Reliable Procedure for Molecular Analysis of Airborne Microflora in Three Indoor Environments: An Office and Two Different Museum Contexts

Biological aerosols from air constitute a significant source of exposure to microorganisms in public places. Airborne microorganisms are involved in the development of certain respiratory symptoms, allergies, or infections among users and occupants. Various sampling instruments have commonly been used in aerobiology to collect bacteria and fungi suspended in the air. The objective of this study was to develop a reliable procedure for sampling in indoor public environments presenting different levels of occupancy, airborne bacteria and fungi to be subjected to molecular analysis (bacteria and fungi quantitative PCR, capillary electrophoresis single strand conformation polymorphism fingerprinting). Four different sampling devices were tested in situ in an office building (open‐plan type) and the sampling strategy chosen was tested in two museum contexts. In accordance with the drawbacks involved to our study (quantitative and qualitative aspects, cost, and overcrowding), cyclone device appeared to be most suitable. The results underline the effectiveness of this high‐volume aerosol sampling device for both qualitative and quantitative molecular analysis. Four in situ sampling collections were carried out in 1 day in the Louvre Museum to study quantitative and qualitative variations of airborne bacterial and fungal diversity. The quantitative results revealed a similar order of magnitude for the numbers of both bacteria and fungi. In the Louvre Museum, the samples yielded between 3.7 × 10⁴ and 4.1 × 10⁴ genome equivalent (GE) bacteria/m³ air and between 5.0 × 10⁴ and 5.9 × 10⁴ GE fungi/m³ air and in the Decorative Arts Museum between, 2.1 × 10⁴ and 2.5 × 10⁴ GE bacteria/m³ air and between 1.4 × 10⁴ and 1.7 × 10⁴ GE fungi/m³ air. The results also indicate that the dominant bacterial community displayed a stable structure over a short period of time whereas dominant eukaryotic airborne community appeared more variable.     

Fundamental Changes in In Situ Air Sparging How Patterns

Two types of gas-phase flow patterns have been discussed and observed in the in situ air sparging (ISAS) literature: bubble flow and air channels. A critical factor affecting the flow pattern at a given location is the grain size of the porous medium. Visualization experiments reported in the literature indicate that a change in the flow pattern occurs around 1 to 2 mm grain diameters, with air channels occurring below the transition size and bubbles above. Analysis of capillary and buoyancy forces suggests that for a given gas-liquid-solid system, there is a critical size that dictates the dominant force, and the dominant force will in turn dictate the flow pattern. The dominant forces, and consequently the two-phase flow patterns, were characterized using a Bond number modified with the porous media aspect ratio (pore throat to pore body ratio). Laboratory experiments were conducted to observe flow patterns as a function of porous media size and air flow rate. The experimental results and the modified Bond number analysis support the relationship of flow patterns to grain size reported in the literature.     

Antimicrobial Activity of Seaweeds

The literature on the bioactivity of seaweeds against bacteria, fungi, viruses and protozoa has been consulted to provide a consolidated report. Information on seaweed metabolites which are antimicrobial in nature is also briefly reported. An appendix provides the details on kind of seaweed, location, period of collection, active compound against microorganisms and reference source. It is possible to derive the details in connection with antimicrobial activity of seaweeds pertaining to regions, seasons, chemical nature and their activity against microorganisms.     

Airborne Microorganisms Emitted from Wastewater Treatment Plant Treating Domestic Wastewater and Meat Processing Industry Wastes

Experiments were conducted to study the airborne microbial contamination generated by a wastewater treatment plant (WWTP). Aerosol samples were collected simultaneously, by sedimentation and impact methods, from the area and the surroundings of the WWTP. Total colony forming units (CFUs) of heterotrophic bacteria (HPC), as well as members of the Enterobacteriaceae, staphylococci, enterococci, actinomycetes, and microscopic fungi were determined. Bacterial (HPC) concentrations ranged between 10¹ and 10⁴ CFU/m³, fungi 0 and 10⁴ CFU/m³. Higher numbers of HPC bacteria in air samples were observed in summer, fungi in autumn. The main emission of microorganisms to atmospheric air was from the mechanical sewage treatment devices of the WWTP. The facilities of the biological sewage treatment of the plant did not generate large amounts of bioaerosols. In the air obtained from the premises of the WWTP, 25 species of the Enterobacteriaceae were isolated (Salmonella spp., Klebsiella pneumoniae, Escherichia coli). At the fence and in the surroundings only Pantoea spp. were identified. This suggests that the sewage bacteria were mainly discharged in the area of the WWTP. The presence of enteric bacteria, especially Enterobacteriaceae reflects the level of air pollution with bioaerosols from sewage and is an important factor during monitoring the quality of the air around WWTPs.     

