Enzyme activities and microbial biomass in coastal soils of India

Soil salinity is a serious problem for agriculture in coastal regions, wherein salinity is temporal in nature. We studied the effect of salinity, in summer, monsoon and winter seasons, on microbial biomass carbon (MBC) and enzyme activities (EAs) of the salt-affected soils of the coastal region of the Bay of Bengal, Sundarbans, India. The average pH of soils collected from different sites, during different seasons varied from 4.8 to 7.8. The average organic C (OC) and total N (TN) content of the soils ranged between 5.2-14.1 and 0.6-1.4 g kg⁻¹, respectively. The electrical conductivity of the saturation extract (ECe) of soils, averaged over season, varied from 2.2 to 16.3 dSm⁻¹. The ECe of the soils increased five fold during the summer season (13.8 dSm⁻¹) than the monsoon season (2.7 dSm⁻¹). The major cation and anion detected were Na⁺ and Cl⁻, respectively. Seasonality exerted considerable effects on MBC and soil EAs, with the lowest values recorded during the summer season. The activities of β-glucosidase, urease, acid phosphatase and alkaline phosphatase were similar during the winter and monsoon season. The dehydrogenase activity of soils was higher in monsoon than in winter. Average MBC, dehydrogenase, β-glucosidase, urease, acid phosphatase and alkaline phosphatase activities of the saline soils ranged from 125 to 346 mg kg⁻¹ oven dry soil, 6-9.9 mg triphenyl formazan (TPF) kg⁻¹ oven dry soil h⁻¹, 18-53 mg p-nitro phenol (PNP) kg⁻¹ oven dry soil h⁻¹, 38-86 mg urea hydrolyzed kg⁻¹ oven dry soil h⁻¹, 213-584 mg PNP kg⁻¹ oven dry soil h⁻¹ and 176-362 mg PNP g⁻¹ oven dry soil h⁻¹, respectively. The same for the non-saline soils were 274-446 mg kg⁻¹ oven dry soil, 8.8-14.4 mg TPF kg⁻¹ oven dry soil h⁻¹, 41-80 mg PNP kg⁻¹ oven dry soil h⁻¹, 89-134 mg urea hydrolyzed kg⁻¹ oven dry soil h⁻¹, 219-287 mg PNP kg⁻¹ oven dry soil h⁻¹ and 407-417 mg PNP kg⁻¹ oven dry soil h⁻¹, respectively. About 48%, 82%, 48%, 63%, 40% and 48% variation in MBC, dehydrogenase activity, β-glucosidase activity, urease activity, acid phosphatase activity and alkaline phosphatase activity, respectively, could be explained by the variation in ECe of saline soils. Suppression of EAs of the coastal soils during summer due to salinity rise is of immense agronomic significance and needs suitable interventions for sustainable crop production.     

Predicting upslope expansion of sub-alpine forest in the Makalu Barun National Park,Eastern Nepal,with a hybrid cartographic model

The natural upper boundary of a forest (forest line) in mountain environments is an indicator of climate conditions. An increase in global average temperatures has resulted in an upward advance of the forest line. This advance may result in fragmentation of the alpine ecosystem and a loss of biodiversity. Therefore, it is important to identify potential areas where current forests can advance under scenarios of future climate change. I used expert knowledge and cartographic modeling to create a hybrid cartographic model considering five topographic variables to predict areas where forest line can expand in the future. The prediction accuracy of the model is around 82%. The model is able to predict areas above the current forest line that are suitable or unsuitable for future forest advance. Further inclusion of high-resolution satellite imagery and digital elevation models, as well as field-based information into the model can help to improve the model accuracy.     

Association of Pedilanthus leaf curl virus with yellow mottling and leaf curl symptoms in two jasmine species grown in India

Association of Pedilanthus leaf curl virus (PeLCV) with yellow mottling of crape jasmine (Tabernaemontana coronaria) and leaf curl of night blooming jasmine (Cestrum nocturnum) was investigated using a sequence analysis of the cloned full-length genome amplified by Rolling circle amplification using Φ-29 DNA polymerase. In the sequence analysis, virus isolates from T. coronaria (JN807764) and C. nocturnum (JQ012790) shared 95 % sequence identity with each other and the highest identity (93 %) and the closest phylogenetic relationships with PeLCV (AM712436); therefore, the virus isolates were identified as PeLCV strains. This report from India is the first on the occurrence of PeLCV on T. coronaria and C. nocturnum anywhere in the world.     

