Environmental Microbiology and Microbial Ecology Commons^™

Escherichia Coli O157:H7 And Other E. Coli Strains Share Physiological Properties Associated With Intestinal Colonization, Lisa Jacobsen, Lisa Durso, Tyrell Conway, Kenneth W. Nickerson

Kenneth Nickerson Papers

Escherichia coli isolates (72 commensal and 10 O157:H7 isolates) were compared with regard to physiological and growth parameters related to their ability to survive and persist in the gastrointestinal tract and found to be similar. We propose that nonhuman hosts in E. coli O157:H7 strains function similarly to other E. coli strains in regard to attributes relevant to gastrointestinal colonization.

An Evaluation Of Methicillin Resistant Staphylococcus Aureus Survival On Five Environmental Surfaces Under Two Different Humidities, With And Without The Addition Of Bovine Serum Albumin, Courtney Ann Coughenour

UNLV Theses, Dissertations, Professional Papers, and Capstones

The spread of antibiotic resistant bacteria is a major public health concern, as they result in greater healthcare costs and increased morbidity and mortality rates. Methicillin resistant Staphylococcus aureus (MRSA) is one organism of particular concern, with the number of infections increasing in epidemic proportion. Bacterial surface contamination with MRSA is significant, as it may serve as a reservoir for transmission and have negative health implications. The purpose of this study was to evaluate survival of MRSA on five environmental surface materials; glass, wood, vinyl, plastic, and cloth. The effect of relative humidity (RH) and bovine serum albumin (BSA) were …

An Essay On Evolution: Evolution And The Origin Of Life Are Separate And Distinct Concepts, Kenneth Nickerson

Kenneth Nickerson Papers

Two years ago on a Saturday morning, I was asked quite pointedly by two friends how I could be both spiritual and a scientist. My questioning friends felt that these qualities were incompatible. It turned out their church taught that scientists were ‘the enemy’ because scientists believe in evolution. Since that time, Letters to the Editor regarding evolution have attracted my attention. Many of the published letters stated that the author did not believe in evolution, and argued in support of his/her position that God had created life. The authors thoroughly confuse two concepts which are separate and distinct: Evolution …

Microbiology Of Oil Fly Larvae, Kenneth Nickerson, Bradley A. Plantz

Kenneth Nickerson Papers

One animal beautifully adapted to the viscous asphalt of the La Brea tar pits is the oil fly Helaeomyia petrolei (Syn. Psilopa). As a normal part of its carnivorous existence the oil fly larval guts are filled with tar, with no adverse effects. Surface sterilized larvae 5 contained ca. 2 x 10 heterotrophic bacteria per larva. These bacteria have been identified as a mixture of enteric bacteria, most commonly Providencia rettgeri, and Acinetobacter spp. These bacteria were clearly growing because their numbers in the larval guts were 100 to 1,000 times greater than in free oil/asphalt. There is …

The Evolution Of Reduced Microbial Killing, Jan A.C. Vriezen Dr., Michael Valliere, Margaret A. Riley Dr.

Jan A.C. Vriezen Dr.

Bacteria engage in a never-ending arms race in which they compete for limited resources and niche space. The outcome of this intense interaction is the evolution of a powerful arsenal of biological weapons. Perhaps the most studied of these are colicins, plasmid-based toxins produced by and active against Escherichia coli. The present study was designed to explore the molecular responses of a colicin-producing strain during serial transfer evolution. What evolutionary changes occur when colicins are produced with no target present? Can killing ability be maintained in the absence of a target? To address these, and other, questions, colicinogenic strains and …

Letter From The Dean, Lalit Verma

Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences

No abstract provided.

Candida Albicans Tup1 Is Involved In Farnesol-Mediated Inhibition Of Filamentous-Growth Induction, Bessie W. Kebaara, Melanie L. Langford, Dhammika H. M. L. P. Navarathna, Raluca Dumitru, Kenneth W. Nickerson, Audrey L. Atkin

Kenneth Nickerson Papers

Candida albicans is a dimorphic fungus that can interconvert between yeast and filamentous forms. Its ability to regulate morphogenesis is strongly correlated with virulence. Tup1, a transcriptional repressor, and the signaling molecule farnesol are both capable of negatively regulating the yeast to filamentous conversion. Based on this overlap in function, we tested the hypothesis that the cellular response to farnesol involves, in part, the activation of Tup1. Tup1 functions with the DNA binding proteins Nrg1 and Rfg1 as a transcription regulator to repress the expression of hypha-specific genes. The tup1/tup1 and nrg1/nrg1 mutants, but not the rfg1/rfg1 mutant, failed to …

