No description available.

From Introduction: It was as early as 1904 that Paul Ehrlich propounded the idea of a “magic bullet”. This “magic bullet”, or chemotherapeutic agent, as he also called it, had to meet certain requirements: (a) a high activity against pathogenic micro-organisms; (b) easy absorption by the body; (c) activity in the presence of body fluids and tissue; (d) a low degree of toxicity; (e) must not allow the development of resistant micro-organisms. The discovery of the sulphonamide, Prentosil, by Domagk in 1935 was one of the initial steps in the search for this “magic bullet”. This, together with the production and purification of the antibiotics penicillin, by Fleming, Florey and Chain in 1942 and streptomycin, by Waksman in 1943, heralded a new era in the fight against bacterial infections. The majority of modern antibacterial agents have to a large extent met the requirements of Ehrlich’s ‘magic bullet”. They have however failed to prevent the development of resistant bacterial strains. This has been particularly noticeable in the past twenty years since the sudden emergence of multiple-resistant bacteria, many of which can transfer to several drugs in one step by a process of conjugation. This phenomenon which has serious medical implications has prompted numerous studies on the origin, epidemiology, biochemistry and genetics of transferable drug resistance.

published_or_final_version / abstract / Ecology and Biodiversity / Doctoral / Doctor of Philosophy

Thesis (Ph. D.)--Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Dept. of Biology; and the Woods Hole Oceanographic Institution), 2009. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 149-162). / Trichodesmium is a colonial, N2-fixing cyanobacterium found in tropical oceans. Species of Trichodesmium are genetically similar but several species exist together in the same waters. In order to coexist, Trichodesmium spp. may occupy different niche spaces through differential utilization of resources such as nutrients and light, and through responses to physical characteristics such as temperature and turbulence. To investigate niche differentiation in Trichodesmium, I characterized cultured strains of Trichodesmium, identified and enumerated Trichodesmium clades in the field, and investigated P stress and N2 fixation in field populations. Species of Trichodesmium grouped into two clades based on sequences from 16S rDNA, the internal transcribed spacer (ITS), and the heterocyst differentiation gene hetR. Clade I contained Trichodesmium erythraeum and Trichodesmium contortum, and clade II contained Trichodesmium thiebautii, Trichodesmium tenue, Trichodesmium hildebrandtii, and Trichodesmium pelagicum. Each clade was morphologically diverse, but species within each clade had similar pigmentation. I developed a quantitative polymerase chain reaction (qPCR) method to distinguish between these two clades. In field populations of the Atlantic and Pacific Oceans, the qPCR method revealed that clade II Trichodesmium spp. were more prominent than clade I in the open ocean. Concentrations of Trichodesmium did not correlate with nutrient concentrations, but clade I had wider temperature and depth distributions than clade II. / (cont.) Temperature and light are physical characteristics that may define niche spaces for species of Trichodesmium. Clade I and II concentrations correlated with each other in the Pacific but not in the Atlantic, indicating that the two clades were limited by the same factors in the Pacific while different factors were limiting the abundance of the two clades in the Atlantic. Trichodesmium populations in the North Atlantic were more P stressed and had higher N2 fixation rates than populations in the western Pacific. While nutrient concentrations didn't directly correlate with Trichodesmium concentrations, the contrasting nutrient regimes found in the Atlantic and Pacific Oceans might influence distributions of the two clades differently. Unraveling the differences among species of Trichodesmium begins to explain their coexistence and enables us to understand factors controlling global N2 fixation. / by Annette Michelle Hynes. / Ph.D.

