Soil In Japan Research Articles

Determining Irrigation Volumes for Enhancing Profit and N Uptake Efficiency of Potato Using WASH_2D Model

Soaring food prices and the intensified scarcity of water resources put a new emphasis on efficient use of water in irrigation. Numerical models for water flow and crop growth can be used to predict crop water stress and make decisions on irrigation management. To this end, a new irrigation scheme was presented to determine the optimum irrigation depths using WASH_2D, a numerical model of water flow and solute transport in soils and crop growth. By using freely available quantitative weather forecasts and volumetric water price as input data to predict soil water flow and give the recommendation of irrigation depths which maximizes net income during each irrigation interval. Field experiments using potato were conducted for two-seasons in a sandy soil in Japan under three irrigation methods, i.e., using the simulation model named treatment “S” (to distinguish, named S1 in first season and S2 in second season), automatic irrigation method using soil moisture sensors named treatment “A”, and refilling irrigation management supplying 100% consumed water named treatment “R”. To compare S with other two treatments, S1 and A was conducted in the first season, then S2 and R was conducted in the second season. Results showed that S1 improved potato yield by 19%, and reduced water by 28%, resulting in an increased net income by 19% compared with A in the first season. There was no significant difference when compared with R in the second season, which was mainly due to the frequent rainfall during second growing season. In addition, S improved the nitrogen uptake efficiency (NUPE) by 39% and 11% compared with A and R, respectively. The simulated values of water content were in fair agreement with those measured in the root zone. In short, simulated irrigation method was effective in improving yield, saving water and increasing NUPE of potato compared with automatic and refilling irrigation methods in sandy field.

Clostridium gelidum sp. nov., a psychrotrophic anaerobic bacterium isolated from rice field soil.

A cold-adapted or psychrotrophic anaerobic bacterial strain (C5S11T) was isolated from rice field soil in Japan using an enrichment culture incubated at 5 °C. C5S11T grew at 0 °C and optimum growth was observed at 10 °C. Cells of C5S11T were Gram-stain-positive, motile, spore-forming rods with peritrichous flagella. C5S11T was assigned to a large branch consisted of various mesophilic species of the genus Clostridium in the phylogenetic trees reconstructed using the 16S rRNA gene sequences. The most closely related species of the strain was Clostridium chromiireducens DSM 23318T (98.5 % sequence similarity). C5S11T fermented various carbohydrates, including polysaccharides (starch, inulin, pectin and xylan), and produced acetate, butyrate and H2 as major products. The major cellular fatty acids were C16 : 0, C16 : 1ω9c, C14 : 0 and C16 : 1ω7c. The diagnostic diamino acid of the cell wall peptidoglycan was meso-diaminopimelic acid. The genome size of C5S11T was 6.04 Mb and the genomic DNA G+C content was 29.0 mol%. Average nucleotide identity by blast (ANIb), avaerage amino acid identity (AAI) and digital DNA–DNA hybridization (dDDH) values between the genomes of C5S11T and C. chromiireducens DSM 23318T were 80.0, 75.2 and 26.4 %, respectively. C5S11T had a gene encoding cold shock protein (RNA chaperone) in the genome, homologues of which have been found in psychrophilic species of the genus Clostridium . On the basis of the differences in the phylogenetic, genomic and phenotypic characteristics of C5S11T from those of the closely related species, a novel species, Clostridium gelidum sp. nov., is proposed to accommodate the strain. The type strain is C5S11T (=NBRC 114689T = DSM 112608T).

Draft Genome Sequence of Paenibacillus sp. Strain L3-i20, Isolated from Soil in Japan.

ABSTRACTThis study describes the draft genome sequence of Paenibacillus sp. strain L3-i20, obtained from an assembly of long reads and subsequently polished using short reads. The draft genome comprises a 5,308,756-bp chromosome with a GC content of 41.6% and no plasmids.

Complete Genome Sequences of Four Parageobacillus Strains Isolated from Soil in Japan.

