosols(Adjacent Digital Politics Ltd, 2023-02-23) Whitby, Corinne; Ferguson, Robert M. W.; Dumbrell, Alex; Colbeck, Ian; Coulon, Frederic; Nasir, Zaheer AhmadBioaerosols are complex mixtures of airborne particles of biological origin (BioPM), which vary in size (~0.05-100 μm) and composition (viruses, bacteria, fungi/mould, pollen, cell fragments, and endotoxins). Many bioaerosols are of inhalable size (< 100 μm), but those < 10 μm are respirable and can penetrate deep into the respiratory system, making them a primary health concern(6). In addition to causing infectious diseases (e.g. tuberculosis and COVID-19), bioaerosols are associated with non-infectious diseases, such as hypersensitivity, allergies, chronic obstructive pulmonary disease (COPD) and asthma, that cause significant mortality and morbidity(4,7). Antimicrobial resistance (AMR) also poses an emerging and uncertain threat to public health worldwide, yet, AMR in bioaerosols is generally ignored leaving a major blindspot in the OneHealth approach to fighting AMR.Item Open Access Size fractionation of bioaerosol emissions from green waste composting(Elsevier, 2020-12-31) Ferguson, Robert M. W.; Neath, Charlotte E. E.; Nasir, Zaheer A.; Garcia Alcega, Sonia; Tyrrel, Sean F.; Coulon, Frederic; Dumbrell, Alex J.; Colbeck, Ian; Whitby, CorinneParticle size is a significant factor in determining the dispersal and inhalation risk from bioaerosols. Green-waste composting is a significant source of bioaerosols (including pathogens), but little is known about the distribution of specific taxa across size fractions. To characterise size fractionated bioaerosol emissions from a compost facility, we used a Spectral Intensity Bioaerosol Sensor (SIBS) to quantify total bioaerosols and qPCR and metabarcoding to quantify microbial bioaerosols. Overall, sub-micron bioaerosols predominated, but molecular analysis showed that most (>75%) of the airborne microorganisms were associated with the larger size fractions (>3.3 µm da). The microbial taxa varied significantly by size, with Bacilli dominating the larger, and Actinobacteria the smaller, size fractions. The human pathogen Aspergillus fumigatus dominated the intermediate size fractions (>50% da 1.1–4.7 µm), indicating that it has the potential to disperse widely and once inhaled may penetrate deep into the respiratory system. The abundance of Actinobacteria (>60% at da < 2.1 µm) and other sub-micron bioaerosols suggest that the main health effects from composting bioaerosols may come from allergenic respiratory sensitisation rather than directly via infection. These results emphasise the need to better understand the size distributions of bioaerosols across all taxa in order to model their dispersal and to inform risk assessments of human health related to composting facilitiesItem Open Access Visualizing the invisible: class excursions to ignite children's enthusiasm for microbes [Editorial](Wiley, 2020-05-14) McGenity, Terry J.; Gessesse, Amare; Hallsworth, John E.; Cela, Esther Garcia; Verheecke-Vaessen, Carol; Wang, Fengping; Chavarría, Max; Haggblom, Max M.; Molin, Søren; Danchin, Antoine; Smid, Eddy J.; Lood, Cédric; Cockell, Charles S.; Whitby, Corinne; Liu, Shuang‐Jiang; Keller, Nancy P.; Stein, Lisa Y.; Bordenstein, Seth R.; Lal, Rup; Nunes, Olga C.; Gram, Lone; Singh, Brajesh K.; Webster, Nicole S.; Morris, Cindy; Sivinski, Sharon; Bindschedler, Saskia; Junier, Pilar; Antunes, André; Baxter, Bonnie K.; Scavone, Paola; Timmis, KennethWe have recently argued that, because microbes have pervasive – often vital – influences on our lives, and that therefore their roles must be taken into account in many of the decisions we face, society must become microbiology‐literate, through the introduction of relevant microbiology topics in school curricula (Timmis et al. 2019. Environ Microbiol 21: 1513‐1528). The current coronavirus pandemic is a stark example of why microbiology literacy is such a crucial enabler of informed policy decisions, particularly those involving preparedness of public‐health systems for disease outbreaks and pandemics. However, a significant barrier to attaining widespread appreciation of microbial contributions to our well‐being and that of the planet is the fact that microbes are seldom visible: most people are only peripherally aware of them, except when they fall ill with an infection. And it is disease, rather than all of the positive activities mediated by microbes, that colours public perception of ‘germs’ and endows them with their poor image. It is imperative to render microbes visible, to give them life and form for children (and adults), and to counter prevalent misconceptions, through exposure to imagination‐capturing images of microbes and examples of their beneficial outputs, accompanied by a balanced narrative. This will engender automatic mental associations between everyday information inputs, as well as visual, olfactory and tactile experiences, on the one hand, and the responsible microbes/microbial communities, on the other hand. Such associations, in turn, will promote awareness of microbes and of the many positive and vital consequences of their actions, and facilitate and encourage incorporation of such consequences into relevant decision‐making processes. While teaching microbiology topics in primary and secondary school is key to this objective, a strategic programme to expose children directly and personally to natural and managed microbial processes, and the results of their actions, through carefully planned class excursions to local venues, can be instrumental in bringing microbes to life for children and, collaterally, their families. In order to encourage the embedding of microbiology‐centric class excursions in current curricula, we suggest and illustrate here some possibilities relating to the topics of food (a favourite pre‐occupation of most children), agriculture (together with horticulture and aquaculture), health and medicine, the environment and biotechnology. And, although not all of the microbially relevant infrastructure will be within reach of schools, there is usually access to a market, local food store, wastewater treatment plant, farm, surface water body, etc., all of which can provide opportunities to explore microbiology in action. If children sometimes consider the present to be mundane, even boring, they are usually excited with both the past and the future so, where possible, visits to local museums (the past) and research institutions advancing knowledge frontiers (the future) are strongly recommended, as is a tapping into the natural enthusiasm of local researchers to leverage the educational value of excursions and virtual excursions. Children are also fascinated by the unknown, so, paradoxically, the invisibility of microbes makes them especially fascinating objects for visualization and exploration. In outlining some of the options for microbiology excursions, providing suggestions for discussion topics and considering their educational value, we strive to extend the vistas of current class excursions and to: (i) inspire teachers and school managers to incorporate more microbiology excursions into curricula; (ii) encourage microbiologists to support school excursions and generally get involved in bringing microbes to life for children; (iii) urge leaders of organizations (biopharma, food industries, universities, etc.) to give school outreach activities a more prominent place in their mission portfolios, and (iv) convey to policymakers the benefits of providing schools with funds, materials and flexibility for educational endeavours beyond the classroom.