Modeling microbial transport in porous media: Traditional approaches and recent developments

A substantial research effort has been aimed at elucidating the role of various physical, chemical and biological factors on microbial transport and removal in natural subsurface environments. The major motivation of such studies is an enhanced mechanistic understanding of these processes for development of improved mathematical models of microbial transport and fate. In this review, traditional modeling approaches used to predict the migration and removal of microorganisms (e.g., viruses, bacteria, and protozoa) in saturated porous media are systematically evaluated. A number of these methods have inherent weaknesses or inconsistencies which are often overlooked or misunderstood in actual application. Some limitations of modeling methods reviewed here include the inappropriate use of the equilibrium adsorption approach, the observed breakdown of classical filtration theory, the inability of existing theories to predict microbial attachment rates, and omission of physical straining and microbe detachment. These and other issues are considered with an emphasis on current research developments. Finally, recently proposed improvements to the most commonly used filtration model are discussed, with particular consideration of straining and microbe motility.     

Applying Quantitative Molecular Tools for Virus Transport Studies: Opportunities and Challenges

Bacteriophages have been used in soil column studies for the last several decades as surrogates to study the fate and transport behavior of enteric viruses in groundwater. However, recent studies have shown that the transport behavior of bacteriophages and enteric viruses in porous media can be very different. The next generation of virus transport science must therefore provide more data on mobility of enteric viruses and the relationship between transport behaviors of enteric viruses and bacteriophages. To achieve this new paradigm, labor intensity devoted to enteric virus quantification method must be reduced. Recent studies applied quantitative polymerase chain reaction (qPCR) to column filtration experiments to study the transport behavior of human adenovirus (HAdV) in porous media under a variety of conditions. A similar approach can be used to study the transport of other enteric viruses such as norovirus. Analyzing the column samples with both qPCR and culture assays and applying multiplex qPCR to study cotransport behavior of more than one virus will provide information to under‐explored areas in virus transport science. Both nucleic acid extraction kits and one‐step lysis protocols have been used in these column studies to extract viral nucleic acid for qPCR quantification. The pros and cons of both methods are compared herein and solutions for overcoming problems are suggested. As better understanding of the transport behavior of enteric viruses is clearly needed, we strongly advocate for application of rapid molecular tools in future studies as well as optimization of protocols to overcome their current limitations.     

Effects of chronic oil pollution from refinery effluent on sediment microflora in a Danish coastal area

Kalundborg Fjord is a Danish marine area which has been heavily oil polluted by refinery effluent, leading to accumulation of petroleum hydrocarbons in the surface sediments. A study of the occurrence in the sediment of heterotrophic bacteria, yeasts and filamentous fungi has been carried out, and the physiological composition of the microbial community has been recorded. Though the abundance of oil-degrading microorganisms was significant, a correlation between the number of these and the oil content of the sediment could not be demonstrated.     

Evaluation of Passive Diffusive-Adsorptive Samplers for Use in Assessing Time-Varying Indoor Air Impacts Resulting from Vapor Intrusion

Passive diffusive-adsorptive samplers are being considered for vapor intrusion (VI) pathway assessment, particularly where multi-week time-weighted average concentrations are desired. Recent studies have shown that passive samplers can produce accurate results under well-controlled steady concentration conditions, and field performance was also demonstrated at several sites. The objective of this study was to examine passive sampler performance in settings with time-varying indoor air concentrations, through a comparison of passive sampler results to concentrations determined by 24-h active sorbent tube sampling in a series of multi-week deployments. Sampling was performed in a well-instrumented residential building as well as industrial buildings, over periods of time ranging from 1 to 7 weeks. Strong linear correlations were noted between passive and active sampling concentration results for some passive samplers, with passive sampling results being similar to or lower than measured active sampling results by about 50% for those samplers in the residential study and about 25% higher in the industrial building study. Other samplers produced poor agreement. The conclusion from this study is that some passive samplers have great potential for use in multi-week indoor air quality monitoring. It was further determined that there is need for accepted procedures to validate and calibrate passive samplers for use in the field.     

