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It is known that the quality factors (Q) of photonic crystal nanocavities vary from sample to sample due to air-hole fabrication fluctuations. In other words, for the mass production of a cavity with a given design, we need to consider that the Q can vary significantly. So far, we have studied the sample-to-sample variation in Q for symmetric nanocavity designs, that is, nanocavity designs where the positions of the holes maintain mirror symmetry with respect to both symmetry axes of the nanocavity. Here we investigate the variation of Q for a nanocavity design in which the air-hole pattern has no mirror symmetry (a so-called asymmetric cavity design). First, an asymmetric cavity design with a Q of about 250,000 was developed by machine learning using neural networks, and then we fabricated fifty cavities with the same design. We also fabricated fifty symmetric cavities with a design Q of about 250,000 for comparison. The variation of the measured Q values of the asymmetric cavities was 39% smaller than that of the symmetric cavities. This result is consistent with simulations in which the air-hole positions and radii are randomly varied. Asymmetric nanocavity designs may be useful for mass production since the variation in Q is suppressed.

SummaryThe family Methanoperedenaceae archaea mediate anaerobic oxidation of methane (AOM) in various terrestrial environments. In this study, we newly developed a high-pressure laboratory incubation system by controlling hydraulic pressure ranging from ambient to 5 MPa. Using the system, we investigated groundwater from 214- and 249-m deep boreholes at Horonobe Underground Research Laboratory, Japan, where the high and low abundances of Methanoperedenaceae archaea have been revealed by genome-resolved metagenomics, respectively. We incubated the groundwater samples amended with or without amorphous Fe(III) as an electron acceptor and 13C-labelled methane at an in-situ pressure of 1.6 MPa. After three to seven-day incubation, AOM activities were not detected from the 249-m deep groundwater but from the 214-m deep groundwater. The AOM rates were 93.7 ± 40.6 and 27.7 ± 37.5 nM/day with and without Fe(III) amendment. To clarify the differences in AOM activity between the 214- and 249-m deep groundwater samples, we characterized Fe(III) contents in suspended particulates collected by filtration. The particulates were not visible in the 249-m deep groundwater on the filter, while they were abundant and contained Fe(III)-bearing phyllosilicates in the 214-m deep groundwater. These results support the in-situ activity of Fe(III)-dependent AOM in the deep subsurface borehole.

Early seedling growth, including seedling emergence and vigor, is crucial in direct seeded rice. In this study, we examined the effects of gibberellic acid (GA3) and ethephon (ET) on the early growth of direct seeded rice, and on α-amylase activity and soluble sugar content in the seeds. Rice seeds were treated with water (control), ET, GA3, or ET+ GA3 and were allowed to grow for 21 days. The results showed that ET and GA3 synergistically improved the lengths of mesocotyl, coleoptile, mesocotyl+ coleoptile, and first leaf. Moderate synergistic effects of ET and GA3 were detected in the second and third leaves. ET+ GA3 treatment induced higher α-amylase activities during early post-germination growth, which is consistent with the longer coleoptile, mesocotyl, mesocotyl+ coleoptile, and first leaf. In addition, ET+ GA3 induced higher α-amylase activity in the seeds, and consequently, higher sucrose and glucose concentrations than other treatments. These results partially explain the regulatory mechanism underlying the synergistic interaction of ET and GA3 on rice seedling growth in terms of starch and sugar metabolism in the seeds, and this knowledge is expected to facilitate the practical use of ET and GA3 in direct seeded rice systems.

At low temperatures (18°C), seedlings of an indica rice (Oryza sativa L.) cultivar Kasalath showed symptoms of chlorosis, although the leaves of a japonica cultivar Arroz da Terra remained green. In this study, transcripts related to the chlorophyll content of rice seedlings grown at 18°C were investigated using RNA-sequencing (RNA-Seq) data for F2 crosses between cultivars Arroz da Terra and Kasalath, as well as their parental cultivars. Differential expression analysis revealed that gene ontology terms related to ‘photosynthesis’ were significantly enriched in lowly expressed genes at 18°C than at 25°C in Kasalath. However, the gene ontology terms related to ‘response to stress’ were significantly enriched in highly expressed genes at 18°C than at 25°C in Kasalath. When the F2 plants were grown at 18°C, their chlorophyll contents varied. Transcripts with expression levels related to chlorophyll content were statistically selected using RNA-Seq data from 21 F2 plants. In regression models, frequently selected genes included four photosynthetic and two stress-responsive genes. The expression values of four photosynthetic and two stress-responsive genes in high-frequency selected genes were significantly correlated with chlorophyll content not only in plants analysed using RNA-Seq but also in 95 F2 plants.

