Rhizosphere Microbiota Research Articles

Two rice cultivars recruit different rhizospheric bacteria to promote aboveground regrowth after mechanical defoliation.

Plants have evolved the ability to regrow after mechanical defoliation and environmental stresses. However, it is unclear whether and how defoliated plants exploit beneficial microbiota from the soil to promote aboveground regrowth. Here, we compared the defoliation-triggered changes in the root exudation and bacterial microbiome of two rice cultivars (Oryza sativa L ssp.), indica/xian cultivar Minghui63 and japonica/geng cultivar Nipponbare. The results show that reciprocal growth promotion existed between defoliated Minghui63 seedlings and soil bacteria. After the leaves were removed, the Minghui63 seedlings displayed approximately 1.5- and 2.1-fold higher root exudation and leaf regrowth rates, respectively, than did the Nipponbare seedlings. In field trials, Minghui63 and Nipponbare enriched taxonomically and functionally distinct bacteria in the rhizosphere and root. In particular, Minghui63 rhizosphere and root communities depleted bacteria whose functions are related to xenobiotics biodegradation and metabolism. The microbiome data implied that the bacterial family Rhodocyclaceae was specifically enriched during the regrowth of defoliated Minghui63 rice. We further isolated a Rhodocyclaceae strain, Uliginosibacterium gangwonense MDD1, from rice root. Compared with germ-free conditions, MDD1 inoculation promoted the aboveground regrowth of defoliated Minghui63 by 61% but had a weaker effect on Nipponbare plants, suggesting cultivar-specific associations between regrowth-promoting bacteria and rice. This study provides novel insight into microbiota‒root‒shoot communication, which is implicated in the belowground microbiome and aboveground regrowth in defoliated rice. These data will be helpful for microbiome engineering to increase rice resilience to defoliation and environmental stresses.IMPORTANCEAs sessile organisms, plants face a multitude of abiotic and biotic stresses which often result in defoliation. To survive, plants have evolved the ability to regrow leaves after stresses and wounding. Previous studies revealed that the rhizosphere microbiome affected plant growth and stress resilience; however, how belowground microbiota modulates the aboveground shoot regrowth is unclear. To address this question, we used rice, an important crop worldwide, to analyze the role of rhizosphere microbiota in leaf regrowth after defoliation. Our data indicate mutual growth promotion between defoliated rice and rhizosphere bacteria and such beneficial effect is cultivar specific. The microbiome analysis also led us to find a Uliginosibacterium gangwonense strain that promoted rice cv. MH63 leaf regrowth. Our findings therefore present a novel insight into plant-microbiome function and provide beneficial strains that potentially enhance rice stress resilience.

Microbial community of cultivated and uncultivated citrus rhizosphere microbiota in Brazil

The rhizosphere microbiome is known to contain beneficial microorganisms that promote plant growth and increase tolerance to abiotic and biotic stresses. Understanding citrus microbiome diversity and the percentage of diversity that can be recovered in the laboratory is essential for developing innovative approaches to improve plant health and promote sustainable agricultural practices. However, information about the citrus root microbiome, especially in the context of exploring commercial citrus growing areas to identify beneficial plant growth-promoting rhizobacteria (PGPR), is scarce. Here, we present the microbiome data of healthy citrus trees sampled from geographical regions of São Paulo and Amazonas States, in Brazil. The resulting rhizosphere microbiome data comprise an average of 126,180 and 138,707 high-quality reads for the 16S rRNA V3–V4 and ITS1-5F regions, respectively. The taxonomic analysis of cultivated diversity revealed a total of 91 bacterial genera recovered in the laboratory. These data provide valuable information for understanding how the microbiome supports citrus plants in different environments and for developing new strategies to improve crop productivity by using PGPR.

