Environmental Microbiology and Microbial Ecology Commons^™

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 …

Cure From The Cave: Volcanic Cave Actinomycetes And Their Potential In Drug Discovery, Naowarat (Ann) Cheeptham Dr., Tara Sadoway, Devon Rule, Kent Watson, Paul Moote, Laiel C. Soliman, Nicholas Azad, Kingsley Donkor, Derrick Horne

International Journal of Speleology

Volcanic caves have been little studied for their potential as sources of novel microbial species and bioactive compounds with new scaffolds. We present the first study of volcanic cave microbiology from Canada and suggest that this habitat has great potential for the isolation of novel bioactive substances. Sample locations were plot ted on a contour map that was compiled in ArcView 3.2. Over 400 bacterial isolates were obtained from the Helmcken Falls cave in Wells Gray Provincial Park, British Columbia. From our preliminary screen, of 400 isolates tested, 1% showed activity against extended spectrum ß-lactamase E. coli, 1.75% against Escherichia …

The Effects Of Uv Light On The Antimicrobial Activities Of Cave Actinomycetes, Devon Rule, Naowarat Cheeptham

International Journal of Speleology

The goal of this study was to determine whether actinomycetes isolated from a volcanic cave in western Canada could produce novel antimicrobial compounds against six multidrugresistant pathogens when exposed to UV light. One hundred and seventy-six actinomycete strains isolated from Helmcken Falls Cave, Wells Gray Provincial Park, BC, were screened against six pathogens using the “plug assay” in UV light and no light conditions. Of the 176 strains tested, 100 or 57% of the cave actinomycete strains had antimicrobial activities against the pathogens in 124 different instances: 35 instances when exposed to UV and no light, 30 when exposed to …

Histone Biotinylation In Candida Albicans, Sahar Hasim, Swetha Tati, Nandakumar Madayiputhiya, Renu Nandakumar, Kenneth W. Nickerson

Kenneth Nickerson Papers

Candida albicans is an opportunistic fungal pathogen in humans. It is a polymorphic fungus: it can live as yeasts, hyphae, or pseudohyphae. Biotin is required for cell growth and fatty acid metabolism because it is used as a cofactor for carboxylases such as acetyl-CoA carboxylase, and pyruvate carboxylase. In addition, we have discovered that biotin is used to modify histones in C. albicans. Biotinylation was detected by Western blots using a monoclonal antibiotin HRP-conjugated antibody as well as with qTOF and LC/MS/MS mass spectrometry. As a precaution, the antibiotin antibody was dialyzed against neutravidin prior to use. During this study, …

Seroprevalence Of Brucellosis In Livestock Within Three Endemic Regions Of The Country Of Georgia, Eliso Mamisashvili, Ian T. Kracalik, Tinatin Onashvili, Lela Kerdzevadze, Ketevan Goginashvili, Tamar Tigilauri, Marina Donduashvili, Marina Nikolaishvili, Irma Beradze, Marina Zakareishvili, Maka Kokhreidze, Makvala Gelashvili, Nino Vepkhvadze, S. Elizabeth Rácz, Philip H. Elzer, Mikeljon P. Nikolich, Jason K. Blackburn

Harold W. Manter Laboratory of Parasitology: Faculty Publications

Brucellosis is the one of most common livestock zoonoses in Georgia, resulting in significant economic losses. Livestock were sampled in three regions of Georgia (Kakheti, Kvemo Kartli, Imereti). Districts that historically reported high numbers of brucellosis related morbidity were selected for serological, bacteriological and molecular surveys. Surveying efforts yielded samples from 10,819 large and small ruminants. In total, 735 serological tests were positive on Rose Bengal and 33 bacterial isolates were recovered and identified as Brucella melitensis or Brucella abortus by microbiology and AMOS-PCR. A Bayesian framework was implemented to estimate the true prevalence of the disease given an imperfect …

Diversity And Biosynthetic Potential Of Culturable Aerobic Heterotrophic Bacteria Isolated From Magura Cave, Bulgaria, Iva Tomova, Irina Lazarkevich, Anna Tomova, Margarita Kambourova, Evgenia Vasileva-Tonkova

International Journal of Speleology

Biocapacity of bacteria inhabiting karstic caves to produce valuable biologically active compounds is still slightly investigated. A total of 46 culturable heterotrophic bacteria were isolated under aerobic conditions from the Gallery with pre-historical drawings in MaguraCave, Bulgaria. Phylogenetic analysis revealed that most of bacterial isolates affiliated with Proteobacteria (63%), followed by Actinobacteria (10.9%), Bacteroidetes (10.9%), and Firmicutes (6.5%). A strong domination of Gram-negative bacteria (total 81%) belonging to nine genera: Serratia, Pseudomonas, Enterobacter, Sphingobacterium, Stenotrophomonas, Commamonas, Acinetobacter, Obesumbacterium, and Myroides, was observed. Gram-positive isolates were represented by the genera Bacillus, Arthrobacter, and Micrococcus. One isolate …

