The bioavailability of iron is limited by the solubility of Fe(III) at circumneutral pH. In the High Nutrient-Low Chlorophyll (HNLC) zones of the ocean, the natural or anthropogenic addition of iron stimulates primary productivity and consumes carbon dioxide. As a result, iron fertilization has been proposed to mitigate anthropogenic carbon emissions and lower global temperatures. The natural sources of iron to the ocean are not fully constrained and include eolian depositions as well as inputs from continental shelf sediments, rivers, hydrothermal vents, and icebergs. Regardless of their source, the effectiveness of iron additions in promoting carbon fixation depends on the presence of organic ligands either natural or produced by microorganisms that stabilize or solubilize Fe(III) at neutral pH. For example, siderophores are well known to be expressed extracellularly by prokaryotes in the photic zones of the oceans to increase the bioavailability of iron. In this dissertation, the production of iron nanoparticles is demonstrated in vent fluids from the 90 North hydrothermal system. These iron nanoparticles may either catalyze the oxidation of sulfide to thiosulfate and produce a potential electron acceptor for microbial respiration or provide a source of iron that stimulates primary production at great distances from the hydrothermal vents. In addition, dissolved iron under the form of soluble organic-Fe(III) complexes is demonstrated to constitute a significant source of iron in estuarine sediments that receive large amounts of particulate iron from flocculation and precipitation at the salinity transition of this estuary. A novel competitive ligand equilibration absorptive cathodic stripping voltammetry (CLE-ACSV) technique reveals that the speciation of iron changes from largely colloidal or particulate in the upper estuary to truly dissolved organic-Fe(III) in the lower estuary. It is also demonstrated that organic-Fe(III) complexes are produced far below the sediment-water interface, suggesting that dissimilatory iron-reducing bacteria may play an important role in their production. These complexes then diffuse across the sediment-water interface and provide a significant source of iron to the continental shelf. The mechanism of reduction of iron oxides by iron-reducing bacteria is not fully understood and presents a unique physiological problem for the organism, as the terminal reductase has to transfer electrons to a solid electron acceptor. In this dissertation, it is demonstrated for the first time using random mutagenesis that the respiration of solid Fe(III) oxides by Shewanella oneidensis, a model iron-reducing prokaryote, first proceeds through a non-reductive dissolution step involving organic ligands that are released extracellularly by the cells. These soluble complexes are then reduced by the organism to produce Fe(II) and recycle the ligand for additional solubilization. Incubations with deletion mutants of the proteins involved in the respiration of Fe(III) revealed that the type-II secretion system, which translocates proteins on the outer membrane of gram-negative bacteria, is involved in the production of organic-Fe(III) complexes by secreting an endogenous iron-solubilizing ligand or a protein involved in the biosynthesis of this ligand on the outer membrane. In addition, periplasmic decaheme cytochromes produced by Shewanella appear to be involved in the mechanism of production of the endogenous organic ligand either directly or through a sensing mechanism that controls its production. In turn, two decaheme cytochromes positioned on the outer-membrane and hypothesized to be involved in the electron transfer to the mineral surface do not appear to be involved in the solubilization mechanism, suggesting either that the cells regulate the ligand production via periplasmic sensing systems or that these cytochromes are not involved in the solubilization mechanism. Altogether this research shows the production of organic-Fe(III) complexes in sediments generates a significant flux of dissolved iron to support primary production in continental shelf waters and that these complexes may be partly produced by iron-reducing bacteria. Indeed, experiments with a model organism demonstrate dissimilatory iron reducing bacteria produce endogenous organic ligands with high iron-binding constants to non-reductively solubilize iron oxides during the anaerobic respiration of iron oxides. The organic ligand is apparently recycled several times to minimize the energy cost associated with its biosynthesis. These findings demonstrate that the solubilization of iron oxides by organic ligands may be an important, yet underappreciated process in aquatic systems.

