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Category: Environmental Microbiology
Manual of Environmental Microbiology is now available on Wiley.comMembers, use the code ASM20 at check out to receive your 20% discount.
The single most comprehensive resource for environmental microbiology
Environmental microbiology, the study of the roles that microbes play in all planetary environments, is one of the most important areas of scientific research. The Manual of Environmental Microbiology, Fourth Edition, provides comprehensive coverage of this critical and growing field.
Thoroughly updated and revised, the Manual is the definitive reference for information on microbes in air, water, and soil and their impact on human health and welfare. Written in accessible, clear prose, the manual covers four broad areas: general methodologies, environmental public health microbiology, microbial ecology, and biodegradation and biotransformation. This wealth of information is divided into 18 sections each containing chapters written by acknowledged topical experts from the international community.
Specifically, this new edition of the Manual
The Manual of Environmental Microbiology is an essential reference for environmental microbiologists, microbial ecologists, and environmental engineers, as well as those interested in human diseases, water and wastewater treatment, and biotechnology.
Hardcover, 1088 pages, full-color illustrations, index.
Environmental microbiology might be considered by some to be an ill-defined subject: Where does the environment begin, and where does it end? From Marcus Terentius Varro's observations regarding unseen “minute creatures” more than two millennia ago to Antonie van Leeuwenhoek's first glimpse of the “animalcula” beneath his lens, there is no place on Earth—from thermophilic, acidic springs to the air we breathe to the deepest subsurface locations we have yet been able to reach—where people have looked and not found microorganisms of some type. The domain of what may be considered environmental microbiology thus continues to expand beyond the textbook definition of “the study of microorganisms existing in natural and artificial environments.” At the same time, our knowledge of microorganisms is increasing at an ever-more rapid rate as the result of incredible improvements in analytical methodology, especially at the molecular level. When compiling a manual of this nature, therefore, how does one determine what to include and what to exclude? In the end, the editors decided to showcase as much information as possible on some of the most important areas of environmental microbiology, to provide a clear sense of the possibilities presented by the existence of microorganisms in various environments. Further and more detailed information can be found in the wealth of expertly chosen references within each chapter.
Enzymatic substrates are widely used in microbiology to study metabolic pathways, to monitor metabolism and to detect, enumerate and identify microorganisms. In general, fluorogenic and chromogenic enzyme substrates have proved to be a powerful tool, utilizing specific enzymatic activities of certain microorganisms. By incorporation of these substrates into primary selective media, enumeration and detection can be performed directly on the isolation plate. Methods and media based on the application of these substrates enable specific and rapid detection of a variety of microorganisms. Examples of target pathogens include Escherichia coli, Staphylococcus aureus, Listeria monocytogenes, Salmonella spp. and Vibrio spp. The inclusion of multiple chromogenic substrates into culture media facilitates the differentiation of polymicrobial cultures.
This paper describes some developments in chromogenic and fluorogenic culture media in microbiological diagnostic in particular in food- and water microbiology.
Anaerobes are key players in global cycles of elements and nutrition in natural and anthropologic ecosystems and are also causative agents of human and veterinary diseases. Numerous studies have sought to develop culturing techniques for anaerobes to enable the elucidation of their basic physiology, pathogenic mechanisms, and ecological functions. This chapter will describe a brief history of the development of anaerobic culturing techniques from the historical Hungate technique to techniques and apparatuses commonly used in modern laboratories. In addition, recent progress in anaerobic culturing techniques (e.g., single-cell manipulation and isolation, the six-well plating method, the co-culture method, bioreactor-based enrichment, and in situ/in vivo cultivation) will be described, with several examples of the application of these techniques for the isolation of anaerobes from natural and artificial ecosystems.
One of the most important observations in microbiology is that the vast majority of microorganisms from most environments on the planet do not grow on artificial media. This is a significant impediment for both academic and applied microbiology, necessitating innovations in cultivation technologies. Several recently advanced methodologies offer a promise to close the gap between the high richness of environmental species and low number of their cultivable representatives. This chapter will describe the state of the art in microbial cultivation methods, their principles and application. These methods are categorized into two types: “in situ cultivation” whereby microbes are cultivated in situ, and “high throughput cultivation”, mostly in vitro. In the first group, the following methods are described in detail, 1) Diffusion chamber, 2) i-chip, 3) Microbial trap, and 4) Hollow Fiber Membrane Chamber. In the second group, we focus on Gel miro-droplets (GMDs) based cultivation and micro-fabrication based technologies. The chapter will also discuss their relative merits and respective biases.
The advent of new sophisticated spectroscopic and tomographic techniques arise interest in the study of environmental conditions within microbial habitats on a submicroscopic level. These methods are based on electromagnetic radiation and result in either elemental characterization or structure visualization. Both aspects are relevant for the investigation of microbe-habitat interactions why a correlative detection of microbial cells would be useful. Fluorescence in situ hybridization is an ideal technique to identify and localize microorganisms but requires a cell-detection via fluorescence microscopy which has a limited optical and elemental resolution. Therefore the utilization of nanogold as marker for in situ hybridization approaches is of great potential. Gold labels can be visualized with one of the aforementioned techniques on resolutions beyond light microscopy and allow the identification and localization of single microbial cells in their habitat in situ. The basic principal and potential of this method is described in this chapter giving an overview on the development steps of gold-targeted cell detection as well. Selected results exemplarily show applications in environmental microbiology both via fluorescence microscopy and electron microscopy including elemental mapping.
The assessment of prokaryotic metabolic function in situ is challenged by the complexity of natural microbial communities, by the lack of information about the genetics of most environmental microbes, and the fact most prokaryotes are yet uncultured. Techniques that measure activity at the single cell level and simultaneously allow for taxonomic identification, despite being labor intensive, provide a window into a world once known only as the microbial black box. In this chapter, three of such approaches that combine microautoradiography with FISH are explored, with a focus on Substrate-Tracking Auto-Radiography Fluorescence In Situ Hybridization (STARFISH). The technical aspects of the protocols were summarized for a better understanding of the applications, their strengths and limitations. These techniques can quantitatively interrogate whether organisms of interest can metabolize particular substrates without the need of cultivation. Examples of various applications are presented. Advancement in high-throughput DNA sequencing technologies has quickly generated large amount of microbial genomic information. Techniques like STARFISH can be applied to validate in silico genetic predictions of microbial metabolic function.
Immunoassay methods for environmental pathogen and toxin detection are well established with formats including lateral flow devices, standard ELISAs, microarray platforms, and biosensor devices. In general, immunoassays provide rapid assay times relative to other conventional methods such as colony counting and PCR approaches. The development of recombinant antibody technologies to produce antibodies with enhanced binding affinities will lead to immunoassays with better sensitivity, specificity and reproducibility. The development of alternative affinity reagents, such as aptamers, engineered proteins and peptides, will provide a greater repertoire of affinity reagents to develop novel immunoassays. Recently, multiplexed assays for the detection of foodborne and waterborne pathogens and toxins have been developed using planar and bead-based microarray approaches. Because environmental pathogens are mostly present in very low numbers, a highly sensitive detection method is necessary. In addition, real-time detection is requisite. Biosensors have the potential to address both of these requirements. Indeed, biosensors are the fastest growing technology for pathogen detection. Integration of biosensors into environmental and food safety monitoring systems is likely to increase in the coming years potentially leading to the development of novel methods that are capable of providing the necessary sensitivity and assay speed to replace the current standards.
The field of molecular biology was revolutionized with the development of the polymerase chain reaction (PCR). This chapter defines PCR, reverse transcription PCR (RT-PCR), real-time PCR, digital PCR and isothermal amplification. Within each subject a brief overview of the process is given along with the required reagents or components and highlighted applications. RT-PCR allows detection and characterization of RNA with options for one-step and two-step RT-PCR procedures with different advantages and disadvantages. Real-time PCR is typically coupled with a fluorescent-based reporter system such as an intercalating dye or a sequence specific probe. Unlike conventional PCR, real-time PCR can be used to quantity the amount of nucleic acid in a given sample where absolute quantification requires the use of known standards to calculate the concentration for a sample, while relative quantification uses a "calibrant" to determine the fold change in a sample. Real-time PCR can be used for direct measurement of DNA targets or it can be coupled with RT-PCR to quantify RNA targets. Digital PCR has only recently become widely available and provides a means to quantify targets in a sample based on direct estimation rather than by making estimates from standard curves. Many isothermal amplification methods have been developed to amplify nucleic acid targets without the need for thermalcycler technologies.
