Rhizosphere Microbiome Research Articles

The Synergistic Impact of a Novel Plant Growth-Promoting Rhizobacterial Consortium and Ascophyllum nodosum Seaweed Extract on Rhizosphere Microbiome Dynamics and Growth Enhancement in Oryza sativa L. RD79

This study investigated the combined effects of novel plant growth-promoting rhizobacteria (PGPR)—Agrobacterium pusense NC2, Kosakonia oryzae WN104, and Phytobacter sp. WL65—and Ascophyllum nodosum seaweed extract (ANE) as biostimulants (PGPR-ANE) on rice growth, yield, and rhizosphere bacterial communities using the RD79 cultivar. The biostimulants significantly enhanced plant growth, shoot and root length, and seedling vigour; however, seed germination was not affected. In pot experiments, biostimulant application significantly increased the richness and evenness of bacterial communities in the rhizosphere, resulting in improvements in rice growth and yield, with increases in plant height (9.6–17.7%), panicle length (14.3–17.9%), and seeds per panicle (48.0–53.0%). Notably, biostimulant treatments also increased post-harvest soil nutrient levels, with nitrogen increasing by 7.7–19.2%, phosphorus by 43.4–161.4%, and potassium by 16.9–70.4% compared to the control. Principal coordinate analysis revealed distinct differences in bacterial composition between the tillering and harvesting stages, as well as between biostimulant treatments and the control. Beneficial bacterial families, including Xanthobacteraceae, Beijerinckiaceae, Acetobacteraceae, Acidobacteriaceae, and Hyphomicrobiaceae, increased in number from the tillering to harvesting stages, likely contributing to soil health improvements. Conversely, methanogenic bacterial families, such as Methanobacteriaceae and Methanosarcinaceae, decreased in number compared to the control. These findings highlight the dynamic responses of the rhizosphere microbiome to biostimulant treatments and underscore their potential benefits for promoting sustainable and productive agriculture.

Plant-Guided Microbiome Selection Produces Transient Effects on Insect Performance and Rhizosphere Community Assembly

Microbial communities are essential for plant health, but using these relationships to enhance growth and pest protection is challenging. Leveraging the natural mechanisms plants employ to manage relationships with microbes is one promising means to selectively engineer whole microbial communities with beneficial properties. This approach, known as host-guided selection, has been successful in some model species targeting performance traits (e.g., biomass). However, few studies use crop plants or focus on defensive traits (e.g., pest resistance). Our goal was to naturally engineer tomato root-associated microbiomes that increase resistance to insect pests. First, we used an iterative soil microbial inoculation process to engineer insect-suppressive rhizosphere soil microbiomes that reduce damage from aphid feeding ( Macrosiphum euphorbiae) or caterpillar defoliation ( Manduca sexta, Spodoptera exigua). We then characterized the bacterial and fungal microbial communities of soils associated with differences in insect performance using metabarcoding approaches. Overall, soil microbiome selection produced transient differences in aphid performance, but caterpillar growth was unaffected. In four of nine generations, the aphid population growth rate was significantly lower on plants with rhizospheres selected for “low” insect performance, where abundance was reduced by up to 20%. Correspondingly minor shifts in fungal and bacterial relative abundance occurred in insect-suppressive communities. However, network analysis indicated that aphid feeding disrupted rhizosphere microbiome assembly, resulting in lower community complexity and connectivity and fewer structurally important taxa compared with uninfested controls. Overall, our results highlight critical factors for successful engineering of beneficial microbiomes, particularly insect feeding guild and microbial community stability.

Long-term garlic‒maize rotation maintains the stable garlic rhizosphere microecology.

