Federico Vita

Barley (Hordeum vulgare L.) is a crucial cereal crop globally, and its productivity is influenced by environmental factors, including elevated carbon dioxide (CO2) levels and water stress. The aim of this study is to investigate the effects of water stress and increased CO2 concentration on the growth, physiological responses, and yield of two-row and six-row barley genotypes. Univariate data analysis revealed significant effects of CO2 concentration on most traits except chlorophyll a (Chla), crop antioxidant capacity as evaluated by the activity of plant extracts to scavenge the 2,2-diphenyl-1-picrylhydrazyl (DPPH), and on the maximum quantum yield of photosystem II (Fv/Fm). Mean comparisons showed that elevated CO2 increased certain traits such as shoot dry weight (ShDW) (34.1%), root dry weight (RDW) (50.8%), leaf area (LA) (12.5%), grain weight (GW) (64.1%), and yield-related traits and combination of significant indices (CSI) (72.5%). In comparison, Proline (−19.3%), Malondial...

Legumes maintain soil fertility thanks to their associated microbiota but are threatened by climate change that causes soil microbial community structural and functional modifications. The core microbiome associated with different chickpea and lentil genotypes was described after an unexpected climatic event. Results showed that chickpea and lentil bulk soil microbiomes varied significantly between two sampling time points, the first immediately after the rainfall and the second 2 weeks later. Rhizobia were associated with the soil of the more productive chickpea genotypes in terms of flower and fruit number. The root‐associated bacteria and fungi were surveyed in lentil genotypes, considering that several parcels showed disease symptoms. The metabarcoding analysis revealed that reads related to fungal pathogens were significantly associated with one lentil genotype. A lentil core prokaryotic community common to all genotypes was identified as well as a genotype‐specific one. A high...

Potatoes are a staple food with high antioxidant properties that can positively affect population health. The beneficial effects of potatoes have been attributed to tuber quality. However, the tuber quality related researches at genetic levels are very few. Sexual hybridization is a powerful strategy for producing new and valuable genotypes with high quality. In this study, 42 breeding potato genotypes in Iran were selected based on appearance characteristics such as shape, size, color, eyes of tubers, and tuber yield and marketability. The tubers were evaluated for their nutritional value and properties, viz. phenolic content, flavonoids, carotenoids, vitamins, sugars, proteins, and antioxidant activity. Potato tubers with white flesh and colored skin had significantly higher levels of ascorbic acid and total sugar. The result showed that higher phenolic, flavonoid, carotenoid, protein concentration, and antioxidant activity were noted in yellow-fleshed. Burren (yellow-fleshed) tub...

The increase in environmental temperature due to global warming is a critical threat to plant growth and productivity. Heat stress can cause impairment in several biochemical and physiological processes. Plants sense and respond to this adverse environmental condition by activating a plethora of defense systems. Among them, the heat stress response (HSR) involves an intricate network of heat shock factors (HSFs) and heat shock proteins (HSPs). However, a growing amount of evidence suggests that reactive oxygen species (ROS), besides potentially being responsible for cellular oxidative damage, can act as signal molecules in HSR, leading to adaptative responses. The role of ROS as toxic or signal molecules depends on the fine balance between their production and scavenging. Enzymatic and non-enzymatic antioxidants represent the first line of defense against oxidative damage and their activity is critical to maintaining an optimal redox environment. However, the HS-dependent ROS burst ...

Olea europaea L. is a glycophyte representing one of the most important plants in the Mediterranean area, both from an economic and agricultural point of view. Its adaptability to different environmental conditions enables its cultivation in numerous agricultural scenarios, even on marginal areas, characterized by soils unsuitable for other crops. Salt stress represents one current major threats to crop production, including olive tree. In order to overcome this constraint, several cultivars have been evaluated over the years using biochemical and physiological methods to select the most suitable ones for cultivation in harsh environments. Thus the development of novel methodologies have provided useful tools for evaluating the adaptive capacity of cultivars, among which the evaluation of the plant-microbiota ratio, which is important for the maintenance of plant homeostasis. In the present study, four olive tree cultivars (two traditional and two for intensive cultivation) were sub...

