Relationship between the vertical distribution of fine roots and residual soil nitrogen along a gradient of hardwood mixture in a conifer plantation.

In forest ecosystems, understanding the relationship between the vertical distribution of fine roots and residual soil nitrogen is essential for clarifying the diversity-productivity-water purification relationship. Vertical distributions of fine-root biomass (FRB) and concentrations of nitrate-nitrogen (NO3 -N) in soil water were investigated in a conifer plantation with three thinning intensities (Control, Weak and Intensive), in which hardwood abundance and diversity were low, moderate and high, respectively. Intensive thinning led to the lowest NO3 -N concentration in soil water at all depths (0-100 cm) and highest FRB at shallow depths (0-50 cm). The NO3 -N concentration at a given depth was negatively correlated with total FRB from the surface to the depth at which NO3 -N concentration was measured, especially at shallow depths, indicating that more abundant fine roots led to lower levels of downward NO3 -N leaching. FRB contributed positively to nitrogen content of hardwood leaves. These findings demonstrate that a hardwood mixture in conifer plantations resulted in sufficient uptake of NO3 -N from soil by well developed fine-root systems, and translocation to canopy foliage. This study suggests that productivity and water purification can be achieved through a hardwood mixture in conifer plantations.

Flavobacterium ammonificans sp. nov. and Flavobacterium ammoniigenes sp. nov., ammonifying bacteria isolated from surface river water.

Three aerobic, Gram-stain-negative, non-motile, rod-shaped bacteria, designated as strains SHINM13T, GENT5T and GENT11 were isolated from surface river water (Saitama Prefecture, Japan). SHINM13T and GENT11 were positive for catalase, whereas GENT5T was negative. Phylogenetic analyses based on the 16S rRNA gene (1341 bp) or 40 marker gene (34,513 bp) sequences revealed that the strains formed distinct phylogenetic lineages within the genus Flavobacterium. The three strains shared 99.3-99.6 % 16S rRNA gene sequence similarity among each other. The average nucleotide identity by orthology (OrthoANI) and digital DNA-DNA hybridization (dDDH) values between strains SHINM13T and GENT11 were 96.56 and 82.1 %, respectively, and those between SHINM13T and GENT5T were 83.46 % and 52.9 %, respectively. The major cellular fatty acids were C15 : 1ω6c, iso-C15 : 0, iso-C15 : 1G, anteiso-C15 : 0 and iso-C15 : 0 3-OH. The major polar lipid was phosphatidylethanolamine. SHINM13T and GENT5T contained menaquinone-6 (MK-6) as the predominant respiratory quinone, and their DNA G+C contents were 34.4 and 35.1 mol%, respectively. Genome sequencing of the three isolates revealed a genome size of 2.26-2.40 Mbp. Furthermore, all three isolates converted dissolved organic nitrogen to ammonium during cell growth. On the basis of the results of phenotypic and phylogenetic analyses, strains SHINM13T and GENT11 and GENT5T represent two distinct novel species in the genus Flavobacterium, for which the names Flavobacterium ammonificans sp. nov. (type strain SHINM13T =JCM 34684T =NCIMB 15379T) and Flavobacterium ammoniigenes sp. nov. (type strain GENT5T =JCM 32249T=NCIMB 15380T) are proposed.

Assessment of nitrous oxide production in eutrophicated rivers with inflow of treated wastewater based on investigation and statistical analysis.

Accurate estimation and control of greenhouse gas emissions have been recognized as imperative in recent years. Therefore, frequent investigations under uniform environmental conditions are required to better understand this concept. Thus, six sampling sites with characteristic concentrations of nitrogen and other water quality parameters were selected to investigate the behavior of water quality parameters throughout the year and to statistically examine the correlations among the parameters. Dissolved nitrous oxide (D-N2O) showed the highest positive correlation coefficient with NO2-N among nitrogen species. The results of the principal component analysis suggested that river water quality could be broadly classified based on photosynthesis and contamination from treated wastewater. Photosynthesis caused an increase in pH, with concomitant decrease in D-N2O concentration. Using the results of multiple regression analysis, D-N2O was accurately estimated based on nitrogen concentration, pH, and concentration of organic matter in various situations. The results of a detailed survey suggested that D-N2O was produced in the river from nitrogen sources released from the wastewater treatment plant. The main roles of the wastewater treatment plant for D-N2O behavior in the river were the supply of the nitrogen source that was the precursor of D-N2O, the supply of the nutrients that induced the photosynthesis, and the direct supply of D-N2O at a low water temperature. The models based on multiple regression analysis could efficiently predict the D-N2O concentration produced in rivers at sites downstream of the wastewater treatment plant, except for the direct supply of D-N2O as an effluent at low water temperature.

