Environmental Microbiology and Microbial Ecology Commons^™

Sulfur Cave (Romania), An Extreme Environment With Microbial Mats In A Co2-H2S/O2 Gas Chemocline Dominated By Mycobacteria, Serban M. Sarbu, Joost W. Aerts, Jean-François Flot, Rob J.M. Van Spanning, Calin Baciu, Artur Ionescu, Boglárka M. Kis, Reka Incze, Sándor Sikó-Barabási, Zoltan Para, Botond Hegyeli, Nicu-Viorel Atudorei, Casey Barr, Kenneth Nealson, Ferenc L. Forray, Cristian Lascu, Emily J. Fleming, Wilbert Bitter, Radu Popa

International Journal of Speleology

Sulfur Cave (Puturosu Mountain, Romania) is an extreme environment, unique for displaying life in a gas chemocline. The lower part of the cave is filled with CO₂, CH₄, and H₂S of mofettic origin, while the upper part contains air that floats above the heavier volcanic gasses. S° and H₂SO₄ (from sulfur-oxidation) cover the cave wall at and below the CO₂-H₂S:O₂ gas/gas interface. On the cave wall, near the interface the pH is < 1 and unusual microbial biofilms occur on the rock’s surface. We provide context information on the geology, mineralogy, chemistry and biology to better understand this unique environment. We have used X-ray diffraction, optical microscopy, scanning electron microscopy with EDAX capabilities, stable isotope analysis and 16S and 18S rDNA amplicon sequencing. The most common taxa in the microbial biofilms are Mycobacteria, Acidithiobacillus and Ferroplasmaceae. Liquid water in this system originates solely from condensation of water …

The Role And Contribution Of Saprotrophic Fungi During Standing Litter Decomposition Of Two Perennial Grass Species, Schizachyrium Scoparium And Schizachyrium Tenerum, Matthew Lodato

Master's Theses

In terrestrial ecosystems, most of the plant biomass produced enters the detrital pool, where microbial decomposers colonize, enzymatically degrade, and assimilate plant litter carbon and nutrients in amounts sufficient to bring about the decomposition of plant litter. Here, I estimated the biomass and production of fungi and microbial respiration associated with decaying Schizachyrium scoparium and Schizachyrium tenerum leaf litter, and constructed a partial organic matter budget estimating C flow into and through fungal decomposers. Significant losses in S. scoparium (57%) and S. tenerum (68%) leaf mass was observed during litter decomposition along with concomitant increases in fungal biomass, which reached …

Monitoring The Influx Of Marine Derived Nitrogen And Characterizing Soil Food Webs Of Riparian Zones Of The Elwha River Watershed, Wa, Usa., Wendal R.H. Kane

EWU Masters Thesis Collection

Nitrogen is often the most limiting nutrient to productivity in terrestrial ecosystems, and can have large effects on ecosystem processes. Two sources of nitrogen to Pacific Northwest riparian areas are marine derived nitrogen (MDN) via anadromous pacific salmon and symbiotic nitrogen fixation via Alnus rubra. The recent removal of two large dams on the Elwha River, WA, opened up ~60 km of previously inaccessible river habitat for pacific salmon. I used naturally abundant stable nitrogen isotopes (denoted as ‰ δ15N) to establish baseline data to monitor the influx of MDN to riparian zones of Elwha River tributaries, post dam removal. …

Microbial Community Response To Light And Heavy Crude Oil In Freshwater Systems, Timothy M. Butler

Dissertations, Master's Theses and Master's Reports

With increased demand for oil, there is an increased risk for oil spills in many environments. A number of pipelines transport oil near or across freshwater systems including the Great Lakes. Microbes are capable of breaking down oil and have thus been proposed as tools for oil spill response through bioremediation. There is a need to understand the microbial response to diverse oil types in freshwater environments due to the lack of research into this topic. This study’s main objectives are to understand how the freshwater microbial communities respond to oil, and how the bacterial communities may respond to different …

Photosynthetic Activity Under Low Light, Danijela Lonco

Williams Honors College, Honors Research Projects

Are bacteria capable of undergoing oxygenic photosynthesis under low-light conditions inside of caves? Inside of an Australian cave, Chlorophyll f was recently discovered. This chlorophyll pigment was found to demonstrate the capability for photosynthesis, suggesting that Chlorophyll f extends the spectrum of usable light needed for oxygenic photosynthesis (Lars, 2015). Due to the findings in this study, a team went to Carlsbad Caverns to see if there were any bacteria capable of undergoing oxygenic photosynthesis under low light.