Before environmental microarrays can fulfill their diagnostic promise, it is necessary to define an environmental diagnostic. In this chapter, I propose a definition for an environmental diagnostic (EVD) that is consistent with the FDA's definition and meaning of an in vitro diagnostic (IVD), where the emphasis is on the use of the diagnostic to make a decision and take action relative to the effect of a particular condition on human health. In this context, the underlying microarray technologies, methods of manufacture, and intended use can significantly impact the quality and reliability of an environmental diagnosis. Current and future technology should therefore focus on reducing the variability of environmental microarrays during manufacture and use, so that repeatable results can be obtained independent of the user. Analytical process simplification, perhaps through amplification microarrays described in this chapter, may help achieve the objective of repeatability for independent users, but technology per se will not substitute for a clearly defined intended use, effective product design, and objective verification and validation data. At present, the absence of regulatory oversight for EVDs is both a blessing and a curse. It is therefore expected that future technical solutions for realizing microarray-based EVDs will only come with a consensus biological and regulatory opinion regarding the meaning of environmental nucleic acid signatures relative to the real or perceived risks associated with each intended use.
Many of the principles underlying rapid detection methods are derived from methods for environmental microbiology, but there is a dearth of literature describing and evaluating field-based detection systems. Thus, the aims of this chapter are to: 1) summarize the different kinds of commercially available sampling kits and field-based biological detectors; 2) highlight some of the continued challenges of sample preparation to stimulate new research towards minimizing the impact of inhibitors on PCR-based detection systems; 3) describe our general rationale and statistically-based approach for instrument evaluation; 4) provide statistical and spatial guidelines for developing valid sampling plans; and 5) summarize some current needs and emerging technologies. This information is presented both to highlight the state of the field, and to also highlight major questions that students may wish to consider investigating further. Where possible we will cite studies that have been conducted and published either in traditional peer-reviewed or other literature (e.g., AOAC International Methods).
In this introduction, we briefly survey developments in next-generation sequencing that have been applied to environmental microbiology, consider both major advances and areas where progress has been slow, and highlight chapters in this and other sections of the MEM4 relevant to nucleic acid-based molecular analyses of microbial communities. Experts on various aspects of next-generation sequencing have contributed to this section, including chapters addressing the analysis of microbial communities through the study of (a) ribosomal RNA gene amplicons (Ionescu); (b) shotgun metagenomic sequence data (Lal and Sangwan); and (c) shotgun metatranscriptomic sequence data (Sarode et al.). In addition, this section includes a chapter reviewing functional metagenomics (Marchesi and Morris) and sequencing platforms for environmental microbiologists (Green).
The fields of microbial ecology and environmental microbiology have been revolutionized by the development of next-generation sequencing technologies. In this chapter we specifically address the use of PCR amplification coupled with high-throughput sequencing for the analysis of microbial community composition and structure, and for subsequent visualization and statistical analyses of this community data.
Using metagenomic approaches to interrogate microbial communities is commonly based on sequencing the total DNA extracted from biomass. However, while this approach predominates in the literature, it does not provide an insight into the novel functions within a system and does not provide physical DNA for manipulation. In order to obtain novel functions from a microbial community, functional metagenomics was developed. This approach, which preceded the advent of large-scale sequence based metagenomics coupled with next generation sequencing, revolves around hosting and expressing heterologous DNA in a suitable surrogate host. Coupled with phenotypic screens functional metagenomics provides an alternative approach to obtaining functionally active genes from a microbial system, without the need to culture any organisms.
Microbial metabolic processes, dynamics and interactions shape the biogeochemistry of the planet. An estimated > 1030 prokaryotic cells and ∼1030 phages inherited in their genomes, inhabit Earth and contain an estimated 350–550 Petagrams (1 Pg = 1015 g) of carbon, 85–130 Pg of nitrogen and 9–14 Pg of phosphorus. These nutrient data have come from nucleic acid based cultivation-independent surveys (CIS) of microbial communities sampled during the past two decades. Often, these communities have been surveyed using PCR-based sequencing approaches targeting organisms at the domain level. The term ‘metagenomics’ can refer to such broad amplicon surveys, but is more commonly used for shotgun sequencing approaches that do not use PCR to select either for specific genes or for specific organisms. Even after a decade of concerted effort of sequence and metadata generation, continuous improvement in sequencing technologies and computational frameworks, our understanding of the microbial dynamics (taxonomical, functional and evolutionary) is still limited in many respects. Specifically, our understanding of the functional potential of the key (eco-genetically adapted) and/or dominating taxa and their interdependencies with the ‘rare biosphere’ (i.e. lesser abundant but genetically diverge species) in complex microbial ecosystems is still largely unknown. In this review, the existing concepts, methodologies and approaches for metagenomic data analysis are outlined in order to highlight the potential of community genomics (metagenomics) to decipher the metabolic potential of microbial assemblages. Significance of closely coupled parameters like ‘individual read versus assembly based functional analysis’ and ‘cross validation (replicates) versus deep coverage’ is also explored.
Analysis of the collective RNA pool from a microbial community - the metatranscriptome - yields valuable information on microbial gene expression patterns and biogeochemical processes in natural environments. Molecular and analytical tools for analyzing metatranscriptomes using high-throughput sequencing have advanced rapidly in recent years and continue to evolve and expand. The technique is increasingly available to individual research projects, even those with a modest budget or lacking an extensive bioinformatics toolkit. A core set of metatranscriptomic practices can now be identified, with key steps including RNA extraction, messenger RNA (mRNA) enrichment, synthesis of complementary DNA (cDNA), shotgun sequencing of cDNA, and bioinformatic analysis of sequence data. This chapter explores key questions that researchers should consider before beginning a metatranscriptomic study and then describes in detail the major steps of a sequencing-based metatranscriptomic analysis, from RNA isolation to functional and taxonomic analysis of sequence data. The questions and methods described here provide an introductory framework for environmental microbiologists interested in using metatranscriptome sequencing to explore microbial community gene expression.
This introduction provides an overview of the QC challenges for environmental microbiological analyses, the role that QC plays in the different settings where analytical methods are used, and the advances that new materials and new approaches have made in increased data reliability and more effective method performance assessments.
A common assumption for conducting microbiological testing is that the laboratory environment and its equipment are properly operated, cleaned, calibrated, and maintained, that the laboratory is a safe working environment, and that the laboratory has a quality assurance plan that it maintains and adheres to. In order to assure that these requirements are met, a QA program needs to be in place.A goal of the QA program is to give management the opportunity to provide input and take responsibility in the planning, implementation, and assessment stages of the environmental microbiology project. The QA Plan should have sections devoted to laboratory facilities, personnel, and equipment; sampling procedures and handling; and deviations, record keeping and audits.
Bacteriological analyses in environmental biology laboratories differ from those performed in their clinical counterparts in that quantitative results are commonly required.
This is a guidance for the development of an environmental virology laboratory quality assurance document with suggested quality control measures detailed.
The following subsections of this chapter presents QA procedures, including practical advice, for laboratories performing USEPA Method 1623 Cryptosporidium and Giardia protozoan analysis. As outlined in the previous QA subsections, a comprehensive QA program is a necessity for an environmental laboratory to accurately and confidently report both presence/absence and quantifiable results. A QA program outlines the components of a laboratory testing scheme that should be monitored whether it be daily, weekly, monthly and yearly, while the QC checks are put into place to ensure the discrete testing method components used throughout the testing protocol contribute minimal amount of error to the results. This outlined section is designed to give an overview of general laboratory QC practices for microscopic detection of microbial organisms.
Environmental microbiologists collect data, lots of data. However these data are not always the appropriate data to answer the questions the researchers are interested in. In this chapter we discuss what needs to be done to ensure that what you think you are discovering is in fact what the data are saying. We encourage a large amount of statistical thinking prior to the first data point being collected or before the first sample is obtained. Statistical thinking is not generally taught in introductory statistics classes. The nuts and bolts of what will be discussed in the chapter do find their way into statistic classes however not necessarily in a way that prepares scientists for the task of doing science. Here we discuss concepts such as defining the problem, experimental design, the weight of evidence, statistical power, and sources of variation, scope of inference, measurement scale, scale transformation and other topics. We show that environmental microbiology done without careful thinking before, during and after data collection rarely can answer any important question - regardless of how big the spreadsheet is. After reviewing countless papers for over three decades it is our experience that many studies in environmental microbiology are statistically weak and more importantly statistically flawed and that one need read no farther than the methods to decide whether to continue to forward.
