Environmental Microbiology and Microbial Ecology Commons^™

Mixing It Up In The Ocean Carbon Cycle And The Removal Of Refractory Dissolved Organic Carbon, Yuan Shen, Ronald Benner

Faculty Publications

A large quantity of reduced carbon is sequestered in the ocean as refractory dissolved molecules that persist through several circuits of global overturning circulation. Key aspects of the cycling of refractory dissolved organic carbon (DOC) remain unknown, making it challenging to predict how this large carbon reservoir will respond to climate change. Herein we investigate mechanisms that remove refractory DOC using bioassay experiments with DOC isolated from surface, mesopelagic and deep waters of the Atlantic Ocean. The isolated DOC was refractory to degradation by native microbial communities, even at elevated concentrations. However, when the refractory DOC was introduced to a …

Bioassessment Of A Drinking Water Reservoir Using Plankton: High Throughput Sequencing Vs. Traditional Morphological Method, Wanli Gao, Zhaojin Chen, Yuying Li, Yangdong Pan, Jingya Zhu, Shijun Guo, Lanqun Hu, Jin Huang

Environmental Science and Management Faculty Publications and Presentations

Drinking water safety is increasingly perceived as one of the top global environmental issues. Plankton has been commonly used as a bioindicator for water quality in lakes and reservoirs. Recently, DNA sequencing technology has been applied to bioassessment. In this study, we compared the effectiveness of the 16S and 18S rRNA high throughput sequencing method (HTS) and the traditional optical microscopy method (TOM) in the bioassessment of drinking water quality. Five stations reflecting different habitats and hydrological conditions in Danjiangkou Reservoir, one of the largest drinking water reservoirs in Asia, were sampled May 2016. Non-metric multi-dimensional scaling (NMDS) analysis showed …

Nevada Desert Dust With Heavy Metals Suppresses Igm Antibody Production, Deborah E. Keil, Brenda J. Buck, Dirk Goossens, Brett Mclaurin, Lacey Murphy, Mallory Leetham-Spencer, Yuanxin Teng, James E. Pollard, Russell Gerads, Jamie C. Dewitt

Geoscience Faculty Research

Systemic health effects from exposure to a complex natural dust containing heavy metals from the Nellis Dunes Recreation Area (NDRA) near Las Vegas, NV, were evaluated. Several toxicological parameters were examined following lung exposure to emissive dust from three geologic sediment types heavily used for recreational off-road activities: yellow sand very rich in arsenic (termed CBN 5); a shallow cover of loose dune sand overlying a gravelly subsoil bordering dune fields (termed CBN 6); and brown claystone and siltstone (termed CBN 7). Adult female B6C3F1 mice were exposed by oropharyngeal administration to these three types of geogenic dusts at 0.01–100 …

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, …

Microbial Community Richness Distinguishes Shark Species Microbiomes In South Florida, Rachael Cassandra Karns

HCNSO Student Theses and Dissertations

The microbiome (microbial community) of individuals is crucial when characterizing and understanding processes that are required for organism function and survival. Microbial organisms, which make up an individual’s microbiome, can be linked to disease or function of the host organism. In humans, individuals differ substantially in their microbiome compositions in various areas of the body. The cause of much of the composition diversity is yet unexplained, however, it is speculated that habitat, diet, and early exposure to microbes could be altering the microbiomes of individuals (Human Microbiome Project Consortium, 2012b, 2012a). To date, only one study has reported on microbiome …

Bacterial Communities Associated With Healthy And Diseased Acropora Cervicornis (Staghorn Coral) Using High-Throughput Sequencing, Charles Walton

HCNSO Student Theses and Dissertations

Coral diseases were first noted in the 1960s and 1970s and have had major impacts globally on coral reef community structures. In the Caribbean, a major outbreak of white band disease has been considered responsible for the drastic decline of Caribbean Acroporids since the 1970s. In addition to white band disease, another more recently described condition known as rapid tissue loss (RTL) has had major impacts on Acropora cervicornis populations, specifically offshore Broward County Southeast Florida. While these diseases have contributed to the population decline, determining their etiologies has been elusive.

