In the past Raina M. Maier has collaborated on articles with Ian L. Pepper and Todd R. Sandrin. One of their most recent publications is Chapter 1 - Introduction to Environmental Microbiology. Which was published in journal .

More information about Raina M. Maier research including statistics on their citations can be found on their Copernicus Academic profile page.

Raina M. Maier's Articles: (17)

Chapter 1 - Introduction to Environmental Microbiology

Publisher SummaryThis chapter provides an introduction to the book that focus on environmental microbiology. The book defines the important microorganisms that are involved in environmental microbiology, the nature of the different possible environments in which they are situated, the methodologies used to monitor microorganisms and their activities, and the possible effects of microorganisms on human activities. The book addresses the new challenges of modern environmental microbiology, in which pathogens and bioremediation remain fundamental to the field. However, in both cases, the subject areas have been greatly enhanced through the application of molecular genetics and biotechnological tools. Another important area that has been included is that of molecular ecology, which involves investigating diversity in the environment and mining and exploiting that diversity for new natural products and activities. Thus, this book can be used in teaching environmental microbiology as well as a general reference book for practitioners in the field of environmental microbiology.

Chapter 8 - Environmental Sample Collection and Processing

Publisher SummaryThis chapter discusses various approaches of sample collection from diverse environments including soil, water, and air. The chapter discusses the microbial analysis of samples through a variety of techniques such as community DNA analysis and culture based analysis. Soil samples can be obtained with a soil auger, and the methods of soil sampling can be random, transect, two-dimensional, or systematic grid. The mechanical approaches using drill rigs are necessary for the sampling the subsurface environment. The traditional methods of bacterial analysis involve either cultural assays utilizing dilution and plating methodology or direct count assays. While the community DNA analysis is nonculture-based approach of DNA extraction, it is thought to be more representative of the actual community present than culture-based approaches. The collection of the water sample is relatively easy; however, processing can be more difficult. The detection and analysis of viruses involves sample collection by adsorption onto the filter such as VIRADEL, elution and reconcentration by change in pH, and virus detection. Detection of bacteria in water is done by two different procedures: the membrane filtration and most probable number (MPN) methodologies. The protozoa detection involves collection of the cysts or oocysts by filtration, extraction, pellet formation, and purification by immunomagnetic separation, and staining with fluorescent monoclonal antibodies. For collection of air samples, many devices are used on the basis of their sampling methods: impingement, impaction, centrifugation, filtration, and deposition. The approaches most commonly used for detection of bacteria on fomites involve Rodac agar plates and the swab-rinse technique, which is also suitable for the sampling of viruses.

Chapter 11 - Physiological Methods

Publisher SummaryMeasurement of microbial activity can provide an indication of the general health of the environment and can be used to evaluate the impact of a disturbance on the microbial community. This chapter describes various types of microbial activity measurements in both pure culture and environmental samples. Activity measurements in pure culture include measurement of substrate utilization, terminal electron acceptor (TEA) utilization, cell mass increase, and carbon dioxide evolution. Utilization of aromatic compounds such as benzene can be measured by the UV spectrophotometer; while, high-performance liquid chromatograph (HPLC) is used for both qualitative and quantitative estimation of a wide variety of compounds such as sugars. The primary activity of the microbial community in undisturbed environments is carbon respiration, and measurement of carbon respiration can be used for the determination of basal rate of microbial activity in soil samples, microbial biomass determination, and biological oxygen demand (BOD). Radiolabelled tracers can be incorporated into the cellular macromolecules—such as proteins or nucleic acids—to monitor the increase in biomass of a bacterial population. The advent of new approaches including functional genomics and proteomics such as microarrays, two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), and matrix-assisted laser desorption ionization time-of-flight mass spectrometer (MALDI-TOF-MS) allows investigation of environmental microbial physiology from a much more holistic perspective.