Relationships Between Factors Influencing Biofilm Formation And Pathogen Retention In Complex Rhizosphere Microbial Communities, Aaron Coristine

Theses and Dissertations (Comprehensive)

Riparian wetlands are unique habitats facilitating all forms of life. The riverbanks of these environments provide ideal conditions for bacteria, plants, and higher organisms. Of particular interest to this research was the variation in microbial community structure at high, intermediate and poor water quality impacted areas. Assessing the capabilities of plants to retain microbial pathogens was identified. Root systems and corresponding soil are ideal locations for bacterial deposition, resulting in attachment at these areas. Biofilm production in these regions is important for long-term establishment, leading to persistence and potential naturalization. Opportunistic pathogens originating from mammalian fecal matter are introduced into …

Fungi Of Forests: Examining The Diversity Of Root-Associated Fungi And Their Responses To Acid Deposition, Donald Jay Nelsen

Graduate Theses and Dissertations

Global importance of forests is difficult to overestimate, given their role in oxygen production, ecological roles in nutrient cycling and supporting numerous living species, and economic value for industry and as recreational zones. Fitness of the forest-forming trees strongly depends on microbial communities associated with tree roots. In particular, fungi impact tree fitness: mycorrhizal species provide water and nutrients for the trees in exchange for C, endophytic fungi play key roles in host defense against pathogenic organisms, and saprotrophic fungi decompose dead organic matter and facilitate nutrient cycling. In addition, pathogenic fungal species strongly affect forest fitness. Despite their importance, …

An Assessment Of Potential False Positive E.Coli Pyroprints In The Cplop Database, Skyler A. Gordon

Master's Theses

The genetic information found in each species of organism is unique, and can be used as a tool to differentiate at the molecular level. This has caused rapid genotyping methods to become the cornerstone of a new area of research dependent on reading the genome as a form of identification. One of these specific identification methods, known as pyroprinting, relies on the small variation of DNA sequences within the same species to develop a unique, reproducible fingerprint. By simultaneously pyrosequencing multiple polymorphic loci within the ribosomal operons known as the intergenic transcribed spacers, a reproducible output is obtained, known as …

The Influence Of The Invasive Chinese Tallow (Triadica Sebifera) Leaf Litter On Aquatic Chemistry And Microbial Community Composition, Raymond D. Montez

Electronic Theses and Dissertations

Global climate change and anthropogenic activity have facilitated the movement and invasive potential of nonnative plants in native environments. These invasions can have negative effects on ecosystem diversity and function. The nonnative and invasive plant, Chinese Tallow (Triadica sebifera), has already invaded much of the south eastern US where it is outcompeting native tree species and changing ecosystem diversity in a variety of habitats. Leaf litter from the Chinese tallow has been shown cause changes in dissolved oxygen and pH in the aquatic environment. Turbidity is also affected when Chinese tallow litter is present in water. A series of …

Presence Of The Cyanotoxin Microcystin In Arctic Lakes Of Southwestern Greenland, Jessica Trout-Haney, Zachary Wood, Kathryn Cottingham

Dartmouth Scholarship

Cyanobacteria and their toxins have received significant attention in eutrophic temperate and tropical systems where conspicuous blooms of certain planktonic taxa release toxins into fresh water, threatening its potability and safe use for recreation. Although toxigenic cyanobacteria are not confined to high nutrient environments, bloom-forming species, or planktonic taxa, these other situations are studied les often studied. For example, toxin production in picoplankton and benthic cyanobacteria—the predominant photoautotrophs found in polar lakes—is poorly understood. We quantified the occurrence of microcystin (MC, a hepatotoxic cyanotoxin) across 18 Arctic lakes in southwestern Greenland. All of the focal lakes contained detectable levels of …

