The Modification of Substrate in the Soilless Cultivation of Raspberries (Rubus Idaeus L.) as a Factor Stimulating the Biosynthesis of Selected Bioactive Compounds in Fruits.

Raspberry fruits are a valuable source of bioactive compounds. The study used the modification of the substrate (coconut fibre), consisting of the use of various organic and mineral additives, in the soilless cultivation of raspberries. The additives influenced the biosynthesis of bioactive compounds in the raspberry fruits by modifying the sorption properties and the abundance of the substrate. The influence of the additives on the content of polyphenols was determined as well as their profile (UPLC-MS), antioxidant potential (ABTS), vitamin C content, and the activity of selected enzymes that are markers of stress and resistance to abiotic factors. In the study, a significant effect of these additives was observed on the biosynthesis of polyphenols in raspberry fruit. The highest increase in the content of these compounds in relation to the control sample (substrate-100% coconut fibre), namely 37.7%, was recorded in the case of fruit produced on coconut substrate enriched with sheep wool. These fruits were also characterised by a significantly different profile of these compounds. These changes were caused by readily available ammonium nitrogen and free amino acids in the decomposition of proteins contained in the sheep wool. This was confirmed by the recorded content of chlorophyll SPAD in the plant leaves and the activity of selected enzymes, which proves a low level of stress and good condition of the plants.

Ensembl 2013.

The Ensembl project (http://www.ensembl.org) provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat. Our resources include evidenced-based gene sets for all supported species; large-scale whole genome multiple species alignments across vertebrates and clade-specific alignments for eutherian mammals, primates, birds and fish; variation data resources for 17 species and regulation annotations based on ENCODE and other data sets. Ensembl data are accessible through the genome browser at http://www.ensembl.org and through other tools and programmatic interfaces.

Ensembl 2012.

The Ensembl project (http://www.ensembl.org) provides genome resources for chordate genomes with a particular focus on human genome data as well as data for key model organisms such as mouse, rat and zebrafish. Five additional species were added in the last year including gibbon (Nomascus leucogenys) and Tasmanian devil (Sarcophilus harrisii) bringing the total number of supported species to 61 as of Ensembl release 64 (September 2011). Of these, 55 species appear on the main Ensembl website and six species are provided on the Ensembl preview site (Pre!Ensembl; http://pre.ensembl.org) with preliminary support. The past year has also seen improvements across the project.

Strategies for managing corn crop residue in the context of greenhouse gas emissions.

Food production is one of the most important sources of greenhouse gas (GHG) emissions, both in primary production and in processing and the logistics chain. The most problematic and risky is the optimization of environmental effects in the stage of primary production. This is due to the significant influence of factors related to climate and soil that are difficult to predict. The scientific literature offers much information on the impact of crop residue management, but the context for assessing the impact of crop residue management in corn production on the carbon footprint is still unclear. The effectiveness of using organic additives like biochar, compost, corn, or straw to maintain soil productivity is well acknowledged. Information about the effects of particular crop residue management strategies on soil carbon sequestration, soil quality, and crop yield in corn cultivation is currently scarce. The research aimed to assess the potential for optimizing corn production through modifications in crop residue management, with a focus on the efficiency indicator being the level of greenhouse gas emissions per functional unit of the product. A 3-year growing experiment was conducted to investigate the impact of different corn crop residue management strategies. The modifications of the corn cultivation technology in terms of the crop residue management strategy had a significant impact on the yield of plants and the amount of GHG emissions. The conversion of corn straw to biochar and its introduction into the soil reduced the GHG emissions from corn cultivation per functional unit, despite the energy expenditure related to straw transport and biochar production. From a 3-year time perspective, a beneficial effect of biochar addition on the size of the commercial yield of plants was observed. In variants with biochar and a reduced level of nitrogen fertilization, no reduction in yields was observed. This confirmed the hypothesis that biochar could be a useful material for the production of slow-acting fertilizers.

The shaping of onion seedlings performance through substrate formulation and co-inoculation with beneficial microorganism consortia.

