Modeling microbial fate in the subsurface environment

Whole Genome Sequencing and Metabolomic Study of Cave Streptomyces Isolates ICC1 and ICC4

The terrestrial subsurface microbiome has gained considerable amount of interests in the recent years because of its rich potential resource for biomining novel genes coding for metabolites possessing antimicrobial activities. In our previous study, we identified two Streptomyces isolates, designated as ICC1 and ICC4, from the Iron Curtain Cave, Chilliwack, Canada that exhibited antagonistic activities against the multidrug resistant strains of Escherichia coli. In this study, the genomes of these two isolates were sequenced by Illumina MiSeq, assembled and annotated. The genes associated with secondary metabolite production were identified and annotated using the bioinformatics platforms antiSMASH and BAGEL. ICC1 and ICC4 were then cultivated and ICC1 metabolome characterized by UHPLC-ESI-HRMS. The Global Natural Products Social Molecular Networking was used to identify metabolites based on the MS/MS spectral data. ICC1 and ICC4 showed a high level of sequence identity with the terrestrial bacteria Streptomyces lavendulae; however, they possess a greater secondary metabolite potential as estimated by the total number of identified biosynthetic gene clusters (BGCs). In particular, ICC1 and ICC4 had a greater number of polyketide and non-ribosomal peptide BGCs. The most frequently detected BGCs were those predicted to generate terpenes, small and low complexity dipeptides and lipids. Spectral analysis clearly identified a number of diketopiperazine products through matched reference spectra for cyclo (Leu-Pro), cyclo (Pro-Val) and cyclo [(4-hydroxyPro)-Leu]. One of the terpenes gene clusters predicted by antiSMASH possesses a seven-gene pathway consistent with diazepinomicin biosynthesis. This molecule contains a very rare core structure and its BGC, to date, has only been identified from a single bacterial genome. The tetrapeptide siderophore coelichelin BGC was unambiguously identified in the genome, however, the metabolite could not be identified from the culture extracts. Two type III polyketides, 2′, 5′ – dimethoxyflavone and nordentatin, were identified from the UHPLC-HRMS data of the aqueous and n-butanolic fractions of Streptomyces sp. ICC1, respectively. A BGC likely encoding these metabolites was predicted in both genomes. The predicted similarities in molecule production and genome shared by these two strains could be an indicative of a cooperative mode of living in extreme habitats instead of a competitive one. This secondary metabolite potential may contribute to the fitness of ICC1 and ICC4 in the Iron Curtain Cave.

Survival of E. coli O157:H7, Salmonella Typhimurium, HAdV2 and MNV-1 in river water under dark conditions and varying storage temperatures

The ability of Escherichia coli O157:H7, Salmonella enterica serovar Typhimurium, Human adenovirus serotype 2 (HAdV2) and Murine Norovirus 1 (MNV-1) to survive in river water at -20, 4, room temperature (~24 °C) and 37 °C, were evaluated under dark conditions. The tested surface water was obtained from the main Nile River in the Dokki area, Giza and sterilized by autoclaving. The pathogens were inoculated separately in the autoclaved river water. Each microcosm was sampled and the test microorganisms counted after zero (immediately following inoculation), 1, 7, 15, 30, 60, 90 and 120 days. Physicochemical parameters including pH, turbidity, electrical conductivity, dissolved oxygen, total dissolved solids, total alkalinity, biological oxygen demand, chemical oxygen demand, nitrates and nitrites, and sulphate, were also measured. For HAdV2, the highest decay rates were observed at 37 °C and room temperature compared to 4 and -20 °C. A similar trend was found for the MNV-1, although unlike the HAdV2, the decay rate was higher at -20 than at 4 °C. Also, 4 °C was the best temperature for the survival of MNV-1 (T₉₀ = 76.9 days), E. coli O157:H7 (T₉₀ = 103 days) and Salmonella Typhimurium (T₉₀ = 105 days). The least survival of the pathogens, except MNV-1, was recorded at 37 °C. These results indicate that under dark conditions and low temperatures, enteric pathogens could be stable for extended periods. No significant statistical correlation was observed between the experimental temperatures and the infectivity of the viral particles. This study provided useful information about the stability of these pathogens in the Nile River water and could serve as an early warning when considering the water of the river for agricultural irrigation or household use in areas with limited or no access to potable water.

Chemotaxis Increases the Retention of Bacteria in Porous Media with Residual NAPL Entrapment

Chemotaxis has the potential to decrease the persistence of nonaqueous phase liquid (NAPL) contaminants in aquifers by allowing pollutant-degrading bacteria to move toward sources of contamination and thus influence dissolution. This experimental study investigated the migratory response of chemotactic bacteria to a distribution of residual NAPL ganglia entrapped within a laboratory-scale sand column under continuous-flow at a superficial velocity of 0.05 cm/min. Naphthalene dissolved in a model NAPL 2,2,4,4,6,8,8-heptamethylnonane partitioned into the aqueous phase to create localized chemoattractant gradients throughout the column. A pulse mixture of equal concentrations of Pseudomonas putida G7, a strain chemotactic to naphthalene, and Pseudomonas putida G7 Y1, a nonchemotactic mutant, was introduced to the column and effluent bacterial concentrations were measured with time. Breakthrough curves (BTCs) for the two strains were noticeably different upon visual inspection. Differences in BTCs (compared to nonchemotactic controls) were quantified in terms of percent recovery and were statistically significant ( p < 0.01). Chemotaxis reduced percent recovery in the effluent by 45% thereby increasing the population of bacteria that were retained within the column in the vicinity of residual NAPL contaminants. An increase in flow rate to a superficial velocity of 0.25 cm/min did not diminish cell retention associated with the chemotactic effect.

