Tuberomics: a molecular profiling for the adaption of edible fungi (Tuber magnatum Pico) to different natural environments

Integrating transcriptome and metabolome analyses to characterize flower development in Salix variegata franch., a typical dioecious plant

Salix variegata, a typical dioecious plant with high reproductive and adaptive ability, has important ecological and ornamental value. To understand the potential mechanisms and metabolite dynamics of male and female flowers development, the first comparative analysis of the transcriptome and metabolome of S. variegata was applied. As a result, 12,245 differentially expressed genes (DEGs) and 4,145 differently expressed metabolites (DEMs) were identified. Transcriptomic analysis showed that the male and female flowers development processes were related to phenylpropanoid and flavonoid biosynthesis. According to the metabolic profile, the main amino acids, flavonoids, phenylpropanoids, and their derivatives were accumulated during the development of male and female flowers of the S. variegata. Combined transcriptomic and metabolomic analyses indicated that the AUX/IAA, bHLH, MIKC, MYB, NAC, ERF and RLK transcription factors (TFs) and their associated key DEGs may mediate the metabolism of phenylpropanoids and flavonoids, which in turn regulate the development of male and female flowers in S. variegata. These results provide important insights to elucidate the development of male and female flowers of S. variegata at the molecular level. Our results will contribute to understanding the molecular and genetic mechanisms of male and female flower development in typical dioecious plants.

Streptomyces improves sugarcane drought tolerance by enhancing phenylalanine biosynthesis and optimizing the rhizosphere environment

Drought stress is a common hazard faced by sugarcane growth, and utilizing microorganisms to enhance plant tolerance to abiotic stress has become an important method for sustainable agricultural development. Several studies have demonstrated that Streptomyces chartreuses WZS021 improves sugarcane tolerance to drought stress. However, the molecular mechanisms underlying tolerance at the transcriptional and metabolomic levels remain unclear. We comprehensively evaluated the physiological and molecular mechanisms by which WZS021 enhances drought tolerance in sugarcane, by performing transcriptome sequencing and non-targeted metabolomics; and examining rhizosphere soil properties and plant tissue antioxidant capacity. WZS021 inoculation improved the rhizosphere nutritional environment (AP, ammonia, OM) of sugarcane and enhanced the antioxidant capacity of plant roots, stems, and leaves (POD, SOD, CAT). Comprehensive analyses of the transcriptome and metabolome revealed that WZS021 mainly affects plant drought tolerance through phenylalanine metabolism, plant hormone signal transduction, and flavonoid biosynthesis pathways. The drought tolerance signaling molecules mediated by WZS021 include petunidin, salicylic acid, α-Linoleic acid, auxin, geranylgeraniol and phenylalanine, as well as key genes related to plant hormone signaling transduction (YUCCA, amiE, AUX, CYPs, PAL, etc.). Interestingly, inoculation with WZS021 during regular watering induces a transcriptome-level response to biological stress in sugarcane plants. This study further elucidates a WZS021-dependent rhizosphere-mediated regulatory mechanism for improving sugarcane drought tolerance, providing a theoretical basis for increasing sugarcane production capacity.

Transcriptomic and metabolomic analysis of poplar response to feeding by Hyphantria cunea

Populus cathayana × canadansis 'Xinlin 1' ('P.'xin lin 1') with the characteristics of rapid growth and high yield, is frequently attacked by herbivorous insects. However, little is known about how it defenses against Hyphantria cunea (H. cunea) at molecular and biochemical levels. Differences in the transcriptome and metabolome were analyzed after 'P. 'xin lin 1' leaves were fed to H. cunea for 0h, 2h, 4h, 8h, 16h and 24h. In the five comparison groups including 2h vs. CK, 4h vs. CK, 8h vs. CK, 16h vs. CK, and 24h vs. CK, a total of 8925 genes and 842 metabolites were differentially expressed. A total of 825 transcription factors (TFs) were identified, which encoded 56 TF families. The results showed that the top four families with the highest number of TFs were AP2/ERF, MYB, C2C2, bHLH. Analyses of leaves which were fed to H. cunea showed that the differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) were significantly enriched in plant hormone signal transduction pathway, MAPK signaling pathway, flavonoid, flavone and flavonol and anthocyanin biosynthesis pathway. Additionally, there were a number of genes significantly up-regulated in MAPK signaling pathway. Some compounds involved in plant hormone signal transduction and flavonoid/flavone and flavonol/ anthocyanin pathways such as jasmonic acid (JA), jasmonoyl-L-Isoleucine (JA-Ile), kaempferol and cyanidin-3-O-glucoside were induced in infested 'P.'xin lin 1'. This study provides a new understanding for exploring the dynamic response mechanism of poplar to the infestation of H. cunea.