The chemical and physical processes controlling contaminant fate and transport in the vadose zone limit the options for application of many remedial technologies. Foam delivery technology (FDT) has been developed as a potential solution to overcome these limitations for remediating subsurface and deep vadose zone environments using reactive amendments. Although there are many advantages to utilizing FDT for treatment in the deep vadose zone, little information is available on how the addition of these surfactants and remedial amendments affect the indigenous microbial communities in the deep vadose zone as well as the impact of biological transformations of surfactant-based foams on remediation efforts. The purpose of this study was to develop a rapid method for assessment of microbial communities in contaminated subsurface environments. This research was divided into two phases: (1) assess the toxicity of proposed FDT components on a single bacterial species, Shewanella oneidensis MR-1; and (2) determine the effects of these components on a microbial community from the vadose zone. In Phase I, S. oneidensis MR-1 was exposed to proposed FDT components to assess potential growth inhibition or stimulation caused by these chemicals. S. oneidensis MR-1 cultures were exposed to the surfactants sodium laureth sulfate (SLES), sodium dodecyl sulfate (SDS), cocamidopropyl betaine (CAPB), and NINOL 40-CO, and the remedial amendment, calcium polysulfide (CPS). Results from this phase revealed that the relative acute toxicity order for these compounds was SDS>>CPS>>NINOL40-CO>SLES≥CAPB. High concentrations of SDS were toxic to the growth of S. oneidensis MR-1 but low concentrations were stimulatory. This benchtop system provided a capability to assess adverse microbial-remediation responses and contributed to the development of in situ remedial chemistries before they are deployed in the field. For Phase II, sediments from the BC Cribs and Trenches (BCCT) area of the Hanford Site, WA, were characterized before and after exposure to potential FDT components. First, the phylogenetic and metabolic diversity of sediment from the BCCT was assessed by sequencing the microbial community and measuring the metabolic activity. The sediment was also incubated with various concentrations of SDS, CAPB, and CPS. Phylogenetic analysis detected phylotypes from the Alpha-, Beta-, Delta-, and Gammaproteobacteria, and Actinobacteria. Unlike the S. oneidensis MR-1 studies conducted in Phase I, the surfactants and CPS stimulated the metabolic activity of the native microbial communities. The observed stimulation could be caused by sorption of the chemicals to the sediment particles, or utilization of the surfactants by the microbial communities. These findings emphasize the importance of monitoring microbial activity at remediation sites in order to determine short and long term efficacy of the treatment, compliance with regulatory mandates, and act as an early warning indicator of unintended changes to the subsurface.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22495号 / 農博第2399号 / 新制||農||1076(附属図書館) / 学位論文||R2||N5275(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 小川 順, 教授 木岡 紀幸 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第18346号 / 農博第2071号 / 新制||農||1024(附属図書館) / 学位論文||H26||N4853(農学部図書室) / 31204 / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 植田 充美, 教授 小川 順 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

京都大学 / 新制・課程博士 / 博士(農学) / 甲第23952号 / 農博第2501号 / 新制||農||1091(附属図書館) / 学位論文||R4||N5387(農学部図書室) / 京都大学大学院農学研究科応用生命科学専攻 / (主査)教授 栗原 達夫, 教授 小川 順, 教授 阪井 康能 / 学位規則第4条第1項該当 / Doctor of Agricultural Science / Kyoto University / DGAM

In the past couple of decades, the discovery that iron is a limiting nutrient in large regions of the ocean has spurred much research into characterizing the biogeochemical controls on iron cycling. While Fe(II) is soluble at circumneutral pH, it readily oxidizes to Fe(III) in the presence of oxygen. Fe(III) is highly insoluble at circumneutral pH, presenting organisms with a bioavailability paradox stemming from the physiological challenge of using a solid phase mineral for assimilatory or dissimilatory purposes. Interestingly, dissolved organic-Fe(III) complexes can be stable in seawater in the presence of oxygen, and an active flux of these complexes has recently been measured in estuarine sediments. Their sources and biogeochemical role, however, remain poorly understood. In this work, a suite of field and laboratory techniques were developed to quantify diagenetic processes involved in the remineralization of carbon in marine sediments in situ, investigate the role of these organic-Fe(III) complexes in sediment biogeochemistry, and characterize the composition of the ligands possibly involved in the solubilization of Fe(III) in marine sediments. The first-of-its-kind in situ electrochemical analyzer and HPLC was used to better constrain diagenetic processes that may lead to the formation of dissolved organic-Fe(III) complexes in the Altamaha estuary and Carolina slope. An intensive study of the Satilla River estuary reveals that dissimilatory iron-reduction contributes to the formation of sedimentary organic-Fe(III) complexes, which are demonstrated to serve as an electron acceptor in subsequent incubations with a model iron-reducing microorganism. Similar observations in deep-sea slope and abyssal plain sediments fed by the Mississippi and Congo Rivers suggest that dissimilatory iron reduction may represent an important component of carbon remineralization in river-dominated ocean margin sediments that may be currently underestimated globally. To confirm that these organic-Fe(III) complexes are produced during microbial iron reduction, novel separation schemes were developed to extract and identify Fe(III)-binding ligands from sediment pore waters. Preliminary results reveal the presence of a few select low-molecular weight compounds in all pore waters extracted, suggesting they might be endogenous ligands secreted by iron-reducing bacteria to non-reductively dissolve Fe(III) minerals prior to reduction.