Interpretation of bacterial composition patterns and community assembly processes in the rhizosphere soil of tea trees in karst areas

Research background and purposeSoil microorganisms that are closely related to plants are important factors affecting plant health. Therefore, elucidating the abundant and rare bacterial species in soil associated with plant diseases is crucial for understanding ecological processes, maintaining the stability of microecological environments, and formulating microbial strategies that are consistent with modern agricultural development.ResultsTea leaf blight leads to an increase in bacterial diversity in the rhizosphere. Random processes dominate the assembly of abundant and rare taxa, while abundant taxa are also influenced by deterministic processes. In the co-occurrence network, the increase in bacterial community diversity mediated by tea cloud leaf blight enhances the stability of the network. Meanwhile, the proportion of positive correlation between rare taxa is relatively high, and the relationship between rare taxa and intermediate taxa is closer. This highly diverse bacteria community maintained the structure and stability of the community to a certain extent.ConclusionThe rare taxa in the rhizosphere and the rhizosphere bacterial community mediated by tea leaf blight have high diversity, which is of great significance for maintaining the stability of the rhizosphere bacterial ecological network. In the future, we will further explore the dynamic changes and interaction patterns of the species in the rhizosphere soil affected by tea tree diseases, and their ecological functions and importance in areas of habitat fragmentation. Overall, there are many microbial resources in the rhizosphere microbiota under the influence of plant diseases that can be used for agricultural practice. The results of this study will enrich the insights into ecodynamics of bacteria in karst areas, especially in karst tea gardens.

Response of Yields, Soil Physiochemical Characteristics, and the Rhizosphere Microbiome to the Occurrence of Root Rot Caused by Fusarium solani in Ligusticum chuanxiong Hort.

Ligusticum chuanxiong Hort. is considered an important medicinal herb with extremely high economic value and medicinal value due to its various effects, including anti-oxidation, sedative action, hepatoprotection, and invigorating blood circulation. However, L. chuanxiong cultivation is hampered by various plant diseases, especially the root rot caused by Fusarium solani, hindering the sustainable development of the L. chuanxiong industry. The occurrence of soil-borne diseases is closely linked to imbalances in the microbial community structure. Here, we studied the yields, rhizosphere microbiota, and soil physiochemical characteristics of healthy and diseased L. chuanxiong plants affected by root rot with high-throughput sequencing and microbial network analysis, aiming to explore the relationships between soil environmental factors, microbiomes, and plant health of L. chuanxiong. According to the results, L. chuanxiong root rot significantly decreased the yields, altered microbial community diversity and composition, enriched more pathogenic fungi, recruited some beneficial bacteria, and reduced microbial interaction network stability. The Mantel test showed that soil organic matter and pH were the major environmental factors modulating plant microbiome assembly. The root rot severity was significantly affected by soil physiochemical properties, including organic matter, cation exchange capacity, available nitrogen, phosphorus, potassium, and pH. Furthermore, two differential microbes that have great potential in the biocontrol of L. chuanxiong root rot were dug out in the obtained results, which were the genera Trichoderma and Bacillus. This study provided a theoretical basis for further studies revealing the microecological mechanism of L. chuanxiong root rot and the ecological prevention and control of L. chuanxiong root rot from a microbial ecology perspective.

Regulation of the Rhizosphere Microenvironment by Arbuscular Mycorrhizal Fungi to Mitigate the Effects of Cadmium Contamination on Perennial Ryegrass (Lolium perenne L.).