Label-free based comparative proteomics approach revealed the changes in proteomic profiles driven by different maturities in two Chinese white truffles, Tuber panzhihuanense and Tuber latisporum

T. panzhihuanense and T. latisporum are white truffle species native to China, of which T. panzhihuanense has significant commercial potential, with high nutritional value and unique flavor. Maturity is an important factor affecting the nutrition and aroma of truffles, which determines their economic status. Here, a label-free-based comparative proteomics method was used to determine the proteomic profiles of T. panzhihuanense and T. latisporum at two different stages of maturity. The results showed that both maturity and species significantly affected the protein expression patterns. T. panzhihuanense responded stronger to maturity than T. latisporum, accompanied by a more complex interaction network between proteins. Some critical proteins were regulated by maturity and variety, including those involved in aroma formation, e.g., S-adenosyl-methionine synthetase. The enrichment of oxidation-reduction processes, glycolysis, and SNARE interactions in vesicular transport were driven by species and maturity. This study provides the first insights into the proteomic profiles of T. panzhihuanense and T. latisporum, revealing the roles of key proteins and biological processes in their maturation.

Fungal and Bacterial Diversity in the Tuber magnatum Ecosystem and Microbiome

Fungi belonging to the genus Tuber produce edible ascocarps known as truffles. Tuber magnatum Picco may be the most appreciated truffle species given its peculiar aroma. While its life cycle is not yet fully elucidated, some studies demonstrated an active role of microorganisms. The main goal of this study was to determine how the T. magnatum microbiome varies across space and time. To address this, we characterized microbial communities associated with T. magnatum through high-throughput amplicon sequencing of internal transcribed spacer (ITS) and 16S rDNAs in three productive natural sites in Italy across 2 years. At each site, four truffles were sampled as well as the soil underneath and at 40, 100, and 200 cm from the harvesting points, to assess for microbial variation between substrates, years, and sites. A statistically significant site-related effect on microbial communities was identified, whereas only the prokaryotic community was significantly affected by the distance of soil from the truffle. Significant differences between sampling years were also found, demonstrating a possible relation among rainfall precipitation and Firmicutes and Actinobacteria. Thirty-six bacterial OTUs in truffles and 11 bacterial OTUs in soils beneath truffles were identified as indicator taxa. As shown for other truffle species, the dominance of Bradyrhizobium, Rhizobium, and Ensifer spp. within the truffle fruiting body suggests an evolutionary adaptation of this microorganism to the genus Tuber. The present work offers novel and relevant insights into the microbial ecology of T. magnatum ecosystems and fruiting bodies. The function and role of these bacteria in the truffle microbiome and life cycle are in need of further investigation.

Role and potentialities of bacteria associated with Tuber magnatum: A mini-review

Among the hypogeous ectomycorrhizal fungi, the white truffle Tuber magnatum Picco is the species of greatest interest, both from an ecological and economic point of view. The increasing market demand of the precious white truffle along with the fall in its natural production led to a growing interest in cultivation techniques and encouraged truffle growers and researchers to deeper investigate factors that could affect and improve T. magnatum productivity. In this context, microbial communities play a central role. Indeed, in the last few years, the hypothesis of a potential link between microbial community composition and truffle orchard productivity is arousing a greater attention. Moreover, since the value of the prized T. magnatum can vary in relation to its provenience, the need to define a reliable tracking system is also emerging and bacteria appear to be a promising tool. Accordingly, the present mini-review summarises the knowledge currently available on T. magnatum microbial communities, focusing on the role of truffle-associated bacteria and highlighting similarities and differences between samples of different origin, to address the following issues: (i) Is there a correlation between microbial taxa and truffle ground productivity? (ii) Can bacteria actually be used as markers of T. magnatum geographic origin? The identification of microorganisms able to promote T. magnatum formation may represent an important advance in the field of truffle farming. Similarly, the detection of bacterial taxa that can be used as markers of T. magnatum origin could have a considerable impact on truffle industry and trade, even at local scale.

