Koki Toyota

Effects of charcoal addition on N2O emissions from soil resulting from rewetting air-dried soil in short-term laboratory experiments

Abstract Laboratory experiments were conducted to examine the effect of charcoal addition on N2O emissions resulting from rewetting of air-dried soil. Rewetting the soil at 73% and 83% of the water-filled pore space (WFPS) caused a N2O emission peak 6 h after the rewetting, and the cumulative N2O emissions throughout the 120-h incubation period were 11 ± 1 and 13 ± 1 mg N m−2, respectively. However, rewetting at 64% WFPS did not cause detectable N2O emissions (−0.016 ± 0.082 mg N m−2), suggesting a severe sensitivity to soil moisture. When the soils were rewetted at 73% and 78% WFPS, the addition of charcoal to soil at 10 wt% supressed the N2O emissions by 89% . In contrast, the addition of the ash from the charcoal did not suppress the N2O emissions from soil rewetted at 73% WFPS. The addition of charcoal also significantly stimulated the N2O emissions from soil rewetted at 83% WFPS compared with the soil without charcoal addition (P < 0.01). Moreover, the addition of KCl and K2SO4 did not show a clear difference in the N2O emission pattern, although Cl− and SO2− 4, which were the major anions in the charcoal, had different effects on N2O-reducing activity. These results indicate that the suppression of N2O emissions by the addition of charcoal may not result in stimulation of the N2O-reducing activity in the soil because of changes in soil chemical properties.

Effects of successive soil freeze-thaw cycles on soil microbial biomass and organic matter decomposition potential of soils

Abstract Effects of soil freeze-thaw cycles on soil microbial biomass were examined using 8 soil samples collected from various locations, including 4 arable land sites and 2 forest sites in temperate regions and 2 arable land sites in tropical regions. The amounts of soil microbial biomass C and N, determined by the chloroform fumigation and extraction method, significantly decreased by 6 to 40% following four successive soil freeze-thaw cycles (- 13 and 4°C at 12 h-intervals) compared with the unfrozen control (kept at 4°C during the same period of time as that of the freeze-thaw cycles). In other words, it was suggested that 60 to 94% of the soil microorganisms might survive following the successive freeze-thaw cycles. Canonical correlation analysis revealed a significantly positive correlation between the rate of microbial survival and organic matter content of soil (r = 0.948*). Correlation analysis showed that the microbial survival rate was also positively correlated with the pore-space whose size ranged from 9.5 to 6.0 μm (capillary-equivalent-diameter; r = 0.995**), pH(KCI) values (r = 0.925**), EC values (r = 0.855*), and pH (H2O) values (r = 0.778*), respectively. These results suggested that the soil physicochemical properties regulating the amount of unfrozen water in soil may affect the rate of microbial survival following the soil freeze-thaw cycles. The potential of organic matter decomposition of the soils was examined to estimate the effects of the soil freeze-thaw cycles on the soil processes associated with the soil microbial communities. The soil freeze-thaw cycles led to significant 6% increase in chitin decomposition and 7% decrease in rice straw decomposition (p < 0.05), suggesting that the partial sterilization associated with the soil freeze-thaw cycles might disturb the soil microbial functions.

Recent trends in control methods for bacterial wilt diseases caused by Ralstonia solanacearum.

Previous studies have described the development of control methods against bacterial wilt diseases caused by Ralstonia solanacearum. This review focused on recent advances in control measures, such as biological, physical, chemical, cultural, and integral measures, as well as biocontrol efficacy and suppression mechanisms. Biological control agents (BCAs) have been dominated by bacteria (90%) and fungi (10%). Avirulent strains of R. solanacearum, Pseudomonas spp., Bacillus spp., and Streptomyces spp. are well-known BCAs. New or uncommon BCAs have also been identified such as Acinetobacter sp., Burkholderia sp., and Paenibacillus sp. Inoculation methods for BCAs affect biocontrol efficacy, such as pouring or drenching soil, dipping of roots, and seed coatings. The amendment of different organic matter, such as plant residue, animal waste, and simple organic compounds, have frequently been reported to suppress bacterial wilt diseases. The combined application of BCAs and their substrates was shown to more effectively suppress bacterial wilt in the tomato. Suppression mechanisms are typically attributed to the antibacterial metabolites produced by BCAs or those present in natural products; however, the number of studies related to host resistance to the pathogen is increasing. Enhanced/modified soil microbial communities are also indirectly involved in disease suppression. New promising types of control measures include biological soil disinfection using substrates that release volatile compounds. This review described recent advances in different control measures. We focused on the importance of integrated pest management (IPM) for bacterial wilt diseases.