Cotransport of clay colloids and viruses through water-saturated vertically oriented columns packed with glass beads: Gravity effects

The cotransport of clay colloids and viruses in vertically oriented laboratory columns packed with glass beads was investigated. Bacteriophages MS2 and ΦX174 were used as model viruses, and kaolinite (ΚGa-1b) and montmorillonite (STx-1b) as model clay colloids. A steady flow rate of Q=1.5 mL/min was applied in both vertical up (VU) and vertical down (VD) flow directions. In the presence of KGa-1b, estimated mass recovery values for both viruses were higher for VD than VU flow direction, while in the presence of STx-1b the opposite was observed. However, for all cases examined, the produced mass of viruses attached onto suspended clay particles were higher for VD than VU flow direction, suggesting that the flow direction significantly influences virus attachment onto clays, as well as packed column retention of viruses attached onto suspended clays. KGa-1b hindered the transport of ΦX174 under VD flow, while STx-1b facilitated the transport of ΦX174 under both VU and VD flow directions. Moreover, KGa-1b and STx-1b facilitated the transport of MS2 in most of the cases examined except of the case where KGa-1b was present under VD flow. Also, the experimental data were used for the estimation of virus surface-coverages and virus surface concentrations generated by virus diffusion-limited attachment, as well as virus attachment due to sedimentation. Both sedimentation and diffusion limited virus attachment were higher for VD than VU flow, except the case of MS2 and STx-1b cotransport. The diffusion-limited attachment was higher for MS2 than ΦΧ174 for all cases examined.

Chemotaxis Increases the Residence Time of Bacteria in Granular Media Containing Distributed Contaminant Sources

The use of chemotactic bacteria in bioremediation has the potential to increase access to, and the biotransformation of, contaminant mass within the subsurface. This laboratory-scale study aimed to understand and quantify the influence of chemotaxis on the residence times of pollutant-degrading bacteria within homogeneous treatment zones. Focus was placed on a continuous-flow sand-packed column in which a uniform distribution of naphthalene crystals created distributed sources of dissolved-phase contaminant. A 10 mL pulse of Pseudomonas putida G7, which is chemotactic to naphthalene, and Pseudomonas putida G7 Y1, a nonchemotactic mutant strain, were simultaneously introduced into the sand-packed column at equal concentrations. Breakthrough curves obtained from experiments conducted with and without naphthalene were used to quantify the effect of chemotaxis on transport parameters. In the presence of the chemoattractant, longitudinal dispersion of PpG7 increased by a factor of 3, and percent recovery decreased by 43%. In contrast, PpG7 Y1 transport was not influenced by the presence of naphthalene. The results imply that pore-scale chemotaxis responses are evident at an interstitial velocity of 1.8 m/day, which is within the range of typical groundwater flow. Within the context of bioremediation, chemotaxis may work to enhance bacterial residence times in zones of contamination, thereby improving treatment.

Bacteria Transport in a Soil-Based Wastewater Treatment System under Simulated Operational and Climate Change Conditions

Bacteria removal efficiencies in a conventional soil-based wastewater treatment system (OWTS) have been modeled to elucidate the fate and transport of bacteria under environmental and operational conditions that might be expected under changing climatic conditions. The HYDRUS 2D/3D software was used to model the impact of changing precipitation patterns, bacteria concentrations, hydraulic loading rates (HLRs), and higher subsurface temperatures at different depths and soil textures. Modeled effects of bacteria concentration shows that greater depth of treatment was required in coarser soils than in fine-textured ones to remove . The initial removal percentage was higher when HLR was lower, but it was greater when HLR was higher. When a biomat layer was included in the transport model, the performance of the system improved by up to 12.0%. Lower bacteria removal (<5%) was observed at all depths under the influence of precipitation rates ranging from 5 to 35 cm, and 35-cm rainfall combined with a 70% increase in HLR. Increased subsurface temperature (23°C) increased bacteria removal relative to a lower temperature range (5-20°C). Our results show that the model is able to effectively simulate bacteria removal and the effect of precipitation and temperature in different soil textures. It appears that the performance of OWTS may be impacted by changing climate.

Interaction of human adenoviruses and coliphages with kaolinite and bentonite

Human adenoviruses (hAdVs) are pathogenic viruses responsible for public health problems worldwide. They have also been used as viral indicators in environmental systems. Coliphages (e.g., MS2, ΦX174) have also been studied as indicators of viral pollution in fecally contaminated water. Our objective was to evaluate the distribution of three viral fecal indicators (hAdVs, MS2, and ΦΧ174), between two different phyllosilicate clays (kaolinite and bentonite) and the aqueous phase. A series of static and dynamic experiments were conducted under two different temperatures (4, 25°C) for a time period of seven days. HAdV adsorption was examined in DNase I reaction buffer (pH=7.6, and ionic strength (IS)=1.4mM), whereas coliphage adsorption in phosphate buffered saline solution (pH=7, IS=2mM). Moreover, the effect of IS on hAdV adsorption under static conditions was evaluated. The adsorption of hAdV was assessed by real-time PCR and its infectivity was tested by cultivation methods. The coliphages MS2 and ΦΧ174 were assayed by the double-layer overlay method. The experimental results have shown that coliphage adsorption onto both kaolinite and bentonite was higher for the dynamic than the static experiments; whereas hAdV adsorption was lower under dynamic conditions. The adsorption of hAdV increased with decreasing temperature, contrary to the results obtained for the coliphages. This study examines the combined effect of temperature, agitation, clay type, and IS on hAdV adsorption onto clays. The results provide useful new information on the effective removal of viral fecal indicators (MS2, ΦX174 and hAdV) from dilute aqueous solutions by adsorption onto kaolinite and bentonite. Factors enabling enteric viruses to penetrate soils, groundwater and travel long distances within aquifers are important public health issues. Because the observed adsorption behavior of surrogate coliphages MS2 and ΦΧ174 is substantially different to that of hAdV, neither MS2 nor ΦΧ174 is recommended as a suitable model for adenovirus.

Survival of Escherichia coli in stormwater biofilters

Biofilters are widely adopted in Australia for stormwater treatment, but the reported removal of common faecal indicators (such as Escherichia coli (E. coli)) varies from net removal to net leaching. Currently, the underlying mechanisms that govern the faecal microbial removal in the biofilters are poorly understood. Therefore, it is important to study retention and subsequent survival of faecal microorganisms in the biofilters under different biofilter designs and operational characteristics. The current study investigates how E. coli survival is influenced by temperature, moisture content, sunlight exposure and presence of other microorganisms in filter media and top surface sediment. Soil samples were taken from two different biofilters to investigate E. coli survival under controlled laboratory conditions. Results revealed that the presence of other microorganisms and temperature are vital stressors which govern the survival of E. coli captured either in the top surface sediment or filter media, while sunlight exposure and moisture content are important for the survival of E. coli captured in the top surface sediment compared to that of the filter media. Moreover, increased survival was found in the filter media compared to the top sediment, and sand filter media was found be more hostile than loamy sand filter media towards E. coli survival. Results also suggest that the contribution from the tested environmental stressors on E. coli survival in biofilters will be greatly affected by the seasonality and may vary from one site to another.

