Search

The importance of plants as complex entities influenced by genomes of the associated microorganisms is now seen as a new source of variability for a more sustainable agriculture, also in the light of ongoing climate change. For this reason, we investigated through metatranscriptomics whether the taxa profile and behaviour of microbial communities associated with the wood of 20-year-old grapevine plants are influenced by the health status of the host. We report for the first time a metatranscriptome from a complex tissue in a real environment, highlighting that this approach is able to define the microbial community better than referenced transcriptomic approaches. In parallel, the use of total RNA enabled the identification of bacterial taxa in healthy samples that, once isolated from the original wood tissue, displayed potential biocontrol activities against a wood-degrading fungal taxon. Furthermore, we revealed an unprecedented high number of new viral entities (~120 new viral species among 180 identified) associated with a single and limited environment and with potential impact on the whole holobiont. Taken together, our results suggest a complex multitrophic interaction in which the viral community also plays a crucial role in raising new ecological questions for the exploitation of microbial-assisted sustainable agriculture.

Genome editing via CRISPR/Cas9 is a powerful technology, which has been widely applied to improve traits in cereals, vegetables and even fruit trees. For the delivery of CRISPR/Cas9 components into dicotyledonous plants, Agrobacterium tumefaciens mediated gene transfer is still the prevalent method, although editing is often accompanied by the integration of the bacterial T-DNA into the host genome. We assessed two approaches in order to achieve T-DNA excision from the plant genome, minimizing the extent of foreign DNA left behind. The first is based on the Flp/FRT system and the second on Cas9 and synthetic cleavage target sites (CTS) close to T-DNA borders, which are recognized by the sgRNA. Several grapevine and apple lines, transformed with a panel of CRISPR/SpCas9 binary vectors, were regenerated and characterized for T-DNA copy number and for the rate of targeted editing. As detected by an optimized NGS-based sequencing method, trimming at T-DNA borders occurred in 100% of the lines, impairing in most cases the excision. Another observation was the leakage activity of Cas9 which produced pierced and therefore non-functional CTS. Deletions of genomic DNA and presence of filler DNA were also noticed at the junctions between T-DNA and genomic DNA. This study proved that many factors must be considered for designing efficient binary vectors capable of minimizing the presence of exogenous DNA in CRISPRed fruit trees.

Domestication processes, amplified by breeding programs, have allowed the selection of more productive genotypes and more suitable crop lines capable of coping with the changing climate. Notwithstanding these advancements, the impact of plant breeding on the ecology of plant-microbiome interactions has not been adequately considered yet. This includes the possible exploitation of beneficial plant-microbe interactions to develop crops with improved performance and better adaptability to any environmental scenario. Here we discuss the exploitation of customized synthetic microbial communities in agricultural systems to develop more sustainable breeding strategies based on the implementation of multiple interactions between plants and their beneficial associated microorganisms.

Reduction of fungicide consumption in agriculture is globally recognized as a priority. Government authorities are fostering research to achieve a reduction of risks associated with conventional pesticides and promoting the development of sustainable alternatives. To address these issues, in the present study, alternative protocols for the control of downy mildew infection in grapevine were compared to the standard protocol. In the first protocol, only resistance inducers were used, comprising a single formulation with Acibenzolar S-methyl, laminarin and disodium-phosphonate. The second and third protocols followed the standard protocol but substituted phosphonates with phosphorus pentoxide and Ecklonia maxima extract.The results showed that at veraison downy mildew incidence and severity in all tested protocols were significantly reduced compared to nontreated controls on both canopy and bunches. Expression analysis of key genes involved in plant stress response, indicated that the two protocols for phosphites substitution induced a remodulation of salicylic acid (SA) and jasmonic acid (JA), with positive impact on yields. Analysis of the first protocol revealed that the primed state induced a short delay in bunch ripening, with a shift of carbohydrate metabolism to boost the plant defences, involving an upregulation of defence related-gene, SAR response and a decreased ROS detoxification. Additionally, analysis on the arthropods populations, in parallel with the positive results achieved using alternatives to conventional fungicides, were enriched by those showing the potential of naturally occurring predators of spider mites.This study provides practical solutions to reduce the environmental impact of treatments for the control downy mildew in viticulture. © 2022 Society of Chemical Industry.

Aims: Soil microbiome roles in agriculture is becoming more and more important. This importance is also reflected on the way plants are seen: complex organisms formed by the plant itself plus the microbes inhabiting its tissues, including the ones on the surface of every organ and the ones adhered or in proximity to the roots. In addition, as already demonstrated, the microbial community associated with a specific soil is able to predetermine the health status of crops. For all the above mentioned reasons, defining the microbial composition of agricultural soils and the factors driving the assemblage is pivotal to achieve more sustainable agriculture and viticulture. Methods: We aimed to investigate how the soil geological characteristics influence the microbiome composition associated with close geographically related vineyards. Moreover, we studied both the top (15 cm in depth) and deep (120 cm in depth) soil layers as anthropically influenced and almost-undisturbed soil, respectively. Results: We observed slightly different microbial communities despite the close geographical proximity of the two vineyards, which is considered one of the main determinants of the soil microbiome composition. In addition, we found that the geological characteristics of the two soils influence both the root distribution and the accumulation of pathogen- and symbiont-related genera. Sensory profiles of the Grillo wines from the two different soils confirmed the tight link between soil origin and wine traits. Conclusions: In the present study, we highlight that the geological characteristics of soil can influence soil microbial composition and assemblage in close geographically related vineyards, with a potential effect on wine features.

It is well known that AM symbiosis provides several ecosystem services leading to plant adaptation in different environmental conditions and positively affects physiological and production features. Although beneficial effects from grapevine and AM fungi interactions have been reported, the impact on growth-defence tradeoff features has still to be elucidated. In this study, the potential benefits of an inoculum formed by two AM fungal species, with or without a monosaccharide addition, were evaluated on young grapevine cuttings grafted onto 1103P and SO4 rootstocks. Inoculated and non-inoculated plants were maintained in potted vineyard substrate under greenhouse conditions for 3 months. Here, agronomic features were combined with biochemical and molecular techniques to assess the influence of the different treatments. Despite the opposite behaviour of the two selected rootstocks, in AM samples, the evaluation of gene expression, agronomic traits and metabolites production revealed an involvement of the whole root microbiome in the growth-defence tradeoff balancing. Noteworthy, we showed that rootstock genotypes and treatments shaped the root-associated microbes, stimulating plant growth and defence pathways. Progresses in this field would open new perspectives, enabling the application of AMF or their inducers to achieve a more sustainable agriculture also in light of the ongoing climate change.

Background The role of soil microbiomes in agriculture is now becoming more and more important, leading to definition of plants as complex organisms formed by the plant itself plus the microbes inhabiting its tissues, the surface of every organ and the ones living adhered or in proximity of the roots. In this context it is important to define the factors able to influence the composition of such microbial communities. In addition, as already demonstrated, the microbial community associated to a specific soil is able to predetermine the health status of the crops in the future. For this reason, we decided to investigate how the soil geological characteristics can influence the microbial community associated to the close geographical related vineyard.Results We decided to analyse a calcarenitic and a marly-limestone soil which are both typical of the viticulture in the Menfi area (Sicily, Italy). Moreover, since vineyard is a semi-anthropic environment we decided to investigate both the top (10-20 cm) and deep (120 cm) soil layers as anthropic influenced and almost-undisturbed soil respectively. Interestingly we observed that, despite the close geographical proximity, the soil microbiomes were slightly different and that in addition, the soil geological characteristics are able to influence the root distribution and the accumulation of both pathogen- and symbiont-related genera. Furthermore, sensory profiles of the Grillo wines obtained from the two different soils confirmed the tight link between soil origin and wine traits.Conclusions In contrast to what observed in other works we pointed out that the geological characteristics of soils can have an important influence on soil microbial composition and assemblage in close geographical related vineyards, with a potential effect on wine features. Furthermore, defining the microbial composition of agricultural soils it’s a crucial step to achieve a more sustainable agriculture and viticulture. In this optic, the observed link between the geological characteristics and the microbiome profiles need to be taken into account when considering a soil for the successful establishment low chemical input agriculture practices.The SRA accession numbers of the NGS reported in this paper are deposited in NCBI under the BioProject PRJNA655455; BioSample SAMN15735114 and SAMN15735115; SRA accession SRR12436974 and SRR12436973