Acoustic monitoring of Amazonian wildlife in human-modified landscapes

Tropical forest covers just 12% of the planet’s land surface, but disproportionately host the planet’s biodiversity, including around two thirds of all terrestrial species. Amazonia retains the largest extent of remaining tropical forest globally, but just over 50% of all tropical forest loss since 2002 has been in the region. Deforestation and disturbance result in significant loss in forest biodiversity, but quantifying the exact nature of those changes can be complex. The Amazon represents a particularly challenging case in which to assess biodiversity change due to the spatiotemporal scales being assessed, because of the high proportion of rare species, and the challenging conditions for conducting biodiversity surveys in tropical forest. Ecoacoustics has been championed as a valuable tool to overcome the difficulties of monitoring in such conditions and at large spatio-temporal scales, but applied analytical methods often remain underdeveloped. In this this thesis I develop and use a range of ecoacoustic methods to help understand the impact of anthropogenic disturbance on Amazonian wildlife, using an extensive audio dataset collected from survey points spanning a degradation gradient in the Eastern Brazilian Amazon. In Chapter 2 I introduce a quick and simple method for the detection of rainfall, tested for efficacy globally and with an accompanying R package. In Chapter 3 I present a new approach to subsampling of acoustic data for manual assessment of avian biodiversity, finding that using a high number of short repeat samples can detect approximately 50% higher alpha diversity than more commonly used approaches. In Chapter 4 I assess the sensitivity and fidelity of two commonly used acoustic indices to biodiversity responses to forest disturbances, finding that measuring indices at narrower, ecologically appropriate time-frequency bins avoids problems with signal masking. In Chapter 5 I use a two-stage, random forest based method to build a multi-taxa classifier for the nocturnal avifaunal community in the study region, and use the classifier-derived data to reveal that the nocturnal bird community is largely robust to less intense forms of forest disturbance. Overall, in this thesis I demonstrate that ecoacoustics can be a highly effective method for inventorying and monitoring biodiversity in one of the most diverse and challenging regions on the planet

Student produced media and the use of web based sites for the assessment of technical and communication skills in engineering students

This paper describes the development of new assessment approaches for engineering students through the use of video production and on-line blogging. The course team in Materials Engineering have developed an approach enabling students to explore ideas and publish work by creating a short film focussing on technical areas. This technical work was previously assessed by a written report and PowerPoint presentations. However, the team wanted to make the reporting more creative and fun for the students and so decided to incorporate a more visual approach introducing video production skills into modules taught on the programme. Discrete modules at all levels of the course were developed in this respect and the outputs of this work have been previously reported. For example, students were given the task of researching a topic in polymers or composites and the end production was a digital video case study handed in on a CD or DVD for assessment. This assessment task replaced a traditional 6 week case study that would have covered the same technical areas, but would have resulted in a group report and PowerPoint presentation. The students were supported with an initial seminar on video production skills, followed by weekly drop-in sessions for technical support on filming and editing. During the last two years students have been asked to produce a website in the form of a technical blog to report their work, both individually and in groups. The result has been an end of module presentation of the sites for summative assessment. The paper will describe the advantages and issues realised with this type of activity, utilising student feedback as part of the evaluation

Using acoustic indices in ecology : guidance on study design, analyses and interpretation

TBL was supported by Leverhulme Trust, research grant number RPG-2020-160; the Lorentz Centre, Leiden, The Netherlands; and UKAN+. AE and OM were supported by UKAN+.The rise of passive acoustic monitoring and the rapid growth in large audio datasets is driving the development of analysis methods that allow ecological inferences to be drawn from acoustic data. Acoustic indices are currently one of the most widely applied tools in ecoacoustics. These numerical summaries of the sound energy contained in digital audio recordings are relatively straightforward and fast to calculate but can be challenging to interpret. Misapplication and misinterpretation have produced conflicting results and led some to question their value. To encourage better use of acoustic indices, we provide nine points of guidance to support good study design, analysis and interpretation. We offer practical recommendations for the use of acoustic indices in the study of both whole soundscapes and individual taxa and species, and point to emerging trends in ecoacoustic analysis. In particular, we highlight the critical importance of understanding the links between soundscape patterns and acoustic indices. Acoustic indices can offer insights into the state of organisms, populations, and ecosystems, complementing other ecological research techniques. Judicious selection, appropriate application and thorough interpretation of existing indices is vital to bolster robust developments in ecoacoustics for biodiversity monitoring, conservation and future research.Publisher PDFPeer reviewe

