Environmental Microbiology and Microbial Ecology Commons^™

18s Rdna Dataset Profiling Microeukaryotic Populations Within Chicago Area Nearshore Waters, Daniel Searle, Emily Sible, Alexandria Cooper, Catherine Putonti

Bioinformatics Faculty Publications

Despite their critical role in the aquatic food web and nutrient cycling, microeukaryotes within freshwater environments are under-studied. Herein we present the first high-throughput molecular survey of microeukaryotes within Lake Michigan. Every two weeks from May 13 to August 5, 2014, we collected surface water samples from the nearshore waters of four Chicago area beaches: Gillson Park, Montrose Beach, 57th Street Beach, and Calumet Beach. Four biological replicates were collected for each sampling date and location, resulting in 112 samples. Eighty-nine of these samples were surveyed through targeted sequencing of the V7 and V8 regions of the 18S rDNA gene. …

Microbial Biofilm Community Variation In Flowing Habitats: Potential Utility As Bioindicators Of Postmortem Submersion Intervals, Jennifer M. Lang, Racheal Erb, Jennifer L. Pechal, John R. Wallace, Ryan W. Mcewan, Mark Eric Benbow

Biology Faculty Publications

Biofilms are a ubiquitous formation of microbial communities found on surfaces in aqueous environments. These structures have been investigated as biomonitoring indicators for stream heath, and here were used for the potential use in forensic sciences. Biofilm successional development has been proposed as a method to determine the postmortem submersion interval (PMSI) of remains because there are no standard methods for estimating the PMSI and biofilms are ubiquitous in aquatic habitats. We sought to compare the development of epinecrotic (biofilms on Sus scrofa domesticus carcasses) and epilithic (biofilms on unglazed ceramic tiles) communities in two small streams using bacterial automated …

An Assessment Of West Virginia Watersheds Through The Use Of Geographic Information System (Gis), Nathan Thomas Hoxie

Theses, Dissertations and Capstones

Analysis of West Virginia Department of Environmental Protection (WVDEP) agency’s Stream Condition Index and habitat assessment data compared two cycles of data. Geographic Information System (GIS) was used to develop a kriging model to project scores. Scores were calculated for Hydrologic Unit Code (HUC) eight and ten using Zonal statistics. The Getis-Ord Gi Star was used to identify high and low value clusters. Land use and impervious surface data was gathered from the United States Geological Survey (USGS) to assess impacts to watersheds. The results for WVSCI and habitat assessment showed that there was an improvement between cycles. Negative WVSCI …

Detection Of Fecal Contamination Using Molecular Methods, Kristina K. Bowen

Independent Research Projects

This study explores the process of designing a molecular method to detect fecal contamination in the urban watersheds of Rock Island and Moline, Illinois. These urban watersheds are known to contain high ammonia levels and total dissolved solids based on previous studies. Additionally there is concern about the aging combined sewer and storm water system. Therefore, these watersheds are thought to have poor water quality including fecal contamination. Existing molecular methods used for detecting fecal contamination require a considerable amount of resources in the laboratory. Our goal was to design a molecular method that requires fewer resources and can continue …

Enhancing The Industrial Potential Of Filamentous Cyanobacteria, Tylor J. Johnson

Electronic Theses and Dissertations

The objectives of this project were to improve the industrial potential of filamentous N2-fixing cyanobacteria by increasing its biofuel tolerance, and to evaluate the economic feasibility and environmental impacts of a theoretical, cyanobacteria-based biofuel production facility. To develop a method to quantify filamentous cyanobacteria in dilute culture media, a dual-stained fluorescence assay was evaluated. While the viable cell stain (SYTO® 9) was accurate, the non-viable cell stain (propidium iodide) also bound to viable cells. Additional non-viable cell stains were evaluated, but none were accurate at quantifying viability. Thus we concluded that the viable cell stain SYTO® 9 is a reliable …

Diversity Of Free-Living Nitrogen Fixing Bacteria In The Badlands Of South Dakota, Bibha Dahal

Electronic Theses and Dissertations

Biological Nitrogen Fixation is carried out by a highly diverse group of members of the domains Bacteria and Archaea which express a nitrogenase enzyme complex and are termed diazotrophs. The best known diazotrophs form symbiotic associations with plants, but free-living nitrogen fixing bacteria also contribute a substantial amount of nitrogen to ecosystems, including arid lands. The aim of this study was to isolate free-living diazotrophs from the soil crusts of sod tables of South Dakota Badlands. Samples were obtained from sod tables and the surrounding base (matrix) in spring and fall of 2014. A culture dependent approach was used to …