Fluviibacter phosphoraccumulans gen. nov., sp. nov., a polyphosphate-accumulating bacterium of Fluviibacteraceae fam. nov., isolated from surface river water.

Three aerobic, Gram-stain-negative, non-motile, rod-shaped bacteria, designated as strains SHINM1T, ICHIJ1 and ICHIAU1, were isolated from surface river water (Saitama Prefecture, Japan). Phylogenetic analyses based on 16S rRNA and 40 marker gene sequences revealed that the strains formed a distinct phylogenetic lineage within the order Rhodocyclales. The three strains shared 100 % 16S rRNA gene similarity. Growth occurred at 15-30 °C and pH 6.0-9.5, but not in the presence of ≥1.0 % (w/v) NaCl. The isolates stained positive for intracellular polyphosphate granules. The major cellular fatty acids were C16 : 0, summed feature 2 (C12 : 1 aldehyde and/or iso-C16 : 1 I and/or C14 : 0 3-OH), summed feature 3 (C16 : 1 ω7c and/or C16 : 1 ω6c) and summed feature 8 (C18 : 1 ω7c and/or C18 : 1 ω6c). The major polar lipids were phosphatidylethanolamine and an unidentified phospholipid. The predominant quinone system of strain SHINM1T was ubiquinone-8 and its DNA G+C content was 56.7 mol%. Genome sequencing of the three isolates revealed a genome size of 2.29-2.43 Mbp and average nucleotide identity by orthology values of ≥98.9 %. Based on the results of phenotypic and phylogenetic analyses, strains SHINM1T, ICHIJ1 and ICHIAU1 represent a novel species of a new genus, for which the name Fluviibacter phosphoraccumulans gen. nov., sp. nov. is proposed, within a new family, Fluviibacteraceae fam. nov. of the order Rhodocyclales. The type strain is SHINM1T (=JCM 32071T=NCIMB 15105T).

Effect of antibiotics on redox transformations of arsenic and diversity of arsenite-oxidizing bacteria in sediment microbial communities.

In the present study, we investigated the effect of antibiotics on microbial arsenate (As(V)) reduction and arsenite (As(III)) oxidation in sediments collected from a small pond and eutrophic lake. The As(V)-reducing activities were less susceptible to chloramphenicol in aerobic conditions than in anaerobic conditions. Aerobic As(V) reduction proceeded in the presence of diverse types of antibiotics, suggesting that As-resistant bacteria are widely antibiotic resistant. In contrast, some antibiotics, e.g., chloramphenicol, strongly inhibited aerobic As(III) oxidation. In addition, bacterial As(III) oxidase genes were scarcely amplified and Proteobacteria -related 16S rRNA genes drastically decreased in chloramphenicol-amended cultures. Erythromycin and lincomycin, which successfully target many Gram-positive bacteria, scarcely affected As(III) oxidation, although they decreased the diversity of As(III) oxidase genes. These results indicate that the aerobic As(III) oxidizers in the sediment cultures are mainly composed of Proteobacteria and are more sensitive to certain types of antibiotics than the aerobic As(V) reducers. Our results suggest that antibiotic disturbance of environmental microbial communities may affect the biogeochemical cycle of As.

Complete Genome Sequence of Aurantimicrobium sp. Strain INA4, Isolated from an Oligotrophic Lake in Japan.

The globally distributed freshwater bacterioplankton of the genus Aurantimicrobium belong to the tribe Luna2. Here, we report the complete genome sequence of Aurantimicrobium sp. strain INA4, which was isolated from an oligotrophic lake surface water in Japan.

Complete Genome Sequences of Three Limnohabitans sp. (Lhab-A3) Strains, INBF002, TEGF004, and MORI2, Isolated from Two Lakes and a River in Japan.

Freshwater bacterioplankton of the genus Limnohabitans represent a dominant group that has worldwide distribution. Here, we report the complete genome sequences of three Limnohabitans sp. (Lhab-A3 tribe) strains, i.e., INBF002, TEGF004, and MORI2, which were isolated from surface water samples from two shallow eutrophic lakes and a river in Japan.

Complete Genome Sequences of Three Polynucleobacter sp. Subcluster PnecC Strains, KF022, KF023, and KF032, Isolated from a Shallow Eutrophic Lake and a River in Japan.

