Microbial ecology of Thiobacillus ferrooxidans

FINAL TECHNICAL REPORT TO U.S. DEPARTMENT OF THE INTERIOR Geological Survey Washington. D.C.The contents of this report were developed in part under a grant from the Department of the Interior, U.S. Geological Survey. Grant number 14-08-0001-61313

Kinetics of chlorine depletion and microbial growth in household plumbing systems

To date, the microbial ecology of water treatment and distribution systems has never been systematically explored. Despite chronic problems with microbial growths in water distribution systems, the waterworks literature would indicate that the fundamentals, techniques and applications of microbial ecology are virtually unknown to the waterworks profession. Microbial ecology is the science that explores the relationships between microorganisms and their environment. A study of microbial ecology involves an assessment of the changes in the total and individual members of the microbial community. In distribution systems, the microbial ecology would be influenced by the influx of organisms, the surface colonization of distribution mains, the invasion of distribution systems by organisms from external sources, variations in flow, the chemical composition of the distributed water and the effective concentration of residual disinfectant. In addition, seasonal water temperature changes would be expected to affect total microbial populations. An assessment of microbial ecology requires the determination of, at least, four basic parameters.Project # G-1235-02 Agreement # 14-08-0001-G-1235-0

Space Microbial Ecology

With the expansion of human space exploration, there is a growing demand to better understand the impacts of space stressors such as microgravity (µG), space radiation, extreme temperatures, and extreme isolation. Research has shown that space stressors alter bacteria response. The changes seen include increases in biofilm formation, antibiotic resistance, and growth rate. Understanding the effects of these changes is vital as they can affect astronaut health, spacecraft life support systems, and space crops used for food. The ERAU Space Microbiology Lab (SML) is working to show how microbial communities are affected by simulated µG. In natural microbial communities (e.g., human gut microbiome), bacteria can develop antagonistic or synergistic relationships between different species. By seeing community development in simulated µG, we can gain insight on how microbial communities adapt to the space environment. Our research was focused on evaluating the changes of a mixed bacteria culture exposed to simulated µG using an EagleStat, a microgravity analog developed by the SML. In the experiment Escherichia coli and Staphylococcus epidermidis were chosen for simulated µG mixed culture exposure due to their visual and physical differentiating characteristics. Results have shown that S.epidermidis can grow to higher colony densities while under sim µG

Space Microbial Ecology

With the expansion of human space exploration, there is a growing demand to better understand the impacts of space stressors. These stressors include microgravity (µG), space radiation, extreme temperatures, and extreme isolation. Ongoing research has demonstrated that the space environment alters the physiology of bacteria. The changes observed have included increases in biofilm formation, antibiotic resistance, and growth rate. Understanding the effects on bacteria in these conditions is vital as they can affect astronaut health, spacecraft life support systems, and space crops used for food. The ERAU Space Microbiology Lab (SML) is working to identify how microbial communities are impacted by simulated µG. In natural microbial communities (e.g., human gut microbiome), bacteria can develop antagonistic or synergistic relationships between different species. Based on what we know about the response of individual species to space conditions, their interaction with other species and the host can change as well. By observing community development in simulated µG, we can gain insight on how microbial communities naturally adapt to the space environment. Our research is focused on observing the changes of a mixed culture of two bacteria subjected to simulated µG using the EagleStat, a microgravity analog developed by the SML. The mixed culture consists of Escherichia coli and Staphylococcus epidermidis bacteria due to the ability to separate the bacteria visually and physically after simulated µG exposure. Bacterial response will be evaluated by colony composition, biofilm development, antibiotic resistance, and differential gene expression of biofilm and virulence related genes

The Community Simulator: A Python package for microbial ecology

Natural microbial communities contain hundreds to thousands of interacting species. For this reason, computational simulations are playing an increasingly important role in microbial ecology. In this manuscript, we present a new open-source, freely available Python package called Community Simulator for simulating microbial population dynamics in a reproducible, transparent and scalable way. The Community Simulator includes five major elements: tools for preparing the initial states and environmental conditions for a set of samples, automatic generation of dynamical equations based on a dictionary of modeling assumptions, random parameter sampling with tunable levels of metabolic and taxonomic structure, parallel integration of the dynamical equations, and support for metacommunity dynamics with migration between samples. To significantly speed up simulations using Community Simulator, our Python package implements a new Expectation-Maximization (EM) algorithm for finding equilibrium states of community dynamics that exploits a recently discovered duality between ecological dynamics and convex optimization. We present data showing that this EM algorithm improves performance by between one and two orders compared to direct numerical integration of the corresponding ordinary differential equations. We conclude by listing several recent applications of the Community Simulator to problems in microbial ecology, and discussing possible extensions of the package for directly analyzing microbiome compositional data.Comment: 14 pages, 6 figure

Effect of Ethanol on Microbial Community Structure and Function During Natural Attenuation of Benzene, Toluene, and \u3cem\u3eo\u3c/em\u3e-Xylene in a Sulfate-reducing Aquifer

Ethanol (EtOH) is a commonly used fuel oxygenate in reformulated gasoline and is an alternative fuel and fuel supplement. Effects of EtOH release on aquifer microbial ecology and geochemistry have not been well characterized in situ. We performed a controlled field release of petroleum constituents (benzene (B), toluene (T), o-xylene (o-X) at ∼1–3 mg/L each) with and without EtOH (∼500 mg/L). Mixed linear modeling (MLM) assessed effects on the microbial ecology of a naturally sulfidic aquifer and how the microbial community affected B, T, and o-X plume lengths and aquifer geochemistry. Changes in microbial community structure were determined by quantitative polymerase chain reaction (qPCR) targeting Bacteria, Archaea, and sulfate reducing bacteria (SRB); SRB were enumerated using a novel qPCR method targeting the adenosine-5′-phosphosulfate reductase gene. Bacterial and SRB densities increased with and without EtOH-amendment (1−8 orders of magnitude). Significant increases in Archaeal species richness; Archaeal cell densities (3–6 orders of magnitude); B, T, and o-X plume lengths; depletion of sulfate; and induction of methanogenic conditions were only observed with EtOH-amendment. MLM supported the conclusion that EtOH-amendment altered microbial community structure and function, which in turn lowered the aquifer redox state and led to a reduction in bioattenuation rates of B, T, and o-X

The maturing of microbial ecology

A.J. Kluyver and C.B. van Niel introduced many scientists to the exceptional metabolic capacity of microbes and their remarkable ability to adapt to changing environments in The Microbe’s Contribution to Biology. Beyond providing an overview of the physiology and adaptability of microbes, the book outlined many of the basic principles for the emerging discipline of microbial ecology. While the study of pure cultures was highlighted, provided a unifying framework for understanding the vast metabolic potential of microbes and their roles in the global cycling of elements, extrapolation from pure cultures to natural environments has often been overshadowed by microbiologists’ inability to culture many of the microbes seen in natural environments. A combination of genomic approaches is now providing a culture-independent view of the microbial world, revealing a more diverse and dynamic community of microbes than originally anticipated. As methods for determining the diversity of microbial communities become increasingly accessible, a major challenge to microbial ecologists is to link the structure of natural microbial communities with their functions. This article presents several examples from studies of aquatic and terrestrial microbial communities in which culture and culture-independent methods are providing an enhanced appreciation for the microbe’s contribution to the evolution and maintenance of life on Earth, and offers some thoughts about the graduate-level educational programs needed to enhance the maturing field of microbial ecology. [Int Microbiol 2006; 9(3):217-223