A hybrid thruster system utilizes propellants in two different stages, traditionally a solid fuel and a gaseous or liquid oxidizer. Recently hybrid thrusters have become a popular topic of research due to the high demand of a ”green” replacement for hydrazine. Not only are hybrid thruster systems typically much safer than hydrazine, but they are also a low-cost system with a high reliability in performance. The Propulsion Research Laboratory (PRL) at Utah State University (USU) has developed a hybrid thruster system using 3-D printed acrylonitrile butadiene styrene (ABS) as the fuel and gaseous oxygen (GOX) as the oxidizer. This system has been spaceflight flown and tested in a hard vacuum environment with success. However, GOX has a low density and must be stored at high pressures to be considered viable. This thesis investigates the use of N2O/O2 mixtures, ”Nytrox”, and more commonly known as ”laughing gas”, as a higher density replacement oxidizer for GOX. Ina manner directly analogous to the creation of soda-water using dissolved carbon dioxide, Nytrox is created by bubbling gaseous oxygen under high pressure into nitrous oxide until the solution reaches saturation level. Oxygen in the mixture ullage dilutes the nitrous oxide vapor, and increases the required decomposition activation energy of the fluid by several orders of magnitude. Data from tests using each oxidizer are analyzed and presented for performance comparisons. Comparisons include, ignition reliability, ignition energy, thrust coefficient, characteristic velocity, specific impulse, and regression rate. Nytrox is shown to work effectively as a “drop in” replacement for gaseous oxygen, exhibiting slightly reduced specific impulse and regression rate, but with the trade of a significantly higher volumetric efficiency.

No description available.

No description available.

The transformations of organic nitrogen to ammonium and nitrate are central processes in the internal soil nitrogen cycle. In most agricultural soils, ammonium is rapidly oxidized to nitrate in the process known as nitrification; often leading to loss of nitrate from the system. Nitrification is mediated by ammonia oxidizing bacteria or archaea, and nitrite oxidizing bacteria. Understanding links between process rates, enzyme activities and the communities of microbes that cycle nitrogen may contribute to sustainable management. Our main objective was to determine the impacts of contrasting nitrogen management on soil microbial communities, enzyme activities, and functional genes for nitrification and nitrogen mineralization in a Utah agricultural system. Process rates and activities were measured in laboratory potential assays and 15N isotope pool dilution experiments. The abundance and diversity of genes involved in nitrification and nitrogen mineralization were examined using quantitative real-time PCR, pyrosequencing, clone libraries, and metagenomics. Key enzymes and their relevant marker genes included ammonia monooxygenase (amoA), nitrite oxidoreductase (nxrB), protease (npr and sub), chitinase (chiA), and urease (ureC). The overall soil microbial community composition was assessed targeting ribosomal genes. Ammonia oxidizing bacteria were more responsive than archaea to ammonium fertilizers while the archaea were competitive under low ammonium levels. The relative contribution of ammonia oxidizing archaea to nitrification increased with increasing temperature and their activity had a higher temperature optimum than bacteria. The abundance of ammonia oxidizers in the organic farming system increased with organic nitrogen fertilizers and their activity was higher in manure than in compost treated soil. Nitrogen fertilizers strongly stimulated the rates of potential nitrite oxidation. Nitrospira was the only known nitrite oxidizer genus recovered from any soil sample. The application of organic nitrogen fertilizers, but not inorganic, increased the diversity of the prokaryotic community and the activities of soil enzymes. In the organic farming system, abundances of functional genes for mineralization were increased by organic nitrogen fertilizer and these abundances were significantly correlated with corresponding enzyme activity. Understanding the link between microbial communities and the biogeochemical functions of nitrification and mineralization may allow ecosystem models to incorporate microorganisms as dynamic components driving nitrogen flux.