ABSTRACTWe isolated four Parageobacillus strains from soil in Japan and completely sequenced their genomes. Three of four strains showed ≥98.9% average nucleotide identity (ANI) to Parageobacillus caldoxylosilyticus S1812T, while one strain, designated KH3-4, showed the highest ANI (91%) to Parageobacillus thermantarcticus M1T, suggesting the species novelty of KH3-4.

Isolation and Characterization of Phosphate Solubilizing Bacteria from Paddy Field Soils in Japan.

Phosphorus (P) is abundant in soil and is essential for plant growth and development; however, it is easily rendered insoluble in complexes of different types of phosphates, which may lead to P deficiency. Therefore, increases in the amount of P released from phosphate minerals using microbial inoculants is an important aspect of agriculture. The present study used inorganic phosphate solubilizing bacteria (iPSB) in paddy field soils to develop microbial inoculants. Soils planted with rice were collected from different regions of Japan. Soil P was sequentially fractionated using the Hedley method. iPSB were isolated using selective media supplemented with tricalcium phosphate (Ca-P), aluminum phosphate (Al-P), or iron phosphate (Fe-P). Representative isolates were selected based on the P solubilization index and soil sampling site. Identification was performed using 16S rRNA and rpoB gene sequencing. Effectiveness was screened based on rice cultivar Koshihikari growth supplemented with Ca-P, Al-P, or Fe-P as the sole P source. Despite the relatively homogenous soil pH of paddy field sources, three sets of iPSB were isolated, suggesting the influence of fertilizer management and soil types. Most isolates were categorized as β-Proteobacteria (43%). To the best of our knowledge, this is the first study to describe the genera Pleomorphomonas, Rhodanobacter, and Trinickia as iPSB. Acidovorax sp. JC5, Pseudomonas sp. JC11, Burkholderia sp. JA6 and JA10, Sphingomonas sp. JA11, Mycolicibacterium sp. JF5, and Variovorax sp. JF6 promoted plant growth in rice supplemented with an insoluble P source. The iPSBs obtained may be developed as microbial inoculants for various soil types with different P fixation capacities.

Correction for Nakao et al., "Complete Genome Sequence of Leptospira kobayashii Strain E30, Isolated from Soil in Japan".

Volume 10, no. 45, e00907-21, 2021, https://doi.org/10.1128/MRA.00907-21. After publication, the authors became aware that the sequences of pE30-2 were derived from the PhiX sequencing control. We apologize for the inconvenience caused.

Complete Genome Sequence of Leptospira kobayashii Strain E30, Isolated from Soil in Japan.

ABSTRACTThe spirochete bacterium Leptospira kobayashii is a recently designated species of the genus Leptospira. Here, we report the complete genome sequence of L. kobayashii strain E30, consisting of two circular chromosomes and two plasmids.

Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov., three new species of endophytes with distinctive morphology and functional traits.

A growing interest in fungi that occur within symptom-less plants and lichens (endophytes) has uncovered previously uncharacterized species in diverse biomes worldwide. In many temperate and boreal forests, endophytic Coniochaeta (Sacc.) Cooke (Coniochaetaceae, Coniochaetales, Sordariomycetes, Ascomycota) are commonly isolated on standard media, but rarely are characterized. We examined 26 isolates of Coniochaeta housed at the Gilbertson Mycological Herbarium. The isolates were collected from healthy photosynthetic tissues of conifers, angiosperms, mosses and lichens in Canada, Sweden and the United States. Their barcode sequences (nuclear ribosomal internal transcribed spacer and 5.8S; ITS rDNA) were ≤97% similar to any documented species available through GenBank. Phylogenetic analyses based on two loci (ITS rDNA and translation elongation factor 1-alpha) indicated that two isolates represented Coniochaeta cymbiformispora, broadening the ecological niche and geographic range of a species known previously from burned soil in Japan. The remaining 24 endophytes represented three previously undescribed species that we characterize here: Coniochaeta elegans sp. nov., Coniochaeta montana sp. nov. and Coniochaeta nivea sp. nov. Each has a wide host range, including lichens, bryophytes and vascular plants. C. elegans sp. nov. and C. nivea sp. nov. have wide geographic ranges. C. montana sp. nov. occurs in the Madrean biome of Arizona (USA), where it is sympatric with the other species described here. All three species display protease, chitinase and cellulase activity in vitro. Overall, this study provides insight into the ecological and evolutionary diversity of Coniochaeta and suggests that these strains may be amenable for studies of traits relevant to a horizontally transmitted, symbiotic lifestyle.

