Microbiology Commons^™

Green Infrastructure Design Influences Communities Of Urban Soil Bacteria, Jessica Lee Joyner, Jordan Kerwin, Maha Deeb, George Lozefski, Bharath Prithiviraj, Anna Paitseva, John Mclaughin, Peter M. Groffman, Zhongqi Cheng, Theodore R. Muth

Publications and Research

The importance of natural ecosystem processes is often overlooked in urban areas. Green Infrastructure (GI) features have been constructed in urban areas as elements to capture and treat excess urban runoff while providing a range of ancillary benefits, e.g., ecosystem processes mediated by microorganisms that improve air and water quality, in addition to the associations with plant and tree rhizospheres. The objective of this study was to characterize the bacterial community and diversity in engineered soils (Technosols) of five types of GI in New York City; vegetated swales, right of way bioswales (ROWB; including street-side infiltration systems and enhanced tree …

Linking Microbial Community Structure And Ecosystem Functions In Acidic Soil From Pennsylvania, Usa, Madison T. James, Sophia T. Farrisi, Shreya Shah, Vishal Shah

Sustainability Research & Creative Activities Grants Reports

Microorganisms play a critical role in the structure and functioning of soil ecosystems. Within acidic soil across the northeastern United States and Canada, we have little understanding of the microbial diversity present and its relationship to the biochemical cycles. The current study is aimed at understanding the taxonomical and functional diversities in the acidic soil obtained from near various types of trees, how the diversities change as a function of depth, and the linkage between taxonomical and functional diversities. From eight sampling locations, soil samples were collected from three horizons (depths). The three depths were 0-10 cm (A), 11-25 cm …

Metaproteomics Reveal That Rapid Perturbations In Organic Matter Prioritize Functional Restructuring Over Taxonomy In Western Arctic Ocean Microbiomes, Molly P. Mikan, H. Rodger Harvey, Emma Timmins-Schiffman, Michael Riffle, Damon H. May, Ian Salter, William S. Noble, Brook L. Nunn

OES Faculty Publications

We examined metaproteome profiles from two Arctic microbiomes during 10-day shipboard incubations to directly track early functional and taxonomic responses to a simulated algal bloom and an oligotrophic control. Using a novel peptide-based enrichment analysis, significant changes (p-value < 0.01) in biological and molecular functions associated with carbon and nitrogen recycling were observed. Within the first day under both organic matter conditions, Bering Strait surface microbiomes increased protein synthesis, carbohydrate degradation, and cellular redox processes while decreasing C1 metabolism. Taxonomic assignments revealed that the core microbiome collectively responded to algal substrates by assimilating carbon before select taxa utilize and metabolize nitrogen intracellularly. Incubations of Chukchi Sea bottom water microbiomes showed similar, but delayed functional responses to identical treatments. Although 24 functional terms were shared between experimental treatments, the timing, and degree of the remaining responses were highly variable, showing that organic matter perturbation directs community functionality prior to alterations to the taxonomic distribution at the microbiome class level. The dynamic responses of these two oceanic microbial communities have important implications for timing and magnitude of responses to organic perturbations within the Arctic Ocean and how community-level functions may forecast biogeochemical gradients in oceans.

Mine Reclamation Using Biofuel Crops: Insights Into The Microbial Ecology Of The Switchgrass (Panicum Virgatum) Microbiome, Brianna L. Mayfield

Graduate Theses, Dissertations, and Problem Reports (ETD)

Bioenergy crop production has steadily increased due to growing political support for renewable energy, thus initiating a demand to find alternative agricultural land. An innovative option is the use of marginal soils, such as reclaimed mine lands, to produce bioenergy crops. Switchgrass (Panicum virgatum) is a promising bioenergy crop that can be grown on marginal lands due to its robust growth in various soil types and climates. However, little is known regarding plant-microbe interactions among switchgrass systems within reclaimed mine lands. A study conducted in 2008 grew switchgrass on high- and low- quality reclaimed mine sites (Hampshire and …