Introduction: Smart management in crop cultivation is increasingly supported by application of arbuscular mycorrhizal fungi (AMF) and plant growth-promoting microorganisms (PGPM), which sustain soil fertility and plant performance. The aim of this study was the evaluation of the effects of consortia composed of (Claroideoglomus claroideum BEG96, Claroideoglomus etunicatum BEG92, Funneliformis geosporum BEG199, Funneliformis mosseae BEG 95, and Rhizophagus irregularis BEG140) and PGPM (Azospirillum brasilense - AZ, or Saccharothrix sp. - S) on onion cultivated in growing media with a composition corresponding to a degraded soil. Methods: Three types of substrate formulations were used, with peat:sand ratios of 50:50, 70:30, 100:0 (v:v). The analysis of substrate parameters crucial for its fertility (pH, salinity, sorption complex capacity, and elements' content) and characteristics reflecting onion seedlings' performance (fresh weight, stress biomarkers, and elements' content) was performed. Results: AMF colonized onion roots in all treatments, showing increasing potential to form intercellular structures in the substrates rich in organic matter. Additionally, co-inoculation with PGPM microorganisms accelerated arbuscular mycorrhiza establishment. Increased antioxidant activity and glutathione peroxidase (GPOX) activity of onion roots sampled from the formulations composed of peat and sand in the ratio of 100:0, inoculated with AMF+S, and positive correlation between GPOX, fresh weight and antioxidant activity of onion roots reflected the successful induction of plant acclimatization response. Total phenols content was the highest in roots and leaves of onion grown in substrates with 70:30 peat:sand ratio, and, in the case of roots, it was correlated with AMF colonization parameters but not with antioxidant activity. Discussion: AMF and PGPM efficiency in supporting onion growth should be linked to the increased onion root system capacity in mineral salts absorption, resulting in more efficient aboveground biomass production. AMF and PGPM consortia were effective in releasing minerals to soluble fraction in substrates rich in organic matter, making elements available for uptake by onion root system, though this phenomenon depended on the PGPM species. Microorganism consortia enhanced onion seedlings' performance also in substrates with lower content of organic carbon through plant biofertilization and phytostimulation.

Assessment of the Possibilities for the Use of Selected Waste in Terms of Biogas Yield and Further Use of Its Digestate in Agriculture.

The utilization of municipal waste and sewage sludge as a source of energy is technically very difficult due to high variability of their physical and chemical properties. The aim of this study was to evaluate the efficiency of the conversion of biomass contained in the whitewater fraction of municipal waste and sewage sludge by means of methanogenesis. The second objective was to assess the chemical composition of the digestate in the context of its use for fertilizer purposes. The whitewater fraction of municipal waste and sewage sludge was subjected to methanogenesis under static experimental conditions, according to DIM DIN 38414 methodology. The methanogenesis of concentrated substrates used in agricultural biogas plants was taken as a reference to evaluate the efficiency of the process. The organic fraction of the municipal waste was characterized by approximately 30% lower value of the soluble COD, with a comparable level of total COD compared to other materials. The total biogas yield, i.e., 404 dm3 per 1 kg of dry weight of the batch, was measured in the facility with sewage sludge. In COD value, this is 0.232 dm3·g O2 COD. In the case of corn, these values were, respectively, 324 dm3 and 0.193, and for the organic sub-sieve fraction of municipal waste, 287 dm3·kg-1 dw or 0.178 dm3·g O2 COD, respectively. The type of fermented material did not affect the intensity of biogas production. The maximum level of biogas production occurred between the 13th and 15th day of the process. The digestate obtained in the process of methanogenesis of corn silage and the organic fraction of municipal waste was characterized by good parameters in terms of possible use for fertilization purposes.

Preparation, Characterization of Granulated Sulfur Fertilizers and Their Effects on a Sandy Soils.

There is a potential for using sulfur waste in agriculture. The main objective of this study was to design a granular fertilizer based on waste elemental sulfur. Humic acids and halloysite were used to improve the properties and their influence on soil properties. This is the first report on the use of proposed materials for fertilizer production. The following granular fertilizers were prepared (the percentage share of component weight is given in brackets): fertilizer A (waste sulfur (95%) + halloysite (5%)), fertilizer B (waste sulfur (81%) + halloysite (5%) + humic acids (14%)), fertilizer C (waste sulfur (50%) + halloysite (50%)) and fertilizer D (waste sulfur (46%) + halloysite (46%) + humic acids (8%)). Basic properties of the obtained granulates were determined. Furthermore, the effect of the addition of the prepared fertilizers on soil pH, electrolytic conductivity, and sulfate content was examined in a 90-day incubation experiment. Enrichment with humic acids and the higher amount of halloysite increased the fertilizer properties (especially the share of larger granules and bulk density). In addition, it stabilized soil pH and increased the sulfur content (extracted with 0.01 mol·L-1 CaCl2 and Mehlich 3) in the soil.

Environmental and Production Aspects of Using Fertilizers Based on Waste Elemental Sulfur and Organic Materials.

