OU - Dissertations

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Open Access
A systematic study of genus
(2008) Chung, Kyong-Sook; Elisens, Wayne J
First, pollen grains of tribe Sanguisorbeae (Rosaceae, Rosoideae) were examined using scanning electron microscopy in order to identify useful characters in the tribe, test taxonomic and phylogenetic hypotheses among genera, and elucidate pollen character evolution. Aperture number, aperture structure, equatorial shape, and exine sculpturing characters grouped the pollen grains into six types. Microverrucate and striate exine sculpturing patterns support a monophyly of Sanguisorbinae and Agrimoniinae respectively. In Agrimoniinae, evolutionary directions of elliptic to circular equatorial shapes and striate to microverrucate sculpturing are apparent and distinguish Hageniafrom the other genera. Pontoperculate apertures are found only in Sanguisorbinae and support close relationships of Acaena, Cliffortia, Margyricarpus, and Polylepis. In chapter 2, phylogeny and biogeography of Agrimoniinae composed of four monotypic endemics (Aremonia, Hagenia, Leucosidea, and Spenceria) and a worldwide genus (Agrimonia) are constructed from nuclear and plastid sequences (GBSSI-1, trnL-trnF, trnS-trnG-trnG). All nucleotide data support the monophyly of Agrimoniinae with a basal group of the Asian monotypic Spenceria (2n=2x=14), the sister relationship of the African genera Hagenia and Leucosidea, and the monophyly of Agrimonia (2n=4x, 6x, and 8x) + Aremonia (2n=6x). In Agrimonia, nuclear data define a lineage of Asian and American tetraploids (Agrimonia coreana, A. microcarpa, A. parviflora, and A. rostellata). These results suggest that the most recent ancestor of the subtribe distributed in Asia (tethyan) and paleo-migration might have occurred between the Northern and Southern Hemispheres and that polyploidy is a major evolutionary process in Agrimoniinae and Agrimonia. Lastly, the genus Agrimonia is characterized as a monophyletic group of 19 species defined by two unique characters, interrupted pinnately compound leaves and bristly epicalyx segments. Species occur primarily in temperate regions throughout North America, Central America, the West Indies, southern South America, Europe, Asia, and southern Africa. Descriptions, nomenclatural histories, distribution maps, and keys are presented to 19 species and three varieties of A. pilosa. Neotypes of A. hirsuta and A. nipponica, an isolectotype of A. pilosa, and a lectotype of A. villosa are designated. The evolution of polyploidy and 12 morphological characters is evaluated within a phylogenetic framework.
Open Access
A systematic study of genus
(2008) Chung, Kyong-Sook; Elisens, Wayne J
First, pollen grains of tribe Sanguisorbeae (Rosaceae, Rosoideae) were examined using scanning electron microscopy in order to identify useful characters in the tribe, test taxonomic and phylogenetic hypotheses among genera, and elucidate pollen character evolution. Aperture number, aperture structure, equatorial shape, and exine sculpturing characters grouped the pollen grains into six types. Microverrucate and striate exine sculpturing patterns support a monophyly of Sanguisorbinae and Agrimoniinae respectively. In Agrimoniinae, evolutionary directions of elliptic to circular equatorial shapes and striate to microverrucate sculpturing are apparent and distinguish Hageniafrom the other genera. Pontoperculate apertures are found only in Sanguisorbinae and support close relationships of Acaena, Cliffortia, Margyricarpus, and Polylepis. In chapter 2, phylogeny and biogeography of Agrimoniinae composed of four monotypic endemics (Aremonia, Hagenia, Leucosidea, and Spenceria) and a worldwide genus (Agrimonia) are constructed from nuclear and plastid sequences (GBSSI-1, trnL-trnF, trnS-trnG-trnG). All nucleotide data support the monophyly of Agrimoniinae with a basal group of the Asian monotypic Spenceria (2n=2x=14), the sister relationship of the African genera Hagenia and Leucosidea, and the monophyly of Agrimonia (2n=4x, 6x, and 8x) + Aremonia (2n=6x). In Agrimonia, nuclear data define a lineage of Asian and American tetraploids (Agrimonia coreana, A. microcarpa, A. parviflora, and A. rostellata). These results suggest that the most recent ancestor of the subtribe distributed in Asia (tethyan) and paleo-migration might have occurred between the Northern and Southern Hemispheres and that polyploidy is a major evolutionary process in Agrimoniinae and Agrimonia. Lastly, the genus Agrimonia is characterized as a monophyletic group of 19 species defined by two unique characters, interrupted pinnately compound leaves and bristly epicalyx segments. Species occur primarily in temperate regions throughout North America, Central America, the West Indies, southern South America, Europe, Asia, and southern Africa. Descriptions, nomenclatural histories, distribution maps, and keys are presented to 19 species and three varieties of A. pilosa. Neotypes of A. hirsuta and A. nipponica, an isolectotype of A. pilosa, and a lectotype of A. villosa are designated. The evolution of polyploidy and 12 morphological characters is evaluated within a phylogenetic framework.