Chapter 12 - Immunological Methods

Publisher SummaryThis chapter presents a discussion of antibodies with respect to the structure and various classes of antibodies and interaction of antibodies with foreign objects. The chapter describes various immunoassays such as fluorescent immunolabeling, enzyme-linked immunosorbent assay (ELISA), magnetic bead antigen capture, and western immunoblotting for the study of microorganisms and chemical contaminants in association with the environment. The five different classes of antibodies or immunoglobulins are IgA, IgD, IgE, IgG, and IgM, which differ in many ways including their overall structures. The types of immunoassays used in environmental microbiology are based on quantitation or detection of antigens, rather than characterization of the antigens. Fluorescent immunolabeling (immunofluorescence) uses the fluorescent signal molecules conjugated to antibodies and can be used to examine the interaction of an antigen of interest with its environment such as E. coli and its interaction with human intestinal epithelial cells. The enzyme-linked immunosorbent assay (ELISA) is a very sensitive method and has been used to quantify biomass within biofilms and even protein production in biofilms. Western immunoblotting is used to identify the target antigens in a complex mixture and can specifically detect extremely low levels of a particular antigen within a heterogeneous matrix. Immunoaffinity chromatography provides a very efficient means of both concentration and purification of antigens. While immunocytochemical assay is used for the detection and determination of the cellular localization of target antigens, immunoprecipitation is used to semiquantitatively determine the amount of antigen or antibody in a sample.

Chapter 14 - Biogeochemical Cycling

Publisher SummaryThis chapter discusses the biogeochemical cycles pertaining to carbon, nitrogen, sulfur, and iron. The carbon cycle involves circulation of carbon between reservoir and sink, through various processes such as photosynthesis, respiration, degradation of organic compounds, and burning of fossil fuels. While photosynthesis is the primary means of carbon fixation and conversion into organic compounds, respiration by the organisms results in the release of carbon dioxide back into the reservoir. Nitrogen cycle is the best studied and most complex of the mineral cycles and includes the microbially catalyzed processes of nitrogen fixation, ammonium oxidation, assimilatory and dissimilatory nitrate reduction, ammonification, and ammonium assimilation. Several bacteria including Azotobacter, Beijerinckia, Azospirillum, and Clostridium can fix N2. Sulfur cycle involves assimilatory sulfate reduction and sulfur mineralization. Two recent practices that have caused a disturbance in the global sulfur reservoirs are strip mining and burning of fossil fuels, resulting in the emission of sulfur dioxide into the atmosphere and subsequent formation of acid rain.

Chapter 17 - Bacterial Communities in Natural Ecosystems

Publisher SummaryComplex bacterial communities are found in essentially all natural ecosystems including soils, plants, and surface and ground water, which exhibit great diversity as well as great redundancy in their activity. This chapter describes the microbial communities and diversity in natural systems, functional diversity and resilience of bacterial communities, and importance of microbial communities as source of natural products. The bacterial diversity in normal healthy soil is necessarily very large; however, under stressed or extreme environments, it tends to be much smaller. DNA–DNA hybridization and sequence based techniques such as 16S rRNA sequencing and multilocus sequence typing (MLST) have been used to study the bacterial diversity in natural systems. Estimates of diversity in soil have also been made using DNA reassociation kinetics and cloning and sequencing 16S rRNA genes; however, the diversity estimates were somewhat different. Natural bacterial communities in marine water have lower numbers than their soil counterparts. The redundancy with respect to functional diversity may enable soil microbial communities to be active even when the environmental parameters change constantly. Microorganisms such as actinomycetes and fungi are rich source of a variety of antibiotics. Paclitaxel, an anticancer drug, is produced by many endophytic fungi associated with yew (Taxus) species. However, the new cultural and cloning techniques are enhancing the availability of beneficial natural products.

Chapter 19 - Microbial Transport

Publisher SummaryTransport of microorganisms is governed by a variety of factors, including filtration effects, physiological state of the cells, porous medium characteristics, water flow rates, predation, and intrinsic mobility of the cells. This chapter describes the factors that determine the transport of microorganisms and nucleic acids through soil and the subsurface such as microbial adhesion to and detachment from solid surfaces and the surrounding solution, the surface properties of the microbe, and the impact of water saturation and flow on movement. The chapter also examines the microbial survival and activity levels during transport, approaches to facilitate transport, and mathematical models that describe and predict microbial transport. Microbial transport is limited by filtration of cells by small pores that may result in bacteria excluded from the microporous domain of porous media; therefore, no microbial activity is expected to be there. The physiological state of microbial cells—such as capsule formation around the cells, nutrient availability, or starvation conditions—also influences its transport potential. Microbial adhesion is controlled primarily by the balance of electrostatic interactions, hydrophobic interactions, and van der Waals forces. Several novel approaches designed to facilitate microbial transport through the terrestrial profile—such as such as formation of ultramicrobacteria, biosurfactants, and gene transfer—are under investigation.

