Microbiology Commons^™

Investigating Physiological Collaborations Between A Lower Termite And Its Symbionts, Brittany F. Peterson

Open Access Dissertations

This project was completed in an effort to better understand the contributions of symbiotic microbes to the biology of Reticulitermes flavipes, the eastern subterranean termite. Lower-termites, like R. flavipes, house symbionts from all three domains of life within their hindgut paunch. This intimate association is reflected in nearly every aspect of termite biology. Here, I investigate these physiological collaborations as they relate to digestion and immunity. My efforts focused on 1) quantifying the role of bacteria in wood digestion within the termite gut, 2) evaluating the role of symbionts in protection against pathogens, and 3) identifying gene products that bacterial …

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. …

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 …

Isolation And Characterization Of Microbial Community Associated With Diadumene Lineata, The Orange-Striped Sea Anemone, Tiffany Lin, Andrew Weir

Student and Faculty Research Days

The orange-striped sea anemone, Diadumene lineata, is a marine invertebrate that can be found in the Northern Hemisphere. Distribution of Diadumene lineata ranges from Japan to the Gulf of Argentina. This invasive anemone originated from the Pacific Coast of Asia and serves as a host for a diverse microbial community including a photosynthetic alga. The epiphytic bacteria adhere to the outer surface as well as to the gastrovascular cavity of the host. The microbial community associated with Diadumene lineata is relatively unknown. This study attempted to isolate and identify bacteria commonly associated with this invasive marine invertebrate. Diadumene lineata was …

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. …

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 …

Expansion Of The Chlorovirus Genus By Studies On Virus Natural History And Chlorella Host Metabolism, Cristian F. Quispe

School of Biological Sciences: Dissertations, Theses, and Student Research

Inland waters cover about 2.5 percent of our planet and harbor huge numbers of known and unknown microorganisms including viruses. Viruses likely play dynamic, albeit largely undocumented roles in regulating microbial communities and in recycling nutrients in the ecosystem. Phycodnaviruses are a genetically diverse, yet morphologically similar, group of large dsDNA-containing viruses (160- to 560-kb) that inhabit aquatic environments. Members of the genus Chlorovirus are common in freshwater. They replicate in eukaryotic, single-celled, chlorella-like green algae that normally exist as endosymbionts of protists in nature. Very little is known about the natural history of the chloroviruses and how they achieve …

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 …

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 …

The Functional And Distributional Ecology Of Mycetozoans Under Changing Edaphic And Climatic Dynamics, Geoffrey Lloyd Zahn

Graduate Theses and Dissertations

Investigations into the distribution and ecosystem functions of fruiting amoebae revealed that local-scale environmental conditions can largely explain broad biogeographical patterns in species assemblage, the way in which amoeboid predators shape bacterial communities and how this top-down influence may affect global biogeochemical processes in a changing climate. The distribution and assemblage of protosteloid amoebae on the islands of New Zealand and Hawaii did not yield any expected patterns of island biogeography, and conformed to other global regions studied. The strongest predictor of species richness in a given region was sampling effort and these species do not appear to have any …

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 …

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 …

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 …

How Does The Exploitation And Degradation Of Finite Natural Resources By Industrial Oil Producers Effect Our Future Planetary Environment?, Zachary J. King Mr.

Symposium of Student Scholars

Zachary King

Dr. Tu

26 March 2015

GEOG 3700

Abstract

The purpose of this presentation is to communicate content of the reports given by credible institution on the degradation and exploitation of finite natural resources by corporate institutions, for short term financial gain, and how it will effect the future planetary environment. Methods used in obtaining this research range from point source observation directly from oil spills in the Gulf or pipe leaks in the Mid-West, to analytical and numerical data quantifications gathered over a period of two decades. This presentation encompasses a wide scope of information concerning the way …

Is There Specificity In A Defensive Mutualism Against Soil Versus Lab Nematodes, Dictyostelium Discoideum Farmers And Their Bacteria?, Boahemaa Adu-Oppong,, David C. Queller, Joan E. Strassmann

