Environmental Microbiology and Microbial Ecology Commons^™

Phylometrics: A Pipeline For Inferring Phylogenetic Trees From A Sequence Relationship Network Perspective, Samuel A. Smits, Cleber C. Ouverney

Faculty Publications, Biological Sciences

Background
Comparative sequence analysis of the 16S rRNA gene is frequently used to characterize the microbial diversity of environmental samples. However, sequence similarities do not always imply functional or evolutionary relatedness due to many factors, including unequal rates of change and convergence. Thus, relying on top BLASTN hits for phylogenetic studies may misrepresent the diversity of these constituents. Furthermore, attempts to circumvent this issue by including a large number of BLASTN hits per sequence in one tree to explore their relatedness presents other problems. For instance, the multiple sequence alignment will be poor and computationally costly if not relying on …

The Human Oral Microbiome, Floyd E. Dewhirst, Tuste Chen, Jacques Izard, Bruce J. Paster, Anne C. R. Tanner, Wen-Han Yu, Abirami Lakshmanan, William G. Wade

Department of Food Science and Technology: Faculty Publications

The human oral cavity contains a number of different habitats, including the teeth, gingival sulcus, tongue, cheeks, hard and soft palates, and tonsils, which are colonized by bacteria. The oral microbiome comprises over 600 prevalent taxa at the species level, with distinct subsets predominating at different habitats. The oral microbiome has been extensively characterized by cultivation and culture-independent molecular methods such as 16S rRNA cloning. Unfortunately, the vast majority of unnamed oral taxa are referenced by clone numbers or 16S rRNA GenBank accession numbers, often without taxonomic anchors. The first aim of this research was to collect 16S rRNA gene …

Growth Of Lactic Acid Bacteria: Influence Of Protocooperation, Bacteriophage Infection, And Prebiotic Carbohydrates, Caitlin D. Goin

School of Biological Sciences: Dissertations, Theses, and Student Research

Lactic acid bacteria are a vital part of the fermented food industry and are the subject of much interest and research. Industry is especially interested in using modern molecular approaches to maintain and improve selected strains; several industrial uses could be improved by closer investigation, namely the protocooperation of S. thermophilus and L. bulgaricus, the role of CRISPRs in phage resistance, and the utilization of prebiotic carbohydrates. Questions such as what genes and pathways are shared during milk fermentation between S. thermophilus and L. bulgaricus, when and what genes are active during bacteriophage infection, and how and where …

Genome Sequence Of The Model Mushroom Schizophyllum Commune, Robin A. Ohm, Jan F. De Jong, Luis G. Lugones, Andrea Aerts, Erika Kothe, Jason E. Stajich, Ronald P. De Vries, Eric Record, Anthony Levasseur, Scott E. Baker, Kirk A. Bartholomew, Pedro M. Coutinho, Susann Erdmann, Thomas J. Fowler, Allen C. Gathmen, Vincent Lombard, Bernard Henrissat, Nicole Knabe, Ursula Kues, Walt W. Lily

Biology Faculty Publications

Much remains to be learned about the biology of mushroom-forming fungi, which are an important source of food, secondary metabolites and industrial enzymes. The wood-degrading fungus Schizophyllum commune is both a genetically tractable model for studying mushroom development and a likely source of enzymes capable of efficient degradation of lignocellulosic biomass. Comparative analyses of its 38.5-megabase genome, which encodes 13,210 predicted genes, reveal the species's unique wood-degrading machinery. One-third of the 471 genes predicted to encode transcription factors are differentially expressed during sexual development of S. commune. Whereas inactivation of one of these, fst4, prevented mushroom formation, inactivation of another, …

Jsphylosvg: A Javascript Library For Visualizing Interactive And Vector-Based Phylogenetic Trees On The Web, Samuel A. Smits, Cleber C. Ouverney

Faculty Publications, Biological Sciences

Background
Many software packages have been developed to address the need for generating phylogenetic trees intended for print. With an increased use of the web to disseminate scientific literature, there is a need for phylogenetic trees to be viewable across many types of devices and feature some of the interactive elements that are integral to the browsing experience. We propose a novel approach for publishing interactive phylogenetic trees.