Crop rotation is a sophisticated agricultural practice that can modify the demographic structure and abundance of microorganisms in the soil, stimulate the growth and proliferation of beneficial microorganisms, and inhibit the development of harmful microorganisms. The stability of the rhizosphere microbiome is crucial for maintaining both soil ecosystem vitality and crop prosperity. However, the effects of extended garlic‒maize rotation on the physicochemical characteristics of garlic rhizosphere soil and the stability of its microbiome remain unclear. To investigate this phenomenon, soil samples from the garlic rhizosphere were collected across four different lengths of rotation in a garlic-maize rotation. There were notable positive associations between the total nitrogen and total phosphorus contents in the soil and the duration of rotation. Prolonged rotation could increase the maintenance of microbiome α diversity. The number of years of rotation and the soil organic carbon (SOC) content emerged as principal determinants impacting the evolution of the bacterial community structure, with the SOC content playing a pivotal role in sculpting the species diversity within the garlic rhizosphere bacterial community. Additionally, SOC remains predominant in shaping the root-associated bacterial community's β-nearest taxon index. However, these factors do not have a notable effect on the fungal community inhabiting the garlic rhizosphere. In comparison with monoculture, rotation can amplify the interconnectivity and intricacy of microbial ecological networks. Long-term rotation can further maintain the stability of both microbial ecological networks and interactions between bacterial and fungal communities. It can enlist a plethora of beneficial Bacillus species microorganisms within the garlic rhizosphere to form a biological barricade that aids in safeguarding garlic against encroachment by the pathogenic fungus Fusarium oxysporum, consequently diminishing disease incidence. This study provides a theoretical foundation for the sustainable development of garlic through long-term crop rotation with maize. Our research results indicate that long-term garlic‒maize rotation maintains stable garlic rhizosphere microecology. Our study provides compelling evidence for the role of long-term crop rotation in maintaining microbiota and community stability, emphasizing the importance of cultivating specific beneficial microorganisms to enhance rotation strategies for garlic farming, thereby promoting sustainability in agriculture.

Biological Nitrification Inhibition by Australian Tussock Grass and Its Impact on the Rhizosphere Ammonia-Oxidizing Microbiome

Certain plant species have developed the ability to express biological nitrification inhibition (BNI), suppressing the activity of nitrifying microbes and thereby reducing the conversion of ammonium to nitrate. This study assessed the BNI capacity and the rhizosphere ammonia-oxidizing microbiome of two grass species: the endemic Australian Barley Mitchell grass (Astrebla pectinata) and the introduced koronivia grass (Urochloa humidicola), using soils from both agricultural land and native vegetation. In agricultural soil, koronivia grass exhibited significantly higher BNI capacity compared with Barley Mitchell grass. However, in native soil, this trend was reversed, with Barley Mitchell grass demonstrating a significantly greater BNI capacity than koronivia grass (52% vs. 38%). Koronivia grass significantly altered the composition of the ammonia-oxidizing bacteria community in its rhizosphere, leading to a decrease in the Shannon index and bacteria number. Conversely, Barley Mitchell grass reduced the Shannon index (1.2 vs. 1.7) and population size (3.28 × 107 vs. 7.43 × 107 gene copy number g−1 dry soil) of the ammonia-oxidizing archaea community in its rhizosphere to a greater extent. These findings suggest that Australian Barley Mitchell grass may have evolved mechanisms to suppress soil archaeal nitrifiers, thereby enhancing its BNI capacity and adapting to Australia’s nutrient-poor soils.

Rhizosphere microbiomes are closely linked to seagrass species: a comparative study of three coastal seagrasses.

Seagrasses are indispensable in marine ecosystems, offering numerous critical services, with their health significantly influenced by associated rhizosphere microbiomes. Although studies have investigated the microbial communities and their ecological roles in seagrass meadows, the correlations between rhizosphere microbiome and seagrass species from a particular geographic region are limited. Some studies concentrated on the bacterial composition within the rhizosphere of various seagrasses, but the functional aspects of these microbiomes remain unexplored. Our research delves into this void, revealing that Ruppia sinensis, Zostera japonica, and Zostera marina host diverse bacterial community in the composition, connections, functions, and metabolism, such as nitrogen and sulfur metabolism. Our study revealed that seagrass species play an important role in shaping the rhizosphere microbiomes in an equivalent environment, emphasizing the importance of seagrass species in shaping the rhizosphere microbial communities.