Rhizosphere microorganisms are crucial for enhancing plant stress resistance. Current studies have shown that Arbuscular mycorrhizal fungi (AMF) can facilitate vegetation recovery in heavy metal-contaminated soils through interactions with rhizosphere microbiota. However, the mechanisms by which AMF influences rhizosphere microbiota and plant growth under cadmium (Cd) stress remain unclear. In this study, Lolium perenne L. was inoculated with AMF (Rhizophagus irregularis) and grown in soils supplemented with Cd (0 mg kg-1, Cd0; 100 mg kg-1, Cd100). Plant biomass, antioxidant enzyme activities, peroxide content, Cd uptake, and rhizosphere bacterial community composition were evaluated. AMF inoculation reduced Cd influx in aboveground tissues, enhanced nutrient availability in the rhizosphere, and mitigated Cd biotoxicity. Additionally, AMF inoculation improved the scavenging efficiency of reactive oxygen species and alleviated oxidative stress in L. perenne, thereby mitigating biomass reduction. Moreover, AMF treatment increased leaf and root biomass by 342.94% and 41.31%, respectively. Furthermore, under the same Cd concentration, AMF inoculation increased bacterial diversity (as measured by the Shannon index) and reduced bacterial enrichment (as indicated by the ACE index). AMF promoted the enrichment of certain bacterial genera (e.g., Proteobacteria and Actinobacteria) in the Cd100 group. These findings suggest that AMF regulated the composition of the rhizosphere bacterial community and promoted the growth of potentially beneficial microorganisms, thereby enhancing the resistance of L. perenne to Cd stress. Cd contamination in soil severely limits plant growth and threatens ecosystem stability, highlighting the need to understand how AMF and rhizosphere microbes can enhance Cd tolerance in L. perenne. Therefore, inoculating plants with AMF is a promising strategy for enhancing their adaptability to Cd-contaminated soils.

Phage biocontrol success of bacterial wilt depends on synergistic interactions with resident rhizosphere microbiota.

Phages can successfully be used invitro and in planta to biocontrol the phytopathogenic Ralstonia solanacearum bacterium-the causal agent of bacterial wilt disease. However, phage biocontrol outcomes are still variable, and it is unclear what causes this. In this study, we assessed the efficiency of four phages in controlled invitro and in planta experiments in all one- and two-phage combinations. We found that using phages in combination did not improve the phage biocontrol efficiency relative to single phage treatments, while certain phages and their combinations were more effective than the others. High intra-treatment variability in phage efficiency was observed across all phage treatments, which was associated with clear shifts in microbiome composition, a reduction in R. solanacearum and an increase in phage densities. We further identified the bacterial taxa that were associated with these 'shifted' microbiomes and conducted additional plant growth experiments, demonstrating that some of the enriched bacterial species could protect plants from R. solanacearum infections-a pattern which was also observed using partial least squares path modelling (PLS-PM). Together, these results suggest that phages could open niche space for beneficial bacteria by reducing pathogen densities and that variability in phage biocontrol outcomes is rhizosphere microbiome-dependent, which can introduce between-replicate variation, even in controlled greenhouse conditions.

Quality traits drive the enrichment of Massilia in the rhizosphere to improve soybean oil content

BackgroundSoybean seeds are rich in protein and oil. The selection of varieties that produce high-quality seeds has been one of the priorities of soybean breeding programs. However, the influence of improved seed quality on the rhizosphere microbiota and whether the microbiota is involved in determining seed quality are still unclear. Here, we analyzed the structures of the rhizospheric bacterial communities of 100 soybean varieties, including 53 landraces and 47 modern cultivars, and evaluated the interactions between seed quality traits and rhizospheric bacteria.ResultsWe found that rhizospheric bacterial structures differed between landraces and cultivars and that this difference was directly related to their oil content. Seven bacterial families (Sphingomonadaceae, Gemmatimonadaceae, Nocardioidaceae, Xanthobacteraceae, Chitinophagaceae, Oxalobacteraceae, and Streptomycetaceae) were obviously enriched in the rhizospheres of the high-oil cultivars. Among them, Oxalobacteraceae (Massilia) was assembled specifically by the root exudates of high-oil cultivars and was associated with the phenolic acids and flavonoids in plant phenylpropanoid biosynthetic pathways. Furthermore, we showed that Massilia affected auxin signaling or interfered with active oxygen-related metabolism. In addition, Massilia activated glycolysis pathway, thereby promoting seed oil accumulation.ConclusionsThese results provide a solid theoretical basis for the breeding of revolutionary soybean cultivars with desired seed quality and optimal microbiomes and the development of new cultivation strategies for increasing the oil content of seeds.7196FtKvsnPuUrhB77D9vLVideo

