Observation of Acoustically Induced Dressed States of Rare-Earth Ions.

Acoustically induced dressed states of long-lived erbium ions in a crystal are demonstrated. These states are formed by rapid modulation of two-level systems via strain induced by surface acoustic waves whose frequencies exceed the optical linewidth of the ion ensemble. Multiple sidebands and the reduction of their intensities appearing near the surface are evidence of a strong interaction between the acoustic waves and the ions. This development allows for on-chip control of long-lived ions and paves the way to highly coherent hybrid quantum systems with telecom photons, acoustic phonons, and electrons.

Microbially produced fertilizer provides rhizobacteria to hydroponic tomato roots by forming beneficial biofilms.

Hydroponic cultivation of Solanum lycopersicum (tomato) is important, and high tomato production depends on the use of nitrogen and phosphate fertilizers. We had developed a microbial fertilizer (MF), which is mainly composed of nitrate. To investigate the effect of MF on plant growth, hydroponic tomato was grown with MF or commercial inorganic fertilizer (IF), and the microbiomes of the rhizosphere and the liquid phase were analyzed by confocal microscopy and high-throughput sequencing. Plant biomass and biofilm formation were increased by growth in MF compared to IF. The microbial community structures of tomato roots and hydroponic water differed between the two conditions, and three operational taxonomic units (OTUs) dominated in plants grown with MF. The three OTUs were related to Rudaea spp., Chitinophaga spp., and Stenotrophobacter terrae, which are reported to be disease-suppressive epiphytic or endophytic microbes of plant roots. Because these three OTUs also predominated in the MF itself, they were likely provided to the rhizosphere or endophytic environments of tomato roots via hydroponic water. KEY POINTS: • Microbial fertilizer for hydroponic growth enhanced biofilm formation on tomato root. • Microbial fertilizer contains tomato-root epiphytic or endophytic microbes. • Microbial fertilizer provided beneficial microbes to the rhizosphere and endophytic environments of tomato roots via hydroponic water.

Epitaxial single-crystal rare-earth oxide in horizontal slot waveguide for silicon-based integrated active photonic devices.

We have epitaxially grown high-quality single-crystal rare-earth oxide thin films, including Gd2O3 and erbium-incorporated (ErGd)2O3, on silicon-on-insulator substrate, and investigated their optical properties when embedded in horizontal slot waveguides. (ErGd)2O3 with an erbium concentration in the mid-1021 cm-3 range shows well-resolved Stark-split photoluminescence emission peaks in the telecommunications band and a photoluminescence lifetime-concentration product as large as 2.67×1018 s·cm-3 at room-temperature. Using these materials, horizontal slot waveguides with strong optical confinement in low-refractive-index rare-earth oxide layers, have been fabricated for silicon-based integrated active photonic devices. Thanks to the strong light-matter interaction, a large waveguide modal absorption of 88 dB/cm related to erbium ions is achieved, leading to a large potential optical gain. Intense emissions from the waveguides are also observed, with a radiation efficiency on the order of 10-4. These results indicate that a combination of epitaxial rare-earth oxide thin films and horizontal slot waveguides provides a promising platform for light amplification and generation on silicon.

Process Description of an Unconventional Biofilm Formation by Bacterial Cells Autoagglutinating through Sticky, Long, and Peritrichate Nanofibers.

In this study, we elucidated the formation process of an unconventional biofilm formed by a bacterium autoagglutinating through sticky, long, and peritrichate nanofibers. Understanding the mechanisms of biofilm formation is essential to control microbial behavior and improve environmental biotechnologies. Acinetobacter sp. Tol 5 autoagglutinate through the interaction of the long, peritrichate nanofiber protein AtaA, a trimeric autotransporter adhesin. Using AtaA, without cell growth or extracellular polymeric substances production, Tol 5 cells quickly form an unconventional biofilm. The process forming this unconventional biofilm started with cell-cell interactions, proceeded to cell clumping, and led to the formation of large cell aggregates. The cell-cell interaction was described by Derjaguin-Landau-Verwey-Overbeek (DLVO) theory based on a new concept, which considers two independent interactions between two cell bodies and between two AtaA fiber tips forming a discontinuous surface. If cell bodies cannot collide owing to an energy barrier at low ionic strengths but approach within the interactive distance of AtaA fibers, cells can agglutinate through their contact. Cell clumping proceeds following the cluster-cluster aggregation model, and an unconventional biofilm containing void spaces and a fractal nature develops. Understanding its formation process would extend the utilization of various types of biofilms, enhancing environmental biotechnologies.

