Biology subjects

Malacrino, A.

Publications and source records attributed to Malacrino, A..

12 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

Fire limits soil microbial dispersal and differentially impacts bacterial and fungal communities

Fire is a globally pervasive force reshaping ecosystems, yet its influence on the ecological processes structuring soil microbiomes remains poorly understood. Using a meta-analysis of >2,600 amplicon sequencing samples across 19 global studies, we tested whether fire alters soil microbiome assembly processes, diversity, and ecological selection for pyrophilic specialists. Contrary to prevailing assumptions, we found that fire did not significantly shift ecological selection processes in bacteria or fungi but instead constrained dispersal, particularly reducing dispersal in bacterial and fungal communities, and increasing ecological drift in fungi. Despite limited evidence for ecological selection, fire consistently filtered for specialist taxa, increasing their relative abundance across microbial communities. Fire also reduced fungal diversity and evenness, while bacterial communities exhibited greater dominance and loss of rare taxa. These findings support the idea that fire promotes microbial post-fire niche specialization while disrupting dispersal pathways. Our results indicate that increasing fire frequency and severity under climate change may homogenize soil microbial communities, reduce microbial resilience, and constrain ecosystem recovery.

ecology↗

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

Terrestrial herbivory drives adaptive evolution in an aquatic community via indirect effects

Indirect ecological effects, which occur when the impact of one species on another is mediated by a third species or the shared environment, are ubiquitous in nature. Given the complexity of natural systems, indirect ecological effects were thought to be important in driving eco-evolutionary processes across community boundaries. However, we know remarkably little about such effects. Here we show that indirect effects of terrestrial insect (aphids) herbivory on macrophytes (duckweed) drives adaptive evolution of water fleas (Daphnia) in large outdoor aquatic mesocosms. Aphid herbivory reduced macrophyte growth and increased the abundance of phytoplankton, which in turn increased the abundance of Daphnia. Whole genome pool sequencing and phenotypic assays revealed an impact on the genetic compositions of the Daphnia populations and transplant experiments indicated that these evolutionary changes were adaptive. Furthermore, these changes in the aquatic community altered the interactions of the aphids and the macrophytes. These results demonstrate that indirect ecological effects can shape eco-evolutionary interactions between different communities.

evolutionary biology↗

bioRxiv2024

Herbivory can increase plant fitness via reduced interspecific competition. Evidence from models and mesocosms

Herbivores are generally considered to reduce plant fitness. However, as in natural communities herbivores often feed on several competing plant species, herbivores can also increase plant fitness by reducing interspecific competition among plants. In this study, we developed a testable model to predict plant fitness in the presence of an interspecific competitor and an herbivore that feeds on both plant species. Our model allows to predict at which herbivore and competitor densities the focal species will benefit from herbivory. This can be estimated by quantifying the effects of the herbivore on the fitness of the focal plant and on its competitor, and by estimating the levels of intra- and interspecific competition in a pair-wise fashion, respectively. We subsequently validated the model in indoor microcosms using three interacting species: an aquatic macrophyte (the giant duckweed Spirodela polyrhiza), its native competitors (green algae), and its native herbivore (the pond snail Lymnaea stagnalis). Additional outdoor mesocosm experiments supported our model under natural conditions. Together, this study provides a conceptual framework to understand how herbivores shape plant fitness in a community context.