Short-term inactivation rates of selected Gram-positive and Gram-negative bacteria attached to metal oxide mineral surfaces: role of solution and surface chemistry

Metal oxides such as ferric or aluminum oxides can play an important role in the retention of bacteria in granular aquatic environments; however, their role in bacterial inactivation is not well understood. Herein, we examined the role of water chemistry and surface chemistry on the short-term inactivation rates of three bacteria when adhered to surfaces. To evaluate the role of water chemistry on the inactivation of attached bacteria, the loss in membrane integrity of bacteria attached to an iron oxide (Fe2O3) surface was measured over a range of water ionic strengths of either monovalent or divalent salts in the absence of a growth substrate. The influence of surface chemistry on the inactivation of attached bacteria was examined by measuring the loss in membrane integrity of cells attached to three surfaces (SiO2, Fe2O3, and Al2O3) at a specific water chemistry (10 mM KCl). Bacteria were allowed to attach onto the SiO2 or metal oxide coated slides mounted in a parallel-plate flow cell, and their inactivation rate (loss in membrane integrity) was measured directly without removing the cells from the surface and without disturbing the system. X-ray photoelectron spectroscopy analysis revealed a high correlation between the amounts of C-metal or O-metal bonds and the corresponding bacterial inactivation rates for each surface. Finally, for all three surfaces, a consistent increase in inactivation rate was observed with the type of bacterium in the order: Enterococcus faecalis, Escherichia coli O157:H7, and Escherichia coli D21f2.

A Review of the Use of Organic Amendments and the Risk to Human Health

Historically, organic amendments—organic wastes—have been the main source of plant nutrients, especially N. Their use allows better management of often-finite resources to counter changes in soils that result from essential practices for crop production. Organic amendments provide macro- and micronutrients, including carbon for the restoration of soil physical and chemical properties. Challenges from the use of organic amendments arise from the presence of heavy metals and the inability to control the transformations required to convert the organic forms of N and P into the minerals available to crops, and particularly to minimize the losses of these nutrients in forms that may present a threat to human health. Animal manure and sewage biosolids, the organic amendments in greatest abundance, contain components that can be hazardous to human health, other animals and plants. Pathogens pose an immediate threat. Antibiotics, other pharmaceuticals and naturally produced hormones may pose a threat if they increase the number of zoonotic disease organisms that are resistant to multiple antimicrobial drugs or interfere with reproductive processes. Some approaches aimed at limiting N losses (e.g. covered liquid or slurry storage, rapid incorporation into the soil, timing applications to minimize delay before plant uptake) also tend to favor survival of pathogens. Risks to human health, through the food chain and drinking water, from the pathogens, antibiotics and hormonal substances that may be present in organic amendments can be reduced by treatment before land application, such as in the case of sewage biosolids. Other sources, such as livestock and poultry manures, are largely managed by ensuring that they are applied at the rate, time and place most appropriate to the crops and soils. A more holistic approach to management is required as intensification of agriculture increases.

A systems analysis of irrigation water quality in environmental assessments related to foodborne outbreaks

Irrigation water quality can affect food safety and health and has been identified as a possible source of pathogens in produce linked to disease outbreaks. Many irrigation water sources are subject to contamination from various sources in surrounding watersheds. A systems-based, watershed scale analysis is therefore necessary to comprehensively identify both sources of contamination and the conditions in the environment that facilitated or created that contamination, termed here 'environmental antecedents'. Three nationwide disease outbreaks linked to produce in the United States (US) are used to illustrate this concept of a watershed scale assessment to investigate potential impacts of irrigation water quality on food safety.

Assessment of sewer source contamination of drinking water wells using tracers and human enteric viruses

This study investigated the source, transport, and occurrence of human enteric viruses in municipal well water, focusing on sanitary sewer sources. A total of 33 wells from 14 communities were sampled once for wastewater tracers and viruses. Wastewater tracers were detected in four of these wells, and five wells were virus- positive by qRT-PCR. These results, along with exclusion of wells with surface water sources, were used to select three wells for additional investigation. Viruses and wastewater tracers were found in the groundwater at all sites. Some wastewater tracers, such as ionic detergents, flame retardants, and cholesterol, were considered unambiguous evidence of wastewater. Sampling at any given time may not show concurrent virus and tracer presence; however, given sufficient sampling over time, a relation between wastewater tracers and virus occurrence was identified. Presence of infectious viruses at the wellhead demonstrates that high-capacity pumping induced sufficiently short travel times for the transport of infectious viruses. Therefore, drinking-water wells are vulnerable to contaminants that travel along fast groundwater flowpaths even if they contribute a small amount of virus-laden water to the well. These results suggest that vulnerability assessments require characterization of "low yield-fast transport" in addition to traditional "high yield-slow transport", pathways.

Interaction between viruses and clays in static and dynamic batch systems

Bacteriophage MS2 and PhiX174 were used as surrogates for human viruses in order to investigate the interaction between viruses and clay particles. The selected phyllosilicate clays were kaolinite and bentonite (>90% montmorillonite). A series of static and dynamic experiments were conducted at two different temperatures (4 and 25 degrees C) to investigate the effect of temperature and agitation (dynamic experiments) on virus adsorption onto clays. Appropriate adsorption isotherms were determined. Electrokinetic features of bacteriophages and clays were quantified at different pH and ionic strength (IS). Moreover, interaction energies between viruses and clays were calculated for the experimental conditions (pH 7 and IS = 2 mM) by applying the DLVO theory. The experimental results shown that virus adsorption increases linearly with suspended virus concentration. The observed distribution coefficient (K(d)) was higher for MS2 than PhiX174. The observed K(d) values were higher for the dynamic than static experiments, and increased with temperature. The results of this study provided basic information for the effectiveness of clays to remove viruses by adsorption from dilute aqueous solutions. No previous study has explored the combined effect of temperature and agitation on virus adsorption onto clays.

