Grey and Black Anti-Hail Nets Ameliorated Apple (Malus × domestica Borkh. cv. Golden Delicious) Physiology under Mediterranean Climate

The use of anti-hail nets on orchards changes the microclimate underneath the net. This might be of great importance in apple growing regions characterized by high radiation levels and hot and dry climates during the summer season. But, depending on the net colour and on the local climatic conditions, the shade promoted triggers different responses by the trees. Grey and black anti-hail nets were applied in an apple orchard (cv. ‘Golden Delicious’) located in Northeast Portugal. Under the nets a lower concentration of glomalin related-soil proteins was observed, along with an improvement on trees water status, stomatal conductance, net photosynthetic rate, total chlorophylls, N, Mg, Fe and Cu concentrations, as well as an increase in mean fruit weight. The major difference between nets was on the photosynthetic efficiency, being higher on black net in sunny days, while grey net performed better under cloudy conditions. The use of netting systems proved to be effective in improving “Golden Delicious” apple trees performance under a Mediterranean climate, mainly when the radiation reaching the plants surpass the tree saturation point for photosynthesis. Therefore, these findings anticipate solutions for current and forecasted negative effects of climate change.

Transcriptomic Analysis of Late-Ripening Sweet Orange Fruits (Citrus sinensis) after Foliar Application of Glomalin-Related Soil Proteins

Glomalin, one of the glycoproteins generated in the spores and hyphae of arbuscular mycorrhizal (AM) fungi, has multiple functions in plants and soil, while the role of foliar spray of easily extractable glomalin-related soil proteins (EE-GRSP) in citrus fruits is not well defined. Our study aimed to use referenced transcriptome sequencing to uncover the mechanism and the role of exogenous EE-GRSP in two late-ripening varieties of sweet orange (Citrus sinensis) fruits including Navel Lane Late (LW) and Rohde Red Valencia (XC). The 1804 and 1861 differentially expressed genes were identified in fruits of LW and XC, respectively, following foliar spray of EE-GRSP. Photosynthesis ranked second in the Kyoto Encyclopedia of Genes and Genomes (KEGG) metabolism in the LW variety, and carbon fixation in photosynthetic organizations ranked first in KEGG metabolism in the XC variety. The response to foliar spray of EE-GRSP affected the fruit starch and sucrose metabolism of KEGG, with 15 (10 up-regulated and 5 down-regulated) and 13 (2 up-regulated and 11 down-regulated) differentially expressed genes identified in the LW and XC variety, respectively. Cs5g19060 (sucrose phosphate synthase 4) was activated and reduced by EE-GRSP on XC and LW, respectively. Cs1g18220 (β-fructofuranosidase) and Cs2g12180 (glycosyl hydrolase family 9) genes were up-regulated and down-regulated in LW and XC, respectively. These results established the involvement of molecular signaling in response to foliar spray of EE-GRSP activating fruit sugar metabolism is dependent on citrus varieties.

Improvement of eukaryotic proteins prediction from soil metagenomes

Background | During the last decades, shotgun metagenomics and metabarcoding have highlighted the diversity of microorganisms from environmental or host-associated samples. Most assembled metagenome public repositories use annotation pipelines tailored for prokaryotes regardless of the taxonomic origin of contigs and metagenome-assembled genomes (MAGs). Consequently, eukaryotic contigs and MAGs, with intrinsically different gene features, are not optimally annotated, resulting in an incorrect representation of the eukaryotic component of biodiversity, despite their biological relevance. Results | Using an automated analysis pipeline, we have filtered eukaryotic contigs from 6,873 soil metagenomes from the IMG/M database of the Joint Genome Institute. We have re-annotated genes using eukaryote-tailored methods, yielding 5,6 million eukaryotic proteins. Our pipeline improves eukaryotic proteins completeness, contiguity and quality. Moreover, the better quality of eukaryotic proteins combined with a more comprehensive assignment method improves the taxonomic annotation as well. Conclusions | Using public soil metagenomic data, we provide a dataset of eukaryotic soil proteins with improved completeness and quality as well as a more reliable taxonomic annotation. This unique resource is of interest for any scientist aiming at studying the composition, biological functions and gene flux in soil communities involving eukaryotes.