Methods/Principal Findings
We present a javascript library, jsPhyloSVG, which facilitates constructing interactive phylogenetic trees from raw Newick or phyloXML formats directly within the browser in Scalable Vector Graphics (SVG) format. It is …

Development Of Pyrf-Based Genetic System For Targeted Gene Deletion In Clostridium Thermocellum And Creation Of A Pta Mutant, Shital A. Tripathi, Daniel G. Olson, D. Aaron Argyros, Bethany B. Miller, Trisha F. Barrett, Daniel M. Murphy, Jesse D. Mccool, Anne K. Warner, Vineet B. Rajgarhia, Lee R. Lynd, David A. Hogsett, Nicky C. Caiazza

Dartmouth Scholarship

We report development of a genetic system for making targeted gene knockouts in Clostridium thermocellum, a thermophilic anaerobic bacterium that rapidly solubilizes cellulose. A toxic uracil analog, 5-fluoroorotic acid (5-FOA), was used to select for deletion of the pyrF gene. The ΔpyrF strain is a uracil auxotroph that could be restored to a prototroph via ectopic expression of pyrF from a plasmid, providing a positive genetic selection. Furthermore, 5-FOA was used to select against plasmid-expressed pyrF, creating a negative selection for plasmid loss. This technology was used to delete a gene involved in organic acid production, namely pta, which encodes …

Alteration Of Microbial Communities Colonizing Leaf Litter In A Temperate Woodland Stream By Growth Of Trees Under Conditions Of Elevated Atmospheric Co2, John J. Kelly, Amit Bansal, Jonathan Winkelman, Lori R. Janus, Shannon Hell, Marie Wencel, Patricia Belt, Kevin A. Kuehn, Steven T. Rier, Nancy C. Tuchman

Faculty Publications

Elevated atmospheric CO₂ can cause increased carbon fixation and altered foliar chemical composition in a variety of plants, which has the potential to impact forested headwater streams because they are detritus-based ecosystems that rely on leaf litter as their primary source of organic carbon. Fungi and bacteria play key roles in the entry of terrestrial carbon into aquatic food webs, as they decompose leaf litter and serve as a source of nutrition for invertebrate consumers. This study tested the hypothesis that changes in leaf chemistry caused by elevated atmospheric CO₂ would result in changes in the size and …

Antimicrobial Activity Of Selected Fungi Isolated From Dee And Barrientos Islands, Antarctica., Shamia Mohamedain Abd Elgadir Younis

Student Works (2010-2019)

This study reports the screening of selected fungi isolated from Dee and Barrientos Islands, Antarctica, for their antimicrobial activities using two methods: a) plug assay method and b) disk diffusion method. The plug assay was carried out as preliminary screening forbiological activity against bacteria: Bacillus subtilis, Staphylococcus aureus,Escherichia coli, pseudomonas aeruginosa, and yeast: Candida albicans. The results showed that 35% from species possessed antibacterial activity; and these included: Geomyces sp.50-1/S7, Unidentified 75-1/S1, Geomyces sp.12-1/S21, Penecillium sp.75-1/S10, Geomyces sp.3-1/S5, Geomyces sp.3-4/S5 and Geomyces sp.146/S5. Most of the strains exhibited antibacterial activity against Gram-positive bacteria S. aureus and B. subtilis …

Analysis Of Bacterial Diversity In Arctic Soil And Sediment Samples From Ny-Alesund, Norway Using Denaturing Gradient Gel Electrophoresis., Yew Wen Chyin

Student Works (2010-2019)

