Evaluating soil nitrate dynamics in an intercropping dripped ecosystem using HYDRUS-2D.

The competition mechanisms between crop species for water and nutrients, especially nitrate (NO3-N), in intercropping ecosystems are still poorly understood. Therefore, an experiment involving high (300 kg ha-1 for corn and 250 kg ha-1 for tomato), medium (210 kg ha-1 for corn and 175 kg ha-1 for tomato), and low (150 kg ha-1 for corn and 125 kg ha-1 for tomato) N-fertilizer applications (HF, MF, LF, respectively) was conducted in the corn and tomato intercropping ecosystem during 2014 (a calibration period for modeling) and 2015 (a validation period for modeling). The modified HYDRUS-2D code was used to analyze soil NO3-N concentrations (SNC) in the middle between corn rows (Pc), between corn and tomato rows (Pb), and between tomato rows (Pt), NO3-N exchange in the horizontal direction between different regions, NO3-N leaching from the corn, the bare, and the tomato region, and N uptake by crops. Simulated SNCs were in good agreement with measurements, with RMSE, NSE, and MRE of 0.01-0.06 mg cm-3, 0.75-0.98, and 8.7-19.1%, respectively, during the validation period (2015). Average SNCs in the 0-40 cm soil layer were different between Pc, Pt, and Pb. Intensive NO3-N exchange in the horizontal direction occurred during the second stage (Day After Sowing [DAS] 37-113 in 2014; DAS 29-120 in 2015). NO3-N exchange between the corn and bare regions was lower than between the tomato and bare regions due to smaller concentration gradients. However, in the vertical direction, NO3-N leaching from the corn region in both years was 4.1 and 8.8 times larger, respectively, than from the tomato region under HF since NO3-N mainly moved from the tomato region to the corn region. Our results reveal the competition between corn and tomato for N and provide a rationale for formulating and optimizing different fertilizer regimes for different crops in the intercropping ecosystem

Metabolic fingerprinting to assess the impact of salinity on carotenoid content in developing tomato fruits

As the presence of health-promoting substances has become a significant aspect of tomato fruit appreciation, this study investigated nutrient solution salinity as a tool to enhance carotenoid accumulation in cherry tomato fruit (Solanum lycopersicum L. cv. Juanita). Hereby, a key objective was to uncover the underlying mechanisms of carotenoid metabolism, moving away from typical black box research strategies. To this end, a greenhouse experiment with five salinity treatments (ranging from 2.0 to 5.0 decisiemens (dS) m(-1)) was carried out and a metabolomic fingerprinting approach was applied to obtain valuable insights on the complicated interactions between salinity treatments, environmental conditions, and the plant's genetic background. Hereby, several hundreds of metabolites were attributed a role in the plant's salinity response (at the fruit level), whereby the overall impact turned out to be highly depending on the developmental stage. In addition, 46 of these metabolites embraced a dual significance as they were ascribed a prominent role in carotenoid metabolism as well. Based on the specific mediating actions of the retained metabolites, it could be determined that altered salinity had only marginal potential to enhance carotenoid accumulation in the concerned tomato fruit cultivar. This study invigorates the usefulness of metabolomics in modern agriculture, for instance in modeling tomato fruit quality. Moreover, the metabolome changes that were caused by the different salinity levels may enclose valuable information towards other salinity-related plant processes as well

Visualization of Tomato Growth Based on Dry Matter Flow

The visualization of tomato growth can be used in 3D computer games and virtual gardens. Based on the growth theory involving the respiration theory, the photosynthesis, and dry matter partition, a visual system is developed. The tomato growth visual simulation system is light-and-temperature-dependent and shows plausible visual effects in consideration of the continuous growth, texture map, gravity influence, and collision detection. In addition, the virtual tomato plant information, such as the plant height, leaf area index, fruit weight, and dry matter, can be updated and output in real time

Review and simulation of homoplasy and collision in AFLP

In this paper we give a short review of the problems of homoplasy and collision in AFLP, and describe a software tool that we developed to illustrate these problems. AFLP is a DNA fingerprinting technique, producing profiles of bands, the result of the separation of DNA fragments by length on a gel or microcapillary system. The profiles are usually interpreted as binary band absence/presence patterns. We focus on two major problems: (1) Within a profile two or more fragments of the same length but of different genomic origin may have been selected, colliding into a single band. This collision problem, akin to the birthday problem, may be surprisingly large. (2) In a pair of profiles two equally long fragments of different genomic origin may have been selected, appearing as identical bands in the two profiles. This is called homoplasy. Both problems are quantified by modeling AFLP as a random sampling technique of fragment lengths. AFLP may be used in phylogenetic studies to estimate the pairwise genetic similarity of individuals. Similarity coefficients like Dice and Jaccard coefficients overestimate the true genetic similarity because of homoplasy, with increasing bias for higher numbers of bands per profile. Corrected estimators are described, which do not suffer from bias. The ideas are illustrated using a new software tool. Data from studies on Arabidopsis and tomato serve as examples. Finally, we make some recommendations with respect to the use of AFLP

High levels of cyclic-di-GMP in plant-associated Pseudomonas correlate with evasion of plant immunity

