Browsing by Author "Ferguson, Robert M. W."

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    Aged-engineered nanoparticles effect on sludge anaerobic digestion performance and associated microbial communities
    (Elsevier, 2017-07-23) Eduok, Samuel; Ferguson, Robert M. W.; Jefferson, Bruce; Villa, Raffaella; Coulon, Frederic
    To investigate the potential effect of aged engineered nanoparticles (a-ENPs) on sludge digestion performance, 150 L pilot anaerobic digesters (AD) were fed with a blend of primary and waste activated sludge spiked either with a mixture of silver oxide, titanium dioxide and zinc oxide or a mixture of their equivalent bulk metal salts to achieve a target concentration of 250, 2000, and 2800 mg kg− 1 dry weight, respectively. Volatile fatty acids (VFA) were 1.2 times higher in the spiked digesters and significantly different (p = 0.05) from the control conditions. Specifically, isovaleric acid concentration was 2 times lower in the control digester compared to the spiked digesters, whereas hydrogen sulfide was 2 times lower in the ENPs spiked digester indicating inhibitory effect on sulfate reducing microorganisms. Based on the ether-linked isoprenoids concentration, the total abundance of methanogens was 1.4 times lower in the ENPs spiked digester than in the control and metal salt spiked digesters. Pyrosequencing indicated 80% decrease in abundance and diversity of methanogens in ENPs spiked digester compared to the control digester. Methanosarcina acetivorans and Methanosarcina barkeri were identified as nano-tolerant as their relative abundance increased by a factor of 6 and 11, respectively, compared to the other digesters. The results further provide compelling evidence on the resilience of Fusobacteria, Actinobacteria and the Trojan horse-like effect of ENPs which offered a competitive advantage to some organisms while reducing microbial abundance and diversity.
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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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    Bioengineering options and strategies for the optimization of anaerobic digestion processes
    (Taylor & Francis, 2014-04-17) Ferguson, Robert M. W.; Villa, Raffaella; Coulon, Frederic
    Anaerobic digestion (AD) is a complex biological process, and the microbial diversity and dynamics within the reactor needs to be understood and considered when process optimization is sought after. Microbial interactions such as competition, mutualism, antagonism and syntrophism affect the function and the survival of single species in the community; hence, they need to be understood for process improvement. Although the relationship between process performance and the microbial community structure is well established, changes in the community might occur without detectable changes in gas production and reactor performance. Recent molecular-based studies have highlighted the complexity of AD systems revealing the presence of several uncultivated species and the need for further research in this area. However, this information is still rarely used for process optimization. The integration of next generation sequencing technologies, such as 454-pyrosequencing, with other techniques, such as phospholipid-derived fatty acids analysis, can provide a holistic understanding of the microbial community. In addition, the in-depth phylogenetic resolution provided can aid environmental ecologists and engineers to better understand and optimize the AD process and consolidate the information collected to date.
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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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    Feedstocks influence on the process parameters and the microbial community in anaerobic digestion
    (Cranfield University, 2013-09) Ferguson, Robert M. W.; Coulon, Frederic; Villa, Raffaella
    To improve our understanding into the key parameters controlling and regulating the microbial groups involved in the anaerobic digestion (AD) process, particularly over multiple changes in operational conditions, triplicate lab-scale digesters fed with sewage sludge were exposed to single and multiple changes in organic loading rate (OLR) using either glycerol waste (a by-product of biodiesel manufacture), or Fats oils and greace (FOG waste) collected from a restaurant grease trap. For the multiple changes in OLR, digesters were either exposed to repeated addition of glycerol waste or repeated addition of both glycerol waste and FOG waste. In all conditions tested, physicochemical variables including volatile fatty acids (VFA), alkalinity, pH, biogas production and composition were analysed. Molecular fingerprint techniques including lipid and ether lipid analysis and 454-pyrosequencing of 16S rRNA genes were used to characterise the microbial communities. These techniques were chosen as they complement each other providing information on the microbial biomass and in-depth phylogenetic analysis of the microbial community, respectively. The key question addressed here was how feedstock composition and variation in OLR would affect the microbial community structure and dynamics and relate this to the performance of the digesters in terms of methane production over a long-term period (> 120 days). Multiple changes in OLR with the same feedstock resulted in faster recovery of methane production (8-10 days faster) compared to digesters exposed to single changes in OLR. This finding was associated specifically with a higher proportion of Clostridia Incertae Sedis XV (closely related to Cloacibacillus genus (83% similarity), family Synergistaceae) in the pre- exposed digesters. It is speculated that members related to Clostridia Incertae Sedis XV play an important role in the syntrophic interactions with the methanogens. Analysis of the VFA profiles supported this by showing that the higher relative abundance of Cloacibacillus was related to higher acetic acid concentrations. The pyrosequencing analysis further showed that community evenness was correlated with the best biogas methane content and shifts in specific bacterial groups was clearly correlated with digester performance. Overall the findings of this PhD provide new insights into the relationships between microbial community structure and digester performance. It also provides new-evidence based knowledge on how molecular microbiological tools can be used in the future to optimise and manage AD plants.
