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.

Biodegradability of legacy crude oil contamination in Gulf War damaged groundwater wells in Northern Kuwait.

During the 1991 Gulf War, oil wells in the oil fields of Kuwait were set aflame and destroyed. This resulted in severe crude oil pollution of the countries only fresh water aquifers. Here, for the first time the natural attenuation and biodegradation of the persisting groundwater contamination was investigated to assess potential processes in the aquifer. Biodegradation experiments were conducted under aerobic and multiple anaerobic conditions using microcosms of the contaminated groundwater from Kuwait. Under the conditions tested, a portion of the total petroleum hydrocarbon (TPH) component was degraded, however there was only a slight change in the bulk concentration of the contaminant measured as dissolved organic carbon (DOC), suggesting the presence of a recalcitrant pollutant. Changes in the associated microbial community composition under different reduction-oxidation conditions were observed and known hydrocarbon degraders identified. The results of this study indicate that lingering contaminant still persists in the groundwater and is recalcitrant to further biodegradation, which presents challenges for future remediation plans.

Competition between Naegleria fowleri and Free Living Amoeba Colonizing Laboratory Scale and Operational Drinking Water Distribution Systems.

Free living amoebae (FLA), including pathogenic Naegleria fowleri, 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 N. fowleri colonization. The aim of this study was to determine if N. fowleri and other FLAs ( Naegleria, Vermamoeba, Willaertia, and Vahlkampfia spp.) cocolonize DWDS biofilm. FLAs commonly isolated from DWDSs ( N. fowleri, V. vermiformis, and N. lovaniensis) were introduced into laboratory-scale biomonitors to determine the impact of these amoebae on N. fowleri's presence and viability. Over 18 months, a single viable amoebae ( N. fowleri, N. lovaniensis, or V. vermiformis) was detected in each biofilm sample, with the exception of N. lovaniensis and N. fowleri, 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% ( n = 242) of samples. Interestingly, various Naegleria spp. did colonize the same DWDS locations but at different times. This knowledge furthers the understanding of ecological factors which enable N. fowleri to colonize and survive within operational DWDSs and could aid water utilities to control its occurrence.

Biodegradability of polar compounds formed from weathered diesel.

Once released into the environment, petroleum is exposed to biological and physical weathering processes which can lead to the formation and accumulation of highly recalcitrant polar compounds. These polar compounds are often challenging to analyse and can be present as an "unresolved complex mixture" (UCM) in total petroleum hydrocarbon (TPH) analyses and can be mistaken for natural organic matter. Existing research on UCMs comprised of polar compounds is limited, with a majority of the compounds remaining unidentified and their long-term persistence unknown. Here, we investigated the potential biodegradation of these recalcitrant polar compounds isolated from weathered diesel contaminant, and the changes in the microbial community composition associated with the biodegradation process. Microcosms were used to study the biodegradability of the polar compounds under various aerobic and anaerobic conditions and the results compared against the biodegradation of fresh diesel. Under all conditions tested, the majority of the polar UCM contaminant remained recalcitrant to biodegradation. The degradation was limited to the TPH portion of the polar UCM, which represented a minor fraction of the total polar UCM concentration. Changes in microbial community composition were observed under different redox conditions and in the presence of different contaminants. This work furthers the understanding of the biodegradation and long-term recalcitrance of polar compounds formed through weathering at contaminated legacy sites.

Development of Untargeted Metabolomics Methods for the Rapid Detection of Pathogenic Naegleria fowleri.

Despite comparatively low levels of infection, primary amoebic meningoencephalitis (PAM) induced by Naegleria fowleri 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 Naegleria in vitro using an untargeted metabolomics approach to identify a panel of diagnostically meaningful compounds that may enable rapid detection of viable pathogenic N. fowleri and augment results from traditional monitoring approaches.

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.

Reduced Efficiency of Chlorine Disinfection of Naegleria fowleri in a Drinking Water Distribution Biofilm.

