Biology subjects

Dini-Andreote, F.

Publications and source records attributed to Dini-Andreote, F..

8 recordsLinked to original sources

bioRxiv2026

Phyllosphere bacterial communities in milkweeds: composition diverge as the season progresses, and links to cardenolides and arthropods depend on host identity

Leaf bacterial communities shape plant defense and interactions with herbivores, yet how host filtering and stochastic processes assemble them remains unclear. We predicted that host identity, chemistry, and arthropods structure them, and that stochastic and deterministic contributions shift seasonally. Across one growing season we sampled leaf bacteria monthly and arthropods weekly on four Asclepias species (Apocynaceae: A. curassavica, A. incarnata, A. syriaca, A. tuberosa) spanning a cardenolide gradient. We sequenced 16S rRNA genes and quantified selection and dispersal contributions to turnover using null models. Host identity shaped bacterial richness and composition, with A. tuberosa hosting the richest communities, and both richness and phylogenetic diversity rose through the season. Early on, homogenizing dispersal made communities more similar among plants; by mid-season no single process dominated turnover, and by late season dispersal limitation prevailed. Homogeneous selection was episodic, not sustained, and arthropod associations were host-specific, negatively so on A. syriaca. Phyllosphere assembly thus shifts from convergence to divergence in one season: young leaves recruit from a shared pool delivered by wind, rain, and arthropods, whereas exchange among ageing plants declines and communities drift apart. Herbivores arriving late meet plant-specific microbial environments, so microbial mediation of herbivory should be host-specific and seasonally contingent.

ecology↗

bioRxiv2026

Bacterial endosymbionts enhance fungal virulence by disrupting the disease-suppressive rhizobiome

The mechanisms by which bacterial endosymbionts (bacteria living within fungal cells) enhance the fitness and virulence of fungal pathogens remain poorly understood. Here, we report that the tomato Fusarium wilt pathogen Fusarium oxysporum f. sp. lycopersici (FOL) hosts Achromobacter sp. endosymbionts that enhance fungal virulence. This virulence potentiation is partially dependent on interactions with the native rhizosphere microbiota. We show that bacterial endosymbiont-harboring FOL reshapes the rhizosphere bacterial community during pathogen infection and decreased the abundance of disease{square}suppressive bacteria, including Streptomyces sp. taxa. This inhibitory effect is mediated by bacterial endosymbiont{square}stimulated production of beauvericin (an antibacterial cyclic hexadepsipeptide) by FOL. Together, our findings reveal a tripartite interaction in which a fungal pathogen leverages its bacterial endosymbiont to weaken rhizosphere microbiome{square}based disease suppression by inhibiting plant-protective bacterial taxa. This work highlights how cross{square}kingdom symbioses can modulate pathogen ecology and virulence in soil environments.

microbiology↗

bioRxiv2025

Spatiotemporal changes in soil properties predict plant health at continental scale

Abiotic and biotic soil properties are strong predictors of plant yield globally1-5, but they become unreliable over large areas when plant health is threatened by pathogen6-8. Here we present a novel approach to predict plant health based on spatiotemporal changes in soil chemical and biological properties. We first demonstrate that plant health and soil properties consistently respond to environmental change (organic fertilization) regardless of the soil type or geographical origin. Second, we experimentally show that trackable shifts in soil properties reliably explain soil suppressiveness to the Ralstonia solanacearum bacterial pathogen and that a scalable spatiotemporal model predicts plant health with 84% accuracy across multiple climatic zones and cropping systems. Our results suggest that this tight coupling between soil properties and plant health could facilitate the development of agricultural practices aimed at sustainably improving crop yields while safeguarding crop health.

ecology↗

bioRxiv2024

Molecular activity mediates the composition and assembly of dissolved organic matter in lake sediments

Lake sediments are hotspots for carbon transformation and burial, where dissolved organic matter (DOM) interacts with microorganisms to regulate global carbon cycling. The potential for individual DOM molecules to undergo biochemical transformations, i.e., their activity, is a critical molecular trait affecting DOM turnover in environment. However, the composition of sediment DOM and how its assembly mechanisms are related to molecular activity remains poorly understood. Here, 63 freshwater sediments were collected from tropical to cold temperate climatic zones in China. We explored the molecular composition and assembly of sediment DOM and the underlying mechanisms driven by climate, physicochemical factors, and microbes along the molecular activity gradient. Sediment DOM was dominated by lipid- (34.8%) and lignin-like compounds (33.01%), and the latter were enriched as molecular activity of DOM increased. Besides, DOM composed of more active molecules had greater compositional similarity across different climatic zones, and was inclined to assemble deterministically. This was supported by the fact that as potential transformations of molecular assemblages increased from 0.4 to 14, the assembly of these molecules was structured by a shift from stochastic to deterministic processes, with the latter accounting for [≥] 75% thereafter. Overall, the molecular assemblage was primarily structured by physicochemical factors, including sediment total organic carbon and electrical conductivity. As molecular activity increased, however, assemblage was increasingly affected by climate and bacterial communities, consistent with the enhanced complexity of bacterial-molecular networks. Collectively, our study highlights that the intrinsic activity of DOM molecules determines their fate through distinct biotic and abiotic mechanisms.

biochemistry↗

bioRxiv2023

Reciprocal interactions between the sorghum root microbiome and the parasitic weed Striga hermonthica