A Diffusive Sampler for Passive Monitoring of Underground Storage Tanks

Passive measurements of volatile organic compounds (VOCs) provide a method for early detection and long-term monitoring of potential leaks from underground storage tanks (USTs) and associated fuel service lines. A diffusive sampler was constructed of a sorbent tube that fits inside a specially designed sampling chamber. VOCs in the soil enter the chamber by molecular diffusion and are collected by the sorbent. The sorbent is easily retrieved for laboratory analyses by thermally desorbing into a gas chromatograph/mass spectrometer (GC/MS), or qualitative concentrations can be determined directly in the field with specific-indicator detectors.
The diffusive samplers were evaluated in an exposure chamber under controlled conditions. Laboratory measurements of the sorbed mass of organic vapor were found to be in close agreement with theoretical values and indicate the passive sampling approach is viable for detecting relatively low concentrations of organic vapors in the vadose zone over a one-day sampling period, as well as providing relatively long-term monitoring periods up to 58 days. A field test found the sampling approach successful in identifying an area where the vadose zone was contaminated by leaking petroleum USTs.     

Automated Time Series Measurement of Microbial Concentrations in Groundwater-Derived Water Supplies

Fecal contamination by human and animal pathogens, including viruses, bacteria, and protozoa, is a potential human health hazard, especially with regards to drinking water. Pathogen occurrence in groundwater varies considerably in space and time, which can be difficult to characterize as sampling typically requires hundreds of liters of water to be passed through a filter. Here we describe the design and deployment of an automated sampler suited for hydrogeologically and chemically dynamic groundwater systems. Our design focused on a compact form to facilitate transport and quick deployment to municipal and domestic water supplies. We deployed a sampler to characterize water quality from a household well tapping a shallow fractured dolomite aquifer in northeast Wisconsin. The sampler was deployed from January to April 2017, and monitored temperature, nitrate, chloride, specific conductance, and fluorescent dissolved organic matter on a minute time step; water was directed to sequential microbial filters during three recharge periods that ranged from 5 to 20 days. Results from the automated sampler demonstrate the dynamic nature of the household water quality, especially with regard to microbial targets, which were shown to vary 1 to 2 orders of magnitude during a single sampling event. We believe assessments of pathogen occurrence and concentration, and related assessments of drinking well vulnerability, would be improved by the time-integrated characterization provided by this sampler.     

Horizontal and Vertical Well Comparison for In Situ Air Sparging

A laboratory study was conducted to determine the effectiveness ol vertical and horizontal well configurations for ground water remediation using in situ air sparging. A lexan lank was designed and constructed to allow both the visualization of air flow and quantitative measurement of the distribution of air flow. Two media, sand and glass beads. were tested with both Vertical and horizontal air sources. In each case, most of the air traveled through preferential channels as continuous flow rather than as discrete bubbles as reported in other studies. Liven though glass beads were selected to have the same grain-size distribution as the sand, air flow was quite different through the two media. Results show that glass beads are not a suitable material for modeling air flow through natural sediments. In this study, the horizontal well proved to be more effective than the vertical well by impacting more of the media with a uniform distribution of air throughout the media. The vertical well resulted in a nonuniform distribution of air flow with most of the air concentrated directly above the well.     

New equations for binary gas transport in porous media,Part 2: experimental validation

A previous study [Water Resour Res 39 (3) (2003) doi:10.1029/2002WR001338] questioned the validity of the traditional advection–dispersion equation for describing gas flow in porous media. In an original mathematical derivation presented in Part 1 [Adv Water Resour, this issue] we have demonstrated the theoretical existence of two novel physical phenomena which govern the macroscopic transport of gases in porous media. In this work we utilize laboratory experiments and numerical modeling in order to ascertain the importance of these novel theoretical terms. Numerical modeling results indicate that the newly derived sorptive velocity, arising from closure level coupling effects, does not contribute noticeably to the overall flux, under the conditions explored in this work. We demonstrate that the newly discovered “slip coupling” phenomenon in the mass conservation equation plays an important role in describing the physics of gas flow through porous solids for flow regimes of both environmental and industrial interest.     