When designing a study to develop/optimize a method, evaluate method performance, validate a method, or test a hypothesis, there are many factors to consider, for example, matrix/matrices (e.g., water, soil), spiking, organism strain, number of replicates, and QC analyses.
This chapter describes options and considerations for choosing water sampling and processing techniques to enable testing for microbes of public health relevance, including pathogens and microbial indicators of fecal contamination. The framework for the discussion draws relationships between investigation goals, conditions and the selection of sampling techniques. Considerations include identifying target microbes, downstream analytical methods, anticipated water quality, acceptable method detection limits, and application of discrete versus composite sampling. Small-volume and large-volume sampling techniques are discussed for application to a wide range of water types, including drinking water, ground water, surface water, recreational water, and marine water. The chapter describes and compares alternative techniques for sample collection and processing for viruses, bacteria, and parasites, as well as identifying techniques that to capture of multiple microbe types. Field sampling techniques are discussed, as well as laboratory-based sample processing techniques to concentrate water samples for analysis. Issues related to sample quality are addressed as they relate to processing inefficiencies and potential for inhibition of analytical procedures.
Whether investigating a disease outbreak, performing environmental monitoring to meet industry standards or guidelines (GMP, USP 797, CODEX Alimentarius, etc.), or ensuring a clean spacecraft before launch, a clear understanding of the intricacies of surface sampling is essential in order to have confidence in the resulting data. Microbial surface sampling appears to be a simple task, but success depends upon knowledge of the molecular target or organism(s), choosing the right sampling strategy, selecting best tool (contact plates, swabs, sponges, wipes, etc.), the optimal storage conditions, and the best elution technique for recovery of the target or organism from a sampling device when one is used. Both current and historical approaches to surface sampling, as well as industry standards and the latest research on microbial surface sampling are discussed.
Environmental microbiology is wrought with difficult to sample environments, not least of which is soil. Soil is a dynamic environment, ripe with changing viral, prokaryotic, and eukaryotic populations, all awaiting assay. Soil sampling, depending on the assay, experiment, or project can vary from simple probes, deep cores, to soil slurry collections. Atop of this, soils must be collected from a statistically sound perspective as well as considerations made for physiological, cultivation, or molecular analysis. This chapter will focus on the use of soil sampling equipment, schemes, assays, and case studies aimed at introducing the reader to the various caveats and potential pitfalls associated with soil sampling. No one chapter can attempt to cover all potential characteristics of a specific soil sampling situation; therefore, this chapter will focus on general trends in microbial soil sampling.
Detection of microorganisms and viruses in wastewater and biosolids provides important information about the functioning of the wastewater treatment process and can provide insight on disease circulation in the population serviced by the treatment. This chapter discusses the wastewater treatment process and provides a description of how sampling should be performed at the different stages. General sampling procedures and considerations are described, including the use of controls and appropriate sample handling conditions. The chapter provides an overview of the required regulatory sampling as well as provides insight on other rationales for sampling of wastewater and biosolids. Sampling for regulatory microorganisms, including indicator organisms (fecal coliforms) and pathogens (Salmonella spp., enteric viruses, and helminth ova) can inform us about the safety of wastewater discharged or biosolids used in land applications. Discussion of standardized methods for the sampling of bacteria, viruses, and eukaryotic microbes are summarized here. This chapter does not focus on the methods used for isolation and detection of microbiological targets, rather concentration and purification techniques are described for a variety of organisms, including bacteria, viruses, protozoan and helminths.
Fecal contamination of freshwaters and drinking waters may result in serious risks to public health that include gastrointestinal and respiratory illnesses, eye and skin infections, many caused by enteric pathogens. The microbiological quality of freshwaters and drinking waters is usually monitored by the detection of traditional indicators that include total and thermotolerant coliforms, Escherichia coli, and Enterococcus spp. Culture methods are usually employed to detect bacterial indicators, but emerging techniques that include the detection of bacteriophages, as well as PCR-based methods amplifying bacterial 16S or 23S rRNA genes also have been developed. Molecular methods targeting indicator bacteria may reduce the time needed to take action to reduce the impact that fecal contamination of freshwaters and drinking waters represent to public health. In freshwaters used for recreation and consumption, identifying the source of the fecal contamination is important in order to reduce or eliminate its impact to pubic health. Microbial Source Tracking (MST) methods have been developed to identify the possible source (e.g. animal vs human) of the fecal contamination and include amplification of nucleic acids of traditional indicator bacteria. While bacterial indicators have successfully been used to protect public health for the last 100 years, and variations on the theme will be in use for decades to come, the target microorganisms would probably need to be revisited, because of the little information we have about their ecology.
Cyanobacterial harmful algal blooms (CyanoHABs) are an increasingly prevalent phenomenon in lakes, rivers, reservoirs, estuaries and coastal regions around the globe. These organisms produce a variety of bioactive secondary metabolites that are of public health concern. Because there is no broadly accepted protocol for monitoring and managing these organisms, the focus of this chapter is to outline all necessary information to develop a CyanoHAB monitoring strategy. Topics covered include: 1) sampling methodology and frequency; 2) sample processing and storage; 3) microscopy identification and enumeration; 4) toxin analysis by ELISA, HPLC and LC/MS; 5) DNA analysis by PCR/QPCR; 6) interpretation of the data and establishment of a monitoring plan.
Wastewater treatment is one of the most important of societal commitments to the health of human populations. This summary provides an overview of analyzing how well the processes meet the goal of providing discharges that do not degrade the environment nor put the health of populations dwelling in or affected by that environment. Basic processes of waste treatment are illustrated and both aqueous and solid discharges are addressed with the most important treatment processes and the parameters that are sampled to assess their efficacy presented. In common with most biological systems studied, recent advances in molecular, whole genome or metagenome techniques and procedures have allowed great advances in our understanding of how these microbial systems function. Bioassays of enormously complex means of biological treatment are shown in context. New methods of understanding whole-system microbiomes are noted with seminal publications. Older bioassay techniques are explained and the empirical underpinnings of many processes that are only now understood more fully are reviewed.
Public health surveillance and epidemiologic research can inform environmental microbiology research and practice. Likewise, advances in environmental microbiology improve our understanding of waterborne disease transmission and support targeted public health actions. Waterborne disease outbreak investigations provide useful information about clusters of uncommon but clinically significant infections caused by recognized pathogens. Furthermore, factors that resulted in outbreaks are often characterized and prevention strategies can be developed. Cohort studies of acute waterborne illness provide information about common but mild sporadic cases of illness. In some settings (but not others) such studies have identified microbial measures of water quality that predict illness occurrence. However, pathogens and environmental factors that caused sporadic cases are generally not identified. The majority of recognized waterborne disease outbreaks in the United States occur in the context of recreation in swimming pools, water parks, and other treated waters, with Cryptosporidium spp. the agent responsible for the vast majority of cases. Recognized outbreaks at lakes and rivers are caused by a wider array of infectious agents. Outbreaks linked to drinking water tend to be caused by deficiencies in water treatment and distribution, with bacteria as the causative agents of most outbreaks. Emerging concerns that have been the focus of recent research include respiratory disease attributable to biofilm-associated microbes in drinking water systems, illness caused by toxins elaborated by algal blooms, and associations between precipitation and waterborne disease.
Enteric viruses are a leading cause of gastroenteritis and they constitute a diverse group. The viruses commonly implicated in gastroenteritis (cases or outbreaks) are classified into the families Picornaviridae (polioviruses, enteroviruses, coxsakieviruses, and echoviruses), Adenoviridae (adenovirus 40 and 41), Caliciviridae (noroviruses, Sapporoviruses,), and Reoviridae (reoviruses). Although enteric virus infections are mainly associated with diarrhea and self-limiting gastroenteritis in healthy humans, they have also been linked to aseptic meningitis, encephalitis, myocarditis and insulin-dependent diabetes.