Dissecting Biological “Dark Matter” With Single-Cell Genetic Analysis Of Rare And Uncultivated Tm7 Microbes From The Human Mouth, Yann Marcy, Cleber C. Ouverney, Elisabeth M. Bik, Tina Lösekann, Natalia Ivanova, Hector Garcia Martin, Ernest Szeto, Darren Platt, Philip Hugenholtz, David A. Relman, Stephen R. Quake

Faculty Publications, Biological Sciences

We have developed a microfluidic device that allows the isolation and genome amplification of individual microbial cells, thereby enabling organism-level genomic analysis of complex microbial ecosystems without the need for culture. This device was used to perform a directed survey of the human subgingival crevice and to isolate bacteria having rod-like morphology. Several isolated microbes had a 16S rRNA sequence that placed them in candidate phylum TM7, which has no cultivated or sequenced members. Genome amplification from individual TM7 cells allowed us to sequence and assemble >1,000 genes, providing insight into the physiology of members of this phylum. This approach …

Farnesol Restores Wild-Type Colony Morphology To 96% Of Candida Albicans Colony Morphology Variants Recovered Following Treatment With Mutagens, Ellen C. Jensen, Jacob M. Hornby, Nicole E. Pagliaccetti, Chuleeon M. Wolter, Kenneth Nickerson, Audrey L. Atkin

Kenneth Nickerson Papers

Candida albicans is a diploid fungus that undergoes a morphological transition between budding yeast, hyphal, and pseudohyphal forms. The morphological transition is strongly correlated with virulence and is regulated in part by quorum sensing. Candida albicans produces and secretes farnesol that regulates the yeast to mycelia morphological transition. Mutants that fail to synthesize or respond to farnesol could be locked in the filamentous mode. To test this hypothesis, a collection of C. albicans mutants were isolated that have altered colony morphologies indicative of the presence of hyphal cells under environmental conditions where C. albicans normally grows only as yeasts. All …

Bacteriophage Migration Via Nematode Vectors: Host-Parasite-Consumer Interactions In Laboratory Microcosms, John J. Dennehy, Nicholas A. Friedenberg, Yul W. Yang, Paul E. Turner

Dartmouth Scholarship

Pathogens vectored by nematodes pose serious agricultural, economic, and health threats; however, little is known of the ecological and evolutionary aspects of pathogen transmission by nematodes. Here we describe a novel model system with two trophic levels, bacteriophages and nematodes, each of which competes for bacteria. We demonstrate for the first time that nematodes are capable of transmitting phages between spatially distinct patches of bacteria. This model system has considerable advantages, including the ease of maintenance and manipulation at the laboratory bench, the ability to observe many generations in short periods, and the capacity to freeze evolved strains for later …

Molecular Assays For Detecting Aphanomyces Invadans In Ulcerative Mycotic Fish Lesions, Mw Vandersea, Rw Litaker, B Yonnish,, Et Al, H Kator, Et Al

VIMS Articles

The pathogenic oomycete Aphanomyces invadans is the primary etiological agent in ulcerative mycosis, an ulcerative skin disease caused by a fungus-like agent of wild and cultured fish. We developed sensitive PCR and fluorescent peptide nucleic acid in situ hybridization (FISH) assays to detect A. invadans. Laboratory-challenged killifish (Fundulus heteroclitus) were first tested to optimize and validate the assays. Skin ulcers of Atlantic menhaden (Brevoortia tyrannus) from populations found in the Pamlico and Neuse River estuaries in North Carolina were then surveyed. Results from both assays indicated that all of the lesioned menhaden (n = 50) collected in September 2004 were …

Determination Of Mrna Half-Lives In Candida Albicans Using Thiolutin As A Transcription Inhibitor, Bessie W. Kebaara, Lindsey E. Nielsen, Kenneth Nickerson, Audrey L. Atkin

