Changes in concentration andδ 13C values of soil-trapped CH4 and C02 in flooded rice soil

Pot experiments were conducted to monitor the changes in compositions and δ¹³C values of soil-trapped CH₄ and C0₂ in flooded rice soil with and without rice plants or rice straw. Incorporation of rice straw increased the concentration of CH₄ and C0₂ accumulated in soil, and the quantities of emitted CH4 to the atmosphere. Rice plants reduced the concentration of soil-trapped CH₄ and CO₂, and the decreased portion of CH₄ was replaced by N₂. A significantly negative correlation was found between soil-trapped CH₄ and N₂. The presence of rice plants increased the δ¹³C values of CH₄. The δ¹³C values of CH₄ tended to increase toward the end of the growing season and were positively correlated with concentration of soil-trapped CH₄. A positive correlation between δ¹³C values of CH₄ and C0₂, and between the δ¹³C values of CH₄ and its concentration, were observed. The CH₄ in the rice stems was 4–14% enriched in¹³C relative to soil-trapped CH₄. In contrast, CO₂ in rice plant stems was 1–9% lighter in¹³C relative to soil-trapped C0₂. These results are discussed in relation to the precursor pools and pathways of methanogenesis.     

Mechanisms of production of soil protease by proteolytic Bacillus subtilis in wetland rice soil

In sterile soil inoculated with proteolytic Bacillus subtilis, the correlation between variations in protease activity and cell numbers was investigated during incubation, and the results were compared with those obtained in different growth media. In sterile soil inoculated with B. subtilis, the extracted soil z-FLase activity (hydrolytic activity towards benzyloxycarbonyl-L-phenylalanyl-L-leucine extracted with 0.1 M phosphate buffer) was correlated with the extracted soil protein content (r=0.95; P<0.01) and the number of vegetative cells (r=0.88, P<0.05), while the extracted soil caseinase activity was well correlated with the number of spores (r=0.82, P<0.05) and not with the number of vegetative cells. Extracellular z-FLase activity in different growth media, inoculated with the proteolytic B. subtilis, was correlated with the extracellular protein concentration (r=0.73, P<0.01) and the number of cells (r=0.73, P<0.01), but extracellular caseinase activity was not correlated with either of these measurements. From these results, we concluded that soil z-FLase production might relate to vegetative growth of the proteolytic B. subtilis and soil caseinase might relate to B. subtilis sporulation.     

Molecular identification of methane oxidizing bacteria in a Japanese rice field soil

By using cultivation-independent techniques, community changes of methane-oxidizing bacteria (MOB) in rice bulk soils were investigated under field conditions in a Japanese rice field. The representative soil samples were collected during the typical rice growing season and nonrice growing period all year round. Statistical characterization of denaturing gradient gel electrophoresis (DGGE) community patterns of MOB pmoA/amoA functional gene fragments showed that MOB community structures in the rice bulk soils remained largely unchanged throughout the investigated period. The total intensity of six common DGGE bands that appeared consistently throughout the investigated period accounted for 64% of the total intensity of all 18 different DGGE bands detected. The low squared distance of the Ward cluster analysis of the DGGE pattern and the high Sorensen similarity coefficient (81%) also implied the high similarity of the MOB community structures. The stable MOB community structure did not couple well with the wide variation of soil water contents all year round. Sequencing analysis of the nine characteristic bands including six common bands revealed the presence of Type I, Type II methanotrophs, and β-proteobacterial ammonia oxidizers in rice bulk soils. In comparison with MOB type species, three DGGE bands showed a wide variation of the highly conserved amino acid residues, implying the presence of novel MOB bacteria inhabiting the rice bulk soil. The high diversity of MOB composition suggested that rice bulk soils might serve as an ideal reservoir for the dynamic changes of MOB in a rice field ecosystem in response to environment changes.     

Method for Estimating the Content of the Chloroform-Extractable Green Fraction (CEGF) in HCl-DMSO Extract of Soils

Chloroform-extractable green fraction (CEGF) was detected in the supernatant obtained by alkali precipitation from the HCI-dimethylsulfoxide (DMSO) extract of Pg-rich soil. In the alkaline solution, the color of CEGF was green and CEGF showed strong Pg-like absorption bands. Ultraviolet and visible (UV-VIS) spectral analysis and gel chromatography on Sephadex G-50 were performed to compare several properties between CEGF and Pg. CEGF, which was purified by gel chromatography on Bio-Beads SX-1, displayed strong absorption bands at 609, 562, 445 and 280 inn in the alkaline solution. These absorption bands were almost similar to those of Pg. Furthermore, the UV-VIS spectrum of CEGF in the organic solvents showed a similar characteristic pattern of 4,9-dihydroxyperylene-3,10-quinone (DHPQ), which was considered to be a chromophore of Pg. Based on the results of gel chromatography on Sephadex G-50, CEGF mainly consisted of two fractions, corresponding to the G₂ and G₃ fractions of Pg. These results indicated that the method for extracting CEGF from Pg-rich soil in the present study was easy and selective and that CEGF was one of the components of, or a closely related substance to Pg. A colorimetric method for the estimation of the CEGF content in soils was developed. The calibration curve of CEGF was linear over a wide range of contents from 2.75 to 220 mg L⁻¹. The CEGF content in twelve samples of various soils was examined. CEGF was detected in all the soil sampled (5 orders) including three samples (3 orders) where Pg was not detected, and the content ranged from 0.07 to 1.66 g kg⁻¹ (dry soil). Therefore, the method for estimating the CEGF content in soils developed in the present study was found to be suitable for various soil orders and it was assumed that CEGF occurred in various soil orders.     