Design, application, and microbiome of sulfate-reducing bioreactors for treatment of mining-influenced water.

Sulfate-reducing bioreactors, also called biochemical reactors, represent a promising option for passive treatment of mining-influenced water (MIW) based on similar technology to aerobic/anaerobic-constructed wetlands and vertical-flow wetlands. MIW from each mine site has a variety of site-specific properties related to its treatment; therefore, design factors, including the organic substrates and inorganic materials packed into the bioreactor, must be tested and evaluated before installation of full-scale sulfate-reducing bioreactors. Several full-scale sulfate-reducing bioreactors operating at mine sites provide examples, but holistic understanding of the complex treatment processes occurring inside the bioreactors is lacking. With the recent introduction of high-throughput DNA sequencing technologies, microbial processes within bioreactors may be clarified based on the relationships between operational parameters and key microorganisms identified using high-resolution microbiome data. In this review, the test design procedures and precedents of full-scale bioreactor application for MIW treatment are briefly summarized, and recent knowledge on the sulfate-reducing microbial communities of field-based bioreactors from fine-scale monitoring is presented.Key points• Sulfate-reducing bioreactors are promising for treatment of mining-influenced water.• Various design factors should be tested for application of full-scale bioreactors.• Introduction of several full-scale passive bioreactor systems at mine sites.• Desulfosporosinus spp. can be one of the key bacteria within field-based bioreactors.

Microbial community in an anaerobic membrane bioreactor and its performance in treating organic solid waste under controlled and deteriorated conditions.

The adoption of anaerobic membrane bioreactors (AnMBRs) for organic solid waste management is important for the recovery of energy and high-quality treated water. However, few studies have focused on AnMBR treatment of high-strength organic solid waste and the microorganisms involved under deteriorated operating conditions. In the present study, a 15-L bench-scale AnMBR was operated using a model slurry of high-strength organic solid waste with the organic loading rate (OLR) increasing from 2.3 g chemical oxygen demand (COD) L-1 day-1 (represented as a controlled condition) to 11.6 g COD L-1 day-1 (represented as a deteriorated condition), and microbial community dynamics over 120 days of operation were analyzed. The abundances of methanogens and bacteria that were dominant under the controlled condition decreased as a result of both high organic loading and sludge withdrawal under the deteriorated condition and did not recover thereafter. Instead, numbers of putative volatile fatty acid (VFA)-producing bacterial operational taxonomic units (OTUs) related to the genus Prevotella increased rapidly, reaching a relative abundance of 43.2%, leading to the deterioration of methanogenic AnMBR operation. Considering that the sequences of these OTUs exhibited relatively low sequence identity (91-95%) to those of identified Prevotella species, the results strongly suggest that the accumulation of VFAs by novel VFA-producing bacteria in the digestion sludge promotes the disruption of the methanogen community under deteriorated conditions.

Desulfosporosinus spp. were the most predominant sulfate-reducing bacteria in pilot- and laboratory-scale passive bioreactors for acid mine drainage treatment.