Complete Genome Sequence of Actinoplanes sp. Strain L3-i22, Isolated from Soil in Japan

ABSTRACTHere, we described the closed complete genome sequence of Actinoplanes sp. strain L3-i22, which was obtained from the assembly with long reads and subsequent polishing with short reads. The complete genome consists of a 12,014,766-bp chromosome, with a GC content of 71.4%, and contains no plasmids.

Constraining models for methane oxidation based on long-term continuous chamber measurements in a temperate forest soil

Upland soils are thought to be a sink of CH4, the second most important anthropogenic greenhouse gas, owing to oxidation by methanotrophs. To better understand CH4 fluxes in upland forests, we quasi-continuously measured CH4 fluxes using an automated closed chamber system over seven years on a larch plantation in a volcanic soil in Japan. We hypothesized that the long-term data sufficiently can calibrate modules for CH4 fluxes, and aimed to predict future pathways of CH4 uptake and their uncertainties in the forest. Based on the observations, a thinning of the overstory only marginally influenced the CH4 fluxes measured by the chambers. Using the data with a Bayesian method, we calibrated four modules for CH4 fluxes in forest soils, which were embedded in the process-based ecosystem model VISIT. The modules well reproduced the observed seasonality, annual budgets, and interannual variability in the CH4 fluxes after calibrating the following parameters: the diffusion coefficient or base CH4 oxidation rate constant and temperature sensitivity. The CH4 fluxes were predicted to increase in the future under the RCP8.5 scenario but to decrease under the RCP 2.6 scenario. The contrasting trajectory was caused by rising and decreasing CH4 concentrations under the RCP 8.5 and 2.6 scenarios, respectively. Furthermore, the magnitudes of the future changes in the fluxes differed in each module because the responses to the changes in the CH4 concentrations were inconsistent among the modules. The observed CH4 fluxes increased with increasing atmospheric CH4 concentration (4.95 mg CH4 m−2 d−1 ppm−1), which was greater in magnitude than those in the modules. Considering the uncertainties in the modules and potential confounding effects in the observations, we conclude that further understanding the responses of CH4 uptake to rising CH4 concentrations is required.

An investigation of upland soil fertility from different soil types

Soil type is a vital determinant of soil fertility because of its characteristic biological, chemical, and physical properties. However, the soil fertility of upland soil is probably changed by different agricultural management practices regardless of soil type. This study investigated the features of soil fertility (bacterial biomass, total carbon (TC), and total nitrogen (TN)) in upland fields in Japan. One thousand soil samples from different soil types were collected from upland fields located on 36 prefectures in Japan. The soil fertility was analyzed using the Soil Fertility Index (SOFIX). There were six soil types included in this study: Organic soils (B), Andosols (D), Lowland soils (F), Red-yellow soils (G), Stagnic soils (H), and Brown Forest soils (I). Of these, the soil types D and F occupied the largest percentage of samples. The values of bacterial biomass, TC, and TN varied greatly, regardless of soil type. The soil fertility does not seem to be characterized by the soil type in upland soils in Japan. The correlations between bacterial biomass and TC (r = 0.23, p < 0.01) and bacterial biomass and TN (r = 0.16, p < 0.01) were relatively weak. Conversely, the correlation between TC and TN (r = 0.68, p < 0.01) was moderate. In soil type D, up to 40% of samples had no bacterial biomass detected and 17% possessed a low bacterial biomass. The effect of the soil types may not be a critical factor in soil fertility in the upland fields.

