We propose a new method to integrate genome-scale metabolic models into biogeochemical reaction modeling. This method predicts rates of microbial metabolisms by combining flux balance analysis (FBA) with microbial rate laws. We applied this new hybrid method to methanogenesis by Methanosarcina barkeri. Our results show that the new method predicts well the progress of acetoclastic, methanol, and diauxic metabolism by M. barkeri. The hybrid method represents an improvement over dynamic FBA. We validated genome-scale metabolic models of Methanosarcina barkeri, Methanosarcina acetivorans, Geobacter metallireducens, Shewanella oneidensis, Shewanella putrefaciens and Shewanella sp. MR4 for application to biogeochemical modeling. FBA was used to predict the response of cell metabolism, and ATP and biomass yield. Our analysis provides improvements to these models for the purpose of applications to natural environments. / 2019-07-28

The redox cycling of iron is intimately linked to the cycling of C, S, N, P as well as the speciation, mobility, and bioavailability of various toxic contaminants in soils and sediments. Within these environments, the cycling of iron is catalytically driven by iron-oxidizing (FeOB) and iron reducing bacteria (FeRB) which mediate the formation, transformation, and dissolution of various iron-bearing minerals. Under oxic conditions, FeOB promote the formation of iron oxides on or in close proximity of their cell walls and extracellular polymeric substances, and such composite, termed biogenic iron oxides (BIOS), offers highly reactive heterogenous sites that efficiently immobilize trace metals and contaminants alike. However, under reducing conditions, FeRB mediate the reductive dissolution of BIOS and in turn lead to the remobilization of associated contaminants. Conversely, contaminants may become immobilized by secondary iron minerals that form from the metabolic activity of FeRB. Therefore, determining the factors that influence the reactivity of BIOS, as well as the formation of secondary iron minerals is of critical importance to develop a better understanding of the geochemical cycling of iron and in turn the transport of contaminants in the environment. This thesis investigated (1) the impact of simulated diagenesis (ageing for ~5 years at 4ºC) on the mineral stability and reactivity of BIOS towards reduction by Shewanella putrefaciens CN32, (2) the effects of phosphate at an environmentally relevant (10µM) and excess (3.9mM) concentration on the rates and extent of microbial reduction of synthetic 2-line ferrihydrite and BIOS, as well as the formation of secondary iron minerals, and (3) the impact of sterilization by γ-irradiation on the mineral stability and reactivity of BIOS. It was found that simulated diagenesis did not affect the mineralogical composition of BIOS but significantly lowered the reactivity of BIOS towards microbial reduction. The concentration of phosphate was found to have contrasting effects on the rates of reduction of ferrihydrite and BIOS, but in general, excess concentration of phosphate enhanced the extent of Fe(III) reduction. The formation of a specific secondary iron mineral was also found to depend on the concentration of phosphate, as well as, in the case for BIOS, the presence of intermixed cell derived organic matter. γ-irradiation did not alter the mineralogy and reactivity of BIOS towards microbial reduction, and it was concluded to be a suitable technique to sterilize BIOS.

Microorganisms control many processes pertinent to the stability of radwaste inventories in nuclear storage and disposal facilities. Furthermore, numerous subsurface bacteria, such as Shewanella spp. have the ability to couple the oxidation of organic matter to the reduction of a range of metals, anions and radionuclides, thus providing the potential for the use of such versatile species in the bioremediation of radionuclide contaminated land. However, the organisms promoting these processes will likely be subject to significant radiation doses. Hence, the impact of acute doses of ionizing radiation on the physiological status of a key Fe(III)-reducing organism, Shewanella oneidensis, was assessed. FT-IR spectroscopy and MALDI-TOF-MS suggested that the metabolic response to radiation is underpinned by alterations to proteins and lipids. Multivariate statistical analysis indicated that the phenotypic response was somewhat predictable although dependent upon radiation dose and stage of recovery. In addition to the cellular environment, the impact of radiation on the extracellular environment was also assessed. Gamma radiation activated ferrihydrite and the usually recalcitrant hematite for reduction by S. oneidensis. TEM, SAED and Mössbauer spectroscopy revealed that this was a result of radiation induced changes to crystallinity. Despite these observations, environments exposed to radiation fluxes will be much more complex, with a range of electron acceptors, electron donors and a diverse microbial community. In addition, environmental dose rates will be much lower than those used in previous experiments. Sediment microcosms irradiated over a two month period at chronic dose rates exhibited enhanced Fe(III)-reduction despite receiving potentially lethal doses. The microbial ecology was probed throughout irradiations using pyrosequencing to reveal significant shifts in the microbial communities, dependent on dose and availability of organic electron donors. The radiation tolerance of an algal contaminant of a spent nuclear fuel pond was also assessed. FT-IR spectroscopy revealed a resistant phenotype of Haematococcus pluvialis, whose metabolism may be protected by the radiation induced production of an astaxanthin carotenoid. The experiments of this thesis provide evidence for a range of impacts of ionizing radiation on microorganisms, including the potential for radiation to provide the basis for novel ecosystems. These results have important implications to the long-term storage of nuclear waste and the geomicrobiology of nuclear environments.

