Molecular biology and DNA microarray technology for microbial quality monitoring of water

Assessment of multiple fecal contamination sources in surface waters using environmental mitochondrial DNA metabarcoding

Waterborne diseases are transmitted to humans through the fecal contamination of water, where homeothermic species are the main reservoir. Fecal indicator bacteria (FIB) are often used to determine the occurrence of fecal contamination. However, FIB cannot provide the source of fecal contamination. Furthermore, as fecal inputs and contamination could originate from multiple sources (e.g., human, livestock, wildlife), multiple source tracking markers are required to identify fecal sources. From a previous study, we developed a mitochondrial DNA (mtDNA) metabarcoding approach to assess the presence of multiple homeotherms in four surface waters. Here, we have broadened our approach by sampling 86 surface water samples from the L'Assomption River and Ville-Marie watersheds (Province of Quebec, Canada). Fecal coliform levels were higher than the expected sanitary recommendations for recreational water (> 200 CFU/100 mL) in 73 % samples. The occurrence of mtDNA from human, livestock, domestic animals, wild mammals and wild birds was found in 40-88 % of the samples. Multivariate analyses showed significant covariations between homeothermic taxa and fecal coliforms, enterococci, β-D-glucuronidase, conductivity, the human-specific Bacteroidales Hf183 genetic marker, and the human population, in the watersheds of L'Assomption River (p = 0.001) and Ville-Marie (p = 0.015) (Province of Quebec, Canada). Through the application of Bayes Theorem, it was determined that fecal coliforms co-occurred with the detection of bovine, beaver, robin and chicken mtDNA in 100 % of cases in the L'Assomption River watershed, and human mtDNA co-occurred with fecal coliforms in 93 % and 76 % of cases in L'Assomption River watershed and Ville-Marie sub-catchment, respectively. This study suggests that fecal contamination could be the result of multiple species, among which some wild animals may contribute to fecal inputs in surface waters, resulting in potential risk to human health. This reinforces the necessity of using the mtDNA metabarcoding method to monitor multi-animal species.

Influence of temperature and water quality on the persistence of human mitochondrial DNA, human Hf183 Bacteroidales, fecal coliforms and enterococci in surface water in human fecal source tracking context

Mitochondrial DNA (mtDNA) is used as a genetic marker to track fecal contamination in surface water. Its potential to effectively discriminate between the nonpoint sources of fecal pollution (e.g. human, livestock) in water environments is relevant for water quality management. However, there is a lack of knowledge about the environmental persistence of mtDNA in relation to those of other microbial parameters, such as fecal indicator bacteria (FIB). In this study, mesocosms composed of water collected from four rivers and tap water were spiked with raw wastewater to mimic human fecal contamination. Mesocosms composed of raw wastewater were also studied. The mesocosms were incubated at 4 °C or at 22 °C for 189 days, from which the levels of human mtDNA (HumtDNA) and human Bacteroidales (Hf183) were measured by qPCR. The levels of FIB (fecal coliforms and enterococci) and heterotrophs were determined by culture methods along with the determination of physicochemical attributes. The decay rates of the genetic markers and FIB were determined with first-order decay rate models. The decay rates of HumtDNA (0.004-0.059 d^-1), Hf183 (0.007-0.082 d^-1), and the two FIBs (0.005-0.066 d^-1) were similar at 4 °C, while the genetic markers both had higher decay rates (0.013-0.919 d^-1) at 22 °C. Different HumtDNA decay rates were observed between the river mesocosms (0.043-0.919 d^-1) and the wastewater and tap water mesocosms (0.004-0.095 d^-1). Covariations of pH and conductivity among the HumtDNA, Hf183 and FIB decay rates were observed. HumtDNA and Hf183 had similar environmental persistence, whereas fecal coliforms and enterococci persisted longer at 22 °C. Finally, HumtDNA had the same trends of persistence in the four river mesocosms, suggesting a relative stability of this marker in different rivers. Our results suggest that HumtDNA could be more suitable for tracking the source of a recent fecal contamination in complement to FIB.

Arbuscular mycorrhizas increased tomato biomass and nutrition but did not affect local soil P availability or 16S bacterial community in the field

While interest in arbuscular mycorrhizal (AM) fungal effects on soil phosphorus (P) have recently increased, field experiments on this topic are lacking. While microcosm studies provided valuable insights, the lack of field studies represents a knowledge gap. Here, we present a field study in which we grew a mycorrhiza-defective tomato (Solanum lycopersicum L.) genotype (named rmc) and its mycorrhizal wild-type progenitor (named 76R) with and without additional fertiliser, using a drip-irrigation system to examine the impacts of the AM symbiosis on soil P availability and plant growth and nutrition. AM effects on fruit biomass and nutrients, soil nutrient availability, soil moisture and the soil bacterial community were examined. At the time of harvest, the AM tomato plants without fertiliser had the same early season fruit biomass and fruit nutrient concentrations as plants that received fertiliser. The presence of roots reduced the concentration of available soil P, ammonium and soil moisture in the top 10 cm soil layer. Arbuscular mycorrhizas did not significantly affect soil P availability, soil moisture, or 16S bacterial community composition. These findings suggest an indirect role for AM fungi in tomato production but not necessarily a direct role in determining soil physicochemical traits, during the one season that this experiment was conducted. While longer-term field studies may be required in the future, the present study provides new insights into impacts of AM fungi on P availability and uptake in a field soil system.