Thesis: Ph. D., Joint Program in Biological Oceanography (Massachusetts Institute of Technology, Department of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2014. / Cataloged from PDF version of thesis. / Includes bibliographical references. / Viral predation on bacteria in the ocean liberates carbon from the particulate fraction, where it is accessible to higher trophic levels, and redirects it to the dissolved fraction, where it supports microbial growth. Although viruses are highly abundant in the ocean little is known about how their interactions with bacteria are structured. This challenge arises because the diversity of both bacteria and viruses is exceedingly high and interactions between them are mediated by specific molecular interactions. This thesis uses heterotrophic bacteria of the genus Vibrio as a model to quantify virus-host interactions in light of host population structure and ecology. The methods developed in this thesis include streamlining of standard bacteriophage protocols, such as the agar overlay, and facilitate higher throughput in the isolation and characterization of novel environmental virus-host systems. Here, >1300 newly isolated Vibrio are assayed for infection by viral predators and susceptibility is found to be common, though total concentrations of predators are highly skewed, with most present at low abundance. The largest phylogenetically-resolved host range cross test available to date is conducted, using 260 viruses and 277 bacterial strains, and highly-specific viruses are found to be prevalent, with nearly half infecting only a single host in the panel. Observations of blocks of multiple viruses with nearly identical infection profiles infecting sets of highly-similar hosts suggest that increases in abundance of particular lineages of bacteria may be important in supporting the replication of highly specific viruses. The identification of highly similar virus genomes deriving from different sampling time points also suggests that interactions for some groups of viruses and hosts may be stable and persisting. Genome sequencing reveals that members of the largest broad host-range viral group recovered in the collection have sequence homology to non-tailed viruses, which have been shown to be dominant in the surface oceans but are underrepresented in culture collections. By integrating host population structure with sequencing of over 250 viral genomes it is found that viral groups are genomically cohesive and that closely-related and co-occurring populations of bacteria are subject to distinct regimes of viral predation. / by Anne Kathryn Marie Kauffman. / Ph. D.

No description available.

Bacteria are ubiquitous in all ecosystems and are often challenged by multiple stresses such as extreme temperatures, high salt concentrations, nutrient limitation, pH variations, radiation, predation and the presence of antibiotics/toxins. The most challenging among them is predation pressure which is one of the major causes of their mortality in different niches. Bacteria have evolved different adaptive measures to counter predation. Some of them include change in shape, size, motility, and unpalatable aggregate formation. Aromatic β-glucosides such as salicin, produced by plants as secondary metabolites, play a significant role in protecting them from herbivores. Members of the family Enterobaceriaceae primarily present in soil, e.g. Erwinia chrysanthemi (a phytopathogen) and Klebsiella aerogenes, can utilize the aromatic β-glucosides salicin and arbutin (likely to be present in soil derived from decomposing plant materials) as a carbon source unlike their fellow members such as Escherichia coli, Shigella sonnei, and Salmonella present in the gut environment. Bacteria can obtain energy by metabolizing β-glucosides in the form of glucose. Whether they can also use these molecules as defense tools in a manner similar to plants is an intriguing possibility. In such an event, Bgl+ bacteria could derive a dual advantage in terms of energy generation and protection from predation. The current study was initiated to investigate a possible link between β-glucoside metabolism and self-defense in Enterobacteriaceae. Different members of Enterobacteriaceae comprising of both laboratory strains and natural isolates were considered as prey. Predators included were laboratory strains and soil isolates of bacteriovorous nematodes of the Rhabditidae family, the amoeba Dictyostelium discoidium and a bacteriovorous Streptomyces sp. The predator-prey interaction was analyzed by performing viability and behavioral assays in the context of β-glucoside metabolism Results presented in Chapter 2 show that active catabolism of aromatic β¬glucosides like salicin, arbutin and esculin by Bgl+ bacteria decreases the viability of their predators. The aglycone products released during β-glucosides metabolism, e.g. saligenin in the case of salicin, are the causative agents of the mortality of the predators. The lethality is reversible up to a specific threshold of exposure. Saligenin acts as a chemo-attractant that lures and kills Caenorhabditis elegans N2. In the case of nematodes that succumb, bacteria can derive nutrition from the dead predators indicating a conversion of prey to predator. Experiments with mutant strains of Caenorhabditis elegans suggest that the dopaminergic receptor dop-1 is involved in mediating saligenin toxicity. Studies mentioned in Chapter 3 revolve around the relevance of the predator-prey interaction discussed in Chapter 2 in the natural environment. Members of Enterobacteriaceae and their predator amoebae (cellular slime molds) and nematodes were isolated from soil. They show coexistence in most of the soil samples analyzed. All the predators isolated from soil and other natural isolates of Caenorhabditis succumb to saligenin as their laboratory counterparts with higher sensitivity in some of the strains. Soil nematodes belonging to genera Oscheius and Mesorhabditis avoid saligenin unlike the members of Caenorhabditis genus which are attracted towards saligenin. This indicates that the soil nematodes are often exposed to saligenin or saligenin-like compounds, resulting in the evolution of a genetic machinery to avoid these toxic compounds. Studies with quasi-natural environments like soil and fruit indicate that β-glucoside metabolism have similar effects on predator prey interaction in these environments, reinforcing the relevance of these observations to the natural ecology of the organisms. The studies reported in Chapter 2 and 3 shed light on a novel defense strategy of otherwise non-pathogenic members of Enterobacteriaceae which comes with a dual advantage. These results have also brought into focus issues such as the benefit derived by bacterial populations that are genetically heterogeneous, consisting of both Bgl+ and Bgl-strains. The broad implications and future directions of the work are discussed in Chapter 4. Work presented in Appendix deals with the investigation of the pattern of cellobiose utilization in Shigella sonnei. As mentioned in Chapter 1, it is known that members of Enterobacteriaceae exhibit diversity in their pattern of β-glucoside utilization. Wild type strains of both E. coli and Shigella sonnei are unable to utilize Arbutin, Salicin and Cellobiose. While E. coli can acquire cellobiose utilizing ability directly from the wild type state (Arb-Sal-Cel-), Shigella sonnei strains, though closely related to E. coli, have to undergo a series of mutations in a specific sequence to become capable of utilizing these sugars. Characterization of a few Shigella sonnei Cel+ mutants showed a different mode of activation of the chb operon (known to be involved in cellobiose utilization in E. coli). Considering the ecological significance of the ability to hydrolyze aromatic β-glucosides, a detailed understanding of the metabolic capability of different strains and the molecular mechanism involved becomes significant.