Bacterial diversity in soil and sediment samples from eighteen sites in and around Dasan Station, Ny-Ålesund, Norway was analyzed using Denaturing Gradient Gel Electrophoresis (DGGE), and was correlated with the environmental variables. Samples analysed included terrestrial soils, beach soil, periglacier soils, inland lake bank sediments, melt lake sediments, and marine sediments. Spearman rank order correlation showed significant correlations (P = 0.001) between conductivity (r = 0.470) and pH (r = 0.294) with the bacterial diversity. Soil from the tundra site (sample 17) appeared to have the most diverse bacterial community while inland lake bank sediment from the …

Isolation And Characterization Of Bacteria From Extended Aeration Wastewater Treatment Plants., Randy Chin Kok Fei

Student Works (2010-2019)

In this study, three different wastewater treatment plants (STP1, STP2 and STP3) were sampled in Klang Valley. STP1 exhibited the best activated sludge health with healthy Sludge Volume (SV), Mixed Liquor Suspended Solids (MLSS) and Mixed Liquor Volatile Suspended Solids (MLVSS). STP2 were constantly disrupted by the mechanical failures which caused its dissolved oxygen (DO) to decrease whereas STP3 was troubled by the inadequate alkalinity in its mixed liquor causing acidic condition in aeration tank. The acidic condition resulted in pin-floc problem and contributed to high Total Suspended Solids (TSS) and low SV. Influent at STP3 was also found to …

Visible And Hyperspectral Imaging Systems For The Detection And Discrimination Of Mechanical And Microbiological Damage Of Mushrooms, Edurne Gaston

Doctoral

Horticultural products such as mushrooms are exposed to environmental conditions during their postharvest life, which may affect product quality. Loss of whiteness during storage is particularly important in the mushroom industry. Rough handling and distribution, fruiting body senescence and bacterial infections are among the main causes of mushroom discolouration. The aim of this work was to study the use of visible and hyperspectral imaging (HSI) systems for the detection and discrimination of mechanical and microbiological damage of mushrooms. This piece of research involved a) monitoring the browning of mushroom with visible computer imaging systems, b) investigating the effect of mechanical …

Response Surface Optimization Of Crystal Violet Decolorization By Pellets Of Pyncnoporus Sanguineus., Siti Suhana Sulaiman

Student Works (2010-2019)

Ligninolytic enzymes of white-rot fungi have broad specificities and have been implicated in transformation and mineralization of organo-pollutant with chemical structure similar to lignin e.g. synthetic dyes. This study was carried out to optimize selected parameters for decolorization of Crystal violet by Pycnoporus sanguineus in shake flasks. The parameters studied were initial dye concentration (ppm), agitation speed (rpm) and process time. They were optimized using response surface methodology (RSM). Subsequent to the optimization, the decolorization process was scaled up in stirred tank reactor (STR). Effect of different geometry of impellers on the decolorization process was studied. Curved blade and angled …

Isolation And Characterization Of Actinobacteria From Soil Samples Of Signy Island, Antarctica., Pan Shing Yi

Student Works (2010-2019)

In this study, ninety five actinobacterial isolates were cultured from seven soils samples collected on Signy Island, maritime Antarctica. Nine different isolation media were used and the isolates plates were incubated at 15ºC for up to four months. SCN agar serves as the better media for the isolation of actinobacteria. Presence of actinobacteria in the soil samples was also detected using PCR with actinobacteria specific primers. The actinobacterial isolates were characterized based on morphology (Gram-stain, coverslip examination, colour grouping), analysis of DAP isomers, antibacterial activities and by molecular methods (ARDRA, analysis of 16S rRNA sequence and detection of NRPS gene). …

Antimicrobial Potential Of Selected Actinomycetes Isolated From The Marine Ecosystem., Nur Rahimatul Hayati Abdul Rahman

Student Works (2010-2019)