Trichloroethylene inhibits nitrogen transformation and microbial community structure in Mollisol

Trichloroethylene (TCE) is the most ubiquitous halogenated organic pollutant in the environment, it is one of the 129 priority control pollutants. In order to clarify the influence of TCE on microorganisms and nitrogen transformation in Mollisol is the core purpose of this study. Results showed that 10 mg kg^-1 TCE is the concentration limit of ammonification in Mollisol. When the concentration of TCE reached 10 mg kg^-1 and the effect lasted for over 7 days, the process of ammonia oxidation to nitric acid in Mollisol will be affected. TCE affected the process of nitrate (NO₃^-) transformation into nitrite (NO₂^-) by affecting the activity of nitrate reductase, thereby affected the denitrification process in soil. When the concentration of TCE is more than 10 mg kg^-1 it reduced the ability of soil microorganisms to obtain nitrogen, thereby affecting soil nitrogen transformation. RDA (Redundancy analysis) showed that the activity of nitrate reductase and the number of nitrifying bacteria and denitrifying bacteria in soil was negatively correlated with the incubation of TCE. In addition, soil nitrate reductase, nitrite reductase, peroxidase activity, ammonifying bacteria, nitrifying bacteria and denitrifying bacteria were negatively correlated with TCE concentration. Beyond that PICRUSt (Phylogenetic Investigation of Communities by Reconstruction of Unobserved States) of functional gene structure depend on KEGG (Kyoto Encyclopedia of Genes and Genomes) showed that 20 mg kg^-1 TCE significantly inhibited the metabolism of energy and other substances in Mollisol. Based on the above, it is found that TCE significantly affected nitrification and denitrification in Mollisol, thus the nitrogen transformation in Mollisol was affected by TCE contamination.

Bacterial community and environmental factors associated to rivers runoff and their possible impacts on coral reef conservation

Rivers potentially conduct important components as result of anthropogenic stressors for coral reefs. Molecular techniques are increasingly being used for monitoring biological and chemical monitoring of rivers and reefs. Here, we use PhyloChips™ to process surface water samples collected along two rivers and associated reefs in an environmental protection area in northeastern Brazil. Our results indicate that a significant part of Operational Taxonomic Units (OTUs) identified were able to survive the transition from freshwater to seawater, several of them belonging to genera implicated in human pathogenesis. The BBC:A ratio and functional prediction suggests that both study rivers are subject to fecal contamination and xenobiotics input and that the bacterial communities were more homogeneous in these environments. We suggest that protection actions adopted for reefs should be broadly extended to the surrounding environment, and that other bacterial group (besides cultivable coliforms) should be included in routine water quality monitoring.

Multi-Faceted Environmental Analysis to Improve the Quality of Anthropogenic Water Reservoirs (Paprocany Reservoir Case Study)

Maintaining good condition of dam reservoirs in urban areas seems increasingly important due to their valuable role in mitigating the effects of global warming. The aim of this study is to analyze possibilities to improve water quality and ecosystem condition of the Paprocany dam reservoir (highly urbanized area of southern Poland) using current data of the water parameters, historical sources, and DPSIR (Driver–Pressure–State–Impact–Response) and 3D modeling concerning human activity and the global warming effects. In its history Paprocany reservoir overcame numerous hydrotechnical changes influencing its present functioning. Also, its current state is significantly influenced by saline water from the coal mine (5 g L⁻¹ of chlorides and sulphates) and biogenic elements in recreational area (about 70 mg L⁻¹ of chlorate and to 1.9 mg L⁻¹ Kjeldahl nitrogen) and in sediments (222.66 Mg of Kjeldahl nitrogen, 45.65 Mg of P, and 1.03 Mg of assimilable phosphorus). Concluding, the best solutions to improve the Paprocany reservoir water quality comprise: increasing alimentation with water and shortening the water exchange time, restoration of the 19th century water treatment plant, and wetlands and reed bed area revitalization. The study also proved the applicability of mathematical models in planning of the actions and anticipating their efficiency.

Short-term impacts of anthropogenic stressors on Aedes albopictus mosquito vector microbiota

Recent studies have highlighted the potential role of microbiota in the biology of the Aedes albopictus mosquito vector. This species is highly anthropogenic and exhibits marked ecological plasticity, with a resulting high potential to colonize a wide range of habitats-including anthropized areas-under various climatic conditions. We put forward the hypothesis that climate and anthropogenic activities, such as the use of antibiotics in agriculture and human medicine, might affect the mosquito-associated bacterial community. We thus studied the additive impact of a temperature decrease and antibiotic ingestion on the temporal dynamics of Ae. albopictus survival and its associated bacterial communities. The results showed no effects of disturbances on mosquito survival. However, short-term temperature impacts on bacterial diversity were observed, while both the community structure and bacterial diversity were affected by early antibiotic ingestion. The genera Elizabethkingia, Chryseobacterium and Wolbachia, as well as an unclassified member of the Bacteroidales order were particularly affected. Antibiotics negatively impacted Elizabethkingia abundance, while Chryseobacterium was completely eliminated following both disturbances, to the benefit of Wolbachia and the unclassified Bacteroidales species. These results generated fresh insight into the effects of climate and anthropogenic activities such as the use of antibiotics on mosquito microbiota.

Experimental procedures for decontamination and microbiological testing in cardiovascular tissue banks

IMPACT STATEMENT

Sterility testing is a critical issue in the recovery, processing, and release of tissue allografts. Contaminated allografts are often discarded, increasing costs, and reducing tissue stocks. Given these concerns, it is important to determine the most effective methodology for sterility testing. This work provides an overview of microbiological methods for sampling and culturing donor grafts for cardiovascular tissue banking.

Impact of nutrient addition on diversity and fate of fecal bacteria

Understanding the variations in the microorganisms associated with human fecal pollution in different types of water is necessary to manage water quality and predict human health risks. Using an Illumina sequencing method, we investigated variations in the fecal bacteria originating from fresh human feces and their decay trends in nutrient-supplemented water and natural river water. Nutrient addition contributed to the growth of heterotrophic bacteria like Comamonadaceae, Cytophagaceae, and Sphingobacteriaceae, but led to lower concentrations for Bacteroidaceae, Lachnospiraceae, and Ruminococcaceae. This result suggests that the utilization of nutrients by high-activity bacteria may suppress other bacteria via depletion of the available nutrient resources. As we did not observe proliferation of Bacteroidales, Lactobacillales, Clostridiales, or Ruminococcaceae in either supplemented or river water, we consider these groups suitable for use as indicators to determine the level of fecal pollution. Moreover, we tested the persistence of Bacteroidales markers, including general-Bacteroidales marker GenBac and human-specific Bacteroidales marker qHS601, by quantitative PCR. We observed similar trends in the decay of the Bacteroidales markers GenBac and qHS601 in the nutrient-supplemented water and natural river water, and the high R² values of the GenBac (R²_{nutrient-supplemented} = 0.93, R²_{natural river} = 0.81) and qHS601 (R²_{nutrient-supplemented} = 0.93, R²_{natural river} = 0.91) suggests they are a good fit for the first-order decay model. We also found stronger correlations between the markers and potential pathogenic anaerobes in the different types of water, demonstrating the validity of the use of GenBac and qHS601 from Bacteroidales for the identification of human-associated pollution sources.