Fate and transport of antibiotic residues and antibiotic resistance genes following land application of manure waste

Antibiotics are used in animal livestock production for therapeutic treatment of disease and at subtherapeutic levels for growth promotion and improvement of feed efficiency. It is estimated that approximately 75% of antibiotics are not absorbed by animals and are excreted in waste. Antibiotic resistance selection occurs among gastrointestinal bacteria, which are also excreted in manure and stored in waste holding systems. Land application of animal waste is a common disposal method used in the United States and is a means for environmental entry of both antibiotics and genetic resistance determinants. Concerns for bacterial resistance gene selection and dissemination of resistance genes have prompted interest about the concentrations and biological activity of drug residues and break-down metabolites, and their fate and transport. Fecal bacteria can survive for weeks to months in the environment, depending on species and temperature, however, genetic elements can persist regardless of cell viability. Phylogenetic analyses indicate antibiotic resistance genes have evolved, although some genes have been maintained in bacteria before the modern antibiotic era. Quantitative measurements of drug residues and levels of resistance genes are needed, in addition to understanding the environmental mechanisms of genetic selection, gene acquisition, and the spatiotemporal dynamics of these resistance genes and their bacterial hosts. This review article discusses an accumulation of findings that address aspects of the fate, transport, and persistence of antibiotics and antibiotic resistance genes in natural environments, with emphasis on mechanisms pertaining to soil environments following land application of animal waste effluent.

Atmospheric movement of microorganisms in clouds of desert dust and implications for human health

Billions of tons of desert dust move through the atmosphere each year. The primary source regions, which include the Sahara and Sahel regions of North Africa and the Gobi and Takla Makan regions of Asia, are capable of dispersing significant quantities of desert dust across the traditionally viewed oceanic barriers. While a considerable amount of research by scientists has addressed atmospheric pathways and aerosol chemistry, very few studies to determine the numbers and types of microorganisms transported within these desert dust clouds and the roles that they may play in human health have been conducted. This review is a summary of the current state of knowledge of desert dust microbiology and the health impact that desert dust and its microbial constituents may have in downwind environments both close to and far from their sources.

Bacteria removal in septic effluent: influence of biofilm and protozoa

Numerous biological, physical and chemical parameters are involved in the retention and removal of bacteria in wastewater treatment systems. Biological parameters, such as biofilms and protozoa grazing activity, are often mentioned but few studies provide a better understanding of their influence. In this study, the effect of bacterivorous protozoa on pathogenic indicator bacteria removal was investigated in septic effluent and in the presence of a biofilm coating glass slides. Endogenous bacteria from septic effluent were quantified. First, bacteria removal was compared between septic effluents treated or not with an inhibitor of protozoa (cycloheximide). The mortality rates were 10 times lower in treated effluent (96 CFU mL(-1) d(-1)) than in untreated effluent (1100 CFU mL(-1) d(-1)). Secondly, the efficiency of bacteria removal was studied (i) with a biofilm surface and active protozoa, (ii) with a biofilm surface and inactivated protozoa, (iii) with a clean surface. Protozoa in the presence of a biofilm were responsible for 60% of bacteria removal. Biofilm without protozoa and a clean surface each removed similar quantities of bacteria. Grazing by protozoa could be an important biological mechanism for bacterial elimination in wastewater treatment systems.

Detection of hepatitis A virus (HAV) in oysters (Crassostrea gigas)

Because shellfish (oysters, clams, and mussels) are filter-feeders, pathogens become concentrated within them, and human consumption of raw, or under-cooked shellfish can result in disease outbreaks. Identification of hepatitis A virus (HAV) in shellfish has been difficult for several reasons: the concentration of virions in shellfish tissues are very low, detection methods based on in vitro propagation are unreliable, recovery of virions from shellfish tissues is inefficient, and PCR inhibitors in shellfish tissues limit the success of RT-PCR. These facts underlie difficulties in determining cause and effect relationships between hepatitis A outbreaks and detection of HAV contamination in shellfish samples. We have developed a reliable and highly sensitive method for detection of HAV in oyster tissues at low levels (0.001 FFU/ml-fluorescent focus units per milliliter). Our method combines dissection of the gastrointestinal oyster tract, organic extraction before PEG precipitation, and RNA extraction with Trizol LS, followed by RT-PCR and hybridization using a digoxigenin-labeled HAV cDNA probe. Our results will benefit both public health officials concerned about hepatitis A infections caused by consumption of HAV-contaminated oysters and shellfish producers who require reliable methods for quality control of commercial oyster production.

Effects of temperature and moisture on coliphage PRD-1 survival in soil

The goal of this study was to quantitatively assess the effects of temperature and soil moisture on the survival of coliphage PRD-1 in soil. PRD-1 was added to sandy loam soil at five different soil moisture levels. The soil seeded with PRD-1 was packed into sterile polyethylene jars and exposed to eight different temperatures in an oven. Samples were collected over 14 to 25 days depending on the temperature. The inactivation rate of PRD-1 increased linearly with increased temperature. The inactivation rate gradually decreased when the soil moisture level decreased from 20.9 to 8.9%. However, the inactivation rate increased when the soil moisture content reached 5.1%, suggesting the existence of an optimal soil moisture condition for PRD-1 survival. It is also possible that there is a threshold soil moisture level below which the inactivation of PRD-1 suddenly increases. Marked reductions in recoveries were observed as the soil moisture approached or fell below 5.0% as a result of evaporation. The increased inactivation of PRD-1 due to strong association with soil particles may have caused rapid reductions in recoveries. The evaporation process appeared to affect PRD-1 survival substantially at higher temperatures whereas little effect was observed at lower temperatures. A model developed from this study predicted PRD-1 survival in subsurface soil in field conditions with an average error of 11.0%.