Five types of sulfate-reducing passive bioreactors with rice bran as substrate were operated at three different mine sites under various operating conditions to investigate and compare the dominant sulfate-reducing bacteria (SRBs) involved in acid mine drainage (AMD) treatment. In all bioreactors, AMD was properly treated under the national effluent standard of Japan when 16 samples in total were taken from different depths of the bioreactors at different sampling times. Analysis of the microbiomes in the five bioreactors by Illumina sequencing showed that Desulfosporosinus spp. were dominant SRBs in all bioreactors (the relative abundances were ~ 26.0% of the total population) regardless of reactor configurations, sizes, and operating conditions. This genus is known to comprise spore-forming, acid-tolerant, and oxygen-resistant SRBs with versatile metabolic capabilities. Microbial populations of AMD water and soil samples (as inocula) from the respective mine sites were also analyzed to investigate the origin of the genus Desulfosporosinus. Desulfosporosinus spp. were detectable in most AMD water samples, even at low relative abundances (0.0025 to 0.0069% of total AMD population), suggesting that the genus Desulfosporosinus is present within the AMD water that flows into the bioreactor. These data strongly imply that the passive treatment system is a versatile and widely applicable process for AMD treatment.

Environmental factors that shape biofilm formation.

Cells respond to the environment and alter gene expression. Recent studies have revealed the social aspects of bacterial life, such as biofilm formation. Biofilm formation is largely affected by the environment, and the mechanisms by which the gene expression of individual cells affects biofilm development have attracted interest. Environmental factors determine the cell's decision to form or leave a biofilm. In addition, the biofilm structure largely depends on the environment, implying that biofilms are shaped to adapt to local conditions. Second messengers such as cAMP and c-di-GMP are key factors that link environmental factors with gene regulation. Cell-to-cell communication is also an important factor in shaping the biofilm. In this short review, we will introduce the basics of biofilm formation and further discuss environmental factors that shape biofilm formation. Finally, the state-of-the-art tools that allow us investigate biofilms under various conditions are discussed.

A case of angioleiomyoma in the buccal space.

Angioleiomyoma in the buccal space is a less common benign neoplasm. To the best of our knowledge, only two cases have been described. We herein describe a new case of angioleiomyoma in the buccal space of a 45-year-old Japanese woman. No specific features were observed on clinical examination or ultrasonography. With an initial diagnosis of an ectopic lymph node or benign tumor, excision via the oral cavity was performed under local anesthesia. Healing was uneventful. Immunohistochemical examination revealed that the excised specimen was progesterone receptor-positive and estrogen receptor-negative.

Low concentrations of ethanol stimulate biofilm and pellicle formation in Pseudomonas aeruginosa.

Biofilms are communities of surface-attached microbial cells that resist environmental stresses. In this study, we found that low concentrations of ethanol increase biofilm formation in Pseudomonas aeruginosa PAO1 but not in a mutant of it lacking both Psl and Pel exopolysaccharides. Low concentrations of ethanol also increased pellicle formation at the air-liquid interface.

Analysis of genes for succinoyl trehalose lipid production and increasing production in Rhodococcus sp. strain SD-74.

Succinoyl trehalose lipids (STLs) are promising glycolipid biosurfactants produced from n-alkanes that are secreted by Rhodococcus species bacteria. These compounds not only exhibit unique interfacial properties but also demonstrate versatile biochemical actions. In this study, three novel types of genes involved in the biosynthesis of STLs, including a putative acyl coenzyme A (acyl-CoA) transferase (tlsA), fructose-bisphosphate aldolase (fda), and alkane monooxygenase (alkB), were identified. The predicted functions of these genes indicate that alkane metabolism, sugar synthesis, and the addition of acyl groups are important for the biosynthesis of STLs. Based on these results, we propose a biosynthesis pathway for STLs from alkanes in Rhodococcus sp. strain SD-74. By overexpressing tlsA, we achieved a 2-fold increase in the production of STLs. This study advances our understanding of bacterial glycolipid production in Rhodococcus species.

Three-dimensional visualization of mixed species biofilm formation together with its substratum.