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 …

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 …

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 …

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 …

Effects Of Elevated Salinity And Oxidative Stress On The Physiology Of The Toxigenic Cyanobacterium Microcystis Aeruginosa, Billy Christopher Warhurst

UNF Graduate Theses and Dissertations

Harmful algal blooms (HABs) are found worldwide, particularly in places where warm, well-lit, and stagnant waters are common. HABs can have negative effects on aquatic plants and wildlife due to the reduction in light availability associated with turbidity, decrease in O₂ availability, and the production of secondary metabolites that can harm or even prove lethal. Aquatic ecosystems are regularly being affected by elevated salinity because of recent water management strategies, episodes of drought, and salt water intrusion. This research focused on how salinity levels ranging from 0-10ppt affected physiological attributes such as cellular growth and abundance, cell mortality, toxin …

Epilithic And Aerophilic Diatoms In The Artificial Environment Of Kungsträdgården Metro Station, Stockholm, Sweden, Lena Norbäck Ivarsson, Magnus Ivarsson, Johannes Lundberg, Therese Sallstedt, Catarina Rydin

International Journal of Speleology

The Kungsträdgården metro station is an artificial and urban subsurface environment illuminated with artificial light. Its ecosystem is almost completely unknown and as a first step to better understand the biology and rock wall habitats the diatom flora was investigated. A total of 12 species were found growing on the rock walls of Kungsträdgården metro station. The results show the diatom flora in Kungsträdgården to be dominated by e.g. Diadesmis contenta, Diadesmis perpusilla, Pinnularia appendiculata, Nitzschia amphibia, Nitzschia sinuata and Diploneis ovalis. One species, Caloneis cf. aerophila, has never been reported from Sweden before. …

Comparative Microbial Community Composition From Secondary Carbonate (Moonmilk) Deposits: Implications For The Cansiliella Servadeii Cave Hygropetric Food Web, Annette Summers Engel, Maurizio G. Paoletti, Mattia Beggio, Luca Dorigo, Alberto Pamio, Tiziano Gomiero, Claudio Furlan, Mauro Brilli, Angelo Leandro Dreon, Roberto Bertoni, Andrea Squartini

International Journal of Speleology

The microbial diversity of moonmilk, a hydrated calcium carbonate speleothem, was evaluated from two Italian caves to provide context for the food web of highly-specialized troglobitic beetles, Cansiliella spp. (Leptodirinae), with distinctive carbon and nitrogen isotope values indicative of a novel food source. The moonmilk and associated percolating waters had low to no extractable chlorophyll, with an average organic C:N ratio of 9, indicating limited allochthonous input and a significant contribution from microbial biomass. The biomass from moonmilk was estimated to be ~10⁴ micro- and meiofaunal individuals per m² and ~10⁷ microbial cells/ml. Betaproteobacteria dominated the …

Litter Conditioning Is Differentially Affected By Leaf Species, Phosphorus Enrichment, And Light Availability, Erin E. Scott

Graduate Theses and Dissertations

Anthropogenic enrichment of nitrogen and phosphorus is one of the most pervasive and detrimental threats to aquatic ecosystems worldwide. In streams that rely on allochthonous basal food resources, such as leaves, nutrient pollution can result in altered food quality and decreased carbon (C) standing stocks. However, the magnitude and mechanisms of this change in quality are poorly understood. Laboratory microcosm studies were conducted to 1) quantify the response of litter C:P to a gradient of phosphorus (P) enrichment (0, 0.05, and 0.5 mg SRP/L) across leaf species with variable levels of degradability (sugar maple and oak), and 2) quantify the …

Control And Passive Treatment Of Runoff From Horse Muck Storage Structures Using Rain Gardens, Hillary K. Otte