© 2018 International Society for Microbial Ecology All rights reserved. Recent single-gene-based surveys of deep continental aquifers demonstrated the widespread occurrence of archaea related to Candidatus Methanoperedens nitroreducens (ANME-2d) known to mediate anaerobic oxidation of methane (AOM). However, it is unclear whether ANME-2d mediates AOM in the deep continental biosphere. In this study, we found the dominance of ANME-2d in groundwater enriched in sulfate and methane from a 300-m deep underground borehole in granitic rock. A near-complete genome of one representative species of the ANME-2d obtained from the underground borehole has most of functional genes required for AOM and assimilatory sulfate reduction. The genome of the subsurface ANME-2d is different from those of other members of ANME-2d by lacking functional genes encoding nitrate and nitrite reductases and multiheme cytochromes. In addition, the subsurface ANME-2d genome contains a membrane-bound NiFe hydrogenase gene putatively involved in respiratory H 2 oxidation, which is different from those of other methanotrophic archaea. Short-term incubation of microbial cells collected from the granitic groundwater with 13 C-labeled methane also demonstrates that AOM is linked to microbial sulfate reduction. Given the prominence of granitic continental crust and sulfate and methane in terrestrial subsurface fluids, we conclude that AOM may be widespread in the deep continental biosphere.

Seedling growth is an important factor for direct seeding of rice. However, the genetic and transcriptomic factors involved in this process are largely unknown. In this study, transcripts affecting shoot weight were identified in rice (Oryza sativa L.) using RNA sequencing (RNA-Seq) data from 20 backcrossed inbred lines (BILs) and their parental cultivars. The selection frequency of the genes for the regression model was determined using repeated analysis of random subsets of the transcriptome. The qLTG3-1gene, controlling low-temperature germinability, and short grain 1 gene (SG1), known to decrease organ elongation, showed high frequency. The quantitative trait loci (QTLs) analysis performed for BILs revealed that qLTG3-1 was included in the QTLs for shoot weight but SG1 was not. No nucleotide polymorphisms were found in the coding region of SG1 in either of the parental cultivars. Quantitative real-time PCR showed that SG1 expression was negatively correlated with shoot weight for all 104 BILs analyzed in this study. Expression QTL (eQTLs) analysis showed an eQTL for SG1 expression located in the same region as the QTL for shoot weight. However, no eQTLs were detected on the same chromosome as SG1, suggesting that nucleotide polymorphisms around the gene do not affect its expression in analyzed growth stage. Overall, these results indicate that RNA-Seq is a useful tool for identifying transcripts that can be related to seedling growth rate.

Deep granitic aquifer is one of the largest, but least understood, microbial habitats. To avoid contamination from the surface biosphere, underground drilling was conducted for 300 m deep granitic rocks at the Mizunami underground research laboratory (URL), Japan. Slightly alkaline groundwater was characterized by low concentrations of dissolved organic matter and sulfate and the presence of > 100 nM H2 . The initial biomass was the highest (∼10(5) cells ml(-1) ) with the dominance of Hydrogenophaga spp., whereas the phylum Nitrospirae became predominant after 3 years with decreasing biomass (∼10(4) cells ml(-1) ). One week incubation of groundwater microbes after 3 years with (13) C-labelled bicarbonate and 1% H2 and subsequent single-cell imaging with nanometer-scale secondary ion mass spectrometry demonstrated that microbial cells were metabolically active. Pyrosequencing of microbial communities in groundwater retrieved at 3-4 years after drilling at the Mizunami URL and at 14 and 25 years after the drilling at the Grimsel Test Site, Switzerland, revealed the occurrence of common Nitrospirae lineages at the geographically distinct sites. As the close relatives of the Nitrospirae lineages were exclusively detected from deep groundwaters and terrestrial hot springs, it suggests that these bacteria are indigenous and potentially adapted to the deep terrestrial subsurface.