Phytostabilization is an emerging technology for the remediation of mine tailings sites. In arid and semiarid environments, mine tailings disposal sites are a major source of environmental pollution as they are subject to eolian dispersion and water erosion. Mine tailings are acidic to neutral, high in metal content, and nutrient poor. Furthermore, these sites remain unvegetated even after decades of no additional mining activity. In arid and semiarid regions, climatic variables such as high winds, salinity, and drought exacerbate the problem. The Klondyke mine tailings site is a model site for studying plant establishment in mine tailings within semiarid regions. It was a lead and zinc ore- processing operation from 1948 to 1958 and is similar in physicochemical characteristics to other acidic pyritic mine tailings.In a greenhouse study, a native drought tolerant halophyte, Atriplex lentiformis (Torr.) S. Wats., was evaluated for its potential as a phytostabilization candidate in compost-amended tailings from the Klondyke site. Germination, plant growth, and metal uptake of A. lentiformis were examined, and the microbial community was monitored by enumeration of autotrophic iron- and sulfur-oxidizing bacteria as well as heterotrophic bacteria. Results demonstrated that with 10 to 15% compost addition, growth of A. lentiformis was not affected and shoot metal concentrations were generally not a concern for foraging animals. Furthermore, the heterotrophic bacterial community is severely stressed but recovers with compost addition and successful plant growth. Therefore, A. lentiformis is a good candidate for phytostabilization of mine tailings with compost amendments.Poor revegetation of mine tailings has been attributed to the microbial community involved in acidifying tailings; however, no thorough microbial studies have been conducted. The second study characterizes the bacterial community of the Klondyke site and compares it to an offsite control sample. Results demonstrate that the heterotrophic community is indicative of soil health as it has a positive relationship with pH, phylotype richness, and diversity. Also, the mine tailings contain an unexplored diversity of acidophiles that are important in maintaining acidity and thus, metal bioavailability. Therefore, the bacterial community in mine tailings should be monitored in phytostabilization studies to evaluate restoration.

No description available.

Electrically controllable propellants (ECPs) provide a new method to increase the control and functionality of rocket motors in particular solid rockets. Traditional solid rockets do not have the capability to modify the burning rate on demand during operation, which greatly limits operational capabilities. The research outlined in this dissertation explores the fundamentals in the creation of ECPs to enable increased control in the burning rate of solid rockets. The research is organized into four studies which step through the fundamentals of ECPs, starting with a focus on the solid oxidizers, then moving into the creation of electrically controllable gel propellants (ECGPs). Next, electrically controllable solid propellants (ECSPs) were explored under atmospheric conditions, and then finally under elevated pressures. The first study explores the ability to electrically control the decomposition characteristics of various solid oxidizers. Typical composite solid propellants are composed of solid fuels and oxidizers and isolating the oxidizer in this study enables the ability to characterize critical components of ECSPs individually. This study discovered that certain solid oxidizers respond differently to applied