Increased microbial complexity and stability in rhizosphere soil: A key factor for plant resilience during mining disturbance

The network-based complexity and stability of the microbial community are critical for host fitness under disturbance, but there are still gaps in our understanding of whether there are general rules governing this relationship. Despite evidence that the rhizosphere microbiome plays an important role in host fitness, it is unclear whether rhizosphere microbial complexity and stability influence host plant fitness under scenarios of environmental disturbance. Here, we investigated the effects of mining disturbance on the complexity and stability of the rhizosphere microbiome and its potential role in plant fitness. Our findings demonstrated that, compared with mildly disturbed mining sites, severely disturbed mining sites exhibited significantly increased complexity and stability indices of the rhizosphere microbial community. Furthermore, we identified a positive feedback relationship between microbial complexity and stability and the functional potential of the microbial community, which ultimately benefits plant fitness. Our study provides empirical evidence that mining disturbance increases microbial complexity and stability, thereby increasing the resilience of host plants to environmental disturbance. Understanding microbially mediated tolerance to mining disturbance may improve our ability to predict and manage plant adaptability in changing environments.

Poly-γ-glutamic acid chelates chromium (III) and copper (II), alleviating their toxicity in cucumber and affecting rhizosphere bacterial community assembly.

The accumulation of chromium (Cr) and copper (Cu) in soil during industrialization and modernization poses an extreme threat to crops. Poly-γ-glutamic acid (γ-PGA) has the potential to stabilize heavy metals in soil through chelation because of the numerous carboxyl groups in its side chain. The rhizosphere microbiome contributes to plant detoxification by participating in heavy metal passivation. However, it is still unclear whether γ-PGA can alleviate the toxicity of Cr and Cu to plants and whether this effect is associated with changes in the rhizosphere microbiome assembly. Here, we found that γ-PGA application significantly reduced the content of Cr or Cu in cucumber plants by 67.45%-86.77% and 94.67%-98.21, respectively, and alleviated the oxidative stress of Cr or Cu to plants. Moreover, γ-PGA significantly increased the biomass of cucumber fruits in the plot experiment by 13.5% and 25.3% under Cr and Cu stress, respectively. The content of Cr or Cu in the cucumber fruit was below limits of detection, in contrast to the 31.23 mg/kg Cr or 9.86 mg/kg Cu detected in the no-γ-PGA treatment. γ-PGA effectively chelated Cr and Cu in vitro, and less than 30% of their chelates were degraded in 20 weeks, suggesting the strong stability of these chelates. γ-PGA significantly altered the rhizosphere bacterial community composition of cucumber by enriching phyla Gemmatimonadota, Acidobacteriota and Firmicutes, and genera Gemmatimonas and Stenotrophomonas, which potentially involved in reducing the mobility of Cr and Cu in soils. Furthermore, γ-PGA significantly enriched taxa assigned to plant growth-promoting bacteria (PGPB). Together, our results suggest that γ-PGA can reduce the Cr and Cu contents in cucumber, and this process is strongly associated with the chelation capacity of γ-PGA and its effects on rhizosphere microbiome composition. These results highlight the exciting potential to use γ-PGA for the remediation of heavy metal-contaminated soils.

Plant growth-promoting fungi improve tobacco yield and chemical components by reassembling rhizosphere fungal microbiome and recruiting probiotic taxa

BackgroundTobacco production faces ongoing challenges due to soil degradation, leading to a persistent decline in yield. Plant growth-promoting fungi (PGPF) have been recognized as an environmentally friendly agricultural strategy. However, many commercial PGPF products exhibit instability due to insufficient environmental compatibility.ResultsIn this study, Penicillium sp. PQxj3 was isolated and assessed for its potential to enhance tobacco productivity under field conditions. The results demonstrated that Penicillium sp. PQxj3 treatment significantly promoted the tobacco growth and improved the crop yield. The height of tobacco in Penicillium sp. PQxj3 treatment group significantly increased by 50.19% and 24.05% compared with CK at exuberant and maturity period (P < 0.05). The average yield of tobacco significantly increased by 36.16% compared to CK (P < 0.05). Fungal microbiome analysis revealed that phylogenetically similar probiotic taxa were recruited by Penicillium sp. PQxj3 and reassembled tobacco rhizosphere fungal microbiome. The key chemical indicators of tobacco such as alkaloid, total sugar, and phosphorus were significantly enhanced in Penicillium sp. PQxj3 treatment. The recruited probiotic taxa (Penicillium brasilianum, Penicillium simplicissimum, Penicillium macrosclerotiorum and Penicillium senticosum) were significantly associated with alkaloid, total sugar etc. (P < 0.05), which were identified as the key drivers for improving the chemical components of tobacco. Transcriptome analysis indicated that Penicillium sp. PQxj3 promoted up-regulation of key functional genes involved in alkaloid, indoleacetic, and gibberellin biosynthesis pathways.ConclusionIn summary, this study assessed the biopromotion mechanism of PGPF Penicillium sp. PQxj3 linking chemical traits, rhizosphere fungal microbiome, and transcriptome profiling. The findings provide a fundamental basis and a sustainable solution for developing fungal fertilizers to enhance agricultural sustainability.