We investigated the morpho-physiological traits of rice (Oryza sativa L.) during the germination and post-germination phases to explore avoidance of hypoxic conditions. We compared four lines selected for anaerobic germination (AG lines) with the variety IR42. The germination capacity of AG lines was higher than that of IR42. The germination percentages and coleoptile elongation differed among the four AG lines; IR06F459 showed the fastest germination and rapid coleoptile elongation. The coleoptiles of IR06F459 were significantly longer than those of IR42. The α-amylase activity in germinating seeds was significantly higher in IR06F459 than in IR42. At 2 days after sowing, the sucrose and glucose concentrations in germinating seeds were higher in IR06F459 than in IR42. These results show that IR06F459, an AG line with a long coleoptile, has high α-amylase activity and high sucrose and glucose concentrations in germinating seeds. These attributes partly explain its vigorous germination and coleoptile growth under hypoxic conditions.

Quantitative trait loci (QTLs) affecting the shoot length and chlorophyll content of seedlings grown at a low temperature (16oC) for 4 weeks were analyzed using inbred lines derived from a cross between an indica rice cultivar, Habataki, and a japonica rice cultivar, Arroz da Terra. Culm length of the inbred lines, measured at the harvesting stage, was also analyzed. The QTLs linked to increased shoot length (qSL1 ) and culm length (qCL1 ) on the Arroz da Terra allele were detected in the same region of chromosome 1, where the gibberellin 20 oxidase-2 gene (identical to Semi Dwarf1 : SD1 ) located. Other QTLs ( qSL and qSL8 ) that were linked to increased shoot length on Arroz da Terra and Habataki alleles, but had no effects on the culm length, were detected on chromosomes 3 and 8, respectively. The alleles of qSL3 and qSL8 might improve early shoot growth without increasing the risk of lodging caused by a long culm length. A novel QTL (qCC1 ) linked to increased chlorophyll content of seedlings ...

Quantitative trait loci (QTL) affecting the germination rate, coleoptile length, and shoot dry weight were analyzed under submerged and low temperature conditions using inbred lines derived from crossing the rice cultivars Ouu 365 and Arroz da Terra. The QTLs that increased the germination rate and shoot dry weight by Arroz da Terra allele were detected on the same region of chromosome 3, where the low temperature germinability gene, qLTG3-1, localized, suggesting that greater germinability might lead to increased shoot growth in paddy fields. The QTLs that increased the coleoptile length by Ouu 365 and Arroz da Terra alleles were detected on chromosome 8 and 11, respectively. The analysis of the known germinability genes suggested that functional allele of qLTG3-1 increased germination rates of the inbred lines. However, Rc which induced red pigmentation in pericarp declined the germination rates of the lines with functional qLTG3-1.

Freshwater aquifers in granitic rocks are widespread microbial habitats in the terrestrial subsurface. Microbial populations in deep granitic groundwater from two recently drilled (1 and 2 years) and two old boreholes (14 and 25 years) were compared. The 16S rRNA gene sequences related to “Candidatus Magnetobacterium bavaricum”, Thermodesulfovibrio spp. of Nitrospirae (90.5–93.1 % similarity) and a novel candidate division with

Microbial metabolic activity within the deep subsurface can potentially impact radionuclide migration during geological disposal of nuclear waste. To evaluate the geomicrobiological properties of Tertiary sedimentary rocks, which are widely distributed in the repository environment in Japan, aseptic and deoxygenated drilling was conducted with the installation of a multi-packer system to collect cores and groundwater. Integrated results from measurements on potential rates of denitrification and pore-size distributions in drill core samples indicated that in situ microbial activity is constrained by the availability of pore spaces larger than 0.1 μm in radius. Comparison of geochemical profiles of porewater extracted from the core samples and groundwater collected within multi-packer intervals revealed that terminal electron acceptors such as nitrite and sulfate were depleted in groundwater. Microbial community structures based on 16S rRNA gene sequences were represented by phylotypes related to Fe-, Mn-, elemental sulfur- and sulfate-reducing bacteria in groundwater. In addition, a phylotype closely related to denitrifying Acidovorax sp. of the β-proteobacteria was dominant in the lower borehole interval. From our results, it is likely that groundwater microorganisms mediate redox reactions that influence the mobility of radionuclides in the deep subsurface.