Additional file 10: Figure S3. Sample gene specificity. Shannon entropy (SH) distribution of T. magnatum genes (n = 6665) based on the expression data (in transcripts per million, TPM). A SH coefficient > 0.6 represents the gene-specific expression associated to each T. magnatum ecotype (i.e. geographical accession, see Additional file 11: Data file S1).

Heat stress (HS) severely affects different cellular compartments operating in metabolic processes and represents a critical threat to plant growth and yield. Chloroplasts are crucial for heat stress response (HSR), signaling to the nucleus the environmental challenge and adjusting metabolic and biosynthetic functions accordingly. GENOMES UNCOUPLED 1 (GUN1), a chloroplast-localized protein, has been recognized as one of the main players of chloroplast retrograde signaling. Here, we investigate HSR in Arabidopsis wild-type and gun1 plantlets subjected to 2 hours of HS at 45°C. In wild-type plants, Reactive Oxygen Species (ROS) accumulate promptly after HS, contributing to transiently oxidize the cellular environment and acting as signaling molecules. After 3 hours of physiological recovery at growth temperature (22°C), the induction of enzymatic and non-enzymatic antioxidants prevents oxidative damage. On the other hand, gun1 mutants fail to induce the oxidative burst immediately aft...

Il presente lavoro di tesi ha avuto come obiettivo lo studio della variabilità proteomica del tartufo bianco di San Miniato con l’intento di individuare profili proteici caratteristici collegabili alle aree di provenienza. Tale scopo è stato perseguito attraverso l’analisi di 7 campioni di Tuber magnatum Pico provenienti da aree della toscana diverse (Crete Senesi, Montaione, Mugello, Lucca, San Miniato), caratterizzate da una elevata vocazione produttiva; nelle analisi sono stati inseiriti anche i tartufi di Alba, di derivazione piemontese. Tali analisi, sono state basate su campioni raccolti in due annate distinte, nel 2007 e nel 2008. Nello specifico, i campioni sono stati inizialmente ripuliti da eventuali contaminazioni, polverizzati in azoto liquido ed utilizzati per l’estrazione delle proteine. In seguito, l’estratto proteico ottenuto è stato impiegato per l’ottenimento di gel elettroforetici bidimensionali, utilizzando la colorazione Blu di Coomassie per evidenziare gli spot...

Tuber magnatum Picco is a greatly appreciated truffle species mainly distributed in Italy. Its price and characteristics mostly depend on its geographical origin. Truffles represent a fundamental step of the life cycle of Tuber species promoting spore dissemination. They consist of two main parts, gleba, the inner part, and peridium, which is in direct contact with ground soil. Within the truffle and around in the growing soil, both the occurrence and abundance of different microbial species seem to play an essential role in truffle production. The development of the next-generation sequencing (NGS) based technology has greatly improved to deepen the role of the composition of microbial communities, thus improving the knowledge of the existing relationships between microbial taxa in a specific condition. Here, we applied a metabarcoding approach to assess the differences in T. magnatum samples collected from three areas in Tuscany (Italy). Peridium and gleba were analyzed separately...

Additional file 14: Figure S4. Relative expression level of the genes selected for the qPCR. Relative levels were expressed, for each gene, as fold change (FC) from the reference sample SM 2014. Data are mean values of transformed data (log10(FC + 1) related to gene expression (n = 4), calculated with the 2-ΔΔCt method [92]. Letters indicate results of Tukey post-hoc test analysis. Sample names correspond to those reported in Table 1. For a reference to RNA-seq transcript IDs, see Additional file 13: Table S9.

