Microbiology Commons^™

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 …

Differential Virus Host-Ranges Of The Fuselloviridae Of Hyperthermophilic Archaea: Implications For Evolution In Extreme Environments, Ruben M. Ceballos, Caleb D. Marceau, Joshua O. Marceau, Steven Morris, Adam J. Clore, Kenneth M. Stedman

Biology Faculty Publications and Presentations

An emerging model for investigating virus-host interactions in hyperthermophilic Archaea is the Fusellovirus-Sulfolobus system. The host, Sulfolobus, is a hyperthermophilic acidophile endemic to sulfuric hot springs worldwide. The Fuselloviruses, also known as Sulfolobus Spindle-shaped Viruses (SSVs), are "lemon" or "spindle"-shaped double-stranded DNA viruses, which are also found worldwide. Although a few studies have addressed the host-range for the type virus, Sulfolobus Spindle-shaped Virus 1 (SSV1), using common Sulfolobus strains, a comprehensive host-range study for SSV-Sulfolobus systems has not been performed. Herein, we examine six bona fide SSV strains (SSV1, SSV2, SSV3, SSVL1, SSVK1, SSVRH) and their respective infection characteristics on …

In Vivo Quantification Reveals Extensive Natural Variation In Mitochondrial Form And Function In Caenorhabditis Briggsae, Kiley Ann Hicks, Dana K. Howe, Aubrey Leung, Dee R. Denver, Suzanne Estes

Biology Faculty Publications and Presentations

We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5Δ) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial phenotypes including reactive oxygen species level, membrane potential, and aspects of organelle morphology, and observed significant among- isolate variation in 18 traits. Although several mitochondrial phenotypes were non-linearly associated with nad5Δ levels, most of the among-isolate phenotypic variation could be accounted for by phylogeographic clade membership. In particular, isolate-specific mitochondrial membrane potential …

A Novel Virus Genome Discovered In An Extreme Environment Suggests Recombination Between Unrelated Groups Of Rna And Dna Viruses, Geoffrey S. Diemer, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Background: Viruses are known to be the most abundant organisms on earth, yet little is known about their collective origin and evolutionary history. With exceptionally high rates of genetic mutation and mosaicism, it is not currently possible to resolve deep evolutionary histories of the known major virus groups. Metagenomics offers a potential means of establishing a more comprehensive view of viral evolution as vast amounts of new sequence data becomes available for comparative analysis.

Results: Bioinformatic analysis of viral metagenomic sequences derived from a hot, acidic lake revealed a circular, putatively single-stranded DNA virus encoding a major capsid protein similar …

Links From Mantle To Microbe At The Lau Integrated Study Site: Insights From A Back-Arc Spreading Center, Margaret K. Tivey, Erin Becker, Roxanne Beinart, Charles R. Fisher, Peter Girguis, Charles H. Langmuir, Peter J. Michael, Anna-Louise Reysenbach

Biology Faculty Publications and Presentations

The Lau Integrated Study Site (ISS) has provided unique opportunities for study of ridge processes because of its back-arc setting in the southwestern Pacific. Its location allows study of a biogeographical province distinct from those of eastern Pacific and mid-Atlantic ridges, and crustal compositions along the ridge lie outside the range of mid-ocean ridge crustal compositions. The Lau ISS is located above a subduction zone, at an oblique angle. The underlying mantle receives water and other elements derived from the downgoing lithospheric slab, with an increase in slab influence from north to south. Water lowers the mantle melting temperature and …

In Situ Enrichment Of Ocean Crust Microbes On Igneous Minerals And Glasses Using An Osmotic Flow‐Through Device, Amy Renee Smith, Martin Fisk, Radu Popa, Mark Nielsen, C. Geoffrey Wheat, Hans W. Jannasch, Andrew T. Fisher, Keir Becker, Stefan M. Sievert, Gilberto Flores

Biology Faculty Publications and Presentations

The Integrated Ocean Drilling Program (IODP) Hole 1301A on the eastern flank of Juan de Fuca Ridge was used in the first long-term deployment of microbial enrichment flow cells using osmotically driven pumps in a subseafloor borehole. Three novel osmotically driven colonization systems with unidirectional flow were deployed in the borehole and incubated for 4 years to determine the microbial colonization preferences for 12 minerals and glasses present in igneous rocks. Following recovery of the colonization systems, we measured cell density on the minerals and glasses by fluorescent staining and direct counting and found some significant differences between mineral samples. …

