Environmental Microbiology and Microbial Ecology Commons^™

Plant-Microbial Interactions Change Along A Prairie Restoration Chronosequence, Anna Herzberger

Undergraduate Honors Theses

Soil microbial communities are critical in determining the performance and density of species in plant communities. However, their role in regulating the success of restorations is much less clear. This study assessed the ability of soil microbial communities to regulate the growth and performance of two potentially dominant grasses and two common forbs in prairie restorations. Specifically, I examined the effects of soil microbial communities along a restoration chronosequence from agricultural fields to remnant prairies using experimentally inoculated soils. The two grass species, Andropogon gerardii and Sorghastrum nutans, produced larger biomass with the agricultural inoculates and experienced a decline …

Bioremediation Of Crude Oil Spills Impacts Microbial Communities And The Magnetic Susceptibility Of Sediments, Carol L. Beaver, Anja Williams, Estella Atekwana, Gamal Abdel Aal, Farag Mewafy, Lee Slater, Silvia Rossbach

Research and Creative Activities Poster Day

A worldwide increase in the production, shipment, and storage of crude oil has led to an increase in oil spills, and efforts to physically remove this oil from the environment are often insufficient. As a result, hydrocarbon contamination that is not eliminated by suction, excavation, or by dispersants remains in the water and sediments to be degraded by microbes. Initially, the bioremediation of oil occurs aerobically, but as oxygen is depleted, microbes must switch to alternate electron acceptors. Gradients of terminal electron acceptors form over time, which in conjunction with the toxic properties of oil, have an effect on the …

Gene And Protein Sequence Optimization For High-Level Production Of Fully Active And Aglycosylated Lysostaphin In Pichia Pastoris, Hongliang Zhao, Kristina Blazanovic, Yoonjoo Choi, Chris Bailey-Kellogg, Karl E. Griswold

Dartmouth Scholarship

Lysostaphin represents a promising therapeutic agent for the treatment of staphylococcal infections, in particular those of methicillin-resistant Staphylococcus aureus (MRSA). However, conventional expression systems for the enzyme suffer from various limitations, and there remains a need for an efficient and cost-effective production process to facilitate clinical translation and the development of nonmedical applications. While Pichia pastoris is widely used for high-level production of recombinant proteins, there are two major barriers to the production of lysostaphin in this industrially relevant host: lack of expression from the wild-type lysostaphin gene and aberrant glycosylation of the wild-type protein sequence. The first barrier can …

The Influence Of Hydrogeomorphology, Soil Redox Conditions, And Salinity On The Spatial Zoning Of Saltgrass, Salt Rush, And Cattails In Scotts Creek Marsh, Swanton Pacific Ranch, Ca, Mark D. Gormley

Master's Theses

Scotts Creek Marsh (SCM) is a small coastal wetland ecosystem in Davenport, CA. The vegetation of SCM is dominated by three halophytic zones comprised of saltgrass, salt rush, cattails. The objectives of the study were (i) to investigate the variables that influence the zoning of the three dominant halophyte communities in SCM and (ii) to the test the effectiveness of Indicator of Reduction in Soil (IRIS) tubes to indicate the reduction of S. The study examined the following parameters from April 6 to July 21, 2013: (i) the HGM of Scotts Creek Marsh, (ii) soil oxidation and reduction (redox) conditions, …

Bacterially-Mediated Formation Of Rock Coatings In Kärkevagge, Swedish Lapland: A Mineralogical And Micro-Environmental Analog For Mars, Cassandra L. Marnocha

Graduate Theses and Dissertations

The search for past or present life on Mars is, for now, limited to surface environments. An often neglected surface environment that could have served as an abode for life and could presently preserve evidence of that life is that of rock coatings. Rock coatings are mineral accretions on rock surfaces. On Earth, they are widespread and occur with considerable chemical diversity. There is growing evidence for a biotic role in their formation on Earth, particularly with respect to rock varnish. As a result, rock varnish has become a target of astrobiological interest on Mars, where varnish-like coatings have been …

Climate Change From Oxygen Isotopic Variation Of Pore Water From Sediments In Punderson Lake, Northeast Ohio, Rachel Daley, Fasong Yuan

