Satoshi Mitsunobu

Geomicrobiology of copper (Cu) and iron (Fe) in circumneutral‐pH drainage from a Japanese Cu mine was investigated, with a focus on Fe(II)‐oxidising microorganisms. Cu in the drainage was rapidly removed through Fe(II) oxidation and subsequent Fe(III) biomineralisation. The resulting Fe(III) biomineral‐rich sediment contained up to ~2 wt% Cu, a percent‐level high content. XAFS and XRD analyses directly demonstrated that Cu was predominantly associated with poorly crystalline Fe(III) oxyhydroxides. The microbial community in the drainage was dominated by chemolithotrophic Fe(II)‐oxidising bacteria of family Gallionellaceae (33.8%), suggesting their key role in Cu and Fe biomineralisation. Using a custom‐made medium, Gallionellaceae bacteria were enriched and a representative strain TK5 was isolated. 16S rRNA gene analysis revealed that TK5 was almost identical to the most abundant taxon at the site and likely represents a novel species of genus Sideroxyarcus . Physiological and genomic analyses confirmed its Fe(II) oxidation ability and a relatively high Cu(II) tolerance (up to 50 μM), which is about 20‐fold higher than on‐site Cu concentration. Strain TK5 is the first known Cu‐tolerant Fe(II)‐oxidising Gallionellaceae isolate. Batch experiments demonstrated that TK5 effectively promoted Cu deposition via Fe(III) biomineralisation. This study highlights the potential of Fe(II)‐oxidising bacteria for Cu bioremediation and biomineralisation under circumneutral‐pH conditions.

Chemolithotrophic neutrophilic iron (Fe)-oxidizing bacteria, which mainly belong to the family Gallionellaceae, universally prevail in terrestrial environments changing Fe cycling. However, they are typically recognized as difficult-to-culture microbes. Despite efforts, there are few Fe(II)-oxidizing lithotroph isolates; hence, their physiological and ecological knowledge remains limited. This limitation is largely owing to difficulties in their cultivation, and we hypothesize that the difficulty exists because substrate and mineral concentrations in the cultivation medium are not tuned to a specific environmental condition under which these organisms live. To address this hypothesis, this study proposes a novel custom-made medium approach for chemolithotrophic Fe(II)-oxidizing bacteria; a method that manipulates medium components through diligent analysis of field environment. A new custom-made medium simulating energy substrates and nutrients under the field condition was prepared by modifying both chemical composition and physical setup in the glass-tube medium. In particular, the modification of the physical setup in the tube had a significant effect on adjusting dissolved Fe(II) and O2 concentrations to the field environment. Using the medium, Gallionellaceae members were successfully enriched and a new Gallionellaceae species was isolated from a natural hot spring site. Compared with conventional medium, the custom-made medium has significantly higher ability in enriching Gallionellaceae members.

In invertebrates inhabiting hydrothermal vent areas, hypotaurine, a precursor of taurine, is thought to mitigate the toxicity of hydrogen sulfide in vent fluids. Information about hypotaurine synthesis pathways in invertebrates is limited, although two pathways, the cysteamine [2-aminoethanethiol (AET)] pathway and the cysteine sulfinate (CSA) pathway are known in mammals. In this study, we cloned a cDNA encoding AET dioxygenase (ADO), the central enzyme of the AET pathway, from the vent mussel Bathymodiolus septemdierum. In the encoded protein (BsADO), functionally important residues, including metal-binding histidines, are conserved. In maximum likelihood phylogenetic analysis, BsADO clustered with ADOs of other invertebrates. By reverse transcription PCR, BsADO mRNA was detected in all tissues examined at similar levels, suggesting that its function is distinct from that of the CSA pathway, predominantly expressed in the gill. BsADO with a His tag, expressed in Escherichia coli in the presence of Fe²⁺, converted AET to hypotaurine, but BsADO expressed in the absence of iron exhibited lower activity. BsADO was active from pH 8 to 11, and from 0 °C to 37 °C, with a peak at 20 °C. This is the first functional characterization of ADO in marine invertebrates.

Pyrite is one of the most common Fe-S minerals found in submarine hydrothermal environments. Previous studies demonstrated that the Fe-S mineral can be a suitable host for Fe(II)-oxidizing microbes in hydrothermal environments; however, the details of microbial Fe(II) oxidation processes with Fe-S mineral alteration are not well known.

The upper oceanic crust is mainly composed of basaltic lava that constitutes one of the largest habitable zones on Earth. However, the nature of deep microbial life in oceanic crust remains poorly understood, especially where old cold basaltic rock interacts with seawater beneath sediment. Here we show that microbial cells are densely concentrated in Fe-rich smectite on fracture surfaces and veins in 33.5- and 104-million-year-old (Ma) subseafloor basaltic rock. The Fe-rich smectite is locally enriched in organic carbon. Nanoscale solid characterizations reveal the organic carbon to be microbial cells within the Fe-rich smectite, with cell densities locally exceeding 10¹⁰ cells/cm³. Dominance of heterotrophic bacteria indicated by analyses of DNA sequences and lipids supports the importance of organic matter as carbon and energy sources in subseafloor basalt. Given the prominence of basaltic lava on Earth and Mars, microbial life could be habitable where subsurface basaltic rocks interact with liquid water.

Ferromanganese minerals are widely distributed in subseafloor sediments and on the seafloor in oceanic abyssal plains. Assessing their input, formation and preservation is important for understanding the global marine manganese cycle and associated trace elements. However, the extent of ferromanganese minerals buried in subseafloor sediments remains unclear. Here we show that abundant (10⁸–10⁹ particles cm⁻³) micrometer-scale ferromanganese mineral particles (Mn-microparticles) are found in the oxic pelagic clays of the South Pacific Gyre (SPG) from the seafloor to the ~100 million-year-old sediments above the basement. Three-dimensional micro-texture, and major and trace element compositional analyses revealed that these Mn-microparticles consist of poorly crystalline ferromanganese oxides precipitating from bottom water. Based on our findings, we extrapolate that 1.5–8.8 × 10²⁸ Mn-microparticles, accounting for 1.28–7.62 Tt of manganese, are globally present in oxic subseafloor sediments. This estimate is at least two orders of magnitude larger than the manganese budget for nodules and crusts on the seafloor. Subseafloor Mn-microparticles thus contribute significantly to the global manganese budget.