Biodesulfurization (BDS) is an alternative to hydrodesulfurization (HDS) as a method to remove sulfur from crude oil. Dibenzothiophene (DBT) was chosen as a model compound for the forms of thiophenic sulfur found in fossil fuels; up to 70% of the sulfur in petroleum is found as DBT and substituted DBTs; these compounds are however particularly recalcitrant to hydrodesulfurization, the current standard industrial method. My thesis deals with enhancing BDS through novel strains and through nanotechnology. Chapter highlights are: Chapter 2. My first aim was to isolate novel aerobic, mesophilic bacteria that can grow in mineral media at neutral pH value with DBT as the sole sulfur source. Different natural sites in Iran were sampled and I enriched, isolated and purified such bacteria. Twenty four isolates were obtained that could utilize sulfur compounds. Five of them were shown to convert DBT into HBP. After preliminary characterization, the five isolates were sent to the Durmishidze Institute of Biotechnology in Tbilisi for help with strain identification. Two isolates (F2 and F4) were identified as Pseudomonas strains, F1 was a Flavobacterium and F3 belonged to the strain of Rhodococcus. The definite identification of isolate F5 was not successful but with high probability it was a known strain. Since no new strains were apparently discovered, I did not work further in this direction. Chapter 3. In a second approach I studied the desulfurization ability of Shewanella putrefaciens strain NCIMB 8768, because in a previous investigation carried out at Cranfield University, it had been found that it reduced sulfur odour in clay. I compared its biodesulfurization activity profile with that of the widely studied Rhodococcus erythropolis strain IGTS8. However, S. putrefaciens was not as good as R. erythropolis. Chapter 4 and 5. I then turned to nanotechnology, which as a revolutionary new technological platform offers hope to solve many problems. There is currently a trend toward the increasing use of nanotechnology in industry because of its potentially revolutionary paths to innovation. I then asked how nanotechnology can contribute to enhancing the presently poor efficiency of biodesulfurization. Perhaps the most problematic difficulty is how to separate the microorganisms at the end of the desulfurization process. To make BDS more amenable, I explored the use of nanotechnology to magnetize biodesulfurizing bacteria. In other words, to render desulfurizing bacteria magnetic, I made them magnetic by decorating their outer surfaces with magnetic nanoparticles, allowing them to be separated using an external magnet. I used the best known desulfurizing bacterial strain, Rhodococcus erythropolis IGTS8. The decoration and magnetic separation worked very well. Unexpectedly, I found that the decorated cells had a 56% higher desulfurization activity compared to the nondecorated cells. I proposed that this is due to permeabilization of the bacterial membrane, facilitating the entry and exit of reactant and product respectively. Supporting evidence for enhanced permeabilization was obtained by Dr Pavel Grigoriev, Institute of Cell Biophysics, Russian Academy of Sciences, Pushchino. In Chapter 6, to optimize attachment of the nanoparticles to the surface of the bacteria I created thin magnetic nanofilms from the nanoparticles and measured the attachment of the bacteria using a uniquely powerful noninvasive optical technique (Optical Waveguide Lightmode Spectroscopy, OWLS) to quantify the attachment and determine how the liquid medium and other factors influence the process.

No description available.