Naegleria fowleri associated with biofilm and biological demand water (organic matter suspended in water that consumes disinfectants) sourced from operational drinking water distribution systems (DWDSs) had significantly increased resistance to chlorine disinfection. N. fowleri survived intermittent chlorine dosing of 0.6 mg/L for 7 days in a mixed biofilm from field and laboratory-cultured Escherichia coli strains. However, N. fowleri associated with an attached drinking water distribution biofilm survived more than 30 times (20 mg/L for 3 h) the recommended concentration of chlorine for drinking water. N. fowleri showed considerably more resistance to chlorine when associated with a real field biofilm compared to the mixed laboratory biofilm. This increased resistance is likely due to not only the consumption of disinfectants by the biofilm and the reduced disinfectant penetration into the biofilm but also the composition and microbial community of the biofilm itself. The increased diversity of the field biofilm community likely increased N. fowleri's resistance to chlorine disinfection compared to that of the laboratory-cultured biofilm. Previous research has been conducted in only laboratory scale models of DWDSs and laboratory-cultured biofilms. To the best of our knowledge, this is the first study demonstrating how N. fowleri can persist in a field drinking water distribution biofilm despite chlorination.

Prokaryotic microbial ecology as an ecosurveillance tool for eukaryotic pathogen colonisation: Meiothermus and Naegleria fowleri.

Naegleria fowleri has been detected in drinking water distribution systems (DWDS) in Australia, Pakistan and the United States and is the causative agent of the highly fatal disease primary amoebic meningoencephalitis. Previous small scale field studies have shown that Meiothermus may be a potential biomarker for N. fowleri. However, correlations between predictive biomarkers in small sample sizes often breakdown when applied to larger more representative datasets. This study represents one of the largest and most rigorous temporal investigations of Naegleria fowleri colonisation in an operational DWDS in the world and measured the association of Meiothermus and N. fowleri over a significantly larger space and time in the DWDS. A total of 232 samples were collected from five sites over three-years (2016-2018), which contained 29 positive N. fowleri samples. Two specific operational taxonomic units assigned to M. chliarophilus and M. hypogaeus, were significantly associated with N. fowleri presence. Furthermore, inoculation experiments demonstrated that Meiothermus was required to support N. fowleri growth in field-collected biofilms. This validates Meiothermus as prospective biological tool to aid in the identification and surveillance of N. fowleri colonisable sites.

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.

The role of predicted chemotactic and hydrocarbon degrading taxa in natural source zone depletion at a legacy petroleum hydrocarbon site.

Petroleum hydrocarbon contamination is a global problem which can cause long-term environmental damage and impacts water security. Natural source zone depletion (NSZD) is the natural degradation of such contaminants. Chemotaxis is an aspect of NSZD which is not fully understood, but one that grants microorganisms the ability to alter their motion in response to a chemical concentration gradient potentially enhancing petroleum NSZD mass removal rates. This study investigates the distribution of potentially chemotactic and hydrocarbon degrading microbes (CD) across the water table of a legacy petroleum hydrocarbon site near Perth, Western Australia in areas impacted by crude oil, diesel and jet fuel. Core samples were recovered and analysed for hydrocarbon contamination using gas chromatography. Predictive metagenomic profiling was undertaken to infer functionality using a combination of 16 S rRNA sequencing and PICRUSt2 analysis. Naphthalene contamination was found to significantly increase the occurrence of potential CD microbes, including members of the Comamonadaceae and Geobacteraceae families, which may enhance NSZD. Further work to explore and define this link is important for reliable estimation of biodegradation of petroleum hydrocarbon fuels. Furthermore, the outcomes suggest that the chemotactic parameter within existing NSZD models should be reviewed to accommodate CD accumulation in areas of naphthalene contamination, thereby providing a more accurate quantification of risk from petroleum impacts in subsurface environments, and the scale of risk mitigation due to NSZD.

Investigation into the microbial communities and associated crude oil-contamination along a Gulf War impacted groundwater system in Kuwait.