The Contribution Of Marine Aggregate-Associated Bacteria To The Accumulation Of Pathogenic Bacteria In Oysters: An Agent-Based Model, Andrew M. Kramer, J. Evan Ward, Fred C. Dobbs, Melissa L. Pierce

OES Faculty Publications

Bivalves process large volumes of water, leading to their accumulation of bacteria, including potential human pathogens (e.g., vibrios). These bacteria are captured at low efficiencies when freely suspended in the water column, but they also attach to marine aggregates, which are captured with near 100% efficiency. For this reason, and because they are often enriched with heterotrophic bacteria, marine aggregates have been hypothesized to function as important transporters of bacteria into bivalves. The relative contribution of aggregates and unattached bacteria to the accumulation of these cells, however, is unknown. We developed an agent-based model to simulate accumulation of vibrio-type bacteria …

Isolation And Identification Of Bacterial Endosymbionts In The Brooding Brittle Star Amphipholis Squamata, Abbey Rose Tedford

Honors Theses and Capstones

Symbiotic associations with subcuticular bacteria (SCB) have been identified and studied in numerous echinoderms, including the SCB of the brooding brittle star, Amphipholis squamata. These SCB, however, have not been studied using current next generation sequencing technologies. Previous studies on the SCB of A. squamata placed these bacteria in the genus Vibrio (γ-Proteobacteria), but subsequent studies suggested that the SCB are primarily composed of α-Proteobacteria. The present study examines the taxonomic composition of SCB associated with A. squamata from the Northwest Atlantic. DNA was extracted using a CTAB protocol and 16S rRNA sequences were amplified …

Endosymbiotic Bacteria In The Bed Bug, Cimex Lectularius L. (Hemiptera: Cimicidae), Mark H. Goodman

Theses and Dissertations--Entomology

The return of bed bugs to prominence as an urban pest has precipitated an emphatic research response from the scientific community in an effort to better understand their biology and management. However, not all aspects of bed bug biology have received equal attention. The role of symbiotic bacteria in the normal function and biology of insects is often underappreciated, and this is true of bed bugs. Bed bugs have two main endosymbiotic bacteria, a Wolbachia species and a poorly-characterized gamma-proteobacterium referred to as BLS. However, their interactions with the host are poorly understood. I explored various aspects of these symbionts …

Attached Algae As An Indicator Of Water Quality: A Study Of The Viability Of Genomic Taxonomic Methods, Allison R. Wood

Honors Theses and Capstones

This research involved evaluating algae as an indicator of water quality in New Hampshire's rivers, with a focus on the Great Bay Estuary. The project had three main goals. First, determining whether or not algae would work as an indicator of water quality in the great bay ecosystem, an environment where tidal currents are strong and water composition is mixed. The second goal was to compare traditional microscopic methods of taxonomy with emerging genomic methods, increasing the economic viability of attached algae monitoring. The third project goal, still underway, is to evaluate massive amounts of genomic data from the Great …

Effects Of Epichloë Coenophiala−Tall Fescue Symbiosis On Plant-Microbe-Soil Interactions In A Temperate Pasture, Lindsey C. Slaughter

Theses and Dissertations--Plant and Soil Sciences

Plants interact in myriad ways with microorganisms to influence ecosystem processes such as nutrient cycling, which can regulate ecosystem response to global change. One important plant-microbe symbiosis occurs between cool-season grasses and asexual fungal Epichloë endophytes, such as tall fescue (Schedonorus arundinaceus) and Epichloë coenophiala. Because the common toxic strain of the endophyte (CTE) harms grazing livestock, non-livestock toxic endophyte (NTE) strains have been developed and are increasingly deployed in pastures. Little is known about how these symbioses impact other plant-microbe interactions and microbe-mediated soil processes in grassland ecosystems. I conducted three studies to determine how E. …

Relationships Between Fecal Indicator Bacteria And Environmental Factors At Edgewater Beach, Anna M. King

Williams Honors College, Honors Research Projects

To provide more timely estimates of indicator bacteria concentrations in recreational waters, environmental agencies are using predictive models to supplement conventional bacteria enumeration methods. As a tool to develop predictive models, correlational relationships between variables can be examined, to determine the statistical significance of explanatory variables. Prior research at Lake Erie beaches suggests that environmental conditions such as average wave height, rainfall, turbidity, and water temperature may demonstrate a strong relationship to concentrations of fecal indicator bacteria Escherichia coli and Enterococcus faecalis (enterococci). These relationships were examined at Edgewater Beach in Cleveland, Ohio, using statistical correlation tests on data collected …

