Environmental Microbiology and Microbial Ecology Commons^™

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 …

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 …

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 …

The Contribution Of Syntrophic Fatty-Acid Degrading Microbial Communities To Anaerobic Digester Function And Stability, Prince Peter Mathai

Dissertations (1934 -)

Anaerobic digestion (AD), the conversion of complex organic matter to methane, occurs through a series of reactions mediated by different guilds of microorganisms. AD process imbalances, such as organic overload or high organic loading rates (OLR), can result in the accumulation of volatile fatty acids (VFA) e.g., propionate, which must be degraded to maintain stable reactor function. VFAs are metabolized by syntrophic fatty-acid degrading bacteria (SFAB) in association with methanogenic archaea (collectively, syntrophic microbial communities, SMC). Despite their indispensable role in AD, little is known about the ecology of SFAB, especially under stressed conditions. To facilitate ecological studies, four quantitative …

Demographics And Transfer Of Escherichia Coli Within Bos Taurus Populations, Joshua Ryan Dillard

Master's Theses

In the United States, symptoms caused by pathogenic strains of Escherichia coli are on the rise. A major source of these pathogenic strains is the E. coli in the digestive tract of cattle. The purpose of this project was to determine if E. coli are transferred between individuals of the same species and if interspecies transmission is possible. Proximity of cattle was also studied as a contributing factor to the transfer of E. coli. To accomplish this goal, E. coli isolates from cattle and cohabitating ground squirrels were compared through a new method of bacterial strain typing called pyroprinting. …

An Exploration Of The Phylogenetic Placement Of Recently Discovered Ultrasmall Archaeal Lineages, Jeffrey M. O'Brien

Honors Scholar Theses

In recent years, several new clades within the domain Achaea have been discovered. This is due in part to microbiological sampling of novel environments, and the increasing ability to detect and sequence uncultivable organisms through metagenomic analysis. These organisms share certain features, such as small cell size and streamlined genomes. Reduction in genome size can present difficulties to phylogenetic reconstruction programs. Since there is less genetic data to work with, these organisms often have missing genes in concatenated multiple sequence alignments. Evolutionary Biologists have not reached a consensus on the placement of these lineages in the archaeal evolutionary tree. There …

Suitability Of Great South Bay, New York To Blooms Of Pfiesteria Piscicida And P. Shumwayae Prior To Superstorm Sandy, October 29, 2012, Pawel Tomasz Zablocki

Theses and Dissertations

Pfiesteria piscicida and P. shumwayae are toxic dinoflagellates implicated in massive fish kills in North Carolina and Maryland during 1990s. A set of physical, chemica l, and biological factors influence population dynamics of these organisms. This study employs i nformation gathered from relevant literature on temperature, salinity, dissolved oxygen, pH, turbulent mixing, and dissolved nutrients, bacteria, algae, microzooplankton, mesozooplankton, bivalve m ollusks, finfish, and other toxic dinoflagellates, which influence Pfiesteria population dynamics. The research focused on whether conditions in the Great South Bay, Long Island, New York were suitable to blooms of Pfiesteria species prior to the passage of superstorm …

You Don’T Have To Go Home But You Carrot Stay Here: Root-Knot Nematode Biological Control In Carrots, Casey R. Martin, Sahar Abdelrazek, Lori A. Hoagland

The Summer Undergraduate Research Fellowship (SURF) Symposium

Root-knot nematodes cause tens of billions of dollars in damages annually in agricultural production. The enormous economic losses brought about by nematodes, combined with the downsides to current methods for handling them, have led to an increased focus in understanding natural plant defense mechanisms and finding alternative methods to lessen the damage done by root-knot nematodes. Endophyte biocontrol agents such as Trichoderma harzianum have shown promise in reducing nematode damage. Recent studies have demonstrated that soil management practices and plant genotype can influence endophyte community structure, but it is unclear whether such differences influence susceptibility to nematode damage. This study …

How Many Particles Are Present In The Air? Bioaerosol Detection Using An Air Particle Counter, Angie Pamela Rivera, Parag Vaishampayan

STAR Program Research Presentations

Relative cleanliness in terms of particle abundance in spacecraft assembly facilities is determined by particle counts carried out in clean rooms during resting conditions. Particle counters assess total particles and particle size distribution, but do not distinguish inert particles from biological particles, which may include bacterial spores that are resistant to standard cleanroom sterilization procedures. Current cleanroom certifications do not fully assess the effects of human presence on spacecraft contamination since humans are known symbionts to enumerate microorganisms and assessments are performed at rest when there is no human presence. In this study, contamination risks and bioburden in spacecraft assembly …