Transport of microsporidium Encephalitozoon intestinales spores in sandy porous media

The retention and transport of microsporidium Encephalitozoon intestinales spores in two water-saturated sandy porous media was investigated in this study. The initial breakthrough of the spores in the column effluent occurred essentially simultaneously with that of a non-reactive tracer, indicating no significant velocity enhancement. A large fraction (45-73%) of the spores injected into the columns was not recovered in the effluent, indicating removal from solution through colloid retention processes of attachment and/or straining. The relative significance of attachment and straining to total retention was evaluated in additional experiments. An experiment was conducted with a sieved coarse fraction of porous media for which straining is unlikely to be of significance based on the relative diameters of the spores and porous-medium pores. The spore recovery for this experiment was similar to the recoveries obtained for microsporidia transport in the un-sieved parent porous medium. An additional experiment was conducted with a subsample of the coarse fraction that was acid-washed to reduce potential surface attachment sites. Spore recovery was complete for this experiment. These results suggest surface deposition was the primary removal mechanism in our system. This conclusion is supported by the results of an experiment wherein deionized water was flushed through a column that was previously flushed with electrolyte solution. The effluent spore concentrations were observed to increase upon injection of deionized water, indicating re-mobilization of spores upon a change in water chemistry. The measured data were successfully simulated using a mathematical model incorporating colloid filtration. The results of this study suggest that the transport of microspordia in sandy porous media is governed by established colloid-transport processes.

Illuminating reactive microbial transport in saturated porous media: demonstration of a visualization method and conceptual transport model

We demonstrate a method to study reactive microbial transport in saturated translucent porous media using the bacteria Pseudomonas fluorescens 5RL genetically engineered to carry a plasmid with bioluminescence genes inducible by salicylate. Induced bacteria were injected into a cryolite grain filled chamber saturated with a sterile non-growth-promoting (phosphorus limited) chemical mixture containing salicylate as an aromatic hydrocarbon analogue. The amount of light produced by the bacteria serves as an estimator of the relative efficiency of aerobic biodegradation since bioluminescence is dependent on both salicylate and oxygen but only consumes oxygen. Bioluminescence was captured with a digital camera and analyzed to study the evolving spatial pattern of the bulk oxygen consuming reactions. As fluid flow transported the bacteria through the chamber, bioluminescence was observed to initially increase until an oxygen depletion zone developed behind the advective front. Bacterial transport was modeled with the advection dispersion equation and oxygen concentration was modeled assuming bacterial consumption via Monod kinetics with consideration of additional effects of rate-limited mass transfer from residual gas bubbles. Consistent with previous measurements, bioluminescence was considered proportional to oxygen consumed. Using the observed bioluminescence, model parameters were fit that were consistent with literature values and produced results in good agreement with the experimental data. These findings demonstrate potential for using this method to investigate the complex spatial and temporal dynamics of reactive microbial transport in saturated porous media.

Vulnerability of drinking-water wells in La Crosse, Wisconsin, to enteric-virus contamination from surface water contributions

Human enteric viruses can contaminate municipal drinking-water wells, but few studies have examined the routes by which viruses enter these wells. In the present study, the objective was to monitor the municipal wells of La Crosse, Wisconsin, for enteric viruses and determine whether the amount of Mississippi River water infiltrating the wells was related to the frequency of virus detection. From March 2001 to February 2002, one river water site and four wells predicted by hydrogeological modeling to have variable degrees of surface water contributions were sampled monthly for enteric viruses, microbial indicators of sanitary quality, and oxygen and hydrogen isotopes. (18)O/(16)O and (2)H/(1)H ratios were used to determine the level of surface water contributions. All samples were collected prior to chlorination at the wellhead. By reverse transcription-PCR (RT-PCR), 24 of 48 municipal well water samples (50%) were positive for enteric viruses, including enteroviruses, rotavirus, hepatitis A virus (HAV), and noroviruses. Of 12 river water samples, 10 (83%) were virus positive by RT-PCR. Viable enteroviruses were not detected by cell culture in the well samples, although three well samples were positive for culturable HAV. Enteroviruses detected in the wells by RT-PCR were identified as several serotypes of echoviruses and group A and group B coxsackieviruses. None of the well water samples was positive for indicators of sanitary quality, namely male-specific and somatic coliphages, total coliform bacteria, Escherichia coli, and fecal enterococci. Contrary to expectations, viruses were found in all wells regardless of the level of surface water contributions. This result suggests that there were other unidentified sources, in addition to surface water, responsible for the contamination.

Retention and removal of pathogenic bacteria in wastewater percolating through porous media: a review

Properly designed biological filters or infiltration systems have the capacity to significantly reduce effluent concentrations of pathogenic microorganisms in wastewater. The retention and elimination of microbial cells in biological wastewater filter systems is influenced by several factors. In this review, these factors are discussed. Immobilization of microbial cells moving through a porous media is influenced by mechanisms such as physical straining as well as adsorption to porous media. The grain size of porous media and bacterial cell size are important factors affecting the straining of bacteria, as are the hydraulic loading rate or the extent of clogging layer development in the filter. Adsorption of cells to the porous media is influenced by the content of organic matter, degree of biofilm development, and electrostatic attraction due to ion strength of the solution or electrostatic charges of cell- and particle surfaces. The rate of inactivation of pathogenic microorganisms, in adsorbed or liquid phases, has been shown to be affected by abiotic and biotic factors such as moisture content, pH, temperature, organic matter, bacterial species, predation, and antagonistic symbiosis between microorganisms in the system.

Influence of groundwater characteristics on the survival of enteric viruses

AIMS

This study was undertaken to further understand the processes affecting the persistence of enteric viruses in groundwater.

METHODS AND RESULTS

Varying temperature, oxygen and nutrient levels were tested in the presence and absence of groundwater micro-organisms to determine which of the factors tested had dominant influence on the decay of Escherichia coli, the bacteriophage MS2, poliovirus and coxsackievirus. The results indicated that the most influential factor affecting the decay of the viruses and E. coli was the presence of groundwater micro-organisms. The results also implied that temperature, the presence of oxygen and nutrient levels indirectly influence viruses and E. coli decay by influencing the activity of the groundwater micro-organisms.

CONCLUSIONS

E. coli and the viruses displayed maximum decay under aerobic conditions, at 28 degrees C without the addition of nutrients in the presence of groundwater micro-organisms.