Modern pig farming production may over burden the environment with organic substances, exposure of bacterial pathogens and introduction of resistance gene. This may be caused by the pig’s droppings, lack of seepage management or accidental spillage of seepage which may impact on the environment and its physicochemical parameters. The objective of this study is to determine and assess the level of bacteriological pollution emanating from the pig farm and their impact on the physicochemical parameters of soil and water as well as to identify the presence of antibiotic resistance gene of these prevailing bacteria. Soil and water samples were collected monthly for a period of six months (March- August 2013). Samples were collected at pig enclosures, soil 20 m and 100 m away from pig enclosures, constructed wetland used for treating pig farm wastewater, soil 20m and 100 m away from constructed wetland. Procedure followed for analysing soil and water samples includes physicochemical analyses, viable cell counts of 10-1 to 10-8 dilutions, identification of bacteria using API 20E test kit, antibiotic susceptibility analyses, and identification of resistance gene using molecular procedures. The media that were used for viable cell counts were, Nutrient agar, MacConkey Agar, Xylose Lysine Deoxycholate agar (XLD agar), and Eosin Methylene Blue (EMB). Physicochemical parameters of water showed unacceptable high levels of analysed parameters for BOD (163 mg/L to 3350 mg/L), TDS (0.77 g/L to 6.48 mg/L), COD (210 mg/L to 9400 mg/L), NO3 (55 mg/L to 1680 mg/L), NO2 (37.5 mg/L to 2730 mg/L), and PO43− (50 mg/L to 1427 mg/L) were higher than the maximum permissible limits set by Department of Water Affairs and Forestry (DWAF). For soil samples TDS (0.01g/L to 0.88 g/L), COD (40 mg/L to 304 mg/L), NO3 (32.5 mg/L to 475 mg/L), and NO2 (7.35 mg/L to 255 mg/L) and PO43- (32.5 mg/L to 475 mg/L ) were observed to be higher than recommended limits set by Federal Ministry for the Environmental (FME). The viable cells in soil samples 30cm depth ranged from 0 cfu/mL to 2.44 x 1010cfu/mL, in soil 5cm depth ranged from 1.00 x 101 cfu/mL to 1.91 x 1010 cfu/mL, and in water samples viable cells ranged from 5.00 x 101 to 5.05 x 109. Pseudomonas luteola (Ps. luteola), Escherichia vulneris (E. vulneris), Salmonella choleraesuis spp arizonae, Escherichia coli 1(E. coli 1), Enterobacter cloacae, Pseudomonas flourescens/putida (Ps. flourescens/putida), Enterobacter aerogenes, Serratia ordoriferal, Pasteurella pneumotropica, Ochrobactrum antropi, Proteus vulgaris group, Proteus vulgaris, Salmonella spp, Aeromonas Hydrophila/caviae/sobria1, Proteus Mirabillis, Vibrio fluvials, Rahnella aquatillis, Pseudomonas aeruginosa (Ps. aeruginosa), Burkholderia Cepacia, Stenotrophomonas maltophilia (St. maltophilia), Shwenella putrefaciens, Klebsiela pneumonia, Cedecea davisa, Serratia liquefaciens, Serratia plymuthica, Enterobacter sakaziki, Citrobacter braakii, Enterobacter amnigenus 2, Yersinia pestis, Serratia ficaria, Enterobacter gergoriae, Enterobacter amnigenus 1, Serratia marcescens, Raoutella terrigena, Hafnia alvei 1, Providencia rettgeri, and Pantoa were isolated from soil and water samples from the pig farm. Isolates were highly resistant to Penicillin G, Sulphamethaxazole, Vancomycin, Tilmocozin, Oxytetracycline, Spectinomycin, Lincomycin, and Trimethoprim. The most resistance genes detected in most isolates were aa (6’)-le-aph (2”)-la, aph (2”)-lb, aph (3”)-llla, Van A, Van B, Otr A and Otr B. Pig farm seepage is causing bacterial pollution which is impacting negatively on the natural environment in the vicinity of pig farm by introducing bacterial pathogens that have an antibiotic resistance gene and is increasing the physicochemical parameters for soil and water in the natural environment at the pig farm. It is therefore recommended that pig farms should consider the need to implement appropriate regulatory agencies that may include the regular monitoring of the qualities of final effluents from waste water treatment facilities. In addition there is a need to limit soil pollution in order to safe guard the natural environment in the vicinity of pig farm from bacteriological pollution and introduction of antibiotic resistance gene. It is also recommended that more advanced technologies should be introduced that will assist pig farms to manages the seepage properly. / Environmental Sciences / M. Sc. (Environmental Sciences)