The F1 plants of crosses between indica and japonica rice cultivars often have black hulls during ripening, even though both of the parental cultivars have yellow hulls. Complementary genes are suggested to be necessary for the black hull phenotype, and one of them is predicted to be Phr1, which encodes polyphenol oxidase. On the other hand, Bh4, which encodes a tyrosine transporter, is known to cause the black hull phenotype in wild rice species, Oryza rufipogon. However, the relationship between Bh4 and Phr1 in the black hull phenotype has not been elucidated. In this study, a genotype analysis of the segregating populations from the cross between an indica cultivar, Habataki, and a japonica cultivar, Arroz da Terra, indicated that only those plants that had both functional genes, Bh4 and Phr1, showed the black hull phenotype, suggesting that a complementarity of Bh4 and Phr1 was necessary for the black hull phenotype.

Deep granitic aquifer is one of the largest, but least understood, microbial habitats. To avoid contamination from the surface biosphere, underground drilling was conducted for 300 m deep granitic rocks at the Mizunami underground research laboratory (URL), Japan. Slightly alkaline groundwater was characterized by low concentrations of dissolved organic matter and sulfate and the presence of 100 nM H2 . The initial biomass was the highest (∼10(5) cells ml(-1) ) with the dominance of Hydrogenophaga spp., whereas the phylum Nitrospirae became predominant after 3 years with decreasing biomass (∼10(4) cells ml(-1) ). One week incubation of groundwater microbes after 3 years with (13) C-labelled bicarbonate and 1% H2 and subsequent single-cell imaging with nanometer-scale secondary ion mass spectrometry demonstrated that microbial cells were metabolically active. Pyrosequencing of microbial communities in groundwater retrieved at 3-4 years after drilling at the Mizunami URL and at 14 and 25 years after the drilling at the Grimsel Test Site, Switzerland, revealed the occurrence of common Nitrospirae lineages at the geographically distinct sites. As the close relatives of the Nitrospirae lineages were exclusively detected from deep groundwaters and terrestrial hot springs, it suggests that these bacteria are indigenous and potentially adapted to the deep terrestrial subsurface.

To achieve super high yield of more than 10 t ha-1 in the Tohoku region (colder area of Japan), we conducted a two-year field experiment using a large grain type high-yielding rice variety Bekoaoba. Although high nitrogen application (HN) increased the top dry weight at the full heading stage only slightly, it increased the sink size (single grain weight x the number of spikelets per area), leaf area index and nitrogen content at the full heading stage and accordingly the dry matter production during the ripening period. As a result, the gross hulled rice yield was higher under HN than under standard nitrogen application (SN). Under HN, early topdressing increased not only the number of differentiated spikelets but also the number of degenerated spikelets. As a result, the sink size and gross hulled rice yield of the plants were not changed by the early topdressing. Under HN, the higher planting density increased the number of panicles per area but decreased the number of spikelets per panicle. As a result, the sink size and gross hulled rice yield were not changed with the planting density. In conclusion, HN produced the gross hulled rice yield of more than 9 t ha-1. However, the gross hulled rice yield could not be increased more than 10 t ha-1 by regulation of the timing of topdressing and /or the planting density. We discussed the strategies for super high-yielding rice in the Tohoku region.

