Complete chloroplast genome sequence of rapeseed (<Emphasis Type="Italic">Brassica napus</Emphasis> L.) and its evolutionary implications

The complete nucleotide sequence of the rapeseed (Brassica napus L.) chloroplast genome (cpDNA) was determined. The 152,860 bp cpDNA contained a pair of 26,035 bp inverted repeat regions (IR), which are separated by small and large single copy regions (SSC and LSC) of 83,030 and 17,760 bp, respectively. The major portion (56.4%) of the B. napus cpDNA consists of gene coding regions, while intergenic spacers make up 43.6% of the complete genome. The average AT content of the B. napus cpDNA is 63.7% and for the LSC, SSC and IR region is 65.9, 70.8 and 57.7%, respectively. Fifteen genes contained one intron, while three genes had two introns. In total, 86 simple sequence repeats were identified. The detailed comparison of the B. napus with one of its putative parents, B. rapa L. cpDNA indicated that the two species were highly similar. The entire gene pool and relative positions of 113 individual genes were identical to those of B. rapa cpDNA. The sequence divergence analysis of B. napus and B. rapa showed only 0.133% in the coding regions, 0.275% in the intron regions, and 0.348% in the intergenic spacer regions. The phylogenies based on 61 protein coding genes from 48 cpDNA sequences provided strong support for monophyly of many major classes of angiosperms and provided support that Amborella could be a sister to all other angiosperms. Our analysis also supported that B. napus is the closest species to B. rapa and B. rapa could be the mathernal parent of B. napus cv. zy036.     

Characterization of Sardinian cork oak (<Emphasis Type="Italic">Quercus suber</Emphasis> L.) genetic resources for economically important traits

Considering the very high socio economic value of cork oak (Quercus suber L.) in Mediterranean areas, a better knowledge of local genetic resources is necessary in order to reach a good balance between the conservation issues and the need of an efficient cork production network. In such frame, local germplasm of Q. suber from the main cork production areas of Sardinia was analysed for DNA and isozyme polymorphisms and for cork quality in relation to some environmental parameters. A total number of 24 sample stands of cork oak were selected, representing typical vegetation, sylvicultural and cork quality features within the eight identified cork growing areas in Sardinia. Considerable variation was found between cork oak stands of the different areas. Results of the principal component analysis performed on the cork quality data and environmental characters of the eight areas, showed that the first three components explain 72.2% of the variation. The major characters involved in this differentiation were cork quality characters such as dimensional recover, moisture and Mg content of the cork and also elevation of stands m a.s.l. for the first component. The second component appears to be determined by some climatic parameters (average annual temperature and average of the minimum temperatures of coldest month) and by the Fe and Zn in the cork. For the third component, major characters involved in differentiation are average annual rainfall, bark thickness and Ca content in the cork.     

Retention and release isotherm of arsenic in arsenic–humic/fulvic equilibrium study

Organic fractions from farm yard manure (FYM), vermicompost, municipal sludge, mustard cake, and surface soil of West Bengal, which was arsenic (As)-contaminated, were extracted and fractionated into fulvic and humic acid (FA and HA, respectively) fractions following standard procedures. These HA and FA samples were characterized by pH-potentiometric titrations, viscometric measurements and visible spectrophotometry. The stability constant (logK) of the complexes formed by these natural with As in aqueous phase was evaluated by the ion-exchange method. The logK values suggest that the organo-As complexes were quite stable. The release isotherm of As from the HA/FA complexes extracted from vermicompost and FYM was assayed in the presence of molybdate, nitrate, phosphate, sulfate and borate. The greatest tendency to displace As from the complexes was shown by sulfate, molybdite, and nitrate.     

Development of new sources of tetraploid <Emphasis Type="Italic">Arachis</Emphasis> to broaden the genetic base of cultivated groundnut (<Emphasis Type="Italic">Arachis hypogaea</Emphasis> L.)

Groundnut, an important crop of many countries of the world, is susceptible to a range of diseases and pests. High levels of resistances are not available in the cultivated gene pool as the crop is said to have a narrow genetic base. Narrow genetic base is attributed to the evolution of the crop which took place by the combination of A and B genome species, and later doubling their chromosome number, giving rise to tetraploid cultivated groundnut. Direct utilization of cross-compatible wild relatives, which are diploids, to broaden the genetic base and introduction of useful traits, is not a straight-forward process due to ploidy differences between the cultivated species and wild relatives. Hence amphiploids and autotetraploids were created by not only combining the putative genomes, but many other A and B genome species, thus producing a highly variable population of tetraploid groundnuts also called new sources of Arachis hypogaea. This study describes the development and characterization of newly generated tetraploid groundnuts and the level of molecular diversity as assessed by DArT markers.     