Collecting Diverse Microorganisms From Rover Spacecraft, Jennifer I. Jacobs, Arianna Jefferson, Heidi Aronson, James Tan, Wayne Schubert, Parag Vaishampayan

STAR Program Research Presentations

. The Planetary Protection discipline at NASA’s Jet Propulsion Laboratory develops and implements procedures to prevent both forward and backward contamination between the Earth and solar system bodies. However, there will always be some microorganisms that will be resistant to the strictest of sterilization methods. In order understand the microorganisms found on spacecraft during assembly, and to rapidly identify them, a mass spectrometry approach was developed. As an experimental approach, a custom database was created for a subset of microorganisms in the Planetary Protection Archive. In order to make the database as accurate and efficient as possible, several different procedures …

Isolation Of Possible Biocontrol Endophytic Bacteria From Solanum Tuberosum Effective Against Streptomyces Scabies., Annie Flatley, Luke Ogle, Adam Noel, Erica Fraley, Alaxandra Goodman, Donna Becker

Poster Sessions

Use of biological control offers a cost effective and environmentally safe method for controlling plant diseases. Biocontrol agents that can colonize roots and live endophytically within plant tissue should allow for effective disease control. The goal of this research was to develop protocols to isolate putative Streptomyces species from potato stem and tuber tissue due to their ability to produce inhibitory compounds which could potentially reduce diseases caused by Streptomyces scabies. Endophyte isolation from Solanum tuberosum (potato) plants (stem and tuber tissues) that were grown in a biocontrol field trial were the focus of this study. Several surface …

Use Of Two Pathogen-Inhibiting Streptomyces Isolates For Biocontrol Of Scab Disease Of Raphanus Sativus, Tyler Park, Nichole Klingler, Adam Noel, Luke Ogle, Annie Flatley, Donna Becker

Poster Sessions

Streptomyces species are ubiquitous soil bacteria that are promising as biological control agents due to their prolific antibiotic production that can inhibit soil-borne plant pathogens. This includes Streptomyces scabies, which causes scab disease on underground storage organs. The goal of this research was to test two Streptomyces isolates that have known inhibitory and biocontrol abilities against S. scabies in a potato (Solanum tuberosum) agricultural system for their effectiveness in biocontrol of this pathogen in a radish (Raphanus sativus) greenhouse assay. Pathogenic S. scabies were mixed into either pasteurized or unpasteurized soil prior to planting. Radish …

Prokaryotic Diversity In The Rhizosphere Of Organic, Intensive, And Transitional Coffee Farms In Brazil, Adam Caldwell, Livia Silva, Cynthia Da Silva, Cleber Ouverney

Faculty Publications, Biological Sciences

Despite a continuous rise in consumption of coffee over the past 60 years and recent studies showing positive benefits linked to human health, intensive coffee farming practices have been associated with environmental damage, risks to human health, and reductions in biodiversity. In contrast, organic farming has become an increasingly popular alternative, with both environmental and health benefits. This study aimed to characterize and determine the differences in the prokaryotic soil microbiology of three Brazilian coffee farms: one practicing intensive farming, one practicing organic farming, and one undergoing a transition from intensive to organic practices. Soil samples were collected from 20 …

Genomic Signatures Of Cooperation And Conflict In The Social Amoeba, Elizabeth A. Ostrowski, Yufeng Shen, Xiangjun Tian, Richard Sucgang, Huaiyang Jiang, Jiaxin Qu, Mariko Katoh-Kurasawa, Debra A. Brock, Christopher Dinh, Fremiet Lara-Garduno, Sandra L. Lee, Christie L. Kovar, Huyen H. Dinh, Viktoriya Korchina, Laronda Jackson, Shobha Patil, Yi Han, Lesley Chaboub, Gad Shaulsky, Donna M. Muzny, Kim C. Worley, Richard A. Gibbs, Stephen Richards, Adam Kuspa, Joan E. Strassmann, David C. Queller

Biology Faculty Research

• Molecular evolution analyses reveal the history of social conflict
• Genes that mediate social conflict show signatures of frequency-dependent selection
• Balanced polymorphisms suggest that cheating may be stable and endemic