Kenneth Nickerson Papers

A method for determining mRNA half-lives in the polymorphic fungus Candida albicans is described. It employs growth in a defined medium, the inhibition of transcription with thiolutin (10–20 μg/mL), and quantitative Northern blotting. The method is effective for the A72, SC5314, and CAI-4 strains of C. albicans, and for mRNAs that have a wide variety of decay rates and steady-state abundances. The range of half-lives detected (from 4–168 min) shows that this method is effective for mRNAs with widely varying half-lives. The mRNA decay rates obtained are compared with those for orthologous mRNAs from Saccharomyces cerevisiae. This procedure …

Methanogenic Archaea And Human Periodontal Disease, Paul W. Lepp, Mary M. Brinig, Cleber C. Ouverney, Katherine Palm, Gary C. Armitage, David A. Relman

Faculty Publications, Biological Sciences

Archaea have been isolated from the human colon, vagina, and oral cavity, but have not been established as causes of human disease. In this study, we reveal a relationship between the severity of periodontal disease and the relative abundance of archaeal small subunit ribosomal RNA genes (SSU rDNA) in the subgingival crevice by using quantitative PCR. Furthermore, the relative abundance of archaeal small subunit rDNA decreased at treated sites in association with clinical improvement. Archaea were harbored by 36% of periodontitis patients and were restricted to subgingival sites with periodontal disease. The presence of archaeal cells at these sites was …

High Phosphate (Up To 600 Mm) Induces Pseudohyphal Development In Five Wild Type Candida Albicans, Jacob M. Hornby, Raluca Dumitru, Kenneth Nickerson

Kenneth Nickerson Papers

A method is described for the formation of nearly 100% pseudohyphae populations of wild-type Candida albicans A72. The method employs fungal growth at 37 °C (ca. 5×10⁶ cells/ml) in a glucose–proline–N-acetyl-glucosamine medium supplemented with up to 600 mM phosphate (KH₂PO₄/K₂HPO₄ 1:1) at pH 6.5. Four other strains of C. albicans (MEN, 10261, SG5314 and CAI-4) also formed pseudohyphae under these conditions, although the phosphate response profiles differed in the concentration required for each strain to form pseudohyphae.

Single-Cell Enumeration Of An Uncultivated Tm7 Subgroup In The, Cleber C. Ouverney, Gary C. Armitage, David A. Relman

Faculty Publications, Biological Sciences

Specific oligonucleotide hybridization conditions were established for single-cell enumeration of uncultivated TM7 and IO25 bacteria by using clones expressing heterologous 16S rRNA. In situ analysis of human subgingival crevice specimens revealed that a greater proportion of samples from sites of chronic periodontitis than from healthy sites contained TM7 subgroup IO25. In addition, IO25 bacterial cells from periodontitis site samples were more abundant and fourfold longer than IO25 cells from healthy site samples.

Cultivation Of Tropheryma Whipplei From Cerebrospinal Fluid, Matthias Maiwald, Axel Von Herbay, David N. Fredricks, Cleber C. Ouverney, Jon C. Kosek, David A. Relman

Faculty Publications, Biological Sciences

Whipple disease (WD) is a systemic disorder caused by the bacterium Tropheryma whipplei. Since the recognition of a bacterial etiology in 1961, many attempts have been made to cultivate this bacterium in vitro. It was eventually isolated, in 2000, from an infected heart valve, in coculture with human fibroblasts. Here we report the isolation of 2 new strains of T. whipplei from cerebrospinal fluid (CSF) of 2 patients with intestinal WD but no neurological signs or symptoms. One culture-positive specimen was obtained before treatment; the other was obtained 12 months after discontinuation of therapy, at a time of intestinal remission. …

Quorum Sensing In Candida Albicans: Probing Farnesol’S Mode Of Action With 40 Natural And Synthetic Farnesol Analogs, Roman Shchepin, Jacob M. Hornby, Erin Burger, Timothy Niessen, Patrick H. Dussault, Kenneth Nickerson

Kenneth Nickerson Papers

The dimorphic fungus Candida albicans produces extracellular farnesol (3,7, 11-trimethyl-2,6,10-dodecatriene- 1-ol) which acts as a quorum-sensing molecule (QSM) to suppress filamentation. Of four possible geometric isomers of farnesol, only the E,E isomer possesses QSM activity. We tested 40 natural and synthetic analogs of farnesol for their activity in an N-acetylglucosamine-induced differentiation assay for germ tube formation (GTF). Modified structural features include the head group, chain length, presence or absence of the three double bonds, substitution of a backbone carbon by S, O, N, and Se heteroatoms, presence or absence of a 3-methyl branch, and the bulkiness of the hydrophobic …