During the First Gulf War (1991) a large number of oil wells were destroyed and oil fires subsequently extinguished with seawater. As a result Kuwait's sparse fresh groundwater resources were severely contaminated with crude oil. Since then limited research has focused on the microbial community ecology of the groundwater and their impact on the associated contamination. Here, the microbial community ecology (bacterial, archaeal and eukaryotic) and how it relates to the characteristics of the hydrocarbon contaminants were examined for the first time since the 1991 event. This study was conducted using 15 wells along the main groundwater flow direction and detected several potential hydrocarbon degrading microorganisms such as Hyphomicrobiaceae, Porphyromonadaceae and Eurotiomycetes. The beta diversity of the microbial communities correlated significantly with total petroleum hydrocarbon (TPH) concentrations and salinity. The TPH consisted mainly of polar compounds present as an unresolved complex mixture (UCM) of a highly recalcitrant nature. Based on the proportions of TPH to dissolved organic carbon (DOC), the results indicate that some minor biodegradation has occurred within highly contaminated aquifer zones. However, overall the results from this study suggest that the observed variations in TPH concentrations among the sampled wells are mainly induced by mixing/dilution with pristine groundwater rather than by biodegradation of the contaminants. The findings make an important contribution to better understand the fate of the groundwater pollution in Kuwait, with important implications for the design of future remediation efforts.

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.

Mobility and recalcitrance of organo-chromium(III) complexes.

Hexavalent chromium [Cr(VI)] is a major industrial pollutant. Bioremediation of Cr(VI) to Cr(III) is a viable clean-up approach. However, Cr(VI) bioreduction also produces soluble organo-Cr(III) complexes, and little is known about their behavior in the environment. When tested with soil columns, citrate-Cr(III) showed little sorption to soil; malate-Cr(III) had limited partitioning with soil; and histidine-Cr(III) exhibited significant interaction with soil. It appears that the mobility varies depending on the organic ligand. Further, Ralstonia eutropha JMP 134 and Pseudomonas aeruginosa pAO1 readily degraded malate, citrate, and histidine, but not the corresponding organo-Cr(III) complexes. The recalcitrance is not due to toxicity, but the complexes are likely to cause hindrance to enzymes, as malate dehydrogenase and amino acid oxidase could not use malate-Cr(III) and histidine-Cr(III), respectively. The data are in agreement with the reports of soluble organo-Cr(III) complexes in the environment.

Application of untargeted metabolomics for the detection of pathogenic Naegleria fowleri in an operational drinking water distribution system.

Found in drinking water distribution systems (DWDSs), swimming pools, and recreational waters, N. fowleri, is the causative agent of primary amoebic meningoencephalitis (PAM). Although cases of N. fowleri infections are rare, the fatality is comparatively high (>95%) and surveillance is essential to minimize N. fowleri infections. However, conventional N. fowleri detection methods are less satisfying owing to their time-consuming and lab intensive characteristics as well as the lack of the ability to determine viability. As a result, an alternative detection approach capable of determining viability as well as species identification is required to better ensure public health. Based on our previous research focusing on distinguishing laboratory cultured N. fowleri from N. lovaniensis and N. italica, this study applies untargeted metabolomics methods to field samples from operational DWDSs. A list of diagnostic features was found to preliminarily discriminate the N. fowleri positive from N. fowleri negative and N. lovaniensis positive field samples with satisfying predictive accuracy. The results outlined in this manuscript further validate and improve the metabolite-based N. fowleri detection approach, potentially aiding water utilities in the detection and management of N. fowleri in drinking water.

Preferential feeding in Naegleria fowleri; intracellular bacteria isolated from amoebae in operational drinking water distribution systems.

