Succession of microbiota estimated by phospholipid fatty acid analysis and changes in organic constituents during the composting process of rice straw

The succession of responsible microbiota during the composting process of rice straw (RS) was studied for 145 d in relation to the changes in the organic constituents of RS. During the composting process, the C / N ratio of RS decreased from 56 to 22. On a C basis, the relative contents of lipid, water-soluble organic matter (WSOM), hemicellulose, cellulose, and lignin fractions in RS changed from 5.6, 8.9, 32.9, 17.9, and 34.0%, to 7.3, 5.8, 30.7, 3.8, and 51.1%, respectively, indicating that the cellulose fraction was mainly decomposed in the composting process. Biomass C accounted for 18.3% (on day 75 when the total amount of phospholipid fatty acids (PLFAs) reached a peak) and 11.5% (at the end of composting) of the total C of RS under the composting process. As for PLFAs, the biomarkers of fungi and Gram-negative bacteria predominated in the RS material used. At the thermophilic stage (the first 2 weeks), biomarkers of Gram-positive bacteria and actinomycetes predominated. After the thermophilic stage, biomarkers of other Gram-positive bacteria became dominant. Finally, at the curing stage, the proportion of the biomarkers of Gram-negative bacteria and eukaryotes increased, indicating the co-contribution of Gram-positive and Gram-negative bacteria and fungi in the decomposition process at this stage. The trans / cis ratio of 16 : 1ω7 PLFA of RS under the composting process ranged from 0.18 to 0.30, indicating that the composting process of RS prepared a significantly lower environmental stress (p < 0.01) compared to the decomposition of RS in a submerged paddy soil.     

Land use dynamics and nutrient characteristics of soils and plants along topo-sequences in inland valley watersheds of Ashanti region,Ghana

Surveys on land use dynamics were conducted over a 3-year period along various toposequences in benchmark inland valley watersheds of the Ashanti region, Ghana. Six typical land use systems were selected for more detailed studies, Le., primary forest (PF), cacao farm (CP), fallow (Fallow), mixed cropping (MC), and lowland rice-based systems including both traditional rice (TR) and sawah{ft1} (paddy)-based rice farming (Sawah). Topsoil samples (0-20 cm) and samples of leaves and bark of various plants were collected from these land use systems for nutrient characterization using laboratory analyses. The remaining primary and secondary forests cover only a patchy area, accounting for less than 20%, in forest reserves and surrounding areas. Cacao farms were developed both in the upland areas, middle slopes, and lowland areas, which occupied about 20% of the watershed. Lowland rice farming is estimated to account for about 10% of the watershed. Oil palm cultivation is also common in the lowland areas. The remaining land use systems were mostly fallow and mixed cropping of maize, cocoyam, cassava, and plantain. Plant leaves of various species in the lowland traditional rice area showed higher concentrations of phosphorus and potassium but lower calcium and strontium concentrations than those of the leaves in the upland surveyed plots, especially, the forest area. Nitrogen, sulfur, magnesium, and the other mineral elements, however, did not show any clear differences among the six land use systems. Bark samples tended to exhibit lower concentrations of nitrogen, phosphorus, sulfur, magnesium, sodium, silicon, aluminum, iron, manganese, and copper but higher concentrations of calcium and strontium. Cacao leaves showed silicon-accumulator characteristics and the magnesium concentration was high too. Cacao bark contained potassium and zinc in appreciable amounts in compared to the leaves. Topsoil samples of the primary forest and cacao farms in the upland areas showed higher levels of TC, TN, exchangeable Ca and Mg, and eCEC while the levels of available P showed a rather reverse trend compared to the lowland traditional and sawah rice plots. Topsoil samples of the fallow and mixed cropping plots at upland and fringe sites showed intermediate levels. The pH at the mixed cropping site was the lowest. These general fertility trends along upland and lowland topo-sequences were different from those of monsoon Asia and Japan. With the implementation of the sawah rice-based farming system, the inland valleys could contribute to the enhancement of sustainable food production in the country.     

Manure application has an effect on the carbon budget of a managed grassland in southern Hokkaido,Japan

Abstract

The carbon (C) budget of managed grassland in a cool-temperate region of Japan was estimated using a combination of eddy covariance and the biometric method for five years, to evaluate the effect of manure application. Chemical fertilizer was applied to the fertilizer (F) plot at a rate of 79 ± 20 kg N ha^?1 yr^?1. In the manure (M) plot, dairy cattle manure was applied at a rate of 10 Mg fresh matter ha^?1 yr^?1 (1923 ± 407 kg C ha^?1 yr^?1, 159 ± 68 kg N ha^?1 yr^?1). There was no significant difference in seasonal gross primary production (GPP) and harvest between the treatment plots, indicating that both fertilizer and manure can increase the biomass production. Annual net ecosystem production (NEP) and ecosystem respiration (RE) was significantly different between the treatment plots. The difference in RE, and between M and F plots approximates heterotrophic respiration of manure (RHm), which ranged from 0.9 to 1.3 Mg C ha^?1 yr^?1. Average annual RHm was 1.1 ± 0.4 Mg C ha^?1 yr^?1, and accounted for 56% of the total amount of applied manure C. The annual net biome production (NBP) in the M plot (from 0.0 to 1.5 Mg C ha^?1 yr^?1) was significantly higher than in the F plot (?1.4 to 0.5 Mg C ha^?1 yr^?1). The long-term effect of manure application combined with chemical fertilizer did not reduce grass production compared with chemical fertilizer only; however, manure application decreased the NEP throughout manure decomposition, and long-term manure application enhanced the NBP.     