Market Integration Predicts Human Gut Microbiome Attributes Across A Gradient Of Economic Development, Keaton Stagaman, Tara J. Cepon-Robins, Melissa A. Liebert, Theresa E. Gildner, Samuel S. Urlacher, Felicia C. Madimenos, Karen Guillemin, J. Josh Snodgrass, Lawrence C. Sugiyama, Brendan J. M. Bohannan

Publications and Research

Economic development is marked by dramatic increases in the incidence of microbiome-associated diseases, such as autoimmune diseases and metabolic syndromes, but the lifestyle changes that drive alterations in the human microbiome are not known. We measured market integration as a proxy for economically related lifestyle attributes, such as ownership of specific market goods that index degree of market integration and components of traditional and nontraditional (more modern) house structure and infrastructure, and profiled the fecal microbiomes of 213 participants from a contiguous, indigenous Ecuadorian population. Despite relatively modest differences in lifestyle across the population, greater economic development correlated with significantly …

The Ecology Of Antibiotic Resistance: Sources And Persistence Of Vancomycin-Resistant Enterococci And Antibiotic Resistant Genes In Aquatic Environments, Suzanne M. Young

USF Tampa Graduate Theses and Dissertations

The growing crisis of antibiotic resistance is a major threat to ecosystems and human health. Infections caused by known and emerging antibiotic resistant pathogens are on the rise globally, with approximately 700,000 deaths per year caused by antibiotic resistant bacteria (1). In the United States, infections from antibiotic resistant bacteria cause more than 2 million illnesses and 23,000 deaths (2). Antibiotic resistant bacteria and antibiotic resistance genes are released into aquatic ecosystems through hospital waste, residential sewer lines and animal agricultural waste streams. Animal agriculture accounts for approximately 70% of antibiotic use in the United States (3). In agricultural ecosystems, …

Survey Of Microbial Urea Degrader Diversity In Two Freshwater Ecosystems: Lake Shenandoah And The Shenandoah River, Naomi E. Gilbert

Senior Honors Projects, 2010-2019

One of the primary drivers of cyanobacterial harmful algal blooms (cHABs) in freshwater systems is nutrient loading, particularly of nitrogen and phosphorus. There has been an increased focus on assessing the role of nitrogen (N) in freshwater lakes and rivers that suffer cHABs. Urea, a widely-used, N-rich fertilizer, is a source of interest due to its abundance in freshwater ecosystems, primarily caused by anthropogenic nutrient loading. While recent work has shown that cHAB population succession may favor the toxic cyanobacterium Microcystis in urea-rich waters, the diversity of the associated bacterial community capable of degrading urea has yet to be determined. …

Incomplete Denitrification In Thermus Species, Chrisabelle Mefferd

UNLV Theses, Dissertations, Professional Papers, and Capstones

Members the bacterial genus Thermus have been shown to be incomplete denitrifiers, terminating with nitrite or nitrous oxide (N2O). However, the ability to carry out denitrification and the evolution of nitrogen oxide reductase genes in Thermus remains poorly understood. This study tests the hypothesis that incomplete denitrification is common in Thermus and seeks to uncover patterns in the evolution of denitrification pathways in Thermus. Denitrification capacity was determined in a collection of 25 strains representing ten species of Thermus and phylogenetic analysis was performed to determine whether denitrification genes evolved horizontally in Thermus. No strains in this study reduced nitrate …

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 …

Microbial Ecology Of Waterborne Pathogens In Sus Scofra And Odocoileus Virginianus In The Jackson Bienville Wildlife Management Area, Jaymes Hunter Collins

Doctoral Dissertations

Previous studies have demonstrated that feral swine (Sus scofra ) are significant reservoirs for a number of pathogens that present a potential threat to wildlife and humans. Despite this, few studies have gone beyond quantifying the incidence of these pathogens to further probe their ecology within a specific habitat or ecosystem.