A World Review Of Fungi, Yeasts, And Slime Molds In Caves, Karen J. Vanderwolf, David Malloch, Donald F. Mcalpine, Graham J. Forbes

International Journal of Speleology

We provide a review of fungi, yeasts, and slime molds that have been found in natural solution caves and mines worldwide. Such habitats provide frequent roost sites for bats, and in eastern North America the environmental conditions that support white-nose syndrome, a lethal fungal disease currently devastating bat populations. A list of 1029 species of fungi, slime moulds, and yeasts in 518 genera have been documented from caves and mines worldwide in 225 articles. Ascomycota dominate the cave environment. Most research has been conducted in temperate climates, especially in Europe. A mean of 17.9±24.4SD fungal species are reported per study. …

La Serreta Endokarst (Se Spain): A Sustainable Value?, Antonia D. Asencio, Teodoro Espinosa

International Journal of Speleology

La Serreta endokarst (SE Spain), which UNESCO declared a World Heritage Site in 1998, was considered a sanctuary with cave art and one of the most important archaeological sites in the Mediterranean region for both the remains it hosts and the spectacular karstic landscape at the site.

To coincide with the 40th anniversary of its discovery, the La Serreta cave-chasm was adapted for public use with the intention of showing visitors the remains, which date back to prehistoric times. The solution included attempts to minimize contact with the valuables in the cave in order to alter the existing remains as …

Metagenome Sequence Analysis Of Filamentous Microbial Communities Obtained From Geochemically Distinct Geothermal Channels Reveals Specialization Of Three Aquificales Lineages, Cristina Takacs-Vesbach, William P. Inskeep, Zackary J. Jay, Markus J. Herrgard, Douglas B. Rusch, Susannah G. Tringe, Mark A. Kozubal, Natsuko Hamamura, Richard E. Macur, Bruce W. Fouke, Anna-Louise Reysenbach, Timothy R. Mcdermott, Ryan Dem. Jennings, Nicolas W. Hengartner, Gary Xie

Biology Faculty Publications and Presentations

The Aquificales are thermophilic microorganisms that inhabit hydrothermal systems world- wide and are considered one of the earliest lineages of the domain Bacteria. We analyzed metagenome sequence obtained from six thermal “filamentous streamer” communities (∼40 Mbp per site), which targeted three different groups of Aquificales found in Yellow- stone National Park (YNP). Unassembled metagenome sequence and PCR-amplified 16S rRNA gene libraries revealed that acidic, sulfidic sites were dominated by Hydrogenobac- ulum (Aquificaceae) populations, whereas the circum-neutral pH (6.5–7.8) sites containing dissolved sulfide were dominated by Sulfurihydrogenibium spp. (Hydrogenothermaceae). Thermocrinis (Aquificaceae) populations were found primarily in the circum-neutral sites with undetectable …

Respiration And Carbon Dioxide Accumulation In Soil Microcosms, Jasity Murphy

Pursuit - The Journal of Undergraduate Research at The University of Tennessee

The thawing of permafrost leads to liberation of soil organic matter and microbial component resulting in significant effect on the carbon cycle. Changes in permafrost soils upon the global climate warming would significantly impact microbial soil activity. Currently, not a great deal is known about what happens to the microbial community after the permafrost thaws. The activity of microbial community was determined in microcosms experiment using respirometry. To assess the CO₂ fluctuations during permafrost thawing a titration experiment was performed. Based on calculations using the respirometric equation it was found that CO₂ production increases with temperature, core depth, …

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 …

Natural And Lignocellulose-Enriched Microbial Communities In Great Boiling Spring, Nv, Jessica Cole

UNLV Theses, Dissertations, Professional Papers, and Capstones

The natural microbial communities present in Great Boiling Spring were investigated and contrasted against those present after in situ enrichment with lignocellulose. High-throughput cultivation-independent DNA sequencing of the V8 region of the small subunit (SSU) rRNA gene generated a total of 274,119 quality-filtered pyrosequencing fragments. Twelve natural spring samples were analyzed, including four high-temperature water samples and eight sediment samples ranging from 87 - 62 °C. Eight lignocellulosic enrichments incubated in the spring sediment and water at two high-temperature sites were analyzed. The natural water communities were found to be extremely uneven but relatively constant throughout time. The natural sediment …

Nitrite Oxidation In Geothermal Springs: Evidence Of An Upper Temperature Limit For Thermophilic Nitrite-Oxidizing Bacteria Of 60 - 65 °C, Tara Edwards

UNLV Theses, Dissertations, Professional Papers, and Capstones

Despite growing evidence of the importance of nitrification in terrestrial geothermal environments, little is known about nitrite oxidation in these environments. In order to further our knowledge, this study combined cultivation-dependent and -independent approaches with measurements of nitrogen speciation along the outflow channels of two Great Basin geothermal springs. Enrichment cultures were inoculated with sediment slurries from sites ranging in temperature from 42 - 87 °C at the sources and along the outflows of >15 hot springs. While attempts to enrich nitrite-oxidizing bacteria (NOB) from sites greater than or equal to 61 °C were unsuccessful, NOB were enriched from five …

