Natural source zone depletion of LNAPL: A critical review supporting modelling approaches

Natural source zone depletion (NSZD) of light non-aqueous phase liquids (LNAPLs) includes partitioning, transport and degradation of LNAPL components. NSZD is being considered as a site closure option during later stages of active remediation of LNAPL contaminated sites, and where LNAPL mass removal is limiting. To ensure NSZD meets compliance criteria and to design enhanced NSZD actions if required, residual risks posed by LNAPL and its long term behaviour require estimation. Prediction of long-term NSZD trends requires linking physicochemical partitioning and transport processes with bioprocesses at multiple scales within a modelling framework. Here we expand and build on the knowledge base of a recent review of NSZD, to establish the key processes and understanding required to model NSZD long term. We describe key challenges to our understanding, inclusive of the dominance of methanogenic or aerobic biodegradation processes, the potentially changeability of rates due to the weathering profile of LNAPL product types and ages, and linkages to underlying bioprocesses. We critically discuss different scales in subsurface simulation and modelling of NSZD. Focusing on processes at Darcy scale, 36 models addressing processes of importance to NSZD are investigated. We investigate the capabilities of models to accommodate more than 20 subsurface transport and transformation phenomena and present comparisons in several tables. We discuss the applicability of each group of models for specific site conditions

Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

Background The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. Results Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. Conclusions In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.publishedVersio

Biofilm and Related Amoebas in an UK Chlorinated Drinking Water System

Drinking water distribution systems (DWDS) can host pathogenic amoebae, but the role of biofilms in supporting the occurrence of these organisms needs to be fully explored in the UK systems. The presence of amoebae and associated bacteria in biofilms attached to inner pipe surfaces was studied in an experimental full-scale chlorinated distribution system in the UK. Quantitative polymerase change reaction (qPCR) was used to identify and quantify amoebae, whilst the bacterial communities in the biofilms were characterised by sequencing the 16S rRNA gene. Despite the maintenance of a chlorine residual in the network (free chlorine ≥ 0.24 mg/L), several species of amoebae belonging to the genera Acanthamoeba, Vermamoeba, and Naegleria were identified in 30-day-old biofilm samples; however, no amoebae were detected in the water samples analysed. The dominant bacterial communities present in the biofilm samples were Variovorax, Pseudomonas, and Aquabacterium. These results indicate that the biofilm samples contained potential pathogenic amoebae and bacteria, such as Acanthamoeba and Pseudomonas, respectively, which implies a potential public health risk if the biofilms are mobilised into the bulk water. Several of the amoebae identified in this study are able to support the presence of resistant bacteria that can remain viable within these prokaryotic organisms until they reach people’s taps. The identification of the microorganisms associated with the pathogenic amoeba species in biofilms could be used to improve the surveillance of DWDS in order to protect public health

Development of Untargeted Metabolomics Methods for the Rapid Detection of Pathogenic <i>Naegleria fowleri</i>

Despite comparatively low levels of infection, primary amoebic meningoencephalitis (PAM) induced by <i>Naegleria fowleri</i> is extremely lethal, with mortality rates above 95%. As a thermophile, this organism is often found in moderate-to-warm climates and has the potential to colonize drinking water distribution systems (DWDSs). Current detection approaches require days to obtain results, whereas swift corrective action can maximize the benefit of public health. Presently, there is little information regarding the underlying in situ metabolism for this amoeba but the potential exists to exploit differentially expressed metabolic signatures as a rapid detection technique. This research outlines the biochemical profiles of selected pathogenic and nonpathogenic <i>Naegleria</i> in vitro using an untargeted metabolomics approach to identify a panel of diagnostically meaningful compounds that may enable rapid detection of viable pathogenic <i>N. fowleri</i> and augment results from traditional monitoring approaches

Competition between <i>Naegleria fowleri</i> and Free Living Amoeba Colonizing Laboratory Scale and Operational Drinking Water Distribution Systems

Free living amoebae (FLA), including pathogenic <i>Naegleria fowleri</i>, can colonize and grow within pipe wall biofilms of drinking water distribution systems (DWDSs). Studies on the interactions between various FLA species in biofilms are limited. Understanding the interaction between FLA and the broader biofilm ecology could help better predict DWDS susceptibility to <i>N. fowleri</i> colonization. The aim of this study was to determine if <i>N. fowleri</i> and other FLAs (<i>Naegleria</i>, <i>Vermamoeba</i>, <i>Willaertia</i>, and <i>Vahlkampfia</i> spp.) cocolonize DWDS biofilm. FLAs commonly isolated from DWDSs (<i>N. fowleri</i>, <i>V. vermiformis</i>, and <i>N. lovaniensis</i>) were introduced into laboratory-scale biomonitors to determine the impact of these amoebae on <i>N. fowleri’s</i> presence and viability. Over 18 months, a single viable amoebae (<i>N. fowleri</i>, <i>N. lovaniensis</i>, or <i>V. vermiformis</i>) was detected in each biofilm sample, with the exception of <i>N. lovaniensis</i> and <i>N. fowleri</i>, which briefly cocolonized biofilm following their coinoculation. The analysis of biofilm and bulk water samples from operational DWDSs revealed a similar lack of cocolonization with a single FLA detected in 99% (<i>n</i> = 242) of samples. Interestingly, various <i>Naegleria</i> spp. did colonize the same DWDS locations but at different times. This knowledge furthers the understanding of ecological factors which enable <i>N. fowleri</i> to colonize and survive within operational DWDSs and could aid water utilities to control its occurrence

Characterization of a Drinking Water Distribution Pipeline Terminally Colonized by Naegleria fowleri

Free-living amoebae, such as Naegleria fowleri, Acanthamoeba spp., and Vermamoeba spp., have been identified as organisms of concern due to their role as hosts for pathogenic bacteria and as agents of human disease. In particular, N. fowleri is known to cause the disease primary amoebic meningoencephalitis (PAM) and can be found in drinking water systems in many countries. Understanding the temporal dynamics in relation to environmental and biological factors is vital for developing management tools for mitigating the risks of PAM. Characterizing drinking water systems in Western Australia with a combination of physical, chemical and biological measurements over the course of a year showed a close association of N. fowleri with free chlorine and distance from treatment over the course of a year. This information can be used to help design optimal management strategies for the control of N. fowleri in drinking-water-distribution systems

Naegleria fowleri Detected in Grand Teton National Park Hot Springs

The free-living thermophilic amoeba Naegleria fowleri (N. fowleri) causes the highly fatal disease primary amoebic meningoencephalitis. The environmental conditions that are favorable to the growth and proliferation of N. fowleri are not well-defined, especially in northern regions of the United States. In this study, we used culture-based methods and multiple molecular approaches to detect and analyzeN. fowleri and other Naegleria spp. in water, sediment, and biofilm samples from five hot spring sites in Grand Teton National Park, Wyoming, U.S.A. These results provide the first detections of N. fowleri in Grand Teton National Park and provide new insights into the distribution of pathogenic N. fowleri and other nonpathogenic Naegleria spp. in natural thermal water systems in northern latitudes

Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri

Background The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. Results Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. Conclusions In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen