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The perennial gramineous grass Miscanthus condensatus functions as a major pioneer plant in colonizing acidic volcanic deposits on Miyake-jima, Japan, despite a lack of nitrogen nutrients. The nitrogen cycle in the rhizosphere is important for the vigorous growth of M. condensatus in this unfavorable environment. In the present study, we identified the nitrogen-cycling bacterial community in the M. condensatus rhizosphere on these volcanic deposits using a combination of metagenomics and culture-based analyses. Our results showed a large number of functional genes related to denitrification and dissimilatory nitrate reduction to ammonium (DNRA) in the rhizosphere, indicating that nitrate-transforming bacteria dominated the rhizosphere biome. Furthermore, nitrite reductase genes (i.e., nirK and nirS) related to the denitrification and those genes related to DNRA (i.e., nirB and nrfA) were mainly annotated to the classes Alpha-proteobacteria, Beta-proteobacteria, and Gamma-proteobacteria. A total of 304 nitrate-succinate-stimulated isolates were obtained from the M. condensatus rhizosphere and were classified into 34 operational taxonomic units according to amplified 16S rRNA gene restriction fragment pattern analysis. Additionally, two strains belonging to the genus Cupriavidus in the class Beta-proteobacteria showed a high in vitro denitrifying activity; however, metagenomic results indicated that the DNRA-related rhizobacteria appeared to take a major role in the nitrogen cycle of the M. condensatus rhizosphere in recent Miyake-jima volcanic deposits. This study elucidates the association between the Miscanthus rhizosphere and the nitrate-reducing bacterial community on newly placed volcanic deposits, which furthers our understanding of the transformation of nitrogen nutrition involved in the early development of vegetation. [ABSTRACT FROM AUTHOR]

Summary: A new species of Xiphinema americanum group was recovered in the rhizosphere of holly (Ilex purpurea) imported from Japan. It is described and illustrated in the present study as X. purpureum n. sp. The new species is characterised by moderately long females 2267 (2115-2550) μ m, round lip region slightly offset from the rest of the body, 103.5 (98.5-109.0) μ m long odontostyle, genital branches without discernible endosymbiotic bacteria, vulva located at 54.1 (51.6-57.1)% of the body, tail 30 (24.3-33.4) μ m long with a broadly rounded terminus, male absent and four juvenile developmental stages. The polytomous codes of the new species are as follows: A4/5, B2/3, C1/2, D2/3, E3, F1, G1, H2, I1/2/3. The new species was molecularly characterised using near full length 18S, ITS1, and 28S D2-D3 regions of rRNA, and mitochondrial cytochrome c oxidase subunit I gene sequences. The phylogenetic analyses placed X. purpureum n. sp. with X. americanum group species, particularly with X. brevicolle complex species. This is the third X. americanum group species described from Japan. [ABSTRACT FROM AUTHOR]

A novel yellowish-white actinobacterial strain, designated as TS60-4C T , was isolated from the rhizosphere soil of the mangrove Bruguiera gymnorhiza (L.) Lam. in Okinawa, Japan, and was subjected to a polyphasic assessment. The strain could grow at 0-3.0% NaCl concentrations (w/v), pH 6.0-10.0, and 20-37 °C. The 16S rRNA gene sequences-based phylogeny showed that the novel isolate belongs to the family Micromonosporaceae and that it shared the highest sequence similarity (98.4%) with Micromonospora craniellae LHW63014 T . The hydrolysate of cell-wall of strain TS60-4C T contained alanine, glutamic acid, glycine, and meso-A2pm. The acyl type of muramic acid was N-glycolyl. The main (> 10%) fatty acids were anteiso-C 17:0 (22.1%), iso-C 16:0 (17.8%), iso-C 15:0 (14.7%), and anteiso-C 15:0 (10.3%) and the predominant menaquinones of the isolate were MK-9(H 6 ) and MK-9(H 4 ). The polar lipids of the isolate were phosphatidylethanolamine, diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol, an unidentified aminolipid, and three unidentified lipids. The genome size of strain TS60-4C T was 6.7 Mbp with a DNA G + C content of 72.4%. The average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity value could differentiate strain TS60-4C T from its closely related taxa. The genome of the strain had 22 putative biosynthetic gene clusters for secondary metabolites, indicating a significant potential as a producer of bioactive chemicals. Consequently, the strain is considered to represent a novel genus and a new species of the family Micromonosporaceae, for which the name Rhizomonospora bruguierae gen. nov., sp. nov. is proposed. The type species is R. bruguierae, with the type strain TS60-4C T (= NBRC 107566 T  = TBRC 2024 T )., (© 2024. The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature.)