Biology Faculty Research

Background: The social amoeba Dictyostelium discoideum is a soil-dwelling microbe, which lives most of its life cycle in the vegetative stage as a predator of bacteria and as prey for nematodes. When bacteria are sparse, amoebae aggregate into a multicellular fruiting body. Some clones of D. discoideum have agriculture (Brock et al., 2011). They carry bacteria through the social stage, eat them prudently, and use some bacteria as defence against non-farming D. discoideum competitors. Caenorhabditis elegans preys on D. discoideum in the laboratory but does not encounter it in nature because C. elegans lives on rotten fruit. The nematode …

Concurrent Coevolution Of Intra-Organismal Cheaters And Resisters, S R. Levin, D A. Brock, David C. Queller, Joan E. Strassmann

Biology Faculty Research

The evolution of multicellularity is a major transition that is not yet fully understood. Specifically, we do not know whether there are any mechanisms by which multicellularity can be maintained without a single-cell bottleneck or other relatedness-enhancing mechanisms. Under low relatedness, cheaters can evolve that benefit from the altruistic behaviour of others without themselves sacrificing. If these are obligate cheaters, incapable of cooperating, their spread can lead to the demise of multicellularity. One possibility, however, is that cooperators can evolve resistance to cheaters. We tested this idea in a facultatively multicellular social amoeba, Dictyostelium discoideum. This amoeba usually exists as …

Iron Deficiency Increases Growth And Nitrogen-Fixation Rates Of Phosphorus-Deficient Marine Cyanobacteria, Nathan S. Garcia, Feixue Fu, Peter N. Sedwick, David A. Hutchins

OES Faculty Publications

Marine dinitrogen (N²)-fixing cyanobacteria have large impacts on global biogeochemistry as they fix carbon dioxide (CO₂) and fertilize oligotrophic ocean waters with new nitrogen. Iron (Fe) and phosphorus (P) are the two most important limiting nutrients for marine biological N₂ fixation, and their availabilities vary between major ocean basins and regions. A long-standing question concerns the ability of two globally dominant N₂-fixing cyanobacteria, unicellular Crocosphaera and filamentous Trichodesmium, to maintain relatively high N₂-fixation rates in these regimes where both Fe and P are typically scarce. We show that under P-deficient …

Heterotrophic And Autotrophic Contribution To Dinitrogen Fixation In The Gulf Of Aqaba, Eyal Rahav, Barak Herut, Margaret R. Mulholland, Natalia Belkin, Hila Elifantz, Ilana Berman-Frank

OES Faculty Publications

We evaluated the seasonal contribution of heterotrophic and autotrophic diazotrophy to the total dinitrogen (N₂) fixation in the photic zone of a pelagic station in the northern Gulf of Aqaba, Red Sea. N₂ fixation rates were highest during a Trichodesmium bloom in winter (0.7 nmol N l^-1 d^-1), decreased 7-fold 1 wk later throughout the upper 200 m (~0.1 nmol N l^-1) d^-1), and were significantly coupled with both primary and bacterial productivity. N₂ fixation rates were generally higher in the upper 200 m (~0.4 nmol N l^{-1 …}

Effects Of Water Column P-Availability And Litter Microbial Mediated Processes And Stoichiometry In Aquatic Systems, Ayla Smartt

Graduate Theses and Dissertations

Anthropogenic nutrient enrichment of aquatic ecosystems is prevalent and can have detrimental effects on biological condition. Many of these effects have been attributed directly or indirectly to changes in autotrophic processes. However, in detrital-based streams changes in course detrital stoichiometry and decomposition have been related to changes community structure and production at higher trophic levels highlighting the importance of considering the heterotrophic microbial responses to enrichment. Leaf litter stoichiometry, which is determined in part by the tree species source and the microbial communities that comprise the associated biofilm, is likely related to decomposition rates, but few studies examine these variables …

Persistence And Stability Of Eastern Afromontane Forests: Evidence From Brevicipitid Frogs, Simon P. Loader, F. Sara Ceccarelli, Michele Menegon, Kim M. Howell, Roman Kassahun, Abebe A. Mengistu, Samy A. Saber, Fikirte Gebresenbet, Rafael O. De Sá, Et Al.