Cooperative systems are susceptible to invasion by selfish individuals that profit from receiving the social benefits but fail to contribute. These so-called "cheaters" can have a fitness advantage in the laboratory, but it is unclear whether cheating provides an important selective advantage in nature. We used a population genomic approach to examine the history of genes involved in cheating behaviors in the social amoeba Dictyostelium discoideum, testing whether these genes experience …

Fungi Inhabiting The Healthy Human Gastrointestinal Tract: A Diverse And Dynamic Community, Heather E. Hallen-Adams, Stephen D. Kachman, Jaehyoung Kim, Ryan Legge, Inés Martínez

Department of Food Science and Technology: Faculty Publications

Fungal DNA was selectively amplified, and the ITS region sequenced, from fecal samples taken from 45 healthy human volunteers at one (21 volunteers) or two (24 volunteers) time points. Seventy-two operational taxonomic units, representing two phyla and ten classes of fungi, were recovered. Candida yeasts, notably C. tropicalis (present in 51 samples), and yeasts in the Dipodascaceae (39 samples), dominated, while 38 OTUs were detected in a single sample each. Fungi included known human symbionts (Candida, Cryptococcus, Malassezia and Trichosporon spp.), common airborne fungi (Cladosporium sp.) and fungi known to be associated with food ( …

Transduction As The Method Of Horizontal Gene Transfer Of The Staphylococcal Chromosomal Cassette Mec (Sccmec), Amber B. Sauder

Senior Honors Projects, 2010-2019

Methicillin-resistant Staphylococcus aureus (MRSA) gains resistance to β-lactam antibiotics through a mutated penicillin binding protein (PBP2a) encoded on the SCCmec element. In combination with the recombinase encoded by ccr, these two genes are used as markers of the mobile genetic element (SCCmec). Due to recent increases in community acquired MRSA infections, the mechanisms of antibiotic resistance gene transfer have gained attention. Transduction, a method of horizontal gene transfer mediated by bacteriophage, is believed to be responsible for the movement of the SCCmec element. Recent studies have shown the transduction of the SCCmec element in clinical isolates; however, this study is …

Comparative Analysis Of Anti-Bd Bacteria From Six Malagasy Frog Species Of Ranomafana National Park, Kelsey Savage

Senior Honors Projects, 2010-2019

As Malagasy amphibians are facing an impending extinction crisis from the lethal skin fungus Batrachochytrium dendrobatidis (Bd), it has become imperative to proactively mitigate the threat. Bd sporangia develop in the skin of infected amphibians and cause the skin to thicken, leading to ionic imbalance and eventual heart failure. It has been shown that certain bacterial species are able to inhibit Bd growth on amphibians by producing antifungal metabolites. Community-based probiotics are one approach used to combat chytridomycosis by inoculating an environment with Bd-inhibitory bacteria so that many amphibian species are treated at once. With this method, it is important …

Epiphytic Diatom Community Structure In A Karst Riverine System, Gregory John Barren

Masters Theses & Specialist Projects

The goal of this study was to assess the epiphytic diatom community structure of two host species along a karst gradient in the upper Green River, Kentucky to a gain a better understanding of the role of diatoms in the food web. The host species studied were Podostemum ceratophyllum and Cladophora. Percent cover of P. ceratophyllum and Cladophora were quantified in the four study reaches. The host species were sampled near-shore and mid-channel in each reach in September and October of 2013. After diatoms were extracted from the host and enumerated the density and diversity were quantified. Twelve genera were …

Management Of A Primordial Problem: Redox-Sensitive Transcriptional Regulation In Methanosarcina Acetivorans, Ryan Christopher Sheehan

Graduate Theses and Dissertations

The primordial Earth which hosted the first forms of life was an environment free of oxygen. Early organisms utilized metabolisms dependent upon anaerobic conditions and incorporated systems to which oxygen is deleterious. As the content of oxygen in Earth's atmosphere increased, anaerobic organisms had to acquire methods to sense and combat oxygen and reactive oxygen species. Several mechanisms were advantageous to such anaerobic organisms which correlated transcriptional processes with the redox state of the cell so that energy may be conserved and oxygen stress recovery genes activated during periods of oxidative stress. Iron sulfur (Fe-S) cluster cofactors incorporated within RNA …