voltages, but generally the decomposition rate of the solid oxidizers is greatly increased when voltage is applied using metal electrodes. The melt layer formed in the decomposition of the solid oxidizers was observed to be critical in the ability to manipulate the decomposition rate of the oxidizers. The second study built upon the knowledge that the melt layer was critical in the functionality of ECPs and explored the utilization of ECGPs which combined a viscous liquid polymer fuel in which solid oxidizers were dissolved. The ECGPs used in this study readily decomposed and ignited when a voltage potential was applied. The composition of the ECGPs along with the magnitude of the voltage being applied greatly impacted the ignition delay and overall burning characteristics of the propellants. This study illustrated the potential to create ECPs that enable increased control over the burning characteristics compared to conventional propellants. The third study utilized a solid polymer binder along with the solid oxidizers to create ECSPs that would readily decompose and ignite when a voltage potential was applied. Compositional changes in the propellant along with the magnitude of the applied voltage potential were observed to impact the regression rate of the ECSPs utilized in this study. The electrochemical decomposition characteristics of the ECSPs were explored to better characterize the contribution of the electrochemical reactions and how they differ from the more conventional thermochemical decomposition. The fourth and final study builds upon the prior ECSP study, but now experiments utilize compositions with electrically conductive additives to increase the responsiveness of the ECSPs to the applied voltage. This enabled the creation of ECSPs which ignite much more readily and with a higher degree of consistency. Experiments were also conducted at elevated pressures to analyze the combined impact that voltage and pressure play on the regression rate of the ECSPs. / Doctor of Philosophy / Solid rockets have many applications in both the civilian and defense industries due to their relatively low costs and long-term storage capabilities. However, traditional solid rockets have a limited degree of control as a result of the fuel and oxidizer being combined in the propellant and the combustion of the propellant being self-sustaining. The ability to change the thrust of the solid rocket motor on demand is something not currently possible without greatly increasing the complexity of the rocket motor, and even then the thrust control is limited. The addition of a simple method to vary the thrust of the rocket motor would drastically improve the functional capabilities and safety of the rocket. The method explored in this study to enable the creation of controllable solid rockets is through the use of electrically controllable propellants. These are propellants whose burning characteristics can be modified when subjected to an electric field. The work outlined in this dissertation develops a fundamental understanding of the methods to create electrically controllable solid and gel propellants. The electrically controllable propellants in this study demonstrated the capability to have their burning rate greatly increase or decrease by increasing or decreasing the voltage being applied to them. In addition to changing the burning rate, several compositions developed in this study were able to have their burning extinguished by removing the voltage and reignited by reapplying the voltage. These capabilities and the fundamentals behind their development enable the creation of much more functional rocket motors that overcome the limitations of current systems.