Truffles are among the most expensive foods available in the market, usually used as flavoring additives for their distinctive aroma. The most valuable species is Tuber magnatum Pico, better known as "Alba white truffle", in which bis(methylthio)methane is the key aroma compound. Given the high economical value of genuine white truffles, analytical approaches are required to be able to discriminate between natural or synthetic truffle aroma. Gas chromatography coupled to combustion-isotope ratio mass spectrometry (GC-C-IRMS), exploiting the 13C/12C ratio abundance of the key flavorings compounds in foods, has been a recognized technique for authenticity and traceability purposes; however, a number of issues have greatly limited its widespread use so far. In the present research, a high-efficiency HS-SPME MDGC-C-IRMS with simultaneous quadrupole MS detection has been applied for the evaluation of bis(methylthio)methane, resolving the coelution occurring with other components. With the aim to minimize the effect of column bleeding on δ13C measurement, a medium polarity ionic liquid-based stationary phase was preferred to a polyethylene glycol one, as the secondary column. In total, 24 genuine white truffles harvested in Italy were analyzed, attaining a δ13C values between -42.6‰ and -33.9‰, with a maximum standard deviation lower than 0.7‰. Two commercial intact truffles and 14 commercial samples of pasta, sauce, olive oil, cream, honey, and fresh cheese flavored with truffle aroma were analyzed, and the results from δ13C measurement were evaluated in comparison with those of genuine "white truffle" range and commercial synthetic bis(methylthio)methane standard.

Roots of the European hazelnut (Corylus avellana L.), i.e., one of the most economically important nut species, form symbiosis with ectomycorrhizal (ECM) fungi, including truffles. Although physical interactions only occur in roots, the presence of mycorrhizal fungi can lead to metabolic changes at a systemic level, i.e., in leaves. However, how root colonization by ECM fungi modifies these processes in the host plant has so far not been widely studied. This work aimed to investigate the response in two C. avellana genotypes, focusing on leaves from plants inoculated with the black truffle Tuber melanosporum Vittad. Transcriptomic profiles of leaves of colonized plants were compared with those of non-colonized plants, as well as sugar and polyphenolic content. Results suggested that T. melanosporum has the potential to support plants in stressed conditions, leading to the systemic regulation of several genes involved in signaling and defense responses. Although further confirmation ...

Simple Summary Carbohydrates play important roles in tolerance to both biotic and abiotic stressors. Xylella fastidiosa, the causal agent of “Olive Quick Decline Syndrome”, is a quarantine pathogen that induces drought stress in the host, aggravated by eventual water shortage, which is a frequent environmental condition in Mediterranean olive groves. At present, the resistance mechanisms shown by few resistant olive cultivars (e.g., cv Leccino) are not completely known; therefore, the aim of this research is to understand whether sugar metabolism is involved in the cross-talk mechanisms of biotic and abiotic responses. The results show that drought stress response induces effects beneficial to resistance of Xylella fastidiosa in cv Leccino. In the current context of global climate change, this study supports the importance of investigating the complex drought–disease interaction to detect resistance traits and thus find ways to counter the threat of this pathogen in the future. Abst...

Additional file 6: Figure S1. Euclidean distance among samples. The heat map shows sample to samples distances indicating the strong correlation between biological replicates. The distance matrix was calculated from the normalized expression dataset using the variance-stabilizing transformations function from the Bioconductor package DESeq2. Data were hierarchically clustered based on sample distances. Biological replicates are indicated as r1 (year 2014) and r2 (year 2015). Shades of grey represent different extents of correlation among samples; black represents perfect positive correlation.

2-DE gel images related to <i>Tuber magnatum </i>Pico samples collected from three different geographical areas (Isernia, San Miniato, Alba). Twelve (Isernia) or sixteen replicate gels (four for each year of collection, Alba, San Miniato) were performed for each biological sample, depending on the overall duration of the study for each of the sampling locations evaluated.<br>

2-DE gel images related to <i>Tuber magnatum </i>Pico samples collected from three different geographical areas (Isernia, San Miniato, Alba). Twelve (Isernia) or sixteen replicate gels (four for each year of collection, Alba, San Miniato) were performed for each biological sample, depending on the overall duration of the study for each of the sampling locations evaluated.<br>