Detecting and reducing heterogeneity of error in acoustic classification

Passive acoustic monitoring can be an effective method for monitoring species, allowing the assembly of large audio datasets, removing logistical constraints in data collection and reducing anthropogenic monitoring disturbances. However, the analysis of large acoustic datasets is challenging and fully automated machine learning processes are rarely developed or implemented in ecological field studies. One of the greatest uncertainties hindering the development of these methods is spatial generalisability—can an algorithm trained on data from one place be used elsewhere? We demonstrate that heterogeneity of error across space is a problem that could go undetected using common classification accuracy metrics. Second, we develop a method to assess the extent of heterogeneity of error in a random forest classification model for six Amazonian bird species. Finally, we propose two complementary ways to reduce heterogeneity of error, by (i) accounting for it in the thresholding process and (ii) using a secondary classifier that uses contextual data. We found that using a thresholding approach that accounted for heterogeneity of precision error reduced the coefficient of variation of the precision score from a mean of 0.61 ± 0.17 (SD) to 0.41 ± 0.25 in comparison to the initial classification with threshold selection based on F-score. The use of a secondary, contextual classification with thresholding selection accounting for heterogeneity of precision reduced it further still, to 0.16 ± 0.13, and was significantly lower than the initial classification in all but one species. Mean average precision scores increased, from 0.66 ± 0.4 for the initial classification, to 0.95 ± 0.19, a significant improvement for all species. We recommend assessing—and if necessary correcting for—heterogeneity of precision error when using automated classification on acoustic data to quantify species presence as a function of an environmental, spatial or temporal predictor variable

Quantifying the importance of plastic pollution for the dissemination of human pathogens: The challenges of choosing an appropriate 'control' material

Discarded plastic wastes in the environment are serious challenges for sustainable waste management and for the delivery of environmental and public health. Plastics in the environment become rapidly colonised by microbial biofilm, and importantly this so-called ‘plastisphere’ can also support, or even enrich human pathogens. The plastisphere provides a protective environment and could facilitate the increased survival, transport and dissemination of human pathogens and thus increase the likelihood of pathogens coming into contact with humans, e.g., through direct exposure at beaches or bathing waters. However, much of our understanding about the relative risks associated with human pathogens colonising environmental plastic pollution has been inferred from taxonomic identification of pathogens in the plastisphere, or laboratory experiments on the relative behaviour of plastics colonised by human pathogens. There is, therefore, a pressing need to understand whether plastics play a greater role in promoting the survival and dispersal of human pathogens within the environment compared to other substrates (either natural materials or other pollutants). In this paper, we consider all published studies that have detected human pathogenic bacteria on the surfaces of environmental plastic pollution and critically discuss the challenges of selecting an appropriate control material for plastisphere experiments. Whilst it is clear there is no ‘perfect’ control material for all plastisphere studies, understanding the context-specific role plastics play compared to other substrates for transferring human pathogens through the environment is important for quantifying the potential risk that colonised plastic pollution may have for environmental and public health

Alpha-v-containing integrins are host receptors for the Plasmodium falciparum sporozoite surface protein, TRAP.

Malaria-causing Plasmodium sporozoites are deposited in the dermis by the bite of an infected mosquito and move by gliding motility to the liver where they invade and develop within host hepatocytes. Although extracellular interactions between Plasmodium sporozoite ligands and host receptors provide important guidance cues for productive infection and are good vaccine targets, these interactions remain largely uncharacterized. Thrombospondin-related anonymous protein (TRAP) is a parasite cell surface ligand that is essential for both gliding motility and invasion because it couples the extracellular binding of host receptors to the parasite cytoplasmic actinomyosin motor; however, the molecular nature of the host TRAP receptors is poorly defined. Here, we use a systematic extracellular protein interaction screening approach to identify the integrin αvβ3 as a directly interacting host receptor for Plasmodium falciparum TRAP. Biochemical characterization of the interaction suggests a two-site binding model, requiring contributions from both the von Willebrand factor A domain and the RGD motif of TRAP for integrin binding. We show that TRAP binding to cells is promoted in the presence of integrin-activating proadhesive Mn2+ ions, and that cells genetically targeted so that they lack cell surface expression of the integrin αv-subunit are no longer able to bind TRAP. P. falciparum sporozoites moved with greater speed in the dermis of Itgb3-deficient mice, suggesting that the interaction has a role in sporozoite migration. The identification of the integrin αvβ3 as the host receptor for TRAP provides an important demonstration of a sporozoite surface ligand that directly interacts with host receptors. Copyright © 2018 the Author(s). Published by PNAS

Clinically important E. coli strains can persist, and retain their pathogenicity, on environmental plastic and fabric waste

Plastic waste is ubiquitous in the environment and there are increasing reports of such waste being colonised by human pathogens. However, the ability of pathogens to persist on plastics for long periods, and the risk that they pose to human health, is unknown. Here, under simulated environmental conditions, we aimed to determine if pathogenic bacteria can retain their virulence following a prolonged period on plastic. Using antibiotic selection and luciferase expression for quantification, we show that clinically important strains of E. coli can survive on plastic for at least 28-days. Importantly, these pathogens also retained their virulence (determined by using a Galleria mellonella model as a surrogate for human infection) and in some cases, had enhanced virulence following their recovery from the plastisphere. This indicates that plastics in the environment can act as reservoirs for human pathogens and could facilitate their persistence for extended periods of time. Most importantly human pathogens in the plastisphere are capable of retaining their pathogenicity. Pathogens colonising environmental plastic waste therefore pose a heightened public health risk, particularly in areas where people are exposed to pollution