Water-Mediated Transmission of Plant, Animal, and Human Viruses

Viruses represent the most abundant and diverse of the biological entities in environmental waters, including the seas and probably also freshwater systems. They are important players in ecological networks in waters and influence global biochemical cycling and community composition dynamics. Among the many diverse viruses from terrestrial environments found in environmental waters, some are plant, animal, and/or human pathogens. The majority of pathogenic viral species found in waters are very stable and can survive outside host cells for long periods. The occurrence of such viruses in environmental waters has raised concerns because of the confirmation of the infectivity of waterborne viruses even at very low concentrations. This chapter focuses mainly on the survival of human, animal, and plant pathogenic viruses in aqueous environments, the possibility of their water-mediated transmission, the ecological implications of viruses in water, the methods adapted for detecting such viruses, and how to minimize the risk of viruses spreading through water.

Review: Microbial analysis in dielectrophoretic microfluidic systems

Infections caused by various known and emerging pathogenic microorganisms, including antibiotic-resistant strains, are a major threat to global health and well-being. This highlights the urgent need for detection systems for microbial identification, quantification and characterization towards assessing infections, prescribing therapies and understanding the dynamic cellular modifications. Current state-of-the-art microbial detection systems exhibit a trade-off between sensitivity and assay time, which could be alleviated by selective and label-free microbial capture onto the sensor surface from dilute samples. AC electrokinetic methods, such as dielectrophoresis, enable frequency-selective capture of viable microbial cells and spores due to polarization based on their distinguishing size, shape and sub-cellular compositional characteristics, for downstream coupling to various detection modalities. Following elucidation of the polarization mechanisms that distinguish bacterial cells from each other, as well as from mammalian cells, this review compares the microfluidic platforms for dielectrophoretic manipulation of microbials and their coupling to various detection modalities, including immuno-capture, impedance measurement, Raman spectroscopy and nucleic acid amplification methods, as well as for phenotypic assessment of microbial viability and antibiotic susceptibility. Based on the urgent need within point-of-care diagnostics towards reducing assay times and enhancing capture of the target organism, as well as the emerging interest in isolating intact microbials based on their phenotype and subcellular features, we envision widespread adoption of these label-free and selective electrokinetic techniques.

Correlations between pathogen concentration and fecal indicator marker genes in beach environments

The concentrations of several potential pathogens were measured using a microfluidic quantitative PCR (MFQPCR) platform in beach water, sand, and sediment samples collected in Duluth, MN. Among the 19 pathogen marker genes examined, eaeA from Escherichia coli and plc from Clostridium perfringens were most frequently detected in all samples. In beach water and wastewater samples, positive correlations were observed between quantities of potential pathogens and most of the fecal indicator genetic markers. Such correlations, however, were not frequently observed in sand and sediment samples. Our results suggest that the behavior of potential pathogens and FIB may vary by sample type and source of contamination. Consequently, appropriate FIB marker genes need to be chosen for reliable water/sand quality monitoring.

The potentiality of cross-linked fungal chitosan to control water contamination through bioactive filtration

Water contamination, with heavy metals and microbial pathogens, is among the most dangerous challenges that confront human health worldwide. Chitosan is a bioactive biopolymer that could be produced from fungal mycelia to be utilized in various applied fields. An attempt to apply fungal chitosan for heavy metals chelation and microbial pathogens inhibition, in contaminated water, was performed in current study. Chitosan was produced from the mycelia of Aspergillus niger, Cunninghamella elegans, Mucor rouxii and from shrimp shells, using unified production conditions. The FT-IR spectra of produced chitosans were closely comparable. M. rouxii chitosan had the highest deacetylation degree (91.3%) and the lowest molecular weight (33.2kDa). All chitosan types had potent antibacterial activities against Escherichia coli and Staphylococcus aureus; the most forceful type was C. elegans chitosan. Chitosan beads were cross-linked with glutaraldehyde (GLA) and ethylene-glycol-diglycidyl ether (EGDE); linked beads became insoluble in water, acidic and alkaline solutions and could effectively adsorb heavy metals ions, e.g. copper, lead and zinc, in aqueous solution. The bioactive filter, loaded with EGDE- A. niger chitosan beads, was able to reduce heavy metals' concentration with >68%, and microbial load with >81%, after 6h of continuous water flow in the experimentally designed filter.

Impact of seasonal variation on Escherichia coli concentrations in the riverbed sediments in the Apies River, South Africa

Many South Africans living in resource-poor settings with little or no access to pipe-borne water still rely on rivers as alternative water sources for drinking and other purposes. The poor microbial quality of such water bodies calls for appropriate monitoring. However, routine monitoring only takes into consideration the microbial quality of the water column, and does not include monitoring of the riverbed sediments for microbial pollution. This study sought to investigate the microbial quality of riverbed sediments in the Apies River, Gauteng Province, South Africa, using Escherichia coli as a faecal indicator organism and to investigate the impact of seasonal variation on its abundance. Weekly samples were collected at 10 sampling sites on the Apies River between May and August 2013 (dry season) and between January and February 2014 (wet season). E. coli was enumerated using the Colilert®-18 Quanti-Tray® 2000 system. All sites tested positive for E. coli. Wastewater treatment work effluents had the highest negative impact on the river water quality. Seasonal variations had an impact on the concentration of E. coli both in water and sediments with concentrations increasing during the wet season. A strong positive correlation was observed between temperature and the E. coli concentrations. We therefore conclude that the sediments of the Apies River are heavily polluted with faecal indicator bacteria and could also harbour other microorganisms including pathogens. The release of such pathogens into the water column as a result of the resuspension of sediments due to extreme events like floods or human activities could increase the health risk of the populations using the untreated river water for recreation and other household purposes. There is therefore an urgent need to reconsider and review the current South African guidelines for water quality monitoring to include sediments, so as to protect human health and other aquatic lives.