Volatiles were analyzed with a PTR-ToF-MS 8000 (IoniconAnalytik GmbH, Innsbruck, Austria) using H<sub>3</sub>O<sup>+</sup> as reagent ion for the proton transfer reaction. The reaction takes place between H<sub>3</sub>O<sup>+</sup> ions and all the biogenic or anthropogenic VOCs having a proton affinity higher than that of water (165.2 kcal mol<sup>−1</sup>). Separation of single ions happens accordingly to their mass to charge (<i>m/z</i>) ratio. Drift applied voltage was set at 600 V, temperature at 110 °C, and pressure at 2.25 mbar. For each sample, about 6 grams of material was transferred in a glass jar provided with a special lid that allowed Teflon connection to a zero-air generator (inlet) and the PTR-ToF system (outlet). The head space was then measured by direct injection into the PTR-ToF drift tube inlet for 150 seconds, after respectively 1 and 20 min of exposure. Preliminary measurements on an empty...

The GC–MS, and GC-FID runs were carried out on a two parallel GC-QP2010 and GC2010 instruments (Shimadzu, Kyoto, Japan). The GC column used was a 30 m × 0.25 mm i.d. × 0.25 μm df Supelcowax-10 column (MilliporeSigma). Helium was exploited as carrier gas, at a constant linear velocity of 30.0 cm/s which corresponding to an inlet pressure of 26.4 kPa for GC-MS and 97.4 kPa for GC-FID. The temperature program was the same in both analysis-type: 40°C at 3° C/min to 250°C, at 10°C/min to 280°C, held 10 min. GC-MS ion source temperature was set at 200°C; the interface temperature, 250°C. Scan range was set to m/z 40–360, with a scanning rate of 2000 amu/s. FFSNC 3.0 (Shimadzu) and NIST11 (Wiley) commercial libraries were used for identification, applying two filters, namely a spectrum similarity match over 85% and Linear Retention Index (LRI) (related to a C4-C24 FAMEs mixture) agreement in the ±15 range. The FID temperature was set at 280°C (sampling rate 40 ms) and gas flows were 40 mL/...

The GC–MS, and GC-FID runs were carried out on a two parallel GC-QP2010 and GC2010 instruments (Shimadzu, Kyoto, Japan). The GC column used was a 30 m × 0.25 mm i.d. × 0.25 μm df Supelcowax-10 column (MilliporeSigma). Helium was exploited as carrier gas, at a constant linear velocity of 30.0 cm/s which corresponding to an inlet pressure of 26.4 kPa for GC-MS and 97.4 kPa for GC-FID. The temperature program was the same in both analysis-type: 40°C at 3° C/min to 250°C, at 10°C/min to 280°C, held 10 min. GC-MS ion source temperature was set at 200°C; the interface temperature, 250°C. Scan range was set to m/z 40–360, with a scanning rate of 2000 amu/s. FFSNC 3.0 (Shimadzu) and NIST11 (Wiley) commercial libraries were used for identification, applying two filters, namely a spectrum similarity match over 85% and Linear Retention Index (LRI) (related to a C4-C24 FAMEs mixture) agreement in the ±15 range. The FID temperature was set at 280°C (sampling rate 40 ms) and gas flows were 40 mL/...

Additional file 7: Figure S2. Volcano plots representing the differentially expressed genes based on RNA-seq data. Pairwise comparisons are shown for San Miniato vs Alba (a) and Isernia vs Alba (b). Yellow dots highlight DEGs selected for |log2 fold change| > 1.5 and FDR

This proteomic dataset comprises 19 mass spectrometry raw data included in the following article:<br><br>Tuberomics: A molecular profiling for the adaption of edible fungi (<i>Tuber magnatum </i>Pico) to different natural environments<br><br><br>

Additional file 11: Data file S1. Differentially expressed genes (DEGs) data related to sample comparisons. Data sheets A) DEGs related to comparison San Miniato (SM) vs Alba (AL); B) DEGs related to comparison Isernia (IS) vs Alba (AL); C) DEGs identified in both the comparisons (SMvsAL, ISvsAL); D) DEGs identified only in San Miniato (SM) vs Alba (AL); E) DEGs identified only in Isernia (IS) vs Alba (AL); F) Gene specificty reported in TPM (transcripts per million) for each sample.