Biofilms, such as dental plaque, are aggregates of microorganisms attached to a surface. Thus, visualization of biofilms together with their attached substrata is important in order to understand details of the interaction between them. However, so far there is limited availability of such techniques. Here, non-invasive visualization of biofilm formation with its attached substratum by applying the previously reported technique of continuous-optimizing confocal reflection microscopy (COCRM) is reported. The process of development of oral biofilm together with its substratum was sequentially visualized with COCRM. This study describes a convenient method for visualizing biofilm and its attached surface.

Sensitivity of human dental pulp cells to eighteen chemical agents used for endodontic treatments in dentistry.

To determine the adverse effects against human dental pulp tissue, the sensitivity of human dental pulp cells (D824 cells) to 18 chemical agents used for endodontic treatments in dentistry was examined. The cytotoxicity, as determined by a decrease in colony-forming ability of cells treated with the chemical agents, increased as the concentration increased. As a quantitative measure of the cytotoxic effect, LC(50), the concentration which induces a 50% lethality, was extrapolated from the concentration-response curves. The rank of the chemical agents according to their cytotoxic effect (LC(50)) was sodium arsenite > formaldehyde > hydrogen peroxide > zinc oxide > thymol ≈ iodoform ≈ eugenol > guaiacol > ethylenediaminetetraacetic acid ≈ iodine > procaine > lidocaine ≈ chloramphenicol ≈ m-cresol > calcium hydroxide ≈ sodium hypochlorite ≈ phenol ≈ p-phenolsulfonic acid. To compare the cytotoxicity and the levels of apoptosis and mRNA expression of five genes related to the function of dental pulp tissue, D824 cells treated with the LC(50) concentrations of chemical agents were assayed by the TUNEL method and quantitative reverse transcription polymerase chain reaction analysis, respectively. The inducibility of apoptotic cells and the level of mRNA expression of the genes varied with the chemical agents, indicating that both effects occurred independent of the rank of cytotoxic effect of the chemical agents. The results not only provide information concerning cytotoxicity of various chemical agents to human dental pulp cells, but also show an insight into the diversity of the pharmacodynamic action of the chemical agents.

Evaluating the Optimal Oil Concentrations in the Startup Performance of a Membrane Bioreactor Treating Oily Noodle-soup Wastewater.

The discharge of high-strength oily wastewater adversely affects the environment; therefore, the treatment of wastewater containing fats, oils, and grease from the food industry is of importance. In this study, we used a membrane bioreactor (MBR) to treat Ramen noodle-soup wastewater, and we evaluated the optimal oil concentration in the wastewater for the startup of the MBR treatment in winter and summer. The MBR system had a sufficient startup in both seasons when fed with a 20-fold dilution of the original oily wastewater, containing approximately 950 to 1,200 mg/L oil and approximately 3,000 to 4,400 mg/L biological oxygen demand (BOD; BOD-SS load of 0.1 to 0.2 kg/kg/d). The reactor performance in winter were relatively stable during the operation. While, activated sludge microbes in summer were not highly active with a 40-fold dilution of wastewater, because of the decreased mixed liquor suspended solid concentration during the operation period. Population shifts in the sludge microbiome with increasing oil concentrations were analyzed using high-throughput sequencing, and the relative abundance of operational taxonomic units belonging to the phylum Bacteroidetes were highest in both winter and summer when fed with 20-fold dilution of the wastewater. In particular, the family Chitinophagaceae was dominant, with relative abundances of 13.5% in winter and 5.1% in summer, suggesting that this family may play important roles in the startup of a MBR treating the wastewater.

Microscopic evidence of sandstone deterioration and damage by fungi isolated from the Angkor monuments in simulation experiments.