Actinomycetes are widespread in marine ecosystem. They are of interest in research field as they are capable to produce bioactive secondary metabolites which can be developed into useful pharmaceutical products. An example of the product is antibiotics which can be used to treat infectious diseases. The potential of antibacterial and antifungal activity of eleven marine derived actinomycetes from the genus Streptomyces were studied. They were tested against bacteria Enterobacter faecalis, Staphylococcus aureus, Bacillus subtilis, Pleisiomonas shigelloides and Pseudomonas aeruginosa and fungi Candida parapsilosis and Candida albicans. Primary screening by the cross streak method and secondary screening by diffusion using paper …

Thermocrinis Minervae Sp. Nov., A Hydrogen And Sulfur-Oxidizing, Thermophilic Member Of The Aquificales From A Costa Rican Terrestrial Hot Spring, Sara L. Caldwell, Yitai Liu, Isabel Ferrera, Terry Beveridge, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

A thermophilic bacterium, designated strain CR11T , was isolated from a filamentous sample collected from a terrestrial hot spring on the south-western foothills of the Rincón volcano in Costa Rica. The Gram-negative cells are approximately 2.4–3.9 mm long and 0.5–0.6 mm wide and are motile rods with polar flagella. Strain CR11T grows between 65 and 85 6C (optimum 75 6C, doubling time 4.5 h) and between pH 4.8 and 7.8 (optimum pH 5.9–6.5). The isolate grows chemolithotrophically with S0 , S2O2{ 3 or H2 as the electron donor and with O2 (up to 16 %, v/v) as the sole electron …

Soil Organic Matter Fractions And Aggregate Distribution In Response To Tall Fescue Stands, I. P. Handayani, Mark S. Coyne, R. S. Tokosh

Plant and Soil Sciences Faculty Publications

The study was conducted to evaluate the influences of tall fescue management on soil organic matter fractions and macro- and microaggregate distribution. Soil samples were collected from four paired adjacent fields consisting of five years of tall fescue mono and poly stands in Western Kentucky. Soil samples from 0 to 15 cm and 15 to 30 cm soil depths were analyzed for soil organic C and N, particulate organic matter C (POM-C) and N (POM-N), macro- and micro aggregate distribution and C-associated with macro- and micro- aggregates. Significant effects were observed between stands for all the properties, except total C, …

Evolutionary Aspects Of Urea Utilization By Fungi, Dhammika H. M. L. P Navarathna, Steven D. Harris, David D. Roberts, Kenneth W. Nickerson

Kenneth Nickerson Papers

The higher fungi exhibit a dichotomy with regard to urea utilization. The hemiascomycetes use urea amidolyase (DUR1,2), whereas all other higher fungi use the nickel-containing urease. Urea amidolyase is an energy-dependent biotincontaining enzyme. It likely arose before the Euascomycete/Hemiascomycete divergence c. 350 million years ago by insertion of an unknown gene into one copy of a duplicated methylcrotonyl CoA carboxylase (MccA). The dichotomy between urease and urea amidolyase coincides precisely with that for the Ni/Co transporter (Nic1p), which is present in the higher fungi that use urease and is absent in those that do not. We suggest that …

Candida Albicans Cellwall Components And Farnesol Stimulate The Expression Of Both Inflammatory And Regulatory Cytokines In The Murine Raw264.7 Macrophage Cell Line, Suman Ghosh, Nina Howe, Katie Volk, Swetha Tati, Kenneth W. Nickerson, Thomas M. Petro

Kenneth Nickerson Papers

Candida albicans causes candidiasis, secretes farnesol, and switches from yeast to hyphae to escape from macrophages after phagocytosis. However, before escape, macrophages may respond to C. albicans’ pathogen-associated molecular patterns (PAMPs) through toll-like receptor 2 (TLR2) and dectin-1 receptors by expressing cytokines involved in adaptive immunity, inflammation, and immune regulation. Therefore, macrophages and the RAW264.7 macrophage line were challenged with C. albicans preparations of live wild-type cells, heat-killed cells, a live mutant defective in hyphae formation, a live mutant producing less farnesol, or an isolate producing farnesoic acid instead of farnesol. Interleukin-6 (IL-6), and IL-1b, IL- 10, and tumor …