Soil Biocrusts May Exert a Legacy Impact on the Rhizosphere Microbial Community of Plant Crops

Biological soil crusts (biocrusts) play important ecological roles in many ecosystems, but their legacy effects in subtropical agricultural systems are poorly understood. This study investigated how biocrusts impact soil properties and subsequent crop rhizosphere microbiomes. Soil with (+BC) and without (−BC) biocrusts was cultivated and used to grow pepper plants in a greenhouse experiment. Soil physicochemical properties and microbial communities in the pre-planting soils, and microbial communities in crop rhizosphere were analyzed. The results showed that soils with biocrust had significantly higher organic matter, total nitrogen, alkaline hydrolyzable nitrogen, total phosphorus, and total potassium content. Microbial community structures differed significantly among treatments, with −BC soils exhibiting higher microbial diversity in pre-planting conditions, while +BC soils showed higher diversity in crop rhizosphere soils. Soil properties, especially extractable potassium, total nitrogen, and organic matter content, were significantly correlated with rhizosphere microbial community structure. Additionally, our results showed that the first principal coordinate (PCoA1) of soil microbial community structure was significantly correlated with rhizosphere microbiota. Multiple regression analysis revealed that pre-planting soil microbial diversity indices and certain soil physicochemical properties could predict crop rhizosphere soil microbial diversity. Our results demonstrate that biocrusts can enhance soil fertility and alter microbial communities in subtropical agricultural soils, with persistent effects on the crop rhizosphere microbiome. This study provides new insights into the ecological legacy of biocrusts in managed subtropical ecosystems and their potential agricultural implications.

The crop mined phosphorus nutrition via modifying root traits and rhizosphere micro‐food web to meet the increased growth demand under elevated CO2

AbstractElevated CO2 (eCO2) stimulates productivity and nutrient demand of crops. Thus, comprehensively understanding the crop phosphorus (P) acquisition strategy is critical for sustaining agriculture to combat climate changes. Here, wheat (Triticum aestivum L) was planted in field in the eCO2 (550 µmol mol−1) and ambient CO2 (aCO2, 415 µmol mol−1) environments. We assessed the soil P fractions, root morphological and physiological traits and multitrophic microbiota [including arbuscular mycorrhizal fungi (AMF), alkaline phosphomonoesterase (ALP)‐producing bacteria, protozoa, and bacterivorous and fungivorous nematodes] in the rhizosphere and their trophic interactions at jointing stage of wheat. Compared with aCO2, significant 20.2% higher shoot biomass and 26.8% total P accumulation of wheat occurred under eCO2. The eCO2 promoted wheat root length and AMF hyphal biomass, and increased the concentration of organic acid anions and the ALP activity, which was accompanied by significant decreases in calcium‐bound inorganic P (Ca‐Pi) (by 16.7%) and moderately labile organic P (by 26.5%) and an increase in available P (by 14.4%) in the rhizosphere soil. The eCO2 also increased the growth of ALP‐producing bacteria, protozoa, and bacterivorous and fungivorous nematodes in the rhizosphere, governed their diversity and community composition. In addition, the eCO2 strengthened the trophic interactions of microbiota in rhizosphere; specifically, the eCO2 promoted the associations between protozoa and ALP‐producing bacteria, between protozoa and AMF, whereas decreased the associations between ALP‐producing bacteria and nematodes. Our findings highlighted the important role of root traits and multitrophic interactions among microbiota in modulating crop P‐acquisition strategies, which could advance our understanding about optimal P management in agriculture systems under global climate changes.