The Angkor monuments have been registered on the World Cultural Heritage List of UNESCO, while the buildings built mostly of sandstone are suffering from serious deterioration and damage. Microorganisms are one of the leading causes for the sandstone deterioration. Identification of the mechanisms underlying the biodeterioration is of significance because it reveals the biochemical reaction involved so that effective conservation and restoration of cultural properties can be achieved. In this study, the fungal colonization and biodeterioration of sandstone in simulation experiments were examined using confocal reflection microscopy (CRM) and scanning electron microscopy-energy dispersive X-ray spectroscopy (SEM-EDS). Aspergillus sp. strain AW1 and Paecilomyces sp. strain BY8 isolated from the deteriorated sandstone of Angkor Wat and Bayon of Angkor Thom, respectively, were inoculated and incubated with the sandstone used for construction of Angkor Wat. With CRM, we could visualize that strain AW1 tightly attached to and broke in the sandstone with extension of the hyphae. Quantitative imaging analyses showed that the sandstone surface roughness increased and the cavities formed under the fungal hyphae deepened during the incubation of strains AW1 and BY8. These highlighted that the massive growth of fungi even under the culture conditions was associated with the cavity formation of the sandstone and its expansion. Furthermore, SEM-EDS indicated the flat and Si-rich materials, presumably quartz and feldspar, were found frequently at the intact sandstone surface. But the flatness was lost during the incubation, possibly due to the detachment of the Si-rich mineral particles by the fungal deterioration. Consequently, this study proposed a biodeterioration model of the sandstone in that the hyphae of fungi elongated on the surface of the sandstone to penetrate into the soft and porous sandstone matrix, damaging the matrix and gradually destabilize the hard and Si-rich minerals, such as quartz and feldspar, to the collapse and cavities.

Startup performance and microbial composition of a pilot-scale rapid sand filter for the treatment of manganese-containing mine water.

The inexpensive removal of soluble manganese [Mn(II)] from mine water that contains large quantities of Mn(II) should be prioritized given that large quantities of alkaline reagents are typically used in the chemical treatment of Mn-rich water from abandoned mines. Rapid sand filter (RSF) systems are widely used as a cost-effective technology in drinking water treatment processes to remove iron and Mn from groundwater. Here, we applied a pilot-scale RSF to treat mine water with a neutral pH and containing approximately 22 mg/L of Mn(II). Following a lag phase from its startup (day 1-day 26), Mn removal rates increased to approximately 40% for around 1 month (day 27-day 55) without the use of alkaline reagents but did not increase during further operation. Quantitative elemental analysis revealed Mn oxides on the sand filters during the Mn removal period. The bacterial communities on the RSFs, recorded on day 42 and day 85, were characterized and compared using 16S rRNA gene amplicon sequencing. Although the well-known Mn-oxidizing bacteria (MOB) were not listed among the ten most dominant operational taxonomic units (OTUs) on the sand filters (relative abundances: >0.68%), a significant increase in the OTUs related to well-known alphaproteobacterial MOB, such as Pedomicrobium spp., were observed during the period.

Evaluation of dye decolorization using anaerobic granular sludge from an expanded granular sludge bed based on spectrometric and microbiome analyses.

The decolorization of 11 dyes by granular sludge from an anaerobic expanded granular sludge bed (EGSB) reactor was evaluated. Biological decolorization of Reactive Red 21, 23, and 180, and Reactive Yellow 15, 17, and 23 in model textile wastewater was observed for the first time after a 7-day incubation (over 94% decolorization). According to the sequencing analysis of 16S rRNA gene amplicons from EGSB granular sludge, the operational taxonomic unit related to Paludibacter propionicigenes showed the highest increase in relative abundance ratios in the presence of dyes (7.12 times on average over 11 dyes) compared to those without dyes.

Metabolic implications for predatory and parasitic bacterial lineages in activated sludge wastewater treatment systems.

