Isolation and characterization of a novel simazine-degrading beta-proteobacterium and detection of genes encoding s-triazine-degrading enzymes

A moderately persistent herbicide, simazine, has been used globally and detected as a contaminant in soil and water. The authors have isolated a simazine-degrading bacterium from a simazine-degrading bacterial consortium that was enriched using charcoal as a microhabitat. The isolate, strain CDB21, was gram-negative, rod-shaped (0.5-0.6 microm x 1.0-1.2 microm) and motile by means of a single polar flagellum. Based on 16S rRNA sequence analysis, strain CDB21 was identified as a novel beta-proteobacterium exhibiting 100% sequence identity with the uncultured bacterium HOClCi25 (GenBank accession number AY328574). PCR using primers that were specific for the genes of the atrazine-degrading enzymes (atzABCDEF) of Pseudomonas sp. strain ADP showed that strain CDB21 also possessed the entire set of genes of these enzymes. Nucleotide sequences of the atzCDEF genes of strain CDB21 were 100% identical to those of Pseudomonas sp. strain ADP. Sequence identity of the atzA genes between these bacteria was 99.7%. The 398-nucleotide upstream fragment of the atzB gene of strain CDB21 was 100% identical to ORF30 of Pseudomonas sp. strain ADP, and the 1526-nucleotide downstream fragment showed 99.8% sequence similarity to the atzB gene of the pseudomonad.     

Biodegradation of methylthio-s-triazines by Rhodococcus sp. strain FJ1117YT, and production of the corresponding methylsulfinyl, methylsulfonyl and hydroxy analogues

A novel bacterial strain FJ1117YT was isolated from an enrichment culture with the herbicide simetryn. The isolate was capable of degrading the herbicide supplied as the sole sulfur source in an aquatic batch culture. The strain FJ1117YT was identified as that belonging to Rhodococcus sp. on the basis of comparative morphology, physiological characteristics and comparison of the 16S rRNA gene sequence. The biodegradation pathway of simetryn was established by isolating the methylsulfinyl analogue as the first metabolite and by identification of the methylsulfonyl intermediate and the hydroxy analogue by liquid chromatography-mass spectrometry (LC-MS) and/or nuclear magnetic resonance (NMR) analysis. The results indicate that the methylthio group was progressively oxidised and hydrolysed by the strain FJ1117YT. The same strain is also able to metabolise other methylthio-s-triazines such as ametryn, desmetryn, dimethametryn and prometryn through similar pathways.     

Uracil DNA glycosylase activity is dispensable for immunoglobulin class switch

Activation-induced cytidine deaminase (AID) is required for the DNA cleavage step in immunoglobulin class switch recombination (CSR). AID is proposed to deaminate cytosine to generate uracil (U) in either mRNA or DNA. In the second instance, DNA cleavage depends on uracil DNA glycosylase (UNG) for removal of U. Using phosphorylated histone gamma-H2AX focus formation as a marker of DNA cleavage, we found that the UNG inhibitor Ugi did not inhibit DNA cleavage in immunoglobulin heavy chain (IgH) locus during CSR, even though Ugi blocked UNG binding to DNA and strongly inhibited CSR. Strikingly, UNG mutants that had lost the capability of removing U rescued CSR in UNG-/- B cells. These results indicate that UNG is involved in the repair step of CSR yet by an unknown mechanism. The dispensability of U removal in the DNA cleavage step of CSR requires a reconsideration of the model of DNA deamination by AID.     

A petiole sap nitrate test for broccoli

Nitrogen (N) status of vegetable crops is often monitored by analysis of dried plant tissues. However, dry tissue analysis often causes a significant delay between sampling and analysis. This study was conducted to examine the accuracy of a portable nitrate meter for determining petiole sap nitrate (NO₃) contents, and the relationship between NO₃‐N concentration in fresh petiole sap and in dried petiole tissue of broccoli grown in southern Arizona during the 1993–94 and 1994–95 winter growing seasons. Experiments were factorial combinations of three irrigation rates and four N rates, both ranging from deficient to excessive. Petioles were sampled throughout each season, and split for sap and dry tissue analysis. A linear correlation was obtained between the two measurements in both seasons, with no consistent effect due to irrigation treatment or crop maturity. The regression coefficients did not differ among seasons. Therefore, a combined regression equation: Y=343+0.047X (r² = 0.799) was derived, in which Y=NO₃‐N (mg/L) in fresh petiole sap, and X=NO₃‐N (mg/kg) in dried petioles. These results suggest that the sap test can be a valuable and rapid technique to predict N needs of broccoli. Differences between the two methods are likely due to interferences in fresh petiole sap and slight differences in pools of extracted NO₃.     

