The effect of chemical and organic N inputs on N2O emission from rain-fed crops in Eastern Mediterranean.

Nitrogen has a significant contribution to global warming and its reduction in agriculture is expected to reduce N2O emissions having however adverse effects on the productivity of agricultural ecosystems. Maintaining systems productivity with alternative N sources i.e manure and composts could be a strategy also to mitigate N2O emissions. In this paper, we present the effect of different N sources (organic and chemical) on field N2O emissions and how these emissions are associated with soil available N forms (NH4+ and NO3-) in three different rain-fed crops namely barley, pea and vetch grown in Cyprus for two growing seasons. The daily emissions ranged from -3.11 to 12.3 g N-N2O/ha/day, while cumulative emissions ranged from 119 g N-N2O/ha to 660 g N-N2O/ha depending on crop and nitrogen source type. The emissions showed a seasonal pattern and WFPS has been identified as a critical soil parameter controlling daily N2O emissions. The daily N2O fluxes in the current study derives mainly from nitrification irrespectively crop type or nitrogen source type. Specific emission factors for each crop cultivated under different N source type were calculated and ranged from 0.03% ± 0.02-0.34% ± 0.09. The application of manure and chemical fertilizers cause similar intensity of N2O emissions while compost exhibited the lower emission factors. These findings suggest that composts could be integrated in a nutrient management strategy of rain-fed crops with less N2O emissions. The high background emissions found suggest also that other factors than external inputs are associated with N2O emissions and further studies including the response of microbial community structure and their contribution and association with N2O emissions.

On the prediction of non-CG DNA methylation using machine learning.

DNA methylation can be detected and measured using sequencing instruments after sodium bisulfite conversion, but experiments can be expensive for large eukaryotic genomes. Sequencing nonuniformity and mapping biases can leave parts of the genome with low or no coverage, thus hampering the ability of obtaining DNA methylation levels for all cytosines. To address these limitations, several computational methods have been proposed that can predict DNA methylation from the DNA sequence around the cytosine or from the methylation level of nearby cytosines. However, most of these methods are entirely focused on CG methylation in humans and other mammals. In this work, we study, for the first time, the problem of predicting cytosine methylation for CG, CHG and CHH contexts on six plant species, either from the DNA primary sequence around the cytosine or from the methylation levels of neighboring cytosines. In this framework, we also study the cross-species prediction problem and the cross-context prediction problem (within the same species). Finally, we show that providing gene and repeat annotations allows existing classifiers to significantly improve their prediction accuracy. We introduce a new classifier called AMPS (annotation-based methylation prediction from sequence) that takes advantage of genomic annotations to achieve higher accuracy.

N-Source Determines Barley Productivity, Nutrient Accumulation, and Grain Quality in Cyprus Rainfed Agricultural Systems.

The Eastern Mediterranean and Middle East (EMME) region is already experiencing the negative effects of increased temperatures and the increase in prolonged drought periods. The use of organic fertilization could be a valuable tool to meet the main challenges of climate change and maintain the productivity, quality, and sustainability of rainfed agricultural ecosystems. In the current study, we compare the effect of manure, compost, and chemical fertilization (NH4NO3) on barley grain and straw yield in a field study for three consecutive growing seasons. The hypothesis that the barley productivity, nutrient accumulation, and grain quality remain similar among the different nutrient management strategies was tested. The results showed that both growing season and type of nutrient source significantly affected barley grain and straw yield (F6,96 = 13.57, p < 0.01). The lowest productivity was noticed in the non-fertilized plots while chemical and organic fertilization exhibited similar grain yield, ranging from 2 to 3.4 t/ha throughout the growing seasons. For straw, the use of compost had no effect on the yield in any of the growing seasons examined. The use of manure and compost had a significant effect on grain macro- and micronutrient content but this was highly related to growing season. Principal component analysis (PCA) clearly demonstrated the discrimination of the different type of fertilization on barley performance during the course of the study, while the application of compost was highly associated with an increase in micronutrients in grain samples. Furthermore, structural equational modeling (SEM) showed that both chemical and organic fertilization had a direct positive effect on macro- (r = 0.44, p < 0.01) and micronutrient (r = 0.88, p < 0.01) content of barley grain and a positive indirect effect on barley productivity through N accumulation in grain (ß = 0.15, p = 0.007). The current study showed that barley grain and straw yield was similar between manure and NH4NO3 treatments, while compost exhibited a residual positive effect causing an increase in grain yield during the growing season. The results highlight that N fertilization under rainfed conditions is beneficial to barley productivity through its indirect effects on N accumulation in grain and straw, while it improves grain quality through the increased accumulation of micronutrients.

Optimizing Resource Allocation in a Cowpea (Vigna unguiculata L. Walp.) Landrace Through Whole-Plant Field Phenotyping and Non-stop Selection to Sustain Increased Genetic Gain Across a Decade.