Analysis of Cryptosporidium parvum oocyst transport in porous media

Cryptosporidium parvum is a protozoan parasite, transmitted through aqueous environments in the form of an oocyst. In this study, a transport model into which sorption, filtration and inactivation mechanisms are incorporated is applied to simulate laboratory column data, and the suitability of a kinetic model to describe the C. parvum oocyst transport and removal in porous media is compared with an equilibrium model. The kinetic model is applied to simulate previous column experimental data and successfully simulates the concentration peak; the late time tailing effect appeared in the breakthrough curves, indicating that the kinetic model is more suitable than the equilibrium one at simulating the fate and transport of the oocysts in porous media. Simulation illustrates that sorption causes retardation along with a tailing in the breakthrough curve. Additionally, filtration acts as a major mechanism of removing the oocysts from the aqueous phase, whereas the role of inactivation in reducing the viable oocyst concentration is minimal. Copyright © 2004 John Wiley & Sons, Ltd.     

Affordable Enteric Virus Detection Techniques Are Needed to Support Changing Paradigms in Water Quality Management

In light of water quality monitoring paradigms shifting to a more holistic approach, it is essential that environmental microbiologists embrace new methodological developments in clinical virology to create rapid, laboratory‐free methods for the identification of wastewater pollution. It is widely accepted that routine monitoring of fecal indicator bacteria (FIB) does not adequately reflect human health risks associated with fecal pollution, especially risks posed by viruses. Enteric viruses are typically more resistant to wastewater treatment and persist longer in the environment than FIB. Furthermore, enteric viruses often have extremely low infectious doses. Currently, the incorporation of sanitary surveys, short‐term monitoring of reference pathogens, exploratory quantitative microbial risk assessments, and predictive ecological models is being championed as the preferred approach to water management. In addition to improved virus concentration methods, simple, point‐of‐use tests for enteric viruses and/or improved viral indicators are needed to complement this emerging paradigm and ensure microbial safety worldwide.

     

A numerical method for simulating non-Newtonian fluid flow and displacement in porous media

Flow and displacement of non-Newtonian fluids in porous media occurs in many subsurface systems, related to underground natural resource recovery and storage projects, as well as environmental remediation schemes. A thorough understanding of non-Newtonian fluid flow through porous media is of fundamental importance in these engineering applications. Considerable progress has been made in our understanding of single-phase porous flow behavior of non-Newtonian fluids through many quantitative and experimental studies over the past few decades. However, very little research can be found in the literature regarding multi-phase non-Newtonian fluid flow or numerical modeling approaches for such analyses.For non-Newtonian fluid flow through porous media, the governing equations become nonlinear, even under single-phase flow conditions, because effective viscosity for the non-Newtonian fluid is a highly nonlinear function of the shear rate, or the pore velocity. The solution for such problems can in general only be obtained by numerical methods.We have developed a three-dimensional, fully implicit, integral finite difference simulator for single- and multi-phase flow of non-Newtonian fluids in porous/fractured media. The methodology, architecture and numerical scheme of the model are based on a general multi-phase, multi-component fluid and heat flow simulator — TOUGH2. Several rheological models for power-law and Bingham non-Newtonian fluids have been incorporated into the model. In addition, the model predictions on single- and multi-phase flow of the power-law and Bingham fluids have been verified against the analytical solutions available for these problems, and in all the cases the numerical simulations are in good agreement with the analytical solutions. In this presentation, we will discuss the numerical scheme used in the treatment of non-Newtonian properties, and several benchmark problems for model verification.In an effort to demonstrate the three-dimensional modeling capability of the model, a three-dimensional, two-phase flow example is also presented to examine the model results using laboratory and simulation results existing for the three-dimensional problem with Newtonian fluid flow.     

A New Method for Collecting Core Samples Without a Drilling Rig

A new piston sampler allows the collection of high-quality core samples from sand, silt or clay, up to depths of 18 meters. The sampler is operated by a one- or two-person crew without a drilling rig. The sampler and ancillary equipment fit easily into a half-ton truck, making this a highly portable sampling system. Other advantages include minimal mechanical disturbance and precisely known sample depth. Casing is not required to maintain an open corehole below the water table and drilling fluid is not used in the corehole, so the solids and pore water of the sample should not be contaminated by foreign fluids. High-quality samples for physical, geochemical, and microbiological characterization of the subsurface are easily obtained with this new device.     