The Evolution Of Host Specificity In The Vertebrate Gut Symbiont Lactobacillus Reuteri, Steven Frese

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The vertebrate gut is home to one of the densest populations of life on Earth. This microbial community has a profound effect on host health, nutrition, development, behavior, and evolution. However, very little is known about how these microbes have evolved with their vertebrate hosts, how and whether they select hosts or how they remain associated with their hosts. Recent work identified Lactobacillus reuteri as an organism that is composed of host-specific sub-populations, each population associated with a different host animal. Representatives from each host-associated population were tested for their ability to colonize gnotobiotic mice, which only rodent strains could …

Form And Function Of Clostridium Thermocellum Biofilms, Alexandru Dumitrache, Gideon Wolfaardt, Grant Allen, Steven N. Liss, Lee R. Lynd

Dartmouth Scholarship

The importance of bacterial adherence has been acknowledged in microbial lignocellulose conversion studies; however, few reports have described the function and structure of biofilms supported by cellulosic substrates. We investigated the organization, dynamic formation, and carbon flow associated with biofilms of the obligately anaerobic cellulolytic bacterium Clostridium thermocellum 27405. Using noninvasive, in situ fluorescence imaging, we showed biofilms capable of near complete substrate conversion with a characteristic monolayered cell structure without an extracellular polymeric matrix typically seen in biofilms. Cell division at the interface and terminal endospores appeared throughout all stages of biofilm growth. Using continuous-flow reactors with a rate …

Amelioration Of Root Disease Of Subterranean Clover (Trifolium Subterraneum) By Mineral Nutrients, Tim Scanlon, Tiernan A. O’Rourke, Megan H. Ryan, Martin J. Barbetti, Krishnapillai Sivasithamparam

Journal articles

Subterranean clover (Trifolium subterraneum) is a key pasture legume across southern Australia and elsewhere. Decline in subterranean clover pastures was first recognised in Australia during the 1960s and manifests as an increase in weeds and a decrease in desirable legume species. While both root disease and poor nutrition contribute to subterranean clover pasture decline, the relationships between root disease and nutrition have not been determined. The objective of this study was to define these relationships. Field experiments were undertaken to determine the nutritional and pathogen status of soils and subterranean clover from three Western Australian field sites. Subsequently, …

Ecology Of Vibrio Parahaemolyticus And Vibrio Vulnificus In The Coastal And Estuarine Waters Of Louisiana, Maryland, Mississippi, And Washington (United States), Crystal N. Johnson, John C. Bowers, Kimberly J. Griffitt, Vanessa Molina, Rachel W. Clostio, Shaofeng Pei, Edward Laws, Rohinee N. Paranjpye, Mark S. Strom, Arlene Chen, Nur A. Hasan, Anwar Huq, Nicholas F. Noriea Iii, D. Jay Grimes, Rita R. Colwell

Faculty Publications

Vibrio parahaemolyticus and Vibrio vulnificus, which are native to estuaries globally, are agents of seafood-borne or wound infections, both potentially fatal. Like all vibrios autochthonous to coastal regions, their abundance varies with changes in environmental parameters. Sea surface temperature (SST), sea surface height (SSH), and chlorophyll have been shown to be predictors of zooplankton and thus factors linked to vibrio populations. The contribution of salinity, conductivity, turbidity, and dissolved organic carbon to the incidence and distribution of Vibrio spp. has also been reported. Here, a multicoastal, 21-month study was conducted to determine relationships between environmental parameters and V. parahaemolyticus …

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 …

One Can’T Stand On Its Own: Are Non-Luminescence Traits Necessary For V. Fischeri Colonization Of E. Scolopes?, Feier Liu

Honors Theses and Capstones

Vibrio fischeri and Euprymna scolopes squid establish mutualistic symbiosis and select for each other in the natural environment. V. fischeri provides bioluminescent camouflage for E. scolopes while E. scolopes provides nutrients for V. fischeri. The most intriguing aspect of this relationship is that E. scolopes is highly selective and only allows sustained colonization by luminous, but not dark V. fischeri. Luminescence is the key symbiosis trait; however, other bacterial factors may also allow squid recognition. We hypothesized that there are luminescence linked traits that contribute to colonization. V. fischeri with luminescence variation was isolated and tested for oxidative resistance, …

Analysis Of Microbial Diversity By Amplicon Pyrosequencing, Ryan Legge

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Microorganisms numerically dominate terrestrial biodiversity, and play important biochemical and geochemical roles in the environments they inhabit. To understand structure and function of complex ecosystems, it is essential to identify primary drivers of microbial diversity and community structure. Historically, the study of microbial ecology was reductive, limited to microbes able to be cultured and enumerated. Microbes meeting this criterion were thought to comprise the dominating members of the environments they were isolated from, however, estimates suggesting up to 99% of the endogenous species are uncultivable with existing methodologies; a concept that reflects experimental failure, rather than a verifiable conclusion. Therefore …