Open Access
Abiotic and biotic drivers of grassland structure: from individual to community responses
(2021-11-02) Castillioni, Karen; Souza, Lara; Martin, Elinor; Patten, Michael; McCarthy, Heather; Kaspari, Michael
Climate has long been recognized as an important factor in determining the spatial-temporal distribution and abundance of species, consequently influencing global biological diversity. Model projections point to changes in precipitation regimes, with some geographic regions experiencing increases and others decline in rainfall; but it is also predicted increase in rainfall variability with lower frequency but higher intensity of precipitation events. Such changes in precipitation regimes will likely have large effects on plant responses. In addition to climate, disturbances can alter the structure and functioning of local systems through disruption in biota, consequently altering resources and conditions. In turn, local biota and their associated species interactions play an important role influencing the response of ecosystems to changes in precipitation and disturbance. Grasslands represent a large proportion of the terrestrial land surface, and provide valuable ecosystem services (e.g., forage production, soil C storage). Thus, it is especially important to understand the magnitude and direction of ecological responses since grasslands are strongly water-limited and experience disturbance by human management. In my dissertation I explore the effects of changing environments on plant communities and how these factors shape plant individual to community responses. In chapter one, 1 explore how organization levels (species-level, functional group level and community level) of the temperate tallgrass prairie are influenced by changes in precipitation and hay harvest (a proxy for human management). I do so by addressing how seven precipitation levels, along with clipping, affect an existing mixed-grass prairie ecosystem. I demonstrated that initial shifts in abundance were detected by examining species- to community-level changes over time. Across years, in dry conditions there was an increase in evenness that was related to the decline of the dominant species and increase in subdominants; whereas mesic conditions mildly promoted plant richness. Hay harvest enhanced plant richness not only over time through species gains, but also in each year. When combining altered precipitation with hay harvest, specifically under mild drought, I observed a decline in evenness that was related to the reduced abundance of C3 species and increase in C4 species. However, in extreme dry levels, clipping muted the effects of precipitation on the dominant plant species, plant evenness, functional groups (C3 and C4 species) and subdominants. These findings could potentially indicate species reordering in abundance of species within a community with experimental climate change and human management. In chapter two, I investigate precipitation and hay harvest effects by incorporating the relative contribution of biotic vs. abiotic factors and the role of species identity in influencing plant performance (measured by cover and height). I was able to provide new insights that acute hay harvest reduces the strength of the precipitation gradient on plant performance. I found that plant performance responds directly to abiotic change with hay harvest, but indirectly without hay harvest through increased precipitation. Hay harvest reduced the strength of precipitation effects on plant performance through changes in bare-ground cover. Conversely, altered precipitation without hay harvest promoted plant species performance through abiotic factors change first, followed by biotic. Most grassland species, including the dominant grass Schizachyrium scoparium, increased their performance with greater canopy structure. These findings provide evidence for hindering positive effects of biotic factors when hay harvest co-occurs with increasing precipitation. In chapter three, I focus on the effects chronic altered precipitation levels to understand the impact of changes in precipitation on plant phenology and reproductive success. Most studies examining the effects of climate change on plant phenology have focused on climate warming, but in grasslands, precipitation is a dominant factor given their water-limited nature. Furthermore, species with different seasonality (especially late-season species) across species of varying origin, growth form, and life cycle have been underrepresented in phenological studies. I, therefore, report the results of precipitation gradient manipulation on plant phenology (flowering/fruiting dates, duration and flower/fruit count) and reproductive success (seed viability) by dividing responses into community-level and its trait factors (bloom time, functional group and life span), and species responses. I found that traits factors are critical for driving different responses of early and late-flowering species, C3 and C4 species, annuals and perennials to drought. Early-blooming plants minimally advanced their flowering date and produced a lower proportion of viable seeds, whereas late-blooming plants responded in the opposite direction by delaying flowering date at a larger magnitude and producing a higher proportion of viable seeds than annuals. Differential drought tolerance also seemed to play a role in the way plant phenology responded to decreasing precipitation, as indicated by functional group (C3 vs. C4 plants), suggesting that water-use strategies may be related to phenological variation among plants growing in grasslands. When grouping species by life span (annual vs. perennial), C3 perennial plants exhibited stronger advances in flowering and fruiting dates than annuals in response to decreasing precipitation. Community-level analysis showed no response to the precipitation gradient, whereas species not only responded in different magnitudes, but also in different directions within the same community. Hence effects of precipitation on plant phenology might be overlooked if trait factors are not considered. This study adds to a growing body of literature showing that precipitation affects phenology, but the mechanism by which precipitation affects phenology is not understood.
Open Access
AEROBIC RESPIRATION AND ECOLOGY OF Escherichia coli IN THE MOUSE CECUM
(2011) Caughron, Joyce Edna; Conway, Tyrrell
The gastrointestinal tract contains a complex microbial ecosystem that exists in a symbiotic relationship with its host and plays an important role in maintaining human health. Escherichia coli, a facultative anaerobe, is a commensal bacterial resident of the gastrointestinal tract and has demonstrated the importance of aerobic respiration for its survival in this competition rich ecosystem. The gastrointestinal tract is also host to a diverse and numerically dominant population of obligately anaerobic bacteria that coexist with E. coli in the mucus layer adjacent to the intestinal wall. This dissertation explores the relationship between E. coli and its oxygen sensitive microbial cohorts in mouse cecum mucus. We produced and in silico model of oxygen diffusion from the intestinal wall into the mucus layer in the absence and presence of aerobically respiring E. coli. The model predicts a decrease in the oxygen concentration of the mucus layer in the presence of aerobically respiring E. coli. In order to confirm the prediction of our model, we performed T2* weighted Magnetic Resonance Imaging (MRI) on the ceca of conventional mice, mice that had their native facultative anaerobes removed by treatment with streptomycin sulfate, and mice that were treated with streptomycin sulfate and subsequently colonized with E. coli MG1655 wild-type Nalr Strr or E. coli MG1655ΔcydAB ΔcyoAB::cat Strr, and isogenic cytochrome oxidase mutant that is unable to respire oxygen but is otherwise identical to the wild-type. T2* weighted MRI confirmed the prediction of our model in that conventional and wild-type colonized mice indicate lower cecal oxygen concentration than streptomycin sulfate only mice or those colonized with the cytochrome oxidase mutant. In order to examine the hypothesis that aerobic respiration in E. coli has an impact on the ecology of cecum mucus, we conducted 16S rRNA pyrosequencing surveys of the same experimental conditions for the MRI experiment. The results indicate a difference in β-diversity between our streptomycin treated only mice and each of those that had been treated with streptomycin and subsequently colonized with the wild-type or the cytochrome oxidase mutant. The results of this work lay the foundation for examinations of the affect of probiotic E. coli strains on the total intestinal microbiota.
Open Access
Allelopathic effects of Polygonum aviculare L.
(1981) Al Saadawi, Ibrahim S.,
Therefore, allelopathy appeared to be the dominant component of the interference, with competition probably accentuating its effects. Polygonum aviculare was inhibitory to Gossypium barbadense L. and Sorghum bicolor (L.) Moench indicating that allelopathy is an important component of the interference by Polygonum against crop yields. In spite of the moderate allelopathic effects against cotton and sorghum it may still be possible to plant Polygonum aviculare between rows of these crops or to supply a light mulch between rows to control various weeds including Cyndon dactylon and some other weeds.