Biology Faculty Publications

Aim: The persistence and stability of habitats through time are considered predictors of high levels of biodiversity in some environments. Long-term habitat persistence and stability may explain the species-rich, endemic forest fauna and flora of the Eastern Afromontane Biodiversity Region (EABR). Using comple- mentary phylogenetic and biogeographical approaches, we examine evolution- ary patterns in EAR brevicipitid frogs. Using these data, we test whether brevicipitid history reflects patterns of long-term forest persistence and/or sta bility across the EABR.

Location: East Africa.

Methods: A dated phylogeny for brevicipitids was constructed using two nuclear and three mitochondrial markers. Alternative diversification modes were used …

Management Of Root Knot Nematode (Meloidogyne Incognita ) In Indiana Soybeans, David Edgardo Perla Martinez

Open Access Theses

The aim of this project was to evaluate different strategies for management of Root Knot Nematode (RKN) on soybean and tomato in Indiana. Seed treatments were evaluated under field and greenhouse conditions, but no effect on RKN populations was observed. Soybean lines evaluated for resistance to RKN under greenhouse conditions showed that six lines may be resistant to RKN. Four different commercial mustard cover crops were evaluated for their bio-fumigant impact on RKN populations in the production of tomato. Euruca sativa, Cv. Nemat was a poor host of RKN. A positive impact on the vigor of the tomato plants followed …

Anthropogenic Litter In Urban Freshwater Ecosystems: Distribution And Microbial Interactions, Timothy Hoellein, Miguel Rojas, Adam Pink, Joseph Gasior, John J. Kelly

Biology: Faculty Publications and Other Works

Accumulation of anthropogenic litter (i.e. garbage; AL) and its ecosystem effects in marine environments are well documented. Rivers receive AL from terrestrial habitats and represent a major source of AL to marine environments, but AL is rarely studied within freshwater ecosystems. Our objectives were to 1) quantify AL density in urban freshwaters, 2) compare AL abundance among freshwater, terrestrial, and marine ecosystems, and 3) characterize the activity and composition of AL biofilms in freshwater habitats. We quantified AL from the Chicago River and Chicago's Lake Michigan shoreline, and found that AL abundance in Chicago freshwater ecosystems was comparable to previously …

Temporal Variations In The Abundance And Composition Of Biofilm Communities Colonizing Drinking Water Distribution Pipes, John J. Kelly, Nicole Minalt, Alessandro Culotti, Marsha Pryor, Aaron Packman

Biology: Faculty Publications and Other Works

Pipes that transport drinking water through municipal drinking water distribution systems (DWDS) are challenging habitats for microorganisms. Distribution networks are dark, oligotrophic and contain disinfectants; yet microbes frequently form biofilms attached to interior surfaces of DWDS pipes. Relatively little is known about the species composition and ecology of these biofilms due to challenges associated with sample acquisition from actual DWDS. We report the analysis of biofilms from five pipe samples collected from the same region of a DWDS in Florida, USA, over an 18 month period between February 2011 and August 2012. The bacterial abundance and composition of biofilm communities …

The Role Of Nitrogen And Phosphorus In The Growth, Toxicity, And Distribution Of The Toxic Cyanobacteria, Microcystis Aeruginosa, James Parrish

Master's Projects and Capstones

Microcystis aeruginosa is among the most common harmful algal-blooming species in the world. Potent microcystins released by M. aeruginosa have been linked to liver failure and death in aquatic mammals, like the endangered California sea otter, and provide a serious public health risk to humans. Once characterized as a freshwater problem, M. aeruginosa is expanding on a global scale, making persistent returns in freshwater, brackish, and coastal marine ecosystems. Though commonly observed dominating aquatic ecosystems in low N:P atomic ratios less than 44:1, the reliability of N:P ratios as a tool for managing and predicting M. aeruginosa blooms is explored …

