Yoshiko Okamura

Group III−V compound semiconductors are essential for electronic and optoelectronic technologies but rely on scarce and toxic elements, necessitating sustainable recovery strategies. Although microorganisms are known to mediate biomineralization of various metal compounds, their ability to form III−V−related phases remains unclear. This study aimed to determine whether microbial consortia can simultaneously accumulate group III (In, Ga) and group V (As) elements and form precursor mineral phases. Marine-derived microbial consortia were enriched in the presence of In3+, Ga3+, and arsenate. Two consortia, IGA-1 and IGA-2, were selected based on their high uptake efficiencies. Mineral formation was analyzed using TEM, EDS, and ICP-OES, and crystallinity was evaluated before and after heat treatment. Both consortia accumulated In, Ga, and As and formed nanoscale mineral particles containing these elements. The particles were predominantly amorphous, although localized lattice fringes were observed within some particles, indicating nanoscale crystalline ordering, although the corresponding crystalline phases could not be identified. Heat treatment at ≥500°C resulted in the formation of crystalline In2O3, accompanied by arsenic loss. These results demonstrate that microbial consortia can co-concentrate group III and V elements and generate multicomponent amorphous precursor materials, highlighting their potential for the biological recovery and preprocessing of semiconductor-related elements.

Indoor microbial communities play a critical role in influencing indoor environmental quality and human health and are shaped by occupant activity, surface characteristics, and environmental conditions. While previous studies have examined these factors individually, systematic evaluations of their combined interactions, particularly involving Heating, Ventilation, and Air Conditioning (HVAC) and drainage systems, remain limited. This controlled, long-term (1.5-year) investigation assessed how human occupancy, surface moisture (dry vs. wet), aquaponics (soilless plant-aquarium systems), and environmental parameters (humidity, ventilation, and seasonal variations) influence bacterial and eukaryotic dynamics in tightly sealed residential units. Continuous air-conditioner operation without fresh-air intake led to elevated CO₂ levels during occupancy and pronounced seasonal humidity fluctuations, emphasizing the need for improved ventilation and adaptive humidity control in compact urban residences. Amplicon sequencing revealed higher microbial diversity on dry surfaces (aerosols, air-conditioner filter dust, and floor dust) than on wet surfaces (waste drains and showerheads). Wet environments supported biofilm-associated taxa adapted to moist conditions (e.g., Methylobacterium, Vermamoeba). Human occupancy significantly enriched air-conditioner filter dust with opportunistic bacteria (e.g., Finegoldia and Streptococcus), underscoring occupant-driven microbial accumulation via recirculated air. Additionally, the small-scale aquaponic system had minimal measurable influence on microbial composition at the room scale, suggesting limited aerosolization or dispersal under typical usage conditions. Indoor relative humidity was significantly correlated with microbial diversity in air systems, notably enhancing moisture-adapted taxa such as Sphingomonas during humid seasons. Seasonal variations markedly influenced eukaryotic communities (e.g., pollen influx), whereas bacterial communities were more strongly influenced by human occupancy. These findings highlight the critical role of human-driven microbial accumulation in air-conditioner filters and the distinct microbial profiles associated with dry and wet indoor surfaces. Although small-scale aquaponics demonstrated minimal room-wide microbial impact, its potential localized influence warrants further exploration. These insights offer practical guidance for targeted hygiene protocols, HVAC system maintenance, and building design strategies aimed at improving indoor microbial quality and supporting occupant health.

Next-generation sequencing has transformed the acquisition of vast amounts of genomic information, including the rapid identification of target gene sequences in metagenomic databases. However, dominant species can sometimes hinder the detection of rare bacterial species. Therefore, a highly sensitive amplification technique that can selectively amplify bacterial genomes containing target genes of interest was developed in this study. The rolling circle amplification (RCA) method can initiate amplification from a single locus using a specific single primer to amplify a specific whole genome. A mixed cell suspension was prepared using Pseudomonas fluorescens ATCC17400 (targeting nonribosomal peptide synthetase [NRPS]) and Escherichia coli (non-target), and a specific primer designed for the NRPS was used for the RCA reaction. The resulting RCA product (RCP) amplified only the Pseudomonas genome. The NRPS was successfully amplified using RCP as a template from even five cells, indicating that the single-priming RCA technique can specifically enrich the target genome using gene-specific primers. Ultimately, this specific genome RCA technique was applied to metagenomes extracted from sponge-associated bacteria, and NRPS sequences were successfully obtained from an unknown sponge-associated bacterium. Therefore, this method could be effective for accessing species-specific sequences of NRPS in unknown bacteria, including viable but non-culturable bacteria.