Arbuscular Mycorrhizal Fungi Of Northern White Cedar (Thuja Occidentalis L.): Habitat Effects On Fungal Communities And Inoculum Effects On Plant Growth On Acid Peat Soils, Guswarni Anwar

Dissertations, Master's Theses and Master's Reports

The relationship of arbuscular mycorrhizal (AM) fungi with northern white cedar (NWC) was examined from the perspective of both fundamental questions about habitat specificity in the root fungal community, as well as applied questions regarding AM fungal efficacy in NWC restoration in peat soils. I performed two experiments testing the effects of AM fungi on survival, growth, and nutrition of NWC seedlings; and one molecular study to determine the habitat effects on community composition of NWC root-associated fungi. First, a greenhouse AM inoculation experiment was conducted in factorial combination with fertilization and liming to examine conditional effectiveness of AM fungal …

Sequence-Based Methods For Detecting And Evaluating The Human Gut Mycobiome, Mallory J. Suhr, Nabaraj Banjara, Heather E. Hallen-Adams

Department of Food Science and Technology: Faculty Publications

We surveyed the fungal microbiota in 16 fecal samples from healthy humans with a vegetarian diet. Fungi were identified using molecular cloning, 454 pyrosequencing and a Luminex analyte specific reagent (ASR) assay, all targeting the ITS region of the rRNA genes. Fungi were detected in each fecal sample and at least 46 distinct fungal operational taxonomic units (OTUs) were detected, from two phyla — Ascomycota and Basidiomycota. Fusarium was the most abundant genus, followed by Malassezia, Penicillium, Aspergillus, and Candida. Commonly detected fungi such as Aspergillus and Penicillium, as well as known dietary fungi Agaricus bisporus and …

Noninvasive Measurement Of Electrical Events Associated With A Single Chlorovirus Infection Of A Microalgal Cell, Seung-Woo Lee, Eun-Hee Lee, Gerhard Thiel, James L. Van Etten, Ravi Saraf

Department of Chemical and Biomolecular Engineering: Faculty Publications

Chlorovirus Paramecium bursaria chlorella virus 1 (PBCV-1) contains a viral-encoded K⁺ channel imbedded in its internal membrane, which triggers host plasma membrane depolarization during virus infection. This early stage of infection was monitored at high resolution by recording the cell membrane depolarization of a single Chlorella cell during infection by a single PBCV-1 particle. The measurement was achieved by depositing the cells onto a network of one-dimensional necklaces of Au nanoparticles, which spanned two electrodes 70 μm apart. The nanoparticle necklace array has been shown to behave as a single-electron device at room temperature. The resulting electrochemical field-effect transistor …

Killer Toxin From Several Food-Derived Debaryomyces Hansenii Strains Effective Against Pathogenic Candida Yeasts, Nabaraj Banjara, Kenneth Nickerson, Mallory J. Suhr, Heather E. Hallen-Adams

Kenneth Nickerson Papers

Candida yeasts are the dominant fungi in the healthy human microbiome, but are well-known for causing disease following a variety of perturbations. Evaluation of fungal populations from the healthy human gut revealed a significant negative correlation between the foodborne yeast, Debaryomyces hansenii, and Candida species. D. hansenii is reported to produce killer toxins (mycocins) effective against other yeast species. In order to better understand this phenomenon, a collection of 42 D. hansenii isolates was obtained from 22 cheeses and evaluated for killer activity against Candida albicans and Candida tropicalis over a range of temperatures and pH values. Twenty three …

The Impact Of Urbanization On Mosquito-Borne Viruses, Nikhita Puthuveetil

Undergraduate Research Posters

Mosquito-borne diseases such as yellow fever, dengue, and West Nile are rapidly emerging across the globe. Their emergence is often aided by the growth of their vector population, or the organisms that transmit the virus to the host. Urbanization and land use often destroys the habitat of the virus and its vector. However, the virus and its vector often survive despite the changes to its environment. The goal of this paper is to find out exactly how urbanization and changes in land use affect mosquito-borne viruses and how these viruses survive despite the destruction of their habitats. To understand how …

Toxicity Of Engineered Nanomaterials To Plant Growth Promoting Rhizobacteria, Ricky W. Lewis