SIGNIFICANCE AND IMPACT OF THE STUDY

The results suggest that if the mode of action of the groundwater micro-organisms could be determined then the decay of viral pathogens in recharged waters may be more easily predicted.

Kinetic studies of attachment and detachment of microbial cells from soil

A mathematical model was developed to describe the kinetics of cell attachment and detachment from soil. Soil-column experiments were performed to evaluate the model parameters. Pseudomonas putida G7 capable of degrading naphthalene was used as a model microorganism. A sediment sample taken from an uncontaminated area near a coal tar waste site in upstate New York, USA was used as a test soil. The kinetics of cell attachment and detachment from the model soil could be described by the developed first-order model. The equilibrium constant of attachment (11.4 ml g(-1)), the rate coefficient of cell attachment (0.299 ml g(-1) min(-1) and the rate coefficient of cell detachment (0.0263 min(-1)) were determined from the soil-column experiment. The equilibrium constant of attachment determined in this study (11.4 ml g(-1)) was within the range of those reported in the literature for bacterial attachment to soil (0.55 to 12.6 ml g(-1)). The kinetic model succesfully predicted the data of batch experiment for cell attachment and detachment soil.

Incidence of enteric viruses in groundwater from household wells in Wisconsin

Recent studies on the contamination of groundwater with human enteric viruses have focused on public water systems, whereas little is known about the occurrence of viruses in private household wells. The objective of the present study was to estimate the incidence of viruses in Wisconsin household wells located near septage land application sites or in rural subdivisions served by septic systems. Fifty wells in seven hydrogeologic districts were sampled four times over a year, once each season. Reverse transcriptase PCR (RT-PCR), followed by Southern hybridization, was used to detect enteroviruses, rotavirus, hepatitis A virus (HAV), and Norwalk-like viruses (NLVs). In addition, cell culture was used to detect culturable enteroviruses. Companion water samples were collected for total coliforms, Escherichia coli, fecal enterococci, F-specific RNA coliphages, nitrate, and chloride analyses. Among the 50 wells, four (8%) were positive for viruses by RT-PCR. Three wells were positive for HAV, and the fourth well was positive for both rotavirus and NLV in one sample and an enterovirus in another sample. Contamination was transient, since none of the wells was virus positive for two sequential samples. Culturable enteroviruses were not detected in any of the wells. Water quality indicators were not statistically associated with virus occurrence, although some concordance was noted for chloride. The present study is the first in the United States to systematically monitor private household wells for virus contamination and, combined with data for public wells, provides further insight on the extent of groundwater contamination with human enteric viruses.

Pathogenic human viruses in coastal waters

This review addresses both historical and recent investigations into viral contamination of marine waters. With the relatively recent emergence of molecular biology-based assays, a number of investigations have shown that pathogenic viruses are prevalent in marine waters being impacted by sewage. Research has shown that this group of fecal-oral viral pathogens (enteroviruses, hepatitis A viruses, Norwalk viruses, reoviruses, adenoviruses, rotaviruses, etc.) can cause a broad range of asymptomatic to severe gastrointestinal, respiratory, and eye, nose, ear, and skin infections in people exposed through recreational use of the water. The viruses and the nucleic acid signature survive for an extended period in the marine environment. One of the primary concerns of public health officials is the relationship between the presence of pathogens and the recreational risk to human health in polluted marine environments. While a number of studies have attempted to address this issue, the relationship is still poorly understood. A contributing factor to our lack of progress in the field has been the lack of sensitive methods to detect the broad range of both bacterial and viral pathogens. The application of new and advanced molecular methods will continue to contribute to our current state of knowledge in this emerging and important field.

Role of the air-water-solid interface in bacteriophage sorption experiments

Batch sorption experiments were carried out with the bacteriophages MS2 and phi X174. Two types of reactor vessels, polypropylene and glass, were used. Consistently lower concentrations of MS2 were found in the liquid phase in the absence of soil (control blanks) than in the presence of soil after mixing. High levels of MS2 inactivation (approximately 99.9%) were observed in control tubes made of polypropylene (PP), with comparatively little loss of virus seen in PP tubes when soil was present. Minimal inactivation of MS2 was observed when the air-water interface was completely eliminated from PP control blanks during mixing. All batch experiments performed with reactor tubes made of glass demonstrated no substantial inactivation of MS2. In similar experiments, bacteriophage phi X174 did not undergo inactivation in either PP or glass control blanks, implying that this virus is not affected by the same factors which led to inactivation of MS2 in the PP control tubes. When possible, phage adsorption to soil was calculated by the Freundlich isotherm. Our data suggest that forces associated with the air-water-solid interface (where the solid is a hydrophobic surface) are responsible for inactivation of MS2 in the PP control tubes. The influence of air-water interfacial forces should be carefully considered when batch sorption experiments are conducted with certain viruses.

Microorganisms as tracers in groundwater injection and recovery experiments: a review

Modern day injection and recovery techniques designed to examine the transport behavior of microorganisms in groundwater have evolved from experiments conducted in the late 1800s, in which bacteria that form red or yellow pigments were used to trace flow paths through karst and fractured-rock aquifers. A number of subsequent groundwater hydrology studies employed bacteriophage that can be injected into aquifers at very high concentrations (e.g., 10(13) phage ml-1) and monitored through many log units of dilution to follow groundwater flow paths for great distances, particularly in karst terrain. Starting in the 1930s, microbial indicators of fecal contamination (particularly coliform bacteria and their coliphages) were employed as tracers to determine potential migration of pathogens in groundwater. Several injection and recovery experiments performed in the 1990s employed indigenous groundwater microorganisms (both cultured and uncultured) that are better able to survive under in situ conditions. Better methods for labeling native bacteria (e.g. by stable isotope labeling or inserting genetic markers, such as the ability to cause ice nucleation) are being developed that will not compromise the organisms' viability during the experimental time course.