Volatile-mediated interspecific plant interaction promotes root colonization by beneficial bacteria via induced shifts in root exudation

BackgroundVolatile organic compounds (VOCs) released by plants can act as signaling molecules mediating ecological interactions. Therefore, the study of VOCs mediated intra- and interspecific interactions with downstream plant physiological responses is critical to advance our understanding of mechanisms underlying information exchange in plants. Here, we investigated how plant-emitted VOCs affect the performance of an interspecific neighboring plant via induced shifts in root exudate chemistry with implications for root-associated microbiota recruitment.ResultsFirst, we showed that VOCs emitted by potato-onion plants stimulate the growth of adjacent tomato plants. Then, we demonstrated that this positive effect on tomato biomass was attributed to shifts in the tomato rhizosphere microbiota. Specifically, we found potato-onion VOCs to indirectly affect the recruitment of specific bacteria (e.g., Pseudomonas and Bacillus spp.) in the tomato rhizosphere. Second, we identified and validated the compound dipropyl disulfide as the active molecule within the blend of potato-onion VOCs mediating this interspecific plant communication. Third, we showed that the effect on the tomato rhizosphere microbiota occurs via induced changes in root exudates of tomato plants caused by exposure to dipropyl disulfide. Last, Pseudomonas and Bacillus spp. bacteria enriched in the tomato rhizosphere were shown to have plant growth-promoting activities.ConclusionsPotato-onion VOCs—specifically dipropyl disulfide—can induce shifts in the root exudate of adjacent tomato plants, which results in the recruitment of plant-beneficial bacteria in the rhizosphere. Taken together, this study elucidated a new mechanism of interspecific plant interaction mediated by VOCs resulting in alterations in the rhizosphere microbiota with beneficial outcomes for plant performance.4wKeniGUxY9GPejLMpvDe9Video

The effects of simulated Martian regolith on Arabidopsis growth, circadian rhythms and rhizosphere microbiota

The effects of simulated Martian regolith on Arabidopsis growth, circadian rhythms and rhizosphere microbiota

Phytostabilisation of arsenic contaminated gold mine waste using the native species Juncus usitatus, Poa labillardieri and Themeda triandra

Arsenic (As) contaminated gold mine waste represents a significant issue for ecosystem and human health, as it is a known carcinogen and environmental toxin. Bendigo in Victoria, Australia, has reported As concentrations up to 22,000 mg/kg, exceeding the national soil guidance values (100 mg/kg) by 220-fold. To reduce exposure and potential human health risk, remediation or risk management strategies are required. Traditional remediation, such as excavation and landfill, often fail to improve soil conditions and are expensive. Biological remediation using plants (phytoremediation) represents a cost-effective strategy that results in the restoration of soil function and ecosystem services. There is a need to identify native plants for phytoremediation as current research focuses on fern species, which are not suitable for Bendigo. This study aimed to identify a native phytostabilising plant by conducting a mesocosm experiment involving Juncus usitatus, Poa labillardieri, and Themeda triandra. Plants grew in mine waste for 100 days; all survived and bioaccumulated As in the roots (phytostabilisation). Poa labillardieri grew significantly more biomass (roots 0.24 ± 0.01 g; shoots 0.22 ± 0.03 g (d/w)) and bioaccumulated the most As (~ 100 mg/kg plant biomass). The bacterial community was investigated to assess soil health and As association. The rhizosphere microbiota stabilised after root colonisation for Poa labillardieri and Themeda triandra, as indicated by richness and evenness changes. The two dominant phyla were Actinobacteriota and Proteobacteria, which displayed As tolerance. A keystone taxon, Latescibacterota, exhibited a positive relative association with As remediation. Poa labillardieri is a good candidate for future phytostabilisation trials.

Diversity and interactions of rhizobacteria determine multinutrient traits in tomato host plants under nitrogen and water disturbances