Acoustic indices perform better when applied at ecologically meaningful time and frequency scales

Acoustic indices are increasingly employed in the analysis of soundscapes to ascertain biodiversity value. However, conflicting results and lack of consensus on best practices for their usage has hindered their application in conservation and land‐use management contexts. Here we propose that the sensitivity of acoustic indices to ecological change and fidelity of acoustic indices to ecological communities are negatively impacted by signal masking. Signal masking can occur when acoustic responses of taxa sensitive to the effect of interest are masked by less sensitive acoustic groups, or target taxa sonification is masked by non‐target noise. We argue that by calculating acoustic indices at ecologically appropriate time and frequency bins, masking effects can be reduced and the efficacy of indices increased. We test this on a large acoustic dataset collected in Eastern Amazonia spanning a disturbance gradient of undisturbed, logged, burned, logged‐and‐burned, and secondary forests. We calculated values for two acoustic indices: the Acoustic Complexity Index and the Bioacoustic Index, across the entire frequency spectrum (0‐22.1 kHz), and four narrower subsets of the frequency spectrum; at dawn, day, dusk and night. We show that signal masking has a large impact on the sensitivity of acoustic indices to forest disturbance classes. Calculating acoustic indices at a range of narrower time‐frequency bins substantially increases the classification accuracy of forest classes by random forest models. Furthermore, signal masking led to misleading correlations, including spurious inverse correlations, between biodiversity indicator metrics and acoustic index values compared to correlations derived from manual sampling of the audio data. Consequently, we recommend that acoustic indices are calculated either at a range of time and frequency bins, or at a single narrow bin, predetermined by a priori ecological understanding of the soundscape

From wastewater discharge to the beach: Survival of human pathogens bound to microplastics during transfer through the freshwater-marine continuum

Large quantities of microplastics are regularly discharged from wastewater treatment plants (WWTPs) into the aquatic environment. Once released, these plastics can rapidly become colonised by microbial biofilm, forming distinct plastisphere communities which may include potential pathogens. We hypothesised that the protective environment afforded by the plastisphere would facilitate the survival of potential pathogens during transitions between downstream environmental matrices and thus increase persistence and the potential for environmental dissemination of pathogens. The survival of Escherichia coli, Enterococcus faecalis and Pseudomonas aeruginosa colonising polyethylene or glass particles has been quantified in mesocosm incubation experiments designed to simulate, (1) the direct release of microplastics from WWTPs into freshwater and seawater environments; and (2) the movement of microplastics downstream following discharge from the WWTP through the river-estuary-marine-beach continuum. Culturable E. coli, E. faecalis and P. aeruginosa were successfully able to survive and persist on particles whether they remained in one environmental matrix or transitioned between different environmental matrices. All three bacteria were still detectable on both microplastic and glass particles after 25 days, with higher concentrations on microplastic compared to glass particles; however, there were no differences in bacterial die-off rates between the two materials. This potential for environmental survival of pathogens in the plastisphere could facilitate their transition into places where human exposure is greater (e.g., bathing waters and beach environments). Therefore, risks associated with pathogen-microplastic co-pollutants in the environment, emphasises the urgency for updated regulations on wastewater discharge and the management of microplastic generation and release

The effectiveness of conventional trickling filter treatment plants at reducing concentrations of copper in wastewaters

This is the post-print version of the final paper published in Science of the Total Environment. The published article is available from the link below. Changes resulting from the publishing process, such as peer review, editing, corrections, structural formatting, and other quality control mechanisms may not be reflected in this document. Changes may have been made to this work since it was submitted for publication. Copyright @ 2009 Elsevier B.V.Eight different sewage treatment works were sampled in the North West of England. The effectiveness of the conventional treatment processes (primary sedimentation and biological trickling filters) as well as various tertiary treatment units in terms of both total and dissolved copper removal was evaluated. The removal of total copper across primary sedimentation averaged 53% and were relatively consistent at all sites, however, at three sites the removal of dissolved copper also occurred at this stage of treatment. Removal of total copper by the biological trickling filters averaged 49%, however, substantial dissolution of copper occurred at two sites, which highlighted the unpredictability of this treatment process in the removal of dissolved copper. Copper removal during tertiary treatment varied considerably even for the same treatment processes installed at different sites, primarily due to the variability of insoluble copper removal, with little effect on copper in the dissolved form being observed. The proportion of dissolved copper increased significantly during treatment, from an average of 22% in crude sewages to 55% in the final effluents. There may be the potential to optimise existing, conventional treatment processes (primary or biological treatment) to enhance dissolved copper removal, possibly reducing the requirement for installing any tertiary processes specifically for the removal of copper.United Utilities PL