Diagnosis of plant diseases using the Nanopore sequencing platform

Reliable detection and identification of plant pathogens are essential for disease control strategies. Diagnostic methods commonly used to detect plant pathogens have limitations such as requirement of prior knowledge of the genome sequence, low sensitivity and a restricted ability to detect several pathogens simultaneously. The development of advanced DNA sequencing technologies has enabled determination of total nucleic acid content in biological samples. The possibility of using the single-molecule sequencing platform of Oxford Nanopore as a general method for diagnosis of plant diseases was examined. It was tested by sequencing DNA or RNA isolated from tissues with symptoms from plants of several families inoculated with known pathogens (e.g. bacteria, viruses, fungi, phytoplasma). Additionally, samples of groups of 200 seeds containing one infected seed of each of two or three pathogens, as well as samples with symptoms but unidentified pathogens were tested. Sequencing results were analysed with Nanopore data analysis tools. In all the inoculated plants, pathogens were identified in real time within 1–2 h of running the Nanopore sequencer and were classified to the species or genus level. DNA sequencing or direct RNA sequencing of samples with unidentified disease agents were validated by conventional diagnostic procedures (e.g. PCR, ELISA, Koch test), which supported the results obtained by Nanopore sequencing. The advantages of this technology include: long read lengths, fast run times, portability, low cost and the possibility of use in every laboratory. This study indicates that adoption of the Nanopore platform will be greatly advantageous for routine laboratory diagnosis.     

Dietary supplementation of dried plum: a novel strategy to mitigate heat stress in broiler chickens

Background: Heat stress is a significant problem in the poultry industry, causing a severe economic loss due to its detrimental effects on chickens' health and performance. Dried plum(DP) is a good source of minerals, vitamins,antioxidants, and phenolic compounds. Studies have suggested that DP has several health benefits, such as maintaining the body's redox system, immune status, and calcium hemostasis. Based on the health benefits of DP,we hypothesized that the dietary supplementation of DP would alleviate the detrimental effects of heat stress on broiler chickens.Results: To test the hypothesis, day-old broiler chicks(n = 72) were randomly allocated to three treatment groups(n = 24/group): no heat stress(NHS), heat stress(HS), and heat stress with dried plum(HS + DP), and reared under standard conditions. The inclusion of 2.5% DP in the feed of the HS + DP group was made during the treatment period, while birds in other groups were provided with a standard finisher diet. After 21 days, birds in the HS and HS + DP groups were exposed to cyclic heat stress conditions(33 °C for 8 h during daytime) for 3 weeks, while those in the NHS group were reared under normal conditions(22–24 °C). Weekly body weight and feed intake were recorded to calculate the average daily gain(ADG), average daily feed intake(ADFI), and feed conversion ratio(FCR). Heat stress significantly decreased the final body weight, ADG, ADFI, and increased FCR compared to the NHS group, whereas dietary supplementation of DP significantly improved these growth performance parameters compared to the HS group. Furthermore, supplementation of DP significantly increased the expression of heat shock protein-related genes(HSF1, HSF3, HSP70, and HSP90), antioxidant-related genes(SOD1, SOD2, GPX1, GPX3,PRDX1, and TXN), tight junction-related genes(CLDN1, and OCLN), and immune-related genes(IL4, MUC2) in the ileum as compared to the HS group. The microbiota analysis showed significant enrichment of Bacillales,Christensenellaceae, Bacillaceae, Peptostreptococcaceae, and Anaerotruncus in heat-stressed birds supplemented with DP as compared to the HS group. Further, DP supplementation also significantly increased the concentration of acetate, propionate, and total VFA in the cecal digesta of the HS + DP group as compared to the HS group.Conclusion: These findings suggest that DP supplementation effectively improved the growth performances and gut health parameters in the heat-stressed birds. Thus, dried plum can be a potential feed supplement to mitigate heat stress in broiler chickens.     

Effect of botanical extracts on the biological activity of granulosis virus against <Emphasis Type="Italic">Pieris brassicae</Emphasis>

A granulosis virus strain infecting Pieris brassicae (PbGV) was isolated from the dry temperate region of northwestern Himalayas as a potential microbial agent for its management. The effect of different botanicals (having insecticidal action against P. brassicae) on the bioefficacy of PbGV was evaluated under laboratory conditions using leaf disc bioassays on cabbage for improving the insecticidal performance of the PbGV. The synergistic action of different botanical extracts was evident in terms of reduction in LC₅₀ values against different botanical extracts. Among different extracts, petroleum-ether extract of neem seed kernel (NSK) when combined with PbGV resulted in maximum reduction of LC₅₀ value (4.39 × 10² occlusion bodies [OBs] ml⁻¹) followed by methanolic extract (7.38 × 10² OBs ml⁻¹) and aqueous extract (9.36 × 10³ OBs ml⁻¹) as compared with PbGV alone (1.85 × 10⁴ OBs ml⁻¹) for 2nd instar larvae of the test insect. These trends were found analogous in cases of 3rd and 4th instars of P. brassicae with different solvent extracts of NSK. The other botanicals evaluated, viz., Eupatorium and Artemesia, also resulted in reduction of LC₅₀ values for 2nd, 3rd and 4th instars as compared with PbGV alone when different extracts were combined with virus for bioassays. The studies suggest that the PbGV in combination with botanical pesticides could be more useful as a bio-pesticide against cabbage butterfly (P. brassicae) in IPM programs.     