Although deep subterranean crystalline rocks are known to harbor microbial ecosystems, geochemical factors that constrain the biomass, diversity, and metabolic activities of microorganisms remain to be clearly defined. To better understand the geochemical and microbiological relationships, we characterized granitic groundwater collected from a 1,148- to 1,169-m-deep borehole interval at the Mizunami Underground Research Laboratory site, Japan, in 2005 and 2008. Geochemical analyses of the groundwater samples indicated that major electron acceptors, such as NO(3)(-) and SO(4)(2-), were not abundant, while dissolved organic carbon (not including organic acids), CH(4) and H(2), was moderately rich in the groundwater sample collected in 2008. The total number of acridine orange-stained cells in groundwater samples collected in 2005 and 2008 were 1.1 x 10(4) and 5.2 x 10(4) cells/mL, respectively. In 2005 and 2008, the most common phylotypes determined by 16S rRNA gene sequence analysis were both related to Thauera spp., the cultivated members of which can utilize minor electron donors, such as aromatic and aliphatic hydrocarbons. After a 3-5-week incubation period with potential electron donors (organic acids or CH(4) + H(2)) and with/without electron acceptors (O(2) or NO(3)(-)), dominant microbial populations shifted to Brevundimonas spp. These geomicrobiological results suggest that deep granitic groundwater has been stably colonized by Thauera spp. probably owing to the limitation of O(2), NO(3)(-), and organic acids.

A deactivating behavior of TiO 2 photocatalysts in NO 2 oxidation to HNO 3 was studied with use of TiO 2 nanoparticulate thin films (0.5-1.5 μm thick) under UV light illumination over 10 h. The photocatalytic activity was decreased with accumulation of HNO 3 on the TiO 2 surface. For thicker TiO 2 films, the deactivation rate was found to be slower. The amount of HNO 3 trapped on the TiO 2 surface was increased and finally saturated, at which the largest amount of HNO 3 was proportional to the thickness of the film. On the basis of the results, we concluded that the produced HNO 3 , inhibiting the reaction as a physical barrier, must be able to diffuse on the TiO 2 surface at a rate of at least more than 1.5 μm h -1 , and finally distributes homogeneously on the whole film. The maximum density of HNO 3 accumulated on the TiO 2 surface was estimated to be ∼2 molecules nm -2 under standard conditions. Finally, when the steady state is reached, the photocatalytic activity remained ∼8% of the initial one.

Sucrose synthase, which catalyzes uridine diphosphate (UDP)-dependent cleavage of sucrose into fructose and UDP-glucose, is induced by oxygen deficiency in rice seedlings and is considered to play an important role in energy production under hypoxic conditions. In this study, we analyzed the relationship between coleoptile elongation and sucrose synthase activity in rice (Oryza sativa L.) cultivars under submerged conditions. We also analyzed the activity of α-amylase, which digests starch reserves in the endosperm and is considered to be important for energy production in young seedlings. The results indicated that different rice cultivars had different sucrose synthase and α-amylase activities under submerged conditions. Moreover, sucrose synthase activity in whole seedlings was significantly correlated with coleoptile length under submerged conditions, whereas the correlation between α-amylase activity and coleoptile length was low. Sugar content of shoots differed with the cultivar. Correlation analysis demonstrated that sucrose content was highly correlated with coleoptile length and sucrose synthase activity, but not with α-amylase activity.

The N-terminal amino-acid sequence of a major rice phloem-sap protein, designated as RPP23, was determined. The complete amino-acid sequence of RPP23 was deduced from the corresponding rice EST- clone and contained an extra 46 amino acids at the N-terminus, that was apparently cleaved off to form mature RPP23 in sieve tubes. RPP23 shared a similarity to plant small heat-shock proteins (smHSPs), though the N-terminal region of RPP23 was distinct from that of known smHSPs. Immunocytological analyses using leaf sections showed that RPP23 was located only in the phloem regions of leaves, and was present in non-stressed plants. In mature leaves, stronger immunocytological signals were detected in sieve elements than in companion cells.

