Natsuko Hamamura

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.

We report the complete genome sequences of two antimony-oxidizing bacteria, Mesorhizobium sp. strain ANAO-SY3R2, comprising one chromosome (4.3 Mbp) and four circular plasmids, and Hydrogenophaga sp. strain ANAO-22, comprising one chromosome (5.8 Mbp) and two circular plasmids. These genome information extend our understanding of physiological versatility of antimony-transforming microorganisms.

Yaku sika deer (Cervus nippon yakushimae) are endemic to Yakushima Island, whose landscape covered with primary evergreen forest is recognized as a World Heritage Site. In this study, the rumen bacterial microbiota (RBM) of wild Yaku sika was characterized using high throughput sequencing of bacterial 16S rRNA genes combined with targeted cultivation and functional analyses. Comparative analyses of RBM datasets from other ruminant animals revealed distinct community structure among domesticated and wild ruminants. Wild Yaku sika RBM exhibited higher species richness than other sika deer (i.e. wild Ezo sika and domesticated sika deer), likely reflecting their dietary variations associated with unique ecosystem in the island. The Yaku sika RBM of high deer population density samples exhibited higher diversity and contained higher proportion of Firmicutes than those of lower density samples. Moreover, the highest abundance of tannase gene were observed in individuals from the highest population density area, consistent with the previous observation that Yaku sika in the high density areas expanded their feed to include tannin-rich unpalatable plants. This study indicated that RBM of unique wild Yaku sika contribute to the flexibility of dietary shift and thus maintaining nutritional status of Yaku sika under high density conditions.

The draft genome sequence of Halomonas sp. strain ANAO-440 contains 3,866 predicted protein-coding sequences. This strain is capable of anaerobic arsenite oxidation and encodes an arxA -type arsenite oxidase within the arxB2AB1CD gene island. This genome sequence provides valuable information regarding the physiological diversity of Arx-dependent arsenite-oxidizing microorganisms.

Cupriavidus sp. strain IK-TO18 was isolated from antimony-contaminated sediment. The draft genome sequence of the isolate contains 6,605 predicted protein-coding sequences, including genes associated with heavy metal resistance and the aerobic degradation of aromatic hydrocarbons. This sequence will provide valuable information regarding the functional versatility of the genus Cupriavidus .

Pseudomonas sp. strain SbOxS1 was isolated from stibnite mine tailing soil for its ability to oxidize antimonite. We present a draft genome sequence of strain SbOxS1, which contains 6,484 predicted protein-coding sequences. This genome information extends our understanding of the physiological versatility of antimony-transforming microorganisms.

The antimony-oxidizing Stenotrophomonas sp. strain SbOxS2 was isolated from stibnite mine tailing soil. The draft genome sequence of strain SbOxS2 comprises 4.76 Mbp with 4,211 predicted protein-coding sequences. This genome will provide useful information for characterizing the molecular mechanisms associated with heavy metal resistance within the genus Stenotrophomonas .

The climatic, biotic, and tectonic events of the Permian are amongst the most profound in Earth history. Global orogeny leading to Pangaean assembly culminated by middle Permian time, and included multiple orogenic belts in the equatorial Central Pangaean Mountains, from the Variscan-Hercynian system (east) to the Ancestral Rocky Mountains (west). Earth’s penultimate global icehouse peaked in early Permian time, transitioning to full greenhouse conditions by late Permian time, thus archiving the only example of icehouse collapse on a fully vegetated Earth. The Late Paleozoic Icehouse was the longest and most intense glaciation of the Phanerozoic, with hypothesized low-elevation glaciation posited for both eastern and western tropical Pangaea during early Permian time. Reconstructions of atmospheric composition record the lowest CO2 and highest O2 levels of the Phanerozoic, with average CO2 levels comparable to the Quaternary, rapidly warming climate. Fundamental shifts occurred in atmospheric circulation: a global megamonsoon developed and the tropics became anomalously arid with time. Extreme environments are well documented in the form of voluminous dust deposits, acid-saline lakes and groundwaters, extreme continental temperatures and aridity, and major extinctions/extirpations, ultimately culminating at the Permo-Triassic boundary with the largest extinction of Earth history.We seek to elucidate paleoclimatic conditions and forcings through the Permian at temporal scales ranging from the millennial to the Milankovitch  and beyond by acquiring continuous core in continental lowlands known to harbor stratigraphically complete records dominated by loess and lacustrine strata. We have identified sites in the western U.S. and Europe as the key sites globally to achieve our objectives, as these represent the western and eastern limits, respectively of the Pangaean tropics. Identified sites harbor arguably the most complete continental Permian sections in the paleoequatorial region, with adjacent paleo-uplands hypothesized to have hosted glaciation. We will also address the nature and character of the modern and fossil microbial biosphere, Mars-analog conditions, and exhumation histories of source regions.

In the present study, the influence of the co-contamination with various chemical forms of antimony (Sb) with arsenite (As[III]) on soil microbial communities was investigated. The oxidation of As(III) to As(V) was monitored in soil columns amended with As(III) and three different chemical forms of Sb: antimony potassium tartrate (Sb[III]-tar), antimony(III) oxide (Sb2O3), and potassium antimonate (Sb[V]). Soil microbial communities were examined qualitatively and quantitatively using 16S rDNA- and arsenite oxidase gene (aioA)-targeted analyses. Microbial As(III) oxidation was detected in all soil columns and 90-100% of added As(III) (200 μmol L-1) was oxidized to As(V) in 9 d, except in the Sb(III)-tar co-amendments that only oxidized 30%. 16S rDNA- and aioA-targeted analyses showed that the presence of different Sb chemical forms significantly affected the selection of distinct As(III)-oxidizing bacterial populations. Most of the 16S rRNA genes detected in soil columns belonged to Betaproteobacteria and Gammaproteobacteria, and some sequences were closely related to those of known As(III) oxidizers. Co-amendments with Sb(III)-tar and high concentrations of Sb2O3 significantly increased the ratios of aioA-possessing bacterial populations, indicating the enrichment of As(III) oxidizers resistant to As and Sb toxicity. Under Sb co-amendment conditions, there was no correlation between aioA gene abundance and the rates of As(III) oxidation. Collectively, these results demonstrated that the presence of different Sb chemical forms imposed a strong selective pressure on the soil bacterial community and, thus, the co-existing metalloid is an important factor affecting the redox transformation of arsenic in natural environments.

Arsenic (As) is a widely distributed toxic element in the environment and microorganisms have developed resistance mechanisms in order to tolerate it. The cellular response of the chemoorganotrophic arsenite (As[III])-oxidizing alpha-Proteobacteria, Sinorhizobium sp. strain A2, to arsenic was examined in the present study. Several proteins associated with arsenite oxidase and As resistance were shown to be accumulated in the presence of As(III). A shift in central carbon metabolism from the tricarboxylic acid pathway to glyoxylate pathway was also observed in response to oxidative stress. Our results revealed the strategy of the As(III)-oxidizing Sinorhizobium strain to mitigate arsenic toxicity and oxidative damage by multiple metabolic adaptations.