Currently, about 140 waterborne viruses are known to infect humans. The waterborne viruses not only show wide diversity in the illness (including diarrhea, fever, hepatitis, paralysis, meningitis, respiratory and heart diseases, they also show broad diversity in their size, shape, infection process and replication mechanisms. Most of waterborne enteric viruses have icosahedral capsid; however, the structural feature on the surface of capsids varies among different virus groups. The rotavirus capsid is composed of three concentric protein layers and the outermost layer comprises the proteins VP4 and VP7. The PV4 forms spike like structures which are responsible for virus attachment to host cell. Adenovirus has an icosahedral capsid composed of hexon the major capsid protein. In addition, capsid has penton with elongated fibers projecting out of each penton. The distal ends of these fibers have a globular "knob" which functions as the major attachment site for host cell receptors. In general, the members of enteroviruses and caliciviruses / norovirus have capsid with less pronounced surface features; but members of these groups have significantly different annotation of their capsid.
Humans are known to be the host to approximately 1500 infectious agents, out of which 66 are protozoa and 287 are helminths. Therefore, from a global perspective helminths and protozoan parasites account for approximately one fourth of the total infectious diseases of humans. A similar trend has been observed in waterborne infectious diseases, among which a significant part is caused by enteric parasites.
Cryptosporidium and Giardia are the leading cause of waterborne outbreaks of gastroenteritis across the globe, and as such, will be discussed in length in this chapter. These parasites are particularly suited for waterborne transmission as the environmentally resistant cysts and oocysts, respectively are shed in large numbers in feces (108-109 oocysts/gram), have a low infectious dose, and are resistant to disinfection practices.
Naegleria fowleri is a pathogenic free-living amoeba found in the environment in both water and soil. There have been over 40 species of Naegleria described to date, but only N. fowleri is pathogenic to humans. N. fowleri was first identified as a human pathogen in 1965 in Australia. The first case in the United States was reported in 1966 and was described as primary meningoencephalitis. Prior to this documented case, free-living amoebae were not considered to be pathogenic. Pathogenic Naegleria fowleri is not easily differentiated from other Naegleria species due to similarities including common morphology when observed microscopically and indistinguishable behavior in cell culture.
One of the Millennium Development Goals is to halve, between 1990 and 2015, the proportion of the population that does not have sustainable access to safe drinking water, which would increase the coverage from 76% to 88% ( 1 ). This goal was met in 2010, with 116 countries meeting the target ( 2 ). Since 1990, more than two billion people have gained access to improved drinking water sources, with 89% of the population covered. There were only three countries (Democratic Republic of the Congo, Mozambique, and Papua New Guinea) where less than half the population had access to an improved drinking water source, and 35 countries (26 of which are in sub-Saharan Africa) in which only 50–75% of the population has access to an improved source of drinking water. Although this represents a substantial improvement, more than 700 million people still lack access to improved sources of drinking water, almost half of which are in sub-Saharan Africa ( 2 ). It is predicted that there will still be more than half a billion people without access to an improved drinking water supply by 2015.
This chapter introduces the study of airborne microorganisms and their by-products, discusses indoor and anthropogenic outdoor sources of airborne microorganisms that affect human health and the environment, reviews the association of bioaerosols and indoor environmental quality, presents background information on airborne microorganisms as potential bioterrorism agents and describes categories of microbial agents common within bioaerosols. Subsequent chapters in this volume are focused on specific topics concerning airborne microorganisms including sampling methods, analysis, fate and transport, fungi and mycotoxins, bacteria and endotoxins, Legionellae, viruses and agricultural pathogens. Interest in the populations of airborne microorganisms in agricultural and industrial settings, health care facilities, residences, offices, and classroom environments has increased in recent years. The threat of purposeful release of microorganisms as bioterrorism agents has prompted renewed interest in aerobiology, and research activity in this area of environmental microbiology has rapidly expanded.
Microbiologists have confronted the challenges of sampling and analysis of airborne microorganisms since the early 20th century. Today, the concentration and composition of airborne microorganisms are of interest in various areas such as agricultural and industrial settings, hospitals, home and office environments, and military installations. In all of these applications, the term "bioaerosol" is used to refer to airborne biological particles, such as bacterial cells, fungal spores, viruses, and pollen grains, and to their fragments and by-products. A wide variety of bioaerosol sampling and analysis methods have been used, and new methods are being developed. However, no single sampling method is suitable for the collection and analysis of all types of bioaerosols and no standardized protocols are currently available. Therefore, data from different studies are often difficult to compare because of differences in sampler designs, collection times, airflow rates, collection media and analysis methods. In addition, human exposure limits have not been established for bioaerosols because of the lack of exposure, dose, and response data.
The purpose of this chapter is to present various bioaerosol sampling and analysis methods that would allow facilitating an intelligent selection of instrumentation and techniques. The principles of bioaerosol sampling are presented, followed by a review of traditional and emerging sampling methods and techniques, including the results of performance evaluations of the various sampler types. Equipment calibration and air sampling considerations such as collection times and the number of samples are discussed. The advantages and disadvantages of surface sampling methods are also described.
Respiratory exposure to certain pathogenic or toxigenic microorganisms and/or elevated concentrations of environmental organisms could result in health effects, such as allergic reactions, irritant responses, toxicosis, and respiratory illness. Determination of the concentration and composition of bioaerosols in indoor environments is necessary for assessment of contamination levels and to estimate potential exposure of occupants. The need for accurate measurement of bioaerosols has received increased attention in recent years owing to concerns with mold contamination in indoor environments and the threat of bioterrorism. Sample analysis methods include culture, microscopic, biochemical, immunological, or molecular biological assays. Traditionally, airborne microorganisms have been analyzed by culturable and microscopic total count determinations. However, limitations to both of these methods have led to the development of techniques that can increase the sensitivity and accuracy of bioaerosol monitoring. The selection of an analysis method is a critical component of a bioaerosol sampling plan, and it should be designated before air sampling is conducted. Factors which influence the choice of an analytical method include the cost and length of time required for analysis, the sensitivity and specificity of the analysis method, the sampling methods to be utilized, and the expected characteristics of the bioaerosol of interest. The purpose of this chapter is to present an overview of available methods for the analysis of bioaerosols. In addition, the potential use of enhanced monitoring of bioaerosols with polymerase chain reaction, biochemical, and immunological assays is discussed.
The study of bioaerosol fate and transport has recently gained more attention due to the recognized importance of both indoor and outdoor events that have been shown to impact applicable populations. In this Chapter current thinking and research are presented in the topic areas of hydrodynamic and kinetic forces affecting fate and transport; environmental condition effects on viability; bioaerosol transport and viability modeling; and microorganism inactivation and repair mechanisms.
This chapter reviews literature on airborne fungi, with emphasis on indoor fungal growth, infestation and contamination, factors affecting airborne fungal spore populations, indoor sources of fungi, and fungal spore discharge mechanisms. It also covers the health effects of fungi and their metabolites (mycotoxins and fungal volatile organic compounds). The diseases associated with indoor fungal exposure, such as infections, allergy, respiratory diseases, hypersensitivity and toxic pneumonitis, mycotoxicoses and mucous membrane/olfactory irritations are discussed.
Airborne bacteria and their associated immunomodulatory ligands, best exemplified by endotoxin, are present in bioactive concentrations in many occupational and some non-occupational environments. Especially high concentrations are found in agricultural settings and in industrial operations handling or processing wet organic matter. Human exposure to these agents induces a variety of respiratory conditions including asthma, asthma-like syndrome, hypersensitivity pneumonitis, organic dust toxic syndrome and pulmonary infections. Endotoxin is an integral component of the bacterial cell membrane and is well-recognized as a potent inducer of lung inflammation. However, low-dose exposure has also been shown to reduce the potential for development of allergic rhinitis and eosinophilic asthma. This chapter presents a critical examination of current knowledge of concentrations and exposures to airborne bacteria and endotoxin in over twenty-five environments. It describes the resulting burden of disease ascertained through epidemiologic studies conducted worldwide. Included in the chapter are detailed methods for the assessment of exposures to endotoxin. New science relating to occupational exposures to the Archaea are also presented along with molecular methods for their identification and quantitation.
Particles containing infectious human or animal viruses can contaminate air indoors or outdoors. The survival of such airborne viruses is influence by a variety of physical and chemical factors, important among these being temperature and relative humidity. Air currents outdoors can carry surviving viruses over several kilometers and such windborne spread is believed have resulted in outbreaks of animal diseases. Movements of air indoors can also transport viruses within houses and buildings. Indoor air can be decontaminated by filtering out viruses or by inactivating them with chemicals or physical agents such as ultraviolet inrradiation. Recent years have seen a revival of interest in airborne viruses in delivering vaccines, biothreat agents, and to better understand and prevent the spread of emerging/reemerging infections such as influenza.