Crop fertilization with sulfur is an important part of agricultural practices, as is the systematic increase in soil organic matter content. Materials of waste origin constitute a source of plant-available sulfur, as well as soil organic matter. The study was to verify the hypothesis assuming that combining waste sulfur pulp and its mixtures with organic materials enables simultaneous soil enrichment with readily available sulfur and organic matter. A 240-day incubation experiment was conducted, on two soils: very light and heavy; with two sulfur doses applied to each soil (20 and 40 mg S/kg d.m. for very light soil, and 30 and 60 mg S/kg d.m. for heavy soil). The sulfate sulfur content in the incubated soil material, treated with the addition of sulfur pulp and its mixtures with organic materials, increased significantly up to day 60 and then decreased. The application of these materials significantly increased the content of available sulfur and decreased the pH value of the incubated material. The effect of the introduced materials on dehydrogenase activity depended on soil granulometric composition (the impact of the applied materials on the activity of these enzymes in very light soil was small, and in heavy soil, their activity was usually limited by the presence of introduced materials). Application of the studied materials had little effect on the total organic carbon content in the incubated soil material (a significant change in the value of this parameter, in relation to the control soil, was recorded in some treatments of heavy soil).

Effects of growth promoting microorganisms on tomato seedlings growing in different media conditions.

Plant growth-promoting microbes (PGPM) play vital roles in maintaining crop fitness and soil health in stressed environments. Research have included analysis-based cultivation of soil-microbial-plant relationships to clarify microbiota potential. The goal of the research was to (i) evaluate the symbiotic microorganism effects on tomato seedling fitness under stressed conditions simulating a fragile soil susceptible to degradation; (ii) compare the plant-microbial interactions after inoculation with microbial isolates and fungi-bacteria consortia; (iii) develop an effective crop-microbial network, which improves soil and plant status. The experimental design included non-inoculated treatments with peat and sand at ratios of 50:50, 70:30, 100:0 (v:v), inoculated treatments with arbuscular mycorrhizal fungi (AMF) and Azospirillum brasilense (AZ) using the aforementioned peat:sand ratios; and treatment with peat co-inoculated with AMF and Saccharothrix tamanrassetensis (S). AMF + AZ increased root fresh weight in peat substrate compared to the control (4.4 to 3.3 g plant-1). An increase in shoot fresh weight was detected in the AMF + AZ treatment with a 50:50 peat:sand ratio (10.1 to 8.5 g plant-1). AMF + AZ reduced antioxidant activity (DPPH) (18-34%) in leaves, whereas AMF + S had the highest DPPH in leaves and roots (45%). Total leaf phenolic content was higher in control with a decreased proportion of peat. Peroxidase activity was enhanced in AMF + AZ and AMF + S treatments, except for AMF + AZ in peat. Microscopic root assays revealed the ability of AMF to establish strong fungal-tomato symbiosis; the colonization rate was 78-89%. AMF + AZ accelerated K and Mg accumulation in tomato leaves in treatments reflecting soil stress. To date, there has been no relevant information regarding the successful AMF and Saccharothrix co-inoculation relationship. This study confirmed that AMF + S could increase the P, S, and Fe status of seedlings under high organic C content conditions. The improved tomato growth and nutrient acquisition demonstrated the potential of PGPM colonization under degraded soil conditions.

Survey of 17 elements, including rare earth elements, in chilled and non-chilled cauliflower cultivars.

This study investigated if genetic diversity among cauliflower cultivars (white 'Xenia' F1, green 'Vitaverde' F1, purple 'Graffiti' F1, orange 'Sunset' F1, romanesco 'Celio' F1) and transplant chilling are reflected in the content of 17 elements in mature curds. Transplants at 40 days after sowing were exposed to 4 °C (chilling) and 18 °C (control) for 7 days and then planted in the field till harvest maturity. The lowest Ag, Al, Co, and Li contents were found in 'Celio' F1 cauliflower, which also had the highest Ba and Sr levels. Orange curds of 'Sunset' F1 were the richest in Al, and high in Li, Sc, and Sn. Chilling applied to the transplants increased Ag, Ba, Co, Sc, Sr, and Tb, and decreased the Y content of mature curds. Transplant chilling can permanently alter plant metabolism, and subsequently may affect the mineral composition of the curds.

Ensembl core software resources: storage and programmatic access for DNA sequence and genome annotation.

The Ensembl software resources are a stable infrastructure to store, access and manipulate genome assemblies and their functional annotations. The Ensembl 'Core' database and Application Programming Interface (API) was our first major piece of software infrastructure and remains at the centre of all of our genome resources. Since its initial design more than fifteen years ago, the number of publicly available genomic, transcriptomic and proteomic datasets has grown enormously, accelerated by continuous advances in DNA-sequencing technology. Initially intended to provide annotation for the reference human genome, we have extended our framework to support the genomes of all species as well as richer assembly models. Cross-referenced links to other informatics resources facilitate searching our database with a variety of popular identifiers such as UniProt and RefSeq. Our comprehensive and robust framework storing a large diversity of genome annotations in one location serves as a platform for other groups to generate and maintain their own tailored annotation. We welcome reuse and contributions: our databases and APIs are publicly available, all of our source code is released with a permissive Apache v2.0 licence at http://github.com/Ensembl and we have an active developer mailing list ( http://www.ensembl.org/info/about/contact/index.html ). Database URL: http://www.ensembl.org.