Coral diseases have been characterized by shifts in their …

Range-Wide Prevalence And Impacts Of Pseudocercosporella Inconspicua On Lilium Grayi And An Assessment Of L. Superbum And L. Michauxii As Reservoirs, Cindy L. Barrett

Electronic Theses and Dissertations

Lilium grayi (Gray’s Lily), a southern Appalachian endemic species, is threatened by a Lilium-specific fungal pathogen, Pseudocercosporella inconspicua. The disease is characterized by tan lesions that can cause early senescence, while also lowering seed production and viability. This project tested for P. inconspicua conidia and accessed health at nine locations. The disease was present and ubiquitous across the range of L. grayi. Through identification of P. inconspicua conidia in the field, L. superbum (Turk’s Cap Lily) was identified as an additional host, while L. michauxii (Michaux’s Lily) was disease-free. However, infection was inducible in both species. With …

Microbial Interactions In The Phyllosphere Increase Plant Performance Under Herbivore Biotic Stress, Muhammad Saleem, Nicole Meckes, Zahida H. Pervaiz, Milton B. Traw

Plant and Soil Sciences Faculty Publications

The phyllosphere supports a tremendous diversity of microbes and other organisms. However, little is known about the colonization and survival of pathogenic and beneficial bacteria alone or together in the phyllosphere across the whole plant life-cycle under herbivory, which hinders our ability to understand the role of phyllosphere bacteria on plant performance. We addressed these questions in experiments using four genetically and biogeographically diverse accessions of Arabidopsis thaliana, three ecologically important bacterial strains (Pseudomonas syringae DC3000, Xanthomonas campestris, both pathogens, and Bacillus cereus, plant beneficial) under common garden conditions that included fungus gnats (Bradysia spp.). …

Analysis Of Microbial Diversity In Disturbed Soil, Tyler G. Sanda

Williams Honors College, Honors Research Projects

This paper uses the composition and abundance of microbial species to analyze soil recovery in disturbed land. Surface mining disturbs ecological communities throughout the world. As organizations seek to reclaim these disturbed lands, a proper analysis of recovery is needed. In previous studies, recovery of disturbed land was limited to surface examinations, which do not characterize the possible unseen devastating effects of the subsoil. Soil microorganisms are extremely sensitive to environmental changes such as strip mining. It is proposed that these microorganisms may serve as better indicators of recovery post disturbance. Our analysis indicates microbial recovery, however it may not …

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 …

Do Novel Weapons That Degrade Mycorrhizal Mutualisms Explain Invasive Species Success?, Philip L. Pinzone Mr.

Biology Theses

Invasive plants often dominate novel habitats where they did not co-evolve with local species. Several hypotheses suggest mechanisms that explain increased exotic plant success, including 'novel weapons' and 'degraded mutualisms'. Japanese knotweed (Fallopia japonica) and European buckthorn (Rhamnus cathartica) are widespread plant invaders in North America that can dominate ecosystems. The goal of this study is to test whether these impacts are more consistent with novel weapons or degraded mutualism hypotheses. I examine tree seedling recruitment, (germination and initial survival) growth, (biomass) and mycorrhizal invasion (AMF content) as a function of F. japonica and R. cathartica …

Regulation Of Pyrroloquinoline Quinone-Dependent Glucose Dehydrogenase Activity In The Model Rhizosphere-Dwelling Bacterium Pseudomonas Putida Kt2440, Ran An, Luke Moe

Plant and Soil Sciences Faculty Publications

Soil-dwelling microbes solubilize mineral phosphates by secreting gluconic acid, which is produced from glucose by a periplasmic glucose dehydrogenase (GDH) that requires pyrroloquinoline quinone (PQQ) as a redox coenzyme. While GDH-dependent phosphate solubilization has been observed in numerous bacteria, little is known concerning the mechanism by which this process is regulated. Here we use the model rhizosphere-dwelling bacterium Pseudomonas putida KT2440 to explore GDH activity and PQQ synthesis, as well as gene expression of the GDH-encoding gene (gcd) and PQQ biosynthesis genes (pqq operon) while under different growth conditions. We also use reverse transcription-PCR to identify transcripts …

Characterization Of The Marine Sponge Amphimedon Compressa Microbiome Across A Spatial Gradient, Renee Michelle Potens

HCNSO Student Theses and Dissertations

Diverse and ecologically important microbial communities (microbiomes) are symbiotic within marine sponges. In this study, the microbiome of Amphimedon compressa from three sample locations (Broward and Dade Counties, Southeast Florida, USA and the Southern Caribbean, Bocas del Toro, Panama) is characterized using 16S rRNA Illumina sequencing. The predominant taxa are Proteobacteria and Cyanobacteria, as expected for Low Microbial Abundance sponges, accounting for over 53% of the total microbiome community. The numbers of Operational Taxonomic Units (OTUs) decrease from Broward County (2,900) to Dade County (2,300) and then Bocas del Toro (1,200). The correlates to a decreasing north-south gradient of …

Dissemination And Persistence Of Plasmid Located, Integron Associated Antibiotic Resistant Genes In Wastewater Treatment Plant Effluent And Stream Water Bacteria, _ Suhartono