Crop plants are subject to diseases caused by viruses, bacteria, oomycetes, and fungi. For many pathogens the aerobiological pathway is important in disease transmission.
Airborne fungal spores and other disease propagules are frequently present in the atmosphere and pose a constant threat to crops as well as plants in the natural environment. This chapter reviews mechanisms of pathogen dispersal with the focus on wind and rain splash and also discusses both local and long distance transport. Various examples of pathogens from the groups above are described with details on the dispersal phase as well as disease forecasting and aspects of control. For many plant diseases, forecasting models are valuable tools alerting the grower regarding the likelihood of disease spread and when to apply control measures. Development of forecasting models requires an understanding of all stages of dispersal from spore takeoff to transport to deposition within the crop. Knowledge of the influence of meteorological conditions on spore development and the ability of spores to survive long-distance transport are also needed for accurately modeling disease spread. In addition to descriptions of well known plant pathogens, several emerging plant diseases are described along with the potential use of plant pathogens in anti-crop biological warfare
This chapter details the ecology of Legionnaires' disease and a description of its history in regards to public health. Also included are methods for detection in environmental samples, identification and environmental approaches to controlling legionellosis.
Soil is a reservoir for a diversity of transient human pathogenic viruses and protozoa that include some species with truly edaphic lifestyles. The ability to detect these pathogens in soil has increased in tandem with concerns about the impact of human activity on soil quality. Separation from the sample matrix and concentration in solution free of interfering contaminants are key preliminary steps to the detection and/or identification of specific species, which is increasingly performed with sensitive molecular methods. The present chapter describes procedures applied in the separation of viruses from soil by desorption from soil particles, their concentration and detection/quantification in laboratory-grown mammalian cell cultures using Quantal methods or plaque assays. Methods for extraction of nucleic acids to permit detection of viruses that are presently difficult or impossible due grow in vitro due to a lack of suitable cell lines (noroviruses, astroviruses, sapoviruses, rotaviruses, hepatitis A and E viruses) by polymerase chain reaction (PCR), conventional reverse-transcription PCR (RT-PCR) or real-time PCR and RT-PCR are also presented. The detection of protozoa against the large background microflora and extraneous components in soil requires a series of variable preliminary elution, concentration and purification steps that are determined by the properties of both sample and target protozoa. Classical methods that rely on microscopic examination for detection/identification of Acanthamoeba spp, Entamoeba histolytica, Naegleria fowleri, Giardia spp., Balantidium coli, Toxoplasma gondii, Cyclospora cayetanensis and Cryptosporidium parvum are presented along with alternative molecular approaches based on the recognition of specific antigens or DNA sequences.
Soils receive inputs of human pathogenic and indicator bacteria through land application of animal manures or sewage sludge, and inputs by wildlife. Soil is an extremely heterogeneous substrate and contains meso- and macrofauna that may be reservoirs for bacteria of human health concern. The ability to detect and quantify bacteria of human health concern is important in risk assessments and in evaluating the efficacy of agricultural soil management practices that are protective of crop quality and protective of adjacent water resources. The present chapter describes the distribution of selected Gram-positive and Gram-negative bacteria in soils. Methods for detecting and quantifying soilborne bacteria including extraction, enrichment using immunomagnetic capture, culturing, molecular detection and deep sequencing of metagenomic DNA to detect pathogens are overviewed. Methods for strain phenotypic and genotypic characterization are presented, as well as how comparison with clinical isolates can inform the potential for human health risk.
Section X of the Manual of Environmental Microbiology addresses the burgeoning area of microbial source tracking (MST), a collection of methodologies and approaches whose aim is to determine the dominant source(s) of fecal contamination of water bodies. Many health- and management-related areas can benefit from MST analyses, including total maximum daily load (TMDL) determinations, beach and water resource management, quantitative microbial risk assessment (QMRA), and epidemiology. This chapter provides a brief overview of the rationale for and theory of MST, followed by chapters that detail MST methodologies and practice. This chapter also suggests future directions for a field that has changed considerably over the last two decades - as it has evolved from an emphasis on building large databases of bacterial phenotypes or genotypes toward the use of culture-independent methods that focus on single genetic targets or microbial community structure. The field is in the process of adopting high-throughput DNA sequencing methods that allow consideration of genomic and metagenomic data to identify host-associated microorganisms and/or patterns in communities that may contribute to accurate identification of fecal pollution sources in the environment.
The goal of this chapter is to provide an overview of MST marker characteristics, to describe performance criteria of detection protocols used and to offer guidelines for the effective interpretation of the results. Since the trend in the research community has shifted towards (q)PCR detection of MST markers targeting either a variable region of the 16S rDNA or functional genes involved in host-microbe interactions, the focus of this chapter is on validation of these specific targets and protocols used to detect them. The most basic performance criteria applied to MST markers are based on the sensitivity and specificity characteristics, which are assessed by testing the marker against fecal material from a broad range of target and non-target hosts. While some information may be gathered through in silico, theoretical testing (e.g. hypergeometric tables, NCBI/BLAST searches), empirical data is needed in order to accurately assess performance of a given marker.
Human fecal waste is thought to contain the largest number of human pathogens representing the greatest public health risk in comparison to other fecal sources. Human fecal pollution can be introduced into water resources from damaged sewer lines, faulty septic systems, combined sewer overflows, illicit dumping activities, and even recreational bathers themselves. Ensuring public safety and adequate water quality therefore requires methods that can confirm the presence or absence, as well as, determine the concentration human fecal pollution sources. This chapter provides an overview of human-associated fecal source identification methods commonly used to assess water quality. In addition to describing various methods, this chapter will also discuss factors to consider for method selection.
The determination of fecal pollution sources in waters is essential in the management of catchments. Although traditional microbial water analyses using indicator microorganisms have been used for water-health management for more than a century, it is known that they cannot provide information about the origin of fecal pollution. The distinction between anthropogenic and non-anthropogenic (animal) fecal pollution in water would greatly support assessment of health risks based on knowledge of the host-specificity of many pathogens. For example, human sewage could constitute a higher health risk to humans than wastewater of animal origin. However, there are some exceptions because some pathogens can infect and cause clinical disease in both humans and animals. Therefore, the fecal pollution source assessment could support different water management strategies, treatment measures and policies to prevent or decrease fecal inputs in water and remediation at the source.
In this chapter, proposed chemical and biological MST indicators for the determination of animal fecal sources are discussed. The biological indicators are grouped based on the phylogenetic description of the proposed target (eukarya, bacteria, and virus). A comprehensive description for each proposed target is provided and the developed methodologies employed are presented. Emphasis is placed on the validation and applicability of each proposed method and animal-MST indicator. New molecular approaches for animal-NST targets based on metagenomics are also presented. Finally, MST assay implementation, their contribution to the assessment of maximum fecal load of water bodies and their relationship to traditional microbial indicators and water-borne pathogens is examined.
Field study design and implementation are critical to the success of fecal source tracking (FST) studies. Significant advances in the field of microbial and chemical source tracking (MST or CST) provide access to a variety of analytical tools, beyond traditional culture-based measurements of fecal indicator bacteria (FIB), in the identification and apportionment of pollution sources adversely impacting water quality and of public health concern. Execution of investigative studies employing these tools requires a phased approach: defining the questions and desired outcome, site assessment, field sampling/laboratory analysis, confirmatory testing, statistical analysis, interpretation of results, and translation of results into actionable items. A sound study design addresses spatial and temporal variability as well as geographic distribution of markers or target organisms used to develop statistically robust data sets from which sound conclusions are drawn. While FST tools may be cutting edge, and informative in their own right, multiple lines of evidence are necessary to adequately characterize pollutant source, loading, and human exposure risk. Assessments of environmental, meteorological and hydrological parameters may increase accuracy in the assignation of relative contributions (from multiple sources) in complex environments. In the absence of strong correlation between FIB, physical attributes and MST or CST markers, a weight of evidence approach may be used to target human exposure interventions, which may take the form of engineered, naturalized, or educational measures. A multi-barrier approach to protecting public health, cognizant of confounding factors impacting the analytical or remediation process, should be stressed and include stakeholder engagement throughout the process.
Mathematical models have been widely applied to surface waters to estimate rates of settling, resuspension, flow, dispersion, and advection in order to calculate movement of particles that influence water quality. Of particular interest are the movement, survival, and persistence of microbial pathogens or their surrogates, which may contaminate recreational water, drinking water, or shellfish. Most models devoted to microbial water quality have been focused on fecal indicator organisms (FIO), which act as a surrogate for pathogens and viruses. Process-based modeling and statistical modeling have been used to track contamination events to source and to predict future events. The use of these two types of models require different levels of expertise and input; process-based models rely on theoretical physical constructs to explain present conditions and biological distribution while data-based, statistical models use extant paired data to do the same. The selection of the appropriate model and interpretation of results is critical to proper use of these tools in microbial source tracking. Integration of the modeling approaches could provide insight for tracking and predicting contamination events in real time. A review of modeling efforts reveals that process-based modeling has great promise for microbial source tracking efforts; further, combining the understanding of physical processes influencing FIO contamination developed with process-based models and molecular characterization of the population by gene-based (i.e., biological) or chemical markers may be an effective approach for locating sources and remediating contamination in order to protect human health better.
Exposure assessment is the evaluation of the magnitude and frequency of exposure to pathogenic organisms via specified exposure pathways. Exposure assessment consists of three steps including: defining the exposure pathway; quantifying each model variable; and finally quantitatively characterizing the magnitude and frequency of exposure. In this chapter, these three steps are described in detail including considerations for data interpretation and statistical inference. Numerical examples related to drinking water consumption, wastewater irrigation of food crops and recreational water quality are provided.
Phylogenomics is aimed at studying functional and evolutionary aspects of genome biology using phylogenetic analysis of whole genomes. Current approaches to genome phylogenies are commonly founded in terms of phylogenetic trees. However, several evolutionary processes are non tree-like in nature, including recombination and lateral gene transfer (LGT). Phylogenomic networks are a special type of phylogenetic networks reconstructed from fully sequenced genomes. The network model, comprising genomes connected by pairwise evolutionary relations, enables the reconstruction of both vertical and gene transfer events. Reconstructing microbial genome evolution in the form of a network enables the use of an extensive toolbox developed for network research. The structural properties of phylogenomic networks open up fundamentally new insights into gene and genome evolution.
An overarching goal of biology is to understand how evolutionary and ecological processes generate and maintain biodiversity. While evolutionary biologists interested in biodiversity tend to focus on the mechanisms controlling rates of evolution and how this influences the phylogenetic relationship among species, ecologists attempt to explain the distribution and abundance of taxa based upon interactions among species and their environment. Recently, a more concerted effort has been made to integrate some of the theoretical and empirical approaches from the fields of ecology and evolutionary biology. This integration has been motivated in part by the growing evidence that evolution can happen on “rapid” or contemporary time scales, suggesting that eco-evolutionary feedbacks can alter system dynamics in ways that cannot be predicted based on ecological principles alone. As such, it may be inappropriate to ignore evolutionary processes when attempting to understand ecological phenomena in natural and managed ecosystems. In this chapter, we highlight why it is particularly important to consider eco-evolutionary feedbacks for microbial populations. We emphasize some of the major processes that are thought to influence the strength of eco-evolutionary dynamics, provide an overview of methods used to quantify the relative importance of ecology and evolution, and showcase the importance of considering evolution in a community context and how this may influence the dynamics and stability of microbial systems under novel environmental conditions.
Within the benthic realm life carpets the sedimentary surface of all aquatic ecosystems including the oceans, lakes, rivers and streams. Microorganisms of all types, bacteria, archaea and eukaryotes, inhabit these environments and through their metabolic activities contribute to the biogeochemical cycles that sustain life on earth. In this chapter we address the question "Why live on or in sediments, or in some cases, attached to rocks or other hard surfaces?" and then explore major questions in the ecology of benthic microbial life in freshwater and shallow marine systems and current methodological approaches used in addressing these questions. Our first focus is on the abiotic and biotic factors that strongly influence the distribution and abundance of benthic microorganisms. Elemental cycles and the possibility of bacterial biogeography within the benthic realm are also addresses. Obtaining high quality samples and methods for determining microbial activity, biomass and community structure are discussed with classical/direct observation, biochemical and molecular approaches highlighted. Characterization of dissolved organic matter, methods for foodweb analysis and identification of the active component of microbial communities are specifically addressed. We conclude with a brief examination of several current questions within the general field of benthic microbial ecology.
Marine planktonic microorganisms, including Bacteria, Archaea, Protozoans (Protists), and Viruses, all play critically important roles in marine ecosystems and global biogeochemical cycles. This chapter focuses on the non-photosynthetic marine plankton organisms, and summarizes information on what organisms are present in the ocean, their diversity, distributions, activities and interactions.
This chapter focuses on microbial biofilms in aquatic environments and attempts to provide a framework for their study based on unifying fundamental concepts of microbial ecology (resilience, resistance, diversity) across micro, community and landscape scales of observation. Biofilm development is briefly considered in terms of classical sequences of events and our current understanding. Growth of microbial communities in natural environments and methods and apparatus for their experimental cultivation at various scales are presented. Critical aspects of biofilm development, the nature and study of exopolymeric substances, predation, grazing, cooperative and trophic interactions, as well as the role of biofilms in the fate of contaminants are reviewed. The essential tools for aquatic biofilm study, from microscale (microscopy), molecular/genomic (FISH/next generation sequencing), to cultivation-based approaches, are laid out for the reader. The effects of environmental stress on aquatic biofilms, as well as their use as bioindicators of ecosystem health and applications in ecotoxicology, risk assessment, and monitoring, are reviewed and discussed.
Extremely acidic environments, defined having a pH of <3, are found in locations as diverse as the Arctic and the Tropics. While these be natural phenomena, human activity, most notoriously mining of metals and coals, are often responsible for the severe acidification of localized environments. The indigenous microflora in extremely acidic environments include species of prokaryotes and eukaryotes, many of which are obligately acidophilic. Acidophiles are widely distributed throughout the "tree of life", and include species of Bacteria, Archaea and Eukarya that are often only very distantly related to each other. Various mechanisms are used by acidophiles to adapt to the challenges they face, which include contending with elevated concentrations of transition metals and metalloids, and severely limited bioavailability of macronutrients such as phosphate.
Inorganic energy sources (reduced iron and sulfur) are highly abundant in many extremely acidic environments. Chemolithotrophic acidophiles are the basis of food webs in subterranean and also contribute to net primary production in deep submarine geothermal vents. However, where solar energy is available phototrophic acidophiles, predominantly species of acidophilic eukaryotic microalgae, proliferate and assume the dominant role of primary producers. Acidophilic microorganisms interact with each other in various ways, including via redox transformations of iron and sulfur, generating electron donors and acceptors for prokaryotic metabolisms, and via provision of organic compounds (supporting heterotrophic species) or inorganic carbon (supporting autotrophs). Acidophiles have long been used to extract metals from ores (biomining) and biotechnologies are emerging that harness their abilities to remediate polluted waters and recover metals.
A great variety of hypersaline environments exist, here defined as environments with salt concentrations exceeding seawater salinity. These include natural inland salt lakes such as Great Salt Lake, Utah, and the Dead Sea, alkaline soda lakes with salt concentrations often close to saturation, and man-made saltern ponds for the production of salt from seawater. There are thalassohaline (seawater-derived) and athalassohaline brines with ionic compositions very different from that of seawater. High salt environments are inhabited by diverse halophilic and/or halotolerant microorganisms belonging to all three domains of life: Archaea, Bacteria, and Eukarya. Many halophilic microorganisms are 'polyextremophiles', able to thrive in environments stressed not only by high salt concentrations but also by extremes of pH, temperature, or both. There are two different strategies that enable microorganisms to live at high salt: some maintain a low-salt cytoplasm and produce organic 'compatible' solutes to provide osmotic balance, while others accumulate molar concentration of KCl intracellularly. Not all physiological types of microorganisms are found up to the highest salinities, and this is probably due to the high energetic cost of osmotic adaptation. At the highest salinities most aerobic heterotrophic activity is due to Archaea of the family Halobacteriaceae, but extremely halophilic Bacteria also exist. The microbial communities inhabiting high salt environments can be studied by culture-dependent and by molecular, culture-independent techniques. Different groups of halophiles have characteristic lipids and pigments, and these can be used as biomarkers for the qualitative and quantitative characterization of the biota of salt lakes, saltern ponds and other hypersaline environments.