Bio-clarification of water from heavy metals and microbial effluence using fungal chitosan

Water pollution is among the most hazardous problems that threaten human health worldwide. Chitosan is a marvelous bioactive polymer that could be produced from fungal mycelia. This study was conducted to produce chitosan from Cunninghamella elegans and to use it for water pollutants elimination, e.g. heavy metals and waterborne microorganisms, and to investigate its antibacterial mode of action against Escherichia coli. The produced fungal chitosan had a deacetylation degree of 81%, a molecular weight of 92.73 kDa and a matched FT-IR spectrum with standard shrimp chitosan. Fungal chitosan exhibited remarkable antimicrobial activity against E. coli, Staphylococcus aureus and Candida albicans. Chitosan was proved as an effective metal adsorbent, toward the examined metal ions, Cu2+, Zn2+ and Pb2+, and its adsorption capacity greatly increased with the increasing of metal concentration, especially for Cu and Zn. The scanning electron micrographs, of treated E. coli cells with fungal chitosan, indicated that the cells began to lyse and combine after 3h of exposure and chitosan particles attached to the combined cells and, after 12 h from exposure, the entire bacterial cell walls were fully disrupted and lysed. Therefore, fungal chitosan could be recommended, as a bioactive, renewable, ecofriendly and cost effective material, for overcoming water pollution problems, from chemical and microbial origins.

On the track for an efficient detection of Escherichia coli in water: A review on PCR-based methods

Ensuring water safety is an ongoing challenge to public health providers. Assessing the presence of fecal contamination indicators in water is essential to protect public health from diseases caused by waterborne pathogens. For this purpose, the bacteria Escherichia coli has been used as the most reliable indicator of fecal contamination in water. The methods currently in use for monitoring the microbiological safety of water are based on culturing the microorganisms. However, these methods are not the desirable solution to prevent outbreaks as they provide the results with a considerable delay, lacking on specificity and sensitivity. Moreover, viable but non-culturable microorganisms, which may be present as a result of environmental stress or water treatment processes, are not detected by culture-based methods and, thus, may result in false-negative assessments of E. coli in water samples. These limitations may place public health at significant risk, leading to substantial monetary losses in health care and, additionally, in costs related with a reduced productivity in the area affected by the outbreak, and in costs supported by the water quality control departments involved. Molecular methods, particularly polymerase chain reaction-based methods, have been studied as an alternative technology to overcome the current limitations, as they offer the possibility to reduce the assay time, to improve the detection sensitivity and specificity, and to identify multiple targets and pathogens, including new or emerging strains. The variety of techniques and applications available for PCR-based methods has increased considerably and the costs involved have been substantially reduced, which together have contributed to the potential standardization of these techniques. However, they still require further refinement in order to be standardized and applied to the variety of environmental waters and their specific characteristics. The PCR-based methods under development for monitoring the presence of E. coli in water are here discussed. Special emphasis is given to methodologies that avoid pre-enrichment during the water sample preparation process so that the assay time is reduced and the required legislated sensitivity is achieved. The advantages and limitations of these methods are also reviewed, contributing to a more comprehensive overview toward a more conscious research in identifying E. coli in water.

An environmental survey of surface waters using mitochondrial DNA from human, bovine and porcine origin as fecal source tracking markers

Fecal contamination of surface waters is one the major sources of waterborne pathogens and consequently, is an important concern for public health. For reliable fecal source tracking (FST) monitoring, there is a need for a multi-marker toolbox as no single all-encompassing method currently exists. Mitochondrial DNA (mtDNA) as a source tracking marker has emerged as a promising animal-specific marker. However, very few comprehensive field studies were done on the occurrence of this marker in surface waters. In this report, water samples were obtained from 82 sites in different watersheds over a six year period. The samples were analyzed for the presence of human, bovine and porcine mtDNA by endpoint nested PCR, along with the human-specific Bacteroidales HF183 marker. These sites represented a mix of areas with different anthropogenic activities, natural, urban and agricultural. The occurrences of mitoHu (human), mitoBo (bovine), mitoPo (porcine) and HF183 specific PCR amplifications from the samples were 46%, 23%, 6% and 50%, respectively. The occurrence of mitoHu and HF183 was high in all environment types with higher occurrence in the natural and urban areas, whereas the occurrence of mitoBo was higher in agricultural areas. FST marker concentrations were measured by real-time PCR for samples positive for these markers. The concentration of the mitoHu markers was one order of magnitude lower than HF183. There was co-linearity between the concentrations of the mitoHu and HF183 markers. Co-linearity was also observed between HF183 concentration and fecal coliform levels. Such a relationship was not observed between the mitoHu concentration and fecal coliform levels. In summary, our results showed a high incidence of human fecal pollution throughout the environment while demonstrating the potential of mtDNA as suitable FST markers.

A disposable bacterial lysis cartridge (BLC) suitable for an in situ water-borne pathogen detection system

A disposable bacterial lysis cartridge (BLC) and a sample handling system for the lysis ofBacillus subtiliswere constructed.

Molecular analysis for screening human bacterial pathogens in municipal wastewater treatment and reuse

Effective and sensitive monitoring of human pathogenic bacteria in municipal wastewater treatment is important not only for managing public health risk related to treated wastewater reuse, but also for ensuring proper functioning of the treatment plant. In this study, three different 16S rRNA gene molecular analysis methodologies were employed to screen bacterial pathogens in samples collected at three different stages of an activated sludge plant. Overall bacterial diversity was analyzed using next generation sequencing (NGS) on the Illumina MiSeq platform, as well as PCR-DGGE followed by band sequencing. In addition, a microdiversity analysis was conducted using PCR-DGGE, targeting Escherichia coli. Bioinformatics analysis was performed using QIIME protocol by clustering sequences against the Human Pathogenic Bacteria Database. NGS data were also clustered against the Greengenes database for a genera-level diversity analysis. NGS proved to be the most effective approach screening the sequences of 21 potential human bacterial pathogens, while the E. coli microdiversity analysis yielded one (O157:H7 str. EDL933) out of the two E. coli strains picked up by NGS. Overall diversity using PCR-DGGE did not yield any pathogenic sequence matches even though a number of sequences matched the NGS results. Overall, sequences of Gram-negative pathogens decreased in relative abundance along the treatment train while those of Gram-positive pathogens increased.