Overall, the objective of this study was to characterize three potential reservoirs in a feral swine infested habitat; two ungulates, and one aquatic reservoir. Our study area was the Jackson-Bienville Wildlife Management Area (J-B WMA). We chose four waterborne bacteria: Brucella spp., Leptospira interrogans, Salmonella enterica, and Helicobacter …

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 …

Intrinsic Challenges In Ancient Microbiome Reconstruction Using 16s Rrna Gene Amplification, Kirsten Ziesemer, Allison Mann, Krithivasan Sankaranarayanan, Hannes Schroeder, Andrew T. Ozga, Bernd W. Brandt, Egija Zaura, Andrea Waters-Rist, Menno Hoogland, Domingo C. Salazar-Garcia, Mark Aldenderfer, Camilla Speller, Jessica Hendy, Darlene A. Weston, Sandy J. Macdonald, Gavin H. Thomas, Matthew J. Collins, Cecil M. Lewis Jr., Corinne Hofman, Christina Warinner

Biology Faculty Articles

To date, characterization of ancient oral (dental calculus) and gut (coprolite) microbiota has been primarily accomplished through a metataxonomic approach involving targeted amplification of one or more variable regions in the 16S rRNA gene. Specifically, the V3 region (E. coli341–534) of this gene has been suggested as an excellent candidate for ancient DNA amplification and microbial community reconstruction. However, in practice this metataxonomic approach often produces highly skewed taxonomic frequency data. In this study, we use non-targeted (shotgun metagenomics) sequencing methods to better understand skewed microbial profiles observed in four ancient dental calculus specimens previously analyzed by amplicon …

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 …

The Pleiotropic Effects Of Beneficial Mutations Of Adapted Escherichia Coli Populations, Brian Scott Van Dam

Honors Theses and Capstones

Mutations that improve fitness in one environment can often be beneficial, deleterious, or neutral in alternative environments. When a single mutation effects fitness in multiple environments, it is said to be a pleiotropic, which can have important consequences for niche specialization, niche expansion, speciation, and even extinction in the face of environmental change. While previous studies have revealed that pleiotropy is nearly universal, the role of adaptive history in the spectrum of pleiotropic effects has yet to undergo detailed experimental observation. Using experimental evolution we gathered beneficial mutations in a previously adapted strain of Escherichia coli growing in the same …

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 …

Biogeography And Microhabitat Distribution Of Myxomycetes In High-Elevation Areas Of The Neotropics, Carlos Alonso Rojas-Alvarado

Graduate Theses and Dissertations

Myxomycetes are a group of amoeboid organisms with the capacity of forming fruiting bodies that resemble some macrofungi. The ecology and global distribution of species within the group have been studied only during the last half century. For this reason, a number of questions regarding the nature of the interactions that exist between myxomycetes and their environment still lack the empirical evidence required to obtain complete answers. In the Neotropical region, species assemblages have been moderately well studied, but their biogeography and macroecology have received little attention. In high-elevation areas of this region, the situation is especially precarious, due the …

Enzymes As Feed Additive To Aid In Responses Against Eimeria Species In Coccidia-Vaccinated Broilers Fed Corn-Soybean Meal Diets With Different Protein Levels, J. Parker, E. O. Oviedo Rondon, Beatrice A. Clack, S. Clemente-Hernandez, J. Osborne, J. C. Remus, H. Kettunen, H. Makivuokko, E. M. Pierson

Faculty Publications

This research aimed to evaluate the effects of adding a combination of exogenous enzymes to starter diets varying in protein content and fed to broilers vaccinated at day of hatch with live oocysts and then challenged with mixed Eimeria spp. Five hundred four 1-d-old male Cobb-500 chickens were distributed in 72 cages. The design consisted of 12 treatments. Three anticoccidial control programs [ionophore (IO), coccidian vaccine (COV), and coccidia-vaccine + enzymes (COV + EC)] were evaluated under 3 CP levels (19, 21, and 23%), and 3 unmedicated-uninfected (UU) negative controls were included for each one of the protein levels. All …