Theses and Dissertations--Plant and Soil Sciences

Engineered nanomaterials (ENMs) have become ubiquitous in consumer products and industrial applications, and consequently the environment. Much of the environmentally released ENMs are expected to enter terrestrial ecosystems via land application of nano-enriched biosolids to agricultural fields. Among the organisms most likely to encounter nano-enriched biosolids are the key soil bacteria known as plant growth promoting rhizobacteria (PGPR). I reviewed what is known concerning the toxicological effects of ENMs to PGPR and observed the need for high-throughput methods to evaluate lethal and sublethal toxic responses of aerobic microbes. I addressed this issue by developing high-throughput microplate assays which allowed me …

Tillage And Fertilization Influences On Autotrophic Nitrifiers In Agricultural Soil, Shuang Liu

Theses and Dissertations--Plant and Soil Sciences

Nitrification is a biological oxidation of NH₃ to NO₂^- and then to NO₃^-. Understanding how the nitrifier community responds to agricultural management is essential because the community composition is complex and functional distinction of subgroups occurs. Better managing nitrifiers could benefit the environment by increasing nitrogen (N) fertilizer use efficiency, decreasing NO₃^- leaching, and reducing NO and N₂O emissions. This study examined how long-term N fertilization and tillage influenced nitrifier density, ratios, nitrification rates, and the community structure of ammonia-oxidizing bacteria (AOB), ammonia-oxidizing archaea (AOA), and nitrite-oxidizing bacteria (NOB). The …

Studies On Regulation Of Pqq-Dependent Phosphate Solubilization Among Rhizosphere Dwelling Bacteria, Ran An

Theses and Dissertations--Plant and Soil Sciences

Plant growth promotion can be enhanced by soil- and rhizosphere-dwelling bacteria by a several different methods. One method is by promoting nutrient acquisition from soil. Phosphorus is an essential nutrient that plants obtain from soil, but in many cases it is immobilized in forms that are not available for plant uptake. Bacteria can solubilize insoluble soil phosphates by secreting gluconic acid. This chemical is produced from glucose by the activity of the bacterial enzyme glucose dehydrogenase, which requires a coenzyme called PQQ. In this dissertation, I studied the regulation of the glucose dehydrogenase enzyme and the PQQ coenzyme in the …

Response Of Soil Microbial Communities To Saltwater Intrusion In Tidal Freshwater Wetlands, Chansotheary Dang

Theses and Dissertations

Saltwater intrusion due to global change is expected to have a detrimental effect on the biogeochemistry of tidal freshwater wetlands. Of particular concern is that fact that salinization can alter the role of these ecosystems in the global carbon cycling by causing shifts in microbial metabolism that alter greenhouse gas emissions and increase carbon mineralization rates. However, our understanding of how wetland microbial community dynamics will respond to saltwater intrusion is limited. To address this knowledge gap and increase our understanding of how microbial communities in tidal freshwater wetlands change over time (1, 3, 12, and 49 weeks) under elevated …

Sulfate-Reducing Bacteria Community Analysis: Isco/Isb Coupled Remediation, Christopher K. Bartlett

Theses and Dissertations (Comprehensive)

Improved techniques for remediating groundwater systems are required for the more than 500,000 contaminated sites in North America. Many of these sites are the legacy of historical industrial operations, inappropriate disposal practices and accidental releases. The most widely observed contaminant at many of these sites is petroleum hydrocarbons (PHCs). Recently, remediation efforts that involve the sequential application of treatment technologies have gained widespread interest. One specific sequential technology application or treatment train employs the aggressive nature of a chemical oxidation followed by bioremediation for polishing. When persulfate is used as the chemical oxidant its natural degradation by-product is sulfate, an …

Super-Killers: Environmental Isolates That Antagonize Pathogenic Vibrio, Abigail Joy

Honors Projects

Vibrio are members of a bacterial group that thrive in diverse aquatic environments including on the surface of aquatic animals, free-living in the water column, and in association with suspended particles. The total Vibrio counts in the coastal ocean ranges from 10³-10⁵ per milliliter of water depending on seasons and water temperature. Although many different species of Vibrio persist in the water column, pathogenic strains, such as Vibrio cholerae and Vibrio parahaemolyticus are absent or rare in marine environments. We hypothesize that the low abundance of these pathogenic species may be due to interspecific competition among environmental …

Fungi On White-Nose Infected Bats (Myotis Spp.) In Eastern Canada Show No Decline In Diversity Associated With Pseudogymnoascus Destructans (Ascomycota: Pseudeurotiaceae), Karen J. Vanderwolf, David Malloch, Donald F. Mcalpine

