The cultivation of soilless tomato in greenhouses has increased considerably, but little is known about the assembly of the root microbiome compared to plants grown in soil. To obtain such information, we constructed an assay in which we traced the bacterial and fungal communities by amplicon-based metagenomics during the cultivation chain from nursery to greenhouse. In the greenhouse, the plants were transplanted either into agricultural soil or into coconut fiber bags (soilless). At the phylum level, bacterial and fungal communities were primarily constituted in all microhabitats by Proteobacteria and Ascomycota, respectively. The results showed that the tomato rhizosphere microbiome was shaped by the substrate or soil in which the plants were grown. The microbiome was different particularly in terms of the bacterial communities. In agriculture, enrichment has been observed in putative biological control bacteria of the genera Pseudomonas and Bacillus and in potential phytopathogenic fungi. Overall, the study describes the different shaping of microbial communities in the two cultivation methods.

Mal secco is a severe vascular citrus disease (MSD) caused by the mitosporic fungus Plenodomus tracheiphilus (Pt). The pathogen enters through wounds on the above- and below-ground parts of the tree. The susceptible species sour orange (Citrus aurantium) is the most commonly used rootstock for lemon trees in Italy. In this study, sour orange seedlings were wound-inoculated with P. tracheiphilus in leaves or roots. Six months post-inoculation, the microbial communities of rhizosphere, endorhizosphere, and xylem endosphere samples from inoculated and healthy plants were analyzed by 16S rRNA and ITS (internal transcribed spacer) amplicon sequencing. The DNA of Pt was quantified by real-time PCR in the three compartments. According to our results, the endorhizosphere of root-inoculated plants showed the highest concentration of the pathogen DNA. Bacterial populations of potentially beneficial taxa (e.g., Pseudomonas and Burkholderia) were depleted in the rhizosphere of the inoculated plants. Infection through leaves and roots also produced a network-wide rewiring of microbial associations in sour orange roots. Overall, our findings revealed community-level changes induced by Pt infection in the sour orange root and xylem microbiome, providing further insights into the beneficial multispecies interactions in Citrus-associated microbial communities.

Climate change has reshaped global weather patterns and intensified extreme events, with drought and soil salinity negatively impacting the yield and quality of crop production. To mitigate the detrimental effects of drought stress, the introduction of beneficial plant growth-promoting rhizobacteria (PGPR) has proven to be a promising approach. In this study, we evaluated a synthetic microbial community (SynCom) comprising bacterial strains belonging to the species Bacillus velezensis, Pseudomonas simiae, P. salmasensis, Glutamicibacter halophytocola, and Leclercia sp., which have been demonstrated to promote tomato growth both individually and collectively. The SynCom and most of its individual bacterial strains were shown to mitigate the detrimental effects of polyethylene glycol (PEG)-induced drought stress in vitro in Arabidopsis thaliana seedlings, either by reducing alterations in xylem elements or promoting the formation of new xylem strands. In a greenhouse trial, soil drenching with the SynCom and two individual strains, B. velezensis PSE31B and P. salmasensis POE54, improved the water stress response in soilless-grown tomato plants under a 40% reduced irrigation regime. Additionally, bacterial treatments positively influenced the diversity of rhizosphere bacterial communities, with distinct changes in bacterial composition, which suggest a treatment-specific interplay between the introduced strains and the native microbiome. These findings highlight the potential of microbial consortia and individual PGPR strains as sustainable tools to improve plant resilience to abiotic stresses.

Mal secco is a vascular disease of citrus caused by the mitosporic fungus Plenodomus tracheiphilus. Soil containing infected plant material constitutes an inoculum source for root infections. In this study, the soil bacterial and fungal communities of five lemon orchards located in Syracuse Province (Sicily, Italy) affected by mal secco were analyzed. Soil samples were collected under lemon tree canopies and subjected to total genomic DNA extraction. The fungal DNA was detected through qPCR in all orchards, with variable concentrations. Bacterial and fungal communities were profiled using 16S and ITS amplicon-based high-throughput sequencing, respectively. According to our results, the relative abundances of the most represented bacterial phyla (e.g., Proteobacteria, Actinobacteriota, Acidobacteriota) changed across the orchards, while in the fungal community, the phylum Ascomycota was dominant, with Basidiomycota and Mortierellomycota abundances fluctuating. On the whole, β diversity analysis showed significant variation in the composition of the soil microbial communities across the orchards. This result was confirmed by the analysis of the core community (taxa present at ≥ 75% of total samples), where putative beneficial bacteria resulted in significantly enriched fungus-infected soil samples, suggesting complex microbial interactions. Our findings shed light on the composition and diversity of the soil microbiome in lemon orchards with the occurrence of mal secco infections.