Growth Phase-Dependent Gene Regulation In Vivo In Sulfolobus Solfataricus, Melissa Deyoung, Michelle Thayer, John Van Der Oost, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Ribosomal genes are strongly regulated dependent on growth phase in all organisms, but this regulation is poorly understood in Archaea. Moreover, very little is known about growth phase-dependent gene regulation in Archaea. SSV1- based lacS reporter gene constructs containing the Sulfolobus 16S/23S rRNA gene core promoter, the TF55a core promoter, or the native lacS promoter were tested in Sulfolobus solfataricus cells lacking the lacS gene. The 42-bp 16S/23S rRNA gene and 39-bp TF55a core promoters are sufficient for gene expression in S. solfataricus. However, only gene expression driven by the 16S/23S rRNA gene core promoter is dependent on …

Potential Fossil Endoliths In Vesicular Pillow Basalt, Coral Patch Seamount, Eastern North Atlantic Ocean, Barbara Cavalazzi, Frances Westall, Sherry L. Cady, Roberto Barbieri, Frédéric Foucher

Geology Faculty Publications and Presentations

The chilled rinds of pillow basalt from the Ampere-Coral Patch Seamounts in the eastern North Atlantic were studied as a potential habitat of microbial life. A variety of putative biogenic structures, which include filamentous and spherical microfossil-like structures, were detected in K-phillipsite-filled amygdules within the chilled rinds. The filamentous structures (similar to 2.5 mu m in diameter) occur as K-phillipsite tubules surrounded by an Fe-oxyhydroxide (lepidocrocite) rich membranous structure, whereas the spherical structures (from 4 to 2 mu m in diameter) are associated with Ti oxide (anatase) and carbonaceous matter. Several lines of evidence indicate that the microfossil-like structures in …

Virus Silicification Under Simulated Hot Spring Conditions, James R. Laidler, Kenneth M. Stedman

Biology Faculty Publications and Presentations

Silicification of organisms in silica-depositing environments can impact both their ecology and their presence in the fossil record. Although microbes have been silicified under laboratory and environmental conditions, viruses have not. Bacteriophage T4 was successfully silicified under laboratory conditions that closely simulated those found in silica-depositing hot springs. Virus morphology was maintained, and a clear elemental signature of phosphorus was detected by energy-dispersive X-ray spectrophotometry (EDS).

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 …

Molecular Coevolution Of Pacific Northwest Hantaviruses And Their Host, The Deer Mouse, Peromyscus Maniculatus, Philip Darren Jones

Dissertations and Theses

Sin Nombre virus (SNV, family Bunyaviridae, genus Hantavirus), hosted by the deer mouse, Peromyscus maniculatus (family Cricetidae, Subfamily Neotominae), is the primary etiological agent of Hantavirus pulmonary syndrome (HPS) in the western United States. HPS, with known pathogenicity only to humans and for which there is no cure or prophylaxis, affects the epithelium of the lungs by making the capillaries leaky, thereby resulting in bilateral infiltrates, and eventually leading to respiratory failure and death by drowning in approximately 38% of hospitalized patients.

In the Americas, Peromyscus has been co-evolving with hantaviruses for approximately 12–20 million years, since the first …

Environmental Controls On The Landscape-Scale Biogeography Of Stream Bacterial Communities, Noah Fierer, Jennifer L. Morse, Sean T. Berthrong, Emily S. Bernhardt, Robert B. Jackson

Environmental Science and Management Faculty Publications and Presentations

We determined the biogeographical distributions of stream bacteria and the biogeochemical factors that best explained heterogeneity for 23 locations within the Hubbard Brook watershed, a 3000-ha forested watershed in New Hampshire, USA. Our goal was to assess the factor, or set of factors, responsible for generating the biogeographical patterns exhibited by microorganisms at the landscape scale. We used DNA fingerprinting to characterize bacteria inhabiting fine benthic organic matter (FBOM) because of their important influence on stream nutrient dynamics. Across the watershed, streams of similar pH had similar FBOM bacterial communities. Streamwater pH was the single variable most strongly correlated with …