Setophoma terrestris, a ubiquitous inhabitant of soil, causes pink root rot in various crops. In the present study, the density of S. terrestris was estimated by quantitative real‐time PCR in onion and non‐onion fields of Hokkaido, the northernmost island of Japan. Three‐year observations in monoculture and rotation fields demonstrated that the fungus grew significantly from the third year onwards, and declined in fields planted with poor hosts (e.g., sugar beet and soybean) that produced few or no chlamydospores of S. terrestris. Seasonal analysis revealed that the population of S. terrestris consistently increased when the tops of onions fell over in summer, which is when root activity declines. However, the soil inoculum potential estimated by a seedling bioassay showed distinct seasonal patterns, which rose from post‐harvest in winter and remained high until the subsequent planting in spring. Detailed surveys on depth distribution in an onion field detected a high population of S. terrestris in the effective layer (10–30 cm deep) but not below the hardpan (40 cm), implying that the fungus is intimately associated with roots. These results indicate that the proliferation of the fungus is closely related to root senescence and that over‐wintered propagules play an important role in primary infections, affecting disease severity. The present study shows that the temporal dynamics of S. terrestris depend exclusively on the activity of infecting roots and provides circumstantial evidence on the deleterious impact of monoculture on crop production. [ABSTRACT FROM AUTHOR]

Aims: Cyperaceae are common on nutrient-poor soils, including in western Japan. We examined the ability of the native Cyperaceae from western Japan to form dauciform roots and assessed the potential resulting contribution to soil phosphorus (P) dynamics. Methods: We assessed dauciform roots for 28 native Cyperaceae. Shoots, roots (including dauciform roots), and bulk and rhizosheath soils of Carex lenta were collected in Seto Inland Sea district (western Japan). The number of dauciform roots, shoot P and nitrogen (N) concentration, and soil P status and fractions were analyzed. Results: We confirmed dauciform-root formation in many Cyperaceae including the genus Carex. The number of dauciform roots of C. lenta showed a negative correlation with total and available soil P concentrations and with shoot P concentration. In the rhizosheath of C. lenta with many mature dauciform roots, we found an increase of readily-available inorganic P (Pi) and a decrease of readily-soluble organic P and sparingly soluble Pi fractions, indicating that the dauciform roots contributed to the acquisition of poorly-available soil P. Conclusions: Our results show negative correlations of the number of dauciform roots with both soil and plant P status. Regosols with a low P availability are common in Seto Inland Sea district; thus the formation of dauciform roots and their exudates induced by low P status are important for the distribution of C. lenta in this region. [ABSTRACT FROM AUTHOR]

Several region-specific vegetable varieties in Japan have an extensive cultivation history. Distinct tastes and aromas make them suitable for use in spices and pickles, and varieties with a high content of functional sulfur-containing compounds have been preferentially selected over the years. In the present study, we investigated the effects of different rhizosphere sulfate concentrations (0, 0.2, 0.4, and 0.8 mM) on the dry weight and sulfur content of 40 varieties of Brassicaceae heirloom vegetables. We also analyzed the expression levels of sulfate transporter genes, such as SULTR1s (sum of SULTR1;1, SULTR1;2, and SULTR1;3) and SULTR2;1, in 20 vegetable varieties. At 0 mM sulfate, plants have small leaves, as well as thin and scarce roots, whereas the mean shoot sulfur content per plant was 10% of that in control. Sulfur content increased by 29% at 0.4 mM and by 66% at 0.8 mM sulfate compared with that in control (0.2 mM sulfate); however, dry weight was not significantly affected. Mean shoot sulfur concentration was 0.12% at 0 mM, 0.52% at 0.2 mM, 0.65% at 4 mM, and 0.86% at 0.8 mM of sulfate. Shoot sulfur concentration exceeded 1% at 0.4 mM sulfate in several varieties. Shoot sulfur content and dry weight were positively correlated, suggesting that the capacity for sulfate ion absorption had a strong effect on biomass production in plants of the Brassicaceae family. Sulfur content and SULTR1s and SULTR2;1 expression were poorly correlated regardless of rhizosphere sulfur concentration. These genes did not respond to shoot sulfur content but responded to sulfate levels in the rhizosphere. Overall, our data indicated that sulfate absorption response to sulfate concentration in the rhizosphere by sulfate transporters in Brassicaceae plants depends on the inherent characteristics of the variety. [ABSTRACT FROM AUTHOR]

Summary: During quarantine inspections, a new species of Hoplotylus was detected from the rhizosphere of the Japanese maple, Acer palmatum , imported into China from Japan. Hoplotylus japonicus n. sp. is characterised by a stout 431-602 μ m long body, well-developed 20.0-24.5 μ m long stylet with tulip-shaped knobs having rounded sides in lateral view and a rounded anterior margin, excretory pore located slightly posterior to the hemizonid, usually empty, spermatheca, conical tail with a spike-like projection, which is distally smooth on the dorsal side, and males not found. It was morphologically compared with four currently known species of the genus, viz., H. femina , H. montanus , H. silvaticus , and H. sjacobi. In molecular phylogenetic analyses using 18S, 28S and internal transcribed spacer (ITS) ribosomal DNA sequences, the new species formed a clade with the only currently sequenced species of the genus, H. femina , in all phylogenies. This is the second species of the genus characterised by molecular data and the second species recovered from Japan. [ABSTRACT FROM AUTHOR]

Plant roots can exude organic compounds into the soil that are useful for plant survival because they can degrade microorganisms around the roots and enhance allelopathy against other plant invasions. We developed a method to collect carbon (C) exudation on a small scale from tree fine roots by C-free filter traps. We quantified total C through root exudation in four conifers from different microbial symbiotic groups (ectomycorrhiza (ECM) and arbuscular mycorrhiza (AM)) in a cool-temperate forest in Japan. We determined the relationship of mass-based exudation rate from three diameter classes (<0.5, 0.5–1.0, and 1.0–2.5 mm) of the intact root system with root traits such as morphological traits including root diameter, specific root length (SRL), specific root area (SRA), root tissue density (RTD) and chemical traits including root nitrogen (N) content and C/N. Across species, the mass-based root exudation rate was found to correlate with diameter, SRA, RTD, N and C/N. When comparing mycorrhizal types, there were significant relationships between the exudation and diameter, SRL, SRA, root N and C/N in ECM species; however, these were not significant in AM species. Our results show that relationships between in situ root exudation and every measured trait of morphology and chemistry were strongly driven by ECM roots and not by AM roots. These differences might explain the fact that ECM roots in this study potentially covaried by optimizing the exudation and root morphology in forest trees, while exudation in AM roots did not change with changes in root morphology. In addition, the contrasting results may be attributable to the effect of degree and position of ECM and AM colonization in fine root system. Differences in fine root exudation relationships to root morphology for the two types of mycorrhizae will help us better understand the underlying mechanisms of belowground C allocation in forest ecosystems. [ABSTRACT FROM AUTHOR]

In forest ecosystems, fine root respiration directly contributes to belowground carbon (C) cycling. Exudation from fine roots indirectly affects C cycling via enhanced microbial decomposition of soil organic matter. Although these root-derived C fluxes are essential components of belowground C cycling, how nitrogen (N) addition affects these fluxes and their correlations remains unclear. In this study, fine root exudation, respiration and chemical/morphological traits were measured in a dominant canopy species, Quercus crispula Blume, found in a cool temperate forest, the Tomakomai Experimental Forest, Hokkaido University, which has undergone 5-year N addition. Soil-dissolved organic carbon (DOC) was also measured in both bulk and rhizosphere soils to evaluate the impact of fine root exudation on soil C cycling. Compared with a control plot with no N treatment, fine roots in the N addition plot exhibited larger diameters and higher N concentrations, but lower specific root lengths and areas. On a root-weight basis, respiration was not different between plots, but exudation was slightly higher under N addition. On a root-area basis, exudation was significantly higher in the N addition plot. Additionally, differences in DOC between rhizosphere and bulk soils were two times higher in the N addition plot than the control plot. Although fine root respiration was positively correlated with exudation in both the control and N addition plots, the ratio of exudation C to respiration C decreased after 5-year N addition. Nitrogen addition also affected absolute C allocation to fine root exudation and changed the C allocation strategy between exudation and respiration fluxes. These findings will help enhance predictions of belowground C allocation and C cycling under N-rich conditions in the future. [ABSTRACT FROM AUTHOR]

Plants allocate a considerable amount of carbon (C) to fine roots as respiration and exudation. Fine-root exudation could stimulate microbial activity, which further contributes to soil heterotrophic respiration. Although both root respiration and exudation are important components of belowground C cycling, how they relate to each other is less well known. In this study, we aimed to explore this relationship on mature trees growing in the field. The measurements were performed on two canopy species, Quercus serrata Thunb. and Quercus glauca, in a warm temperate forest. The respiration and exudation rates of the same fineroot segment were measured in parallel with a syringe-basis incubation and a closed static chamber, respectively. We also measured root traits and ectomycorrhizal colonization ratio because these indexes commonly relate to root respiration and reflect root physiology. The microbial activity enhanced by root exudation was investigated by comparing the dissolved organic carbon (DOC) and microbial biomass carbon (MBC) between rhizosphere soils and bulk soils. Mean DOC concentration and MBC were ca two times higher in the rhizosphere soils and positively related to exudation rates, indicating that exudation further relates to the C dynamics in the soils. Flux rates of exudation and respiration were positively correlated with each other. Both root exudation and respiration rates positively related to ectomycorrhizal colonization and root tissue nitrogen, and therefore the relationship between the two fluxes may be attributed to fine-root activity. The flux rates of root respiration were 8.7 and 10.5 times as much as those of exudation on a root-length basis and a root-weight basis, respectively. In spite of the fact that flux rates of respiration and exudation varied enormously among the fine-root segments of the two Quercus species, exudation was in proportion to respiration. This result gives new insight into the fine-root C-allocation strategy and the belowground C dynamics. [ABSTRACT FROM AUTHOR]

Root-colonizing fluorescent pseudomonads, represented by Pseudomonas protegens , produce a number of antibiotic secondary metabolites and extracellular enzymes that contribute to the suppression of pathogens in the rhizosphere. An antibiotic exoproduct that is commonly produced by P. protegens and related strains is 2,4-diacetylphloroglucinol (DAPG). We recently screened and characterized DAPG-producing strains among ca. 3000 fluorescent pseudomonads isolated from samples collected in the field in Japan. The genome data obtained will provide insights into the characteristics of novel factor(s) contributing to the antibiotic activities of newly isolated strain(s). DAPG-producing strains were subjected to a comparative genomic analysis, and the results obtained showed the accumulation of strain-specific genomic repertoires for the biosynthesis of secondary metabolites that prevent soil-borne diseases. Exoproduct expression levels were dependent on the Gac/Rsm signal transduction pathway, indicating the conservation of this mechanism in these strains. We herein propose a number of strategies to control these useful strains by promoting this signal transduction pathway in the rhizosphere. • Screening of beneficial strains among ca. 3000 pseudomonads has been done. • Their genome data revealed novel factor(s) involved in the antibiotic activity. • Each genome features revealed the uniqueness of the species. • The production of secondary metabolites is regulated in common mechanisms. • Primary metabolites regulate bacterial behavior in rhizosphere. [ABSTRACT FROM AUTHOR]

The search for bacteria that can be used as biocontrol agents to control crop diseases yielded a promising candidate, Sm006 T , which was isolated from the rhizosphere of eggplant ( Solanum melongena ) growing in a field in Aichi Prefecture, Japan, in 2006. The cells were Gram-stain-negative, aerobic, non-spore-forming, rod-shaped and motile with one polar flagellum. The results of homology searches and phylogenetic analyses based on the 16S rRNA gene sequence indicated that Sm006 T represents a member of the genus Pseudomonas . The genomic DNA G+C content was 66.3 mol% and the major cellular fatty acids (more than 5 % of the total fatty acids) were summed feature 8 (C 18 : 1 ω7 c and/or C 18 : 1 ω6 c ), summed feature 3 (C 16 : 1 ω7 c and/or C 16 : 1 ω6 c ), C 16 : 0 and C 12 : 0 . Phylogenetic analyses using the rpoD gene sequence and phylogenomic analysis of the whole genome sequence revealed that Sm006 T represents a member of the Pseudomonas resinovorans group; however, its phylogenetic position does not match that of any known species of the genus Pseudomonas . The average nucleotide identity and digital DNA-DNA hybridisation values between the strain and closely related species were lower than the thresholds for prokaryotic species delineation (95-96 and 70 %, respectively), with the highest values observed for Pseudomonas tohonis TUM18999 T (92.05 and 46.3 %, respectively). Phenotypic characteristics, cellular fatty acid composition and possession of 2,4-diacetylphloroglucinol biosynthetic gene cluster could be used to differentiate the strain from its closest relatives. The phenotypic, chemotaxonomic and genotypic data obtained during this study indicated that Sm006 T represents a novel species of the genus Pseudomonas , for which we propose the name Pseudomonas solani sp. nov., with Sm006 T (= MAFF 212523 T = ICMP 24689 T ) as the type strain.

The occurrence of a parthenogenetic population of Longidorus jonesi in the rhizosphere of a Prunus sp. tree in a mixed evergreen forest is reported for the first time in Miyazaki ( Miyazaki prefecture), southern Japan, and constitutes the first report of this species in Japan. Nematode diagnosis matched well with the original description in India and a subsequent report in China. Morphometric traits of the Japanese population were characterized by a longer odontostyle length (123-142.5 vs. 107-120 μm) and some differences in c ratio (95.9-131.5 vs. 140-185) with respect to the original description, but closer to the Chinese population. This difference could be considered as geographical intraspecific variability. Molecular characterization from nuclear ribosomal RNA genes [ D2- D3 expansion segments of large ribosomal subunit (28 S) and internal transcribed spacer 1 ( ITS1)] was provided for the first time. Molecular analysis of D2- D3 and ITS1 showed a close relationship with L. diadecturus, a virus-vector nematode, by 94 and 79% similarity, respectively. The similarities in morphology, molecular and ecology ( L. jonesi and L. diadecturus are feeding mainly on Prunus species) suggest that this species could be a potential virus vector, as it is the case with L. diadecturus and peach rosette mosaic virus. [ABSTRACT FROM AUTHOR]

As part of the Kushiro Wetland Restoration Project, we evaluated the effect of the tree-cutting (February 2003) on soil water chemistry for 3 years in an alder ( Alnus japonica) shrubland on the peat soil in the Kushiro Wetland, the largest wetland in Japan. The alder stand was divided into two types; low stature and high stature stands, mean heights being 1.5 and 2.6 m, respectively. The treatment plot with tree cutting and the reference plot measuring 25 m × 25 m each were established in both stands, and a soil incubation experiment was also conducted by trenching the root zone of wetland vegetation in the treatment plots in both stands in the summer of 2004. The tree cutting did not substantially increase the concentrations of ammonium ion (NH) and nitrate ion (NO) in the soil water, although a gradual and slight increase of NO concentration was found after the tree-cutting only in the high stature stand (<10 μmol/l). This increase in the NO concentration in the high stature stand was probably due to the rhizosphere oxidation of wetland herbaceous vegetation, and was accompanied by the increase of Ca concentration. The soil incubation experiment showed no significant change of the nitrogen concentration, suggesting that inorganic nitrogen was immobilized and NO was denitrified intensively in this wetland peat soil. The results of this study suggested that this wetland ecosystem had a high potential to stabilize the soil water chemistry. [ABSTRACT FROM AUTHOR]

Populations of Athyrium yokoscense, a fern that hyperaccumulates Zn and Cd, have often been found at abandoned mining sites in Japan, and are often accompanied by another Zn and Cd hyperaccumulating plant, Arabis flagellosa. We compared the Zn and Cd uptake characteristics of At. yokoscense and Ar. flagellosa and examined the influences of community development on Zn and Cd uptake by each plant. A soil culture experiment was conducted using a rhizobox system with seven compartments, each filled with a metalliferous soil taken from Ikuno-cho, Hyogo Prefecture, Japan. The treatments consisted of the following three planting schemes: two plants of At. yokoscense (AY), two plants of Ar. flagellosa (AF) and a mixed planting of two plants of each species (AY+AF). After 3 months of cultivation, the Zn and Cd concentrations in the shoots were approximately 4.0 and 0.9 g kg−1 for At.  yokoscense in the AY treatment and 24 and 0.3 g kg−1 for Ar. flagellosa in the AF treatment, respectively. These results indicated that Ar. flagellosa was more efficient at accumulating Zn in the shoots than At. yokoscense. In the AY+AF treatment, the amounts of water-soluble Zn and Cd in the soil of the central compartments were significantly higher than those in the AY and AF treatments. Despite this, the Zn and Cd concentrations in the shoots of Ar. flagellosa in the AY+AF treatment were not significantly different from those in the AF treatment. The Cd content in the shoots of At. yokoscense was higher in the AY+AF treatment than in the AY treatment, owing to a growth enhancement in the AY+AF treatment. Consistent with the results for the AY and AF treatments, Ar. flagellosa accumulated higher shoot concentrations of Zn than At. yokoscense and At. yokoscense accumulated higher concentrations of Cd than Ar. flagellosa in the AY+AF treatment. These results suggested that the levels of Zn and Cd accumulated by these two plants were not largely affected by their community development, and implied that communities of these plants do not develop as a result of mutual effects on metal uptake. [ABSTRACT FROM AUTHOR]

We studied the effects of the application of organic matter (OM) and chemical fertilizer (CF) on soil alkaline phosphatase (ALP) activity and ALP-harboring bacterial communities in the rhizosphere and bulk soil in an experimental lettuce field in Hokkaido, Japan. The ALP activity was higher in soils with OM than in soils with CF, and activity was higher in the rhizosphere for OM than in the bulk soil. Biomass P and available P in the soil were positively related to the ALP activity of the soil. As a result, the P concentration of lettuce was higher in OM soil than in CF soil. We analyzed the ALP-harboring bacterial communities using polymerase chain reaction based denaturing gradient gel electrophoresis (DGGE) on the ALP genes. Numerous ALP genes were detected in the DGGE profile, regardless of sampling time, fertilizer treatment or sampled soil area, which indicated a large diversity in ALP-harboring bacteria in the soil. Several ALP gene fragments were closely related to the ALP genes of Mesorhizobium loti and Pseudomonas fluorescens. The community structures of the ALP-harboring bacteria were assessed using principal component analysis of the DGGE profiles. Fertilizer treatment and sampled soil area significantly affected the community structures of ALP-harboring bacteria. As the DGGE bands contributing to the principal component were different from sampling time, it is suggested that the major bacteria harboring the ALP gene shifted. Furthermore, there was, in part, a significant correlation between ALP activity and the community structure of the ALP-harboring bacteria. These results raise the possibility that different ALP-harboring bacteria release different amounts and/or activity of ALP, and that the structure of ALP-harboring bacterial communities may play a major role in determining overall soil ALP activity. [ABSTRACT FROM AUTHOR]

The article presents a study on recombinant deoxyribonucleic acid sequencing in Japan. The research was done by observing strain SA7, a new agar-degrading bacterium, that was isolated from plant roots. Hypothesis of the study revealed that the bacterium produces extracellular agarase and developed through its own agar. The investigation also uses zymogram analysis to determine its secretion extracellularly.

The environment of plant rhizosphere soil differs from that of non-rhizosphere soil due to the secretion of mucilage polysaccharides from the roots. This environment is regarded as one of the preferential habitats for agar-degrading bacteria. In a previous study, agar-degrading Steroidobacter agariperforans KA5-B T was isolated from agar-enriched agricultural soil using diffusible metabolites from Rhizobiales bacteria. Based on the hypothesis that similar characteristic bacteria still exist in the rhizosphere, isolation was performed using rhizosphere soils. Agar-degrading SA29-B T and YU21-B were isolated from onion and soybean rhizosphere soils. The 16S rRNA genes of these strains showed ≥98.7% identities with the most closely related strain KA5-B T . However, differences were noted in polysaccharide utilization, and average nucleotide identities were <95-96% against strain KA5-B T , indicating that they are different species from S. agariperforans KA5-B T . To investigate the distribution of bacterial sequences affiliated with novel strains, a primer set was designed and a meta-analysis of the 16S rRNA gene was performed. Sequences were widely distributed in rhizospheres throughout Japan, but varied in plant- and region-dependent manners. Regarding phenotypic characterization, distinguishable features were observed in growth temperatures, pH, and dominant fatty acids. SA29-B T and YU21-B grew at 15-40°C and pH 6.0-12 and contained C 16:0 as the dominant cell fatty acid, whereas KA5-B T showed no growth at 40°C and pH 12 and contained a moderate amount of C 16:0 . Based on these characteristics, SA29-B T (JCM 333368 T =KCTC 72223 T ) and YU21-B (JCM 333367=KCTC 72222) represent novel species in the genus Steroidobacter, for which the name Steroidobacter agaridevorans sp. nov. is proposed.

More than 3,000 isolates of fluorescent pseudomonads have been collected from plant roots in Japan and screened for the presence of antibiotic-synthesizing genes. In total, 927 hydrogen cyanide (HCN)-, 47 2,4-diacetylphloroglucinol (PHL)-, 6 pyoluteorin (PLT)-, 14 pyrrolnitrin (PRN)-, and 8 phenazine (PHZ)-producing isolates have been detected. A cluster analysis (≥99% identity) identified 10 operational taxonomic units (OTUs) in antibiotic biosynthesis gene-possessing pseudomonads. OTU HLR (PHL, PLT, and PRN) contained four antibiotics: HCN, PHL, PLT, and PRN, while OTU RZ (PRN and PHZ) contained three: HCN, PRN, and PHZ. OTU H1, H2, H3, H4, H5, H6, and H7 (PHL1-7) contained two antibiotics: HCN and PHL, while OTU H8 (PHL8) contained one: PHL. Isolates belonging to OTU HLR and RZ suppressed damping-off disease in cabbage seedlings caused by Rhizoctonia solani. Effective strains belonging to OTU HLR and RZ were related to Pseudomonas protegens and Pseudomonas chlororaphis, respectively. Antibiotic biosynthesis gene-possessing fluorescent pseudomonads are distributed among different geographical sites in Japan and plant species.

Microbial community structures associated with halophytes and their compositions among different habitats, particularly natural saline sites, have not yet been investigated in detail. In the present study, we examined the diversity and composition of the rhizosphere and root endosphere bacteria of two halophytes, Salicornia europaea L. and Glaux maritima L., collected from two adjacent brackish lakes, Lake Notoro and Lake Tofutsu, in Japan. The bacterial species richness and diversity indices of the two halophytes collected from both lakes showed no significant differences in the rhizosphere or root endosphere. In contrast, beta diversity and taxonomic analyses revealed significant differences in the bacterial communities from each halophyte between the two lakes even though the two locations were natural saline sites, indicating that the bacterial communities for S. europaea and G. maritima both fluctuated in a manner that depended on the geographical location. Common and abundant genera associated with each halophyte across the two lakes were then identified to verify the bacterial genera specifically inhabiting each plant species. The results obtained showed that the composition of abundant genera inhabiting each halophyte across two lakes was distinct from that reported previously in other saline soil areas. These results suggest that each halophyte in different geographical sites had an individual complex bacterial community.

Phosphorus (P) is an essential nutrient for crop production, while most soil P is the less labile P associated with Aluminum (Al) and Iron (Fe) in acidic soils of Japan. The objectives of this study were to evaluate the effects of two contrasting P-efficient legumes (white lupin, WL (Lupinus albus L.); and groundnut, GN (Arachis hypogaea L.)) on rhizosphere soil P dynamics in different soil types of Japan, such as Al-rich volcanic-soil, Fe-rich red-yellow-soil, and sandy-soil, with or without historical fertilization managements (3 soil types × 2 managements = 6 soil samples). We conducted a 56-day pot experiment, and analyzed the plant P uptake and fractionated P of rhizosphere and bulk soils, based on the Hedley-fractionation method. We observed that GN P uptake was generally larger than that in WL in most soil types and managements. WL significantly decreased the labile P in most soils and also decreased the less labile inorganic P (Pi) and organic P (Po) in fertilized Red-yellow-soil, which has much crystalline Fe, though GN did not. In contrast, both WL and GN significantly decreased the less labile Pi in fertilized volcanic-soil, which has much non-crystalline Al. These results indicate that (1) characteristics of less labile P uptake by P efficient legumes were different between the soil types and managements, and (2) WL efficiently solubilized the less labile P than GN in fertilized red-yellow soil, while GN efficiently absorbed the larger amount of P than WL, especially in volcanic- and sandy-soil. [ABSTRACT FROM AUTHOR]

In 1984 at Mt. Ontake in Japan, an earthquake caused a devastating landslide, and as a result, the vegetation on the south slope of the mountain was completely eliminated. In higher elevation (2000 m) areas, revegetation has not yet been completed even 30 years after the landslide. Revegetation progress throughout the area was heterogeneous. In the partially revegetated areas, actinorhizal plant species such as Alnus maximowiczii and Alnus matsumurae have been found. In the present study, we investigated the Frankia communities in the higher-elevation area using sequence analysis of the amplified nifH (dinitrogenase reductase) gene from nodule and soil samples collected in the disturbed region, undisturbed forest, and in the boundary between the disturbed region and the undisturbed forest. Phylogenetic analysis of partial nifH sequences revealed the presence of six clusters, each of which consisted of highly similar (> 99%) sequences. Four clusters showed significant sequence similarity to Frankia (three Alnus- and a Casuarina-infecting strains). Diversity in the Frankia community was relatively low-only one or two clusters were detected in a site. At most of the sampling sites, a dominant cluster in a nodule coincided with that in rhizosphere soil, indicating that community structure in the rhizosphere is a primary factor that determines occupancy in a nodule. No significant difference in community structure was observed between plant species. Diversity in the Frankia community varied depending on revegetation progress. Cluster A, which was the most dominant in the disturbed region, was likely to have invaded from undisturbed forest.

A novel actinobacterium, designated strain NEAU-TPG4(T) was isolated from rhizosphere soil of Pinus koraiensis Sieb. et Zucc. collected from Luobei, Heilongjiang Province, north China, and characterized using a polyphasic approach. Morphological and chemotaxonomic properties of strain NEAU-TPG4(T) were consistent with the description of the genus Dactylosporangium. The strain formed finger-shaped sporangia on short sporangiophores that emerged directly from substrate hyphae. The cell-wall peptidoglycan consisted of meso- and 3-hydroxy-diaminopimelic acids; arabinose, xylose and glucose were found as whole-cell sugars. The phospholipid profile contained diphosphatidylglycerol, phosphatidylethanolamine, phosphatidylglycerol and phosphatidylinositol. The predominant menaquinones were identified as MK-9(H8) and MK-9(H6). The predominant cellular fatty acids were identified as iso-C16:0, anteiso-C15:0, anteiso-C17:0 and C18:0. Phylogenetic analysis using 16S rRNA gene sequences also indicated that the strain should be classified in the genus Dactylosporangium and showed that the closest relatives were Dactylosporangium maewongense Japan Collection of Microorganism (JCM) 15933(T) (99.6 %), Dactylosporangium siamense NBRC 106093(T) (99.6 %), Dactylosporangium aurantiacum JCM 3083(T) (99.5 %) and Dactylosporangium luteum JCM 17685(T) (99.5 %). However, the low level of DNA-DNA relatedness and several cultural and physiological characteristics allowed the strain to be distinguished from its closest relatives. Thus, it is proposed that strain NEAU-TPG4(T) represents a novel Dactylosporangium species. Dactylosporangium cerinum sp. nov. The type strain of D. cerinum is NEAU-TPG4(T) (=CGMCC 4.7152(T) = DSM 46712(T)).

A polyphasic approach was used to determine the taxonomic position of actinomycete strain R1-NS-10(T), which was isolated from a sample of strawberry root rhizosphere obtained from Hokuto, Yamanashi, Japan. Strain R1-NS-10(T) was Gram-staining-positive and aerobic, and formed brownish-white aerial mycelia and grayish-brown substrate mycelia on ISP-2 medium. The strain grew in the presence of 0-5% (w/v) NaCl and optimally grew without NaCl. The strain grew at pH 5-8, and the optimum for growth was pH 7. The optimal growth temperature was 30 °C, but the strain grew at 5-37 °C. Whole-cell hydrolysates of strain R1-NS-10(T) contained A2pm, galactose, mannose and rhamnose. The predominant menaquinones were MK-9(H6) and MK-9(H8). The major cellular fatty acids were anteiso-C15:0 and iso-C16:0. Comparative 16S rRNA gene sequence analysis revealed that strain R1-NS-10(T) was most closely related to Streptomyces prunicolor NBRC 13075(T) (99.4%). The draft genome sequences of both strains were determined for characterization of genome sequence-related parameters such as average nucleotide identity (ANI) and the diversity of secondary metabolite biosynthetic gene clusters. DNA-DNA hybridization (DDH) and ANI values for both strains were below the species delineation cutoff, and differences in physiological and biochemical characteristics differentiated strain R1-NS-10(T) from its closest phylogenetic relative. On the basis of these data, we propose that strain R1-NS-10(T) (=NBRC 108812(T)=KCTC 29186(T)) should be classified as the type strain of a novel Streptomyces species named Streptomyces hokutonensis sp. nov.

A novel strain of Gram-staining-positive bacterium, designated HI08-69(T), was isolated from the rhizosphere of a mangrove on Iriomote Island, Japan, and its taxonomic position was investigated by a polyphasic approach. The strain had peptidoglycan of the A4α type, with lysine as the diagnostic diamino acid. The predominant menaquinone was demethylmenaquinone DMK-9(H(4)) and the major fatty acids were anteiso-C(15:0), anteiso-C(17:0) and C(16:0). The major polar lipids were diphosphatidylglycerol, phosphatidylglycerol, phosphatidylinositol and an unidentified polar lipid but minor amounts of other polar lipids were also detected. The genomic DNA G+C content of strain HI08-69(T) was 71.7 mol%. In phylogenetic analyses based on 16S rRNA gene sequences, the novel strain and members of the genus Demequina formed a monophyletic cluster, with pairwise sequence similarities of 95.6-96.8%. However, strain HI08-69(T) was clearly distinguishable from all established members of the genus Demequina in terms of several chemotaxonomic characteristics. On the basis of the phenotypic and genotypic characteristics, strain HI08-69(T) represents a novel species in a new genus for which the name Lysinimicrobium mangrovi gen. nov., sp. nov. is proposed. The type strain of the type species is HI08-69(T) ( = NBRC 105856(T) = DSM 24868(T)).

A total of 100 isolates of chitinolytic bacteria were obtained from the rhizospheres of various agronomic plants, and the 16S rRNA gene sequences of these isolates were determined. Phylogenetic analyses revealed that 81 isolates belonged to the classes Betaproteobacteria (39 isolates) and Gammaproteobacteria (42 isolates). Of the remaining 19 isolates, 16 belonged to the phylum Firmicutes. Clustering analysis identified 6 and 3 operational taxonomic units (OTUs) in Gammaproteobacteria and Betaproteobacteria, respectively, at the genus level. The majority of chitinolytic bacteria in Gammaproteobacteria belonged to the genera Serratia, Stenotrophomonas, and Lysobacter (14, 15, and 7 isolates, respectively) while those in Betaproteobacteria belonged to the genus Mitsuaria (37 isolates). The 16 isolates placed in Firmicutes belonged to 2 genera, Paenibacillus and Bacillus (8 isolates each). The isolates in the remaining OTUs belonged to the genera Erwinia, Aeromonas, Pseudomonas, Achromobacter, Flavobacterium, and Microbacterium, in less abundance. These results showed a wide distribution of culturable chitinolytic bacteria in the rhizospheres of various agronomic plants. Considering the potential antagonistic activity of chitinolytic enzymes against phytopathogenic fungi, which is exhibited by fungal cell wall degradation, the above-mentioned native chitinolytic bacteria in rhizospheres could potentially be utilized for the biological control of soil-borne phytopathogenic fungi.