Modern pig farming production may over burden the environment with organic substances, exposure of bacterial pathogens and introduction of resistance gene. This may be caused by the pig’s droppings, lack of seepage management or accidental spillage of seepage which may impact on the environment and its physicochemical parameters. The objective of this study is to determine and assess the level of bacteriological pollution emanating from the pig farm and their impact on the physicochemical parameters of soil and water as well as to identify the presence of antibiotic resistance gene of these prevailing bacteria. Soil and water samples were collected monthly for a period of six months (March- August 2013). Samples were collected at pig enclosures, soil 20 m and 100 m away from pig enclosures, constructed wetland used for treating pig farm wastewater, soil 20m and 100 m away from constructed wetland. Procedure followed for analysing soil and water samples includes physicochemical analyses, viable cell counts of 10-1 to 10-8 dilutions, identification of bacteria using API 20E test kit, antibiotic susceptibility analyses, and identification of resistance gene using molecular procedures. The media that were used for viable cell counts were, Nutrient agar, MacConkey Agar, Xylose Lysine Deoxycholate agar (XLD agar), and Eosin Methylene Blue (EMB). Physicochemical parameters of water showed unacceptable high levels of analysed parameters for BOD (163 mg/L to 3350 mg/L), TDS (0.77 g/L to 6.48 mg/L), COD (210 mg/L to 9400 mg/L), NO3 (55 mg/L to 1680 mg/L), NO2 (37.5 mg/L to 2730 mg/L), and PO43− (50 mg/L to 1427 mg/L) were higher than the maximum permissible limits set by Department of Water Affairs and Forestry (DWAF). For soil samples TDS (0.01g/L to 0.88 g/L), COD (40 mg/L to 304 mg/L), NO3 (32.5 mg/L to 475 mg/L), and NO2 (7.35 mg/L to 255 mg/L) and PO43- (32.5 mg/L to 475 mg/L ) were observed to be higher than recommended limits set by Federal Ministry for the Environmental (FME). The viable cells in soil samples 30cm depth ranged from 0 cfu/mL to 2.44 x 1010cfu/mL, in soil 5cm depth ranged from 1.00 x 101 cfu/mL to 1.91 x 1010 cfu/mL, and in water samples viable cells ranged from 5.00 x 101 to 5.05 x 109. Pseudomonas luteola (Ps. luteola), Escherichia vulneris (E. vulneris), Salmonella choleraesuis spp arizonae, Escherichia coli 1(E. coli 1), Enterobacter cloacae, Pseudomonas flourescens/putida (Ps. flourescens/putida), Enterobacter aerogenes, Serratia ordoriferal, Pasteurella pneumotropica, Ochrobactrum antropi, Proteus vulgaris group, Proteus vulgaris, Salmonella spp, Aeromonas Hydrophila/caviae/sobria1, Proteus Mirabillis, Vibrio fluvials, Rahnella aquatillis, Pseudomonas aeruginosa (Ps. aeruginosa), Burkholderia Cepacia, Stenotrophomonas maltophilia (St. maltophilia), Shwenella putrefaciens, Klebsiela pneumonia, Cedecea davisa, Serratia liquefaciens, Serratia plymuthica, Enterobacter sakaziki, Citrobacter braakii, Enterobacter amnigenus 2, Yersinia pestis, Serratia ficaria, Enterobacter gergoriae, Enterobacter amnigenus 1, Serratia marcescens, Raoutella terrigena, Hafnia alvei 1, Providencia rettgeri, and Pantoa were isolated from soil and water samples from the pig farm. Isolates were highly resistant to Penicillin G, Sulphamethaxazole, Vancomycin, Tilmocozin, Oxytetracycline, Spectinomycin, Lincomycin, and Trimethoprim. The most resistance genes detected in most isolates were aa (6’)-le-aph (2”)-la, aph (2”)-lb, aph (3”)-llla, Van A, Van B, Otr A and Otr B. Pig farm seepage is causing bacterial pollution which is impacting negatively on the natural environment in the vicinity of pig farm by introducing bacterial pathogens that have an antibiotic resistance gene and is increasing the physicochemical parameters for soil and water in the natural environment at the pig farm. It is therefore recommended that pig farms should consider the need to implement appropriate regulatory agencies that may include the regular monitoring of the qualities of final effluents from waste water treatment facilities. In addition there is a need to limit soil pollution in order to safe guard the natural environment in the vicinity of pig farm from bacteriological pollution and introduction of antibiotic resistance gene. It is also recommended that more advanced technologies should be introduced that will assist pig farms to manages the seepage properly. / Environmental Sciences / M. Sc. (Environmental Sciences)