Morphological Biosignatures And The Search For Life On Mars, Sherry L. Cady, Jack D. Farmer, John P. Grotzinger, J. William Schopf, Andrew Steele

Geology Faculty Publications and Presentations

This report provides a rationale for the advances in instrumentation and understanding needed to assess claims of ancient and extraterrestrial life made on the basis of morphological biosignatures. Morphological biosignatures consist of bona fide microbial fossils as well as microbially influenced sedimentary structures. To be recognized as evidence of life, microbial fossils must contain chemical and structural attributes uniquely indicative of microbial cells or cellular or extracellular processes. When combined with various research strategies, high-resolution instruments can reveal such attributes and elucidate how morphological fossils form and become altered, thereby improving the ability to recognize them in the geological record …

Enrichments And Isolations Of Mesophilic And Thermophilic Iron-Reducing Microbes From Deep-Sea Hydrothermal Vents And The Deep Subsurface, Melissa Mary Kendall

Dissertations and Theses

Microbes inhabiting the deep subsurface play an important role in geochemical processes and may be of practical value in bioremediation and biotechnology. Hydrothermal vents and the deep gold mines of South Africa have be likened to "windows" into the subsurface biosphere. The aim of this research was to isolate and characterize microbes involved in iron-cycling from deep-sea hydrothermal vents and from the deep gold mines of the Witwatersrand Basin. Three mesophilic bacteria, strains BB4, W3, and A6 were isolated from sulfide chimneys at 13°N and a thermophilic bacterium, strain GB21 was isolated from Guaymas Basin on the East Pacific Rise. …

Cullin-3 Targets Cyclin E For Ubiquitination And Controls S Phase In Mammalian Cells, Jeffrey D. Singer, Mark Gurian-West, Bruce Clurman, James M. Roberts

Biology Faculty Publications and Presentations

Cyclin E is an unstable protein that is degraded in a ubiquitin- and proteasome- dependent pathway. Two factors stimulate cyclin E ubiquitination in vivo: when it is free of its CDK partner, and when it is phosphorylated on threonine 380. We pursued the first of these pathways by using a two-hybrid screen to identify proteins that could bind only to free cyclin E. This resulted in the isolation of human Cul-3, a member of the cullin family of E3 ubiquitin–protein ligases. We found that Cul-3 was bound to cyclin E but not to cyclin E-Cdk2 complexes in mammalian cells, and …

Gene Expression In Two Cyanobacteria, Freshwater Synechococcus Sp. Pcc 7942 And Oceanic Synechococcus Sp. Wh 7803, In Response To Ammonium, Nitrate Or Iron, Abbas Sadeghi

Dissertations and Theses

The transcriptional response of freshwater Synechococcus sp. PCC 7942 and oceanic Synechococcus sp. WH 7803 to ammonium, nitrate or iron was studied in single or multiple factor limited cultures. Both strains showed maximum production of NiR mRNA when grown in nitrate-containing media. When grown in ammonium-containing medium, they did not show any signal for NiR mRNA synthesis. The influence on the transcription of NiR mRNA by iron as sole limiting nutrient was also evaluated. Iron increased the NiR mRNA whether or not the positive effect of nitrate was already present. The hybridization signal of mRNA for the large subunit of …

The Morphology, Physiology, And Fine Structure Of A Toluene-Oxidizing Strain Of Pseudomonas Putida, Barry Clayton Anderson

Dissertations and Theses

The role of microorganisms in the degradation of xenobiotics in the environment is well established. Bacteria from the genus Pseudomonas are particularly well adapted to the degradation of hydrocarbons, aromatics, and numerous other natural and introduced substrates. We have isolated a strain of Pseudomonas putida, designated PC2P15, that uses toluene, phenol, benzene, and a number of other substrates as its sole sources of carbon and energy.