Significant variation in epidermal bladder cell (EBC) density and salt tolerance (ST) exists amongst quinoa accessions, suggesting that salt sequestration in EBCs is not the only mechanism conferring ST in this halophyte. In order to reveal other traits that may operate in tandem with salt sequestration in EBCs and whether these additional tolerance mechanisms acted mainly at the root or shoot level, two quinoa (Chenopodium quinoa) accessions with contrasting ST and EBC densities (Q30, low ST with high EBC density versus Q68, with high ST and low EBC density) were studied. The results indicate that responses in roots, rather than in shoots, contributed to the greater ST in the accession with low EBC density. In particular, the tolerant accession had improved root plasma membrane integrity and K+ retention in the mature root zone in response to salt. Furthermore, superior ST in the tolerant Q68 was associated with faster and root-specific H2O2 accumulation and reactive oxygen species...

Capsicum plant species are globally cultivated in warm and temperate regions, being important for agro-economic, biological and cultural aspects. While their worldwide spread and their ability of cross-pollination to easily hybridize play an important role in the formation of numerous species and varieties but also create confusion for their classification. For this reason, the categorization of species and varieties is complex and several methods have been used to evaluate pepper plant origin and evolution. Therefore, the objectives of this study were to compare a wild pepper (Capsicum chacoense) with other two domesticated cultivars belonging to different species such as Capsicum annuum and C. baccatum and draw conclusions about their origins using different approaches. For this purpose three methodologies have been used and compared: the comparison of their fruits volatile organic compounds (VOCs) emissions , their capsaicin and dihydrocapsaicin content and the leaves proteomic p...

Soil salinity is among the major abiotic stresses that plants must cope with, mainly in arid and semiarid regions. The tolerance to high salinity is an important agronomic trait to sustain food production. Quinoa is a halophytic annual pseudo-cereal species with high nutritional value that can secrete salt out of young leaves in external non-glandular cells called epidermal bladder cells (EBC). Previous work showed high salt tolerance, but low EBC density was associated with an improved response in the early phases of salinity stress, mediated by tissue-tolerance traits mainly in roots. We compared the transcript profiling of two quinoa genotypes with contrasting salt tolerance patterning to identify the candidate genes involved in the differentially early response among genotypes. The transcriptome profiling, supported by in vitro physiological analyses, provided insights into the early-stage molecular mechanisms, both at the shoot and root level, based on the sensitive/tolerance traits. Results showed the presence of numerous differentially expressed genes (DEGs) among genotypes, tissues and treatments, with genes involved in hormonal and stress response upregulated mainly in the sensitive genotype, suggesting that tolerance may be correlated to restricted changes in gene expression, at least after a short salt stress. These data, showing constitutive differences between the two genotypes, represent a solid basis for further studies to characterize the salt tolerance traits. Additionally, new information provided by this work might be useful for the development of plant breeding or genome engineering programs in quinoa.

Background Truffles are symbiotic fungi that develop underground in association with plant roots, forming ectomycorrhizae. They are primarily known for the organoleptic qualities of their hypogeous fruiting bodies. Primarily, Tuber magnatum Pico is a greatly appreciated truffle species mainly distributed in Italy and Balkans. Its price and features are mostly depending on its geographical origin. However, the genetic variation within T. magnatum has been only partially investigated as well as its adaptation to several environments. Results Here, we applied an integrated omic strategy to T. magnatum fruiting bodies collected during several seasons from three different areas located in the North, Center and South of Italy, with the aim to distinguish them according to molecular and biochemical traits and to verify the impact of several environments on these properties. With the proteomic approach based on two-dimensional electrophoresis (2-DE) followed by mass spectrometry, we were ab...