Graduate Theses and Dissertations

Transmissible plasmid-mediated integrons play important role in the persistence and dissemination of antibiotic resistance throughout the environment. Plasmids from 139 multi-antibiotic resistant Escherichia coli recovered from wastewater treatment plant effluent and upstream and downstream receiving stream water in Northwest Arkansas were extracted and profiled. Genes of class 1 and class 2 integrase (intI), mobilization (mob), sulfamethoxazole resistance (sul), and trimethoprim resistance (dfr) were detected using PCR and confirmed through DNA sequencing. Plasmids from almost half of the isolates (47%) were transmissible with mobF12 gene as the most frequently detected mobilization gene. Plasmid-borne class 1 with and without class 2 integrons …

Global Worming: A Quantitative Study About Greenhouse Gas Flux In Surface Soils Facilitated By The Anecic Earthworm, Lumbricus Terrestris, Under Rising Global Temperature, Rachel Briden Frei, Jose A. Amador

Senior Honors Projects

Climate change is the long-term alteration in the Earth’s average weather conditions believed to be driven by greenhouse gases (GHG): carbon dioxide (CO₂), methane (CH₄) and nitrous oxide (N₂O). These alterations are expected to cause more extreme weather events, gradually warmer global temperatures and greater amounts of precipitation. Roughly 20% of the Earth’s CO₂, one-third of CH₄ and two-thirds of N₂O emissions, originate from soils, and earthworms are known to accelerate GHG. As climate change proceeds, there is expected to be an increase in global temperature of 2-6ºC. Temperature …

Soil Microbial Community Composition And Respiration Along An Experimental Precipitation Gradient In A Semiarid Steppe, Cancan Zhao, Yuan Miao, Chengde Yu, Lili Zhu, Feng Wang, Lin Jiang, Dafeng Hui, Shiqiang Wan

Biology Faculty Research

As a primary limiting factor in arid and semiarid regions, precipitation strongly influences soil microbial properties. However, the patterns and mechanisms of soil microbial responses to precipitation have not been well documented. In this study, changes in soil microorganisms along an experimental precipitation gradient with seven levels of precipitation manipulation (i.e., ambient precipitation as a control and ±20%, ±40% and ±60% of ambient precipitation) were explored in a semiarid temperate steppe in northern China. Soil microbial biomass carbon and respiration as well as the ratio of fungal to bacterial biomass varied along the experimental precipitation gradient and peaked under the …

Novel Mitochondrial Complex I Inhibitors Restore Glucose-Handling Abilities Of High-Fat Fed Mice, Darren Martin, Siobhan Leonard, Robert Devine, Clara Redondo, Gemma Kinsella, Conor Breen, Victoria Mceneaney, Mary Rooney, Tim Munsey, Richard Porter, Asipu Sivaprasadarao, John Stephens, John Findlay

Articles

Metformin is the main drug of choice for treating type 2 diabetes, yet the therapeutic regimens and side effects of the compound are all undesirable and can lead to reduced compliance. The aim of this study was to elucidate the mechanism of action of two novel compounds which improved glucose handling and weight gain in mice on a high-fat diet. Wildtype C57Bl/6 male mice were fed on a high-fat diet and treated with novel, anti-diabetic compounds. Both compounds restored the glucose handling ability of these mice. At a cellular level, these compounds achieve this by inhibiting complex I activity in …

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. …

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

Theses and Dissertations--Plant and Soil Sciences

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

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 …

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

Master's Theses

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

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

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 …

Methane Emissions From Direct-Seeded, Delayed-Flood Rice Grown On A Clay Soil, Alden Daniel Smartt

Graduate Theses and Dissertations

Due to the production of methane (CH4) under flooded-soil conditions, rice (Oryza sativa L.) cultivation is a major contributor to agricultural CH4 emissions. Studies examining CH4 emissions from rice have only recently been initiated in Arkansas and no data have been collected from rice produced on clay soils in Arkansas. Therefore, research was conducted in 2012 and 2013 at the Northeast Research and Extension Center in Keiser, Arkansas to examine the factors affecting CH4 emissions from rice produced on a Sharkey clay (very-fine, smectitic, thermic Chromic Epiaquerts). The objectives of this study were to determine: 1) the effect of vegetation …

Potential For Biocontrol Of Environmental Vibrio Spp. By Predatory Bacteria Bacteriovorax, Patrick Tennis

OES Theses and Dissertations

The scale of predator-prey interactions varies from the iconic (e.g., lions and gazelles) to the microscopic (e.g., protists and bacteria). Bdellovibrio-and-like-organisms (BALOs) are bacteria that prey upon other Gram-negative bacteria, including pathogens. In particular, the halophilic genus Vibrio, many species of which are disease agents, has been shown to be susceptible to attack by BALOs. One motivation of the present research is to assess the potential for biocontrol of Vibrio by Bacteriovorax. This investigation is the first to test the susceptibility of Vibrio strains (n = 26) originating from a variety of geographic locations to predation by …