The genus Polynucleobacter subcluster PnecC consists of bacteria representing the ubiquitous taxon of freshwater bacterioplankton. Here, we report the complete genome sequences of three Polynucleobacter sp. (PnecC) strains, namely, KF022, KF023, and KF032, which were isolated from surface water of a temperate shallow eutrophic lake and its inflow river in Japan.

Complete Genome Sequences of Polynucleobacter sp. Subcluster PnecA Strains SHI2 and SHI8, Isolated from an Oligotrophic-Dystrophic Lake in Japan.

Members of the genus Polynucleobacter belonging to the subcluster PnecA comprise freshwater bacterioplankton with worldwide distribution. Here, we report the complete genome sequences of two Polynucleobacter sp. strains (PnecA), SHI2 and SHI8, isolated from the surface water of an oligotrophic-dystrophic lake in a humid continental climate in Japan.

Ecological niche separation in the Polynucleobacter subclusters linked to quality of dissolved organic matter: a demonstration using a high sensitivity cultivation-based approach.

The free-living, cosmopolitan, freshwater betaproteobacterial bacterioplankton genus Polynucleobacter was detected in different years in 11 lakes of varying types and a river using the size-exclusion assay method (SEAM). Of the 350 strains isolated, 228 (65.1%) were affiliated with the Polynucleobacter subclusters PnecC (30.0%) and PnecD (35.1%). Significant positive correlations between fluorescence in situ hybridization and SEAM data were observed in the relative abundance of PnecC and PnecD bacteria to Polynucleobacter communities (PnecC + PnecD). Isolates were mainly PnecC bacteria in the samples with a high specific UV absorbance at 254 nm (SUVA(254) ), and a low total hydrolysable neutral carbohydrate and amino acid (THneutralCH + THAA) content of the dissolved organic matter (DOM) fraction, which is known to be correlated with a high humic content. In contrast, the PnecD bacteria were abundant in samples with high chlorophyll a and/or THneutralCH + THAA concentrations, indicative of primary productivity. With few exceptions, differences in the relative abundance of PnecC and PnecD in each sample, determined using a high-sensitivity cultivation-based approach, were due to DOM quality. These results suggest that the major DOM component in the field, which is allochthonously or autochthonously derived, is a key factor for ecological niche separation between PnecC and PnecD subclusters.

Structural origin of enhanced slow dynamics near a wall in glass-forming systems.

Spatial confinement is known to induce a drastic change in the viscosity, relaxation times, and flow profile of liquids near the glass (or jamming) transition point. The essential underlying question is how a wall affects the dynamics of densely packed systems. Here we study this fundamental problem, using experiments on a driven granular hard-sphere liquid and numerical simulations of polydisperse and bidisperse colloidal liquids. The nearly hard-core nature of the particle-wall interaction provides an ideal opportunity to study purely geometrical confinement effects. We reveal that the slower dynamics near a wall is induced by wall-induced enhancement of 'glassy structural order', which is a manifestation of strong interparticle correlations. By generalizing the structure-dynamics relation for bulk systems, we find a quantitative relation between the structural relaxation time at a certain distance from a wall and the correlation length of glassy structural order there. Our finding suggests that glassy structural ordering may be the origin of the slow glassy dynamics of a supercooled liquid.

Complete Genome Sequences of Two Flavobacterium ammonificans Strains and a Flavobacterium ammoniigenes Strain of Ammonifying Bacterioplankton Isolated from Surface River Water.

Flavobacterium ammonificans and Flavobacterium ammoniigenes are ammonifying freshwater bacterioplankton. Here, we report the complete genome sequences of two F. ammonificans strains (SHINM13T and GENT11) and one F. ammoniigenes strain (GENT5T) that were isolated from surface river water in Japan.

Complete Genome Sequences of Rhodoluna sp. Strains KAS3 and KACHI23, Isolated from Lake and River Surface Water.

The genus Rhodoluna belongs to the ubiquitous freshwater bacterioplankton tribe Luna1-A2. Here, we report the complete sequences of Rhodoluna sp. strains KAS3 and KACHI23, which were isolated from freshwater lake and river surface water in Japan.

Whole-Genome Sequence of Sediminibacterium sp. Strain TEGAF015, Isolated from a Shallow Eutrophic Freshwater Lake in Japan.

The genus Sediminibacterium comprises bacteria representing the ubiquitous taxa of freshwater bacterioplankton. Here, we report the whole-genome sequence of Sediminibacterium sp. strain TEGAF015, isolated from a shallow eutrophic freshwater lake in Japan.

Complete Genome Sequence of Aquiluna sp. Strain KACHI24, Isolated from River Surface Water.