Prevalence Of Bacteria Of Division Tm7 In Human Subgingival Plaque And Their Association With Disease, Mary M. Brinig, Paul W. Lepp, Cleber C. Ouverney, Gary C. Armitage, David A. Relman

Faculty Publications, Biological Sciences

Members of the uncultivated bacterial division TM7 have been detected in the human mouth, but little information is available regarding their prevalence and diversity at this site. Human subgingival plaque samples from healthy sites and sites exhibiting various stages of periodontal disease were analyzed for the presence of TM7 bacteria. TM7 ribosomal DNA (rDNA) was found in 96% of the samples, and it accounted for approximately 0.3%, on average, of all bacterial rDNA in the samples as determined by real-time quantitative PCR. Two new phylotypes of this division were identified, and members of the division were found to exhibit filamentous …

Eight Gram-Negative Bacteria Are 10,000 Times More Sensitive To Cationic Detergents Than To Anionic Detergents, Soumitra Rajagopal, Nicole Eis, Kenneth Nickerson

Kenneth Nickerson Papers

In liquid culture, eight typical Gram-negative bacteria were ca. 10,000-fold more sensitive to cationic detergents than to the anionic detergent sodium dodecyl sulfate. Cetyltrimethylammonium bromide (CTAB) was inhibitory at concentrations ranging from 0.0006% to 0.01%. Four pseudomonads able to form biofilms were ca. 1000-fold more resistant to CTAB on Luria–Bertani agar plates than they were in liquid culture. A lasI mutant of Pseudomonas aeruginosa was only able to tolerate 0.1% CTAB on Luria–Bertani agar plates but could tolerate 5% CTAB when supplemented with homoserine lactone containing culture supernatants.

En culture liquide, huit bactéries Gram négatif typiques étaient ca. 10,000 fois …

Escherichia Coli O157:H7 In Free-Ranging Deer In Nebraska, David G. Renter, Jan M. Sargeant, Scott E. Hygnstrom, Jeff D. Hoffmann, Jerry R. Gillespie

School of Natural Resources: Faculty Publications

In order to determine the prevalence and distribution of the human pathogen, Escherichia coli O157:H7, in free-ranging deer, hunters were asked to collect and submit fecal samples from deer harvested during a regular firearm season (14–22 November 1998). Prior to the season, 47% of the hunters with permits in the southeastern Nebraska (USA) study area indicated a willingness to participate in the study. Approximately 25% of successful hunters in the area submitted deer fecal samples. Escherichia coli O157:H7 was cultured from four (0.25%) of 1,608 total samples submitted. All of the fecal samples that were properly identified (1,426) and all …

Marine Planktonic Archaea Take Up Amino Acids, Cleber C. Ouverney, Jed A. Fuhrman

Faculty Publications, Biological Sciences

Archaea are traditionally thought of as “extremophiles,” but recent studies have shown that marine planktonic Archaea make up a surprisingly large percentage of ocean midwater microbial communities, up to 60% of the total prokaryotes. However, the basic physiology and contribution of Archaea to community microbial activity remain unknown. We have studied Archaea from 200-m depths of the northwest Mediterranean Sea and the Pacific Ocean near California, measuring the archaeal activity under simulated natural conditions (8 to 17°C, dark and anaerobic) by means of a method called substrate tracking autoradiography fluorescence in situ hybridization (STARFISH) that simultaneously detects specific cell types …

Integronlike Structures In Campylobacter Spp. Of Human And Animal Origin, Brigid Lucey, D. Crowley, P. Moloney, B. Cryan, M. Daly, F. O'Halloran, E. J. Threlfall, S. Fanning

Department of Biological Sciences Publications

Resistance to antimicrobial agents used to treat severe Campylobacter spp. gastroenteritis is increasing worldwide. We assessed the antimicrobial resistance patterns of Campylobacter spp. isolates of human and animal origin. More than half (n = 32) were resistant to sulphonamide, a feature known to be associated with the presence of integrons. Analysis of these integrons will further our understanding of Campylobacter spp. epidemiology.