Transport of bacteria through geologic media

A review of the current literature on transport of bacteria through geologic media is presented. The review addresses the major controls on bacterial transport. These controls include the nature of the substratum, the solute, and the bacterial cell. Most knowledge on the transport of bacteria through geologic media has been gained from column studies. There is need for some standardization of approaches, particularly with regard to data collection and controls on factors such as ionic strength and flow velocity. Other systems including glass micromodels have been used in conjunction with microscopy and scanning confocal laser microscopy to examine the controls on transport at the pore scale rather than porous medium scale of column studies. Many inconsistencies exist regarding the effect of the numerous variables that impact bacterial sorption in porous media. These variables include the nature of the substratum (i.e., the presence or absence of coatings), chemical composition of the solute (particularly ionic strength), system hydrodynamics, and bacterial variables such as size, shape, hydrophobicity, and electrostatic charge. Mathematical models based on the advective–dispersion equation have been developed to simulate bacterial transport. Within specific limits, these models can approximate most aspects of bacterial transport; however, they neglect parameters such as growth and behavior of bacteria. There is a need for theoretical development, extensive laboratory investigation, and model development before the goal of prediction of bacterial transport at field scale may be realized.Key words: sorption, advection, dispersion, models, facilitated transport.

Occurrence of fecal indicator bacteria in surface waters and the subsurface aquifer in Key Largo, Florida

Sewage waste disposal facilities in the Florida Keys include septic tanks and individual package plants in place of municipal collection facilities in most locations. In Key Largo, both facilities discharge into the extremely porous Key Largo limestone. To determine whether there was potential contamination of the subsurface aquifer and nearby coastal surface waters by such waste disposal practices, we examined the presence of microbial indicators commonly found in sewage (fecal coliforms, Clostridium perfringens, and enterococci) and aquatic microbial parameters (viral direct counts, bacterial direct counts, chlorophyll a, and marine vibriophage) in injection well effluent, monitoring wells that followed a transect from onshore to offshore, and surface waters above these wells in two separate locations in Key Largo in August 1993 and March 1994. Effluent and waters from onshore shallow monitoring wells (1.8- to 3.7-m depth) contained two or all three of the fecal indicators in all three samples taken, whereas deeper wells (10.7- to 12.2-m depth) at these same sites contained few or none. The presence of fecal indicators was found in two of five nearshore wells (i.e., those that were < or = 1.8 miles [< or = 2.9 km] from shore), whereas offshore wells (> or = 2.1 to 5.7 miles [< or = 3.4 to 9.2 km] from shore) showed little sign of contamination. Indicators were also found in surface waters in a canal in Key Largo and in offshore surface waters in March but not in August. Collectively, these results suggest that fecal contamination of the shallow onshore aquifer, parts of the nearshore aquifer, and certain surface waters has occurred.(ABSTRACT TRUNCATED AT 250 WORDS)

Transport behavior of groundwater protozoa and protozoan-sized microspheres in sandy aquifer sediments

Transport behaviors of unidentified flagellated protozoa (flagellates) and flagellate-sized carboxylated microspheres in sandy, organically contaminated aquifer sediments were investigated in a small-scale (1 to 4-m travel distance) natural-gradient tracer test on Cape Cod and in flow-through columns packed with sieved (0.5-to 1.0-mm grain size) aquifer sediments. The minute (average in situ cell size, 2 to 3 (mu)m) flagellates, which are relatively abundant in the Cape Cod aquifer, were isolated from core samples, grown in a grass extract medium, labeled with hydroethidine (a vital eukaryotic stain), and coinjected into aquifer sediments along with bromide, a conservative tracer. The 2-(mu)m flagellates appeared to be near the optimal size for transport, judging from flowthrough column experiments involving a polydispersed (0.7 to 6.2 (mu)m in diameter) suspension of carboxylated microspheres. However, immobilization within the aquifer sediments accounted for a log unit reduction over the first meter of travel compared with a log unit reduction over the first 10 m of travel for indigenous, free-living groundwater bacteria in earlier tests. High rates of flagellate immobilization in the presence of aquifer sediments also was observed in the laboratory. However, immobilization rates for the laboratory-grown flagellates (initially 4 to 5 (mu)m) injected into the aquifer were not constant and decreased noticeably with increasing time and distance of travel. The decrease in propensity for grain surfaces was accompanied by a decrease in cell size, as the flagellates presumably readapted to aquifer conditions. Retardation and apparent dispersion were generally at least twofold greater than those observed earlier for indigenous groundwater bacteria but were much closer to those observed for highly surface active carboxylated latex microspheres. Field and laboratory results suggest that 2-(mu)m carboxylated microspheres may be useful as analogs in investigating several abiotic aspects of flagellate transport behavior in groundwater.

Effect of Solution Ionic Strength and Iron Coatings on Mineral Grains on the Sorption of Bacterial Cells to Quartz Sand

Understanding the interaction between bacterial cells and solid surfaces is essential to our attempts to quantify and predict the transport of microbes in groundwater aquifers, whether from the point of view of contamination or from that of bioremediation. The sorption of bacterial cells suspended in groundwater to porous medium grains was examined in batch studies. Bacterial sorption to clean quartz sand yielded equilibrium, linear, adsorption isotherms that varied with the bacterial strain used and the ionic strength of the aqueous solution. Values of K d (the slope of the linear sorption isotherm) ranged from 0.55 to 6.11 ml g -1 , with the greatest sorption observed for the highest groundwater ionic strength. These findings are consistent with the interpretation that an increasingly compressed electrical double layer results in stronger adsorption between the like-charged mineral surface and the bacterial cells. When iron-oxyhydroxide-coated sand was used, however, all of the added bacteria were adsorbed up to a threshold of 6.93 × 10 8 cells g of coated sand -1 , beyond which no further adsorption occurred. The irreversible, threshold adsorption is the result of a strong electrostatic attraction between the sesquioxide coating and the bacterial cells. Experimental results of adsorption in mixtures of quartz and Fe(III)-coated sand were successfully predicted by a simple additive model for sorption by the two substrate phases. Even small amounts of Fe(III)-coated sand in a mixture influenced the extent of adsorption of bacterial cells. A quantitative description of adsorption in the mixtures can be realized by using a linear isotherm for reversible adsorption to the quartz grains with a y intercept that represents the number of cells irreversibly adsorbed to the Fe(III)-coated sand.