Bacterial Communities in the Fruiting Bodies and Background Soils of the White Truffle Tuber magnatum

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 with the aim to distinguish them based on their microbial composition. Also, soil samples were collected and analyzed to compare productive and unproductive truffle grounds to confirm the presence of specific patterns linked to truffle production. Results indicate that differences occurred between truffle compartments (gleba and peridium) as well as between analyzed soils (productive and unproductive), with distinctive taxa associated. Furthermore, findings also demonstrated specific characteristics associated with truffle collection areas, thus indicating a degree of microbial selection related to different environments.

Heterogeneity of the white truffle Tuber magnatum in a limited geographic area of Central-Southern Italy

Molise region (Central-Southern Italy) is one of the Italian richest areas of truffles and contributes significantly to the national production of the precious Tuber magnatum. Nevertheless, Molise truffle has received little scientific attention. Accordingly, in the present study, two T. magnatum populations collected in two different sites of Molise region were characterised from a morphological, genetic and microbiological point of view. A considerable variability between and within the two analysed groups emerged, suggesting an interesting heterogeneity of Molise white truffle populations. Ascocarps of the two groups significantly differed in size and maturation degree, although no linear correlation between weight and maturity was found. Genetic investigations focused on the Sequence-Characterised Amplified Region SCAR A21-inf. Three haplotypes, randomly distributed within the two truffle groups regardless of their collection sites, were detected. The 16S rRNA gene amplicon high-throughput sequencing provided an overview of the composition of the ascocarp-associated bacterial communities. A predominance of α-Proteobacteria was observed, with Bradyrhizobium among the main genera. However, some truffles showed unusual microbial profiles, with Pedobacter, Polaromonas and other bacterial genera as dominant taxa.

An Overview on Truffle Aroma and Main Volatile Compounds

Truffles are underground edible fungi that grow symbiotically with plant roots. They have been globally considered as one of the most expensive foods because of their rarity, unique aroma, and high nutritional value as antioxidant, anti-inflammatory, antiviral, hepatoprotective, anti-mutagenic, antituberculoid immunomodulatory, antitumor, antimicrobial, and aphrodisiac. The unique flavor and fragrance of truffles is one of the main reasons to get worldwide attraction as a food product. So, the aim of this review was to summarize the relevant literature with particular attention to the active aroma components as well as the various sample preparation and analytical techniques used to identify them. The major analytical methods used for the determination of volatile organic compounds (VOC) in truffles are gas chromatography (GC), proton-transfer-reaction mass spectrometry (PTR-MS), and electronic nose sensing (EN). In addition, factors influencing truffle aroma are also highlighted. For this reason, this review can be considered a good reference for research concerning aroma profiles of different species of truffles to deepen the knowledge about a complex odor of various truffles.

Differentiation of European and Chinese Truffle (Tuber sp.) Species by Means of Sterol Fingerprints

The increasing demand of valuable truffles (Tuber sp.) has prompted new areas of naturally growing truffles entering the market. Hence, the identification of valueless Tuber species is an important task to prevent food fraud. Here, we show that sterol patterns are suited to differentiate five Tuber species (Tuber magnatum, Tuber melanosporum, Tuber aestivum, Tuber albidum, and Tuber indicum varieties) from each other. Next to the known main sterols of Tuber, ergosterol and brassicasterol, occurrence of minor sterols in differing shares resulted in characteristic fingerprints in the five Tuber species, irrespective of the country of origin. A total of 27 sterols were evaluated, and we proposed assignment criteria of main sterol relations as well as eight distinct biomarkers within the minor compounds for the differentiation of European and Chinese truffles.

Can We Discover Truffle's True Identity?

This study used elemental and stable isotope composition to characterize Slovenian truffles and used multi-variate statistical analysis to classify truffles according to species and geographical origin. Despite the fact that the Slovenian truffles shared some similar characteristics with the samples originating from other countries, differences in the element concentrations suggest that respective truffle species may respond selectively to nutrients from a certain soil type under environmental and soil conditions. Cross-validation resulted in a 77% correct classification rate for determining the geographical origin and a 74% correct classification rate to discriminate between species. The critical parameters for geographical origin discriminations were Sr, Ba, V, Pb, Ni, Cr, Ba/Ca and Sr/Ca ratios, while from stable isotopes δ18O and δ13C values are the most important. The key variables that distinguish T.magnatum from other species are the levels of V and Zn and δ15N values. Tuber aestivum can be separated based on the levels of Ni, Cr, Mn, Mg, As, and Cu. This preliminary study indicates the possibility to differentiate truffles according to their variety and geographical origin and suggests widening the scope to include stable strontium isotopes.