Effects Of Conalbumin Bound Iron On The Growth Of Salmonella Paratyphi B And Salmonella Thompson, John Nicholas Mason

Dissertations and Theses

I have investigated the possibility that specific conalbumin (ovotransferrin) iron saturation levels enable less virulent strains of Salmonella to become more virulent. Iron starved cells of two pathogenic Salmonella strains, S. paratyphi B var. java and S. thompson, were cultured in iron limited media at 3 different iron conalbumin saturation levels. Results indicate that strains differ significantly at both low and high iron saturation conalbumin. These differences depict a growth advantage for S. paratyphi B which correlates with reports by the Centers for Disease Control that S. paratyphi B was 3 times more frequent in blood isolates than S. …

Restriction Mapping And Expression Of Recombinant Plasmids Containing The Arsenic Resistance Genes Of The Plasmid R45, Terry M. Coons

Dissertations and Theses

The trivalent (arsenite) and pentavalent (arsenate) forms of arsenic are introduced into the environment through the use of arsenic in herbicides, pesticides, fertilizers, and the smelting of arsenic-bearing ores. Bacteria resistant to arsenic are readily isolated from surface waters, sewage, and clinical infections. Although some bacterial resistance is provided by inducible phosphate transport systems that discriminate against arsenate, marked resistance is carried on bacterial plasmids.

A 6.9 kilobase fragment previously derived from one such plasmid, R45, and containing the genes for inducible resistance to arsenite and arsenate was ligated into the cloning vectors puce and pUC9 in opposite orientations and …

Characterization Of A New Freshwater Methanogen, Methanogenium Wolfei Sp. Nov., Theodore B. Moore

Dissertations and Theses

A recently isolated freshwater methanogenium species, Methanogenium wolfei, is characterized. Cells were irregular cocci, measuring 1.5 to 2.0 micrometers in diameter. No motility was observed, but 1 to 2 flagella per cell were observed after staining with Gray's Flagella Stain. Colonies formed by this species were small, shiny, and green-brown in color. Formate or hydrogen plus carbon dioxide served as substrates for growth. The optimal temperature for growth was found to be 45 degrees centigrade with minimal growth below 30 degrees centigrade and above 55 degrees centigrade. The optimal pH for growth was determined to be 6.8. Optimal growth was …

A Genetic And Physiological Study Of An Arsenite Resistant, Uncoupled Mutant Of Escherichia Coli, Daniel Gordon Smiley

Dissertations and Theses

Chromosomally determined arsenate resistance in Escherichia coli is well characterized. Little, however, is known about chromosomally determined arsenite resistance in E. coli. Accordingly, spontaneous arsenite resistant mutants were selected in a plasmid free strain of E. coli. One mutant strain was analyzed in detail, genetically and physiologically. The mutation confering arsenite resistance was shown to be a single gene mutation. Genetic mapping studies using conjugation and transduction showed that the mutation was closely linked to the ilv region of the E. coli map.

Physiological studies of this mutant showed that it shared characteristics common to those of mutants …

Characterization Of Gram-Positive Bacterial Isolates From Burn Victims, Trisha A. Hannan

Dissertations and Theses

Streptococcus and Staphylococcus were collected from patients hospitalized at the Oregon Burn Center, Emanuel Hospital, Portland, Oregon, between October 27, 1980 and January 1, 1981. Forty-five isolates of Staphylococcus and twenty-one isolates of Streptococcus, Lancefield Group D, were included in the investigation.

The objectives of the investigation were: (i) to identify to the species level all isolates, (ii) to determine their susceptibility to antimicrobial agents, (iii) to test the organisms. over time for increasing resistance to silver, (iv) to determine, if present, a bacterium harbored within the burn unit (nosocomial bacterium), and (v) to determine any recognizable pattern of successive …

Plasmid-Mediated Resistance To Arsenite And Arsenate In Escherichia Coli, Thomas Patrick Trezona

Dissertations and Theses

Bacterial strains resistant to arsenite, arsenate (or both) are readily isolated from nature. The resistance, in many cases, can be shown to be determined by conjugal plasmids. The mechanisms by which these plasmids confer resistance to arsenic compounds are entirely unknown. This study was undertaken to shed light on some of the physiological and genetic aspects of this resistance using plasmid-bearing strains of Escherichia coli which are highly resistant to both arsenite and arsenate. Most studies were carried out using E. coli J53 (R773) or the plasmid-free strain J53.