Chlorella Virus Pbcv-1 Encodes A Functional Homospermidine Synthase, Annette Kaiser, Michael Vollmert, Dorothea Tholl, Michael V. Graves, James Gurnon, Weimei Xing, Amber D. Lisec, Kenneth Nickerson, James L. Van Etten

Kenneth Nickerson Papers

Sequence analysis of the 330-kb genome of chlorella virus Paramecium bursaria chlorella virus 1 (PBCV-1) revealed an open reading frame, A237R, that encodes a protein with 34% amino acid identity to homospermidine synthase from Rhodopseudomonas viridis. Expression of the a237r gene product in Escherichia coli established that the recombinant enzyme catalyzes the NAD⁺-dependent formation of homospermidine from two molecules of putrescine. The a237r gene is expressed late in PBCV-1 infection. Both uninfected and PBCV-1-infected chlorella, as well as PBCV-1 virions, contain homospermidine, along with the more common polyamines putrescine, spermidine, and cadaverine. The total number of polyamine …

Increase In Fluorescence Intensity Of 16s Rrna In Situ Hybridization In Natural Samples Treated With Chloramphenicol, Cleber C. Ouverney, Jed A. Fuhrman

Faculty Publications, Biological Sciences

Despite the numerous advantages of fluorescent in situ hybridization for the identification of single prokaryotic cells with 16S rRNA probes, use of the technique with natural samples, especially those from the marine environment, is still problematic. The low percentage of fluorescently labeled cells constitutes the primary problem for in situ hybridization of natural samples, probably due to low cellular rRNA content. This study represents an attempt to improve detection of marine prokaryotes by increasing cellular rRNA content without changing the species composition. Cells from three California coastal sites were treated with chloramphenicol, an inhibitor of protein synthesis and rRNA degradation, …

Prevalence Of Extreme Detergent Resistance Among The Enterobacteriaceae, Vance Kramer, Kenneth Nickerson, Nancy V. Hamlett, Caroline O'Hara

Kenneth Nickerson Papers

The detergent-resistance properties of 208 independent isolates of the Enterobacteriaceae have been examined. Of these bacterial strains, 200 were able to grow in the presence of ≥5% sodium dodecyl sulfate, including all members of the Klebsielleae tribe. This resistance does not appear to be plasmid encoded. It is proposed that detergent-resistant organisms he termed saponotolerant or saponophilic, by analogy with other microorganisms occupying harsh ecological niches. In contrast to their prevalent resistance to anionic detergents, not one of the 208 strains tested was found to grow in the presence of three different cationic detergents. This sensitivity to cationic detergents may …

Phomopsis : The Causal Fungus Of Lupinosis, P Mcr Wood, A. G. P. Brown

Journal of the Department of Agriculture, Western Australia, Series 4

It is now well known that lupinosis of sheep and cattle follows ingestion of lupin stubble colonised by the fungus Phomopsis rossiana. The fungus infects green lupins but persists on the stubble and under certain conditions apparently produces a toxin which causes the disease.

As Phomopsis is now widespread on lupins in Western Australia its ecology has been studied in detail as a basis for possible control measures.

This article outlines what is known so far of the disease and its control.

Euryhelmis Cotti N. Sp. (Trematoda: Heterophyidae) With Observations On Its Life Cycle, Michael Joseph Simon

Dissertations and Theses

Fish of the genus Cottus were found infected with heterophyid metacercariae. Laboratory animals were infected with the metacercariae, and adult heterophid trematodes were recovered. These flukes were found to represent an undescribed species of the genus Euryhelmis. Various streams in the Willamette Valley and coastal areas were sampled for infected Cottus sp. Snails of the genera Oxytrema and Fluminicola were collected. Several possible definitive hosts were examined. A partial review of the subfamily Apophallinae and a complete review of the genus Euryhelmis are presented. Euryhelmis cotti n. sp. is placed in the subfamily Apophallinae, and its life cycle …

Life History Of Philophthalmus Megalurus (Cort, 1914) In Western Oregon, Toni Anne Mcmillan

Dissertations and Theses

The specific identification of a megalurous cercaria found in the snail Oxytrema plicifera was accomplished by completing the life cycle in the laboratory. This species is compared with the eastern Philophthalmus megalurus and P. gralli with which it was once confused. The eggs, miracidia, and rediae of the Oregon species were found to be similar to those of the above species. The body and organ sizes and sucker ratios for the cercariae and adult stages obviously indicate that the Oregon species is Philophthalmus megalurus.