TOL proteins mediate vacuolar sorting of the borate transporter BOR1 in Arabidopsis thaliana

Boron (B) is an essential micronutrient for plants; however, it shows cytotoxicity at high concentrations. A borate transporter BOR1 is required for efficient transport of B toward the root stele in Arabidopsis thaliana. BOR1 shows polar localization in the plasma membrane of various root cells toward the stele-side under B limitation. To avoid over-accumulation of B, BOR1 in the plasma membrane is rapidly internalized and transported into the vacuole for proteolysis after high-B supply in an ubiquitination-dependent manner. Although BOR1 has been predicted to be transported into multi-vesicular bodies/late endosomes (MVB/LEs) via the endosomal sorting complex required for transport (ESCRT) machinery, experimental evidence was absent so far. In this study, we investigated the intracellular localization of BOR1 by visualizing endomembrane compartments, and tested the involvement of ESCRT-0-like proteins TOM1-LIKEs (TOLs) in the vacuolar sorting of BOR1. Under low-B conditions, a large portion of cytoplasmic BOR1 was localized in the trans-Golgi networks/early endosomes (TGN/EEs) labeled with VHA-a1 subunit. Pharmacological interference of endosomal recycling using brefeldin A-induced colocalization of BOR1 with RabA5D, which labels recycling vesicles associated with the TGN. On the other hand, under high-B conditions, BOR1 was localized in the inside of TOL5-positive MVB/LEs. To examine the roles of TOL proteins in intracellular trafficking of BOR1, we analyzed BOR1-GFP localization in the TOL quintuple mutant (tolQ; tol2-1tol3-1tol5-1tol6-1tol9-1) after high-B supply. In the tolQ mutant, vacuolar sorting of BOR1 was delayed, while the polar localization of BOR1 was not disturbed. Taken together, BOR1 is constantly transported to the TGN/EE by endocytosis and recycled to the plasma membrane likely via RabA5D-positive endomembrane compartments under low-B conditions. On the other hand, BOR1 is transported to the vacuole via TOL5-positive MVB/LEs under high-B conditions. TOL proteins are required for sorting of ubiquitinated BOR1 into MVB/LE for vacuolar degradation.     

Site-level model–data synthesis of terrestrial carbon fluxes in the CarboEastAsia eddy-covariance observation network: toward future modeling efforts

Based on the model–data comparison at the eddy-covariance observation sites from CarboEastAsia datasets, we report the current status of the terrestrial carbon cycle modeling in monsoon Asia. In order to assess the modeling performance and discuss future requirements for both modeling and observation efforts in Asia, we ran eight terrestrial biosphere models at 24 sites from 1901 to 2010. By analyzing the modeled carbon fluxes against the CarboEastAsia datasets, the strengths and weaknesses of terrestrial biosphere modeling over Asia were evaluated. In terms of pattern and magnitude, the carbon fluxes (i.e., gross primary productivity, ecosystem respiration, and net ecosystem exchange) at the temperate and boreal forest sites were simulated best, whereas the simulation results from the tropical forest, cropland, and disturbed sites were poor. The multi-model ensemble mean values showed lower root mean square errors and higher correlations, suggesting that composition of multiple terrestrial biosphere models would be preferable for terrestrial carbon budget assessments in Asia. These results indicate that the current model-based estimation of terrestrial carbon budget has large uncertainties, and future research should further refine the models to permit re-evaluation of the terrestrial carbon budget.     

Effect of increased harvests on saccharification ratio of waste mushroom medium from the cultivation of shiitake mushroom (Lentinula edodes)

Waste mushroom medium (WM) was saccharized with cellulase to obtain glucose after shiitake fruiting bodies were harvested 3 and 5 times (WM-3 and WM-5, respectively). Glucose can be used as a feedstock for the production of bioethanol or other bioproducts. WM-3 and WM-5 were analyzed for the amounts of shiitake fruiting bodies harvested and chemical components. The fresh weight ratio of shiitake fruiting bodies from the 4th and 5th harvests relative to the total fresh weight of shiitake fruiting bodies until the 5th harvest was 4.1 %. The additional 2 harvests decreased WM dry weight to 78.0 % and slightly decreased acid-insoluble lignin and xylan contents from 11.9 and 12.0 % to 10.0 and 9.6 %, respectively. The additional 2 harvests did not decrease glucan content. WM-5 included 31.6 % of glucan relative to dry weight, and 54.5 % of the glucan was saccharized to glucose with Meicelase (5 FPU/g substrate) at 40 °C for 48 h without pretreatment. The saccharification ratio of WM-3 was 45.0 % under the same saccharification condition. The amounts of saccharized glucose in WM-3 and WM-5 were 155.1 ± 9.8 mg/g substrate and 191.3 ± 9.2 mg/g substrate, respectively.     

