Renée Abou Jaoudé

Traditional holobiont research has largely focused on bacterial taxonomy, often overlooking the functional diversity among strains within a taxon. Using a phenotype-first approach, we evaluated the responses of lettuce (Lactuca sativa L.) to culture-enriched rhizosphere microbial communities (transplanted inocula; RMs) derived from three stress-tolerant Mediterranean species: Juniperus phoenicea (JP), Rosmarinus officinalis (RO), and Pistacia lentiscus (PL). Responses were assessed by growth and physiological measurements together with untargeted LC–MS metabolomics on pooled leaf samples. The JP- and PL-derived RMs significantly increased average leaf mass, and all three produced healthy plant phenotypes, whereas only PL-RM significantly enhanced aboveground biomass, with higher leaf mass per area and maintained photosystem II quantum yield despite lower stomatal conductance. Metabolomic analysis revealed a consistent decrease in phenylpropanoids and resistance-associated alkaloids across all inoculated plants, consistent with a shift between primary and defense-related metabolism; PL-RM specifically promoted protective flavonoids, apocarotenoids, and tryptophan-derived alkaloids, whereas JP-RM and RO-RM reduced primary carbohydrates without increasing biomass, possibly reflecting altered carbon allocation. Overall, the three inocula, each from a single donor community, elicited distinct physiological and metabolic responses. By linking plant phenotypes to microbiome-induced metabolic shifts, this host-centered framework offers a scalable strategy for comparing microbiomes and selecting those suited to a given research objective.

Sweet basil (Ocimum basilicum L.) is a popular aromatic and medicinal crop cultivated globally. While its essential oils possess inherent antimicrobial properties, the plant remains highly susceptible to various pathogens. This study investigated the impact of a beneficial synthetic microbial community (SynCom)—composed of eight strains with proven antimicrobial and plant growth-promoting activities—on basil growth, ecophysiology, and metabolic profile in an aeroponic system. Although SynCom inoculation significantly enhanced photochemical efficiency, it did not yield significant gains in total biomass. Instead, inoculated plants exhibited a strategic reallocation of resources toward structural and chemical defenses. This physiological shift was physically manifested as denser plant canopies and lower specific leaf area (SLA). Untargeted metabolomic profiling identified 167 significantly altered metabolites. Notably, SynCom inoculation increased abscisic acid (ABA) turnover and redirected tryptophan metabolism from growth-promoting auxins to defense-related indoles and kynurenine derivatives. Furthermore, inoculation enriched the leaves with essential amino acids and a diverse array of protective secondary metabolites, including phenylpropanoids, flavonoids, and terpenoids. These findings demonstrate that specialized microbial inoculants can induce a transition toward fortified phenotypes and likely enhance plant resilience, even in the absence of traditional biomass gains.

Rosmarinus officinalis L. is known for its drought tolerance; however, its growth is adversely affected by both mild and severe water stress. This study investigates the potential of rhizomicrobiome (RM) transplantation to strengthen water stress resilience. Three RMs derived from native plants—R. officinalis (RO), Pistacia lentiscus L. (PL), and Juniperus phoenicea L. (JP)—collected from a semi-arid Mediterranean garrigue were inoculated into R. officinalis subjected to severe drought stress for 30 days. Although RM transplantation did not result in an increase in biomass, it led to the accumulation of intermediates within the phenylpropanoid/coumarin pathway and significant source-specific alterations in other leaf metabolites. Specifically, PL-RM increased the abundance of lignans and stress signaling metabolites. JP-RM improved the root-to-shoot ratio and the sugar and sugar-alcohol accumulation in leaves. Both JP-RM and RO-RM treatments reduced the abundance of abscisic acid, cyclic GMP, and purine recycling pathways. Additionally, RO-RM decreased the abundance of fifteen defense-related metabolites, indicating a direct interference of the inoculum with the plant immune system. In conclusion, these findings suggest that targeted RM manipulation can be an effective strategy to modulate R. officinalis leaf metabolism.

