Community structure of bacteria and fungi responsible for rice straw decomposition in a paddy field estimated by PCR-RFLP analysis

Rice straw including leaf sheaths and blades put in nylon mesh bags was placed in the plow layer of a Japanese paddy field after harvest under upland conditions and after transplanting of rice seedlings under flooded conditions. In addition, rice straw that was decomposed under the upland conditions during the off-crop season in winter was placed again in soil at the time of transplanting. The materials were collected periodically to analyze the community structure of the bacteria and fungi responsible for rice straw decomposition by PCR-RFLP analysis. The PCR products with 27f and 1492r primers designed for bacterial 16S rDNA and with EF3 and EF4 primers designed for fungal 18S rDNA were digested with four restriction endonucleases (Hinf I, Sau3A I, Hae III, EeoR I). Bacterial communities in the decomposing rice straw were different from each other between upland and flooded conditions, between leaf sheaths and blades, and between straw samples with and without decomposition under upland conditions during the off-crop season. Fungal communities in the decomposing rice straw were also different between the leaf sheaths and blades under upland soil conditions. Score plots of bacterial and fungal communities in the principal component analysis were separated from the plot of the straw materials along with the duration of the placement, indicating the succession of bacterial and fungal communities in decomposing rice straw with time.     

Bacterial communities associated with nodal roots of rice plants along with the growth stages: Estimation by PCR-DGGE and sequence analyses

Bacterial communities in rice roots that developed from different nodes and at different growth stages were compared by using polymerase chain reaction (PCR)-denaturing gradient gel electrophoresis (DGGE) analysis of 16S rDNA. Rice root samples were collected at three stages, namely tillering (July 2), maximum tillering (July 21), and ripening (September 12). The bacterial diversity in rice roots was found to increase along with the growth stages of the rice plants as well as the root age from the numbers of DGGE bands. The community structure of the bacteria was also found to change with the growth stages and root age from cluster analysis. Sequence analysis of the DGGE bands indicated that the dominant bacteria associated with rice roots were Gram-negative bacteria, especially β-Proteobacteria irrespective of the growth stages and root age. DGGE bands related to Janthinobacterium agaricidamnosum W1r3T and Clostridium sp. FCB90-3 were ubiquitous in many roots irrespective to the sampling date. Principal component analysis enabled to characterize the DGGE bands related to nitrogen-fixing Azoarcus spp., and Azovibrio sp. BS20-3 in the samples collected on July 2 and on July 21, and the myxobacteria collected on September 12, respectively, as representative bacteria in the bacterial communities. The habitat around older rice roots at every sampling date was more reductive than that around younger rice roots, and the DGGE bands related to Spirochaeta spp. were specific in older roots at every sampling date. Some specific bacteria that were most closely related to the DGGE bands were found from principal component analysis to characterize young and old. roots at each growth stage as follows: aerobes Flavobacterium sp. 90 clone 2 and Janthinobacterium agaricidamnosus W1r3T in young roots and facultative anaerobes Dechloromonas sp. MissR and Anaeromyxobacter dehalogenans 2CP-3 in old nodal roots on July 2, strict anaerobe Geobacter pelophilus Dfr2 and aerobes Nitrosospira sp. Nsp17 and uncultured Nitrospira sp. clone 4-1 in old roots on July 21, and different Clostridium spp. in both young and old roots and Desulfovibrio magneticus RS-1 in old roots on September 12, respectively. A larger number of the closest relatives of anaerobic bacteria grew at the late stage than at the early stages, and in old roots than in younger roots. Thus, the environment of paddy roots was remarkably heterogeneous as a bacterial habitat, where not only the whole root system but also a root may create oxic and anoxic environments.     

On the semi-micro determination of total nitrogen (part 4) the decision of number of samples in rice experiment fields

To obtain a value of soil total nitrogen, which represents nitrogen content of soils of rice field under experiment, statistical consideration will be required, because the value of total nitrogen of soil may differ from sample to sample, owing to heterogeneity of the soil in the field.     

Microbial communities responsible for the decomposition of rice straw compost in a Japanese rice paddy field determined by phospholipid fatty acid (PLFA) analysis