Metabolic and Physiological Effects of Antibiotic-Induced Dysbiosis in Citrus

Streptomycin (Str) and oxytetracycline (Otc) are widely used antibiotics to manage bacterial diseases in citrus and other crops. However, their impacts on the rhizosphere bacterial assembly and plant physiology are poorly understood. The aim of this study was to examine the effects of Str and Otc on the physiology (assimilation, transpiration rate, intracellular CO2, and stomatal conductance to water vapor), rhizosphere bacterial assemblages (16S rRNA gene high-throughput amplicon sequencing), and rhizosphere metabolite profiles in healthy Citrus reticulata trees. The results indicated a reduction in photosynthesis after Str and Otc treatments, whereas CO2 outflow stayed constant. Both antibiotics decreased the culturable numbers of bacteria. Analysis of the microbiome showed changes in relative abundance of bacterial groups, specifically Pseudomonas, Agrobacterium, and Streptomyces, in response to the antibiotics. Metabolite profiles changed in streptomycin- and oxytetracycline-treated citrus plants suggesting response to microbe targets or induction of stress responses. This study advances knowledge of antibiotic-driven effects on the rhizosphere microbiome, rhizosphere metabolome, and plant physiology, which is essential for managing plant diseases while safeguarding rhizosphere ecology and long-term plant health.

Foliar application of bioorganic fertilizers enhances plant nutrients uptake and citrus yield by regulating rhizosphere and phyllosphere microbiome

Foliar application of bioorganic fertilizers enhances plant nutrients uptake and citrus yield by regulating rhizosphere and phyllosphere microbiome

Synergistic effects of AMF and PGPR on improving saline-alkaline tolerance of Leymus chinensis by strengthening the link between rhizosphere metabolites and microbiomes

Synergistic effects of AMF and PGPR on improving saline-alkaline tolerance of Leymus chinensis by strengthening the link between rhizosphere metabolites and microbiomes

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.

Breed Selection of Poplars Imposes Greater Selection Pressure on the Rhizosphere Bacterial Community

Breed selection alters the coevolution of plant–microbiome associations that have developed over long periods of natural evolution. We investigated the effects of breed selection on the rhizosphere microbiomes and metabolites of hybrid parents (I101 and 84K) and their offspring (Q1–Q5) using metagenomics and untargeted metabolomics. Rhizosphere archaeal, bacterial and fungal community β-diversity significantly differed among hybrid parents and offspring, but only the dominant bacterial phyla and bacterial community α-diversity revealed significant differences. Approximately 5.49%, 14.90% and 7.86% of the archaeal, bacterial and fungal species significantly differed among the poplar hybrid parents and offspring. Rhizosphere microbial functional genes and metabolites were both clustered into the following three groups: I101 and 84K; Q2 and Q4; and Q1, Q3 and Q5. Compared with the hybrid parents, 15 phytochemical compounds were enriched in the hybrid offspring and explained 7.15%, 18.24% and 6.68% of the total variation in the archaeal, bacterial and fungal community compositions, respectively. Rhizosphere metabolites significantly affected the bacterial community, rather than the archaeal and fungal communities. Our observations suggested that poplar breed selection imposed greater selection pressure on the rhizosphere bacterial community, which was mainly driven by metabolites.

