Browsing by Author "Dumbrell, Alex J."

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    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, Ian
    Bioerosols (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.
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    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, Frederic
    Air 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.
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    Defining recovery potential in river restoration: a biological data-driven approach
    (MDPI, 2021-11-24) Wilkes, Martin A.; Mckenzie, Morwenna; Naura, Marc; Allen, Laura; Morris, Mike; Van De Wiel, Marco; Dumbrell, Alex J.; Bani, Alessia; Lashford, Craig; Lavers, Tom; England, Judy
    Scientists and practitioners working on river restoration have made progress on understanding the recovery potential of rivers from geomorphological and engineering perspectives. We now need to build on this work to gain a better understanding of the biological processes involved in river restoration. Environmental policy agendas are focusing on nature recovery, reigniting debates about the use of “natural” reference conditions as benchmarks for ecosystem restoration. We argue that the search for natural or semi-natural analogues to guide restoration planning is inappropriate due to the absence of contemporary reference conditions. With a catchment-scale case study on the invertebrate communities of the Warwickshire Avon, a fifth-order river system in England, we demonstrate an alternative to the reference condition approach. Under our model, recovery potential is quantified based on the gap between observed biodiversity at a site and the biodiversity predicted to occur in that location under alternative management scenarios. We predict that commonly applied restoration measures such as reduced nutrient inputs and the removal of channel resectioning could be detrimental to invertebrate diversity, if applied indiscriminately and without other complementary measures. Instead, our results suggest considerable potential for increases in biodiversity when restoration measures are combined in a way that maximises biodiversity within each water body
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    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.
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    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, Frederic
    The 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.
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    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, Corinne
    Particle 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 facilities