Effects Of Feed Additives And Mixed Eimeria Species Infection On Intestinal Microbial Ecology Of Broilers, M. E. Hume, S. Clemente-Hernandez, E. O. Oviedo Rondon

Faculty Publications

Evaluation of digestive microbial ecology is necessary to understand effects of growth-promoting feed. In the current study, the dynamics of intestinal microbial communities (MC) were examined in broilers fed diets supplemented with a combination of antibiotic (bacitracin methylene disalicylate) and ionophore (Coban 60), and diets containing 1 of 2 essential oil (EO) blends, Crina Poultry (CP) and Crina Alternate (CA). Five treatments were analyzed: 1) unmedicated uninfected control; 2) unmedicated infected control; 3) feed additives monensin (bacitracin methylene disalicylate) + monensin (Coban 60; AI); 4) EO blend CP; and 5) EO blend CA. Additives were mixed into a basal feed …

Characterization Of Microbial Activity, Mark P. Buttner, Patricia Cruz, Klaus J. Stetzenbach, Abe Van Luik, Thomas Williams, Amy J. Smiecinski

Publications (YM)

The overall goal of this study is to investigate the phenomena that affect the fate and transport of radionuclides in the environment. The objective of this task, “Characterization of Microbial Activity”, is to develop a molecular biological method for the characterization of the microbial population indigenous to the Yucca Mountain Project site, with emphasis in detection and measurement of species or groups of microorganisms that could be involved in actinide and/or metal reduction, and subsurface transport. Subtasks consist of QA planning and preparation, and literature review. This task is part of a cooperative agreement between the UNLV Research Foundation and …

Microbial Endemism And Biogeography, Brian P. Hedlund, James T. Staley

Life Sciences Faculty Research

The topic of microbial biogeography is almost 100 years old, however, when confronted with questions about the existence and extent of endemism in the microbial world, many microbiologists respond with opinions and theoretical arguments rather than examples of well-conducted studies. We begin this chapter with an overview of this debate as it applies to free-living prokayotes in part because there are relatively few good microbial biogeography studies. Furthermore, the arguments help to frame microbial biogeography in the larger context of biodiversity in that if endemism is common, then many more species exist.

The Molecular Microbial Ecology And Mechanisms Of Biomarker Degradation In Crude Oil, Fredrick Daniel Bost

MUSC Theses and Dissertations

Biomarkers are structurally complex components of petroleum derived from biological molecular precursors, such as chlorophyll, sterols, and hopanoids (Peters and Moldowan, 1993). The biomarker profile of a crude oil is distinctive and diagnostic, often allowing correlation of an oil to its source rock. Many biomarkers in crude oil are resistant to biodegradation and are used by petroleum geochemists to assess genetic relationships, thermal maturity, and biodegradation. However, the reliability of these biomarkers depends on this recalcitrance to biodegradation. The studies presented here used bacterial enrichment cultures to examine the distribution and extent of biomarker­ degrading activity in aerobic and anaerobic …

So You Want To Be A Soil Microbiologist?, Mark S. Coyne

Plant and Soil Sciences Faculty Book Gallery

A tongue-in-cheek look at soil microbiology.

The Microbial Biochemical Potential Of Two Detention-Retention Marshes In The Kissimmee River Valley Watershed, Douglas A. Winkelmann

Retrospective Theses and Dissertations

One of the major programs to abate the deterioration of water quality in the Lake Okeechobee watershed was the addition of detention-retention facilities. The microbial biochemical potential of two different detention-retention marshes in the Kissimmee River Valley were examined to determine their effectiveness to improve water quality. The kinetics of decomposition and nutrient mineralization and assimilation, as mediated by microorganisms, and the enumeration of microorganisms capable of utilizing various substrates were studied. Various communities within each marsh were studied during a 2-year period. The decomposition rates of 3 plant substrates were determined. Chitin was used as a standard for organic …