Deciphering unclear microbial interactions is key to improving biological wastewater treatment processes. Microbial predation and parasitism in wastewater treatment ecosystems are unexplored survival strategies that have long been known and have recently attracted attention because these interspecies interactions may contribute to the reduction of excess sludge. Here, microbial community profiling of 600 activated sludge samples taken from six industrial and one municipal wastewater treatment processes (WWTPs) was conducted. To identify the shared lineages in the WWTPs, the shared microbial constituents were defined as the family level taxa that had ≥ 0.1% average relative abundance and detected in all processes. The microbial community analysis assigned 106 families as the shared microbial constituents in the WWTPs. Correlation analysis showed that 98 of the 106 shared families were significantly correlated with total carbon (TC) and/or total nitrogen (TN) concentrations, suggesting that they may contribute to wastewater remediation. Most possible predatory or parasitic bacteria belonging to the phyla Bdellovibrionota, Myxococcota, and Candidatus Patescibacteria were found to be the shared families and negatively correlated with TC/TN; thus, they were frequently present in the WWTPs and could be involved in the removal of carbon/nitrogen derived from cell components. Shotgun metagenome-resolved metabolic reconstructions indicated that gene homologs associated with predation or parasitism are conserved in the Bdellovibrionota, Myxococcota, and Ca. Patescibacteria genomes (e.g., host interaction (hit) locus, Tad-like secretion complexes, and type IV pilus assembly proteins). This study provides insights into the complex microbial interactions potentially linked to the reduction of excess sludge biomass in these processes.

Optimal start-up conditions for the efficient treatment of acid mine drainage using sulfate-reducing bioreactors based on physicochemical and microbiome analyses.

Typically, sulfate-reducing bioreactors used to treat acid mine drainage (AMD) undergo an initial incubation period of a few weeks to acclimatize sulfate-reducing bacteria (SRB), although necessity of this preincubation has rarely been evaluated. To reduce time and economic cost, we developed an SRB acclimatization method using the continuous flow of AMD into bioreactors fed with rice bran, and compared with the conventional acclimatization method. We found that the SRB sufficiently acclimatized without the preincubation phase. Furthermore, we examined the performance and SRB communities in bioreactors operated for >200 days under seven different conditions, in which the amount of rice bran added and hydraulic retention times (HRTs) were varied. A comparison of the various bioreactor conditions revealed that the lowest rice bran amount (50 g) and the shortest HRT (6 h) caused a deterioration in reactor performance after day 144 and 229, respectively. In both cases, relatively aerobic environments developed due to the lack of organic matter seemed to inhibit sulfate reduction. Of the conditions tested, operation of the bioreactors with 200 g of rice bran and an HRT of 12.5 h was the most effective in treating AMD, showing a sulfate reduction rate of 20.7-77.9% during days 54-242. DATA AND MATERIALS AVAILABILITY: All data needed to evaluate the conclusions of this study are presented in the paper and/or the appendix.

Aqueous mechano-bactericidal action of acicular aragonite crystals.

Nanoneedle structures on dragonfly and cicada wing surfaces or black silicon nanoneedles demonstrate antibacterial phenomena, namely mechano-bactericidal action. These air-exposed, mechano-bactericidal surfaces serve to destroy adherent bacteria, but their bactericidal action in the water is no precedent to report. Calcium carbonate easily accumulates on solid surfaces during long-term exposure to hard water. We expect that aragonite nanoneedles, in particular, which grow on TiO2 during the photocatalytic treatment of calcium-rich groundwater, exhibit mechano-bactericidal action against bacteria in water. Here, we showed that acicular aragonite modified on TiO2 ceramics prepared from calcium bicarbonate in mineral water by photocatalysis exhibits mechanical bactericidal activity against E. coli in water. Unmodified, calcite-modified and aragonite-modified TiO2 ceramics were exposed to water containing E. coli (in a petri dish), and their bactericidal action over time was investigated under static and agitated conditions. The surfaces of the materials were observed by scanning electron microscopy, and the live/dead bacterial cells were observed by confocal laser scanning microscopy. As a result, the synergistic bactericidal performance achieved by mechano-bactericidal action and photocatalysis was demonstrated. Aragonite itself has a high biological affinity for the human body different from the other whisker-sharpen nanomaterials, therefore, the mechano-bactericidal action of acicular aragonite in water is expected to inform the development of safe water purification systems for use in developing countries.