Undergraduate Research Posters 2013

The environment in Ohio has changed over time. The hydroclimate, which is the climate of the water, shows changes from the Industrial Revolution to the present. Evidence for these changes can be found in levels of δ18O and δ2H isotopes in the layers of sediment and water in the lakes of Northeast Ohio. Mass spectrometry can be used to test the levels of δ18O and δ2H isotopes from pore water samples within sediment cores. In this study, surface soil and water samples were collected from cores in Punderson Lake at Punderson State Park in Newbury, Ohio. Pore water was extracted …

Aerobic Degradation Of Α-, Β-, Γ-Hexachlorocyclohexane By Narragansett Bay Bacterioplankton, Ian M. Rambo

Senior Honors Projects

Hexachlorocyclohexanes (HCHs) are a family of chlorinated organic compounds that were previously used as agricultural insecticides. HCHs are recognized as persistent organic pollutants due to their toxicity, recalcitrant properties, and tendency to bioaccumulate in food webs. Although HCH was first synthesized in 1825, its use was not widespread until the discovery of the insecticidal activity of the γ-HCH isomer in 1942. γ-HCH and its toxic waste isomers α-HCH and β-HCH were banned from production and use by the United Nations in 2009, yet these chemicals still present environmental problems due to their persistence in soils and surface waters. HCHs continue …

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 …

Managing Soil Microbial Communities With Organic Amendments To Promote Soil Aggregate Formation And Plant Health, Shawn T. Lucas

Theses and Dissertations--Plant and Soil Sciences

The effects of managing soil with organic amendments were examined with respect to soil microbial community dynamics, macroaggregate formation, and plant physio-genetic responses. The objective was to examine the possibility of managing soil microbial communities via soil management, such that the microbial community would provide agronomic benefits. In part one of this research, effects of three amendments (hairy vetch residue, manure, compost) on soil chemical and microbial properties were examined relative to formation of large macroaggregates in three different soils. Vetch and manure promoted fungal proliferation (measured via two biomarkers: fatty acid methyl ester 18:2ω6c and ergosterol) and also stimulated …

Interactions Of Zooplankton And Phytoplankton With Cyanobacteria, Rebecca Alexander

School of Natural Resources: Dissertations, Theses, and Student Research

Cyanobacteria are a major concern in Nebraska reservoirs and are capable of producing toxins that can cause skin irritations and gastrointestinal problems, as well as affect the nervous system. It is important to determine the mechanisms that can cause cyanobacteria blooms due to the effect they can have on human health. The interaction of zooplankton and other phytoplankton groups with cyanobacteria is important because there is a biological component in surface waters that should be taken into consideration along with the physical and chemical parameters that have been noted to promote cyanobacteria. For example, zooplankton have the ability to alter …

Fecal Indicator Bacteria In Knitting Mill Creek With A Comparison Of Methods Used To Enumerate E. Coli, Manju Nagarajan

OES Theses and Dissertations

This research seeks to evaluate the impact of an urban, multi-use neighborhood on the bacteriological quality of water in Knitting Mill Creek, a blind arm of the Lafayette River, a sub-estuary of the lower Chesapeake Bay. A principal objective was to determine the effects of rainfall, a surrogate for run-off, on water-column concentrations of fecal-indicator bacteria (FIB). I collected water samples weekly (September 2009-December 2010) and biweekly (January 2010-December 2011) at a storm-sewer outfall and a nearby marina and quantified their E. coli and enterococci concentrations using Colilert-18 and Enterolert, most-probable-number assays. In addition, I took monthly samples for these …

The Use Of Diatoms To Infer Environmental Change Of The Lower White River, Southeastern Arkansas, Ruchi Bhattacharya

Graduate Theses and Dissertations

This dissertation describes the limnology of the lower White River oxbow lakes in southeast Arkansas, inundated by the major 2008 spring flood. The flood water and sediment deposited in oxbow lakes were analyzed for water chemistry, sediment geochemistry and diatom assemblages and used as an analogue for past floods. The 2008 spring flood inundated and homogenized the entire floodplain; also represented by the predominantly planktonic diatom assemblage suggesting riverine input. Indicator species for eutrophication were also recorded consistent with the high nutrient content in the lakes. However, the variance in the surface diatom assemblage was best explained by the lake …

Chemoorganotrophic Bacteria Isolated From Biodeteriorated Surfaces In Cave And Catacombs, Filomena De Leo, Agnese Iero, Gabrielle Zammit, Clara E. Urzi