Plant Growth-Promoting Rhizobacteria (PGPR) are emerging as a sustainable alternative in agriculture due to their environmentally friendly properties and their ability to enhance crop productivity. Among these, Pantoea agglomerans has gained attention for its versatility as both a biofertilizer and a biocontrol agent. In this study, we use comparative genomics to gain insight into the genetic diversity and functional specialization of members of this species. The pan-genome analysis of 20 representative P. agglomerans strains revealed that 32% of the genes constitute the core genome (2856 out of 8899), while the remaining 68% are classified as accessory or singleton genes, indicating a high level of genomic diversity within the species. Functional annotation showed that core genes are predominantly involved in central metabolic processes, whereas genes associated with specialized metabolic functions are found within the accessory and singleton categories. The comparative analysis demonstrated a mosaic distribution of genes related to nitrogen and sulfur metabolism, heavy metal resistance, defense mechanisms, and oligopeptide uptake, suggesting niche-specific adaptations and metabolic capabilities within this species. Exometabolome profiling of strains associated with different hosts, specifically plant (C1) or human (DSM3493^T), demonstrated that omics-centered approaches can be utilized to select P. agglomerans strains tailored to specific agronomic requirements.

Water scarcity can negatively affect crop yield, posing a significant threat to global food security, such as drought. Plant growth-promoting rhizobacteria (PGPR), either as single strains or synthetic communities (SynComs), has shown promise in alleviating drought stress in various plant species. In this study, we examined the effects of water limitation on Salvia officinalis and the potential of a SynCom composed of five phosphate-solubilizing, auxin-producing, and/or nitrogen-fixing Gram-negative bacteria to enhance plant growth and drought tolerance. Plant growth, morphology, physiology, and leaf metabolomic profiles were assessed using a combination of physiological measurements and LC-MS untargeted metabolomics. Mild water stress induced a conservative water-use strategy in S. officinalis, characterized by increased root-to-shoot ratio and altered leaf morphology, without compromising photosynthetic performance. SynCom inoculation under well-watered conditions elicited drought-like responses, including transient reductions in stomatal conductance. Leaf metabolomic analysis revealed that inoculation influenced the abundance of several metabolites, including biogenic amines and dipeptides, under both irrigation regimes. Notably, drought stress and SynCom inoculation increased histamine and α-ketoglutaric acid levels, highlighting potential impacts on food quality. Under reduced irrigation, inoculation further modulated leaf morphology and biomass allocation, promoting thicker leaves and increased root biomass allocation. These results demonstrate the ability of the SynCom to modulate plant physiology and metabolism in response to both optimal and reduced irrigation, potentially enhancing drought resilience without directly improving growth. The study also highlights the complex interactions among microbial inoculation, plant stress responses, and leaf metabolite profiles, emphasizing the importance of considering the effects on the production of bioactive compounds when developing microbial inoculants for edible plants.

Introduction: Soil microbiome transplantation is a promising technique for enhancing plant holobiont response to abiotic and biotic stresses. However, the rapid assessment of microbiome-plant functional integration in short-term experiments remains a challenge.Methods: This study investigates the potential of three evergreen sclerophyll species, Pistacia lentiscus (PL), Rosmarinus officinalis (RO), and Juniperus phoenicea (JP), to serve as a reservoir for microbial communities able to confer enhanced tolerance to drought in Salvia officinalis cultivated under water shortage, by analyzing biomass production, plant phenotype, plant ecophysiological responses, and leaf metabolome.Results: Our results showed that the inoculation with the three rhizomicrobiomes did not enhance total plant biomass, while it significantly influenced plant architecture, ecophysiology, and metabolic responses. The inoculation with the JP rhizomicrobiome led to a significant increase in root biomass, resulting in smaller leaves and a higher leaf number. These morphological changes suggest improved water acquisition and thermoregulation strategies. Furthermore, distinct stomatal conductance patterns were observed in plants inoculated with microbiomes from PJ and PL, indicating altered responses to drought stress. The metabolome analysis demonstrated that rhizomicrobiome transplantation significantly influenced the leaf metabolome of S. officinalis. All three rhizomicrobiomes promoted the accumulation of phenolic compounds, terpenoids, and alkaloids, known to play crucial roles in plant defense and stress response. Five molecules (genkwanin, beta-ionone, sumatrol, beta-peltatin-A-methyl ester, and cinnamoyl-beta-D-glucoside) were commonly accumulated in leaves of inoculated sage, independently of the microbiome. Furthermore, unique metabolic alterations were observed depending on the specific inoculated rhizomicrobiome, highlighting the specialized nature of plant-microbe interactions and the possible use of these specific molecules as biomarkers to monitor the recruitment of beneficial microorganisms.Discussion: This study provides compelling evidence that microbiome transplantation can induce phenotypic and metabolic changes in recipient plants, potentially enhancing their resilience to water scarcity. Our findings emphasize the importance of considering multiple factors, including biomass, physiology, and metabolomics, when evaluating the effectiveness of microbiome engineering for improving plant stress tolerance.