Theses and Dissertations--Forestry and Natural Resources

Runoff from livestock operations may contain a variety of pathogens and high levels of nutrients and other harmful contaminants, and is of particular concern in central Kentucky as watersheds are threatened by waste generated from a high concentration of equine activity. Rain gardens are a type of stormwater management tool used to capture and passively treat runoff. This project aimed to incorporate rain gardens into the horse muck storage structures at a thoroughbred facility in the Canr Run watershed in Lexington, Kentucky. Water quality data from soil water within two rain garden muck pads and two control pads, and grab …

Bacterial Community Structure Of Contrasting Soils Underlying Bornean Rain Forests: Inferences From Microarray And Next-Generation Sequencing Methods, Sabrina E. Russo, Ryan Legge, Karrie A. Weber, Eoin L. Brodie, Katherine C. Goldfarb, Andrew K. Benson, Sylvester Tan

School of Biological Sciences: Faculty Publications

Soil microbial diversity is vast, and we lack even basic understanding of how this diversity is distributed ecologically. Using pyrosequencing and microarray methods, we quantified the structure of bacterial communities in two contrasting soils underlying Bornean rain forest (clay and sandy loam) that differ markedly in soil properties, aboveground tree flora, and leaf litter decomposition rates. We found significant soil-related taxonomic and phylogenetic differences between communities that, due to their proximity, are independent of climate. Bacterial communities showed distinct compositional and taxon-abundance distributions that were significantly correlated with the structure of the overlying tree community. Richness of bacteria was greater …

Human Pathogen Shown To Cause Disease In The Threatened Elkhorn Coral Acropora Palmata, Kathryn Patterson Sutherland, Sameera Shaban, Jessica L. Joyner, James W. Porter, Erin K. Lipp

Faculty Publications

Coral reefs are in severe decline. Infections by the human pathogen Serratia marcescens have contributed to precipitous losses in the common Caribbean elkhorn coral, Acropora palmata, culminating in its listing under the United States Endangered Species Act. During a 2003 outbreak of this coral disease, called acroporid serratiosis (APS), a unique strain of the pathogen, Serratia marcescens strain PDR60, was identified from diseased A. palmata, human wastewater, the non-host coral Siderastrea siderea and the corallivorous snail Coralliophila abbreviata. In order to examine humans as a source and other marine invertebrates as vectors and/or reservoirs of the APS pathogen, challenge experiments …

A Spatial And Temporal Analysis Of Microbial Communities In Great Boiling Spring, Nevada, U.S.A., Jessica K. Guy, Joseph P. Peacock, Jeremy A. Dodsworth, Tanja Woyke, Tijana G. Del Rio, Brian P. Hedlund

Undergraduate Research Opportunities Program (UROP)

Great Boiling Spring (GBS) is a large, circumneutral, long residence time geothermal spring in the US Great Basin. Twelve samples were taken from four different sediment sites and the planktonic community in the bulk water of GBS on up to four different dates. Microbial community composition and diversity was assessed by using a barcoded, improved universal primer set targeting the V8 portion of the 16S rRNA gene and PCR. Over 200,000 products were sequenced using the Roche 454 GS FLX Titanium System. Sediment and planktonic microbial communities were distinct with very little overlap, regardless of the sampling location or temperature. …

Biodiversity And Antimicrobial Activity Of Cold-Adapted Soil Microfungi From: Deception Island, Wilhelmina Bay And Yankee Bay, Maritime Antarctica., Mohammed Ahmed Mohammed Abneuf

Student Works (2010-2019)

Decades ago, the Antarctic regions have been exploited for cold-tolerant microorganisms, prospecting various biological benefits, mainly psychrophilic enzymes and bioactive compounds. The first half of the present research aimed to study the occurrence of microfungi in samples of soil taken from Deception Island, Wilhelmina Bay and Yankee Bay, Maritime Antarctica. Attempt made to screen the biodiversity using conventional media and soil plating technique, yielded population of 27 species from the total of 14 soil samples. Of that, 13 fungal species were recorded from Deception Island, 8 from Wilhelmina Bay and 6 from Yankee Bay. Among the genera were Aspergillus, …