Nodulation and competitiveness of gusA-marked Bradyrhizobium japonicum A1017 in soybean

Attempts to improve the symbiotic nitrogen fixation with effective (Brady) rhizobium strains do not always succeed under field conditions due to the lower nodulation competitiveness of the introduced strains than that of the indigenous rhizobia (Triplett and Sadowsky 1992). An introduced strain needs to be marked for monitoring its nodule occupancy under competitive nodulation conditions.     

Nutritional characteristics of mineral elements in tree species of tropical rain forest,West Sumatra,Indonesia

The nutritional characteristics of mineral elements in tree species were studied in a 1 ha permanent observation plot at Mt. Gadut area near Padang, West Sumatra, Indonesia. The elemental composition of the 42 leaf and the 457 bark samples from the 1 ha plot was analyzed. Most of the elements, such as S, K, AI, CI, Si, B, and Sr, showed a significant correlation between leaf and bark, suggesting that bark can also be used to study the nutritional characteristics of trees instead of leaves as the first approximation. The concentrations of elements in 457 bark samples showed a wide range, indicating the considerable diversity of nutritional characteristics of mineral elements among these tree species. The concentration ranges expressed in mg kg-¹ were Mn (0.1–3,800), Sr (0.1–1,070), Si (2–1,700), Fe (0.6–4,100), Al (10–46,000), Mg (10–7,200), Zn (0.4–290), K (60–22,000), Cu (0.8–150), P (19–2,540), CI (110–9,200), S (170–13,600), Ca (2,300–100,000), B (4–70), and N a (130–700). Accumulator species were defined as trees with concentrations higher than logarithmic mean + 2std., whereas excluder species were defined as trees with concentrations lower than logarithmic mean — 2std. Among the 113 tree species identified, the accumulators were A. maingayi, M. glaberrimus, M. laurinum, P. axillaris, S. javensis, and M. sericea for S, A. frutescens, A. maingayi, M. laurinum, M. corymbosus, and E. acuminata for Al, F. ribes for Ca, B. pendula and U. maerophyllum for Cl, M. affinis and M. sereea for Si, M. affinis, L. elegans, G. maerophyllum, C. seorteehinii, and E. decipiens for Na, G. macrophyllum, E. opaea, E. latifolia, and C. arborea for B, E. opaea for Cu, F. lepicarpa for Fe, G. maerophyllum and E. opaea for P, A. malaccensis for Zn. The excluders were L. conoearpus for S, V. umbonata, L. conocarpus, S. elongata, G. forbesii, and M. serieea for Al, V. umbonata, L. conocarpus, P. grandis, P. eaeruleseens, G. forbeii, and H. arthoearpoid for Ca, V. perakensis, L. conocarpus, C. seorteehinii, and P. grandis for Mg, V. perakensis, B. tokbrai, C. zollingeriana, G. forbesii, and E. fastigiata for Na, P. exeelsa for Cu, A. porteri for Fe, P. alnifolia for Mn, L. conocarpus and G. forbesii for Sr. Specific Al accumulators were observed. M. corymbosus and U. macrophyllum accumulated Al at very high concentrations, 40 and 20 g kg-¹, respectively. Moreover, Al was accumulated not only in the mature leaves but also in the new leaves. A significant correlation between Al and P concentrations in the 457 bark samples was also observed. These observations suggest that Al exerts a beneficial effect on plant growth for certain tree species in the plot by stimulating P absorption.     

Isolation and partial characterization of endophytic diazotrophs associated with Japanese sugarcane cultivar

Endophytic bacteria were isolated from the juice of a 6 month-old sugarcane cv. NiF-8, which was collected from Miyako, Okinawa and planted in a field lysimeter in Tsukuba, Ibaraki, Japan. The most probable number of N₂-fixing endophytes was 4.5 × 10⁵ cells per gram of fresh weight sample and 21 isolates have a positive reaction for ARA in an N₂-free semi-solid medium with 10% crystallized sugarcane sugar and 0.5% sugarcane juice. Analyses of some of the biochemical properties of the N₂-fixing isolates indicated that 13 isolates were putative strains of Acetobacter diazotrophicus, 4 isolates showed similar characteristics to those of Herbaspirillum seropedicae, and 4 isolates consisted of Herbaspirillum rubribalbicans-like strains. This study confirmed the existence of N₂-fixing endophytic bacteria in the Japanese sugarcane cv. NiF-8.     