Chemical and microbial contamination baseline in the Saguenay-St. Lawrence Marine Park (Eastern Canada): concentrations and fluxes from land-based sources

Stretching halfway between the Canadian Great Lakes and the Atlantic Ocean, the Saguenay-St. Lawrence Marine Park is subject to environmental issues being exposed to untreated or uncontrolled point and non-point sources of anthropogenic contamination. This article provides a first estimation of chemical and microbial contamination entering the marine park from the discharges of local municipal effluents and the inputs of tributaries in the summer period. Suspended particulate matter (SPM), nutrients, particulate carbon (PC) and nitrogen, trace metals, and fecal coliform bacteria were determined in surface brackish waters at upstream boundaries, in freshwater of 11 tributaries, and in nine sewage effluents from small communities settled along the marine park. Most tributaries have SPM < 10 mg L(-1) and contributed to a total of ~47 tons day(-1), thus representing a small proportion of daily SPM transported by Saguenay River (200 tons day(-1)) and St. Lawrence River (6.3 × 10(3) tons day(-1)). As expected, untreated sewage effluents showed high fecal contamination (0.2-6.0 × 10(6) CFU 100 mL(-1)), high NO x levels (4-33 μmol L(-1)) and high concentrations of particulate organic carbon (7-62 mg L(-1)). However, all tributaries had low coliforms (<230 CFU 100 mL(-1)), low PC (0.3-1.1 mg L(-1)), and low nutrients (NO(x) < 3.3 μmol L(-1)), with the exception of the Moulin-à-Baude River, a small tributary (2.3 × 10(5) m(3) day(-1)) clearly contaminated by human activities. Detailed analysis of 14 metals and metalloids in SPM did not show any clear contamination trend between sewage effluents and tributaries, except for Grandes-Bergeronnes River, where most trace metals appeared to be greater than for other rivers. Regarding global inputs, results showed that despite their relatively high pollutants load, inputs from local sewages and small tributaries remained minor contributors compared with upstream inputs, i.e., Saguenay River and St. Lawrence River. However, we illustrate that some local hydrodynamic factors in bays and inlets must be taken into account when evaluating risks associated with sewage discharges.

Evaluation of commercial kits for the extraction and purification of viral nucleic acids from environmental and fecal samples

The extraction and purification of nucleic acids is a critical step in the molecular detection of enteric viruses from environmental or fecal samples. In the present study, the performance of three commercially available kits was assessed: the MO BIO PowerViral Environmental DNA/RNA Isolation kit, the Qiagen QIAamp Viral RNA Mini kit, and the Zymo ZR Virus DNA/RNA Extraction kit. Viral particles of adenovirus 2 (AdV), murine norovirus (MNV), and poliovirus type 1 (PV1) were spiked in molecular grade water and three different types of sample matrices (i.e., biosolids, feces, and surface water concentrates), extracted with the kits, and the yields of the nucleic acids were determined by quantitative PCR (qPCR). The MO BIO kit performed the best with the biosolids, which were considered to contain the highest level of inhibitors and provided the most consistent detection of spiked virus from all of the samples. A qPCR inhibition test using an internal control plasmid DNA and a nucleic acid purity test using an absorbance at 230 nm for the nucleic acid extracts demonstrated that the MO BIO kit was able to remove qPCR inhibitors more effectively than the Qiagen and Zymo kits. These results suggest that the MO BIO kit is appropriate for the extraction and purification of viral nucleic acids from environmental and clinical samples that contain high levels of inhibitors.

Fecal source tracking in water using a mitochondrial DNA microarray

A mitochondrial-based microarray (mitoArray) was developed for rapid identification of the presence of 28 animals and one family (cervidae) potentially implicated in fecal pollution in mixed activity watersheds. Oligonucleotide probes for genus or subfamily-level identification were targeted within the 12S rRNA - Val tRNA - 16S rRNA region in the mitochondrial genome. This region, called MI-50, was selected based on three criteria: 1) the ability to be amplified by universal primers 2) these universal primer sequences are present in most commercial and domestic animals of interest in source tracking, and 3) that sufficient sequence variation exists within this region to meet the minimal requirements for microarray probe discrimination. To quantify the overall level of mitochondrial DNA (mtDNA) in samples, a quantitative-PCR (Q-PCR) universal primer pair was also developed. Probe validation was performed using DNA extracted from animal tissues and, for many cases, animal-specific fecal samples. To reduce the amplification of potentially interfering fish mtDNA sequences during the MI-50 enrichment step, a clamping PCR method was designed using a fish-specific peptide nucleic acid. DNA extracted from 19 water samples were subjected to both array and independent PCR analyses. Our results confirm that the mitochondrial microarray approach method could accurately detect the dominant animals present in water samples emphasizing the potential for this methodology in the parallel scanning of a large variety of animals normally monitored in fecal source tracking.

Quantification of diarrhea risk related to wastewater contact in Thailand

Wastewater reuse contributes to closing the nutrient recycling loop as a sustainable way of managing water resources. Bangkok has over a thousand man-made drainage and irrigation canals for such purposes. Its use for agricultural and recreational purposes has a long tradition in rural and peri-urban areas. However, the continuation of these practices is increasingly questioned since potential health risks are an issue if such practices are not appropriately managed. The microbial and chemical quality of canal water has considerably deteriorated over the last decade, mainly because of discharged, untreated domestic and industrial wastewater. It is important to understand the health risks of wastewater reuse and identify risky behaviors from the most highly exposed actors promote the safe use of wastewater. This study assessed diarrhea infection risks caused by the use of and contact with wastewater in Klong Luang municipality, a peri-urban setting in Northern Bangkok, using quantitative microbial risk assessment. Wastewater samples were collected from canals, sewers at household level, and vegetables grown in the canals for consumption. Samples were also collected from irrigation water from the agricultural fields. Two protozoa, Giardia lamblia and Entamoeba histolytica, were quantified and analyzed by real-time PCR, exposure assessment was conducted, and finally, the risk of infection due to contact with wastewater in different scenarios was calculated. The results showed that canal water and vegetables were heavily contaminated with G. lamblia and E. histolytica. Infection risk was high in tested scenarios and largely exceeded the acceptable risk given by WHO guidelines.