Legume residue influence arbuscular mycorrhizal colonisation and P uptake by wheat

Legumes have been shown to increase growth and P uptake of the following cereal. This could, in part, be due to nutrients released by the decomposing legume residues. To investigate the effect of P added with legume residues on wheat growth, P uptake and arbuscular mycorrhizal (AM) colonisation, a number of experiments were conducted with different legume residues added to a soil with low P availability under conditions in which N was not limiting. Young and mature faba bean shoots (FYS, FMS) and mature chickpea shoots (CP) were added to soil at different rates (0.5–2%, w/w) with the P concentration being the greatest in the young faba bean shoots and least in the mature chickpea residues. Other treatments included addition of inorganic P at different rates (0–80 mg P kg⁻¹). Available P, growth and P uptake and AM colonisation of wheat were measured after 6 weeks. As expected, inorganic P addition increased growth and P uptake but decreased AM colonisation. The effect of the residues was more complex. AM colonisation was not correlated with available P in the soil amended with residues, whereas there was significant negative correlation between available P and AM colonisation in the treatments with inorganic P. Addition of FYS increased wheat shoot growth and P uptake and decreased AM colonisation. However, FMS and CP addition not only decreased wheat growth and P uptake but also AM colonisation despite low soil P availability. It is concluded that addition of some legume residues can improve the growth of subsequent cereals, but others have a negative effect on wheat growth and AM colonisation which cannot be explained solely by soil P availability.     

AFLP analysis in pigeonpea (<Emphasis Type="Italic">Cajanus cajan</Emphasis> (L.) Millsp.) revealed close relationship of cultivated genotypes with some of its wild relatives

A total of 561 amplified fragment length polymorphism (AFLP) loci were generated and used to study the genetic diversity of wild and cultivated genotypes of pigeonpea. Out of 561 marker loci, 558 were polymorphic with an average of 76.12 bands. Analysis of molecular variation (AMOVA) revealed significant strong population structure when genotypes were structured according to continent of origin (F_ST = 0.22) also when structured into cultivated and wild genotypes (F_ST = 0.16). Maximum polymorphic loci were observed in cultivated species C. cajan (352) which is due to more number of genotypes used while, a minimum number of 45 polymorphic bands were obtained in C. acutifolius. Highest (0.291) average gene diversity was recorded in species C. mollis and lowest (0.079) average gene diversity was recorded in C. acutifolius. The 33 genotypes grouped into 14 clusters at 26% Jaccard’s similarity coefficients. Clustering analysis revealed most cultivated genotypes grouped into one major cluster while, the wild genotypes grouped into many clusters at 26% Jaccard’s similarity revealing greater diversity within wild species as compared to cultivated genotypes. From among the various cultivated genotypes studied, four genotypes BRG 3, ICP 7035, TTB 7 and ICP 8863 were molecularly and morphologically diverse and were used as parental genotypes to study nature of inheritance and to identify markers linked to sterility mosaic disease.     

Interpreting the temperature-induced response of ammonia oxidizing microorganisms in soil using nitrogen isotope fractionation

Purpose  

Although nitrification plays a key role in the fate of soil nitrogen (N) under global warming, little information is available for the nitrifiers’ response to changing temperatures. Nitrogen isotope fractionation associated with nitrification can be a proxy of nitrifiers’ sensitivity to changing temperature. We hypothesized that the temperature-induced balance between the transport of substrate NH₄⁺ into the microbial cell (supply) and the intracellular NH₄⁺ oxidation (consumption) governs the intracellular NH₄⁺ concentration and then affects nitrification rates and associated isotope fractionations. This study was conducted to understand the microbial response of NH₄⁺ oxidation to changing temperatures by examining the effect of changing temperature on nitrification rate and apparent isotope fractionation.     

Sorption and persistence of wastewater-borne psychoactive and antilipidemic drugs in soils

Purpose  

Although the ubiquity of pharmaceuticals in treated wastewater has now been well documented, their fate and risk during beneficial wastewater reuse are far less understood. Soil sorption and degradation are important processes affecting the leaching potential of trace contaminants in irrigated soil. To this end, we examined the sorption and attenuation of six psychoactive and antilipidemic drugs, i.e., carbamazepine, diazepam, Dilantin, meprobamate, primidone, and gemfibrozil, in a loam (LVL) and a loamy sand representative of golf course soils in the southwestern United States.     

Biodegradation of carbofuran by <Emphasis Type="Italic">Pichia anomala</Emphasis> strain HQ-C-01 and its application for bioremediation of contaminated soils

A novel yeast named HQ-C-01 was isolated from activated sludge and identified as Pichia anomala based on the morphology and 18S rDNA sequence analysis. The HQ-C-01 strain degraded 95.2% of carbofuran when the insecticide was used as the only C source and added at 50 mg/L in a mineral salts medium within 48 h. The optimal concentration, temperature, and pH of medium for degradation of carbofuran were 50 mg/L, 30°C, and pH 7.5, respectively. Strain HQ-C-01 could also effectively degrade other carbamate insecticides including carbaryl, indoxacarb, and fenobucarb, and the degradation rates were 99%, 85%, and 67%, respectively. Gas chromatography–mass spectrometry analysis showed that the strain metabolized carbofuran to produce benzofuranol as the intermediate metabolite, which was further degraded. Degradation of carbofuran added at 50 mg/kg of soil was higher in yeast-inoculated soil than in the control. These results indicated that strain HQ-C-01 may potentially be used in bioremediation of carbofuran-contaminated soil.     

Influence of two-phase olive mill waste application to soil on terbuthylazine behaviour and persistence under controlled and field conditions

Purpose  

Terbuthylazine is one of the most common herbicides used to control weeds in olive groves. Application of two-phase olive mill waste (OW) to soils may play a fundamental role in the management of leaching losses of pesticides, especially in Mediterranean areas where soils are characterized by low organic matter levels. We evaluated the impact of OW amendments on the sorption–desorption, degradation, leaching, and persistence of the herbicide terbuthylazine in a representative olive grove soil from Portugal.