Geomesophilobacter sediminis gen. nov., sp. nov., Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., three novel members in the family Geobacterecace isolated from river sediment and paddy soil

Bacteria in the family Geobacteraceae have been proven to fill important niches in a diversity of anaerobic environments and global biogeochemical processes. Here, three bacterial strains in this family, designated Red875T, Red259T, and Red421T were isolated from river sediment and paddy soils in Japan. All of them are Gram-staining-negative, strictly anaerobic, motile, flagellum-harboring cells that form red colonies on agar plates and are capable of utilizing Fe(III)-NTA, Fe(III) citrate, ferrihydrite, MnO2, fumarate, and nitrate as electron acceptors with acetate, propionate, pyruvate, and glucose as electron donors. Phylogenetic analysis based on the 16S rRNA gene and 92 concatenated core proteins sequences revealed that strains Red259T and Red421T clustered with the type strains of Geomonas species, whereas strain Red875T formed an independent lineage within the family Geobacteraceae. Genome comparison based on  average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH) values clearly distinguished these three strains from other Geobacteraceae members, with lower values than the thresholds for species delineation. Moreover, strain Red875T also shared low average amino acid identity (AAI) and percentage of conserved proteins (POCP) values with the type species of the family Geobacteraceae. Based on these physiological, chemotaxonomic, and phylogenetic distinctions, we propose that strain Red875T (=NBRC 114290T = MCCC 1K04407T) represents a novel genus in the family Geobacteraceae, namely, Geomesophilobacter sediminis gen. nov., sp. nov., and strains Red259T (=NBRC 114288T = MCCC 1K05016T) and Red421T (=NBRC 114289T = MCCC 1K06216T) represent two novel independent species in the genus Geomonas, namely, Geomonas propionica sp. nov. and Geomonas anaerohicana sp. nov., respectively.

Ultrasonic Removal of Clogging and Evaluation of Flow Capacity of Geotextile Drain

Clogging of geotextile drains is very common when used in fine-grained soil geo-structure such as reinforced earth retaining wall, slopes, embankments. As on date the index properties of the embedded drains are usually standardized with respect to factory-defined parameters. This paper explains the application of ultrasonic excitation for the removal of clogging of geotextiles drains extracted from two fine-grained soils, Kanto Loam, a naturally occurring soil in Japan and a commercially available clayey silt, whose drainage capacity was tested with consolidation from slurry stage. The mechanism of ultrasound for the cleaning of clogging as well as various other similar industrial applications has been explained. The amounts fine-grained soil entrapped within geotextile pores, before and after cleansing in an ultrasonic water tub was evaluated. Several terms, such as clogging index, clogging potential, cleansing efficiency, have been explained and evaluated based on the experimental data. The in-plane and cross-plane flows of clogged geotextile drains, both before and after ultrasonic cleaning, showed that cleansing efficiency was greater than 80%, which were irrespective of the type of geotextile selected and the nature of clogging by both fine-grained soils. Compared to the clogged geotextile specimens’ transmissivity and permittivity recovered nearly to 75% and above after ultrasonic cleaning. The importance of geotextile drains under confinement and in situ removal of its clogging by ultrasonics is elaborated.

Winter CH4 oxidation in cold-temperate grassland soils of northern Japan: 222Rn as a proxy for the validation of CH4 diffusivity

Amidst changing seasonal snow-covered periods and extents in northern high latitude regions, winter CH4 oxidation is susceptible to drastic climate change, all of which modulates an accurate assessment of regional carbon balance. The importance of winter CH4 oxidation to the soils in these regions has previously been recognized; in this study, concentrations of CH4 and 222Rn were observed in the snowpack and underlying cold temperate soils during the winters of 1995/96 and 1996/97. These observations were carried out in order to 1) validate the 222Rn tracer as a proxy for variations in CH4 diffusivity within a snowpack containing many seasonal ice lenses, and to 2) estimate winter CH4 oxidation through the snowpack to the soils. Winter CH4 oxidations estimated by snow density (method 1); using the 222Rn tracer under steady (method 2) and non-steady (method 3) conditions; and using a static chamber (method 4) during the winter of 1996/97 yielded 16.7 ± 6.3; 8.2 ± 2.9; 9.8 ± 7.4; and 4.5 ± 2.5 mg CH4–C m−2, respectively. These results suggest that contributions from average CH4 oxidation represent 23.3% (range: 12.7–35.1%) of the annual CH4 oxidation into cold temperate soils. Wintertime CH4 oxidation significantly reflects temporal variation in the snowpack, demonstrating that soil temperature depends on snow cover, and that a threshold snow depth of 40 cm does not prevent, but rather promotes, atmospheric CH4 oxidation through snowpack to the soils. These findings demonstrate that the 222Rn tracer was useful for estimating winter CH4 diffusivity and oxidation, using a one-dimensional vertical diffusion box model in cold temperate soils in Japan during multiple snow-covered seasons.