Microbial community indigenous to the earthworm Eisenia foetida

Abstract Microbial populations of the earthworm Eisenia foetida, their casts and farmyard manure (FYM) in which E. foetida had lived were enumerated with the dilution plate method using several media. The microbial community of earthworms appeared to be similar to that of the FYM in which they had lived, while that of earthworms starved in distilled water for 24 h greatly differed from that of the FYM. The community of the starved earthworms consisted exclusively (more than 90%) of fast growers, which were defined as those that formed their colonies within 2 days, unlike that of the FYM (10–30%). About 30 isolates were randomly chosen and some physiological properties were examined. The community of starved earthworms consisted exclusively of Gram-negative, oxidase-positive, fermentative bacteria, whereas bacteria from the FYM were much more diverse and there were no fermentative bacteria in the FYM. The predominant bacteria species of the starved earthworms were identified as Aeromonas hydrophila and considered to be indigenous to the earthworm E. foetida.

Impact of Fumigation with Metam Sodium upon Soil Microbial Community Structure in Two Japanese Soils

Abstract The effects of fumigation with sodium methyl dithiocarbamate (metam sodium) on the microbial community structure and function in 2 soils were investigated using a variety of techniques. In both soils ca. 50% and 90% of the populations of total and culturable bacteria, respectively, were killed by fumigation, with recovery to levels prevailing in control soils 26 d after cessation of fumigation. The size of the ammonium and nitrite oxidiser populations was reduced by up to 4 orders of magnitude by fumigation, with the latter showing a slight recovery 105 d later. There were substantial changes in the C-utilisation (Biolog GN) profiles in the fumigated soils even 105 d later. The number and pattern of amplified 16S ribosomal DNA restriction analysis (ARDRA) fragments was changed by fumigation, and there was a shift in the %G+C profile toward a greater proportion of lower %G+C classes in treated soils. It appeared that DNA released from killed cells remained for some time after fumigation, and maske...

Development of a real-time PCR method for the potato-cyst nematode Globodera rostochiensis and the root-knot nematode Meloidogyne incognita

Abstract The primers PCN280f and NEPCN398r were designed for the quantitative detection of the potato-cyst nematode Globodera rostochiensis using real-time polymerase chain reaction (PCR). One, five, 50, 125 and 250 individuals of the second-stage juveniles (J2) of G. rostochiensis were mixed with various stages of vermiform Caenorhabditis elegans to make a total of 500 individuals and DNA was extracted from the nematode mixture. There was a significant correlation (r 2 = 0.9355, P < 0.001) between the threshold cycle values and the number of G. rostochiensis added. When nematodes were extracted from soils artificially infested with G. rostochiensis to various degrees and real-time PCR was conducted using DNA templates from the nematodes extracted, there was a highly significant correlation in the numbers of G. rostochiensis J2 from the real-time PCR method and morphological identification. Real-time PCR sensitively detected a single G. rostochiensis J2 out of 1,000 individuals of free-living nematodes. Similarly, real-time PCR primers RKNf and RKNr were designed for the detection of the root-knot nematode Meloidogyne incognita. This study demonstrated that the real-time PCR assay for the potato-cyst nematode and the root-knot nematode provides a sensitive and reliable means for the rapid quantification of these vermiform pests.

Fungal N2O production in an arable peat soil in Central Kalimantan, Indonesia

Abstract To clarify the microbiological factors that explain high N2O emission in an arable peat soil in Central Kalimantan, Indonesia, a substrate-induced respiration-inhibition experiment was conducted for N2O production. The N2O emission rate decreased by 31% with the addition of streptomycin, whereas it decreased by 81% with the addition of cycloheximide, compared with a non-antibiotic-added control. This result revealed a greater contribution of the fungal community than bacterial community to the production of N2O in the soil. The population density of fungi in the soil, determined using the dilution plate method, was 5.5 log c.f.u. g−1 soil and 4.9 log c.f.u. g−1 soil in the non-selective medium (rose bengal) and the selective medium for Fusarium, respectively. The N2O-producing potential was randomly examined in each of these isolates by inoculation onto Czapek agar medium (pH 4.3) and incubation at 28°C for 14 days. Significant N2O-producing potential was found in six out of 19 strains and in five out of seven strains isolated from the non-selective and selective media, respectively. Twenty-three out of 26 strains produced more than 20% CO2 during the 14-day incubation period, suggesting the presence of facultative fungi in the soil. These strains were identified to be Fusarium oxysporum and Neocosmospora vasinfecta based on the sequence of 18S rDNA, irrespective of the N2O-producing potential and the growth potential in conditions of low O2 concentration.

Seasonal variations of phospholipid fatty acid composition in the floodwater of a Japanese paddy field under a long-term fertilizer trial

Abstract The concentration and composition of phospholipid fatty acids (PLFAs) in the floodwater of a Japanese paddy field under a long-term fertilizer trial for more than 70 y [no fertilizers (NoF) plot, chemical fertilizers (CF) plot, chemical fertilizers and composts (CM) plot] were determined. The amount of PLFAs ranged from 2.8 to 14.1 μg L-1 for the NoF plot, from 3.2 to 8.6 μg L-1 for the CF plot, from 4.4 to 13.0 μg L-1 for the CM plot, respectively. Dominant PLFAs in the floodwater were 16: lω7, 16: 0, 18: 1ω7 in all the plots. Straight, mono-unsaturated PLFAs accounted for about 40% of the total, suggesting the predominance of Gram-negative bacteria in the floodwater. Principal component analysis and cluster analysis of PLFA composition clearly revealed the variations of microbiota in the floodwater with the kinds of fertilizer and the growth stages of rice plants. An indicator of the environmental stress imposed upon microbiota expressed by the trans vs. cis ratio of 16: 1ω7 was consistently low, indicating that the floodwater environment was a low-stress environment upon the microbiota.

Complete genome sequence of Bradyrhizobium sp. S23321: insights into symbiosis evolution in soil oligotrophs.

Bradyrhizobium sp. S23321 is an oligotrophic bacterium isolated from paddy field soil. Although S23321 is phylogenetically close to Bradyrhizobium japonicum USDA110, a legume symbiont, it is unable to induce root nodules in siratro, a legume often used for testing Nod factor-dependent nodulation. The genome of S23321 is a single circular chromosome, 7,231,841 bp in length, with an average GC content of 64.3%. The genome contains 6,898 potential protein-encoding genes, one set of rRNA genes, and 45 tRNA genes. Comparison of the genome structure between S23321 and USDA110 showed strong colinearity; however, the symbiosis islands present in USDA110 were absent in S23321, whose genome lacked a chaperonin gene cluster (groELS3) for symbiosis regulation found in USDA110. A comparison of sequences around the tRNA-Val gene strongly suggested that S23321 contains an ancestral-type genome that precedes the acquisition of a symbiosis island by horizontal gene transfer. Although S23321 contains a nif (nitrogen fixation) gene cluster, the organization, homology, and phylogeny of the genes in this cluster were more similar to those of photosynthetic bradyrhizobia ORS278 and BTAi1 than to those on the symbiosis island of USDA110. In addition, we found genes encoding a complete photosynthetic system, many ABC transporters for amino acids and oligopeptides, two types (polar and lateral) of flagella, multiple respiratory chains, and a system for lignin monomer catabolism in the S23321 genome. These features suggest that S23321 is able to adapt to a wide range of environments, probably including low-nutrient conditions, with multiple survival strategies in soil and rhizosphere.

Suppression of ammonia volatilization from a paddy soil fertilized with anaerobically digested cattle slurry by wood vinegar application and floodwater management

Abstract Ammonia (NH3) volatilization from animal manure application is detrimental to the environment, crop nutrition and human health and investigations into mitigation strategies are a great challenge among agro-environmental issues. The objective of the present study was to reduce NH3 volatilization in a paddy soil fertilized with anaerobically digested cattle slurry (ADCS). In laboratory experiments, several mitigation methods for NH3 volatilization were tested. Among these methods, acidification of ADCS with wood vinegar (WV) from pH 7.8 to pH 6.0 was the most effective in suppressing NH3 volatilization. Increasing the depth of the floodwater threefold also reduced NH3 volatilization by more than 80%. A lysimeter (1 m square with 0.5 m depth) experiment was conducted in triplicate with the following treatments: (1) chemical fertilizer ([CF] N:P:K = 14:14:14), (2) ADCS, (3) acidifying ADCS with WV to pH 6.0, (4) keeping a deeper floodwater level (DFW) at 10 cm at the ADCS applications (3–4 cm in the other treatments). A total fertilization of 30 g NH+ 4–N m−2 (basal and three times as a top dressing) was done for all treatments either with CF or ADCS and other fertilizations were not conducted. The NH3 volatilization was measured using the dynamic flow chamber method for 1 week after each fertilizer application. The results highlighted that the use of ADCS, instead of CF, enhanced NH3 volatilization approximately eightfold, and the total amount of NH3 volatilization corresponded to 13% of the applied NH+ 4–N in the ADCS treatment. This increased N loss was effectively (63–82%) reduced by adding WV and by keeping the floodwater level deeper. Biomass production was not significantly different between the CF (2880 ± 226 g [dry basis] m−2) treatment and the three ADCS treatments (3320 ± 249, 2720 ± 384 and 3330 ± 359 g [dry basis] m−2 in the ADCS, ADCS + WV and ADCS + DFW treatments, respectively). These results demonstrated that enhanced NH3 volatilization in soil fertilized with ADCS was mitigated by the simultaneous application of an acid residue, such as WV, and by the management of the floodwater level.