International Journal of Speleology

The main objective of this work was the comparative analysis of a large number of bacterial strains isolated from biodeteriorated surfaces in three different sites, namely the catacombs of St. Callistus in Rome, Italy, the catacombs dedicated to St. Agatha in Rabat, Malta and the Cave of Bats in Zuheros, Spain. Our results showed that even considering only culturable chemoorganotrophic bacteria the variability is very high, reflecting the great variety of microhabitats present. Hence any strategies to prevent, control or eliminate the biofilm-embedded microbiota from an archeological surface should take into account a number of considerations as stipulated in our …

Bacterial Community Survey Of Sediments At Naracoorte Caves, Australia, Eric M. Adetutu, Krystal Thorpe, Esmaeil Shahsavari, Steven Bourne, Xiangsheng Cao, Ramin Mazaheri Nezhad Fard, Greg Kirby, Andrew S. Ball

International Journal of Speleology

Bacterial diversity in sediments at UNESCO World Heritage listed Naracoorte Caves was surveyed as part of an investigation carried out in a larger study on assessing microbial diversity in caves. Cave selection was based on tourist accessibility; Stick Tomato and Alexandra Cave (> 15000 annual visits) and Strawhaven Cave was used as control (no tourist access). Microbial analysis showed that Bacillus was the most commonly detected microbial genus by culture dependent and independent survey of tourist accessible and inaccessible areas of show (tourist accessible) and control caves. Sediment bacterial groups were assigned to the Firmicutes, Actinobacteria and Proteobacteria. The survey …

Biological Effects On Serpentinite Weathering, Mary H. Evert, Julie Baumeister, Elisabeth Hausrath

Undergraduate Research Opportunities Program (UROP)

Serpentinites, perhaps more than any other rock type, control the composition and evolution of the development of the surrounding ecosystems. The bulk chemistry of serpentinite rocks, high in Mg and trace elements, and low in nutrients such as Ca, K, P, and N, causes an extreme and stressful environment for ecosystems. However, the role that those serpentine ecosystems play in development of serpentine soils has not been examined.

Due to the unusual chemistry of serpentine soils, serpentine ecosystems have deeper and better-developed root systems than other ecosystems. The rhizosphere of serpentine systems, documented to produce abundant organic acids and siderophores, …

Cellulose- And Xylan-Degrading Thermophilic Anaerobic Bacteria From Biocompost, M. V. Sizova, J. A. Izquierdo, N. S. Panikov, L. R. Lynd

Dartmouth Scholarship

Nine thermophilic cellulolytic clostridial isolates and four other noncellulolytic bacterial isolates were isolated from self-heated biocompost via preliminary enrichment culture on microcrystalline cellulose. All cellulolytic isolates grew vigorously on cellulose, with the formation of either ethanol and acetate or acetate and formate as principal fermentation products as well as lactate and glycerol as minor products. In addition, two out of nine cellulolytic strains were able to utilize xylan and pretreated wood with roughly the same efficiency as for cellulose. The major products of xylan fermentation were acetate and formate, with minor contributions of lactate and ethanol. Phylogenetic analyses of 16S …

Potential Fossil Endoliths In Vesicular Pillow Basalt, Coral Patch Seamount, Eastern North Atlantic Ocean, Barbara Cavalazzi, Frances Westall, Sherry L. Cady, Roberto Barbieri, Frédéric Foucher

Geology Faculty Publications and Presentations

The chilled rinds of pillow basalt from the Ampere-Coral Patch Seamounts in the eastern North Atlantic were studied as a potential habitat of microbial life. A variety of putative biogenic structures, which include filamentous and spherical microfossil-like structures, were detected in K-phillipsite-filled amygdules within the chilled rinds. The filamentous structures (similar to 2.5 mu m in diameter) occur as K-phillipsite tubules surrounded by an Fe-oxyhydroxide (lepidocrocite) rich membranous structure, whereas the spherical structures (from 4 to 2 mu m in diameter) are associated with Ti oxide (anatase) and carbonaceous matter. Several lines of evidence indicate that the microfossil-like structures in …

Iron Oxide And Calcite Associated With Leptothrix Sp. Biofilms Within An Estavelle In The Upper Floridan Aquifer, Lee J. Florea, Chasity L. Stinson, Josh Brewer, Rick Fowler, B Joe Kearns, Anthony M. Greco