Culture And Growth Of Closterium Ehrenbergii (Desmidiaceae), David Bruce Renstrom

Dissertations and Theses

Methods were devised for the isolation and pure culture in defined mineral medium of Closteriurn ehrenbergii Menegh (Chlorophyceae). The effect of pH, type of nitrogen source, nitrate concentration, total hardness, and various buffers on growth were investigated. Best growth rates were obtained at pH 8 to 9, but good growth was observed even at pH 9.4. Nitrate, ammonia, or urea nitrogen could be utilized, but at concentrations greater than 10^-2M urea was toxic to growth. At higher concentrations of ammonia and nitrate longer lag phases of growth were obtained but eventual higher cell yields were obtained. Good growth …

Purification And Properties Of Lysozyme From Pseudomonas Aeruginosa Bacteriophage 7v, Lynne Vernice Mcfarland

Dissertations and Theses

A lysozyme from Bacteriophage 7v was purified 7.7 fold over the original lysates of the bacteriophage 7v and Pseudomonas aeruginosa PS-7. This purification process includes ultracentrifugation, ammonium sulfate precipitation, dialysis, and fractionation in a Sephadex G-150 column. The phage lysozyme exhibits a greater specificity when assayed with P. aeruginosa cells as a substrate, but still is capable of acting on the standard lysozyme Micrococcus lysodeikticus substrate. The pH optimum, heat inactivation range, and action on other bacteria is described. The molecular weight was found to be 14,300. The values of this 7v phage lysozyme are in close agreement with values …

The Life Cycle Of Lissorchis Heterorchis, Macy And Krygier (1969), Brendan P. H. Onyejekwe

Dissertations and Theses

Many Flumenicola virens (Lea) collected from Crystal Springs Creek and Tualatin River, Portland, Oregon, were found to shed large numbers of a species of microcercous cercariae containing refractile granules. They resembled the cercariae of Triganodistomum mutabile (=Lissorchis mutabile Cort, 1918 as described by Wallace (1939), and subsequent experiments proved that they were the larval stages of what was described by Macy and Krygier (1969), as Lissorchis heterorchis. Encystment of these cercariae was induced experimentally in uninfected adult brown planarians collected partly from Crystal Springs Creek and partly from Carolina Biological Research Station in Gladstone, Portland, Oregon. Adult flukes …

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 …

Repression Of Β-Galactosidase Synthesis In Escherichia Coli By Salicylates, Joan Carlyn Olson

Dissertations and Theses

Salicylic acid, and to a lesser extent aspirin, have been shown to repress β-galactosidase synthesis in Escherichia coli. The repression is not due to decreased inducer uptake, nor does it result from competition with inducer for repressor. Dinitrophenol does not exert similar effects on β-galactosidase synthesis. Cyclic adenosine 31, 51-monophosphate partially relieves the repression. The extent or the relief by cyclic adenosine monophosphate seems to depend on the concentration of salicylic acid. This indicates there may be direct interaction between the actions of cyclic adenosine monophosphate and salicylic acid in E. coli cells.

Effects Of Insulin, Sodium And D-Glucose On Amino Acid Absorption In The Intestine Of Rats, Andre-Gerard Craan

Dissertations and Theses

Amino acid absorption across rat intestine in vitro was inhibited or stimulated by insulin depending on the hormone serosal concentration.

The absence of sodium ions from the incubating solution resulted in a significant decrease of L-alanine absorption. However, L-alanine was enhanced in a sodium-free medium by the addition of insulin on the serosal side of the intestine.

A sizable decrease in L-alanine and L-lysine absorption was produced by introduction of D-glucose (0.2 % and 2 %) in the Krebs-Ringer's incubating buffer. Nevertheless, the presence of D-glucose did not prevent the stimulatory effect of insulin on amino acid absorption.

The Effect Of Antibiotics On Thermophilic Blue-Green Algae, Erleen Blanche Christenson

Dissertations and Theses

The nature of the action of penicillin on the cell walls of bacteria is reviewed. The composition of bacterial cell walls is compared to cell walls of blue-green algae.

The test organisms used were thermophilic: Anacystis nidulans grew optimally at 35⁰C, whereas Synechococcus lividus grew best at 45⁰ C. Growth was recorded by reading optical densities.

Cells of these two thermophilic blue-green algae were treated with varying dosages of penicillin and streptomycin. Penicillin inhibited growth of Anacystis nidulans and Synechococcus lividus in concentrations of 3.0 µg/ml and 0.03 µg/ml respectively. However, when 0.3 µg/ml of penicillin was added to Anacystis …