Soil organic carbon was more strongly linked with soil phosphate fixing capacity than with clay content across 20,000 agricultural soils in Japan: a potential role of reactive aluminum revealed by soil database approach

ABSTRACT Identifying the soil properties that control soil organic carbon (SOC) storage is a critical step to monitor and manage SOC at regional and global scales. While clay content has been commonly used to explain SOC variation and to model SOC dynamics, recent studies point to the significant control of extractable metal phases such as pyrophosphate extractable Al (Alp) for a range of soil types. Phosphate adsorption coefficient (PAC), soil’s capacity to adsorb phosphate, is known to show strong positive correlation with Alp. The soil database maintained by the national farmland fixed–point survey contains basic soil attributes including SOC and PAC and covers approximately 20,000 sites that belong to Andosols and Lowland soil great groups, representing roughly 70% of the arable land in Japan (MAT range from 5.3 to 22.3 °C). Using the database, we found that PAC showed more significant positive correlation with SOC compared to clay and silt–clay contents for both Lowland soils and Andosols. The OC:Alp ratio was estimated from the slope of SOC:PAC regression line for all soil groups and great groups ranged from 3.35 to 10.5 (mol:mol), which was within the range shown in previous studies on volcanic and spodic soils. The ANCOVA test further revealed that the SOC–PAC relationship was significantly affected by soil temperature regime in both soil group and soil great group levels (both p < 0.0001). All four soil groups within Lowland soils showed a similar temperature-dependent trend in the SOC:PAC ratio with little variation among the groups. The soil groups within Andosols, however, had no clear temperature trend, suggesting the influence of other factors that remain to be elucidated in future. We concluded that PAC was the more effective indicator of SOC than clay content for the major arable soils in Japan and that the PAC–SOC relationship was partly controlled by soil temperature and soil group. Further study to assess the role of Alp and the contribution of other factors such as land use and management type is important as major portions of the SOC variation was not explained by PAC.

Quantification of Phytophthora infestans population densities and their changes in potato field soil using real-time PCR

Tuber infection of Phytophthora infestans often occurs at harvest. However, it is difficult to accurately estimate the population densities of P. infestans in soil, especially Japanese soil. In the present study, P. infestans DNA was extracted from soil samples using a modified CTAB-bead method and quantified using real-time PCR to accurately, rapidly and easily estimate the P. infestans population densities in upland soils in Japan. P. infestans was well quantified in eleven types of soil samples, including nine types of upland soils in Japan, that were artificially inoculated with a zoosporangia suspension. The amounts of P. infestans DNA estimated by the real-time PCR were proportional to the inoculum densities. In the non-controlled experimental potato field, P. infestans population densities in soil corresponded to the development of symptoms and were correlated with the number of lesions on the potato foliage. These results imply that the proposed real-time PCR assay is suitable for the estimation or monitoring of P. infestans population densities in upland soils in Japan. The population densities at the ridge bottoms were larger than those at any other location in commercial potato fields. These results were similar to those of a previous report using a bioassay. Moreover, a correlation between DNA quantity and inoculum potential was observed. In conclusion, the real-time PCR assay developed in this study is suitable for indirect estimation of the inoculum potential of P. infestans.

Complete Genome Sequence of Kaistia sp. Strain 32K, Isolated from Soil as a Mixed Single Colony with Methylobacterium sp. Strain ME121.