Open Access
Allelopathic potential of wheat accessions /
(1984) Spruell, James Alton,
Root exudates of 286 accessions of hard red winter wheat (Triticum aestivum L.) were compared with that of a commercial strain 'T 64' for their relative ability to inhibit root and shoot growth of Japanese brome (Bromus japonicus L.) and common lambsquarters (Chenopodium album L.). Five accessions produced root exudates significantly more inhibitory to root growth in indicator plants than the commercial strain. When Japanese brome was grown in the presence and absence of wheat in sand cultures, wheat significantly retarded growth of the brome, with two of the test accessions of wheat significantly more effective than 'T 64' in reducing weed growth. When CI 13633 was grown with Japanese brome on a one-on-one basis in U-tubes containing aerated Hoagland's solution, growth of the brome was approximately 53% of that obtained by growing it with 'T64'. Respiration rates of roots and shoots of young seedlings and of newly emerged whole seedlings of Japanese brome were significantly reduced by root exudates from two of the test accessions. The consistent and superior inhibition of the indicator species by the test accessions indicates a strong allelopathic character which could be incorporated into commercial cultivars.
Open Access
ANAEROBACULUM HYDROGENIFORMANS: INSIGHTS INTO THE NOVEL BIOCHEMICAL AND PHYSIOLOGICAL ABILITY OF A THERMOPHILIC BIOCATALYST THAT CAN UTILIZE BOTH DEFINED AND UNDEFINED SUBSTRATES FOR THE PRODUCTION OF RENEWABLE HYDROGEN ENERGY
(2011) Maune, Matthew W.; Tanner, Ralph S
This body of work describes the bacterium Anaerobaculum hydrogeniformans strain OS1, a novel anaerobic, moderately thermophilic, NaCl-requiring fermentative bacterium that was isolated from oil production water collected from Alaska, USA. A. hydrogeniformans produces 4 moles of H2 per mole of glucose. Aside from the characterization of A. hydrogeniformans, production of H2 from undefined wastewaters was also evaluated. An optimal ratio of wastewater to mineral medium was obtained for all feedstocks and used for batch fermentations. Clarified wastewaters resulted in higher H2 yields. This study shows that A. hydrogeniformans can be used to produce H2 from waste feedstocks while significantly reducing COD at values higher that others reported in the literature for pure and mixed cultures as well as electrolytic cells. Determination of the optimal fermentation conditions for A. hydrogeniformans and elucidate limiting factors during glucose fermentation. A. hydrogeniformans grew optimally and produced H2 from 0.2 M to 0.6 M, and tolerated up to 1.2 M NaCl, making it the most NaCl tolerant organism producing approximately 4 H2 per mole of glucose. A. hydrogeniformans was able to grow in the presence of high initial sodium/potassium acetate concentrations. Ionic strength was not responsible for inhibition of growth or product production. Inhibition of total glucose oxidation was affected by a decrease in the culture pH, where by pH adjustment with additional buffer or bicarbonate during growth resulted in total glucose oxidation. Hydrogen removal from the headspace marginally increased glucose utilization and growth rates, but the total H2 production rate was not affected. Glucose was not oxidized totally, in cultures with lowered H2 partial pressures, supporting the hypothesis that increasing H2 partial pressure is not the only limiting factor during fermentation. Growth rate and glucose utilization increased when the concentration of yeast extract was increased in the medium. The physiological pathway for anaerobic glucose oxidation was evaluated. Enzyme activities for the Embden-Meyerhoff-Parnas pathway were all detected. However, Glyceraldehyde-3-phosphate dehydrogenase was not be detected in cell free extracts of A. hydrogeniformans using NAD⁺ or NADP⁺ as electron acceptors. However there was enzyme activity for a glyceraldehyde-3-phosphate oxidoreductase. The oxidation of pyruvate to acetate is accomplished by a pyruvate:oxidoreductase, phosphotransacetylase and acetate kinase. Labeling of the C-1 and C-3 of glucose showed the production of CO2 from the 3-C of glucose and the incorporation of the C-1 of glucose into the methyl position of acetate, which is indicative of the Embden Meyerhof pathway and further confirmed by the detection of key metabolites from glucose grown cultures of A. hydrogeniformans. This is the first report of an eubacterial species that oxidizes glucose to acetate, H2 and CO2 via a ferredoxin dependent pathway, such as that previously thought to only be present in hyperthermophilic archaeal species.
Open Access
The anaerobic biodegradation of ethylcyclopentane and intermediates of benzoate metabolism by microorganisms from a hydrocarbon-contaminated aquifer.
(2003) R√≠-hern√ʻez, Luis A.,; Suflita, Joseph M.,
In this thesis, I examine the microbial degradation of an alicyclic hydrocarbon and the intermediates of benzoate decay under anaerobic conditions. Ethylcyclopentane was chosen as a model alicyclic hydrocarbon because GC analysis of contaminated core samples suggested that ECP was depleted relative to other hydrocarbons present in the gas condensate (a hydrocarbon mixture). This observation suggested that ECP might have been biologically attenuated in this aquifer in a manner similar to that previously demonstrated for BTEX hydrocarbons by other researchers. I obtained a bacterial enrichment which could mineralize ECP coupled to the reduction of sulfate in stoichiometrically expected amounts. In addition, I was able to propose a pathway for the degradation of this alicyclic hydrocarbon based on the identification of various transient metabolites produced during biodegradation. Furthermore, I describe the organisms in the ECP-degrading enrichment by denaturing gradient gel electrophoresis (DGGE) using a portion of the 16S rDNA gene. This study suggests that alicyclic hydrocarbons such as ECP can be anaerobically activated by the addition to the double bond of fumarate to form alkylsuccinate derivatives under sulfate-reducing conditions and that the reaction occurs in the laboratory and in hydrocarbon-impacted environments.
Open Access
The anaerobic biodegradation of petroleum-related compounds.