Soil Metaproteomics for the Study of the Relationships Between Microorganisms and Plants: A Review of Extraction Protocols and Ecological Insights

Soil is a complex matrix where biotic and abiotic components establish a still unclear network involving bacteria, fungi, archaea, protists, protozoa, and roots that are in constant communication with each other. Understanding these interactions has recently focused on metagenomics, metatranscriptomics and less on metaproteomics studies. Metaproteomic allows total extraction of intracellular and extracellular proteins from soil samples, providing a complete picture of the physiological and functional state of the “soil community”. The advancement of high-performance mass spectrometry technologies was more rapid than the development of ad hoc extraction techniques for soil proteins. The protein extraction from environmental samples is biased due to interfering substances and the lower amount of proteins in comparison to cell cultures. Soil sample preparation and extraction methodology are crucial steps to obtain high-quality resolution and yields of proteins. This review focuses on the several soil protein extraction protocols to date to highlight the methodological challenges and critical issues for the application of proteomics to soil samples. This review concludes that improvements in soil protein extraction, together with the employment of ad hoc metagenome database, may enhance the identification of proteins with low abundance or from non-dominant populations and increase our capacity to predict functional changes in soil.

Evaluation of Changes in Glomalin-Related Soil Proteins (GRSP) Content, Microbial Diversity and Physical Properties Depending on the Type of Soil as the Important Biotic Determinants of Soil Quality

The aim of the study was to evaluate the changes in glomalin-related soil proteins (GRSP) content, microbial diversity and soil physical quality depending on the type of soil measures of soil improvement and changes in soil health. The study was based on a 100-year stationary field microplot experiment where the soil profiles were collected with preserving the natural soil horizons. The microplot experiment was carried out on eight different soil types: Brunic Arenosol (Dystric I), Rendzic Leptosol, Fluvic Cambisol, Haplic Cambisol (Eutric), Gleyic Phaeozem, Brunic Arenosol (Dystric II), Haplic Cambisol (Eutric II) and Haplic Cambisol (Dystric). These soils are the most common types of agricultural soils in Poland. Relatively significant correlations with the soil quality, physical parameters and the glomalin-related soil proteins have been found. The study determined the total GRSP (T-GRSP) and easily extractable GRSP (EE-GRSP) levels in soils as well as the soil physical quality index and soil’s microbial biodiversity. The GRSP depended on the type of soil and correlated with S-Index and also was responsible for the unique chemical and physical properties of soils. Soils characterized by the highest T-GRSP content belonged to the group of very good and good soil physical quality characterized also by high biological activity, for which there were strong correlations with such parameters as dehydrogenase activity (DHA), microbial biomass content (MBC), microbial nitrogen content (MBN) and total bacteria number (B). The highest T-GRSP content and higher microbial diversity were found in Gleyic Phaeozem, Rendzic Leptosol and Fluvic Cambisol. The T-GRSP and EE-GRSP content were additionally correlated with the number of AMF spores. Very poor and poor soil physical quality according to S-Index characterized Brunic Arenosol (Dystric I) and Haplic Cambisol (Dystric). This research indicates that a specific edaphone of soil microorganisms and GRSP content may be of great importance when assessing a soil’s quality and improvements in soil health. The abundance of glomalin-producing fungi significantly affects the quality of the soil. This effect is particularly important for agricultural soils are threatened by ongoing land degradation.

Mode of application influences the biofertilizing efficacy of cyanobacterial biofilm formulations in chrysanthemum varieties under protected cultivation

Availability of nutrients in soil plays an important role in the productivity and quality of flowers in chrysanthemum. A set of novel biofilm inoculants- Anabaena-Azotobacter, Anabaena-Pseudomonas fluorescens (An-Psf) and Anabaena-Trichoderma (An-Tr) were applied as carrier based dry formulation or soil drench and their performance compared in two varieties of chrysanthemum (White Star and Zembla), in a climate-controlled greenhouse. Both the An-Psf and (An-Tr) inoculants enhanced glomalin related soil proteins in the rhizosphere of White Star, while in terms of polysaccharide content of soil, both these inoculants performed better in Zembla variety. Significant increases in the availability of selected macro and micronutrients in rhizosphere soil samples, in both chrysanthemum varieties were recorded, particularly when the inoculants were applied as soil drench. Principal Component analysis illustrated the significant interaction among soil and plant parameters, more specifically, the distinct effect of the inoculants, as compared to the application of carrier alone or control treatment. This investigation demonstrated the varietal effects on soil biological activities and significance of mode of application of microbial inoculants in influencing plant growth and rhizospheric metabolic activities.