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.     

Changes with time in the potassium content and phyllosilicates in the soil of the Broadbalk continuous wheat experiment at Rothamsted

The transformations of phyllosilicates and the changes in potassium (K) balances caused by long-term cropping have been examined in soil from the 153-year-old Broadbalk experiment. Samples taken between 1856 and 1987 and kept in archive were fractionated for particle size and analysed for changes in mineralogy by X-ray diffraction and changes in total K of the coarser and fine fractions. These were compared with K balances made from records of cropping and fertilizer application. No change in mica due to cropping and K-depletion could be detected. Deep ploughing after 1925 mixed chlorite from the subsoil into the surface soil, but this had weathered by 1987. Potassium balances did not agree with measured changes in total K presumably because of unquantified uptake of K from the subsoil and poorly quantified K leaching.     

Genetic variability for seed oil content and seed index in some wild species and perennial races of cotton

A 3‐year study was made on genetic variability of seed oil content and seed index with 20 wild species, two cultivated species and six perennial races of Gossypium arboreum cotton maintained at the Central Institute for Cotton Research, Nagpur, India. The mean seed oil content varied from 10.26 to 22.89% in 22 species of Gossypium and six races of G. arboreum. In this material the weight of delinted seed varied from 43.33 to 54.54 mg/seed. The highest seed oil content was recorded in the species G. lobatum followed by G. harknessii. On average, for both traits, the means were higher for G. arboreum and its races. However, G. africanum and G. harknessii reached the level of G. arboreum and its races for seed weight, while five wild species surpassed the best races and G. arboreum in seed oil content, among them was G. harknessii. To breed simultaneously for seed oil content and seed weight, crosses between races of G. arboreum and wild species of Gossypium seem to be promising.     

Efficacy of fermented prawn shell waste as a feed ingredient for Indian white prawn, Fenneropenaeus indicus

Prawn shell waste collected from shrimp‐processing plants in Cochin, India, was subjected to fermentation using 20 chitinoclastic and proteolytic/non‐proteolytic bacterial strains. The products generated were analysed for protein, lipid, total sugars, N‐acetyl glucosamine, free amino acids and ash. Shrimp diets were prepared using these 20 fermented products and a control diet using raw prawn shell waste. Feeding experiment was conducted with postlarvae (PL21) of Indian white prawn, Fenneropenaeus indicus for a period of 21 days. Biogrowth parameters such as mean weight gain, feed conversion ratio, specific growth rate and protein efficiency ratio were estimated and the animals were challenged with white spot virus orally via diet. Enhanced growth could be observed in prawns fed F134 and F124, incorporated with the fermentation products generated using Bacillus spp., C134 and C124 respectively. The percentage survival of prawns after 7 days of challenge was found to be highest for groups fed diet F111 incorporated with fermentation product generated using Bacillus sp. These products of bacterial fermentation hold promise as growth enhancers and immunostimulants in aquaculture.     

Gharials (Gavialis gangeticus) in Bardiya National Park,Nepal: Population,habitat and threats

1. The Critically Endangered gharial (Gavialis gangeticus) residing within Bardiya National Park (BNP) in Nepal constitutes the sixth major sub-population of this unique lineage; however, this population is not well studied. A 46 km protected stretch of the Babai River and a 60 km stretch of the Karnali River in and around BNP were surveyed for gharials in early 2017 and in 2019.
2. Gharial counts in 2017 – 17 from the Babai and one from the Karnali rivers – consisted of 10 adults, five sub-adults and three juveniles. In 2019, 19 gharials were counted – 18 for the Babai and one for the Karnali – comprising 11 adults, six sub-adults and two juveniles. In the Babai River within BNP, four breeding groups were identified. Gharials in BNP prefer sandy vs. rocky banks for basking and completely avoid sand-grass and clay banks. Habitat preference did not vary with size class.
3. Protected stretches of both rivers inside BNP (76 km) have resident gharial, intact habitats and few human threats. In contrast, the unprotected stretch of the Karnali (30 km) is threatened by boulder quarrying, sand mining and unlicensed fishing, and is avoided by gharials despite the availability of habitat.
4. This study established baseline data, including indices of population size, distribution and habitat preferences, and documented resident gharials that are breeding in the Babai River in BNP. The conservation of this Babai population is crucial for the species’ survival in BNP.
5. Based on this study, we recommend the following conservation actions on the Babai stretch: (a) determine hatching success; (b) assess juvenile recruitment; (c) consider supplementation by releasing captives; (d) study riverine features important as baselines; (e) accommodate upstream movements on the protected Babai stretch; and (f) protect the downstream Babai outside the boundary of the BNP.

     

盐条件下产胞外多糖植物促生细菌研究

Salt-tolerant plant growth-promoting rhizobacteria (PGPR) can play an important role in alleviating soil salinity stress during plant growth and bacterial exopolysaccharide (EPS) can also help to mitigate salinity stress by reducing the content of Na + available for plant uptake.In this study,native bacterial strains of wheat rhizosphere in soils of Varanasi,India,were screened to identify the EPS-producing salt-tolerant rhizobacteria with plant growth-promoting traits.The various rhizobacteria strains were isolated and identified using 16S rDNA sequencing.The plant growth-promoting effect of inoculation of seedlings with these bacterial strains was evaluated under soil salinity conditions in a pot experiment.Eleven bacterial strains which initially showed tolerance up to 80 g L -1 NaCl also exhibited an EPS-producing potential.The results suggested that the isolated bacterial strains demonstrated some of the plant growth-promoting traits such as phosphate solubilizing ability and production of auxin,proline,reducing sugars,and total soluble sugars.Furthermore,the inoculated wheat plants had an increased biomass compared to the un-inoculated plants.     

Rapid detection of Corynebacterium pseudotuberculosis in clinical samples from sheep

Corynebacterium pseudotuberculosis, a Gram-positive bacterium is the causative agent of caseous lymphadenitis (CLA), a chronic disease of sheep, goats and other warm blooded animals. In the present study, a total of 1,080 sheep reared under semi-intensive system on organized farms situated in the semi arid tropical region of Rajasthan, India, was clinically examined. Pus samples from superficial lymph nodes of 25 (2.31 %) adult sheep showing clinical lesions similar to CLA were collected for laboratory analyses. On the basis of morphological, cultural and biochemical characteristics 12 (48 %) bacterial isolates from pus identified it as C. pseudotuberculosis. A polymerase chain reaction (PCR) assay targeting Putative oligopeptide/dipeptide ABC transporter, nicotinamide adenine dinucleotide phosphate (NADP) oxidoreductase coenzyme F420-dependent and proline iminopeptidase (PIP) genes of C. pseudotuberculosis was developed that showed 14 pus samples as positive. All C. pseudotuberculosis isolates were also found positive for these genes in the PCR. The specificity of the PCR products was confirmed by sequencing of the amplified products that showed 98–100 % homology with published sequences available in the NCBI database. The present study shows the incidence of CLA as 2.31 %, 1.1 % and 1.29 % based on clinical, bacterial culture and direct pus PCR assay, respectively. The PCR assay was rapid, specific and as significant as bacterial culture in detecting bacteria directly in the clinical pus samples. The PCR assay developed in the study can be applied for the diagnosis and control of CLA. Furthermore, the assay can also be applied to detect C. pseudotuberculosis in various clinical samples.