The amoeba Naegleria fowleri is the causative agent of the highly fatal disease, primary amoebic meningoencephalitis, and estimated to cause 16 deaths per year in the United States alone. Colonisation of drinking water distribution systems (DWDSs) by the N. fowleri is a significant public health issue. Understanding the factors which enable this pathogen to colonise and thrive in DWDSs is critical for proper management. The microbial ecology within DWDSs may influence the ability of N. fowleri to colonise DWDSs by facilitating the availability of an appropriate food source. Using biofilm samples obtained from operational DWDSs, 16S rRNA amplicon metabarcoding was combined with genus-specific PCR and Sanger sequencing of intracellular associated bacteria from isolated amoeba and their parental biofilms to identify Meiothermus chliarophilus as a potential food source for N. fowleri. Meiothermus was confirmed as a food source for N. fowleri following successful serial culturing of axenic N. fowleri with M. chliarophilus or M. ruber as the sole food source. The ability to identify environmental and ecological conditions favourable to N. fowleri colonisation, including the detection of appropriate food sources such as Meiothermus, could provide water utilities with a predictive tool for managing N. fowleri colonisation within the DWDS.

Comparison of biofilm ecology supporting growth of individual Naegleria species in a drinking water distribution system.

Free-living amoebae (FLA) are common components of microbial communities in drinking water distribution systems (DWDS). FLA are of clinical importance both as pathogens and as reservoirs for bacterial pathogens, so identifying the conditions promoting amoebae colonisation of DWDSs is an important public health concern for water utilities. We used high-throughput amplicon sequencing to compare eukaryotic and bacterial communities associated with DWDS biofilms supporting distinct FLA species (Naegleria fowleri, N. lovaniensis or Vermamoeba sp.) at sites with similar physical/chemical conditions. Eukaryote and bacterial communities were characteristics of different FLA species presence, and biofilms supporting Naegleria growth had higher bacterial richness and higher abundance of Proteobacteria, Bacteroidetes (bacteria), Nematoda and Rotifera (eukaryota). The eukaryotic community in the biofilms had the greatest difference in relation to the presence of N. fowleri, while the bacterial community identified individual bacterial families associated with the presence of different Naegleria species. Our results demonstrate that ecogenomics data provide a powerful tool for studying the microbial and meiobiotal content of biofilms, and, in these samples can effectively discriminate biofilm communities supporting pathogenic N. fowleri. The identification of microbial species associated with N. fowleri could further be used in the management and control of N. fowleri in DWDS.

Elimination of Naegleria fowleri from bulk water and biofilm in an operational drinking water distribution system.

Global incidence of primary amoebic meningoencephalitis cases associated with domestic drinking water is increasing. The need for understanding disinfectant regimes capable of eliminating the causative microorganism, Naegleria fowleri, from bulk water and pipe wall biofilms is critical. This field study demonstrated the successful elimination of N. fowleri from the bulk water and pipe wall biofilm of a persistently colonised operational drinking water distribution system (DWDS), and the prevention of further re-colonisation. A new chlorination unit was installed along the pipe line to boost the free chlorine residual to combat the persistence of N. fowleri. Biofilm and bulk water were monitored prior to and after re-chlorination (RCl), pre-rechlorination (pre-RCl) and post-rechlorination (post-RCl), respectively, for one year. A constant free chlorine concentration of > 1 mg/L resulted in the elimination of N. fowleri from both the bulk water and biofilm at the post-RCl site. Other amoeba species were detected during the first two months of chlorination, but all amoebae were eliminated from both the bulk water and biofilm at post-RCl after 60 days of chlorination with free chlorine concentrations > 1 mg/L. In addition, a dynamic change in the biofilm community composition and a four log reduction in biofilm cell density occurred post-RCl. The pre-RCl site continued to be seasonally colonised by N. fowleri, but the constant free chlorine residual of > 1 mg/L prevented N. fowleri from recolonising the bulk and pipe wall biofilm at the post-RCl site. To our knowledge, this is the first study to demonstrate successful removal of N. fowleri from both the bulk and pipe wall biofilm and prevention of re-colonisation of N. fowleri in an operational DWDS. The findings of this study are of importance to water utilities in addressing the presence of N. fowleri and other amoeba in susceptible DWDSs.

Rapid detection of Naegleria fowleri in water distribution pipeline biofilms and drinking water samples.