(1997) Londry, Kathleen Louise.; Suflita, Joseph M.,
The toxicity and biodegradation of mixtures of thiols, thiophenes, thiophenic acids and aromatic sulfides were determined under anaerobic conditions. Toxicity effects were dependent on the structure of the organosulfur compounds, the amounts added to cultures, and the available electron acceptor. The anaerobic biodegradation of eight different organothiols was observed under nitrate-reducing conditions but not methanogenic or sulfate-reducing conditions. Degradation of hexanethiol was linked to nitrate reduction and nitrite production.
Open Access
THE ANAEROBIC MICROBIAL METABOLISM OF ENERGY SUBSTRATES: AN EXPLORATION INTO COALBED METHANOGENESIS, THE BIODETERIORATION OF DIESEL FUEL, AND BIOCORROSION
(2013-12) Lyles, Christopher N.; Suflita, Joseph M.; McInerney, Michael J.; Stevenson, Bradley S.; Lawson, Paul A.; Nanny, Mark A.
Under anaerobic conditions the complete mineralization of energy substrate can be achieved by specialized individual microorganisms or through syntrophic partnerships involving bacteria and archaea that ultimately convert parent compounds to methane and carbon dioxide. Such biotransformations generally result in the production of several fatty acids (i.e. acetate, propionate, butyrate, benzoate) that are particularly diagnostic for in situ microbial activity as well as postulated intermediates for anaerobic hydrocarbon degradation. The metabolic fate of these organic acid intermediates has been the subject of multiple investigations. However, what seems clear is that fatty acid-oxidizing bacteria generally catalyze the subsequent conversion of these intermediate compounds under a thermodynamically-based microbial syntrophism in co-culture with hydrogen/formate-utilizing microorganisms. Thus, C1-C5 volatile fatty acid (VFA) compounds are used throughout these chapters to represent metabolic intermediates of coal or hydrocarbon degradation. The ecological consequences of these anaerobic bioconversions are highly dependent on the prevailing geochemical conditions as well as the interrelationships between microorganisms and carbon sources. This dissertation focuses on the degradation of hydrocarbons or proposed fatty acid intermediates either relating to the production of coal bed methane (CBM) or the biodeterioration of fuels and how the latter subsequently impacts the biocorrosion of carbon steel. Coal is extremely difficult to chemically characterize; the organic fraction varies based on the starting plant material, the conditions of decomposition, and the physical and chemical changes that occur during the process of coalification. Thus, coal does not make for amenable methanogenic substrate, and requires a diverse microbial assemblage along with a thermodynamically based microbial syntrophism for the bioconversion of coal to methane. Considering the vast worldwide reserves of coal, the ever-expanding need for energy across the globe, and the environmental benefits of methane utilization as an energy source, there is considerable interest in stimulating the modern bioconversion of coal to methane. It has been previously proposed that ecological factors such as substrate bioavailability, coal recalcitrance, the absence of the requisite microorganisms, and chemical/nutrient limitations might contribute to the inhibition of biogenic CBM production. To assess coalfield methanogenesis, formation water from 17 sites collected from the Illinois and Powder River Basins as well as the Cook Inlet gas field was used as inocula for nutrient-replete incubations amended with C1-C5 fatty acids. Methanogenic rates for these incubations were extremely slow with long lag times and expected stoichiometric values of methane were typically not produced. Additionally, a functional gene microarray indicated that the genetic potential associated with a variety of microbial functions was present in all samples. Out of the three coalfields, the Cook Inlet incubations produced the most methane, particularly when amended with butyrate or valerate, a result that correlated with the number of unique mcr gene sequences and is consistent with the in situ detection of C4-C5 alkanoic acids. Collectively, these results suggested that the soft lignite coal in the Cook Inlet is easier to degrade than the sub-bituminous and bituminous coals of the Illinois and Powder River Basins. The degradation of the lignite coal in turn leads to the production of intermediate polar organic compounds (i.e. butanoic, pentanoic acids) within production waters that are then syntrophically converted to methane. These findings highlight the role of syntrophy in CBM production, and we concluded that coal methanogenesis is probably not limited by the inherent lack of metabolic potential, the presence of alternate electron acceptors, or the lack of available nutrients, but more likely restricted by the recalcitrant nature of the coal itself. Stringent regulations have been imposed worldwide mandating that diesel fuels contain ≤15 ppm sulfur; as a consequence ultra-low sulfur diesel (ULSD) has been fully integrated into the worldwide infrastructure to reduce chemical and particulate emissions. The process of desulfurization results in several changes to the physical properties of diesel fuel, which might differentially impact the biodeterioration of ULSD, compared to traditional diesel fuel formulations. We hypothesized that the removal of potentially inhibitory organosulfur compounds could alleviate the negative impact of these substances on the microbes responsible for diesel fuel biodegradation and that the intense process of desulfurization leads to the production of residual lower-molecular weight by products, which might increase the proliferation of problematic microbes relative to the fuel hydrocarbons. To test these hypotheses, an inoculum from a seawater-compensated ballast tank, along with two other known hydrocarbon- degrading inocula, were amended with fuel from the same ship or with refinery fractions of ULSD, low- (LSD), and high sulfur diesel (HSD) and monitored for sulfate depletion. The rates of sulfate removal in incubations amended with the refinery fuels were elevated relative to the fuel-unamended controls, but indistinguishable from one another. Thus, anaerobic hydrocarbon metabolism likely occurred in these incubations regardless of fuel sulfur content. The microbial community structure from each incubation was also largely independent of the fuel amendment type, based on molecular analysis of 16S rRNA gene sequences. Our results suggest that removal of organosulfur compounds and the production of easily amenable low molecular weight hydrocarbons via desulfurization do not significantly influence sulfate reduction rates or the structure of microbial communities. Thus, the process of desulfurization cannot explain the propensity of ULSD to decay faster than traditional diesel fuel formulations. The major implications of this work are that the biodegradation of diesel hydrocarbons or, by inference, the degree of biocorrosion is not influenced by the concentration of organosulfur species in the fuel. There is no doubt that the anaerobic degradation of hydrocarbons can be accomplished axenically by microbial pure cultures under a variety of electron accepting conditions as well as syntrophically by nutritionally diverse microbial consortia. However, the environmental consequences of anaerobic hydrocarbon transformation depend on the geochemical setting. Under sulfate-reducing conditions the production of sulfide can lead to health and safety concerns, reservoir souring, and metal biocorrosion; whereas the consequences under methanogenic conditions include the overall diminishment of petroleum quality and the production of methane, a greenhouse gas. Given that syntrophic bacteria are common in oil production facilities, we focused our efforts to understanding the impact of syntrophic hydrocarbon and fatty acid intermediates on the deleterious process of biocorrosion under both methanogenic and sulfate reducing conditions. Thus, defined microbial incubations using the hydrocarbon-degrading, sulfate-reducing bacterium Desulfoglaeba alkanexedens strain ALDC, was cultured with either