[Truncated abstract] Acidic mine lakes are formed as a result of the oxidation and dissolution of metal sulfide minerals and are primarily characterized by low pH values of 2 – 4. Many strategies for the bioremediation of acidic mine lakes depend on the alkalinity generation capabilities of microbial ferric and/or sulfate reducing bacteria. However nearly all mine lakes are oligotrophic, with very low concentrations of available organic carbon and nutrients; all required for healthy microbial growth. There is also an unusual class of mine lakes characterized by low concentrations of organic carbon and also very low concentrations of dissolved iron and sulfate. Our ability to promote microbial activity in these systems is especially challenging. This study focuses on one of these systems, Lake Kepwari, a coal mine lake in Western Australia. Numerical modeling of remediation strategies is an efficient way of testing scenarios prior to expensive in-field trials. However such modeling relies on good descriptions of microbial processes, including kinetic parameterizations of ferric and sulfate reduction. There has been little research to date on the study of kinetic parameterizations of the chemical and biological alkalinity generation in acidic mine lakes. The objectives of this thesis were to investigate the viability of microbial ferric and sulfate reduction in an ultraoligotrophic, acidic mine lake, to assess the impact of these microbial processes on water quality and to parameterize the Dual Monod kinetics of neutralization under dual limitation conditions. Molecular analyses including most probable number, DNA extraction, polymerase chain reaction, polymerase chain reaction – denaturing gradient gel electrophoresis were used to examine the microbial communities in the lake sediments. ... The Monod maximum specific microbial growth rates with respect to dissolved organic carbon and ferric, and as determined in batch experiments, were 0.07 ± 0.01 and 0.048 ± 0.02 day-1, respectively, and their corresponding Monod half saturation constants and were 14.37 and 5.6 mmol L-1. The Monod maximum consumption rates under ferric and OC limitation were also estimated. The Monod maximum specific microbial growth rates with respect to dissolved organic carbon and sulfate, , and were 0.05 ± 0.01, 0.08 ± 0.01 and 0.07 ± 0.02 day-1, respectively, and their corresponding Monod half saturation constants, and were 75.5, 131.8 and 10.2 mmol L-1. The Monod maximum consumption rates under sulfate and OC limitation were also estimated. The results of this study suggest that strategies for the remediation of ultraoligotrophic, acidic mine lakes may rely on microbial ferric and sulfate reduction, however additions of both organic carbon and sulfate/ferric are essential. These results can be immediately applied to mesocosm studies in outdoor enclosures and to the management of acidic mine lakes. Furthermore, this thesis has provided a new, valuable understanding on the Dual Monod kinetic parameterizations of neutralization for an ultraoligotrophic, acidic mine lake environment. These parameterizations are essential for the lake ecological models that will be used to investigate remediation scenarios for acidic mine lakes.