Morphometric Studies On Subadult Liza Subviridis And Sillago Sihama From Sonmiani Bay (Miani Hor), Balochistan, Pakistan, Muhammad A. Gondal, Naureen A. Qureshi, Noor U. Saher

Journal of Bioresource Management

Length-weight relationship of Liza subviridis and Sillago sihama (Family: Mugilidae; Class: Pisces and Family: Sillaginidae; Class: Pisces) in subadults sampled from Somiani Bay Balochistan, Pakistan during 2002, 2003 and 2006 was analyzed. Liza subviridis showed positive allometry (3.23) in 2002, and negative allometry during 2003 (2.95) and 2006 (1.95). Sub adults of Sillago sihama showed positive allometry during 2002 (3.10) and 2003 (3.13). An isometric condition (3.02) was observed in the samples of Sillago sihama collected from Bhaira in 2006.

On Individual, Sex And Age Differentiation Of Indian House Crow (Corvus Splendens) Call: A Preliminary Study In Potohar, Pakistan, Waqas Hameed, Inayat Ullah, Safia Janjua, Fakhar -I- Abbas, Afsar Mian

Journal of Bioresource Management

Considering importance of acoustics studies in population biology, 500 calls of the Indian House Crow (Corvus splendens) were recorded in morning - mid-afternoon hours (January-February, 2009) from 23 sites of urban areas of Potahar (Punjab, Pakistan). Calls were recorded using Sony CFS 1030 S sound records (sampling rate = 48 KHz) and edited using Sound Analysis Pro (Version 1.02). software using FFT method rate 50%, data window 9.27 ms, advanced window 1.36 ms. Through editing of calls, we selected 60 (37 ♂♂, 17 ♀♀, 6 Juvenile ♂♂) good quality spectrograms for detailed analysis. Spectrograms were characterized by rapid frequency modulations …

Review: Pollination, Pollinated And Pollinators Interaction In Pakistan, Mohammad Irshad, Elizabeth Stephen

Journal of Bioresource Management

The agriculture sector is important in the overall economy and export earnings of Pakistan. Pollination is an essential ecosystem service that depends on symbiosis between species, the pollinated and the pollinator. Animal mediated pollination contributes to the sexual production of over 90% species of modern angiosperms. Effective pollination results in increased crop production, quality improvement and more seed production. Many fruits, vegetables, edible oil crops, stimulant crops and nuts are highly dependent on bee pollination. Worldwide value of pollinators is €153 billion (217 billion US dollars). The production value of pollinated dependent crop in Pakistan is quantified to be 1.59 …

Research Note: Contribution To Mushroom Flora Of Rawalpindi-Islamabad, Pakistan, Kishwar Sultana, Naveeda Riaz, Gulshan Irshad, Ali Nauman Khan

Journal of Bioresource Management

Seven hymenomycetous fungi (mushrooms) were collected from the twin cities area during July 2008. These were identified as the members of the order Agaricales, class Basidiomycetes. They belong to five genera: *Clitocybe fragrans, *Collybia cookie, *Coprinus radians, *Coprinus sterculinus, *Volvariella bingensis, Volvariella parvula, and Termitomyces microcarpus. Five of them, marked with asterisk were reported for the first time from Pakistan.

Diagnostic Accuracy Of C-Reactive Protein In Neonatal Sepsis, Sidra Younis, Muhammad Ali Sheikh, Amjad Ali Raza

Journal of Bioresource Management

Sepsis is the most common cause of neonatal mortality and is responsible for 30-50% of total neonatal deaths each year in developing countries. The objective of the study was to determine the diagnostic accuracy of C-reactive protein (CRP) in neonatal sepsis. Fifty nine consecutive patients with risk factors and clinical features suggestive of CRP sepsis were selected as per operational definition and fulfilling the inclusion and exclusion criteria. Detailed physical examination was carried out. Blood sample for culture and CRP was taken from all the patients. Results of blood culture and CRP were noted down in the performa. Statistical analysis …