sulfate or Methanospirillum hungatei strain JF-1 as electron acceptors and tested for the ability to corrode carbon steel coupons. The anaerobic biodegradation of hydrocarbons can also lead to the formation of a suite of fatty acid intermediates that can then be syntrophically metabolized, thus the corrosive potential of a model fatty acid-oxidizing bacteria S. aciditrophicus strain SB was assessed both in axenic culture, as well as syntrophically in co-culture with both Desulfovibrio sp. strain G11 and M. hungatei strain JF-1. Corrosion was measured using both electrochemical and profilometry techniques. Our results suggested that the corrosion of carbon steel decreased when D. alkanexedens strain ALDC was in co-culture with M. hungatei strain JF-1 and increased when S. aciditrophicus strain SB was co-cultured with Desulfovibrio sp. strain G11. The results highlight the role of acetate and sulfide production on the corrosion of carbon steel, and suggest that the metabolic interactions between syntrophs and hydrogen/formate utilizing microorganisms can substantially influence both instantaneous corrosion rates (1/Rp) and localized corrosion of the metal coupon. Despite these trends, corrosion was highly variable between replicate incubations. Differences in the amount of biomass, initial substrate concentrations, metabolic activity, end product production, and experimental conditions within the defined incubations did not account for this variation. Thus, the variability was ascribed to differences in the elemental composition of the metal coupons.
Open Access
Anaerobic reduction of hexavalent chromium by subsurface microorganisms.
(1999) Marsh, Tamara L.; McInerney, Michael J.,
Anaerobic sediments from an aquifer contaminated with landfill leachate were used to study the potential for microbial reduction of Cr(VI) to Cr(III). The lightly colored, sandy sediments slowly reduced Cr(VI) in viable, but not heat-killed, microcosms indicating a biological process. Microcosms containing sandy sediments and mineral medium were amended with various electron donors to determine those most important for biological Cr(VI) reduction. More than 500 muM Cr(VI) was reduced when formate, lactate, hydrogen, and glucose, but not benzoate or acetate, were added as electron donors. Chromate reduction in microcosms was not inhibited by the addition of sulfate, selenate, or Fe(III). However, the presence of nitrate partially inhibited Cr(VI) reduction. Nearly complete inhibition of Cr(VI) reduction was observed when microcosms were shaken in the presence of oxygen. The addition of molybdate to the microcosms did not affect Cr(VI) reduction in sandy sediments until very high concentrations (40 times the Cr(VI) concentration) were used. The addition of bromoethanesulfonic acid (BESA) in amounts less than, or slightly greater than, the Cr(VI) concentration partially inhibited Cr(VI) reduction in the microcosms. An anaerobic Cr(VI)-utilizing enrichment was obtained that was dependent upon hydrogen for both growth and Cr(VI) reduction. Growth and Cr(VI) reduction by the enrichment were completely inhibited by the addition of formaldehyde, partially inhibited by molybdate, and completely unaffected by BESA. No methane was produced by the enrichment, which reduced about 750 muM Cr(VI) in less than six days. These studies showed that Cr(VI) reduction in sandy aquifer sediments is a biologically mediated, anaerobic process that is inhibited by oxygen and nitrate. In addition, electron donors which resulted in increased available hydrogen showed a greater extent of Cr(VI) reduction.
Open Access
Analysis of the functional conservation of genes in a plant single cell type: the root hair cell
(2017-12) Qiao, Zhenzhen; Libault, Marc; Holt, Ben F.; Masly, John P.; Bartley, Laura E.; Russell, Scott D.
The evolution of plant species is tightly associated with major changes in their genome such as their allopolyploidy and autopolyploidy. These paleopolyploid events and recent genome duplications have contributed to the large sizes of the plant genomes and to the abundance of duplicated genes. This increases genomic content and, as a consequence, provides material for genetic mutations, drift, and selection. Therefore, genome duplication creates new possibilities of molecular evolution. Several studies focusing on the evolution of duplicated genes during plant development and in response to environmental stresses has been conducted. However, the cellular complexity of the plant organs used in these studies represents a difficulty to precisely characterize the molecular and functional conservation and divergence of duplicated genes. In this dissertation, taking advantage of publicly available genomic and transcriptomic sequences and functional genomic datasets, we aimed to precisely delineate the conservation and divergence of plant gene transcription and protein function. This analysis has been conducted with an unprecedented level of resolution using a single plant cell type, the root hair cell which emerged around 400 million years ago (mya). The rationale of the selection of this single plant cell type to conduct the projects is the following: the molecular response of a plant tissue or organ, which is often selected when conducting plant molecular studies, is a reflection of the average molecular reponses of the different cell types composing the tissue/organ. This cellular complexity is a limitation in our understanding of the molecular evolution of plant genes. This concept will be largely discussed in the introduction of this dissertation (Chapter 1). In chapter two, we described the development of an innovative plant culture system, the ultrasound aeroponic system, to access the root hair cells. This innovative plant culture system not only provides easy access to isolated root hair cells but also facilitates root hair observation and isolation, as well as the generation of transgenic root hair cells to enhance functional genomic studies. Finally, the ultrasound aeroponic system is compatible with the application of biotic and abiotic treatments on the plant root system. This is important because it opens avenues to precisely understand the adaptation of different plant species to environmental stresses and the evolution of these responses. In chapter 3, mining the Arabidopsis (Arabidopsis thaliana) and soybean (Glycine max) genome sequence and root hair transcriptomes, we performed a comparative analysis to reveal the molecular evolution of plant genes at the single cell type level. Our analysis revealed that the transcriptional activity of plant genes and the mechanisms controlling their expression in root hair cells are highly conserved between plant species. Focusing on nodulation, a biological process initiated by the symbiotic interaction between nitrogen-fixing bacteria (Rhizobia) and the legume root hair cell, we also performed a comparative genomic and transcriptomic analysis of the major regulators of the nodulation process and their homologs. This analysis is reported in Chapter 4. This study revealed the level of conservation and divergence of the nodulation-related genes across various legume species. In chapter 5, we further examined the molecular and functional conservation of genes and proteins by performing a comparative functional analysis of two regulators of the nodulation process: GmFWL1 and its interaction partner, a flotillin protein. Both proteins are microdomain-associated proteins. In response to rhizobial infection, these proteins translocate to the root hair cell tip where rhizobial recognition and invasion occur prior to the initiation of the infection process. Similar localization patterns of the Medicago (Medicago truncatula) flotillin ortholog in response to rhizobial infection (i.e., translocation at the tip of the root hair cell) suggests the conservation of the soybean and Medicago flotillin cellular functions and, more broadly, the role of plasma membrane microdomains during the nodulation process. This dissertation describes the use of a plant single cell type, the root hair cell, to study the conservation of plant genes expression and function. This work will expand our knowledge in plant evolutionary biology.