Effects of supplemental xylanase and xylooligosaccharides on production performance and gut health variables of broiler chickensOA

Background: This study evaluated the effects of supplemental xylanase and xylooligosaccharides(XOS) in a cornsoybean meal(SBM)-based diet on growth performance and intestinal health of broilers. A total of 288 day-old chicks(Cobb 500) were allocated to 36 floor pens(8 birds/pen) equally in 9 dietary treatments in a 3 × 3 factorial arrangement. The treatments were combinations of 3 levels of xylanase(0, 0.005% and 0.01% Econase XT) and 3 levels of prebiotics(0, 0.005% and 0.01% XOS) added to basa...     

Quality of brackish aquaculture sludge and its suitability for anaerobic digestion and methane production in an upflow anaerobic sludge blanket (UASB) reactor

Intensive recirculating aquaculture systems (RAS) produce high volumes of biosolid waste. The high salinity of brackish/marine sludge limits its use in landfill sites and waste outflows and it is a source of pollution. A reduction in sludge mass would therefore minimize the potential environmental hazard and economic burden stemming from its disposal. The aims of the current study were: 1) to characterize brackish aquaculture sludge (BAS) from three RAS in order to test for potentially suitable treatments, and 2) to test the BAS's suitability for anaerobic digestion in an upflow anaerobic sludge blanket reactor (UASB). Brackish sludge from three intensive RAS was collected periodically and analyzed for a variety of physical and chemical parameters. The mean sludge electrical conductivity and pH values ranged from 4.0 to 8.6 mS cm^− 1 and 7.0 to 7.7, respectively. A low sludge redox potential averaging − 80 mV and dissolved oxygen concentrations of less than 1 mg l^− 1 indicated the existence of anaerobic conditions. Volatile solids comprised 56 to 76% of the dry weight and the sludge volume index ranged from 44 to 69 ml g ^− 1. High concentrations of total nitrogen and total carbon were also observed, resulting in a C:N ratio ranging between 8.1 and 10.3. Toxic and/or inhibitory compounds for methanogenesis such as nitrites, nitrates and sulfides were almost absent. Sludge BOD₅ ranged from 10 to 30% dry weight. These data suggest that BAS may be used in anaerobic digestion and methanogenesis without pretreatment. This concept was tested by digesting aquaculture sludge in UASB reactors. Despite the high sulfate and phosphate concentrations in the BAS, these were found not to be inhibitory to methanogenesis. Up to 70% sludge-mass reduction and an average of 40% methane production were demonstrated.     

A Novel Method for Combined Biowaste Stabilization and Production of Nitrate-Rich Liquid Fertilizer for Use in Organic Horticulture

A novel system for organic waste stabilization and reuse, combined with production of nitrate-rich liquid fertilizer was developed by manure digestion followed by volatilization of ammonia-rich gas (originating in manure extract) and its nitrification and recovery. This approach has several advantages, including biowaste stabilization and high recovery (over 60%) of manure N mainly as nitrate which is a better N form for many plants as compared to ammonium as the sole fertilizer N. Moreover, the potential utilization of different wastes as N sources in organic horticulture is possible as well as removal of suspended particles and microorganisms (including pathogens) that might otherwise clog the irrigation system and pose health risks, respectively. In a pilot-scale study, the system yielded several hundred liters of nitrate-rich (ca. 11 g N L⁻¹) liquid fertilizer using guano as substrate. In a fertilization experiment, lettuce fertigated with the nitrate-rich extract exhibited better growth and quality compared to the common organic practice of fertigation with guano extract. The resulting stabilized biowaste was estimated as “low-risk” according to current guidelines and may be used for liming or land application.     

Interaction effect of nitrogen,phosphorus, and zinc fertilization on growth,yield, and nutrient contents of aromatic rice varieties

Abstract

Studies on nutrient interactions in aromatic rice are needed for proper understanding of impact of imbalanced use of nutrients in the era of multi and micro-nutrient deficiencies. A pot experiment was conducted during the rainy/wet season (June–October) of 2013 at New Delhi, to study the interaction effects of two levels each of nitrogen (N) (0 and 120?kg?ha^?1), phosphorus (P; 0 and 25.8?kg?ha^?1), and zinc (Zn; 0 and 5?kg?ha^?1) in two aromatic rice (Oryza sativa L.) varieties, viz. Pusa Rice Hybrid 10 and Pusa Basmati 1121. Application of N, P, and Zn resulted in increase of dry matter (0.91, 0.32, and 0.24?g plant^?1, respectively) 60?days after sowing (DAS) and grain yield of rice (3.68, 1.67, and 1.17?g plant^?1). The increase in yield of rice owing to N application was relatively higher by 0.98, 0.22, and 1.05?g plant^?1, respectively, when either P or Zn or both were applied with N than alone application of N, indicating synergetic effect of P and Zn application with N. The higher concentration and uptake of K in grain (0.25% vs 0.10%) and straw (1.32% vs 0.94%) were observed in the treatment received N than no N, though K was applied uniformly in all the treatments. It indicates positive interaction of N and K. The higher uptake of P in grain and straw was observed when P was applied with N and Zn (3.34 and 2.15?mg plant^?1), or with N (3.26 and 2.11?mg plant^?1) signifying positive effect of N on P uptake in rice.     