Chapter 17 - Microorganisms and Organic Pollutants

The objective of this chapter is to describe the interaction of microorganisms with organic pollutants. In particular, the ability of heterotrophic microbes to degrade organic pollutants via a process known as bioremediation is examined. The overall process of biodegradation is discussed, including the role of contaminant structure on bioavailability and toxicity. The influence of environmental factors on biodegradation is also described including essential nutrient requirements in addition to carbon substrate; redox conditions; moisture, temperature and other soil characteristics. Degradation of specific types of organic compounds is evaluated under both aerobic and anaerobic conditions. Major classes of compounds discussed include: aliphatics; alicyclics and aromatics including polyaromatic hydrocarbons (PAHs), polychlorinated biphenyls (PCBs) and pesticides. Finally, bioremediation technologies and strategies to enhance bioremediation effectiveness are described.

Chapter 20 - Microbial Communication: Bacteria/Bacteria and Bacteria/Host

It is now well recognized that most bacteria produce signals that allow communication between cells by emitting specific chemical signals. This cell–cell communication can be within a single population of bacteria (intraspecies signaling), between bacterial populations (interspecies signaling) or between bacteria and other organisms (interkingdom signaling). This chapter discusses the current understanding of bacterial signaling using examples of communication systems including: signaling in Gram-negative bacteria via quorum sensing with N-acyl homoserine lactones; signaling in Gram-positive bacteria via λ-butyryl lactones and small peptide signals; and signaling via Autoinducer-2 and -3, and bacterial neuropeptides. In addition are covered: bacterial eavesdropping; bacterial signal interference; and interkingdom signaling.

Surficial weathering of iron sulfide mine tailings under semi-arid climate

AbstractMine wastes introduce anthropogenic weathering profiles to the critical zone that often remain unvegetated for decades after mining cessation. As such, they are vulnerable to wind and water dispersion of particulate matter to adjacent ecosystems and residential communities. In sulfide-rich ore tailings, propagation to depth of the oxidative weathering front controls the depth-variation in speciation of major and trace elements. Despite the prevalence of surficial mine waste deposits in arid regions of the globe, few prior studies have been conducted to resolve the near-surface profile of sulfide ore tailings weathered under semi-arid climate. We investigated relations between gossan oxidative reaction-front propagation and the molecular speciation of iron and sulfur in tailings subjected to weathering in a semi-arid climate at an EPA Superfund Site in central Arizona (USA). Here we report a multi-method data set combining wet chemical and synchrotron-based X-ray diffraction (XRD) and X-ray absorption near-edge spectroscopy (XANES) methods to resolve the tight coupling of iron (Fe) and sulfur (S) geochemical changes in the top 2 m of tailings. Despite nearly invariant Fe and S concentration with depth (130–140 and 100–120 g kg−1, respectively), a sharp redox gradient and distinct morphological change was observed within the top 0.5 m, associated with a progressive oxidative alteration of ferrous sulfides to (oxyhydr)oxides and (hydroxy)sulfates. Transformation is nearly complete in surficial samples. Trends in molecular-scale alteration were co-located with a decrease in pH from 7.3 to 2.3, and shifts in Fe and S lability as measured via chemical extraction. Initial weathering products, ferrihydrite and gypsum, transform to schwertmannite, then jarosite-group minerals with an accompanying decrease in pH. Interestingly, thermodynamically stable phases such as goethite and hematite were not detected in any samples, but ferrihydrite was observed even in samples with the lowest pH, indicating its metastable persistence in these semiarid tailings. The resulting sharp geochemical speciation gradients in close proximity to the tailings surface have important implications for plant colonization, as well as mobility and bioavailability of co-associated toxic metal(loid)s.

Optimization of plant growth-promoting bacteria-assisted phytostabilization of mine tailings

AbstractRecent studies have indicated that plant growth-promoting bacteria (PGPB) can improve revegetation of arid mine tailings as measured by increased biomass production. The goals of the present study were first to evaluate how mode of application of known PGPB affects plant growth, and second to evaluate the effect of this inoculation on rhizosphere microbial community structure. PGPB application strategies investigated include preliminary surface sterilization of seeds (a common practice in phytoremediation trials) followed by a comparison of two application methods; immersion and alginate encapsulation. Results with two native desert plant species, Atriplex lentiformis and Buchloe dactyloides, suggest that seed surface sterilization prior to inoculation is not necessary to achieve beneficial effects of introduced PGPB. Both PGPB application techniques generally enhanced plant growth although results were both plant and PGPB specific. These results demonstrate that alginate encapsulation, which allows for long-term storage and easier application to seeds, is an effective way to inoculate PGPB. In addition, the influence of PGPB application on B. dactyloides rhizosphere community structure was evaluated using PCR-DGGE (denaturing gradient gel electrophoresis) analysis of bacterial DNA extracted from rhizosphere samples collected 75 d following planting. A comparative analysis of DGGE profiles was performed using canonical correspondence analysis (CCA). DGGE-CCA showed that rhizosphere community profiles from PGPB-inoculated treatments are significantly different from both uninoculated tailings rhizosphere profiles and profiles from the compost used to amend the tailings. Further, community profiles from B. dactyloides inoculated with the best performing PGPB (Arthro Mix) were significantly different from two other PGPB tested. These results suggest that introduced PGPB have the potential to influence the development of the rhizosphere community structure found in plants grown in mine tailings.

Synthesis and biological activities of flavolipids

AbstractSyntheses of the bacterial surfactants 6S,6S-, 9S,9S-, and 9U,9U-flavolipids confirmed the structures proposed for them from spectroscopic analysis of a flavolipid mixture and made pure flavolipids available for the first time. All three synthetic flavolipids and a straight chain analogue were found to be weakly cytotoxic and to inhibit metastatic cancer cell migration, with 9U,9U-flavolipid (the most abundant natural flavolipid) having the most activity. Biosynthetic routes to the branched side-chains of the flavolipids are suggested, and it is proposed that branched chains are employed to hinder biodegradation.

The impact of unconfined mine tailings in residential areas from a mining town in a semi-arid environment: Nacozari, Sonora, Mexico

AbstractPast mining activities in northern Mexico left a legacy of delerict landscapes devoid of vegetation and seasonal formation of salt efflorescence. Metal content was measured in mine tailings, efflorescent salts, soils, road dust, and residential soils to investigate contamination. Climatic effects such as heavy wind and rainfall events can have great impact on the dispersion of metals in semi-arid areas, since soils are typically sparsely vegetated. Geochemical analysis of this site revealed that even though total metal content in mine tailings was relatively low (e.g. Cu = 1000 mg kg−1), metals including Mn, Ba, Zn, and Cu were all found at significantly higher levels in efflorescence salts formed by evaporation on the tailings impoundment surface following the rainy season (e.g. Cu = 68,000 mg kg−1). Such efflorescent fine-grained salts are susceptible to wind erosion resulting in increased metal spread to nearby residential soils. Our results highlight the importance of seasonally dependent salt-formation and wind erosion in determining risk levels associated with potential inhalation or ingestion of airborne particulates originating from contaminated sites such as tailings impoundments. In low metal-content mine tailings located in arid and semi-arid environments, efflorescence salts could represent a human health risk and a challenge for plant establishment in mine tailings.

Effect of arbuscular mycorrhizal fungi on plant biomass and the rhizosphere microbial community structure of mesquite grown in acidic lead/zinc mine tailings

AbstractMine tailings in arid and semi-arid environments are barren of vegetation and subject to eolian dispersion and water erosion. Revegetation is a cost-effective strategy to reduce erosion processes and has wide public acceptance. A major cost of revegetation is the addition of amendments, such as compost, to allow plant establishment. In this paper we explore whether arbuscular mycorrhizal fungi (AMF) can help support plant growth in tailings at a reduced compost concentration. A greenhouse experiment was performed to determine the effects of three AMF inocula on biomass, shoot accumulation of heavy metals, and changes in the rhizosphere microbial community structure of the native plant Prosopis juliflora (mesquite). Plants were grown in an acidic lead/zinc mine tailings amended with 10% (w/w) compost amendment, which is slightly sub-optimal for plant growth in these tailings. After two months, AMF-inoculated plants showed increased dry biomass and root length (p < 0.05) and effective AMF colonization compared to controls grown in uninoculated compost-amended tailings. Mesquite shoot tissue lead and zinc concentrations did not exceed domestic animal toxicity limits regardless of whether AMF inoculation was used. The rhizosphere microbial community structure was assessed using denaturing gradient gel electrophoresis (DGGE) profiles of the small subunit RNA gene for bacteria and fungi. Canonical correspondence analysis (CCA) of DGGE profiles showed that the rhizosphere fungal community structure at the end of the experiment was significantly different from the community structure in the tailings, compost, and AMF inocula prior to planting. Further, CCA showed that AMF inoculation significantly influenced the development of both the fungal and bacterial rhizosphere community structures after two months. The changes observed in the rhizosphere microbial community structure may be either a direct effect of the AMF inocula, caused by changes in plant physiology induced by AMF, or a combination of both mechanisms.

Home gardening near a mining site in an arsenic-endemic region of Arizona: Assessing arsenic exposure dose and risk via ingestion of home garden vegetables, soils, and water

Highlights•Daily arsenic intake decreased in order of: water > soil > homegrown vegetables.•The excess cancer risk range for consumption of homegrown vegetables was 10− 8 to 10− 4.•The excess cancer risk range for incidental soil ingestion was 10− 6 to 10− 4.•Risk-based maximum As levels in garden soils are estimated.

Asthma and lower airway diseaseBacterial microbiota of the upper respiratory tract and childhood asthma

BackgroundPatients with asthma and healthy controls differ in bacterial colonization of the respiratory tract. The upper airways have been shown to reflect colonization of the lower airways, the actual site of inflammation in asthma, which is hardly accessible in population studies.ObjectiveWe sought to characterize the bacterial communities at 2 sites of the upper respiratory tract obtained from children from a rural area and to relate these to asthma.MethodsThe microbiota of 327 throat and 68 nasal samples from school-age farm and nonfarm children were analyzed by 454-pyrosequencing of the bacterial 16S ribosomal RNA gene.ResultsAlterations in nasal microbiota but not of throat microbiota were associated with asthma. Children with asthma had lower α- and β-diversity of the nasal microbiota as compared with healthy control children. Furthermore, asthma presence was positively associated with a specific operational taxonomic unit from the genus Moraxella in children not exposed to farming, whereas in farm children Moraxella colonization was unrelated to asthma. In nonfarm children, Moraxella colonization explained the association between bacterial diversity and asthma to a large extent.ConclusionsAsthma was mainly associated with an altered nasal microbiota characterized by lower diversity and Moraxella abundance. Children living on farms might not be susceptible to the disadvantageous effect of Moraxella. Prospective studies may clarify whether Moraxella outgrowth is a cause or a consequence of loss in diversity.

The influence of system complexity on bacterial transport in saturated porous media

AbstractA series of miscible-displacement column experiments were conducted under saturated flow conditions to systematically investigate the influence of physical and biological complexity on bacterial activity and fate in the presence and absence of a non-sorbing growth substrate, salicylate. Bacterial elution was monitored for three different systems; System I—a sterilized, inoculated, well-sorted sand, System II—a sterilized, inoculated, heterogeneous loamy sand (Hayhook), and System III—two different unsterilized loamy sands (Hayhook and Vinton) each with their associated indigenous microbial community. Results show that System I behaved ideally with respect to both cell and substrate transport, wherein: (1) growth occurred in response to substrate addition, (2) cell elution increased in response to the substrate pulse, and (3) breakthrough curves were reproducible for both substrate and cell elution. In contrast, System II showed ideal behavior with respect to substrate transport but showed variable behavior for cell transport. Further, there was no measurable growth in response to substrate addition and no increase in cell elution during the salicylate pulse. System III exhibited non-ideal behavior for both substrate and cell transport. Of particular interest is the fact that the indigenous communities of the two soils behaved differently. Specifically, for the Hayhook soil, an increased elution response was observed for the heterotrophic population while the salicylate-degrading community was preferentially retained in the column. In contrast for the Vinton soil, the substrate pulse did not elicit an elution response from either the heterotrophic or salicylate-degrading community from the culturable, indigenous Vinton microorganisms. For Systems II and III, the observed variability appears to be associated with the biological component of the system, since sterile controls were reproducible. This type of systematic study is critical for understanding cell and substrate transport behavior in complex, heterogeneous systems, and illustrates the potential uncertainty associated with measurements in such systems.

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