Morpho-physiological and molecular mechanisms of phenotypic root plasticity for rice adaptation to water stress conditions

Different types of water stress severely affect crop production, and the plant root system plays a critical role in stress avoidance. In the case of rice, a cereal crop cultivated under the widest range of soil hydrologic conditions, from irrigated anaerobic conditions to rainfed conditions, phenotypic root plasticity is of particular relevance. Recently, important plastic root traits under different water stress conditions, and their physiological and molecular mechanisms have been gradually understood. In this review, we summarize these plastic root traits and their contributions to dry matter production through enhancement of water uptake under different water stress conditions. We also discuss the physiological and molecular mechanisms regulating the phenotypic plasticity of root systems.     

Isolation of antagonistic <Emphasis Type="Italic">Streptomyces</Emphasis> sp. against a potato scab pathogen from a field cultivated with wild oat

Fungi, actinomycetes, and bacteria isolated from soil and plant samples from a potato field in which wild oat (Avena strigosa) had been pre-cultivated were screened for microorganisms that can be used as biocontrol agents for common scab of potato. Of 342 isolates assessed in initial pot trials for their suppressive effect on the severity of potato scab caused by Streptomyces turgidiscabies, 26 isolates were selected as antagonistic candidates based on their ability to reduce disease severity, then tested in a second pot trial. Of the 26, five actinomycetes, isolated from either the rhizosphere soil of wild oat or the soil adhering to potato stolons and tubers, were selected as antagonists. A comparison of partial sequences of 16S rRNA genes from the five isolates indicated that they belong to the genus Streptomyces. Of these five, WoRs-501 most strongly inhibited in vitro mycelial growth of S. turgidiscabies and was also the most effective in suppressing potato scab in a third field pot trial. In that pot trial, a 10% (v/v) mix of WoRs-501 (6.2 × 10⁸ colony-forming units [CFU]/g dry mass) decreased the disease severity by 78–94% in comparison with the untreated control at 5 × 10⁴ to 5 × 10⁶ CFU S. turgidiscabies/g dry soil. WoRs-501 also grew well in vitro at a wide range of pH levels and temperatures. These results suggest that WoRs-501 is a promising candidate for biocontrol of potato scab.     

Immunohistochemical analysis of cartilage-derived retinoic acid-sensitive protein (CD-RAP)/melanoma inhibitory activity (MIA) in murine, canine, bovine and equine cerebrospinal tissues

Cartilage-derived retinoic acid-sensitive protein (CD-RAP)/melanoma inhibitory activity (MIA), which appears abundantly in hypertrophic cartilage at the stage of endochondral ossification, is also detected in cerebrospinal fluid (CSF) following spinal cord injury. In this study, the localization of the CD-RAP/MIA molecule in normal tissues of the spine and brain obtained from mice, rats, dogs, cattle and horses was examined using immunohistochemistry with a specific antibody. The positive signals of CD-RAP/MIA were found at nerve cells in the spinal cords of all species and were especially strong at cerebellar Purkinje cells. The results suggested that CD-RAP/MIA included in normal cerebrospinal tissues could be a biomarker associated with tissue injuries, as the molecules might flow into the CSF.     

Prediction of superovulatory response in Japanese Black cattle using ultrasound, plasma anti-Müllerian hormone concentrations and polymorphism in the ionotropic glutamate receptor AMPA1/GRIA1

The aim of this study was to improve the reliability of predicting the superovulatory response in Japanese Black cattle. Follicle counts and plasma anti-Müllerian hormone concentrations were analyzed within four days prior to the initiation of superovulation. The single nucleotide polymorphism (guanine or adenine) of the ionotropic glutamate receptor AMPA1 was determined. The plasma anti-Müllerian hormone concentration was positively correlated (P<0.001) with the numbers of all follicles and small (<5 mm) follicles and with the numbers of ova/embryos (P<0.001), fertilized embryos (P<0.001) and transferable embryos (P=0.005). There was no significant difference in follicle counts and superovulatory responses between donor cows bearing guanine/adenine or guanine/guanine alleles of AMPA1. Donor cows with a high plasma anti-Müllerian hormone concentration and homozygous for the guanine-containing allele of AMPA1 were most responsive to superovulation. The results suggest that physiological and genetic markers of superovulation have a synergistic effect on the accuracy of predictions of responsiveness.