Development of sustainable performance index based on production,reproduction, health and longevity for genetic improvement of Sahiwal cattle

An attempt was made for the first time in India to develop the performance indices for quantifying the relative emphasis to be given to production, reproduction, health and longevity traits for selection and genetic improvement of Sahiwal cattle in a sustainable manner. The study was conducted using information related to various production, reproduction, health and longevity traits spread over a period of 29 years in Sahiwal cattle. Using income and expenditure method, the relative economic values for 305 days milk yield (305DMY), average daily milk yield (ADMY), calving to first insemination interval (CFI), days open (DO) and longevity (LNG) were estimated as 1, 1, −6.62, −6.62 and 5.96 in Sahiwal cattle. A total of three performance indices were constructed using three-trait combination, that is production, reproduction and longevity before and after excluding the days suffered by the animals. Correlation between the aggregate genotype and index (R_IH) was computed to determine the accuracy of each performance index, and based on highest R_IH value, best performance index was identified for selection of Sahiwal cattle. Developed indices were further assessed for robustness by increasing the relative economic values of the traits by 25% and 50%. The performance index (305DMY, DO and LNG) was found to be the best index before as well as after excluding days suffered by the animals, but in later case emphasis to be given to different traits was found to be more balanced. The best index indicated that about 47, 42 and 11% relative emphasis to be assigned to 305 days milk yield, days open and longevity for selection of Sahiwal animals for sustainable genetic improvement.     

Direct and maternal (co)variance components and heritability estimates for body weights in Chokla sheep

Estimates of (co)variance components were obtained for weights at birth, weaning and 6, 9 and 12 months of age in Chokla sheep maintained at the Central Sheep and Wool Research Institute, Avikanagar, Rajasthan, India, over a period of 21 years (1980–2000). Records of 2030 lambs descended from 150 rams and 616 ewes were used in the study. Analyses were carried out by restricted maximum likelihood (REML) fitting an animal model and ignoring or including maternal genetic or permanent environmental effects. Six different animal models were fitted for all traits. The best model was chosen after testing the improvement of the log-likelihood values. Direct heritability estimates were inflated substantially for all traits when maternal effects were ignored. Heritability estimates for weight at birth, weaning and 6, 9 and 12 months of age were 0.20, 0.18, 0.16, 0.22 and 0.23, respectively in the best models. Additive maternal and maternal permanent environmental effects were both significant at birth, accounting for 9% and 12% of phenotypic variance, respectively, but the source of maternal effects (additive versus permanent environmental) at later ages could not be clearly identified. The estimated repeatabilities across years of ewe effects on lamb body weights were 0.26, 0.14, 0.12, 0.13, and 0.15 at birth, weaning, 6, 9 and 12 months of age, respectively. These results indicate that modest rates of genetic progress are possible for all weights.     

Rearing advanced fry of major Indian carp species in recirculatory-filtering ponds at Barrackpore,West Bengal

This paper describes an experiment using a recirculatory-filtering system operating in two rectangular cemented ponds (160 and 190 m², 1.5 m deep) to rear fry (25 mm–50 mm) of the major Indian carp species Labeo rohita (Hamilton) and Catla catla (Hamilton) to fingerlings (100 mm–125 mm). These operations were concluded in both the species in 32 days at stocking densities of 0.46 million/ha and 0.55 million/ha, and showed survival rates of 96.6% and 84.4% respectively. In the presently followed practices of modern fish culturists, corresponding operations in earth ponds usually take 90 days and have a stocking density of 0.2 million/ha with survival rates more or less similar to those obtained in the recirculatory-filtering system. If followed by industry, the technique described will enable production of major Indian carp fingerlings with great saving in time, the use of water and the space occupied by the production system. These advantages greatly enhance the economic viability of rearing carp fingerling in India.     

Low levels of genetic diversity detected by RAPD analysis in geographically distinct accessions of Bacopa monnieri

Brahmi (Bacopa monnieri) is atraditional Indian medicinal plant known for its natural nootropicaction of saponins present in large amount in its shoots. Acollection of 24 B.monnieri accessions from differentagro-climatic zones of India and an introduction from Malaysiamaintained in the field genebank at CIMAP was analysed for RAPDvariation. Among the 40 random primers tested, 29 primers generatedone or more polymorphic bands. The number of polymorphic bandsgenerated was primer dependent, ranging from 2 to maximum of 8.Similarity matrices were generated from the RAPD data on the basis ofNei's estimates of similarity indices and dendrograms wereconstructed based on UPGMA clustering. All the accessions were foundto be in the range of 0.8–1.0 of similarity, which isindicative of a narrow genetic base among the various accessions witha medium level of polymorphism. It was possible to differentiateindividual accessions, showing differences in morphological andgrowth properties at DNA level. The observed low levels of geneticvariation were attributed to interplay of sexual and vegetative modesof reproduction and similarity of local environments in habitats ofB. monnieri.     

Biochemical analysis of uterine fluid for identification of indicators for subclinical endometritis in the water buffalo (Bubalus bubalis)

Alterations in biochemical constituents of uterine fluid have been suggested for diagnosis of subclinical uterine infection in the bovine. This study was undertaken to investigate whether uterine fluid biomolecules could act as tool for diagnosis of subclinical endometritis in the buffalo. Uterine fluid samples from normal (n = 22) and subclinical endometritis (n = 18; diagnosed based on uterine cytology)‐affected buffaloes were subjected to biochemical analysis. Among the different biochemical constituents estimated, urea, urea N, cholesterol, total bilirubin and alkaline phosphatase (ALP) concentrations were significantly (p < 0.05) higher in uterine fluid obtained from subclinical endometritis‐affected buffaloes. The extent of difference between normal and subclinical endometritis‐affected buffaloes was highest in ALP (69%) followed by cholesterol (55%), bilirubin (48%), urea (30%) and urea N (30%) concentrations. Receiver operating characteristic (ROC) analysis indicated that the likelihood ratio (LR) was 3.63 for urea, indicating that buffaloes having less than the threshold concentration (47.5 mg/dl) of urea in their uterine fluid were at 3.6 times more risk to be affected with SE. The LRs for urea N, cholesterol, ALP and bilirubin were 2.33, 2.54, 2.12 and 1.65, respectively. It was concluded that ALP, urea, urea N and cholesterol concentrations in uterine fluid may serve as an aid for diagnosing subclinical endometritis in the buffalo.     

Virome identification in wheat in the Czech Republic using small RNA deep sequencing

High-throughput deep-sequencing technology and bioinformatics analysis of the small RNA(sRNA) population isolated from plants allows universal virus detection and complete virome reconstruction for a given sample. In the present sRNA deep-sequencing analysis of virus-infected wheat samples in the Czech Republic, samples were firstly tested for barley yellow dwarf viruses(BYDVs), wheat streak mosaic virus(WSMV) and wheat dwarf virus(WDV) using ELISA, RT-PCR and PCR. Subsequent sRNA sequencing of these samples yielded more than ～60 million single-end 50-bp reads with high confidence for nine field samples of wheat. Overall, 16.5% of reads were virus-specific and 83.5% were mapped to the host. More 21-nt reads(～7.7 E+06 reads) were found than 24-nt(～6.20 E+06 reads) or 22-nt(～4.30 E+06 reads) reads. De novo assembly of the high-quality contigs revealed the presence of three earlier reported viruses in the Czech Republic: BYDVs(31.48%), WSMV(24.23%) and WDV(26.66%). We also showed the presence of cereal yellow dwarf virus(14.33%; two species CYDV-RPS and CYDV-RPV(family Luteoviridae/Polerovirus) and wheat yellow dwarf virus(WYDV, 3.30%; Luteoviridae). Phylogenetic analysis showed CYDV and WYDV grouped separately from BYDVs. Furthermore, several recombination breakpoints were found among the groups of yellow dwarf viruses(BYDVs, CYDV, and WYDV). Using RNA deep sequencing, we confirmed the presence of the three known viruses(BYDVs, WSMV, and WDV) and the first record of two species of CYDV and WYDV in wheat in the Czech Republic.     

H2O2 degradation is suppressed in kumquat leaves infected with Xanthomonas axonopodis pv. citri

We found in a previous study that after leaves of kumquat [Fortunella margarita (Lour.) Swingle] cv ‘Nagami’ were inoculated with Xanthomonas axonopodis pv. citri (Xac), total superoxide dismutase activity (SOD) increased to promote higher H₂O₂ concentrations that coincided with a 4-fold decline in Xac populations ( Kumar et al., 2011a). The objective of the current study was to determine how activities and isoforms of important enzymes that catabolize H₂O₂, specifically catalase (CAT), ascorbate peroxidase (APOD), and the Class III peroxidases (POD) that are located in the apoplast, change in infected kumquat leaves to affect concentration and compartmentalization of H₂O₂. DAB (3,3-diaminobenzidine) staining of the Xac-infected leaves confirmed higher overall concentration of H₂O₂ as in our earlier study. One day after inoculation (dai), APOD activity declined below the controls and declines steadily up to 10 dai when the experiment was terminated. CAT activity was similar to the controls until 4 dai then declined rapidly to about 60% the activity of the controls by 6 dai, after which it remained fairly constant until 10 dai. There were 4 CAT isoforms in control leaves and 5 isoforms in infected leaves. The CAT-1 isoform band was much smaller in infected plants than the control at all sampling times. The CAT-3 isoform band disappeared at 10 dai. The CAT-5 isoform band, which was not observed in control leaves, appeared only at 4 dai in infected leaves. POD activity of infected leaves increased above the controls starting 1 dai and reached a maximum of about 3-fold higher than the controls 8 dai after which it declined. Two POD isoforms were detected in control and infected plants. This study demonstrated that the higher accumulation of H₂O₂ in kumquat leaves infected with Xac was promoted during pathogenesis first by the suppression of APOD activity and later by suppression of CAT activity. We propose that the higher SOD and lower APOD and CAT activities in the symplast contributed H₂O₂ substrate for the higher POD activity in the apoplast, which is known to be involved in plant defense against pathogens.