Abstract Coevolution within the plant holobiont extends the capacity of host plants for nutrient acquisition and stress resistance. However, the role of the rhizospheric microbiota in maintaining multinutrient utilization (i.e., multinutrient traits) in the host remains to be elucidated. Multinutrient cycling index (MNC), analogous to the widely used multifunctionality index, provides a straightforward and interpretable measure of the multinutrient traits in host plants. Using tomato as a model plant, we characterized MNC (based on multiple aboveground nutrient contents) in host plants under different nitrogen and water supply regimes and explored the associations between rhizospheric bacterial community assemblages and host-plant multinutrient profiles. Rhizosphere bacterial community diversity, quantitative abundance, predicted function, and key topological features of the co-occurrence network were more sensitive to water supply than to nitrogen supply. A core bacteriome comprising 61 genera, such as Candidatus Koribacter and Streptomyces, persisted across different habitats and served as a key predictor of host-plant nutrient uptake. The MNC index increased with greater diversity and higher core taxon abundance in the rhizobacterial community, while decreasing with higher average degree and graph density of rhizobacterial co-occurrence network. Multinutrient absorption by host plants was primarily regulated by community diversity and rhizobacterial network complexity under the interaction of nitrogen and water. The high biodiversity and complex species interactions of the rhizospheric bacteriome play crucial roles in host-plant performance. This study supports the development of rhizosphere microbiome engineering, facilitating effective manipulation of the microbiome for enhanced plant benefits, which supports sustainable agricultural practices and plant health.

Aeration treatment promotes transformation of soil phosphorus fractions to plant-available phosphorus by modulating rice rhizosphere microbiota

Microorganisms play an important role in affecting the content of available phosphorus (P) in plant rhizosphere soil. However, the effect of aeration on available P in rice rhizosphere soil and its microbial mechanism remain unclear. This study aimed to elucidate the effects of aeration strategies on available P and P-solubilizing microorganisms in rhizosphere soil, employing three different aeration methods (continuous flooding (CF), continuous flooding and aeration (CFA), and alternate wetting and drying (AWD)). We analyzed the bacterial and fungal community structures in rice rhizosphere soil via Illumina sequencing techniques and quantified the abundance of P transformation functional genes related to inorganic P solubilization (pqqC) and organic P mineralization (phoC, phoD, and appA) through quantitative PCR. Our findings revealed that the AWD treatment significantly increased soil pH and Eh; Both AWD and CFA treatments markedly increased soil Olsen-P content at the tillering and heading stages, as well as the microbial carbon-to-phosphorus ratio (MBC/MBP) at the heading and maturity stages. Cluster analysis showed distinct bacterial communities at the heading and maturity stages under AWD, which differed from those in other treatments. Fungal communities at the tillering and heading stages under CFA and AWD grouped together. AWD and CFA treatments consistently enhanced labile-P in the rhizosphere soil throughout the entire growth stages, while reducing moderately labile-P during the tillering and heading stages. Compared to CF, at the heading and maturity stages, the copy numbers of pqqC, phoD, phoC, and appA were higher under AWD compared to other treatments. In conclusion, this study posits that the increase in Olsen-P in paddy fields due to aeration results from improved oxygen conditions in the rhizosphere, alterations in pH and Eh, effects on microbial stoichiometry, and adjustments in the abundance and composition of P-solubilizing microorganisms, thereby promoting P transformation. This conclusion provides new insights into the conversion of soil P Fractions into plant-available forms.

The rootstock genotype shapes the diversity of pecan (Carya illinoinensis) rhizosphere microbial community.