International Journal of Speleology

The introduction of the fungal pathogen Pseudogymnoascus destructans (Pd) to North America has stimulated research on the poorly known mycology of caves. It is possible that the introduction of Pd reduces the diversity of fungi associated with bats hibernating in caves. To test this hypothesis we examined the fungal assemblages associated with hibernating bats (Myotis spp.) pre- and post- white-nose syndrome (WNS) infection in eastern Canada using culture-dependent methods. We found the mean number of fungal taxa isolated from bats/hibernaculum was not significantly different between pre-infection (29.6 ± 6.1SD) and post-infection with WNS (32.4 ± 4.3). Although …

The Human Gut Mycobiome: Pitfalls And Potentials — A Mycologist's Perspective, Mallory J. Suhr, Heather E. Hallen-Adams

Department of Food Science and Technology: Faculty Publications

We have entered the Age of the Microbiome, with new studies appearing constantly and whole journals devoted to the human microbiome. While bacteria outnumber other gut microbes by orders of magnitude, eukaryotes are consistently found in the human gut, and are represented primarily by the fungi. Compiling 36 studies spanning from 1917 to 2015, we found at least 267 distinct fungal taxa have been reported from the human gut, and seemingly every new study includes one or more fungi not previously described from this niche. This diversity, while impressive, is illusory. If we examine gut fungi, we will quickly observe …

Production And Harvest Of Microalgae In Wastewater Raceways With Resource Recycling, Alexander Colin Roberts

Master's Theses

Microalgae can be grown on municipal wastewater media to both treat the wastewater and produce feedstock for algae biofuel production. However the reliability of treatment must be demonstrated, as well as high areal algae productivity on recycled wastewater media and efficient sedimentation harvesting. This processes was studied at pilot scale in the present research.

A pilot facility was operated with nine CO₂-supplemented raceway ponds, each with a 33-m² surface area and a 0.3-m depth, continuously from March 6, 2013 through September 24, 2014. The ponds were operated as three sets of triplicates with two sets continuously fed …

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Biology Faculty Articles

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon …

Seeps And Springs At A Platteville “Observatory” On The River Bluffs, Bj Bonin, Greg Brick, Julia R. Steenberg

Sinkhole Conference 2015

Residential building construction along the Mississippi River bluffs in the 1970s created a unique enclosed outcrop of the Late Ordovician Platteville Formation at Lilydale, Minnesota. This outcrop was examined in early 2013 after a newly-formed spring flooded an elevator shaft the previous year, drawing attention to the foundation conditions. The Lexington Riverside property is a six story condominium complex constructed within the top of the bluff. A two-level underground parking garage was built into the bluff. Bedrock was mechanically excavated to accommodate the construction of the building, creating an unweathered rock surface. The space between the structure and the excavated …

A Tail Of Two Phages: Genomic And Functional Analysis Of Listeria Monocytogenes Phages Vb_Lmos_188 And Vb_Lmos_293 Reveal The Receptor-Binding Proteins Involved In Host Specificity, Aidan Casey, Kieran Jordan, Horst Neve, Aidan Coffey, Olivia Mcauliffe

Department of Biological Sciences Publications

The physical characteristics of bacteriophages establish them as viable candidates for downstream development of pathogen detection assays and biocontrol measures. To utilize phages for such purposes, a detailed knowledge of their host interaction mechanisms is a prerequisite. There is currently a wealth of knowledge available concerning Gram-negative phage-host interaction, but little by comparison for Gram-positive phages and Listeria phages in particular. In this research, the lytic spectrum of two recently isolated Listeria monocytogenes phages (vB_LmoS_188 and vB_LmoS_293) was determined, and the genomic basis for their observed serotype 4b/4e host-specificity was investigated using comparative genomics. The late tail genes of these …

Bacteriophages Isolated From Lake Michigan Demonstrate Broad Host-Range Across Several Bacterial Phyla, Kema Malki, Alex Kula, Katherine Bruder, Emily Sible, Thomas Hatzopoulos, Stephanie Steidel, Siobhan C. Watkins, Catherine Putonti

Biology: Faculty Publications and Other Works

BACKGROUND:

The study of bacteriophages continues to generate key information about microbial interactions in the environment. Many phenotypic characteristics of bacteriophages cannot be examined by sequencing alone, further highlighting the necessity for isolation and examination of phages from environmental samples. While much of our current knowledge base has been generated by the study of marine phages, freshwater viruses are understudied in comparison. Our group has previously conducted metagenomics-based studies samples collected from Lake Michigan - the data presented in this study relate to four phages that were extracted from the same samples.

FINDINGS:

Four phages were extracted from Lake Michigan …