This research assessed the seasonal effects of contrasting tillage and crop rotation systems on soil ammonia oxidizing bacteria (AOB) and archaea (AOA). Four different cropping systems under till and no-till were analyzed in a 30 year-old agricultural field trial. Samples were collected during the 2010 growing season at times corresponding with agronomic events. Nucleic acids were preserved in the field and subsequently analyzed by quantitative real-time polymerase chain reactions (qPCR). Tillage decreased AOB activity and abundance in the plow layer (0-15 cm) immediately after fall moldboard plow events, but observed AOB dynamics at other times suggest tillage had a long-term distribution effect across depth (0-30 cm). AOA abundance was significantly greater in no-till plots at all times indicating tillage had longer-term effects on these communities. Crop rotation had minimal effect on AOB and AOA, but there was a noted yield advantage for corn following wheat, regardless of tillage treatment. / OMAFRA Highly Qualified Personnel Program, NSERC

Acidophilic iron oxidizing bacteria of the betaproteobacterial genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) habitats worldwide. Since their isolation and maintenance in the laboratory has proved to be extremely difficult, members of this genus are not accessible to a “classical” microbiological characterization with exception of the designated type strain “Ferrovum myxofaciens” P3G. The present study reports the characterization of “Ferrovum” strains at genome and transcriptome level. “Ferrovum” sp. JA12, “Ferrovum” sp. PN-J185 and “F. myxofaciens” Z-31 represent the iron oxidizers of the mixed cultures JA12, PN-J185 and Z-31. The mixed cultures were derived from the mine water treatment plant Tzschelln close to the lignite mining site in Nochten (Lusatia, Germany). The mixed cultures also contain a heterotrophic strain of the genus Acidiphilium. The genome analysis of Acidiphilium sp. JA12-A1, the heterotrophic contamination of the mixed culture JA12, indicates an interspecies carbon and phosphate transfer between Acidiphilium and “Ferrovum” in the mixed culture, and possibly also in their natural habitat. The comparison of the inferred metabolic potentials of four “Ferrovum” strains and the analysis of their phylogenetic relationships suggest the existence of two subgroups within the genus “Ferrovum” (i.e. the operational taxonomic units OTU-1 and OUT-2) harboring characteristic metabolic profiles. OTU-1 includes the “F. myxofaciens” strains P3G and Z-31, which are predicted to be motile and diazotrophic, and to have a higher acid tolerance than OTU-2. The latter includes two closely related proposed species represented by the strains JA12 and PN-J185, which appear to lack the abilities of motility, chemotaxis and molecular nitrogen fixation. Instead, both OTU-2 strains harbor the potential to use urea as alternative nitrogen source to ammonium, and even nitrate in case of the JA12-like species. The analysis of the genome architectures of the four “Ferrovum” strains suggests that horizontal gene transfer and loss of metabolic genes, accompanied by genome reduction, have contributed to the evolution of the OTUs. A trial transcriptome study of “Ferrovum” sp. JA12 supports the ferrous iron oxidation model inferred from its genome sequence, and reveals the potential relevance of several hypothetical proteins in ferrous iron oxidation. Although the inferred models in “Ferrovum” spp. share common features with the acidophilic iron oxidizers of the Acidithiobacillia, it appears to be more similar to the neutrophilic iron oxidizers Mariprofundus ferrooxydans (“Zetaproteobacteria”) and Sideroxydans lithotrophicus (Betaproteobacteria). These findings suggest a common origin of ferrous iron oxidation in the Beta- and “Zetaproteobacteria”, while the acidophilic lifestyle of “Ferrovum” spp. may have been acquired later, allowing them to also colonize acid mine drainage habitats.