The soil microbiome plays a crucial role in protecting plants against various pests and pathogens. However, its impact on interactions between plants and parasitic weeds, such as Striga hermonthica, is poorly understood. In this study, sorghum plants susceptible to Striga were grown in 22 different field soils infested with parasite seeds. Significant variations in Striga infections were observed among the soils. When the most Striga-suppressive soil was gamma-irradiated, there was a significant increase in Striga attachments, highlighting the importance of the soil microbiome in disrupting parasite infection. In the presence of the soil microbiome, the Striga-susceptible sorghum plants performed similarly to three Striga-resistant genotypes. This effect was lost when the soil microbiome was eliminated by gamma-irradiation. Subsequent analysis revealed that Striga substantially affected the sorghum rhizosphere microbiome and that both the sorghum rhizosphere mycobiome and bacteriome composition significantly correlated with Striga attachment. Interestingly, certain fungal species in the sorghum rhizosphere mycobiome were only detected when Striga seeds were present. Further investigation showed that these fungal taxa originated from the Striga seeds and are known sorghum pathogens, suggesting a potential partnership between Striga and fungal pathogens to invade their shared host. Overall, our study demonstrated that the soil microbiome influences Striga infection and sorghum performance in a genotype-dependent manner, and the microbiome of Striga seeds affects the composition of the sorghum rhizosphere microbiome.

ecology↗

bioRxiv2022

The soil microbiome reduces Striga infection of sorghum by modulation of host-derived signaling molecules and root development

Sorghum bicolor is one of the most important cereals in the world and a staple crop for smallholder famers in sub-Saharan Africa. However approximately 20% of sorghum yield is annually lost on the African continent due to infestation with the root parasitic weed Striga hermonthica. Existing Striga management strategies often show an inconsistent to low efficacy. Hence, novel and integrated approaches are needed as an alternative strategy. Here, we demonstrate that the soil microbiome suppresses Striga infection in sorghum. We associate this suppression with microbiome-mediated induction of root endodermal suberization and aerenchyma formation, and depletion of haustorium inducing factors (HIFs), root exudate compounds that are critical for the initial stages of Striga infection. We further identify microbial taxa associated with reduced Striga infection with concomitant changes in root cellular anatomy and differentiation as well as HIF degradation. Our study describes novel microbiome-mediated mechanisms of Striga suppression, encompassing repression of haustorium formation and induction of physical barriers in the host root tissue. These findings open new avenues to broaden the effectiveness of Striga management practices.

plant biology↗

bioRxiv2021

Microbial phylogenetic relatedness links to distinct successional patterns of bacterial and fungal communities

Development of soil microbial communities along ecological succession is crucial for ecosystem recovery and maintenance. However, mechanisms mediating microbial community dynamics and co-occurrence patterns along ecological succession remain unclear. Here, we explored community dynamics and taxa co-occurrence patterns in bacterial and fungal communities across a well-established chronosequence of post-mining lands spanning 54 years of recovery. Meanwhile, by synthesizing previous studies and ecological theories, we devised two conceptual models that integrate microbial phylogeny with patterns in community dynamics and in taxa co-occurrence. We further tested these models by using empirical data. At early successional stages, bacterial community structures became increasingly phylogenetically clustered with soil age, which was co-determined by the environmental selection from soil vegetation cover and by heterogeneous responses of less phylogenetically similar bacteria to the increasing resource availability along succession. At later successional stages, bacterial community phylogenetic structures displayed progressively lower variability. The fungal community phylogenetic structures varied relatively less and were independent of soil age, soil properties and vegetation cover, which was attributed to the dominance of stochastic processes in community turnover along succession. Network analysis revealed a decrease in bacterial co-occurrence complexity along succession, which aligned with a decrease in average pairwise phylogenetic distances between co-occurring bacteria. These patterns together implied a decrease in potential bacterial cooperation that was probably mediated by increasing resource availability along succession. The increased complexity of fungal co-occurrence along succession was independent of phylogenetic distances between co-occurring fungi. This study provides new sights into ecological mechanisms underlying bacterial and fungal community succession.

microbiology↗

bioRxiv2020

Belowground changes to community structure alter methane-cycling dynamics in Amazonia

Amazonian rainforest is undergoing increasing rates of deforestation, driven primarily by cattle pasture expansion. Forest-to-pasture conversion has been associated with changes to ecosystem processes, including substantial increases in soil methane (CH4) emission. The drivers of this change in CH4 flux are not well understood. To address this knowledge gap, we measured soil CH4 flux, environmental conditions, and belowground microbial community attributes across a land use change gradient (old growth primary forest, cattle pasture, and secondary forest regrowth) in two Amazon Basin regions. Primary forest soils exhibited CH4 uptake at modest rates, while pasture soils exhibited CH4 emission at high but variable rates. Secondary forest soils exhibited low rates of CH4 uptake, suggesting that forest regrowth following pasture abandonment could reverse the CH4 sink-to-source trend. While few environmental variables were significantly associated with CH4 flux, we identified numerous microbial community attributes in the surface soil that explained substantial variation in CH4 flux with land use change. Among the strongest predictors were the relative abundance and diversity of methanogens, which both increased in pasture relative to forests. We further identified individual taxa that were associated with CH4 fluxes and which collectively explained ~50% of flux variance. These taxa included methanogens and methanotrophs, as well as taxa that may indirectly influence CH4 flux through acetate production, iron reduction, and nitrogen transformations. Each land type had a unique subset of taxa associated with CH4 fluxes, suggesting that land use change alters CH4 cycling through shifts in microbial community composition. Taken together, our results suggest that changes in CH4 flux from agricultural conversion could be driven by microbial responses to land use change in the surface soil, with both direct and indirect effects on CH4 cycling. This demonstrates the central role of microorganisms in mediating ecosystem responses to land use change in the Amazon Basin.

ecology↗