International Journal of Speleology

In Thornton’s Cave, an estavelle in west-central Florida, SEM, EDS, and XRD data reveal biofilms that are predominantly comprised of FeOOH-encrusted hollow sheaths that are overgrown and intercalated with calcite. Fragments of this crystalline biofilm adhere to the walls and ceiling as water levels vary within the cave. Those on the wall have a ‘cornflake’ appearance and those affixed to the ceiling hang as fibrous membranes. PCR of DNA in the active biofilm, combined with morphologic data from the tubes in SEM micrographs, point to Leptothrix sp., a common Fe-oxidizing bacteria, as the primary organism in the biofilm. Recent discoveries …

Baseline Microbial Characterizations Of An Imperiled Aquatic Diversity Hotspot: Ash Meadows National Wildlife Refuge, Jessica Newburn, Jim Bruckner, Jenny C. Fisher, Duane P. Moser

Undergraduate Research Opportunities Program (UROP)

Located in the discharge zone of the Death Valley Flow System, Ash Meadows National Wildlife Refuge is a spring-fed desert oasis and biodiversity hotspot about 90 miles northwest of Las Vegas. These critical wetlands are potentially threatened by groundwater pumping, exotic species invasions, and climate change. Although a major component of the lower food web, very little is known about the microbial makeup of this ecosystem. As a first step towards understanding the microbial and biogeochemical aspects of this system, a detailed molecular-based characterization of microbial communities, baseline chemistry, and physical characteristics of various springs of Ash Meadows will be …

Biogeochemical Behavior Of Dissolved Arsenic And Uranium Concentrations In Public Water Supply Wells, Kevin J. Mcvey

School of Natural Resources: Dissertations, Theses, and Student Research

Public water supply (PWS) wells currently contain dissolved uranium concentrations above the federally mandated maximum contaminant level (MCL) of 30 ppb (parts per billion) and dissolved arsenic concentrations above the 10 ppb MCL. Both uranium and arsenic are known to cause various forms of cancer in humans. Variations in total uranium concentrations in PWS wells in Nebraska indicate a relationship to the duration and rate of pumping in specific wells. Although total arsenic concentrations show some variability over time in specific wells, the relationship to pumping is not as clear. Previous studies show that iron and sulfur bacteria present in …

The Influence Of Carbon Source Types And Nitrate On The Performance Of The Enhanced Biological Phosphorus Removal Systems, Shamim Ara Begum

UNLV Theses, Dissertations, Professional Papers, and Capstones

This research focuses on two issues in enhanced biological phosphorus removal (EBPR). The first issue encompasses the effect of the type of carbon sources (i.e. volatile fatty acids and non volatile fatty acids) on the microbiology of EBPR. The second issue deals with the influence of denitrification on EBPR. Few studies have been performed to investigate these two issues. The recent findings on these areas are summarized below to establish the knowledge gaps this dissertation attempted to address. Details on the specific findings can be found in the literature review portion of this proposal.

Multimeric Hemicellulases Facilitate Biomass Conversion, Zhanmin Fan, Kurt Wagschal, Wei Chen, Michael D. Montross, Charles C. Lee, Ling Yuan

Plant and Soil Sciences Faculty Publications

Two highly active trifunctional hemicellulases were constructed by linking the catalytic portion of a xylanase with an arabinofuranosidase and a xylosidase, using either flexible peptide linkers or linkers containing a cellulose-binding domain. The multifunctional enzymes retain the parental enzyme properties and exhibit synergistic effects in hydrolysis of natural xylans and corn stover.

Diversity Of Estrogen Degrading Microorganisms In Las Vegas Wash And Lake Mead, Nevada, Usa, Susanna Blunt, Jim Bruckner, Jenny C. Fisher, Duane P. Moser

Lake Mead Science Symposium

Endocrine disrupting chemicals (EDCs) are a subject of intense research as more studies reveal their persistence in the environment and detrimental effects on wildlife. Steroid hormones, including the natural and synthetic estrogens estrone (E1), 17-beta-estradiol (E2) and 17- alpha-ethinyl estradiol (EE2), are among the most bioactive and have been detected at low concentrations in waterways downstream from wastewater treatment plants. Las Vegas Wash, a stream flowing into Lake Mead and fed primarily by treated wastewater, provides a unique experimental system in which to study the role microorganisms play in the fate and dispersal of these compounds in surface waters.