Open Access
Arthrobacter atrocyaneus as a system for the study of procaryotic morphogenesis /
(1976) Stanlake, Gary James,
Open Access
Assessing the impact of microorganisms capable of degrading biodiesel and diesel fuel in storage tanks
(2021-12-06) Floyd, James; Stevenson, Bradley; Dunn, Anne; De León, Kara; Madden, Andrew
Microbiological contamination in petroleum-based fuels has been exacerbated with the addition of fatty acid methyl esters to diesel fuels. Consequences of microbiological contamination of these fuels can lead to degraded fuels, fouling and clogging of infrastructure, and potentially lead to microbiologically influenced corrosion (MIC) from the formation of organic acids as these microbes metabolize the fuel components. Additionally, operators are typically unaware of any potential contamination in their fuel tanks as the formation of biofilms can interfere with current technology designed to alert them of ongoing problems. As part of this dissertation, the fungal isolates Paecilomyces AF001 and Wickerhamomyces SE3 were characterized as being capable of degrading B20 biodiesel and using it as the sole carbon and energy source. The metabolism of B20 biodiesel led to an acidification of the medium and caused an increase in pitting corrosion and generalized corrosion on carbon steel. Additionally, this research has provided evidence that corrosion risks in contaminated fuel storage tanks are greatest at the interface of the fuel and any water that becomes entrapped in the fuels. Prior to this research, limited information was known about the microbiological communities in ultra-low sulfur diesel (ULSD) and B20 biodiesel. This research expands the knowledge of microbial communities in fouled fuels by analyzing contaminated fuels from 106 fuel tanks at 17 military bases across the continental U.S. This research has demonstrated the bacterial communities in contaminated fuels are far more diverse than fungal communities in fuels when they are present. When fungal contamination occurred in fuels it was primarily composed of the filamentous fungal family Trichocomaceae. Fuel composition of B5 ULSD and B20 biodiesel was determined and used to correlate microbial community families to the fuel components. The same problematic fungal isolates Paecilomyces AF001 and Wickerhamomyces SE3 used to evaluate corrosion of carbon steel when grown on B20 were used to determine if the correlations predicted by RDA analysis were accurate. Trichocomaceae (representative isolate Paecilomyces AF001) had positive correlations with fuels containing more palmitoleic acid methyl ester and the fungal family Debaryomycetaceae (representative isolate Wickerhamomyces SE3) had a positive correlation with increases in pentadecanoic acid methyl esters in fuels. Both isolates were grown on these substrates to determine their ability to utilize them as a sole carbon and energy source. Paecilomyces AF001 was able to grow on palmitoleic acid methyl ester and was unable to grow on pentadecanoic acid methyl esters while Wickerhamomyces SE3 was able to grow on both substrates. Fungal families are less diverse than bacterial families in contaminated fuels and were primarily present when contamination occurred. Due to this, the fungal family Trichocomaceae which was present at many contaminated fuel storage tanks, was selected for enzymatic and transcriptomic analyses on B5 ULSD and B20 biodiesel as the sole carbon and energy sources. Paecilomyces AF001, a member of the Trichocomaceae family, has already been shown to be able to utilize hydrocarbons and FAME (Fatty Acid Methyl Ester) components in fuels and leads to increased corrosion risks. Transcriptomics was done to see any differences in metabolic utilization of genes associated with the metabolism of hydrocarbons and FAME. Paecilomyces was able to grow on both B5 ULSD and B20 biodiesel. Transcripts associated with hydrocarbon degradation, such as mono and dioxygenases, were higher than those seen when this fungus grew in B20 biodiesel. Additionally, lipase activity and transcripts associated with lipase genes were observed in both fuel types; however, more lipase activity and transcripts were found when Paecilomyces AF001 was grown on B20 fuel instead of B5 ULSD. Understanding how Paecilomyces AF001 grows on different fuel types can lead to the development of biosensors that can help operators detect contamination in their tanks sooner and hopefully lead to less costs associated with remediating contaminated tanks. Overall, this work has demonstrated that microbial contamination of B5 ULSD and B20 is a rampant problem across the U.S. This work has linked the filamentous fungus Paecilomyces AF001 to increased corrosion risks to carbon steel when grown on B20 biodiesel, demonstrated that the fungal family Trichocomaceae (representative isolate Paecilomyces AF001) is a predominant fouler when storage tanks are contaminated, and demonstrates that this organism transcribes different genes associated with fuel metabolism based on if this organism is grown on B5 ULSD or B20 biodiesel.
Open Access
Assessing the influence of electron donor and cell-cell interactions on in situ microbial sulfate and hydrogen consumption using field and laboratory approaches.
(2004) Harris, Steve H., Jr.; Suflita, Joseph M.,
*This dissertation is a compound document (contains both a paper copy and a CD as part of the dissertation).
Open Access
Assessing the influence of physical and chemical properties of sediments on microbial distribution and activity in the terrestrial subsurface.