The capability to (1) systematically collect, process, and archive nucleic acids from "extremely low-biomass" spacecraft-related environments, and (2) effectively assess the diversity of microorganisms present on spacecraft and associated cleanroom surfaces was developed, and validated. This capability enabled generation of the most comprehensive (bacterial, archaeal, and fungal) assessment of spacecraft-associated biodiversity to date. The capability to provide a passenger list of the microorganisms associated with flight hardware developed and validated in this study bridges a significant gap in technology and dramatically increases NASA's ability to explore and verify the scientific findings of both in-situ life detection and sample-return missions.
Although there is a growing understanding of the biodiversity associated with low biomass surfaces, it remains challenging to provide a comprehensive inventory of microbes present. In this study three molecular approaches were attempted: conventional cloning techniques, PhyloChip DNA microarrays, and 454 tag-encoded pyrosequencing, together with a methodology to systematically collect, process, and archive nucleic acids, to assess the phylogenetic breadth of microorganisms present on spacecraft and associated surfaces. The analysis methods yielded very different results; traditional approaches provided the least comprehensive assessment of microbial diversity, while PhlyoChip and pyrosequencing detected more diverse microbial populations. The findings of this pioneering study provided new and important insights into the benefits and limitations of modern molecular approaches for assessing the microbial diversity associated with samples extremely low in total biomass. These are of particular relevance to current and future NASA endeavors, as well as homeland security, medical, pharmaceutical, and semiconductor applications.
A variety of thermal systems exist on Earth, spanning wide ranges of temperature and other physicochemical parameters, including the deep continental and marine subsurface, terrestrial and marine geothermal systems at tectonic plate boundaries, spreading centers, and "hotspots", and a wide variety of natural and engineered systems. A variety of hyperthermophilic and thermophilic microorganisms inhabit many of these environments; however, microbial diversity is inversely proportional to temperature at temperatures inhabited by thermophiles. Above ~80 {degree sign}C, microbial communities are almost entirely composed of thermophilic specialists, including Archaea such as Thermoprotei (Crenarchaeota), Archaeoglobi (Euryarchaeota), Methanopyri (Euryarchaeota), Thermococci (Euryarchaeota); Bacteria such as Aquificae, Thermi, Thermotogae, Thermodesulfobacteria, and Dictyoglomi; and a variety of yet-uncultivated lineages that are abundant globally. The decrease in diversity and change in microbial community composition associated with high temperatures is driven by bioenergetic stresses associated with increased degradation and racemization rates at high temperature. One key molecular adaptation to life at high temperature is the tetraether membrane lipid. Biodiversity losses driven by high temperature lead to losses in ecosystem functions that impact key biochemical processes, such as the absence of photosynthesis above ~73 {degree sign}C. The impact of high temperature on other biogeochemical cycles is still poorly understood, but likely includes limitations on the oxidative nitrogen cycle. A significant recent advancement of the study of life at high temperature is the use of single-cell genomics and metagenomics approaches to probe yet-uncultivated lineages in high-temperature habitats; however, this progress must be matched with an equally vigorous program to test functions predicted from these genomes.
The last decades have seen a development of the research on animal-microbe interactions that is showing that animals, and in general higher organisms, are embedded in a microbial world. The recent developments in the research of the associations of microbes with the invertebrate gut are confirming that also in these animals the interactions with symbiotic microorganisms had a major role in the host evolution with important consequences, among others, on physiology, behavior, stress adaptation and ecology of the host. In this chapter such kind of interactions are analyzed and an overview of the different roles that gut-microbe symbiosis plays on the host fitness is presented. The profound effects of symbionts on the invertebrate biology are also discussed in the light of their potential exploitation for controlling invertebrate related problems such as, for instance and among others, controlling agriculture insect pest and transmission of vector borne diseases.
The gastrointestinal (GI) tract of humans and animals is colonized by microorganisms immediately after birth. The composition of the GI tract microbiota undergoes remarkable alterations during early age, reaches a relative stable status in adulthood, and is driven by external factors such as habitual diet, location along the intestine, antibiotic therapy and maternal microbiota, and intrinsic factors such as host species and genotype. Whereas usually faecal samples are used for assessing the impact on the microbiota in human intervention studies, in vitro and animal models provide an easier way to collect many (invasive) samples, have multiple comparisons and regulating the genotype background. Animal models, and in particular mammalian models, provide an alternative way to study the in vivo responses to beneficial, commensal and pathogenic microorganisms in the GI tract, including studies that aim to see the impact of the host system as well. The main animals used to study the mammalian GI tract are rodents (mainly mice and rats) and pigs. Rodent and pig models, including gnotobiotic and humanized rodents and pigs and minipigs, have been extensively employed in gut microbiota studies, and especially the piglet model has been suggested as an appropriate model for human infant studies. With pig models, several intestinal sampling techniques can be applied in kinetic microbiota studies, including small intestinal segment perfusion and cannulation. In many cases, to test a certain treatment, a tiered approach consisting of complementary methods is employed, comprising in vitro, in vivo animal models, eventually leading towards human intervention studies.
Any organism with a gut system will make use of microbes to enable the most efficient digestion of food that it ingests. The gut microbiota is a complex community of many different bacteria, archaea, viruses and lower eukaryotes that are required to act in unison to break down a wide variety of foodstuffs and even associated toxins (see below) to maintain the health of their host. The structure of this microbial community is influenced by many factors, including host (immune) response to the non-host cells, food intake and interactions between and competition within the members of the microbiota themselves. Understanding these interactions and the processes that lead to the establishment of a stable gut microbiota is a rapidly expanding area of microbial ecology. Whilst initially focused on understanding the human gut microbiota, researchers are now turning to the study of animal gut microbiota, and in particular those animals that we rely on for food, such as ruminant livestock (cattle and sheep) and poultry.
A large number of microorganisms capable of degrading xenobiotic aromatic compounds has been isolated, and applications of them for bioremediation to remove the contamination by these compounds have been studied. Recently, genome sequences of dioxin-like compound-degrading bacteria have been determined, including degraders of biphenyl, dibenzofuran, dibenzo-p-dioxin, and their chlorinated derivatives such as Burkholderia xenovorans LB400, Rhodococcus jostii RHA1, and Sphingomonas wittichii RW1. Their key enzymes and pathways to metabolize these compounds have been elucidated, and molecular mechanisms to regulate their expression have been analyzed in detail. Some of their degradative genes are located on mobile genetic elements, such as a large plasmid and an integrative and conjugative element, which could have an important role for distribution of their degradative genes. Comparisons of crystal structures of the degrading enzymes showed their putative evolutional relationships. Genome-wide analyses including transcriptome, proteome, and mutagenesis have revealed how the degraders expressed their degradative genes, how they survived in different environments, and what the key environmental factors to express their degrading ability. Combination of phytoremediation and bioaugmentation treatments was shown to be efficient for decontamination. These aspects could be essential to improve decontamination by bioremediation.
The widespread use of organochlorine pesticides (OCPs), mainly in the past, has caused serious environmental problems. Many OCPs were recently categorized as persistent organic pollutants (POPs) that should be controlled as toxic environmental contaminants. On the other hand, many bacterial strains and consortia have been identified that can degrade OCPs, including man-made ones, and various pathways for the biodegradation of OCPs have been clarified. Especially, aerobic OCP-degrading bacteria have been analyzed in detail as an excellent model for studying the bacterial adaptation and evolution in the environment. In fact, most such degradation pathways are thought to be established by the assembly of preexisting and newly evolved pathways, involving enzymes whose functions are thought to have evolved during relatively short period. Furthermore, a large amount of bacterial genomic information is now available, and the appearance and evolution of bacteria capable of degrading man-made OCPs can be discussed on the basis of such genomic information and mobile genetic elements. These accumulating knowledge on the biodegradation of OCPs will also be useful for practical bioremediation.