Simultaneous detection of multiple fish pathogens using a naked-eye readable DNA microarray

We coupled 16S rDNA PCR and DNA hybridization technology to construct a microarray for simultaneous detection and discrimination of eight fish pathogens (Aeromonas hydrophila, Edwardsiella tarda, Flavobacterium columnare, Lactococcus garvieae, Photobacterium damselae, Pseudomonas anguilliseptica, Streptococcus iniae and Vibrio anguillarum) commonly encountered in aquaculture. The array comprised short oligonucleotide probes (30 mer) complementary to the polymorphic regions of 16S rRNA genes for the target pathogens. Targets annealed to the microarray probes were reacted with streptavidin-conjugated alkaline phosphatase and nitro blue tetrazolium/5-bromo-4-chloro-3′-indolylphosphate, p-toluidine salt (NBT/BCIP), resulting in blue spots that are easily visualized by the naked eye. Testing was performed against a total of 168 bacterial strains, i.e., 26 representative collection strains, 81 isolates of target fish pathogens, and 61 ecologically or phylogenetically related strains. The results showed that each probe consistently identified its corresponding target strain with 100% specificity. The detection limit of the microarray was estimated to be in the range of 1 pg for genomic DNA and 10³ CFU/mL for pure pathogen cultures. These high specificity and sensitivity results demonstrate the feasibility of using DNA microarrays in the diagnostic detection of fish pathogens.

Integration of gene chip and topological network techniques to screen a candidate biomarker gene (CBG) for predication of the source water carcinogenesis risks on mouse Mus musculus

Screening of a candidate biomarker gene (CBG) to predicate the carcinogenesis risks in the Yangtze River source of drinking water in Nanjing area (YZR-SDW-NJ) on mouse (Mus musculus) was conducted in this research. The effects of YZR-SDW-NJ on the genomic transcriptional expression levels were measured by the GeneChip(®) Mouse Genome and data treated by the GO database analysis. The 298 genes discovered as the differently expressed genes (DEGs) were down-regulated and their values were ≤-1.5-fold. Of the 298 DEGs, 25 were cancer-related genes selected as the seed genes to build a topological network map with Genes2Networks software, only 7 of them occurred at the constructed map. Smad2 gene was at the constructed map center and could be identified as a candidate biomarker gene (CBG) primarily which involves the genesis and development of colorectal, leukemia, lung and prostate cancers directly. Analysis of the gene signal pathway further approved that smad2 gene had the relationships closely to other 16 cancer-related genes and could be used as a CBG to indicate the carcinogenic risks in YZR-SDW-NJ. The data suggest that integration of gene chip and network techniques may be a way effectively to screen a CBG. And the parameter values for further judgment of the CBG through signal pathway relationship analysis also will be discussed.

Comparative phylogenetic microarray analysis of microbial communities in TCE-contaminated soils

The arrival of chemicals in a soil or groundwater ecosystem could upset the natural balance of the microbial community. Since soil microorganisms are the first to be exposed to the chemicals released into the soil environment, we evaluated the use of a phylogenetic microarray as a bio-indicator of community perturbations due to the exposure to trichloroethylene (TCE). The phylogenetic microarray, which measures the presence of different members of the soil community, was used to evaluate unpolluted soils exposed to TCE as well as to samples from historically TCE polluted sites. We were able to determine an apparent threshold at which the microbial community structure was significantly affected (about 1ppm). In addition, the members of the microbial community most affected were identified. This approach could be useful for assessing environmental impact of chemicals on the biosphere as well as important members of the microbial community involved in TCE degradation.

Microbial diagnostic microarray for food- and water-borne pathogens

A microbial diagnostic microarray for the detection of the most relevant bacterial food- and water-borne pathogens and indicator organisms was developed and thoroughly validated. The microarray platform based on sequence-specific end labelling of oligonucleotides and the pyhylogenetically robust gyrB marker gene allowed a highly specific (resolution on genus/species level) and sensitive (0.1% relative and 10(4) cfu absolute detection sensitivity) detection of the target pathogens. Validation was performed using a set of reference strains and a set of spiked environmental samples. Reliability of the obtained data was additionally verified by independent analysis of the samples via fluorescence in situ hybridization (FISH) and conventional microbiological reference methods. The applicability of this diagnostic system for food analysis was demonstrated through extensive validation using artificially and naturally contaminated spiked food samples. The microarray-based pathogen detection was compared with the corresponding microbiological reference methods (performed according to the ISO norm). Microarray results revealed high consistency with the reference microbiological data.

Comparing microarrays and next-generation sequencing technologies for microbial ecology research

Recent advances in molecular biology have resulted in the application of DNA microarrays and next-generation sequencing (NGS) technologies to the field of microbial ecology. This review aims to examine the strengths and weaknesses of each of the methodologies, including depth and ease of analysis, throughput and cost-effectiveness. It also intends to highlight the optimal application of each of the individual technologies toward the study of a particular environment and identify potential synergies between the two main technologies, whereby both sample number and coverage can be maximized. We suggest that the efficient use of microarray and NGS technologies will allow researchers to advance the field of microbial ecology, and importantly, improve our understanding of the role of microorganisms in their various environments.