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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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    Insights into the effect of mixed engineered nanoparticles on activated sludge performance
    (Oxford University Press, 2015-07-16) Eduok, Samuel; Hendry, Callum; Ferguson, Robert M. W.; Martin, Ben; Villa, Raffaella; Jefferson, Bruce; Coulon, Frederic
    In this study, the effects, fate and transport of ENPs in wastewater treatment plants (WWTP) were investigated using three parallel pilot WWTPs operated under identical conditions. The WWTPs were spiked with (i) an ENP mixture consisting of silver oxide, titanium dioxide and zinc oxide, and (ii) bulk metal salts. The third plant served as control (unspiked). ENP effects were evaluated for (i) bulk contaminant removal, (ii) activated sludge (AS) process performance, (iii) microbial community structure and dynamics and (iv) microbial inhibition. ENPs showed a strong affinity for biosolids and induced a specific oxygen uptake rate two times higher than the control. The heterotrophic biomass retained its ability to nitrify and degrade organic matter. However, non-recovery of ammonia- and nitrite-oxidizing bacteria such as Nitrosomonas, Nitrobacter or Nitrospira in the ENP spiked reactors suggests selective inhibitory effects. The results further suggest that ENPs and metal salts have antimicrobial properties which can reduce synthesis of extracellular polymeric substances and therefore floc formation. Scanning electron microscopy evidenced selective damage to some microbes, whereas lipid fingerprinting and 454 pyrosequencing indicated a temporal shift in the microbial community structure and diversity. Acidovorax, Rhodoferax, Comamonas and Methanosarcina were identified as nano-tolerant species. Competitive growth advantage of the nano-tolerant species influenced the removal processes and unlike other xenobiotic compounds, ENPs can hasten the natural selection of microbial species in AS.
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    Organic loading rate: a promising microbial management tool in anaerobic digestion
    (Elsevier, 2016-05-06) Ferguson, Robert M. W.; Coulon, Frederic; Villa, Raffaella
    This study investigated the effect of changes in organic loading rate (OLR) and feedstock on the volatile fatty acids (VFAs) production and their potential use as a bioengineering management tool to improve stability of anaerobic digesters. Digesters were exposed to one or two changes in OLR using the same or different co-substrates (Fat Oil and Grease waste (FOG) and/or glycerol). Although all the OLR fluctuations produced a decrease in biogas and methane production, the digesters exposed twice to glycerol showed faster recovery towards stable conditions after the second OLR change. This was correlated with the composition of the VFAs produced and their mode of production, from parallel to sequential, resulting in a more efficient recovery from inhibition of methanogenesis. The change in acids processing after the first OLR increase induced a shift in the microbial community responsible of the process optimisation when the digesters were exposed to a subsequent OLR increase with the same feedstock. When the digesters were exposed to an OLR change with a different feedstock (FOG), the recovery took 7d longer than with the same one (glycerol). However, the microbial community showed functional resilience and was able to perform similarly to pre-exposure conditions. Thus, changes in operational conditions can be used to influence microbial community structure for anaerobic digestion (AD) optimisation. Finally, shorter recovery times and increased resilience of digesters were linked to higher numbers of Clostridia incertae sedis XV, suggesting that this group may be a good candidate for AD bioaugmentation to speed up recovery after process instability or OLR increase.
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    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 Ahmad
    Bioaerosols 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.
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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
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    Understand microbial ecology can help improve biogas production in AD
    (Elsevier, 2018-06-17) Ferguson, Robert M. W.; Coulon, Frederic; Villa, Raffaella
    454-Pyrosequencing and lipid fingerprinting were used to link anaerobic digestion (AD) process parameters (pH, alkalinity, volatile fatty acids (VFAs), biogas production and methane content) with the reactor microbial community structure and composition. AD microbial communities underwent stress conditions after changes in organic loading rate and digestion substrates. 454-Pyrosequencing analysis showed that, irrespectively of the substrate digested, methane content and pH were always significantly, and positively, correlated with community evenness. In AD, microbial communities with more even distributions of diversity are able to use parallel metabolic pathways and have greater functional stability; hence, they are capable of adapting and responding to disturbances. In all reactors, a decrease in methane content to <30% was always correlated with a 50% increase of Firmicutes sequences (particularly in operational taxonomic units (OTUs) related to Ruminococcaceae and Veillonellaceae). Whereas digesters producing higher methane content (above 60%), contained a high number of sequences related to Synergistetes and unidentified bacterial OTUs. Finally, lipid fingerprinting demonstrated that, under stress, the decrease in archaeal biomass was higher than the bacterial one, and that archaeal Phospholipid etherlipids (PLEL) levels were correlated to reactor performances. These results demonstrate that, across a number of parameters such as lipids, alpha and beta diversity, and OTUs, knowledge of the microbial community structure can be used to predict, monitor, or optimise AD performance.