The benzene ring moiety is found in biological compounds accounting for ~25% of the land-based organic matter on Earth. Hence, the biosynthesis and biodegradation of aromatic ring compounds constitutes an important part of natural carbon cycle. Microorganisms capable of using aromatic compounds as carbon and energy sources can be found in a range of very different habitats and redox conditions. In anoxic ecosystems where dissolved oxygen is depleted, degradation of aromatic compounds depends on the availability of inorganic electron acceptors such as nitrate, iron, sulfate or carbon dioxide. Developing efficient and effective bioremediation technologies requires an in-depth understanding of the microbial communities responsible for degradation of contaminants. Anaerobic microorganisms use a strategy of attacking the aromatic ring via reductive transformations. Anaerobic degradation of aromatic compounds (e.g. benzene, toluene and xylene (BTX), lignoaromatics, polycyclic aromatic hydrocarbons (PAHs) and halogenated aromatic compounds) has now been demonstrated under different redox conditions. One of the fundamental challenges has been to elucidate the microorganism(s) responsible for degradation of aromatic compounds in anaerobic environments. The recent advancements in molecular techniques have provided an opportunity to unravel the veil of the microbial activity responsible for the anaerobic degradation of aromatic compounds. This chapter provides an overview of some techniques and approaches to elucidate anaerobic degradation of aromatic compounds and how the active microorganisms can be identified, classified and enumerated.
Waste organic matters such as organic compounds in wastewater and waste biomass from agricultural practices contain tremendous amount of energy. Recently microbial electrochemical technology (MET) receives great attention as promising technology to harvest energy from waste organics and produce directly electricity and valuable chemicals. MET use the bioelectrochemical system (BES) where microorganisms are used as catalyst for various electrochemical reactions. Two main mechanisms of extracellular electron transfer (EET), i.e. direct EET and indirectly mediated EET, from bacteria into anode or from cathode to bacteria have been reported. Microorganisms, which can transfer electrons into anode or receive electrons from cathode, are designated as electron transfer microorganisms (ETMs). The activity of ETMs directly and substantially affects the BES performance to produce electricity in MFCs and valuable products in MECs. Tremendous variety of ETMs has been reported and the variety seems to be depending on substrate types, substrate concentrations, poised electrode potentials, and electron acceptors. Most progress of MET in BES has been achieved from researches on application for wastewater treatment to produce electricity. MET is also used for biosensors, bioremediation, producing biofuels and industrial chemicals, and reverse electrodialysis. The present chapter will summarize recent reports of MET focusing on the developments of microbial aspects such as detailed EET mechanisms and diversity of ETMs. In addition, the newest various applications of MET will be briefly introduced.
The aim of this chapter is to give an overview of aerobic biodegradation of petroleum aromatic compounds. Among the wide variety of petroleum aromatic compounds that occur, BTEX, PAHs, and HACs are the principal components of petroleum and their toxicities are relatively higher than other components, such as alkanes. This chapter will focus on degradation pathways and enzymes used by microorganisms capable of metabolizing BTEX, four representative PAHs, naphthalene, phenanthrene, fluorene, and pyrene and three HACs, carbazole, dibenzothiophene and dibenzofuran.
Environmental Systems Microbiology is well positioned to move forward in dynamic complex system analysis probing new questions and developing new insight into the function, robustness and resilience in response to anthropogenic perturbations. Recent studies have demonstrated that natural bacterial communities can be used as quantitative biosensors in both groundwater and deep ocean water, predicting oil concentration from the Gulf of Mexico Deep Water Horizon spill and from groundwater at nuclear production waste sites (16, 17, 25). Since the first demonstration of catabolic gene expression in soil remediation (34) it has been clear that extension beyond organismal abundance to process and function of microbial communities as a whole using the whole suite of omic tools available to the post genomic era. Metatranscriptomics have been highlighted as a prime vehicle for understanding responses to environmental drivers (35) in complex systems and with rapidly developing metabolomics, full functional understanding of complex community biogeochemical cycling is an achievable goal. Perhaps more exciting is the dynamic nature of these systems and their complex adaptive strategies that may lead to new control paradigms and emergence of new states and function in the course of a changing environment.
Dissimilatory Fe(III)-reducing bacteria occupy a central position in a variety of environmentally important processes, including the biogeochemical cycling of carbon and iron, the bioremediation of radionuclides and organohalides, and the generation of electricity in microbial fuel cells. Fe(III)-reducing bacteria are scattered and deeply rooted throughout both prokaryotic domains, an indication that microbial Fe(III) reduction may also have been one of the first respiratory processes to have evolved on early Earth. The metal-reducing γ-proteobacterium Shewanella oneidensis is one of the most extensively studied Fe(III)-reducing bacteria. This chapter examines the molecular mechanism by which S. oneidensis transfers electrons to Fe(III) ranging from highly soluble organic-Fe(III) complexes to highly insoluble Fe(III) oxides. S. oneidensis employs four novel respiratory pathways for dissimilatory Fe(III) reduction, including: i) localization of c-type cytochromes to the cell surface where they deliver electrons to external Fe(III) (Mechanism No. 1, Direct contact by outer membrane-localized c-type cytochromes); ii) localization of c-type cytochromes along extracellular nanowires where they deliver electrons to external Fe(III) (Mechanism No. 2, Direct contact by nanowire-localized c-type cytochromes); iii) delivery of electrons to external Fe(III) via endogenous or exogenous electron shuttles (Mechanism No. 3, Extracellular electron shuttling); and iv) non-reductive dissolution of Fe(III) oxides to form more readily reducible soluble organic-Fe(III) complexes (Mechanism No. 4, Fe(III) oxide solubilization followed by reduction of the produced soluble organic-Fe(III) complexes); The chapter highlights the mechanistic details associated with each of the four Fe(III) reduction pathways of S. oneidensis, including a concluding discussion of the future research directions for each pathway.
Geomicrobiology involves the study of microbes that rely on certain geochemical conditions and substrates for growth and survival. Field and laboratory methods need to be carefully considered in order to thoroughly understand unique biogeochemical environments. Choices of field site as well as culture-dependent and culture-independent approaches are central to the study of systems where geomicrobiological processes such as metal oxidation, reduction, and adsorption predominate. We describe general considerations for fieldwork including choice of site, safety issues, and sampling options. Development of powerful ‘omics’ approaches such as metaproteomics and metagenomics now allow researchers to more fully understand complex geomicrobiological phenomena from the molecular to ecosystem scales. Examples are presented where combined 'omics' analyses have shown what biogeochemical processes are occurring and how these influence the geochemical environment. When combined with geochemical analyses, microbiological data from a given system can reveal what key metal transformation processes are occurring, their relative importance in the environment, and the ultimate impact that microbes have on the geochemistry of a system. This chapter serves as a practical guide for initiating and developing a variety of geomicrobiology projects, and can be used in conjunction with microbiology courses and teaching laboratories where questions regarding microbial transformation of metals are being explored.
Metal(loid)-impacted soils represent one of the more difficult environmental systems to remediate. Physicochemical heterogeneities combined with varying environmental conditions challenge both abiotic and biotic mitigation efforts. Yet, metal toxicities within soil systems are a growing concern that due to the recalcitrance of metals and metalloids will continue to persist. With renewed efforts, microbial-based technologies are being examined in the identification, prevention and remediation of metal-impacted soils, resulting in a re-emergence of old technologies with new perspectives and novel microbial uses. This chapter summarizes some of these efforts and provides a look into the future of microbial-based soil remediation.
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©Doody’s Review
This book covers microbes in air, water, and soil and their impact on human health and welfare. This edition provides critical updates regarding the microbial risk assessment process, a summary of updates to study environmental microorganisms, and the assessment of microbial presence in natural and built environments.
Environmental microbiology is part of the broader American Society for Microbiology. As such, the book provides critical references for practicing clinical and environmental microbiologists.
The composition of the senior editorial board serves as a guide to potential readership. Dr. Yates is in a department of environmental sciences (UC-Riverside), while Dr. Nakatsu serves in a department of agronomy (Purdue), Dr. Miller works in a department of microbiology and molecular genetics (Oklahoma State), and Dr. Pillai is posted at the National Center for Electron Beam Research (Texas A&M). The contributor list numbers over 180, spanning four continents and many sub-disciplines. I would expect the readership to derive from similar diverse affiliations. Water and wastewater specialists also will number among readers.
This book actually contains four volumes: general methodology (analytical detection to sample collection); environmental public health microbiology (surveying microorganisms in water, air, or soil); microbial ecology (means of classifying and explaining relationships); and bio degradation and bio transformation (transformations and degradation of natural- and man-made chemicals).
ASM Press has prepared a wonderful book essential to the science of environmental microbiologists, microbial ecologists, and environmental engineers. The new features in this edition justify this update.
Reviewer: J. Thomas, Pierce Navy Environmental Health Center
Review Date: 12 May 2017
©Doody’s Review Service