Kaistia sp. strain 32K, an aerobic Gram-negative bacterium, was isolated from soil in Japan. Here, we report the complete genome sequence of this bacterium, which has a 5.4-Mbp genome sequence, containing 4,919 protein-coding sequences.

Laboratory and field measurement of magnetic susceptibility of Japanese agricultural soils for rapid soil assessment

Measuring volume magnetic susceptibility (κ) of soil allows rapid soil assessment. In this study, we measured the κ value of agricultural surface soils in Japan at national and farm scales in order to evaluate the scale-dependent relationship between soil κ and other soil properties and to examine the repeatability of the κ value measured in the laboratory and in the field. A handheld field sensor was used to measure two sample sets: (1) 164 samples collected throughout Japan (national scale), and (2) 246 samples collected from paddy fields in Takatsuki and 117 (39 sites × 3 times) samples collected from paddy fields in Mifune (farm scale). Laboratory measurements showed that the coefficients of variation of soil κ were 112% for the national scale samples, 13% for the Takatsuki samples, and 33–37% for the Mifune samples. The large variation at the national scale was due to several positive outliers, which were classified as Vitric or Silandic Andosols by the WRB classification. Repeated measurement of samples enabled estimation of the within-sample variation in κ, and the data was considered unreliable if the coefficient of variation exceeded 10%. The correlation analysis using the reliable data indicated that at the national scale, the κ value was most positively correlated with structural Fe (total Fe minus Fed) followed by Alo and the andic properties (Alo + 1/2Feo). In contrast, for the Mifune samples collected at the farm scale, the κ value was most positively correlated with sand content followed by K saturation percentage. Field measurements of soil κ at the 39 Mifune sites indicated that the coefficients of variation of κ at the same site were almost all below 10%. The within-site variations were due probably to the incomplete contact between the soil surface and the sensor. Our results suggest that measuring κ of agricultural surface soils in Japan can help to distinguish Vitric or Silandic Andosols from other soils, and to estimate the κ-related soil properties at the farm and national scales.

Complete Genome Sequence of the Cesium-Accumulating Bacterium Rhodococcus qingshengii CS98, Isolated from Soil in Japan.

Rhodococcus qingshengii CS98 is a bacterium isolated from soil in Japan that shows strong cesium-accumulating ability. Here, we report the complete genome sequence of R. qingshengii (6.7 Mb), which may provide useful genetic information supporting its bioremediation features.

Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov., isolated from terrestrial environments, and emended description of the genus Geomonas

Three bacterial strains, designated Red330T, Red736T and Red745T, were isolated from forest and paddy soils in Japan. Strains Red330T, Red736T and Red745T are flagella-harbouring and strictly anaerobic bacteria forming red colonies. A 16S rRNA gene sequence-based phylogenetic tree showed that all three strains were located in a cluster, including the type strains of Geomonas species, which were recently separated from the genus Geobacter within the family Geobacteraceae. Similarities of the 16S rRNA gene sequences among the three strains and Geomonas oryzae S43T, the type species of the genus Geomonas, were 96.3-98.5 %. The genome-related indexes, average nucleotide identity, digital DNA-DNA hybridization, and average amino acid identity, among the three strains and G. oryzae S43T were 74.7-86.8 %, 21.2-33.3 % and 70.4-89.8 %, respectively, which were lower than the species delineation thresholds. Regarding the phylogenetic relationships based on genome sequences, the three strains clustered with the type strains of Geomonas species, which were independent from the type strains of Geobacter species. The distinguishableness of the three isolated strains was supported by physiological and chemotaxonomic properties, with the profile of availability of electron donors and cellular fatty acids composition being particularly different among them. Based on genetic, phylogenetic and phenotypic properties, the three isolates represent three novel independent species in the genus Geomonas, for which the names Geomonas silvestris sp. nov., Geomonas paludis sp. nov. and Geomonas limicola sp. nov. are proposed. The type strains are Red330T (=NBRC 114028T=MCCC 1K03949T), Red736T (=NBRC 114029T=MCCC 1K03950T) and Red745T (=NBRC 114030T=MCCC 1K03951T), respectively.