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

Induced responses contribute to rapid plant adaptation to herbivory

Herbivory-induced responses in plants are typical examples of phenotypic plasticity, and their evolution is thought to be driven by herbivory. However, direct evidence of the role of induced responses in plant adaptive evolution to herbivores is scarce. Here, we experimentally evolved populations of an aquatic plant (Spirodela polyrhiza, giant duckweed) and its native herbivore (Lymnaea stagnalis, freshwater snail) testing whether herbivory drives rapid adaptive evolution in plant populations using a combination of bioassays, pool-sequencing, metabolite analyses, and amplicon metagenomics. We found that snail herbivory drove rapid phenotypic changes, increased herbivory resistance, and altered genotype frequencies in the plant populations. Additional bioassays suggested that evolutionary changes of induced responses contributed to the rapid increase of plant resistance to herbivory. This study provides direct evidence that herbivory-induced responses in plants can be subjected to selection and have an adaptive role by increasing resistance to herbivores.

evolutionary biology↗

bioRxiv2022

Natural rubber reduces herbivory and alters the microbiome below ground

O_LILaticifers are hypothesized to mediate both plant-herbivore and plant-microbe interactions. However, there is little evidence for the dual function of these secretory structures. C_LIO_LIWe investigated whether the major constituent of natural rubber, cis-1,4-polyisoprene, a phylogenetically widespread and economically important latex polymer, alters plant resistance and the root microbiome of the Russian dandelion (Taraxacum koksaghyz) under attack of a root herbivore, the larva of the May cockchafer (Melolontha melolontha). C_LIO_LIRubber-depleted transgenic plants lost more shoot and root biomass upon herbivory than normal rubber content near-isogenic lines. M. melolontha preferred to feed on artificial diet supplemented with rubber-depleted rather than normal rubber content latex. Likewise, adding purified cis-1,4-polyisoprene in ecologically relevant concentrations to diet deterred larval feeding and reduced larval weight gain. Metagenomics and metabarcoding revealed that abolishing biosynthesis of natural rubber alters the structure but not the diversity of the rhizosphere and root microbiota in a herbivore-dependent manner. Roots from rubber-depleted plants, however, did not exhibit a higher pathogen load compared to normal rubber content roots. C_LIO_LITaken together, our data demonstrate that natural rubber biosynthesis reduces herbivory and alters the plant microbiota in a herbivore-dependent manner, which highlights the role of plant specialized metabolites and secretory structures in shaping multitrophic interactions. C_LI

plant biology↗

bioRxiv2022

Soil microbiota and herbivory influence the structure of plant-associated microbial communities in tomato plants

Plant-associated microbial communities are key to shaping many aspects of plant biology. In this study, we tested whether soil microbial communities and herbivory influence the bacterial community of tomato plants and whether their influence in different plant compartments is driven by microbial spillover between compartments or whether plants are involved in mediating this effect. We grew our plants in soils hosting three different microbial communities and covered (or not) the soil surface to prevent (or allow) passive microbial spillover between compartments, and we exposed them (or not) to herbivory by Manduca sexta. The results showed that the soil-driven effect on aboveground compartments was consistently detected regardless of soil coverage, whereas soil cover influenced the herbivore-driven effect on belowground microbiota. Together, our results suggest that the soil microbiota influences aboveground plant and insect microbial communities via changes in plant metabolism and physiology or by sharing microorganisms via xylem sap. In contrast, herbivores influence the belowground plant microbiota via a combination of microbial spillover and changes in plant metabolism. These results demonstrate the important role of plants in linking aboveground and belowground microbiota, and can foster further research on soil microbiota manipulation for sustainable pest management.

ecology↗

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↗

bioRxiv2020

Biological invasions alter environmental microbiomes: a meta-analysis

Biological invasions impact both agricultural and natural systems. The damage can be quantified in terms of both economic loss and reduction of biodiversity. Although the literature is quite rich about the impact of invasive species on plant and animal communities, their impact on environmental microbiomes is underexplored. Here, we re-analyze publicly available data using a common framework to create a global synthesis of the effects of biological invasions on environmental microbial communities. Our findings suggest that non-native species are responsible for the loss of microbial diversity and shifts in the structure of microbial populations. Therefore, the impact of biological invasions on native ecosystems might be more pervasive than previously thought, influencing both macro- and micro-biomes. We also identified gaps in the literature which encourage research on a wider variety of environments and invaders, and the influence of invaders across seasons and geographical ranges.

ecology↗