La nanoscience est basée sur les changements de propriétés des particules lorsque leur diamètre est inférieur à 100 nm (i.e. nanoparticules, NPs). Devant l’utilisation croissante de tels NPs, et leur déversement probable dans l’environnement, l’évaluation de leurs risques sur la santé humaine et l’environnement est un enjeu majeur. Dans le cadre de la protection des eaux et des sols, l’évaluation de la qualité des eaux de surface est particulièrement importante, notamment dans les zones humides (ZHs), où la dynamique des métaux toxique (i.e. As, Pb, Ni, Cr, Hg) est complexe et dépend des conditions redox du milieu. Comme les NPs de magnétite (nano-Fe3O4), naturelles ou manufacturées, sont reconnues pour leur capacité d’adsorption importante face aux métaux lourds, leurs interactions dans les ZHs ripariennes (ZHRs) avec les ETMs restent critiques quant à leurs impacts directs ou indirects. Ainsi, l’objectif de cette thèse était d’étudier le rôle des nano-Fe3O4 manufacturées (~10nm) et des oxydes de fer naturels sur la dynamique des ETMs dans les eaux de surfaces et les sols de ZHRs. Ainsi, dans un premier volet portant sur des précipités colloïdaux naturels provenant de produits de reoxydation en milieu riparian (soumis à des oscillations redox), la distribution spatiale des éléments a été effectuée par cartographie isotopique nanoSIMS (i.e. 75As-, 56Fe16O-, le soufre (32S-) et la matière organique (12C14N-), alors que la spéciation du soufre a été évaluée par adsorption des rayons X au seuil K du soufre (S) (XANES). Ces analyses ont permis de mettre en évidences les interactions entre les oxydes de fer naturels, la matière organique naturelle (MON) et un métalloïde toxique, l’arsenic. Nos résultats suggèrent, par colocalisation statistique des images nanoSIMS, l’existence de deux types d’interaction : (1) 12C14N-, 32S-, 56Fe16O- et 75As-, et (2) 12C14N-, 32S- et 75As-. La coexistence des formes de S oxydées et réduites, confirmées par les analyses XANES, pourrait être attribuée à la lente cinétique d’oxydation de la MON. Ainsi, ce premier volet montre qu’en plus des interactions MON, oxydes de fer et As, de possibles interactions directes entre As et NOM à travers des groupements fonctionnels soufrés (e.g. thiols) sont aussi possibles en milieu oxydé. Dans un second volet, l’effet des nano-Fe3O4 (~ 10 nm) sur la mobilité des éléments traces (ETs) et des colloïdes, dans l'horizon organominéral d’un sol naturel de ZHR, a été évaluée à l’aide de colonnes de sol. Nos résultats montrent que l’enrobage des nanoparticules semble influencer la mobilité de la MON et des ETs du sol. En effet, la mobilité des ETs semble augmenter en présence de nano-Fe3O4 nus, suggérant des associations où la MON stabiliserait les nanoparticules et augmenterait leur mobilité ainsi que celle des ETs associés. / Nanoscience is based on changes in particle properties when their diameter is below 100 nm (ie nanoparticles, NPs). Considering the increasing use of such NPs and their discharge into the environment, the assessment of their risks to human health and the environment is a major issue. Underneath the protection of waters and soils, the surface water assessment quality is particularly important, especially in wetlands, where the toxic metals dynamic (e.g. As, Pb, Ni, Cr , Hg) is complex and depends on the redox conditions of the environment. As magnetite (nano-Fe3O4), a natural or manufactured NP, is known for its significant adsorption capacity with heavy metals, their interactions in riparian wetlands with trace metals (TMs) remain critical concerning their direct of indirect impact on trace metals (TMs) mobility. The objective of this thesis was to study the role of manufactured nano-Fe3O4 (~ 10nm) and natural iron oxides on the TMs dynamics in wetland surface waters and soils. Therefore, in a first part considering natural colloidal precipitates from reoxidation products from riparian areas (subject to redox oscillations), a spatial distribution of elements was performed using nanoSIMS isotope mapping (i.e. 75As-, 56Fe16O-, sulfur (32S-) and organic matter (12C14N-), while the sulfur speciation was evaluated X-ray adsorption at K edge of the sulfur (S) (XANES). These analyzes allowed to highlight the interactions between natural iron oxides, natural organic matter (NOM) and a toxic metalloid, As. Our results suggest, with a statistical colocalization of nanoSIMS images, the existence of two interaction types: (1) 12C14N-, 32S-, 56Fe16O- and 75As-, and (2) 12C14N-, 32S- and 75As-. The coexistence of the oxidized and reduced forms of S, confirmed by the XANES analyses might be attributed to the slow oxidation kinetic of MON. Thus, this first part shows that in addition to the known interactions between MON, iron oxides and As, a possible direct interaction between As and NOM through sulfur functional groups (e.g. thiols) are also possible in oxidized environment. In a second part, the effect of nano-Fe3O4 (~ 10 nm) on trace elements (TEs) and colloids mobility in the organomineral horizon of a natural wetland soil was assessed using soil columns. Our results show that the nanoparticles coating influences the mobility of NOM and TMs. Indeed, the TMs mobility increases in presence of naked nano-Fe3O4, suggesting associations where NOM stabilizes the nanoparticles and increase the nanoparticles and associated TMs mobility. This mechanism seems less possible with coated nano-Fe3O4 where MON blocks the coating adsorption sites and therefore the adsorption of metals.

No description available.