Potential microbial bioinvasions via ships' ballast water, sediment, and biofilm

A prominent vector of aquatic invasive species to coastal regions is the discharge of water, sediments, and biofilm from ships' ballast-water tanks. During eight years of studying ships arriving to the lower Chesapeake Bay, we developed an understanding of the mechanisms by which invasive microorganisms might arrive to the region via ships. Within a given ship, habitats included ballast water, unpumpable water and sediment (collectively known as residuals), and biofilms formed on internal surfaces of ballast-water tanks. We sampled 69 vessels arriving from foreign and domestic ports, largely from Western Europe, the Mediterranean region, and the US East and Gulf coasts. All habitats contained bacteria and viruses. By extrapolating the measured concentration of a microbial metric to the estimated volume of ballast water, biofilm, or residual sediment and water within an average vessel, we calculated the potential total number of microorganisms contained by each habitat, thus creating a hierarchy of risk of delivery. The estimated concentration of microorganisms was greatest in ballast water>sediment and water residuals>biofilms. From these results, it is clear microorganisms may be transported within ships in a variety of ways. Using temperature tolerance as a measure of survivability and the temperature difference between ballast-water samples and the water into which the ballast water was discharged, we estimated 56% of microorganisms could survive in the lower Bay. Extrapolated delivery and survival of microorganisms to the Port of Hampton Roads in lower Chesapeake Bay shows on the order of 10(20) microorganisms (6.8 x 10(19) viruses and 3.9 x 10(18) bacteria cells) are discharged annually to the region.     

Paraxial approximation for poroelastic media

Amongst different existing techniques developed for absorbing boundaries in transient dynamic analysis, the paraxial approximation represents an elegant framework. This approach is extended to the case of saturated porous media, which is of vital interest in many earthquake engineering problems. With respect to the frequency content of the dynamic process, several formulations exist for modelling the two-phase behaviou of soil or rock materials. The existence of a shear wave and two dilatational waves, which are standard features of porous media, is verified for the adopted formulation. The paraxial approximation is presented in the case of the u – p Biot two-phase dynamic formulation, suitable for seismic analyses and implemented by using a finite element approach. The efficiency of these boundaries is further verified through same numerical examples.     

Bioestimation: A new method for the control of water self-purification process and its comparison with bioindication

A new line in the studies of water bodies is proposed: the assessment and correction of the process of biotic purification of water (biological treatment and self-purification). The proposed approach is based on a principally new hydrobiological method of monitoring and control of water quality formation process—bioestimation. The principal novelty of bioestimation is due to the fact that it controls not the quality of the aquatic medium, but the object that has not been controlled before—water purification process and organic matter transformations in the process of vital activity of saprotrophic bacteria. Three critical groups of factors were found to govern the activity of these bacteria: the dynamic characteristics of the aquatic environment; the load on destructors in terms of organic matter; and the impact of substances, which are atypical of natural water and most often are discharged in it with industrial wastes. A group of indicator microorganisms—bioestimators—is chosen for each group of factors. The population size of such estimators can be used to identify and next eliminate the disturbing factor. The bioestimators are not species but ecological groups of microorganisms, commonly inhabiting any waters, either salt or fresh. Bioestimation also helps to identify disturbances in water purification process even in the cases where analyses of aquatic environment quality do not signal alarm. The proposed method is described and its major distinctions from the well-known hydrobiological method (bioindication in its original, saprobiological meaning) are demonstrated.     

Survival rate of pathogenic bacteria and viruses in groundwater

The results of an analytical review of publications on the process of inactivation of pathogenic microorganisms in groundwater are considered. The process of inactivation is described by a mathematical model based on an exponential dependence. The values of the inactivation rate factor for a number of pathogenic microorganisms are given. Recommendations are given regarding formulas for determining the dependence of the inactivation rate factor of bacteria and viruses on water temperature.Translated from Vodnye Resursy, Vol. 32, No. 2, 2005, pp. 232–237.Original Russian Text Copyright © 2005 by Nevecherya, Shestakov, Mazaev, Shlepnina.