京都大学 / 0048 / 新制・課程博士 / 博士(農学) / 甲第22507号 / 農博第2411号 / 新制||農||1078(附属図書館) / 学位論文||R2||N5287(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 植田 充美, 教授 山口 信次郎 / 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21161号 / 農博第2287号 / 新制||農||1060(附属図書館) / 学位論文||H30||N5135(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

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A dissertation is presented on the bioreduction of hematite (α-Fe2O3) nanoparticles. The study shows that an alternative extracellular electron transfer mechanism other than the classical 'direct-contact' mechanism may be simultaneously employed by Shewanella oneidensis MR-1 during solid-phase metal reduction. This conclusion is supported by analysis of the bioreduction kinetics of hematite nanoparticles coupled with microscopic investigations of cell-mineral interactions. The reduction kinetics of metal-oxide nanoparticles were examined to determine how S. oneidensis utilizes these environmentally-relevant solid-phase electron acceptors. Nanoparticles involved in geochemical reactions show different properties relative to larger particles of the same phase, and their reactivity is predicted to change as a function of size. To demonstrate these size-dependent effects, the surface area normalized reduction rates of hematite nanoparticles by S. oneidensis MR-1 with lactate as the sole electron donor were measured. As evident from whole cell TEM analysis, the mode of nanoparticle adhesion to cells is different between the more aggregated, pseudo-hexagonal to irregular shaped 11 nm, 12 nm, 99 nm and the less aggregated 30 nm and 43 nm rhombohedral particles. The 11 nm, 12 nm and 99 nm particles show less cell contact and coverage than the 30 nm and 43 nm particles but still show significant rates of reduction. This leads to the provisional speculation that S. oneidensis MR-1 employs a pathway of indirect electron transfer in conjunction with the direct-contact pathway, and the relative importance of the mechanism employed depends upon aggregation level and the shape of the particles or crystal faces exposed. In accord with the proposed increase in electronic band-gap for hematite nanoparticles, the smallest particles (11 nm) exhibit one order of magnitude decrease in reduction when compared with larger (99 nm) particles, and the 12 nm rates fall in between these two. This effect may also be due to the passivation of the mineral and cell surfaces by Fe(II), or decreasing solubility due to decrease in size. / Ph. D.

The concomitant occurrence and reported discrepant behavior of uranium and arsenic in water bodies is a major health and environmental concern. This study combined batch and column experiments, hydrogeochemical simulations and XAFS spectroscopy to uncover the exchange mechanisms governing uranium fate between water and scrap metallic iron, minerals and Shewanella putrefaciens surfaces in the presence of arsenic. The main results suggest that both water chemistry and the solid phase composition influence uranium fate in the presence of arsenic. The importance of uranyl-arsenate species as a major control of uranium behavior in the presence of arsenic is shown. The toxicity of arsenic and the presence of nitrate are interpreted as limiting factors of the enzymatic reduction of both toxins. Besides, XANES fingerprinting and EXAFS modeling have confirmed precipitation/co-precipitation of uranyl-arsenates as a major mechanism controlling uranium behavior in the presence of arsenic.

The concomitant occurrence and reported discrepant behavior of uranium and arsenic in water bodies is a major health and environmental concern. This study combined batch and column experiments, hydrogeochemical simulations and XAFS spectroscopy to uncover the exchange mechanisms governing uranium fate between water and scrap metallic iron, minerals and Shewanella putrefaciens surfaces in the presence of arsenic. The main results suggest that both water chemistry and the solid phase composition influence uranium fate in the presence of arsenic. The importance of uranyl-arsenate species as a major control of uranium behavior in the presence of arsenic is shown. The toxicity of arsenic and the presence of nitrate are interpreted as limiting factors of the enzymatic reduction of both toxins. Besides, XANES fingerprinting and EXAFS modeling have confirmed precipitation/co-precipitation of uranyl-arsenates as a major mechanism controlling uranium behavior in the presence of arsenic.