Pecans (Carya illinoinensis), one of the most valuable native North American nut crops, are commonly propagated through grafting to preserve the desired characteristics from parent trees. Since successful cultivation of pecan trees relies on the interplay among scion varieties, rootstocks, and soil conditions, this study investigated the microbial change to communities in the soils and roots of southern (87MX5-1.7) and northern (Peruque) rootstocks in a rootstock test orchard. Both grafted with the 'Pawnee' scion cultivar. Bacterial 16S ribosomal RNA and fungal ITS were amplified from both roots and rhizosphere soils of the two 10-year-grafted trees, then sequenced and annotated into trophic and nutrient-related groups to characterize the rhizosphere microbiota. The Peruque roots had a higher relative abundance of saprotroph fungi, while 87MX5-1.7 exhibited higher levels of symbiotroph fungi and nitrogen fixation-related bacteria. Among them, the presence of symbiotroph fungi, particularly ectomycorrhizal fungi, notably differed between these two rootstocks, with a significantly higher presence observed in the root of 87MX5-1.7 compared to Peruque. This variation likely leads to divergent pathways of nutrient translocation: Peruque was in favor of multiple fungi (Russula and Inocybe) to gain nutrition, while 87MX5-1.7 preferred a specific domain of fungi (Tuber) and nitrogen fixation-related bacteria (Bradyrhizobia) to form beneficial symbiosis. Moreover, the presence of pathogens suggested a potential risk of Fusarium patch and snow molds in 87MX5-1.7, while canker and black foot disease pose threats in Peruque. The findings of this study suggest that rootstocks from different origins shape rhizosphere microbes differently, potentially affecting nutrient uptake and nut yield. Exploring rootstock-microbe combinations could provide insights into optimizing scion growth and ultimately increasing nut yield. By understanding how different rootstock-microbe interactions influence pecan tree development, growers can strategically select combinations that promote beneficial symbiotic relationships, enhancing nutrient uptake, disease resistance, and overall tree vigor.

Interspecific allelopathic interaction primes direct and indirect resistance in neighboring plants within agroforestry systems

The agroforestry system with high biodiversity enhances ecosystem stability and reduces vulnerability to environmental disturbances and diseases. Investigating the mechanisms of interspecies allelopathic interactions for disease suppression in agroforestry offers a sustainable strategy for plant disease management. Here, we used Panax ginseng cultivated under Pinus koraiensis forests, which have low occurrences of Alternaria leaf spot, as a model to explore the role of allelochemicals in disease suppression. Our findings demonstrate that foliar application of P. koraiensis needle leachates effectively enhanced the resistance of P. ginseng against Alternaria leaf spot. Using gas chromatography-mass spectrometry, we identified and quantified endo-borneol as a key compound in P. koraiensis leachates and confirmed its ability to prime resistance in neighboring P. ginseng plants. We discovered that endo-borneol not only directly activates defense-related pathways in P. ginseng to confer resistance but also indirectly recruits its beneficial rhizospheric microbiota by promoting the secretion of ginsenosides, thereby triggering induced systemic resistance. Notably, higher concentrations of endo-borneol, ranging from 10 to 100 mg/l, have a greater capacity to induce plant resistance and enhance root secretion, thereby recruiting more microbiota compared to lower concentrations ranging from 0.01 to 1 mg/l. Additionally, endo-borneol exhibits antifungal activities against the growth of the pathogen Alternaria panax when concentrations exceeded 10 mg/l. These results reveal the multifaceted functions of allelochemical endo-borneol in disease suppression within agroforestry systems and highlight its potential as an environmentally friendly agent for sustainable agriculture.

A "love match" score to compare root exudate attraction and feeding of the plant growth-promoting rhizobacteria Bacillus subtilis, Pseudomonas fluorescens, and Azospirillum brasilense.

The rhizosphere is the zone of soil surrounding plant roots that is directly influenced by root exudates released by the plant, which select soil microorganisms. The resulting rhizosphere microbiota plays a key role in plant health and development by enhancing its nutrition or immune response and protecting it from biotic or abiotic stresses. In particular, plant growth-promoting rhizobacteria (PGPR) are beneficial members of this microbiota that represent a great hope for agroecology, since they could be used as bioinoculants for sustainable crop production. Therefore, it is necessary to decipher the molecular dialog between roots and PGPR in order to promote the establishment of bioinoculants in the rhizosphere, which is required for their beneficial functions. Here, the ability of root exudates from rapeseed (Brassica napus), pea (Pisum sativum), and ryegrass (Lolium perenne) to attract and feed three PGPR (Bacillus subtilis, Pseudomonas fluorescens, and Azospirillum brasilense) was measured and compared, as these responses are directly involved in the establishment of the rhizosphere microbiota. Our results showed that root exudates differentially attracted and fed the three PGPR. For all beneficial bacteria, rapeseed exudates were the most attractive and induced the fastest growth, while pea exudates allowed the highest biomass production. The performance of ryegrass exudates was generally lower, and variable responses were observed between bacteria. In addition, P. fluorescens and A. brasilense appeared to respond more efficiently to root exudates than B. subtilis. Finally, we proposed to evaluate the compatibility of each plant-PGPR couple by assigning them a "love match" score, which reflects the ability of root exudates to enhance bacterial rhizocompetence. Taken together, our results provide new insights into the specific selection of PGPR by the plant through their root exudates and may help to select the most effective exudates to promote bioinoculant establishment in the rhizosphere.