Spatial And Temporal Patterns In The Microbial Diversity Of A Meromictic Soda Lake In Washington State, Pedro A. Dimitriu, Holly C. Pinkart, Brent M. Peyton, Melanie R. Mormile

All Faculty Scholarship for the College of the Sciences

The microbial community diversity and composition of meromictic Soap Lake were studied using culture-dependent and culture-independent approaches. The water column and sediments were sampled monthly for a year. Denaturing gradient gel electrophoresis of bacterial and archaeal 16S rRNA genes showed an increase in diversity with depth for both groups. Late-summer samples harbored the highest prokaryotic diversity, and the bacteria exhibited less seasonal variability than the archaea. Most-probable-number assays targeting anaerobic microbial guilds were performed to compare summer and fall samples. In both seasons, the anoxic samples appeared to be dominated by lactate-oxidizing sulfate-reducing prokaryotes. High numbers of lactate- and acetate-oxidizing …

Ship Ballast Tanks: How Microbes Travel The World, Fred C. Dobbs

OES Faculty Publications

As the international shipping fleet travels the oceans, it carries with it hidden cargoes of microbes. Fred C. Dobbs explores the hazards posed and what can be done to counteract them.

Environmental Controls On The Landscape-Scale Biogeography Of Stream Bacterial Communities, Noah Fierer, Jennifer L. Morse, Sean T. Berthrong, Emily S. Bernhardt, Robert B. Jackson

Environmental Science and Management Faculty Publications and Presentations

We determined the biogeographical distributions of stream bacteria and the biogeochemical factors that best explained heterogeneity for 23 locations within the Hubbard Brook watershed, a 3000-ha forested watershed in New Hampshire, USA. Our goal was to assess the factor, or set of factors, responsible for generating the biogeographical patterns exhibited by microorganisms at the landscape scale. We used DNA fingerprinting to characterize bacteria inhabiting fine benthic organic matter (FBOM) because of their important influence on stream nutrient dynamics. Across the watershed, streams of similar pH had similar FBOM bacterial communities. Streamwater pH was the single variable most strongly correlated with …

Microbial Nitrogen Limitation Increases Decomposition, Joseph M. Craine, Carl Morrow, Noah Fierer

Dartmouth Scholarship

With anthropogenic nutrient inputs to ecosystems increasing globally, there are long-standing, fundamental questions about the role of nutrients in the decomposition of organic matter. We tested the effects of exogenous nitrogen and phosphorus inputs on litter decomposition across a broad suite of litter and soil types. In one experiment, C mineralization was compared across a wide array of plants individually added to a single soil, while in the second, C mineralization from a single substrate was compared across 50 soils. Counter to basic stoichiometric decomposition theory, low N availability can increase litter decomposition as microbes use labile substrates to acquire …

Sulfur-Oxidizing Bacteria In Soap Lake (Washington State), A Meromictic, Haloalkaline Lake With An Unprecedented High Sulfide Content, Dimitry Y. Sorokin, Mirjam Foti, Holly C. Pinkart, Gerard Muyzer

All Faculty Scholarship for the College of the Sciences

Culture-dependent and -independent techniques were used to study the diversity of chemolithoautotrophic sulfur-oxidizing bacteria in Soap Lake (Washington State), a meromictic, haloalkaline lake containing an unprecedentedly high sulfide concentration in the anoxic monimolimnion. Both approaches revealed the dominance of bacteria belonging to the genus Thioalkalimicrobium, which are common inhabitants of soda lakes. A dense population of Thioalkalimicrobium (up to 10⁷ cells/ml) was found at the chemocline, which is characterized by a steep oxygen-sulfide gradient. Twelve Thioalkalimicrobium strains exhibiting three different phenotypes were isolated in pure culture from various locations in Soap Lake. The isolates fell into two groups …

Analysis Of Bacterial Population And Distribution In The Developing Strata Of A Constructed Wetland Used For Chlorinated Ethene Bioremediation, Milton J. Clausen Jr.

Theses and Dissertations

Chlorinated hydrocarbons and their degradation products are among of the most common organic groundwater contaminates in the United States. These compounds attack the central nervous system in animals and can affect the photosynthesis of plants. These compounds are also resistant to degradation in the environment and, because of this, pose a risk to any ecosystem in which they are present. This study identified the dominant microbial species in a constructed treatment wetland at Wright-Patterson AFB, Dayton, Ohio using 16S rRNA gene sequence analysis. Samples were taken from three different depths and during each of the four seasons. These samples were …

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.