Acidophilic iron oxidizing bacteria of the betaproteobacterial genus “Ferrovum” are ubiquitously distributed in acid mine drainage (AMD) habitats worldwide. Since their isolation and maintenance in the laboratory has proved to be extremely difficult, members of this genus are not accessible to a “classical” microbiological characterization with exception of the designated type strain “Ferrovum myxofaciens” P3G. The present study reports the characterization of “Ferrovum” strains at genome and transcriptome level. “Ferrovum” sp. JA12, “Ferrovum” sp. PN-J185 and “F. myxofaciens” Z-31 represent the iron oxidizers of the mixed cultures JA12, PN-J185 and Z-31. The mixed cultures were derived from the mine water treatment plant Tzschelln close to the lignite mining site in Nochten (Lusatia, Germany). The mixed cultures also contain a heterotrophic strain of the genus Acidiphilium. The genome analysis of Acidiphilium sp. JA12-A1, the heterotrophic contamination of the mixed culture JA12, indicates an interspecies carbon and phosphate transfer between Acidiphilium and “Ferrovum” in the mixed culture, and possibly also in their natural habitat. The comparison of the inferred metabolic potentials of four “Ferrovum” strains and the analysis of their phylogenetic relationships suggest the existence of two subgroups within the genus “Ferrovum” (i.e. the operational taxonomic units OTU-1 and OUT-2) harboring characteristic metabolic profiles. OTU-1 includes the “F. myxofaciens” strains P3G and Z-31, which are predicted to be motile and diazotrophic, and to have a higher acid tolerance than OTU-2. The latter includes two closely related proposed species represented by the strains JA12 and PN-J185, which appear to lack the abilities of motility, chemotaxis and molecular nitrogen fixation. Instead, both OTU-2 strains harbor the potential to use urea as alternative nitrogen source to ammonium, and even nitrate in case of the JA12-like species. The analysis of the genome architectures of the four “Ferrovum” strains suggests that horizontal gene transfer and loss of metabolic genes, accompanied by genome reduction, have contributed to the evolution of the OTUs. A trial transcriptome study of “Ferrovum” sp. JA12 supports the ferrous iron oxidation model inferred from its genome sequence, and reveals the potential relevance of several hypothetical proteins in ferrous iron oxidation. Although the inferred models in “Ferrovum” spp. share common features with the acidophilic iron oxidizers of the Acidithiobacillia, it appears to be more similar to the neutrophilic iron oxidizers Mariprofundus ferrooxydans (“Zetaproteobacteria”) and Sideroxydans lithotrophicus (Betaproteobacteria). These findings suggest a common origin of ferrous iron oxidation in the Beta- and “Zetaproteobacteria”, while the acidophilic lifestyle of “Ferrovum” spp. may have been acquired later, allowing them to also colonize acid mine drainage habitats.:EIDESSTATTLICHE ERKLÄRUNG ... 2 CONTENT ... 4 SUMMARY ... 9 CHAPTER I ... 11 ORIGIN AND MICROBIOLOGY OF ACID MINE DRAINAGE ... 11 ACIDOPHILIC IRON OXIDIZING BACTERIA OF THE GENUS “FERROVUM” ... 12 APPLICATION OF OMICS-BASED APPROACHES TO CHARACTERIZE ACIDOPHILES ... 14 AIMS OF THE PRESENT WORK ... 15 CHAPTER II ... 17 ABSTRACT ... 18 INTRODUCTION ... 18 METHODS ... 19 GENOME PROJECT HISTORY ... 