The plant innate immune system employs plasma membrane-localized receptors that specifically perceive pathogen/microbe-associated molecular patterns (PAMPs/MAMPs). This induces a defence response called pattern-triggered immunity (PTI) to fend off pathogen attack. Commensal bacteria are also exposed to potential immune recognition and must employ strategies to evade and/or suppress PTI to successfully colonize the plant. During plant infection, the flagellum has an ambiguous role, acting as both a virulence factor and also as a potent immunogen as a result of the recognition of its main building block, flagellin, by the plant pattern recognition receptors (PRRs), including FLAGELLIN SENSING2 (FLS2). Therefore, strict control of flagella synthesis is especially important for plant-associated bacteria. Here, we show that cyclic-di-GMP [bis-(3'-5')-cyclic di-guanosine monophosphate], a central regulator of bacterial lifestyle, is involved in the evasion of PTI. Elevated cyclic-di-GMP levels in the pathogen Pseudomonas syringae pv. tomato (Pto) DC3000, the opportunist P. aeruginosa PAO1 and the commensal P. protegens Pf-5 inhibit flagellin synthesis and help the bacteria to evade FLS2-mediated signalling in Nicotiana benthamiana and Arabidopsis thaliana. Despite this, high cellular cyclic-di-GMP concentrations were shown to drastically reduce the virulence of Pto DC3000 during plant infection. We propose that this is a result of reduced flagellar motility and/or additional pleiotropic effects of cyclic-di-GMP signalling on bacterial behaviour

A morphogenetic crop model for sugar-beet (Beta vulgaris L.)

This paper is the instructions for the proceeding of the International Symposium on Crop. Sugar beet crop models have rarely taken into account the morphogenetic process generating plant architecture despite the fact that plant architectural plasticity plays a key role during growth, especially under stress conditions. The objective of this paper is to develop this approach by applying the GreenLab model of plant growth to sugar beet and to study the potential advantages for applicative purposes. Experiments were conducted with husbandry practices in 2006. The study of sugar beet development, mostly phytomer appearance, organ expansion and leaf senescence, allowed us to define a morphogenetic model of sugar beet growth based on GreenLab. It simulates organogenesis, biomass production and biomass partitioning. The functional parameters controlling source-sink relationships during plant growth were estimated from organ and compartment dry masses, measured at seven different times, for samples of plants. The fitting results are good, which shows that the introduced framework is adapted to analyse source-sink dynamics and shoot-root allocation throughout the season. However, this approach still needs to be fully validated, particularly among seasons

Challenges and opportunities for quantifying roots and rhizosphere interactions through imaging and image analysis

The morphology of roots and root systems influences the efficiency by which plants acquire nutrients and water, anchor themselves and provide stability to the surrounding soil. Plant genotype and the biotic and abiotic environment significantly influence root morphology, growth and ultimately crop yield. The challenge for researchers interested in phenotyping root systems is, therefore, not just to measure roots and link their phenotype to the plant genotype, but also to understand how the growth of roots is influenced by their environment. This review discusses progress in quantifying root system parameters (e.g. in terms of size, shape and dynamics) using imaging and image analysis technologies and also discusses their potential for providing a better understanding of root:soil interactions. Significant progress has been made in image acquisition techniques, however trade-offs exist between sample throughput, sample size, image resolution and information gained. All of these factors impact on downstream image analysis processes. While there have been significant advances in computation power, limitations still exist in statistical processes involved in image analysis. Utilizing and combining different imaging systems, integrating measurements and image analysis where possible, and amalgamating data will allow researchers to gain a better understanding of root:soil interactions

Metabolic profiling reveals coordinated switches in primary carbohydrate metabolism in grape berry (Vitis vinifera L.), a non-climacteric fleshy fruit

Changes in carbohydrate metabolism during grape berry development play a central role in shaping the final composition of the fruit. The present work aimed to identify metabolic switches during grape development and to provide insights into the timing of developmental regulation of carbohydrate metabolism. Metabolites from central carbon metabolism were measured using high-pressure anion-exchange chromatography coupled to tandem mass spectrometry and enzymatic assays during the development of grape berries from either field-grown vines or fruiting cuttings grown in the greenhouse. Principal component analysis readily discriminated the various stages of berry development, with similar trajectories for field-grown and greenhouse samples. This showed that each stage of fruit development had a characteristic metabolic profile and provided compelling evidence that the fruit-bearing cuttings are a useful model system to investigate regulation of central carbon metabolism in grape berry. The metabolites measured showed tight coordination within their respective pathways, clustering into sugars and sugar-phosphate metabolism, glycolysis, and the tricarboxylic acid cycle. In addition, there was a pronounced shift in metabolism around veraison, characterized by rapidly increasing sugar levels and decreasing organic acids. In contrast, glycolytic intermediates and sugar phosphates declined before veraison but remained fairly stable post-veraison. In summary, these detailed and comprehensive metabolite analyses revealed the timing of important switches in primary carbohydrate metabolism, which could be related to transcriptional and developmental changes within the berry to achieve an integrated understanding of grape berry development. The results are discussed in a meta-analysis comparing metabolic changes in climacteric versus non-climacteric fleshy fruits