Some Physico-chemical characteristics of soils influenced by Taal Volcano in reference to soil productivity

Soils of the northwestern part of the Taal Volcano in the Philippines representing four geomorphological units (upper, middle, and lower slopes and alluvial plains) were investigated and related to soil productivity. Results revealed that the soils on the upper and middle slopes contained higher amounts of organic matter and available P and displayed a low P retention together with more favorable physical properties such as loamy soil texture, loose and friable and well-drained soils compared to those on the lower slopes and in the alluvial plains. Due to these favorable soil characteristics, sustained agricultural production was higher at the upper elevations than at the lower elevations. Year-round multistorey / mixed cropping systems of cultivation in the upper and middle landscapes were also made possible because the higher precipitation was evenly distributed coupled with cooler temperatures compared the conditions on the lower slopes and in the alluvial plains. On the other hand, the soils on the lower slopes and in the alluvial plains had a clayey texture and contained a lower amount of organic matter and available P, in addition to the lower precipitation, resulting in reduced land utilization, as indicated by the limited types of crops grown and lower yield of crops.     

Evaluation of readily available nonexchangeable potassium in soil by sequential extractions with 0.01 molar hydrochloric acid

Nonexchangeable potassium (K-ne), i.e. 1 M NH₄OAc-nonexchangeable K, often contributes significantly to plant nutrition. However conventional extraction methods often extract much more K-ne than plants even after intensive cropping, suggesting the difficulty in evaluating the amount of readily available soil K-ne. In this study, we used a milder extraction method (0.01 M HCl method) to examine its applicability to evaluate the amount of readily available K-ne in soil. In the first experiment, the concentration of K-ne in twenty surface soils sampled from agricultural fields in Japan and K-bearing minerals was determined by the 0.01 M HCl method, i.e. sequential extraction with 0.01 M HCl over a period of 10 d after removal of exchangeable K, and by conventional methods. The average percentage of the soil K-ne extracted by the 0.01 M HCl method amounted to 0.66% of the total K amount, and was much lower than that by a single extraction with 1 M HNO₃ (2.0%) or with 0.2 M sodium tetraphenylboron for 2 d (22%). In the second experiment, the amount of K-ne removed by chemical extractions was compared with that of K-ne removed by maize plants grown for 29 d in five of the above soils. The amount of the K-ne evaluated by the 0.01 M HCl method gave the highest correlation (p < 0.05) with that of the K-ne utilized by plants among the extraction methods applied. The amount of soil K-ne extracted by the 0.01 M Hel method could therefore become a suitable index of the amount of readily available K-ne in soil. Extraction of K-ne in soils after maize planting further indicated that plants had removed K-ne more intensively than the 0.01 < HCl method probably only from the rhizosphere, although a high correlation was observed between the amount of K-ne removed by the 0.01 M Hel method and that by plants. This implies that the estimation of the amount of K-ne utilized by plants requires not only soil chemical analysis but also the evaluation of the percentage of the soil volume where the plant-induced release of K-ne actually occurs.     

Characterization of Rehmannia mosaic virus isolated from chili pepper (<Emphasis Type="Italic">Capsicum annuum</Emphasis>) in Japan

In 2010, severe necrotic mosaic disease and fruit distortion were observed on greenhouse-grown chili pepper (Capsicum annuum cv. Fushimi-amanaga) plants in Kyoto Prefecture, Japan. Electron microscopic imaging and genomic RNA sequencing indicated that the virus responsible was a new isolate of Rehmannia mosaic virus (ReMV), which had not been previously reported in Japan. Although ReMV systemically infected many Solanaceae species, including chili pepper and tomato (Solanum lycopersicum), tobamovirus-resistance genes from species of Capsicum (L ^1a , L ² , L ³ , and L ⁴ ) and tomato (Tm-1, Tm-2, and Tm-2 ^a ) conferred resistance against ReMV.