The globally distributed bacterioplankton of the genus Aquiluna belong to the tribe Luna1-A1. Here, we report the complete genome sequence of Aquiluna sp. strain KACHI24, which was isolated from river surface water in Japan.

Critical-like behaviour of glass-forming liquids.

Recently it has been revealed that when approaching the glass-transition temperature, T(g), the dynamics of a liquid not only drastically slows down, but also becomes progressively more heterogeneous. From our simulations and experiments of six different glass-forming liquids, we find that the heterogeneous dynamics is a result of critical-like fluctuations of static structural order, contrary to a common belief that it is purely of dynamic origin. The static correlation length and susceptibility of a structural order parameter show Ising-like power-law divergence towards the ideal glass-transition point. However, this structural ordering accompanies little density change, which explains why it has not been detected by the static structure factor so far. Our results suggest a far more direct link than thought before between glass transition and critical phenomena. Indeed, the glass transition may be a new type of critical phenomenon where a structural order parameter is directly linked to slowness.

Screening for lectin-like protein-producing microorganisms based on cell surface proteins.

A method for screening lectin-producing microorganisms was developed. The presence of lectin on microbial cell surfaces was used as an index for their selective isolation. The lectin-producing microorganisms adhered to sugar-modified agarose beads and were selectively eluted with specific saccharide solutions. Spin columns were an effective tool for excluding non-lectin producers. Eighty-seven percent of the microorganisms that were eluted from the beads showed hemagglutination. The results of sequence analysis indicated that some of the eluted microorganisms have not been previously identified as lectin-producing microorganisms.

Complete Genome and Plasmid Sequences of Three Fluviibacter phosphoraccumulans Polyphosphate-Accumulating Bacterioplankton Strains Isolated from Surface River Water.

Fluviibacter phosphoraccumulans is a polyphosphate-accumulating freshwater bacterioplankton which is detected mainly from riverine environments. The type strain, SHINM1, and two other strains, ICHIJ1 and ICHIAU1, were isolated from surface river water in Japan. Here, we report the complete genome and plasmid sequences of three F. phosphoraccumulans strains.

Light-induced root hair formation in lettuce (Lactuca sativa L. cv. Grand Rapids) roots at low pH is brought by chlorogenic acid synthesis and sugar.

Previously, we reported that chlorogenic acid (CGA) facilitated root hair formation at pH 4.0 in lettuce (Lactuca sativa L. cv. Grand Rapids). Light was essential for this process. In the present study, we determined relationships between CGA, light, and sugar during root hair formation in lettuce seedlings. The amount of CGA increased with white light in intact seedlings. Exogenously applied CGA restored root hair formation in dark-grown intact seedlings at pH 4.0. However, no root hair formation was induced in decapitated seedlings regardless of light exposure and CGA application. Application of sucrose or glucose induced both root hair formation and CGA synthesis in light-grown decapitated seedlings at pH 4.0. Blue light was the most effective for both root hair formation and CGA synthesis when supplied with sucrose to decapitated seedlings. Addition of sucrose and CGA together induced root hair formation at pH 4.0 in dark-grown decapitated seedlings. Results suggest that light induced CGA synthesis from sugar in the roots. Sugar was also required for root hair formation other than starting material of CGA synthesis. In addition, an unknown low pH-induced factor was essential for lettuce root hair formation.

Effective isolation of bacterioplankton genus Polynucleobacter from freshwater environments grown on photochemically degraded dissolved organic matter.

Effective isolation of freshwater bacterioplankton belonging to genus Polynucleobacter from a shallow eutrophic lake and its tributary was achieved by size-selective filtration with a 0.7-mum pore filter and cultivation on R2A agar medium. Partial 16S rRNA gene analysis showed that over 80% of all the strains were highly similar to the Polynucleobacter cluster. Essential medium components for effective cultivation are pyruvate, yeast extract and peptone, whereas soluble starch and glucose are not necessary. Isolate KF001 (affiliated with Polynucleobacter subcluster D) has a strict requirement for organic acids as carbon sources, and we hypothesize that the Polynucleobacter cluster of bacteria could utilize compounds formed via photochemically dissolved organic matter (DOM) degradation for growth. Because organic acids form from solar radiation of DOM in aquatic environments, carbon sources that are typical products of DOM photochemical degradation were added to the medium. These compounds were readily utilized by KF001 in this study. Finally, we observed the stimulation of strain KF001 activity by photochemical degradation of natural lake water. Our findings suggest a carbon flow of DOM photoproducts to Polynucleobacter in the freshwater microbial loop.