In sustainable agriculture, the application of microorganisms to soil is a widely adopted strategy aimed at enhancing soil microbiome functionality, restoring fertility, and recovering biodiversity diminished by intensive farming. While introducing individual beneficial microbes often encounters issues with establishment and persistence, multispecies microbial consortia offer a more robust alternative, providing complementary functions that enhance both their resilience and effectiveness. To test this approach, we designed three synthetic bacterial communities (SynComs), each composed of varying combinations of ten bacterial endophytes previously shown to promote plant growth and exert biocontrol effects. The SynComs were designed with ascending levels of richness (4, 6, and 10 members) and diversity (ranging from 3 to 6 bacterial genera). In growth chamber trials with tomatoes, the SynComs not only promoted plant growth but also induced significant shifts in the rhizosphere bacterial communities, primarily affecting less abundant taxa. The SynComs MIX2 and MIX3, which included Pseudomonas species, exhibited the greatest impact on both plant growth enhancement and shifts within the resident microbial community. Monitoring of the introduced strains over time demonstrated that most bioinoculants successfully established although at very low concentration in the rhizosphere.

Microbial communities associated with the rhizosphere and phyllosphere are recognized as fundamental components influencing essential plant processes, including nutrient acquisition, growth promotion, and tolerance to stress. Biological control agents (BCAs), such as Trichoderma spp. and Bacillus spp., are widely applied in citrus crops. However, while BCAs effectiveness against plant pathogens is widely established, their resulting impact on indigenous, non-target bacterial and fungal communities remains poorly understood. The aim of this study was to evaluate the non-target effects of two commercial microbial formulations—one containing Trichoderma asperellum ICC 012 and T. gamsii ICC 080, and the other Bacillus amyloliquefaciens QST 713—on the resident microbiomes of Citrus volkameriana seedlings by using the amplicon-based metagenomic analysis, targeting the 16S rRNA and ITS1 regions. The application of the Trichoderma formulation as a soil drench in the rhizosphere resulted in minimal changes to the overall composition and diversity (α- and β-diversity) of the bacterial communities. This stability is considered a desirable trait for overall soil health. However, specific taxonomic changes were observed, such as a notable decrease in the genus Rhodococcus (0.4% vs. 1.5% in controls) among bacteria. In the fungal communities, the treatment led to a significant shift in phylum relative abundance, characterized by an increase in Basidiomycota (38% vs. 28% in controls) and a corresponding decrease in Ascomycota (51% vs. 56% in controls). Successful colonization was confirmed by a substantially higher relative abundance of the inoculated Trichoderma genus compared to control plants (1.4% vs. 0.1% in controls). Conversely, the foliar application of the Bacillus product induced a substantial restructuring of the phyllosphere bacterial community. This treatment caused a statistically significant reduction in bacterial α-diversity and a clear differentiation in community composition (β-diversity) relative to untreated controls. The successful colonization by the BCA resulted in the dominance of the Bacillus genus in the treated samples (27% vs. 2% in controls). Importantly, this ecological shift was accompanied by the enrichment of other beneficial bacterial taxa, including Sphingomonas (15% vs. 4% in controls) and the Burkholderia-Caballeronia-Paraburkholderia group (4% vs. 2% in controls). While fungal phyla abundances remained generally stable in the phyllosphere, specific genera such as Cladosporium (15% vs. 23% in controls) and Symmetrospora (21% vs. 13% in controls) prevailed post-treatment. In conclusion, these findings highlight the importance of considering non-target microbiome shift when implementing microbial biocontrol strategies in citrus production systems, since in this study was demonstrated that commercial BCAs exert a markedly differential influence based on the compartment of application: Trichoderma promoted ecological stability in the rhizosphere, whereas Bacillus induced a directional community shift in the phyllosphere.