19 GROWTH CONDITIONS AND GENOMIC DNA PREPARATION ... 20 GENOME SEQUENCING AND ASSEMBLY ... 20 GENOME ANNOTATION ... 21 RESULTS ... 21 CLASSIFICATION AND FEATURES ... 21 GENOME PROPERTIES ... 24 INSIGHTS FROM THE GENOME SEQUENCE ... 24 COMPARATIVE GENOMICS ... 28 CONCLUSIONS ... 30 ACKNOWLEDGMENTS ... 32 AUTHOR CONTRIBUTIONS ... 32 CHAPTER III ... 33 ABSTRACT ... 34 INTRODUCTION ... 34 METHODS ... 36 ORIGIN AND CULTIVATION OF “FERROVUM” STRAIN JA12 ... 36 GENOME SEQUENCING, ASSEMBLY AND ANNOTATION ... 37 VISUALIZATION OF THE NEARLY COMPLETE GENOME ... 38 PHYLOGENETIC ANALYSIS ... 39 PREDICTION OF MOBILE GENETIC ELEMENTS ... 39 NUCLEOTIDE SEQUENCE ACCESSION NUMBER ... 39 RESULTS AND DISCUSSION ... 39 PHYLOGENETIC CLASSIFICATION OF “FERROVUM” STRAIN JA12 ... 39 GENOME PROPERTIES ... 40 NUTRIENT ASSIMILATION AND BIOMASS PRODUCTION ... 44 Carbon dioxide fixation ... 44 Central carbon metabolism ... 45 Nitrogen ... 47 Phosphate ... 49 Sulfate ... 50 ENERGY METABOLISM ... 50 Ferrous iron oxidation ... 50 Other redox reactions connected to the quinol pool ... 54 Predicted formate dehydrogenase ... 55 STRATEGIES TO ADAPT TO ACIDIC ENVIRONMENTS, HIGH METAL LOADS AND OXIDATIVE STRESS ... 55 Acidic environment ... 55 Strategies to cope with high metal and metalloid loads ... 58 Oxidative stress ... 59 HORIZONTAL GENE TRANSFER ... 60 CONCLUSIONS ... 61 ACKNOWLEDGMENTS ... 62 AUTHORS\' CONTRIBUTIONS ... 62 CHAPTER IV ... 63 ABSTRACT ... 64 INTRODUCTION ... 64 METHODS ... 66 ORIGIN AND CULTIVATION OF “FERROVUM” STRAINS PN-J185 AND Z-31 ... 66 GENOME SEQUENCING, ASSEMBLY AND ANNOTATION ... 66 PREDICTION OF MOBILE GENETIC ELEMENTS ... 67 COMPARATIVE GENOMICS ... 68 Phylogenomic analysis ... 68 Assignment of protein-coding genes to the COG classification ... 68 Identification of orthologous proteins ... 68 Comparison and analysis of genome architectures ... 69 RESULTS ... 69 GENERAL GENOME FEATURES AND PHYLOGENETIC RELATIONSHIP OF THE FOUR “FERROVUM” STRAINS ... 69 COMPARISON OF INFERRED METABOLIC TRAITS ... 71 Identification of core genes and flexible genes ... 71 Comparison of the central metabolism ... 74 Central carbon metabolism ... 74 Nitrogen metabolism ... 77 Energy metabolism ... 78 Cell mobility and chemotaxis ... 78 Diversity of predicted stress tolerance mechanisms ... 78 Maintaining the intracellular pH homeostasis ... 78 Coping with high metal loads ... 79 Oxidative stress management ... 79 IDENTIFICATION OF POTENTIAL DRIVING FORCES OF GENOME EVOLUTION ... 80 Prediction of mobile genetic elements ... 81 Linking the differences in the predicted metabolic profiles to the genome architectures ... 82 Gene cluster associated with flagella formation and chemotaxis in “F. myxofaciens” ... 84 Gene clusters associated with the utilization of alternative nitrogen sources ... 86 Gene cluster associated with carboxysome formation in “F. myxofaciens” and OTU-2 strain JA12 ... 87 Putative genomic islands in the OTU-strain JA12 ... 89 CRISPR/Cas in “F. myxofaciens” Z-31: a defense mechanism against foreign DNA ... 91 DISCUSSION ... 92 THE COMPARISON OF THEIR METABOLIC PROFILES INDICATES THE EXISTENCE OF OTU- AND STRAIN-SPECIFIC FEATURES ... 92 GENOME EVOLUTION OF THE “FERROVUM” STRAINS APPEARS TO BE DRIVEN BY HORIZONTAL GENE TRANSFER AND GENOME REDUCTION ... 94 Horizontal gene transfer ... 94 Mechanisms of genome reduction ... 95 CONCLUDING REMARKS ... 98 ACKNOWLEDGMENTS ... 98 AUTHOR CONTRIBUTIONS ... 98 CHAPTER V ... 99 ABSTRACT ... 100 INTRODUCTION ... 100 METHODS ... 102 CULTIVATION OF THE “FERROVUM”-CONTAINING MIXED CULTURE JA12 ... 102 Up-scaling of pre-cultures for the transcriptome study ... 103 Experimental setup of the transcriptome study ... 103 Cell harvest from large culture volumes ... 106 EXTRACTION OF TOTAL RNA ... 106 LIBRARY CONSTRUCTION AND SEQUENCING ... 107 DATA ANALYSIS ... 107 Processing of raw data ... 107 Quantification of gene expression levels ... 108 Functional analysis ... 108 RESULTS ... 108 CULTIVATION OF THE MIXED CULTURE JA12 IN THE MULTIPLE BIOREACTOR SYSTEM ... 108 Growth monitoring ... 108 Microbial composition ... 111 RNA SEQUENCING (RNA-SEQ) ... 112 FUNCTIONAL CATEGORIZATION OF EXPRESSED GENES ... 113 Functional assignment of highly expressed genes ... 117 Functional assignment of poorly expressed genes ... 121 COMPARISON OF EXPRESSION LEVELS OF GENES PREDICTED TO BE INVOLVED IN OXIDATIVE STRESS MANAGEMENT ... 122 DISCUSSION ... 124 METABOLIC PATHWAYS RELEVANT UNDER CULTURE CONDITIONS MIMICKING THE NATURAL CONDITIONS IN THE MINE WATER TREATMENT PLANT ... 125 Novel insights into the energy metabolism of “Ferrovum” sp. JA12 ... 125 Insights from poorly expressed genes ... 126 VARIATION OF GENE EXPRESSION PATTERNS UNDER THE DIFFERENT CONDITIONS ... 128 EVALUATION OF THE EXPERIMENTAL SET-UP INVOLVING THE MULTIPLE BIOREACTOR SYSTEM ... 129 CONCLUDING REMARKS: SIGNIFICANCE OF THE PRESENT TRANSCRIPTOME STUDY ... 130 ACKNOWLEDGMENTS ... 131 AUTHOR CONTRIBUTIONS ... 131 CHAPTER VI ... 133 ABSTRACT ... 133 EXTENDED INSIGHTS INTO THE FERROUS IRON OXIDATION IN BETAPROTEOBACTERIA ... 133 MECHANISMS OF PHYLOGENETIC AND METABOLIC DIVERSIFICATION WITHIN THE GENUS “FERROVUM” ... 136 INFERRED ROLES OF “FERROVUM” SPP. IN THE MICROBIAL NETWORK OF THE MINE WATER TREATMENT PLANT ... 138 PERSPECTIVES ... 143 REFERENCES ... 145 SUPPLEMENTARY MATERIAL ... 170 DATA DVD ... 170 SUPPLEMENTARY MATERIAL FOR CHAPTER III ... 171 NUCLEOTIDE ACCESSION NUMBERS ... 171 PHYLOGENETIC ANALYSIS ... 171 GENOME PROPERTIES ... 173 NUTRIENT ASSIMILATION ... 174 Carbon metabolism ... 174 FERROUS IRON OXIDATION ... 176 HORIZONTAL GENE TRANSFER ... 179 SUPPLEMENTARY MATERIAL FOR CHAPTER IV ... 180 PHYLOGENETIC ANALYSIS ... 180 ASSIGNMENT OF PROTEIN-CODING GENES TO THE COG CLASSIFICATION ... 180 COMPARISON OF THE CENTRAL METABOLISM ... 181 Predicted metabolic potential of the four “Ferrovum” strains ... 181 Genes predicted to be involved in the central metabolism, energy metabolism, cell motility and stress management in the four “Ferrovum” strains ... 183 PREDICTED MOBILE GENETIC ELEMENTS IN THE GENOMES OF THE FOUR “FERROVUM” STRAINS ... 184 THE FLAGELLA AND CHEMOTAXIS GENE CLUSTER ... 184 THE UREASE GENE CLUSTER ... 185 THE CARBOXYSOME GENE CLUSTER ... 186 PUTATIVE GENOMIC ISLANDS IN “FERROVUM” SP. JA12 ... 187 Gene content of the genomic islands ... 187 Flanking sites of the putative genomic islands 1 and 2 ... 188 SUPPLEMENTARY MATERIAL FOR CHAPTER V ... 189 ORGANIZATION AND OPERATION OF THE LABFORS 5 MULTIPLE BIOREACTOR SYSTEM ... 189 INVESTIGATION OF THE MICROBIAL COMPOSITION IN THE IRON OXIDIZING MIXED CULTURE JA12 ... 192 SUPPLEMENTARY DATA OF THE TRANSCRIPTOME DATA ANALYSIS ... 193 RNA-Seq statistics ... 193 Expression strength of protein-coding genes ... 194 Expression of genes involved in carboxysome formation ... 197 Expression of a ribosomal proteins-encoding gene cluster ... 199 Expression of a gene cluster presumably involved in ferrous iron oxidation ... 202 Lowest expressed genes ... 205 Expression of genes predicted to be involved in oxidative stress response ... 206 ACKNOWLEDGMENTS ... 208 COLLEAGUES ... 208 ERFOLGSTEAM “JUNGE FRAUEN AN DIE SPITZE” (“YOUNG WOMEN TO THE TOP“) ... 208 FAMILY AND FRIENDS ... 209 FUNDING ... 209 CURRICULUM VITAE ... 210 LIST OF PUBLICATIONS ... 212 RESEARCH ARTICLES ... 212 CONFERENCE PROCEEDINGS ... 212 ORAL PRESENTATIONS AND POSTERS ... 213