(2005) Musslewhite, Christopher L.; McInerney, Michael J.,
To maximize the possibility for success, accurate assessment of the distribution and activity of microorganisms in the subsurface is essential for implementing bioremediation strategies at contaminated sites. It is clear that large variations in microbial activity and abundance occur between strata with markedly different sedimentological features. However, the relationship between microbial activity and abundance and sedimentological properties within a single geological unit have not been quantified to the same extent as between strata. The central hypothesis driving this investigation was that the major controls of microbial activity in the subsurface are strongly correlated with a statistical description of the variation in the physical and chemical properties of the formation. To test this hypothesis, the relationships between sedimentological and microbiological parameters in the vadose zone of a barrier sediment and in a shallow, microaerophilic aquifer, both located on the eastern shore of Virginia, were examined. For the vadose zone sediment, pairs of samples were taken 10-cm apart in the vertical direction and 2 cm apart in the horizontal direction along three transects with one sample from each depth being processed aerobically and the other being processed anaerobically. Little variation was observed in the sedimentological and microbiological parameters tested. The sediment of all samples was fine to coarse sand with the grain sizes varying by less than an order of magnitude. Sediment moisture was low for all samples, but increased near the top and bottom of each sampling transect. These were regions where bioavailable Fe(III) concentrations were highest. Zero-order rates of H2 uptake were low throughout and ranged from below detection limit to 0.064 mumol H2 • day-1 • g -1 of sediment with a median rate of 0.01 mumol H2 • day-1 • g-1 of sediment. The variation in bacterial numbers was slightly more than an order of magnitude range over the entire sampling face. Phospholipid fatty acid analysis showed a diverse but fairly uniform microbial community from sample to sample. Statistical analysis revealed that the quartile of aerobically processed samples with the highest H2 uptake rates had statistically higher moisture content and bioavailable iron content than did the rest of the samples. The quartile of aerobically processed samples with the lowest H2 uptake rates had significantly more gravel, less moisture, and less bioavailable Fe(III) than did the rest of the samples. Similar trends were observed for anaerobically processed samples, but the differences were not significant. The data indicate that the spatial variation in microbial parameters is low within strata with uniform grain sizes. (Abstract shortened by UMI.)
Open Access
An Assessment of Microbial Communities and Their Potential Activities Associated with Oil Producing Environments
(2015-06) Nunn, Heather; Stevenson, Bradley; Lawson, Paul; Krumholz, Lee; Suflita, Joseph; Madden, Andrew
Microbial populations have been found in oil-associated environments as early as the 1920s. The proliferation and metabolic activities of these microorganisms can have profound deleterious effects on the infrastructure associated with oil reservoirs, production, transport and storage. Biodegradation of hydrocarbons by reservoir microorganisms can lead to the formation of ‘heavy oil’ that is of lower economic value and is more difficult to recover. Some members of reservoir microbial communities also participate in microbial influenced corrosion. By applying modern sequencing technologies, much can be learned about the microorganisms present and their metabolic capabilities. The focus of this dissertation was to provide a comprehensive characterization of microbial communities in two oil production facilities and define their metabolic activity by profiling metabolites of hydrocarbons and sequencing their metagenomes. The most common samples available from oil production facilities are fluids collected at valve openings. These samples are chemically and biologically representative of the bulk fluids at any given location within an oil facility (e.g. pipelines). Microorganisms commonly attach to surfaces and form biofilms that can provide the microbial inhabitants protection from the external environment, allow for localized changes in chemistry, and represent sites of corrosion. Common maintenance of pipelines includes the use of “pigs” which physically disrupt and remove biofilms, corrosion products, and other solids associated with the inner surfaces of a pipeline. Libraries of partial 16S rRNA gene sequences were used to compare the microbial communities in bulk fluids from several locations throughout an oil production facility with the community associated with a “pig envelope”, the fluids enriched with solids removed by a pig. The microbial communities in bulk fluids and biofilms of the oil production facility contained only a few taxa. All samples had similar compositions, but different structure (relative abundances of taxa). An estimation of population density based on qPCR of 16S rRNA gene copy number showed that there was a five-fold increase in the number of bacteria in the pig envelope. The numerically abundant taxa were members of the genera Thermoanaerobacter, Thermacetogenium and Thermovirga, which should be studied further to determine their ability to degrade hydrocarbons and influence corrosion. The community structure, genomic potential, and function of microbial assemblages from two oilfields under different management practices were characterized to measure their potential for hydrocarbon biodegradation. High throughput sequencing of 16S rRNA genes was combined with shotgun metagenomic sequencing and a targeted environmental metabolomics survey to interrogate two oil production facilities. The genomic potential for the abundant taxa was thoroughly interrogated for currently known pathways for hydrocarbon metabolism. Several sequences were identified that are closely related to known hydrocarbon degradation genes; however, there is no conclusive evidence that directly links these taxa and the hydrocarbon metabolites that were identified. The presence of microorganisms and putative signature metabolites in oil-associated environments suggests hydrocarbon degradation is occurring. Hydrocarbon degradation causes souring and ‘heavy oil’ which is harder to extract and of less value. Additionally, when microorganisms are identified in close association with corroded surfaces, they are potentially implicated as participating in surface corrosion. In order to directly associate a particular microorganism with a specific activity, there is still a need for controlled experiments. A better understanding of the microorganisms and their activities in oil production facilities will lead to improved monitoring and mitigation for the future.
Open Access
Bacillus lipopeptide biosurfactants: Purification, structure-activity relationship, and in-situ production in oil reservoirs.
(2006) Youssef, Noha.; McInerney, Michael J.,
Alternatively, biosurfactant activity can be manipulated by formulation of biosurfactant mixtures with different properties. The efficacy of biosurfactants from individual strains, and mixtures of biosurfactants from different strains with and without synthetic surfactants was tested for enhanced interfacial activity. To design (bio)surfactant formulations effective in lowering IFT, information about both the bio/surfactant structure and the nature of targeted non-aqueous phase liquids (NAPL) was required. The IFT against toluene was lowered by using lipopeptide biosurfactants with a heterogeneous fatty acid composition or by using mixtures of lipopeptide and rhamnolipid biosurfactants. Conversely, the IFT against hydrophobic NAPL was lowered by mixing lipopeptide biosurfactants with a more hydrophobic synthetic surfactants.
Open Access
Bacillus mojavensis and Bacillus subtilis require DNA or deoxyribonucleosides for anaerobic growth.
(2004) Folmsbee, Martha Jean.; McInerney, Michael J.,
Bacillus mojavensis strain JF-2 grows to an A600 of 0.8 to 1.0 in aerobic medium E but growth in this medium under strict anaerobic conditions is difficult to establish and replicate. Anaerobic growth of JF-2 was not improved by the addition of vitamins, amino acids, ribonucleic acids, polyglutamate, polyglutamine, polytryptophan, rumen fluid, fatty acids or Tween 80 to medium E. The addition of enzymatic digests of protein to medium E improved anaerobic growth of JF-2. DNA from various sources replaced the requirement for enzymatic digests of protein for anaerobic growth of Bacillus mojavensis JF-2 and two other B. mojavensis strains. The addition of a mixture of four deoxyribonucleosides to medium E replaced the requirement for DNA. The addition of a mixture of five nucleic acid bases, four ribonucleotides or four ribonucleosides to medium E did not replace the requirement for four deoxyribonucleosides. The addition of four deoxyribonucleosides to aerobic medium rescued B. mojavensis JF-2 from hydroxyurea-induced, aerobic growth inhibition. DNA was not used as a sole carbon and energy source.
Open Access
BET-HEDGING IN HETEROCARPIC GRINDELIA CILIATA (ASTERACEAE)
(2017-05-12) Kistenmacher, Michael; Gibson, John; Hoagland, Bruce; McCarthy, Heather; Souza, Lara; Moore, Abigail
A challenge for all living organisms is to offset the fitness associated risks of environmental uncertainty. Bet-hedging strategies are adaptive in unpredictable environments and are documented in a wide range of taxa spanning all kingdoms (Simons 2011, see Appendix A). There are two general types of bet-hedging strategies, a conservative strategy exemplified by the phrase "a jack of all trades and master of none" and the more common diversified strategy best described by the phrase "don't put all your eggs in one basket" (Seger and Brockman, 1987; Simons, 2011, see Appendix A). Although there are differences between them, both are based on the principle that mean geometric fitness increases by reducing fitness variation among years (Cohen, 1966; Gillespie, 1974; Philippi and Seger, 1989, see Appendix A). In annual plants, small germination fractions and high seed survival in the seed bank are adaptive when good years occur unpredictably or in a low frequency. The opposite is true for environments when the probability of a good year is high. Mathematical models have derived these theoretical predictions (Cohen 1966; Levin et al. 1984; Venable and Brown, 1988; Venable and Lawlor 1980, see Appendix A), but empirical tests of these models remains problematic, primarily because documentation of changes in geometric mean fitness are not realized until different environmental conditions are experienced by the study organism. Since bet-hedging strategies are adapted on an evolutionary time scale, environmental conditions to hedge against may not be experienced in a human lifetime, or longer. Thus, field experiments are not optimal for testing bet-hedging theory. However a few long term observational studies support theoretical expectations (see Pake and Venable 1996; Venable, 2007, see Appendix A), and long-term manipulative experiments that alter environmental conditions (e.g. precipitation frequency) are feasible approaches (Petru and Tielboerger 2008, see Appendix A). Modeling is another method for testing theoretical predictions, specifically by combining demographic models that are coupled with environmental models that alter soil temperature and soil water content. Demographic models have been applied to estimate population growth rates in desert annuals by deriving parameters such as reproductive output, recruitment from the seed bank, and survivorship in response to simulated precipitation regimes (Gremer and Venable 2014; Salguero-Gomez et al. 2012, see Appendix A). Bet-hedging literature consists of a mixture of results that support and reject theoretical predictions, particularly in regard to seed germination and dormancy. This is due, in part, to the inability to incorporate mechanisms such as phenotypic plasticity and maternal effects that confound observations of demographic traits (i.e., seed production and seed dormancy) in natural populations. Another shortcoming is that comparisons of demographic traits at the population level are not incorporated into predictive models, resulting in hampered understanding of underlying genetic differences in the expression of bet hedging strategies, which are important variables determining population persistence and range dynamics. Lastly, and potentially the greatest shortcoming, is that risk avoidance from alternative selection agents (i.e., herbivores) are almost entirely non-existent. For example, frequent pre and post dispersal seed predation (i.e., granivory) may favor adaptations that reduce the risk of predation, such as increased lignification, or accumulation of tannins and similar defense compounds in fruit or seed coats (i.e., pericarp, and testa), that simultaneously alter germination or dormancy. Since plant-animal interactions are ubiquitous, and because the selective pressure animals impose on plant fitness can be extremely strong, we cannot truly understand plant bet hedging strategies without accounting this selective force. Chapter one is an explanation of why the Cox Proportional Hazard (CPH) model is an excellent choice for analyzing germination data. Historically, germination data was analyzed by analysis of variance, however the nature of germination data requires more complicated statistical analysis. The CPH is a suitable choice, but certain shortcomings in the standard CPH were identified (Ritz et al. 2013, see Appendix A). This chapter presents the use of the extended CPH (Kleinbaum and Klein 2012, see Appendix A), and demonstrates its ability to overcome the shortcomings of the standard CPH. The major strength of the extended CPH is the flexibility to statistically compare time intervals of interest to the user. Chapter two presents an investigation into the variability in germination and dormancy among G. ciliata populations in Oklahoma. The germination trends that were observed in chapter one are explained in chapter two and it is shown that significant differences in dormancy exist among populations. Such variation may strongly affect how seedbank and population dynamics. Chapter three is an investigation of how reproductive bet-hedging in an Oklahoma native forb Grindelia ciliata (Asteraceae), is affected by the seed herbivore Schinia mortua (Noctuidae). Female S. mortua moths determine the time, location, and abundance of S. mortua larvae that will consume the G. ciliata seeds. By manipulating location, timing, and abundance of larvae I evaluate the impact that this herbivore has on plant fitness.