Prevalence And Serovars Of Salmonella In The Feces Of Free-Ranging White-Tailed Deer (Odocoileus Virginianus) In Nebraska, David G. Renter, David P. Gnad, Jan M. Sargeant, Scott E. Hygnstrom

School of Natural Resources: Faculty Publications

To determine the prevalence and serovars of Salmonella in free-ranging deer, we cultured feces from white-tailed deer (Odocoileus virginianus) harvested by hunters during a regular firearm season in southeastern Nebraska (USA). We recovered Salmonella from 5 (1%; 95% confidence interval: 0.37– 2.20%) of 500 samples and identified four different Salmonella enterica serovars [Litchfield (1), Dessau (1), Infantis (2), and Enteritidis (1)]. Although the prevalence of Salmonella in free-ranging deer appears to be low, the serovars recovered are known to be pathogenic to humans and animals.

Ua3/9/5 Conservation Reserve Enhancement Program (Crep), Wku President's Office

WKU Administration Documents

Talking points used by WKU president Gary Ransdell regarding WKU's partnering with Conservation Reserve Enhancement Program.

The Diversity And Abundance Of Parasites In Age Groups Of Yellow Perch In Lake Bemidji, Mn Applied To A Whittaker Curve, Kelly J. Main

Honors Capstones

Capstone submitted as a graduation requirement for the BSU Honors Program.

A Common Pattern Of Somite Cell Rotation In Three Species Of Pipidae, Shou-Yuan Fan, Rafael O. De Sá, Gary P. Radice

Biology Faculty Publications

During amphibian somitogenesis, presumptive myotome cells change shape from round or polygonal to elongated and aligned parallel to the notochord (for reviews see Radice, et al., 1989; Keller, 2000). Although the final orientation of myotomal cells is always axial, the movements that achieve this final arrangement can differ greatly between species. The simplest movement is that seen in Bombina variegata, Pelobates fuscus, and Bufo bufo (Brustis et al., 1976; Brustis, 1979; Kielbowna, 1981 ). In these anurans, after segmentation myotomal cells simply elongate along the embryo’s anteroposterior axis. The urodeles Ambystoma mexicanum and Pleurodeles waltl have a very different pattern; …

Escherichia Coli O157:H7 In Free-Ranging Deer In Nebraska, David G. Renter, Jan M. Sargeant, Scott E. Hygnstrom, Jeff D. Hoffmann, Jerry R. Gillespie

School of Natural Resources: Faculty Publications

In order to determine the prevalence and distribution of the human pathogen, Escherichia coli O157:H7, in free-ranging deer, hunters were asked to collect and submit fecal samples from deer harvested during a regular firearm season (14–22 November 1998). Prior to the season, 47% of the hunters with permits in the southeastern Nebraska (USA) study area indicated a willingness to participate in the study. Approximately 25% of successful hunters in the area submitted deer fecal samples. Escherichia coli O157:H7 was cultured from four (0.25%) of 1,608 total samples submitted. All of the fecal samples that were properly identified (1,426) and all …

Comparison Between Two Analytical Methods For Fecal Coliform Analysis In Natural Water: Membrane Filtration And Multiple Tube Fermentation, Mona M. Hafez

Theses & Honors Papers

This study compares two different analytical methods for the determination of coliform bacteria within natural waters. The two methods are: 1) membrane Filtration, and 2) multiple tube fermentation. Water samples from ten different locations within the Appomattox River watershed were collected by technicians from the Piedmont Soil and Water Conservation District and the Piedmont Region TMDL Initiative in Farmville, Virginia.

The Membrane filtration (MF) method utilizes m-FC broth to isolate and differentiate total fecal coliform bacteria (E.coli, Klebsiella, Pseudomonas) in natural water samples. A 1% dilution of each water sample is filtered through a 0.45 micron (um) Millipore filter …