Marine Sequestration Of Carbon In Bacterial Metabolites, Oliver J. Lechtenfeld, Norbert Hertkorn, Yuan Shen, Matthias Witt, Ronald Benner

Faculty Publications

Linking microbial metabolomics and carbon sequestration in the ocean via refractory organic molecules has been hampered by the chemical complexity of dissolved organic matter (DOM). Here, using bioassay experiments and ultra-high resolution metabolic profiling, we demonstrate that marine bacteria rapidly utilize simple organic molecules and produce exometabolites of remarkable molecular and structural diversity. Bacterial DOM is similar in chemical composition and structural complexity to naturally occurring DOM in sea water. An appreciable fraction of bacterial DOM has molecular and structural properties that are consistent with those of refractory molecules in the ocean, indicating a dominant role for bacteria in shaping …

Effects Of Sex And Mycorrhizal Fungi On Gas Exchange In The Dioecious Salt Marsh Grass Distichlis Spicata, Kassandra Reuss-Schmidt, Todd N. Rosenstiel, Sally R. Rogers, Allie G. Simpson, Sarah M. Eppley

Biology Faculty Publications and Presentations

Premise of research. In dioecious plant species, males and females often differ in physiology, and mycorrhizal fungal relationships are likely to influence these differences. However, few data are available on the potential role of mycorrhizal fungi in altering sex-specific physiology and population sex ratios of dioecious plant species.

Methodology. In this study, we measured leaf gas exchange in a multifactorial greenhouse experiment with and without mycorrhizal fungal additions and under field conditions in Distichlis spicata, a dioecious C4 salt marsh grass, displaying extreme spatial sex ratio variation.

Pivotal results. We found a significant interaction between gas exchange, plant sex, and …

Effects Of Treated Wastewater Effluent On Microbial Community Structure In A Natural Receiving Aquatic System, Matthew D. Hladilek

Masters Theses

Despite our dependency on treatment facilities to condition wastewater for eventual release to the environment, our knowledge regarding the effects of treated water on the local watershed is extremely limited. Responses of these lotic systems to the treated wastewater effluent have been traditionally investigated by examining the benthic macroinvertebrate assemblages and community structure; however, these studies do not address the microbial diversity of the water systems. In the present study, planktonic and benthic bacterial community structure were examined at fourteen sites (from 60 m upstream to 12,100 m downstream) and at two time points along an aquatic system receiving treated …

Methane Production By A Packed-Bed Anaerobic Digester Fed Dairy Barn Flush Water, Sean Richard Thomson

Master's Theses

Packed-bed digesters are an alternative to covered lagoon digesters for methane production and anaerobic treatment of dilute wastewaters such as dairy barn flush water. The physical media of packed-beds retain biofilms, often allowing increased treatment rates. Previous studies have evaluated several types of media for digestion of dilute wastewaters, but cost and media fouling have setback commercial development. A major operational cost has been effluent recirculation pumping.

In the present effort, a novel approach to anaerobic digestion of flush dairy water was developed at pilot-scale: broken walnut shells were used as a low-cost packed-bed medium and effluent recirculation was replaced …

Phylogenetic Diversity Of Microbial Isolates From The Mars Pathfinder, Kyla Bradylong, Adriana Blachowicz, Parag Vaishampayan, James N. Benardini, Wayne Schubert

STAR Program Research Presentations

As spacecraft are sent to different planets, they take with them microscopic pieces of life from Earth. It is the task of the Biotechnology and Planetary Protection Group to keep as much of this life off other planets as possible as well as document any life that may have been sent. During the construction of the Mars Pathfinder, samples were collected from various locations on the spacecraft to test for contamination. These samples were then isolated, grown, documented, preserved and their 16S rRNA genes were sequenced for identification. The 16S rRNA gene sequence is utilized because it is a highly …

Interactions Of Various Bacterial Populations With Chemical And Physical Factors From Seasonal Inputs And Outputs Of Retention Ponds, Felicia A. Krelwitz

All Student Theses and Dissertations

Retention ponds at Governors State University play an important role in collecting and treating storm water runoff before leaving campus and entering Thorn Creek. Many chemical and physical factors influence the diversity of bacterial populations in freshwater ecosystems. The main objective of this study was to compare the interactions of various bacterial populations with chemical and physical factors from seasonal inputs and outputs of Governors State University retention ponds before being discharged into Thorn Creek. The retention ponds studied include the Café Settling pond, Café pond and Beaver pond. Water and sediment were collected from inputs and outputs every other …