Diversity of microbial, biocontrol agents and nematode abundance on a susceptible Prunus rootstock under a Meloidogyne root gradient infection.

Root-knot nematodes (RKNs) of the genus Meloidogyne are one of the most damaging genera to cultivated woody plants with a worldwide distribution. The knowledge of the soil and rhizosphere microbiota of almonds infested with Meloidogyne could help to establish new sustainable and efficient management strategies. However, the soil microbiota interaction in deciduous woody plants infected with RKNs is scarcely studied. This research was carried out in six commercial almond groves located in southern Spain and infested with different levels of Meloidogyne spp. within each grove. Several parameters were measured: nematode assemblages, levels and biocontrol agents in Meloidogyne's eggs, levels of specific biocontrol agents in rhizoplane and soil, levels of bacteria and fungi in rhizoplane and soil, fungal and bacterial communities by high-throughput sequencing of internal transcribed spacer (ITS), and 16S rRNA gene in soil and rhizosphere of the susceptible almond hybrid rootstock GF-677 infested with Meloidogyne spp. The studied almond groves showed soil degradation by nematode assemblies and fungi:bacterial ratio. Fungal parasites of Meloidogyne eggs were found in 56.25% of the samples. However, the percentage of parasitized eggs by fungi ranged from 1% to 8%. Three fungal species were isolated from Meloidogyne eggs, specifically Pochonia chlamydosporia, Purpureocillium lilacinum, and Trichoderma asperellum. The diversity and composition of the microbial communities were more affected by the sample type (soil vs rhizosphere) and by the geographical location of the samples than by the Meloidogyne density, which could be explained by the vigorous hybrid rootstock GF-677 and a possible dilution effect. However, the saprotrophic function in the functional guilds of the fungal ASV was increased in the highly infected roots vs the low infected roots. These results indicate that the presence of biocontrol agents in almond fields and the development of new management strategies could increase their populations to control partially RKN infection levels.

Artificially selected rhizosphere microbiota modify plant growth in a soil-independent and species-dependent way

Artificially selected rhizosphere microbiota modify plant growth in a soil-independent and species-dependent way

Evolutionarily conserved core microbiota as an extended trait in nitrogen acquisition strategy of herbaceous species.

Microbiota have co-evolved with plants over millions of years and are intimately linked to plants, ranging from symbiosis to pathogenesis. However, our understanding of the existence of a shared core microbiota across phylogenetically diverse plants remains limited. A common garden field experiment was conducted to investigate the rhizosphere microbial communities of phylogenetically contrasting herbaceous families. Through a combination of metagenomic sequencing, analysis of plant economic traits, and soil biochemical properties, we aimed to elucidate the eco-evolutionary role of the core rhizosphere microbiota in light of plant economic strategies. We identified a conserved core microbiota consisting of 278 taxa that was closely associated with the phylogeny of the plants studied. This core microbiota actively participated in multiple nitrogen metabolic processes and showed a strong correlation with the functional potential of rhizosphere nitrogen cycling, thereby serving as an extended trait in the plant nitrogen acquisition. Furthermore, our examination of simulated species loss revealed the crucial role of the core microbiota in maintaining the rhizosphere community's network stability. Our study highlighted that the core microbiota, which exhibited a phylogenetically conserved association with plants, potentially represented an extension of the plant phenotype and played an important role in nitrogen acquisition. These findings held implications for the utilization of microbiota-mediated plant functions.