To identify the microbial communities responsible for the decomposition of rice straw compost in soil during the rice cultivation period, phospholipid fatty acid (PLFA) composition of rice straw compost was determined by periodically sampling the compost from a Japanese rice field under flooded conditions. About 21% of the compost was decomposed within a period of 3 months. The total amount of PLFAs, as an indicator of microbial biomass, was significantly lower under drained conditions than under flooded conditions and was relatively constant during the flooding period. This indicates that the microbial biomass in the compost samples did not increase during the gradual decomposition of rice straw compost under flooded conditions. The proportion of branched-chain PLFAs (biomarker of Grampositive and anaerobic Gram-negative bacteria) slightly decreased during the early period after placement, and increased gradually afterwards. Among the branched-chain PLFAs, i15:0, ail5:0, i16:0 and i17:0 PLFAs predominated and their proportions increased gradually except for i16:0. The proportion of straight mono-unsaturated PLFAs (biomarker of Gramnegative bacteria) was almost constant throughout the period, and 18:1ω9 and 18:1ω7 PLFAs predominated. The proportion of straight poly-unsaturated PLFAs as a biomarker of eukaryotes including fungi was also constant throughout the period, except for a decrease under drained conditions. Straight poly-unsaturated PLFAs consisted mainly of 18:2ω6c PLFA. Therefore, these results suggest that the proportions of Gram-positive and anaerobic Gram-negative bacteria increased during the decomposition of rice straw compost in flooded paddy field. Statistical analyses enabled to divide PLFA patterns of microbiota in the rice straw compost into two groups, one group consisting of rice straw compost samples collected before mid-season drainage and the other of samples collected after mid-season drainage. Small squared distances among samples in cluster analysis indicated that the community structure of microbiota was similar to each other as a whole. These results suggest that the microbial communities changed gradually during the period of placement, and that mid-season drainage may have affected the community structure of microbiota. Principal component analysis of the PLFA composition suggested that the succession of microbiota along with the decomposition in flooded soil was similar between rice straw compost and rice straw and that the changes in the community structure during the decomposition in flooded soil were more conspicuous for rice straw than for rice straw compost.     

Nutrient storage in termite (Macrotermes bellicosus) mounds and the implications for nutrient dynamics in a tropical savanna Ultisol

The role of mounds of the fungus-growing termite Macrotermes bellicosus (Smeathman) in nutrient recycling in a highly weathered and nutrient-depleted tropical red earth (Ultisol) of the Nigerian savanna was examined by measuring stored amounts of selected nutrients and estimating their rates of turnover via the mounds. A study plot (4?ha) with a representative termite population density (1.5?mounds?ha^?1) and size (3.7?±?0.4?m in height, 2.4?±?0.2?m in basal diameter) of M. bellicosus mounds was selected. The mounds were found to contain soil mass of 9249?±?2371?kg?ha^?1, composed of 7502?±?1934?kg?ha^?1 of mound wall and 1747?±?440?kg?ha^?1 of nest body. Significant nutrient enrichment, compared to the neighboring topmost soil (Ap1 horizon: 0–16?cm), was observed in the nest body for total nitrogen (N) and exchangeable calcium (Ca), magnesium (Mg) and potassium (K), and in the mound wall for exchangeable K only. In contrast, available (Bray-1) phosphorus (P) content was found to be lower in both the mound wall and the nest body than in the adjacent topmost soil horizon. Consequently, the mounds formed by M. bellicosus contained 1.71?±?0.62?kg?ha^?1 of total N, 0.004?±?0.003?kg?ha^?1 of available P, 3.23?±?0.81?kg?ha^?1 of exchangeable Ca, 1.11?±?0.22?kg?ha^?1 of exchangeable Mg and 0.79?±?0.21?kg?ha^?1 of exchangeable K. However, with the exception of exchangeable K (1.2%), these nutrients amounted to less than 0.5% of those found in the topmost soil horizon. The soil nutrient turnover rate via M. bellicosus mounds was indeed limited, being estimated at 1.72?kg?ha^?1 for organic carbon (C), 0.15?kg?ha^?1 for total N, 0.0004?kg?ha^?1 for available P, 0.15?kg?ha^?1 for exchangeable Ca, 0.05?kg?ha^?1 for exchangeable Mg, and 0.06?kg?ha^?1 for exchangeable K per annum. These findings suggest that the mounds of M. bellicosus, while being enriched with some nutrients to create hot spots of soil nutrients in the vicinity of the mounds, are not a significant reservoir of soil nutrients and are therefore of minor importance for nutrient cycling at the ecosystem scale in the tropical savanna.     

Downy mildew of busy lizzie caused by Plasmopara obducens in Japan

In June 2010 and March 2012, busy lizzie (Impatiens sultanii) plants in a glasshouse in Yamagata Prefecture and in nurseries in a plastic house in Shimane Prefecture, Japan were observed with yellowing of the adaxial surface of leaves or cotyledons and a white downy growth on the abaxial surface of leaves or cotyledons. We identified the causal pathogen as Plasmopara obducens based on the morphologies and rDNA-large subunit sequences. This new disease was named “downy mildew of busy lizzie” in Japan.     

Eremothecium ashbyi causes soybean yeast-spot and is associated with stink bug, Riptortus clavatus

Many fusiform ascospores observed on soybean seeds with yeast spot disease symptoms differed significantly from those of Eremothecium coryli, the known causal agent of yeast spot disease in soybean. On the basis of morphological and physiological characteristics and sequence data of the internal transcribed spacer regions including the 5.8S rDNA and D1/D2 regions of 26S rDNA, this fungus was identified as E. ashbyi. Pathogenicity of E. ashbyi was confirmed by reinoculation test. This report is the report on E. ashbyi causing soybean yeast spot disease. In addition, this study showed that E. ashbyi was transmitted by the stink bug, Riptortus clavatus, as was E. coryli, the two Eremothecium yeasts may have been acquired when the stink bug fed on infected soybeans and overwintered in this insect species. The nucleotide sequence data reported are available in the GeneBank/EMBL/DDBJ database as accessions AB294407 to AB294412 for E. ashbyi EA1, EA7 and EA11.     

Overexpression of the LASAP2 gene for secretory acid phosphatase in white lupin improves the phosphorus uptake and growth of tobacco plants

Secretion of acid phosphatase (APase) from the roots to take up phosphorus (P) is a well-known strategy of plants under P-deficient conditions. White lupin, which shows vigorous growth in low-P soils, is noted for its ability to secrete APase under P-deficient conditions. The APase secreted by white lupin roots is stable in soil solution and shows low substrate specificity, suggesting that genetic modification of plants using the APase gene LASAP2 might improve their ability to use organic P. The objective of the present study was to evaluate the potential of LASAP2 transgenic plants to increase organic P utilization. Dry matter production and P accumulation were higher in LASAP2 transgenic tobacco plants grown in gel media containing soluble phytate as the sole P source than in wild-type tobacco plants. Phosphorus uptake by the transgenic plants also increased in soil culture conditions. LASAP2 was apparently more effective in the liberation of organic P, including phytate, in the soil than the native tobacco APase. Thus, the enzymatic stability of LASAP2 in the soil appears to be an important factor for P acquisition.     

Physicochemical and morphological properties of termite (Macrotermes bellicosus) mounds and surrounding pedons on a toposequence of an inland valley in the southern Guinea savanna zone of Nigeria

Termites play a significant role in soil-forming processes of the tropics. The influence of termites on pedogenesis as affected by the toposequence, however, has rarely been explored. We investigated the soil physicochemical and morphological characteristics of epigeal mounds constructed by Macrotermes bellicosus (Smethman) compared with those of surrounding pedons along a toposequence (bottom, fringe and upland sites) of an inland valley in central Nigeria. The physicochemical and morphological properties of the mound soils varied according to structural units but were generally different from those of the adjacent pedons. The differences included finer texture, higher electrical conductivity, total N, exchangeable bases (Ca, Mg and K) and effective cation exchange capacity and lower C/N ratio and exchange acidity in the mound than the pedon at each toposequence position. This tendency to modify the soil properties was more prominent in the nest body where the termites actually live, that is, in the hives, royal cell and base-plate, than in the soils below the nest and the other mound parts, that is, the external wall, internal wall and pillars. We found this trend to a greater or lesser degree at all toposequence positions. Our findings suggest that: (1) M. bellicosus can manipulate the mound soils according to functional applications of structure units or environmental requirements for its livelihood, regardless of local soils; (2) M. bellicosus makes ecological patches (hot spots) at all toposequence positions in the same measure; (3) the influence of M. bellicosus on the pedogenesis is reduced in the lowlands compared with the uplands because the number and volume of the mounds were substantially lower in the bottom and fringe sites compared with the upland site.     

Effect of temperature on survival,growth and malformation of cultured larvae and juveniles of the seven-band grouper Epinephelus septemfasciatus

The effects of rearing temperature (23–29 °C) during the larval and juvenile stage on survival, growth and skeletal malformations in the seven-band grouper Epinephelus septemfasciatus were investigated. The survival rate of juveniles 30–40 mm in total length emerging from eggs was higher at 25 and 26 °C (0.1–1.3 %) than at 23 °C or 27–29 °C (0.004–1.5 %). Growth (increase in total length) was accelerated at higher temperatures. The frequency of malformed individuals was lower at 25–27 °C (36.0–61.5 %) than at 23, 28 or 29 °C (65.3–76.9 %). Specific incidences of spinal curvature and centrum fusion or defects in juveniles were not related to rearing temperature. However, incidences of twisted or compressed vertebrae (6.5–64.0 %) were higher at higher temperatures, while the incidence of bifurcated neural spine was significantly higher at 23 °C (43.6–54.4 %) than at other temperatures (3.3–22.7 %). The incidence rate of spinal curvature (23.3 %) was significantly higher in juveniles with a deflated swim bladder, regardless of rearing temperature. The results of this study suggest that the optimum culture temperature for seven-band grouper is 25–26 °C, collectively considering the survival, growth and incidences of abnormalities. Our results also demonstrate the significance of identifying the conditions for swim bladder inflation to prevent spinal curvature in seven-band grouper.