Rapid detection of pathogenic Naegleria fowler in water distribution networks is critical for water utilities. Current detection methods rely on sampling drinking water followed by culturing and molecular identification of purified strains. This culture-based method takes an extended amount of time (days), detects both nonpathogenic and pathogenic species, and does not account for N. fowleri cells associated with pipe wall biofilms. In this study, a total DNA extraction technique coupled with a real-time PCR method using primers specific for N. fowleri was developed and validated. The method readily detected N. fowleri without preculturing with the lowest detection limit for N. fowleri cells spiked in biofilm being one cell (66% detection rate) and five cells (100% detection rate). For drinking water, the detection limit was five cells (66% detection rate) and 10 cells (100% detection rate). By comparison, culture-based methods were less sensitive for detection of cells spiked into both biofilm (66% detection for <10 cells) and drinking water (0% detection for <10 cells). In mixed cultures of N. fowleri and nonpathogenic Naegleria, the method identified N. fowleri in 100% of all replicates, whereastests with the current consensus primers detected N. fowleri in only 5% of all replicates. Application of the new method to drinking water and pipe wall biofilm samples obtained from a distribution network enabled the detection of N. fowleri in under 6 h, versus 3+ daysforthe culture based method. Further, comparison of the real-time PCR data from the field samples and the standard curves enabled an approximation of N. fowleri cells in the biofilm and drinking water. The use of such a method will further aid water utilities in detecting and managing the persistence of N. fowleri in water distribution networks.

Isolation and characterization of an NAD+-degrading bacterium PTX1 and its role in chromium biogeochemical cycle.

Microorganisms can reduce toxic chromate to less toxic trivalent chromium [Cr(III)]. Besides Cr(OH)(3) precipitates, some soluble organo-Cr(III) complexes are readily formed upon microbial, enzymatic, and chemical reduction of chromate. However, the biotransformation of the organo-Cr(III) complexes has not been characterized. We have previously reported the formation of a nicotinamide adenine dinucleotide (NAD(+))-Cr(III) complex after enzymatic reduction of chromate. Although the NAD(+)-Cr(III) complex was stable under sterile conditions, microbial cells were identified as precipitates in a non-sterile NAD(+)-Cr(III) solution after extended incubation. The most dominant bacterium PTX1 was isolated and assigned to Leifsonia genus by phylogenetic analysis of 16S rRNA gene sequence. PTX1 grew slowly on NAD(+) with a doubling time of 17 h, and even more slowly on the NAD(+)-Cr(III) complex with an estimated doubling time of 35 days. The slow growth suggests that PTX1 passively grew on trace NAD(+) dissociated from the NAD(+)-Cr(III) complex, facilitating further dissociation of the complex and formation of Cr(III) precipitates. Thus, organo-Cr(III) complexes might be an intrinsic link of the chromium biogeochemical cycle; they can be produced during chromate reduction and then further mineralized by microorganisms.

Formation of soluble organo-chromium(III) complexes after chromate reduction in the presence of cellular organics.

Microbial reduction of hexavalent chromium [Cr(VI)] to trivalent chromium [Cr(III)] has been investigated as a method for bioremediation of Cr(VI) contaminated environments. The produced Cr(III) is thought to be insoluble Cr(OH)3; however, recent reports suggested a more complex fate of Cr(III). A bacterial enzyme system, using NADH as the reductant, converts Cr(VI)to a soluble NAD+-Cr(III) complex, and cytochrome c-mediated Cr(VI) reduction produces cytochrome c-Cr(III) adducts. In this study, Cr(VI) reduction in the presence of cellular organic metabolites formed both soluble and insoluble organo-Cr(III) end-products. Several soluble end-products were characterized by absorbance spectroscopy and electron paramagnetic resonance spectrometry as organo-Cr(III) complexes, similar to the known ascorbate-Cr(III) complex. The complexes remained soluble and stable upon dialysis against distilled H20 and over a broad pH range. The ready formation of stable organo-Cr(III) complexes suggests that organo-Cr(III) complexes are rather common, likely representing an integral part of the natural cycling of chromium. Thus, organo-Cr(III) complexes may account for the mobile form of Cr(II) detected in the environment.