The British river of the future: how climate change and human activity might affect two contrasting river ecosystems in England

The possible effects of changing climate on a southern and a north-eastern English river (the Thames and the Yorkshire Ouse, respectively) were examined in relation to water and ecological quality throughout the food web. The CLASSIC hydrological model, driven by output from the Hadley Centre climate model (HadCM3), based on IPCC low and high CO(2) emission scenarios for 2080 were used as the basis for the analysis. Compared to current conditions, the CLASSIC model predicted lower flows for both rivers, in all seasons except winter. Such an outcome would lead to longer residence times (by up to a month in the Thames), with nutrient, organic and biological contaminant concentrations elevated by 70-100% pro-rata, assuming sewage treatment effectiveness remains unchanged. Greater opportunities for phytoplankton growth will arise, and this may be significant in the Thames. Warmer winters and milder springs will favour riverine birds and increase the recruitment of many coarse fish species. However, warm, slow-flowing, shallower water would increase the incidence of fish diseases. These changing conditions would make southern UK rivers in general a less favourable habitat for some species of fish, such as the Atlantic salmon (Salmo salar). Accidental or deliberate, introductions of alien macrophytes and fish may change the range of species in the rivers. In some areas, it is possible that a concurrence of different pressures may give rise to the temporary loss of ecosystem services, such as providing acceptable quality water for humans and industry. An increasing demand for water in southern England due to an expanding population, a possibly reduced flow due to climate change, together with the Water Framework Directive obligation to maintain water quality, will put extreme pressure on river ecosystems, such as the Thames.

Automated analytical microarrays: a critical review

Microarrays provide a powerful analytical tool for the simultaneous detection of multiple analytes in a single experiment. The specific affinity reaction of nucleic acids (hybridization) and antibodies towards antigens is the most common bioanalytical method for generating multiplexed quantitative results. Nucleic acid-based analysis is restricted to the detection of cells and viruses. Antibodies are more universal biomolecular receptors that selectively bind small molecules such as pesticides, small toxins, and pharmaceuticals and to biopolymers (e.g. toxins, allergens) and complex biological structures like bacterial cells and viruses. By producing an appropriate antibody, the corresponding antigenic analyte can be detected on a multiplexed immunoanalytical microarray. Food and water analysis along with clinical diagnostics constitute potential application fields for multiplexed analysis. Diverse fluorescence, chemiluminescence, electrochemical, and label-free microarray readout systems have been developed in the last decade. Some of them are constructed as flow-through microarrays by combination with a fluidic system. Microarrays have the potential to become widely accepted as a system for analytical applications, provided that robust and validated results on fully automated platforms are successfully generated. This review gives an overview of the current research on microarrays with the focus on automated systems and quantitative multiplexed applications.

The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray

The effects of glass surfaces and probe GC content on signal intensities of a 60-mer diagnostic microarray were studied. Twelve virus-specific oligonucleotide probes for severe acute respiratory syndrome coronavirus (SARS-CoV) were divided into a high GC content group (≥ 50%) and a low GC content group (< 50%), and spotted onto four different chemically-modified glass surfaces: a poly-amine coating activated by 1,4-phenylene diisothiocyanate (Poly-Amine surface), an acrylic acid-co-acrylamide copolymer coating activated by 1-(3-dimethylamino propyl)-3-ethylcarbodiimide hydrochloride and N-hydroxysuccinimide (AACA-Copolymer surface), a commercial Corning CMT-GAPS amino surface, and a Telechem SuperAmine amino surface. RNA samples from cultured SARS-CoV strain were labelled using direct cDNA labelling with restriction display in a single colour format. The background-subtracted signal intensities were analysed using two-way analysis of variance. The effects of glass surfaces on background-subtracted signal intensities were significant (p=0.003). Multiple comparisons showed that differences existed mainly between the AACA-Copolymer surface and the other glass surfaces, and that the AACA-Copolymer surface had the highest background-subtracted signal intensity. The probe GC content had no significant effect on signal intensities in the narrow range of GC content represented (p=0.07). The results suggested that the AACA-Copolymer surface may be a novel choice of microorganism survey based on long oligonucleotide microarray.

Fecal source tracking, the indicator paradigm, and managing water quality

Fecal source tracking is used because standard methods of measuring fecal contamination in water by enumerating fecal indicator bacteria (FIB) do not identify the sources of the contamination. This paper presents a critical review of source tracking with emphasis on the extent to which methods have been tested (especially in comparison with other methods and/or with blind samples), when methods are applicable, their shortcomings, and their usefulness in predicting public health risk or pathogen occurrence. In addition, the paper discusses the broader question of whether fecal source tracking and fecal indicator monitoring is the best approach to regulate water quality and protect human health. Many fecal source-tracking methods have only been tested against sewage or fecal samples or isolates in laboratory studies (proof of concept testing) and/or applied in field studies where the "real" answer is not known, so their comparative performance and accuracy cannot be assessed. For source tracking to be quantitative, stability of ratios between host-specific markers in the environment must be established. In addition, research is needed on the correlation between host-specific markers and pathogens, and survival of markers after waste treatments. As a result of the exclusive emphasis on FIB in legislation, monitoring has concentrated on FIB and lost sight of pathogens. A more rational approach to regulating water quality would start with available epidemiological data to identify pathogens of concern in a particular water body, and then use targeted pathogen monitoring coupled with targeted fecal source tracking to control them. Baseline monitoring of indicators would become just one tool among many.

Depuration dynamics of oysters (Crassostrea gigas) artificially contaminated by Salmonella enterica serovar Typhimurium

The State of Santa Catarina produces the greatest quantity of edible mollusks in Brazil. To guarantee sanitary qualify, mollusk cultures should be monitored for contamination by pathogenic microorganisms. A self-purification or "depuration" system that eliminates Salmonella enterica serovar Typhimurium contamination from oysters has been developed and evaluated. The depuration process occurred within a closed system, in which 1000 L of water was recirculated for 24 h. The water was sterilized with ultraviolet (UV) light, chlorine, or both together. Oysters (Crassostrea gigas) artificially contaminated with S. typhimurium were harvested every 6 h. Samples of oyster tissue were excised and both the presence and numbers of bacteria were determined. Combined UV light and chlorine treatments resulted in total elimination of bacteria within 12 h. Polymerase chain reaction detected bacteria in water exposed to the three treatments. This pioneering study is the first of its kind in Brazil and represents a major contribution to commercial mollusk culture in this country.