Including root architecture in a crop model improves predictions of spring wheat grain yield and above‐ground biomass under water limitations

Although the root length density (RLD) of crops depends on their root system architecture (RSA), the root growth modules of many 1D field crop models often ignored the RSA in the simulation of the RLD. In this study, two model set‐up scenarios were used to simulate the RLD, above‐ground biomass (AGB) and grain yield (GY) of water‐stressed spring wheat in Germany, aiming to investigate the impact of improved RLD on AGB and GY predictions. In scenario 1, SlimRoot, a root growth sub‐model that does not consider the RSA of the crop, was coupled to a Lintul5‐SlimNitrogen‐SoilCN‐Hillflow1D crop model combination. In scenario 2, SlimRoot was replaced with the Somma sub‐model which considered the RSA for simulating RLD. The simulated RLD, AGB and GY were compared with observations. Scenario 2 predicted the RLD, AGB and GY with an average root mean square error (RMSE) of 0.43 cm/cm³, 0.59 t/ha and 1.03 t/ha, respectively, against 1.03 cm/cm³, 1.20 t/ha and 2.64 t/ha for scenario 1. The lower RMSE under scenario 2 shows that, even under water‐stress conditions, predictions of GY and AGB can be improved by considering the RSA of the crop for simulating the RLD.     

Zinc nutrition of rice as influenced by crop establishment methods,rates of nitrogen and phosphorus fertilization and inoculation with microbial consortia

Abstract

Zinc (Zn) fertilization in rice is important to enhance productivity and increase Zn concentration in rice grain to improve its nutritional status. A field experiment was conducted in wet seasons of 2013 and 2014 to study Zn nutrition of rice in three different crop establishment methods (CEMs) viz. puddled transplanted rice (PTR), system of rice intensification (SRI) and aerobic rice system (ARS), under three different rates of nitrogen (N) and phosphorus (P) viz. 0, 75 and 100% of recommended dose of fertilizer (RDF) (120?kg N ha^?1 and 25.8?kg P ha^?1) and two different sources of N and P viz. chemical fertilizer and microbial inoculation (MI). Concentration and uptake of Zn at different growth stages and in straw and milled rice was significantly higher in PTR and SRI than ARS. Soil DTPA–extractable Zn content of soil was increased by 1142.4, 1140.3 and 755.8?g ha^?1 in PTR, SRI and ARS after two year of Zn fertilization (soil application of 5?kg Zn ha^?1). Zinc nutrition increase its Zn concentration in straw and milled rice and improvement in total uptake was 38.1, 40.3 and 40.8?g ha^?1 when Zn was applied with RDF, 75% RDF + Anabaena sp. (CR1) + Providencia sp (PR3) consortia (MI1) and 75% RDF + Anabaena-Pseudomonas biofilmed bio-fertilizer (MI2), respectively. Positive correlation between milled rice yield and Zn concentration (R²= 0.95 and 0.97) showed the importance of Zn nutrition in improving rice yield. Zinc concentration at 70?days after sowing (DAS) and 100 DAS was also found positively correlated with dehydrogenase activity and microbial biomass carbon in soil.     

Reuse of Stabilized Fowl Manure as Soil Amendment and Its Implication on Organic Agriculture Nutrition Management

A major input in intensive organic agriculture is nutrient-rich liquid fertilizers. Guano and other fowl manure are frequently digested in water extracts, and the supernatant is supplied as fertilizer. The resultant manure biowaste (MBW) is commonly disposed of to the environment, posing potential pollution and health risks. The study aims were to determine two types of fowl MBWs for their chemical properties before and after lime treatment and to test their reuse potential as soil amendment. Guano and layer manure were digested, and the residues?? chemical properties were analyzed before and after lime treatment. MBWs were then air-dried and used as a soil amendment in a parsley-growing experiment. The lime-treated MBW composition met the European standards for high-quality biowaste compost. Both digested and lime-treated MBWs had residual nitrogen, 3% and 1% in guano and layer manure, respectively. Parsley grown in soil amended with layer MBW had 100% survival, high yield, and good crop quality compared with controls. Plants grown with soil amended with guano biowaste exhibited lower yield and only 50% survival. These findings indicate that the current practice of disposing guano biowaste to the environment may pollute soil and water bodies, while the land spread of lime-treated layer MBW is safe and may improve soil fertility.