Heavy metals in a polluted environment are toxic to life. However, some microorganisms can remove or immobilize heavy metals through biomineralization. These bacteria also form minerals with compositions similar to those of semiconductors. Here, this bioprocess was used to fabricate semiconductors with low energy consumption and cost. Bacteria that form lead sulfide (PbS) nanoparticles were screened, and the crystallinity and semiconductor properties of the resulting nanoparticles were characterized. Bacterial consortia that formed PbS nanoparticles were obtained. Extracellular particle size ranged from 3.9 to 5.5 nm, and lattice fringes were observed. The lattice fringes and electron diffraction spectra corresponded to crystalline PbS. The X-ray diffraction (XRD) patterns of bacterial PbS exhibited clear diffraction peaks. The experimental and theoretical data of the diffraction angles on each crystal plane of polycrystalline PbS were in good agreement. Synchrotron XRD measurements showed no crystalline impurity-derived peaks. Thus, bacterial biomineralization can form ultrafine crystalline PbS nanoparticles. Optical absorption and current–voltage measurements of PbS were obtained to characterize the semiconductor properties; the results showed semiconductor quantum dot behavior. Moreover, the current increased under light irradiation when PbS nanoparticles were used. These results suggest that biogenic PbS has band gaps and exhibits the general fundamental characteristics of a semiconductor.

Nitratireductor sp. OM-1 can accumulate butenoic acid, which is a short-chain unsaturated carboxylic acid utilized for chemical products. So far, we have predicted the thioesterase gene, te, as a candidate gene for butenoic acid biosynthesis, based on comparative transcriptome analysis. To confirm the function of te, the gene transfer system in Nitratireductor sp. OM-1 was required. Thus, in this study, we used electroporation as a transformation system and pRK415, a broad host range plasmid, and optimized the conditions. As a result, a maximum transformation efficiency of 7.9 × 10⁴ colonies/µg DNA was obtained at 22.5 kV/cm. Moreover, an expression vector, pRK415-te, was constructed by insertion of te, which was successfully transferred into strain OM-1, using electroporation. The recombinant OM-1 strain produced butenoic acid at 26.7 mg/g of dried cell weight, which was a 254% increase compared to transformants harboring an empty vector. This is the first report of a gene transfer system for Nitratireductor sp., which showed that the te gene was responsible for butenoic acid production.

Marine sponge-associated bacteria are known as bio-active compound produce. We have constructed metagenome libraries of the bacteria and developed a metagenomic screening approach. Activity-based screening successfully identified novel genes and novel enzymes; however, the efficiency was only in 1 out of 10⁴ clones. Therefore, in this study, we thought that bioinformatics could help to reduce screening efforts, and combined activity-based screening with database search. Neutrophils play an important role for the immune system to recognize excreted bacterial by-products as chemotactic factors and are recruited to infection sites to kill pathogens via phagocytosis. These excreted by-products are considered critical triggers that engage the immune system to mount a defense against infection, and identifying these factors may guide developments in medicine and diagnostics. We focused on genes encoding amino acid ligase and peptide synthetase and selected from an in-house sponge metagenome database. Cell-free culture medium of each was used in a neutrophil chemiluminescence assay in luminol reaction. The clone showing maximum activity had a genomic sequence expected to produce a molecule like a phospho-N-acetylmuramyl pentapeptide by the metagenome fragment analysis.

Recently, we developed an in situ mRNA detection method termed RNase H-assisted rolling circle amplification-fluorescence in situ hybridization (RHa-RCA-FISH), which can detect even short mRNA in a bacterial cell. However, because this FISH method is sensitive to the sample condition, it is necessary to find a suitable cell permeabilization and collection protocol. Here, we demonstrate its further applicability for detecting intrinsic mRNA expression using lactic acid bacteria (LAB) as a model consortium. Our results show that this method can visualize functional gene expression in LAB cells and can be used for monitoring the temporal transition of gene expression. In addition, we also confirmed that data obtained from bulk analyses such as RNA-seq or microarray do not always correspond to gene expression in individual cells. RHa-RCA-FISH will be a powerful tool to compensate for insufficient data from metatranscriptome analyses while clarifying the carriers of function in microbial consortia. By extending this technique to capture spatiotemporal microbial gene expression at the single-cell level, it will be able to characterize microbial interactions in phytoplankton–bacteria interactions.

A Correction to this paper has been published: https://doi.org/10.1007/s10126-020-10008-1

Meta-analyses using next generation sequencing is a powerful strategy for studying microbiota; however, it cannot clarify the role of individual microbes within microbiota. To know which cell expresses what gene is important for elucidation of the individual cell’s function in microbiota. In this report, we developed novel fluorescence in situ hybridization (FISH) procedure using RNase-H-assisted rolling circle amplification to visualize mRNA of interest in microbial cells without reverse transcription. Our results show that this method is applicable to both Gram-negative and Gram-positive microbes without any noise from DNA, and it is possible to visualize the target mRNA expression directly at the single-cell level. Therefore, our procedure, when combined with data of meta-analyses, can help to understand the role of individual microbes in the microbiota.