Soilless cultivation allows for the exploitation of the benefits of plant growth-promoting rhizobacteria (PGPR) without the loss of efficacy observed with soil inoculation. In this study, we investigated the effects of a PGPR consortium on the plant growth, ecophysiology, and metabolic profile of lettuce (Lactuca sativa L.) grown in an aeroponic system under a low-nutrient regime. Overall, the plant biomass increased by 25% in the PGPR-inoculated plants due to enhanced leaf and root growth. The rise in the leaf biomass was primarily due to an increase in the leaf number and average leaf mass, coupled with a higher total leaf area. In addition, the inoculated plants exhibited an altered leaf anatomy characterized by an increased palisade parenchyma thickness and reduced airspace area, suggesting an improved photosynthetic efficiency and changes in the mesophyll conductance. The root morphology was also altered, with the PGPR-inoculated plants showing higher lateral root development. Furthermore, PGPR inoculation induced significant metabolic reprogramming in the leaves, affecting several pathways related to growth, development, and stress responses. These findings provide valuable insights into the intricate metabolic dialog between plants and beneficial microbes and demonstrate that the integration of soilless culture with an analysis of the ecophysiological, anatomical, and metabolomic plant responses can be a powerful approach to accelerate the design of new PGPR consortia for use as microbial biostimulants.

Plant microbiomes represent a reservoir of adaptive traits that can enhance plant resilience and productivity. In this study, we investigated the potential of a synthetic microbial consortium (SynCom), composed of five nitrogen-fixing Bacillaceae derived from the phyllosphere of Pistacia lentiscus L., to promote the growth of Lactuca sativa L. under nutrient-limiting availability. The short-term effects of the SynCom were evaluated in a hydroponic system, and four inoculation treatments were compared. The root and leaf inoculation (RL) significantly increased total plant biomass, driven by higher above-ground (+33%) and below-ground (+31%) biomass. The number of leaves per plant and leaf mass per area were also significantly enhanced in RL (+12% and +34%, respectively). While root-only inoculation (R) did not alter plant biomass, structure, or leaf traits, foliar spraying (L) significantly decreased the total leaf area and increased root biomass and the root-to-shoot ratio compared to non-inoculated plants, suggesting a direct influence of microbial metabolites on root growth and nutrient uptake. Compared to the individual R and L treatments, the synergistic effect observed in RL highlights the complex interplay between plant–microbe interactions in the rhizosphere and phyllosphere and the importance of ensuring adequate nutrient availability to nitrogen-fixing bacteria to achieve their growth-promoting potential fully. These findings suggest the potential for utilizing SynComs as bioinoculants to promote plant growth, emphasizing the need to optimize application strategies, considering both the SynCom composition and the host plant’s nutritional status to ensure efficacy.

“Pecorino” is a typical semi-hard cheese obtained with raw or heat-treated sheep milk using procedures to valorize the raw material’s chemical and microbiological properties. In the present study, using a high-throughput method of 16S rRNA gene sequencing, we assessed the evolution of the microbiome composition from milk to Pecorino-like cheese in artisanal processes using milk from Comisana and Lacaune sheep breeds. The comparative analysis of the bacterial community composition revealed significant differences in the presence and abundance of specific taxa in the milk microbiomes of the Comisana and Lacaune breeds. Next-Generation Sequencing (NGS) analysis also revealed differences in the curd microbiomes related to dairy farming practices, which have a relevant effect on the final structure of the Pecorino cheese microbiome.

“Pecorino” is a typical semi-hard cheese obtained with raw or heat-treated sheep milk using procedures to valorize the raw material's chemical and microbiological properties. In the present study, using a high throughput method of 16S rRNA gene sequencing, we assessed the evolution of the microbiome composition from milk to Pecorino cheese in artisanal processes using milk from Comisana and Lacaune sheep breeds. The comparative analysis of the bacterial com-munity composition revealed significant differences in the presence and abundance of specific taxa in the milk microbiome of the Comisana and Lacaune breeds. NGS analysis also revealed differences in the curd microbiome related to dairy farming practices, which have a relevant effect on the final structure of the Pecorino-cheese microbiome.