VIRTUS, a model of virus transport in unsaturated soils

As a result of the recently proposed mandatory groundwater disinfection requirements to inactivate viruses in potable water supplies, there has been increasing interest in virus fate and transport in the subsurface. Several models have been developed to predict the fate of viruses in groundwater, but few include transport in the unsaturated zone and all require a constant virus inactivation rate. These are serious limitations in the models, as it has been well documented that considerable virus removal occurs in the unsaturated zone and that the inactivation rate of viruses is dependent on environmental conditions. The purpose of this research was to develop a predictive model of virus fate and transport in unsaturated soils that allows the virus inactivation rate to vary on the basis of changes in soil temperature. The model was developed on the basis of the law of mass conservation of a contaminant in porous media and couples the flows of water, viruses, and heat through the soil. Model predictions were compared with measured data of virus transport in laboratory column studies and, with the exception of one point, were within the 95% confidence limits of the measured concentrations. The model should be a useful tool for anyone wishing to estimate the number of viruses entering groundwater after traveling through the soil from a contamination source. In addition, model simulations were performed to identify parameters that have a large effect on the results. This information can be used to help design experiments so that important variables are measured accurately.

Dispersal dynamics of groundwater bacteria

Dispersal of bacteria in saturated, porous soils can be characterized by the partitioning of cells between the aqueous and solid phases, as a result of the physical and chemical nature of the soil and water and cell surface modifications. The purpose of this work is to understand variations in partitioning as a consequence of the nutrient conditions and to use this information in mathematical models to predict the dispersal rate of bacteria in aquifer material. Two different models were used to describe dispersal: an advective-dispersive-sorptive model with a first order kinetic sink term to account for irreversible cell reactions, such as death and sorption; and a two-site reaction model, in which the retardation was assumed to be determined by two types of sites, one characterized by instantaneous equilibrium sorption reactions and the other by kinetic nonequilibrium reactions. Water-saturated sand columns were used as continuous-flow groundwater microcosms to test the models under different nutrient regimes. Two strains of indigenous groundwater bacteria were isolated from aquifer material and labelled with(3)H-alanine,(14)C-pyruvic acid,(3)H-glucose, and(3)H-adenosine for different measurements of sorption and dispersal, which were estimated from breakthrough curves. Both experimental data and model variables showed that dispersal of bacteria was a dynamic nonequilibrium process, possibly shaped by two subpopulations, one strongly, even irreversibly, adsorbing to the solid particles, and one with very slow adsorption kinetics. The cell surfaces were modified in response to the growth conditions, which was demonstrated by hydrophobic and electrostatic interaction chromatography. Cell surface hydrophobicity was about eight times higher in groundwater than in eutrophic lake water. The partition coefficient varied between 12.6 in the groundwater and 6.4 in the lake water, indicating the prime importance of hydrophobic binding for attachment in low nutrient conditions. The partitioning was also sensitive to the hydrodynamics of the system and the oxygen supply, as demonstrated by comparison of sorption in agitated test tubes, gently shaken vials, and air-flushed bottles. Sorption kinetics were demonstrated in a continuous flow cell. About 45% of a population was associated with sand particles with a continuous flow of pure groundwater and as little as 20% in lake water. However, more than 50% of the bacteria in the aqueous phase were associated with suspended material of less than 60 μm in diameter. This association may enhance dispersal for example, by size exclusion of the colloidal material in the interstitial pores.

Effect of sodium chloride on transport of bacteria in a saturated aquifer material

Determinations were made of the influence of NaCl concentration, cell density, and flow velocity on the transport of Pseudomonas sp. strain KL2 through columns of aquifer sand under saturated conditions. A pulse-type boundary condition was used. The experiments were conducted by using 0.3-m-long Plexiglas columns with an internal diameter of 0.05 m. When a 1-h pulse of a 0.01 M NaCl solution containing 10(8) cells per ml was added at a flow rate of 10(-4) m s-1, the bacterial density in the effluent never exceeded 2.2% of the density of cells added, and only 1.5% of the bacteria passed through the aquifer material. In contrast, when the bacteria were applied in distilled water, the relative cell density in the effluent approached 100%, and 60% of the bacteria were transported through the aquifer solids. Under these conditions, the breakthrough of Pseudomonas sp. strain KL2 was slower than chloride. When the flow rate was 2.0 x 10(-4) m s-1, the cell density in the effluent reached 7.3% of that added in 0.01 M NaCl solution, but only 3.9% of the bacteria were transported through the aquifer particles. On the other hand, the density in the effluent approached 100% of that added in deionized water, and 77% of the added bacteria were recovered. When the density of added cells was 10(9) cells per ml at a flow rate of 10(-4) m s-1, the densities in the effluent reached 70 and 100% of those added in salt solution and deionized water, respectively, and 44 and 57% of the bacteria were transported through the aquifer solids.(ABSTRACT TRUNCATED AT 250 WORDS)

Microbiological Comparison of Surface Soil and Unsaturated Subsurface Soil from a Semiarid High Desert

Thirty-two chemoheterotrophic bacteria were isolated from unsaturated subsurface soil samples obtained from ca. 70 m below land surface in a high desert in southeastern Idaho. Most isolates were gram positive (84%) and strict aerobes (79%). Acridine orange direct counts of microbes in one subsurface sample showed lower numbers than similar counts performed on surface soils from the same location (ca. 5 × 10 5 versus 2 × 10 6 cells per g [dry weight] of soil), but higher numbers than those from plate counts performed on the subsurface material. Another sample taken from the same depth at another location showed no evidence of colonies under identical conditions. Soil analyses indicated that subsurface sediments versus surface soils were slightly alkaline (pH 7.9 versus 7.4), had a higher water content (25.7 versus 6.3%), and had lower organic carbon concentrations (0.05 to 0.17 versus 0.25% of soil dry weight). Analyses of biologically relevant gases from the unsaturated subsurface indicated an aerobic environment. As in other unsaturated soil environments, either a high proportion of bacteria in these subsurface sediments are not viable or they are incapable of growth on conventional media under aerobic conditions. The presence and numbers of bacteria in these deep sediments may be influenced by colonization opportunities afforded by periodic percolation of surface water through fractures in overlying strata.