Remediation of Acid Rock Drainage by Regenerable Natural Clinoptilolite

Clinoptilolite is investigated as a possible regenerable sorbent for acid rock drainage based on its adsorption capacity for Zn, adsorption kinetics, effect of pH, and regeneration performance. Adsorption of Zn ions depends on the initial concentration and pH. Adsorption/Desorption of Zn reached 75% of capacity after 1–2 h. Desorption depended on pH, with an optimum range of 2.5 to 4.0. The rank of desorption effectiveness was EDTA?>?NaCl?>?NaNO₃?>?NaOAc?>?NaHCO₃?>?Na₂CO₃?>?NaOH?>?Ca(OH)₂. For cyclic absorption/desorption, adsorption remained satisfactory for six to nine regenerations with EDTA and NaCl, respectively. The crystallinity and morphology of clinoptilolite remained intact following 10 regeneration cycles. Clinoptilolite appears to be promising for ARD leachate treatment, with significant potential advantages relative to current treatment systems.     

The abundance of heterocystous blue-green algae in rice soils and inocula used for application in rice fields

Summary Algal populations were quantified (as colony-forming units [CFU] per square centimetre) in 102 samples of rice soils from the Philippines, India, Malaysia and Portugal, and in 22 samples of soil-based inocula from four countries. Heterocystous blue-green algae (BGA) were present in all samples. Nostoc was the dominant genus in most samples, followed by Anabaena and Calothrix. In soils, heterocystous BGA occurred at densities ranging from 1.0 × 10² to 8.0 × 10⁶ CFU/cm² (median 6.4 × 10⁴) and comprised, on average, 9% of the total CFU of algae. Their abundance was positively correlated with the pH and the available P content of the soils. In soil-based inocula, heterocystous BGA occurred at densities ranging from 4.6 × 10⁴ to 2.8 × 10⁷ CFU/g dw (dry weight), comprising only a moderate fraction (average 13%) of the total algae. In most soils, the density of indigenous N₂-fixing BGA was usually higher than that attained by applying recommended rates of soil-based inoculum. Whereas research on the practical utilization of BGA has been mostly directed towards inoculation with foreign strains, our results suggest that attention should also be given to agricultural practices that enhance the growth of indigenous strains already adapted to local environmental conditions.Maître de Recherches ORSTOM (France), Visiting Scientist at IRRI     

Quantification of genetically modified soybean by quenching probe polymerase chain reaction

Quenching probe (QProbe) polymerase chain reaction (PCR) is a simple and cost-effective real-time PCR assay in comparison with other real-time PCR assays such as the TaqMan assay. We used QProbe-PCR to quantify genetically modified (GM) soybean (Roundup Ready soybean). We designed event-specific QProbes for Le1 (soy endogenous gene) and RRS (recombinant gene), and we quantified certified reference materials containing 0.1, 0.5, 1, 2, and 5% GM soybean. The TaqMan assay was also applied to the same samples, and the results were compared. The accuracy of QProbe-PCR was similar to that of TaqMan assay. When GM soybean content was 0.5% or more, the relative standard deviations of QProbe-PCR were less than 20%. QProbe-PCR is sensitive enough to monitor labeling systems and has acceptable levels of accuracy and precision.     

Effect of land management and soil texture on seasonal variations in soil microbial biomass in dry tropical agroecosystems in Tanzania

Soil microbes are an essential component of most terrestrial ecosystems; as decomposers they are responsible for regulating nutrient dynamics, and they also serve as a highly labile nutrient pool. Here, we evaluated seasonal variations in microbial biomass carbon (MBC) and nitrogen (MBN) as well as microbial activity (as qCO₂) for 16 months with respect to several factors relating to soil moisture and nutrients under different land management practices (plant residue application, fertilizer application) in both clayey (38% clay) and sandy (4% clay) croplands in Tanzania. We observed that MBC and MBN tended to decrease during the rainy season whereas they tended to increase and remain at high levels during the dry season in all treatment plots at both of our test sites, although soil moisture did not correlate with MBC or MBN. qCO₂ correlated with soil moisture in all treatment plots at both sites, and hence soil microbes act as decomposers mainly during the rainy season. Although the effect of seasonal variation of soil moisture on the dynamics of MBC, MBN, and qCO₂ was certainly greater than that attributable to plant residue application, fertilizer application, or soil texture, plant residue application early in the rainy season clearly increased MBC and MBN in both clayey and sandy soils. This suggests that plant residue application can help to not only counter the N loss caused by leaching but also synchronize crop N uptake and N release from soil microbes by utilizing these microbes as an ephemeral nutrient pool during the early crop growth period. We also found substantially large seasonal variations in MBC and MBN, continuously high qCO₂, and rapid turnover of soil microbes in sandy soil compared to clayey soil. Taken together, our results indicate that soil microbes, acting as both a nutrient pool and decomposers, have a more substantial impact on tropical sandy soil than on clayey soil.