We showed that the photocatalytic effect of a coating of TiO(2) greatly reduces the formation of a biofilm by Phormidium tenue (P. tenue), a filamentous cyanobacterium, on glass plates. Sample plates were immersed in P. tenue culture solution (OD(730)=0.3) under concurrent illumination with white fluorescent (WF) and UV light (0.3 mW cm(-2), each) for 11 days. TiO(2)-coated glass plates showed greatly reduced adhesion of P. tenue over 11 days compared to bare plates. The number of P. tenue adhering to bare glass plates increased to over 10(6) cells cm(-2) in 6 days. The photocatalytic anti-biofilm effect was also observed under WF light, although it was small and lasted only a few days. The addition of 1 mM mannitol, a scavenger for the hydroxyl radical (·OH), suppressed the effect. The surface of TiO(2)-coated plates was maintained in a highly hydrophilic state for 11 days, regardless of the addition of mannitol. Therefore, we conclude that the photocatalytic oxidation of P. tenue is effective in preventing the formation of a biofilm.

In contrast to the deep subseafloor biosphere, a volumetrically vast and stable habitat for microbial life in the terrestrial crust remains poorly explored. For the long-term sustainability of a crustal biome, high-energy fluxes derived from hydrothermal circulation and water radiolysis in uranium-enriched rocks are seemingly essential. However, the crustal habitability depending on a low supply of energy is unknown. We present multi-isotopic evidence of microbially mediated sulfate reduction in a granitic aquifer, a representative of the terrestrial crust habitat. Deep meteoric groundwater was collected from underground boreholes drilled into Cretaceous Toki granite (central Japan). A large sulfur isotopic fractionation of 20–60‰ diagnostic to microbial sulfate reduction is associated with the investigated groundwater containing sulfate below 0.2 mM. In contrast, a small carbon isotopic fractionation (

Sieve tubes are comprised of sieve elements, enucleated cells that are incapable of RNA and protein synthesis. The proteins in sieve elements are supplied from the neighboring companion cells through plasmodesmata. In rice plants, it was unclear whether or not all proteins produced in companion cells had the same distribution pattern in the sieve element-companion cell complex. In this study, the distribution pattern of four proteins, beta-glucuronidase (GUS), green fluorescent protein (GFP), thioredoxin h (TRXh) and glutathione S-transferase (GST) were analyzed. The foreign proteins GUS and GFP were expressed in transgenic rice plants under the control of the TRXh gene promoter (PTRXh), a companion cell-specific promoter. Analysis of leaf cross-sections of PTRXh-GUS and PTRXh-GFP plants indicated high accumulation of GUS and GFP, respectively, in companion cells rather than in sieve elements. GUS and GFP were also detected in phloem sap collected from leaf sheaths of the transgenic rice plants, suggesting these proteins could enter sieve elements. Relative amounts of GFP and endogenous phloem proteins, TRXh and GST, in phloem sap and total leaf extracts were compared. Compared to TRXh and GST, GFP content was higher in total leaf extracts, but lower in phloem sap, suggesting that GFP accumulated mainly in companion cells rather than in sieve elements. On the other hand, TRXh and GST appeared to accumulate in sieve elements rather than in companion cells. These results indicate the evidence for differential distribution of proteins between sieve elements and companion cells in rice plants.

We describe the alteration of protein contents in the phloem sap of rice plants by introduction of transgenes. The coding sequences of rice thioredoxin h (TRXh) and oryzacystatin-I (OC-I) were fused in sense and antisense orientations to the promoter region of the rice TRXh gene. These proteins are present in rice phloem sap. The contents of TRXh and OC-I were reduced in the phloem sap of the transgenic plants carrying the corresponding antisense cDNAs. The content of OC-I protein increased in the phloem sap of transgenic plants carrying the TRXh promoter sense OC-I cDNA. This is the first demonstration of the control of the phloem protein contents in rice plants by analysis of phloem sap of transgenic plants.

Many kinds of proteins have been found in the sieve element–companion cell complexes by the analyses of phloem sap and microscopic observations. The cDNAs, which encode some of these sieve-tube proteins, have already been cloned. As mature sieve elements lack nuclei and most ribosomes, sieve-tube proteins have been hypothesized to be synthesized in the companion cells and then transported to the lumina of the functional sieve tubes through the plasmodesmata connecting the companion cells and sieve elements. Soluble proteins present in the sieve tubes can be collected by several techniques, such as incision or the aphid technique. The composition of the proteins in the phloem sap is unique compared with that of tissue extract, suggesting these proteins have important roles for the development and functions of sieve tubes.