Biology subjects

Schena, L.

Publications and source records attributed to Schena, L..

6 recordsLinked to original sources

bioRxiv2026

Foliar pathogen and drought impose reproducible but community-dependent influence on the root microbiome

Plant microbiomes are assembled from environmental pools that differ substantially in composition, yet whether their responses to stress follow general rules or depend on the resident community remains unclear. We tested the generality of root microbiome responses to stress by growing three tomato (Solanum lycopersicum) genotypes in 20 independently sourced microbial communities under controlled abiotic and biotic stress. Microbial communities were transferred into a common sterile substrate, allowing to vary microbial community identity independently of soil physicochemical properties, and plants were exposed to drought, the foliar pathogen Pseudomonas syringae pv. tomato, or no stress. We analyzed the root microbiota using 16S rRNA amplicon sequencing. Stressor identity explained more variation in bacterial community composition than inoculum identity or plant genotype. Hierarchical models showed that many bacterial taxa responded consistently across distinct starting communities, with taxon identity contributing far more variation in stress response than microbial community of origin. Both stressors shifted between-community dissimilarity from taxon turnover toward nestedness, indicating increasingly similar patterns of taxon loss, but the pathogen produced stronger effects and increased variability among replicate plants. Drought reduced phylogenetic redundancy, whereas pathogen increased dispersal limitation. Together, these results show that stress imposes reproducible ecological filters across diverse starting microbiomes, while the magnitude and resulting community state remain contingent on the resident microbial community. This provides a basis for identifying transferable microbial targets for microbiome-based crop stress management, while also managing the local microbiome to maximize their beneficial effects.

microbiology↗

bioRxiv2025

Beneficial fungi are major drivers of root fungal microbiome assembly and network robustness

Despite the critical role of soil microbiomes in ecosystem stability, how soil disturbance impacts these communities and their interactions with plants remains poorly understood. In this study, we investigate how different levels of soil disturbance influence the assembly and robustness of the root fungal microbiome. Using a microcosm experiment, we inoculated plants with soil from environments with decreasing levels of disturbance -- agricultural field, field margin, and uncultivated field -- and tested the variation in composition, assembly process, and network stability of the root fungal microbiome. Our results reveal that more disturbed systems, i.e. agricultural soils, harbor microbiomes with less robust networks compared to systems with lower disturbance. Network analysis identified arbuscular mycorrhizal fungi as key taxa contributing to microbiome stability, suggesting their critical role in maintaining the robustness of root-associated fungal microbiomes. Furthermore, stochastic processes dominated fungal community assembly across all soil treatments, yet the key taxa that deviated from null-model predictions include those with a major role in network robustness, and were mainly identified as arbuscular mycorrhizal fungi. Together, our results suggest that arbuscular mycorrhizal fungi are major actors in assembling robust plant microbiomes, and soil disturbance is a key factor in disrupting these interactions.

ecology↗

bioRxiv2024

Lettuce seedlings rapidly assemble their microbiome from the environment through deterministic processes

Plant-associated microorganisms have significant impacts on plant biology, ecology, and evolution. Although several studies have examined the factors driving variations in plant microbiomes, the mechanisms underlying the assembly of the plant microbiome are still poorly understood. In this study, we used gnotobiotic plants to test (i) whether seedlings create a selective environment and drive the assembly of root and leaf microbiomes through deterministic or stochastic processes, and (ii) whether seedlings structure the microbiome that is transferred through seeds using deterministic processes and whether this pattern changes when seedlings are exposed to the environmental microbiome. Our results show that the microbiome of gnotobiotic plants (i.e., inherited through seeds) is not under the selective influence of the host plant but changes quickly when plants are exposed to soil microbiomes. Within one week, plants were able to select microorganisms from the inocula, assemble the root microbiome, and assemble the shoot microbiome. This study supports the hypothesis that plants at early developmental stages might exert strong selective activity on their microbiomes and contribute to clarifying the mechanisms of plant microbiome assembly.

plant biology↗

bioRxiv2022

Plant genotype influence the structure of cereal seed fungal microbiome

Plant genotype is a crucial factor for the assembly of the plant-associated microbial communities. However, we still know little about the variation of diversity and structure of plant microbiomes across host species and genotypes. Here, we used six species of cereals (Avena sativa, Hordeum vulgare, Secale cereale, Triticum aestivum, Triticum polonicum, and Triticum turgidum) to test whether the plant fungal microbiome varies across species, whether plant species use different mechanisms for microbiome assembly focusing on the plant ears. Using ITS2 amplicon sequencing, we found that host species influences the diversity and structure of the seed-associated fungal communities. Then, we tested whether plant genotype influences the structure of seed fungal communities across different cultivars of T. aestivum (Aristato, Bologna, Rosia, and Vernia) and T. turgidum (Capeiti, Cappelli, Mazzancoio, Trinakria, and Timilia). We found that cultivar influences the seed fungal microbiome in both species. We found that in T. aestivum the seed fungal microbiota is more influenced by stochastic processes, while in T. turgidum selection plays a major role. Collectively, our results contribute in filling the knowledge gap on the wheat seed microbiome assembly and might help in understanding how we can manipulate this process to improve agriculture sustainability.

microbiology↗

bioRxiv2020

Soil microbial diversity impacts plant microbiomes more than herbivory

Interactions between plants and microbiomes play a key role in ecosystem functioning and are of broad interest due to their influence on nutrient cycling and plant protection. However, we do not yet have a complete understanding of how plant microbiomes are assembled. Here, we tested and quantified the effect of different factors driving the diversity and composition of plant-associated microbial communities. We manipulated soil microbial diversity (high or low diversity), plant species (Solanum tuberosum or Solanum vernei), and herbivory (presence or absence of a phloem-feeding insect Macrosiphum euphorbiae), and found that soil microbial diversity influenced the herbivore-associated microbiome composition, but also plant species and herbivory influenced the soil microbiome composition. We quantified the relative strength of these effects and demonstrated that the initial soil microbiome diversity explained the most variation in plant- and herbivore-associated microbial communities. Our findings strongly suggest that soil microbial community diversity is a driver of the composition of multiple associated microbiomes (plant and insect), and this has implications for the importance of management of soil microbiomes in multiple systems.

ecology↗

bioRxiv2018

Impact of Bactrocera oleae on the fungal microbiota of ripe olive drupes.

The olive fruit fly (OFF), Bactrocera oleae is the most devastating pest affecting olive fruit worldwide. Previous investigations have addressed the fungal microbiome associated with olive drupes or B. oleae, but the impact of the insect on fungal communities of olive fruit remains undescribed. In the present work, the fungal microbiome of olive drupes, infested and non-infested by the OFF, was investigated in four different localities and cultivars. Olive fruit fly infestations caused a general reduction of the fungal diversity, a higher quantity of the total DNA and an increase in taxa that remained unidentified or had unknown roles. The infestations led to imbalanced fungal communities with the growth of taxa that are usually outcompeted. While it was difficult to establish a cause-effect link between fly infestation and specific fungi, it is clear that the fly alters the natural microbial balance, especially the low abundant taxa. On the other hand, the most abundant ones, were not significantly influenced by the insect. In fact, despite the slight variation between the sampling locations, Aureobasidium, Cladosporium, and Alternaria, were the dominant genera, suggesting the existence of a typical olive fungal microbiome.

microbiology↗