Cowpea is a warm-season legume, often characterized as an orphan or underutilized crop, with great future potential, particularly under the global change. A traditional cowpea landrace in Cyprus is highly valued for fresh pod consumption in the local cuisine. In order to improve the yield potential of the landrace, the long-term response to direct selection for fresh pod yield and the associated changes in fodder and root biomass were investigated in a variety of fertility regimes under real field conditions. The non-stop selection process employed comprehensive pod, fodder, and root phenotyping at the level of the individual plant and resulted in the creation of a range of highly improved sibling lines with differential adaptation to micro-environments and with an improved ratio of pod to shoot and root biomass. The average rate of increase per year for fresh pod yield is at the level of 180 g per plant despite the relatively narrow genetic base of a single landrace and it is seemingly inexhaustible testifying to the great plasticity of the cowpea genome and the potential of the methodology to capture it. The corresponding high genetic gain was also confirmed under dense stands where the difference in pod yield between the best selection and the control amounted to 31.37%. Thus, the new focus apart from the simple variety maintenance should also include the continuous improvement and exploitation of micro-adaptation processes specific for individual fields that allow quick responses to environmental and climatic changes. This work presents also a novel approach to the multiple challenges encountered in root phenotyping and a method to meaningfully associate it with whole-plant performance in field conditions.

Converting environmental risks to benefits by using spent coffee grounds (SCG) as a valuable resource.

Coffee is perhaps one of the most vital ingredients in humans' daily life in modern world. However, this causes the production of million tons of relevant wastes, i.e., plastic cups, aluminum capsules, coffee chaff (silver skin), and spent coffee grounds (SCG), all thrown untreated into landfills. It is estimated that 1 kg of instant coffee generates around 2 kg of wet SCG; a relatively unique organic waste stream, with little to no contamination, separated directly in the source by the coffee shops. The produced waste has been under researchers' microscope as a useful feedstock for a number of promising applications. SCG is considered a valuable, nutrients rich source of bioactive compounds (e.g., phenolics, flavonoids, carotenoids, lipids, chlorogenic and protocatechuic acid, melanoidins, diterpenes, xanthines, vitamin precursors, etc.) and a useful resource material in other processes (e.g., soil improver and compost, heavy metals absorbent, biochar, biodiesel, pellets, cosmetics, food, and deodorization products). This paper aims to provide a holistic approach for the SCG waste management, highlighting a series of processes and applications in environmental solutions, food industry, and agricultural sector. Thus, the latest developments and approaches of SCG waste management are reviewed and discussed.

Application of sodium nitroprusside results in distinct antioxidant gene expression patterns in leaves of mature and senescing Medicago truncatula plants.

Sodium nitroprusside (SNP) represents one of the most commonly used NO donors in biological sciences, which acts as a signal molecule in plants responsible for the regulation of the expression of many defense-related enzymes. This study attempts to provide novel insight into the effect of application of low (100 µΜ) and high (2.5 mM) concentrations of SNP on antioxidant gene expression (cAPX, GST, FeSOD, CAT, and AOX) in mature (40 day) and senescing (65 day) Medicago truncatula plants. Quantitative real-time RT-PCR suggests that low concentration of SNP applied in mature leaves leads to an overall induction of antioxidant gene expression, while increasing concentration results in suppression of these genes. Conversely, older plants demonstrate a much more variable regulation which appears to be time dependent. The observed transcriptional regulation pattern in mature M. truncatula plants comes in support of the previously documented protective or damaging effect of SNP depending on concentration applied, whereas senescing M. truncatula plants demonstrated a general suppression in antioxidant gene expression levels regardless of SNP concentration, indicative of reduced overall plant defense capacity against free radicals.

Developmental stage- and concentration-specific sodium nitroprusside application results in nitrate reductase regulation and the modification of nitrate metabolism in leaves of Medicago truncatula plants.

Nitric oxide (NO) is a bioactive molecule involved in numerous biological events that has been reported to display both pro-oxidant and antioxidant properties in plants. Several reports exist which demonstrate the protective action of sodium nitroprusside (SNP), a widely used NO donor, which acts as a signal molecule in plants responsible for the expression regulation of many antioxidant enzymes. This study attempts to provide a novel insight into the effect of application of low (100 µΜ) and high (2.5 mM) concentrations of SNP on the nitrosative status and nitrate metabolism of mature (40 d) and senescing (65 d) Medicago truncatula plants. Higher concentrations of SNP resulted in increased NO content, cellular damage levels and reactive oxygen species (ROS) concentration, further induced in older tissues. Senescing M. truncatula plants demonstrated greater sensitivity to SNP-induced oxidative and nitrosative damage, suggesting a developmental stage-dependent suppression in the plant's capacity to cope with free oxygen and nitrogen radicals. In addition, measurements of the activity of nitrate reductase (NR), a key enzyme involved in the generation of NO in plants, indicated a differential regulation in a dose and time-dependent manner. Furthermore, expression levels of NO-responsive genes (NR, nitrate/nitrite transporters) involved in nitrogen assimilation and NO production revealed significant induction of NR and nitrate transporter during long-term 2.5 mM SNP application in mature plants and overall gene suppression in senescing plants, supporting the differential nitrosative response of M. truncatula plants treated with different concentrations of SNP.