Daniele Nicotra

Ciclo: XXXVII

Data inizio: 01/12/2021

Curriculum: Agroalimentari

Borsa: MIUR PON R&I

Titolo tesi: Microbiome and plant health, beneficial bacteria for the eco-sustainable protection of tomato from stresses

Abstract: 

My thesis project aimed to uncover the mechanisms driving complex interactions within the plant microbiome, with the ultimate goal of developing new bioinoculants as sustainable alternatives to chemical products in tomato cultivation. As one of the world’s most widely cultivated and economically significant horticultural crops, tomato production faces major challenges due to biotic and abiotic stress factors that reduce both yield and quality. Growing environmental and health concerns regarding the intensive use of chemical treatments in tomato farming have increased the interest in alternative approaches, particularly focusing on biological control agents (BCA). Building on a previous project that developed a model system for New Generation Sequencing (NGS)-based analysis of the tomato microbiome’s traceability and profile, the first objective of this thesis was to isolate and select bacterial endophytes with potential as bioinoculants for promoting growth and controlling diseases in tomatoes.

The selected endophytic strains were isolated from the endosphere of seeds and roots of tomato plants at different stages of the production chain and were chosen based on the core microbiome analysis. These bacterial strains included both well-known biofertilizers and biocontrol agents (e.g., Pseudomonas and Bacillus) and lesser-known genera. Interestingly, the selected strains demonstrated beneficial activities in planta, enhancing tomato growth and controlling diseases like Fusarium Crown and Root Rot and Bacterial Spot, regardless of their in vitro performance. High-quality genomes of each strain were obtained through Oxford Nanopore long-read and Illumina short-read sequencing, enabling an in-depth analysis of their genetic profiles to identify phyto-beneficial traits.

From the ten selected strains, three synthetic communities (SynComs) with varying richness and diversity levels were designed and tested for their in vivo potential to enhance plant growth and stress resilience in tomato. One SynCom, designated MIX2, exhibited the most robust activity in our trials, prompting further investigation into its effects on resident microbial communities and plant gene expression. In growth chamber trials, MIX2 application in the soil reshaped the rhizosphere bacterial communities, notably affecting low-abundance taxa. Under greenhouse conditions with water-stressed tomato plants, MIX2 mitigated the stress impact, enhancing both growth and fruit quality. This beneficial effect may be linked to MIX2 positive influence on rhizosphere microbiome diversity, which was significantly compromised by water deficiency but successfully restored by the SynCom treatment.

II

In a biocontrol trial carried out in the growth chamber, MIX2 reduced the incidence and severity of Bacterial Spot disease caused by Xanthomonas euvesicatoria pv. perforans (Xep). Analyses of the phyllosphere and rhizosphere microbial community highlighted that both the pathogen and the SynCom treatments reshaped resident community assembly compared to control plants. Transcriptomic analysis of the plant-pathogen-BCA interaction on tomato leaves revealed that Xep inoculation significantly affected gene expression compared to MIX2. Interestingly, only in the presence of the pathogen, MIX2 triggered a priming effect, upregulating plant hormone signaling and phenylpropanoid biosynthesis pathways, notably those related to jasmonic acid (JA) and lignin biosynthesis.

Overall, these findings suggest the potential of PGPR as a promising tool for enhancing tomato plant growth and health. A top-down selection approach based on microbiome analysis proved effective in identifying potential bioinoculants. Additionally, a proper SynCom design appears crucial for the successful establishment of the inoculants within the resident microbiome, where they actively interact with the native microbes to promote a more resilient and efficient microbiome assembly. A diverse mixture of bacterial strains may also combine multiple mechanisms of action

Tutor: Catara

Data Conseguimento Titolo:

Linkedin: www.linkedin.com/in/daniele-nicotra

Email: donata.arena@phd.unict.it

Periodi all'estero- Sede e data: Swedish University of Agricultural Sciences 03/08/2022 - 31/10/2022, 15/05/2023 - 12/08/2023, 02/05/2024 – 31/07/2024

Esperienze post-Dottorato ed attuale occupazione: