Engineering lithoheterotrophy in an obligate chemolithoautotrophic Fe(II) oxidizing bacterium

Neutrophilic Fe(II) oxidizing bacteria like Mariprofundus ferrooxydans are obligate chemolithoautotrophic bacteria that play an important role in the biogeochemical cycling of iron and other elements in multiple environments. These bacteria generally exhibit a singular metabolic mode of growth which prohibits comparative “omics” studies. Furthermore, these bacteria are considered non-amenable to classical genetic methods due to low cell densities, the inability to form colonies on solid medium, and production of copious amounts of insoluble iron oxyhydroxides as their metabolic byproduct. Consequently, the molecular and biochemical understanding of these bacteria remains speculative despite the availability of substantial genomic information. Here we develop the first genetic system in neutrophilic Fe(II) oxidizing bacterium and use it to engineer lithoheterotrophy in M. ferrooxydans, a metabolism that has been speculated but not experimentally validated. This synthetic biology approach could be extended to gain physiological understanding and domesticate other bacteria that grow using a single metabolic mode.

Hydrothermal formation of iron-oxyhydroxide chimney mounds in a shallow semi-enclosed bay at Satsuma Iwo-Jima Island, Kagoshima, Japan

Hydrothermal iron-oxyhydroxide chimney mounds (iron mounds) have been discovered in a fishing port in Nagahama Bay, located on the southwest coast of Satsuma Iwo-Jima Island, south of Kyushu Island, Japan. In the fishing port, uncovered ∼1.0-m-high iron mounds in shallow waters formed under relatively calm conditions. Typically, the fishing port has orange-colored turbid waters that mix with outer ocean waters during high tide. Colloidal iron-oxyhydroxides form due to the oxidation of ferrous iron in hydrothermal waters (pH = 5.5; temperature = 55 °C) as they mix with seawater. The mounds are made of two types of material: hard, dark brown–orange, high-density material; and soft, brownish orange–yellow, low-density material. Computed tomography scans of the harder iron mound material revealed a cabbage-like structure consisting of micropipe structures with diameters of 2–5 mm. These micropipes have relatively hard walls made of iron oxyhydroxides (FeOH) and are identified as discharge pipes. Nucleic acid staining genetic sequencing and scanning electron microscope observations suggest that the mounds formed mainly from bacterial stalks with high concentrations of FeOH colloidal matter. In the harder parts of the mounds, these “fat stalks,” which contain oxyhydroxide colloidal aggregates, are entwined and concentrated. The softer material contains twisted stalk-like structures, which are coated with FeOH colloidal particles. Deoxyribonucleic acid (DNA) examination of the iron mounds revealed the presence of iron-oxidizing bacteria, especially at the mound surface. We estimate that the iron mounds accumulated at a rate of ∼1700 tons/1000 m2/yr. This is an order of magnitude higher than the rate of FeOH sedimentation via chemical precipitation of FeOH colloids within the fishing port. This suggests that biogenic activity, resulting in the production of entwined FeOH stalks, leads to the rapid accumulation of FeOH beds and that biogenic activity within the water mass rich in FeOH colloids is an efficient means of generating thick iron-rich sedimentary sequences. As such, we propose that some ancient iron formations may have also formed through the biogenic production of FeOH stalks rather than solely through chemical sedimentation in a water mass rich in FeOH colloids. It appears that these rapidly forming biogenic FeOH iron mounds, distributed over a wide area of ocean floor, are also relatively protected from erosion and diagenetic alteration (reduction). Previous studies have reported that ancient iron formations were commonly deposited in deeper environments via direct iron oxidation from the water column in a ferruginous ocean. However, there are several hydrothermal vent inflows preserved with FeOH that would have formed appropriate redox boundary conditions in an otherwise anoxic ocean. Under these conditions, iron mound mat-type sedimentary deposits might have formed and been well preserved and affected by early diagenesis where higher heat flow occurred in the Archean ocean. The FeOH mounds in Nagahama Bay provide an example of the iron formation sedimentary environment and important information for estimating the past depositional state of iron formations.

Pedofeatures Associated to Soil Processes

As stipulated by G. Stoops, “the aim of micropedology is to contribute to solving problems related to the genesis, classification and management of soils, including soil characterization in palaeopedology and archaeology. The interpretation of features observed in thin sections is the most important part of this type of research, based on an objective detailed analysis and description” (Stoops et al. 2018). To answer such questions, two major books contributed to the comparative knowledge necessary to tackle this objective: the first one was published in 1985 and used micromorphology to distinguish between different classes of soils (Douglas and Thompson 1985); the second one is an extensive guide of more than 1000 pages to the interpretation of micromorphological features encountered in thin sections of soil (Stoops et al. 2018). The aim of this Atlas is neither to be a substitution for these books nor a way to enter directly into the interpretation of soil genesis and classification. Nonetheless, this chapter presents the imprints of major soil processes that can be easily deduced from specific features observed in thin sections. These processes involve the dynamics of (a) clay, both translocation and swelling, (b) water, such as waterlogging, evaporation, and its role as ice and frost, (c) carbonate, gypsum, and iron oxyhydroxides, and finally (d) biogeochemical reactions within the solum.

Modeling of the Phase Formation Processes on the Steel Surface Contacting with Water Medium under Conditions of Deep Geological Repository

The experimental modeling of the corrosive phase formation processes was performed under conditions approaching the initial and transitional stages of evolution of the deep geological repository (the hydrogen index of the medium lied in the range of 9–12 and a temperature was 50–70 °C). The specificity of the system of rotating disk electrode made it possible to determine the phase composition of corrosion products formed under oxidative conditions (the near surface layer, NSL) and, conditionally, reductive — on the steel surface (SL) covered by NSL, that significantly complicated the access of oxygen into the reaction area. It was determined that phase composition of the corrosion products at the pH0 values 9–11 was identical and it is regulated by the compensative action of cathodic half-reaction of oxygen reducing on the steel surface. Green Rust and magnetite or non-stoichiometric spinel ferrite characterized by coagulative type of the structure and spherical particle shape were determined as the main phases of SL. Iron oxyhydroxides — goethite and lepidocrocite were presented as the phases of NSL. Increase in the pH0 to 12 changes the chemical mechanism of the corrosion process and it leads to the formation of weak crystallized iron oxyhydroxide phases. It was proved the main phase formed under corrosion of steel at 50–70 °C was spinel ferrite. Its morphology is presented as the cubic shaped particles that evidences about condensingcrystallizing mechanism of their formation. Generally, the presence of Co2+ and Mn2+ cations does not influence on the phase formation process and the phase composition as well, whereas the iron oxyhydroxides with admixture of Mn2+ and Mn3+ oxygen compounds are dominant in the sediment compositions when they are formed in the presence of Mn7+.

Tracking high-valent surface iron species in the oxygen evolution reaction on cobalt iron (oxy)hydroxides

The oxygen evolution reaction (OER) is the bottleneck reaction of water splitting, which can be used to generate green hydrogen from renewable electricity. Cobalt iron oxyhydroxides (CoFeOxHy) are among the...