Current and future uses of real-time polymerase chain reaction and microarrays in the study of intestinal microbiota, and probiotic use and effectiveness

Probiotics are defined as live microorganisms that confer a health benefit to the host when administered in adequate amounts. In addition to human health benefits, probiotics can improve various aspects of growth and performance in livestock and poultry, as well as control undesirable microorganisms in food animals. Studies indicate that probiotics can prevent or treat certain conditions, including atopic disease in infants, food allergy, infection after surgery, acute diarrhea, and symptoms associated with irritable bowel syndrome. Understanding the complete mechanism, effectiveness, and potential use of probiotics is limited by the availability and sensitivity of current methods (i.e., culturing techniques). In recent years, real-time polymerase chain reaction (PCR) and microarrays have become prominent and promising methods to examine quantitative changes of specific members of the microbial community and the influence of probiotics on the structure and function of human and animal intestinal ecosystems. Culture-independent studies have established that only a fraction of organisms present in feces are cultivable, therefore, results obtained by cultivation are limited. Conversely, in-depth knowledge of microbial genomes has enabled real-time PCR and microarrays to be more sensitive and has resulted in precise methods for comprehensive analysis of the complex gut microbiota. Additionally, these technologies can assess the influence of intestinal microorganisms on host metabolism, nutrient status, and disease. This paper reviews method technologies and applications of real-time PCR and microarray assays as they relate to the effect and use of probiotics on the intestinal microbiota and gastrointestinal disease.

Multiplex approach for screening genetic markers of microbial indicators

Genetic markers are expected to provide better specificity in epidemiological studies and potentially serve as better indicators of waterborne pathogens. Methods used to assess genetic markers of emerging microbial indicators include pulsed field gel electrophoresis, polymerase chain reaction (PCR), and microarrays. This paper outlines a high-throughput approach to screen for such genetic markers using a set of theoretical and experimental screening tools. The theoretical screening involves evaluating genes related to the ribosomal RNA and specific functions from emerging indicator groups, followed by experimental validation with appropriate sampling schemes and high-throughput and economical screening methods, such as microarrays, real time PCR, and on-chip PCR. Analysis of a wide range of samples covering temporal variability in location, host, and waterborne disease outbreaks is essential. The proposed approach is expected to shorten the time and cost associated with searching for new genetic markers of emerging indicators by at least 10-fold.

Waterborne norovirus outbreaks

Noroviruses (NoVs) are the most common nonbacterial causative agents of waterborne outbreaks. Due to the mild and short-lived disease of gastroenteritis, even large epidemics may go unnoticed, since patients do not necessarily visit a doctor. NoVs have several means by which to survive both in the environment and in a population. The nonenveloped small virus retains its infectivity in the environment, and particularly in cold water, for a long time. Unlike most enteric viruses, it causes disease both in children and adults. A large number of genotypes combined with a small infective dose and short-term immunity guarantee efficient circulation of these viruses. The world of NoVs has been revealed to us predominantly by molecular methods. Having learned to detect these viruses first in patients, the emphasis is now in searching for methods sensitive enough to find them in environmental samples. In this review, the latest methods and their use in monitoring of these viruses are discussed.

DetectiV: visualization, normalization and significance testing for pathogen-detection microarray data

DNA microarrays offer the possibility of testing for the presence of thousands of micro-organisms in a single experiment. However, there is a lack of reliable bioinformatics tools for the analysis of such data. We have developed DetectiV, a package for the statistical software R. DetectiV offers powerful yet simple visualization, normalization and significance testing tools. We show that DetectiV performs better than previously published software on a large, publicly available dataset.

Improvement of Potato virus Y (PVY) detection and quantitation using PVY(N)- and PVY(O)-specific real-time RT-PCR assays

A Potato virus Y (PVY) single nucleotide polymorphism (A/G(2213)), recently identified as a molecular determinant of the tobacco leaf necrosis symptom induced by PVY(N) isolates, has been used as a target to develop two PVY group-specific (PVY(N) and PVY(O)) fluorescent (TaqMan-based) real-time RT-PCR assays. These procedures allow detection, characterisation, and quantitation of a wide range of PVY isolates in samples containing 10(3)-10(8) viral transcripts. Moreover, the high specificity of these two new assays make the simultaneous detection and the reliable quantitation of PVY(N) and PVY(O) isolates in mixed solutions, regardless of the Y(N)/Y(O) ratio, feasible. The high sensitivity (threshold of 10(3) copies per reaction) and the PVY group specificity of these two new PVY detection tools clearly improve previously published PVY detection tests and offer new opportunities for PVY research programs.

Selective removal of DNA from dead cells of mixed bacterial communities by use of ethidium monoazide

The distinction between viable and dead bacterial cells poses a major challenge in microbial diagnostics. Due to the persistence of DNA in the environment after cells have lost viability, DNA-based quantification methods overestimate the number of viable cells in mixed populations or even lead to false-positive results in the absence of viable cells. On the other hand, RNA-based diagnostic methods, which circumvent this problem, are technically demanding and suffer from some drawbacks. A promising and easy-to-use alternative utilizing the DNA-intercalating dye ethidium monoazide bromide (EMA) was published recently. This chemical is known to penetrate only into "dead" cells with compromised cell membrane integrity. Subsequent photoinduced cross-linking was reported to inhibit PCR amplification of DNA from dead cells. We provide evidence here that in addition to inhibition of amplification, most of the DNA from dead cells is actually lost during the DNA extraction procedure, probably together with cell debris which goes into the pellet fraction. Exposure of bacteria to increasing stress and higher proportions of dead cells in defined populations led to increasing loss of genomic DNA. Experiments were performed using Escherichia coli O157:H7 and Salmonella enterica serovar Typhimurium as model pathogens and using real-time PCR for their quantification. Results showed that EMA treatment of mixed populations of these two species provides a valuable tool for selective removal of DNA of nonviable cells by using conventional extraction protocols. Furthermore, we provide evidence that prior to denaturing gradient gel electrophoresis, EMA treatment of a mature mixed-population drinking-water biofilm containing a substantial proportion of dead cells can result in community fingerprints dramatically different from those for an untreated biofilm. The interpretation of such fingerprints can have important implications in the field of microbial ecology.