Environment, plant genetics, and their interaction shape important aspects of sunflower rhizosphere microbial communities.

Associations with soil microorganisms are crucial for plants' overall health and functioning. While much work has been done to understand drivers of rhizosphere microbiome structure and function, the relative importance of geography, climate, soil properties, and plant genetics remains unclear, as results have been mixed and comprehensive studies across many sites and genotypes are limited. Rhizosphere microbiomes are crucial for crop resistance to pathogens, stress tolerance, nutrient availability, and ultimately yield. Here, we quantify the relative roles of plant genotype, environment, and their interaction in shaping soil rhizosphere communities, using 16S and ITS gene sequencing of rhizosphere soils from 10 genotypes of cultivated sunflower (Helianthus annuus) at 15 sites across the Great Plains of the United States. While site generally outweighed genotype overall in terms of effects on archaeal, bacterial, and fungal richness, community composition, and taxa relative abundances, there was also a significant interaction such that genotype exerted a significant influence on archaeal, bacterial, and fungal microbiomes in certain sites. Site effects were attributed to a combination of spatial distance and differences in climate and soil properties. Microbial taxa that were previously associated with resistance to the fungal necrotrophic pathogen Sclerotinia were present in most sites but differed significantly in relative abundance across sites. Our results have implications for plant breeding and agronomic microbiome manipulations for agricultural improvement across different geographic regions.IMPORTANCEDespite the importance of plant breeding in agriculture, we still have a limited understanding of how plant genetic variation shapes soil microbiome composition across broad geographic regions. Using 15 sites across the Great Plains of North America, we show that cultivated sunflower rhizosphere archaeal, bacterial, and fungal communities are driven primarily by site soil and climatic differences, but genotype can interact with site to influence the composition, especially in warmer and drier sites with lower overall microbial richness. We also show that all taxa that were previously found to be associated with resistance to the fungal pathogen Sclerotinia sclerotiorum were widespread but significantly affected by site, while a subset was also significantly affected by genotype. Our results contribute to a broader understanding of rhizosphere archaeal, bacterial, and fungal community assembly and provide foundational knowledge for plant breeding efforts and potential future microbiome manipulations in agriculture.

Priestia aryabhattai Improves Soil Environment and Promotes Alfalfa Growth by Enhancing Rhizosphere Microbial Carbon Sequestration Capacity Under Greenhouse Conditions.

Plant Growth-Promoting Rhizobacteria (PGPR) are gaining increasing attention, but their interactions with indigenous rhizosphere microbiomes remain unclear. To address this issue, we isolated a strain of Priestia aryabhattai with a growth-promoting effect. Under greenhouse conditions, its growth-promoting effect on alfalfa was evaluated, and amplicon sequencing was used to analyze changes in the rhizosphere microbial community to explore the growth promotion mechanism. Our study shows that inoculation with Priestia aryabhattai increases the α-diversity index of the alfalfa rhizosphere microbiome and enhances the abundance of beneficial bacterial genera. This is likely because inoculation with Priestia aryabhattai increased the abundance of carbon-sequestering genera, particularly Gemmatimonas, thereby improving the soil environment. The increased abundance of beneficial bacteria stimulates root development in alfalfa and enhances nutrient uptake, particularly phosphorus, which in turn boosts photosynthesis and promotes alfalfa growth. In summary, Priestia aryabhattai improves soil environment and promotes alfalfa growth by enhancing the carbon sequestration capacity of the rhizosphere microbial community. This work provides theoretical support and insight for the development of PGPR inoculants and for further research on their mechanisms.

Unveiling the hidden world: How arbuscular mycorrhizal fungi and its regulated core fungi modify the composition and metabolism of soybean rhizosphere microbiome

BackgroundThe symbiosis between arbuscular mycorrhizal fungi (AMF) and plants often stimulates plant growth, increases agricultural yield, reduces costs, thereby providing significant economic benefits. AMF can also benefit plants through affecting the rhizosphere microbial community, but the underlying mechanisms remain unclear. Using Rhizophagus intraradices as a model AMF species, we assessed how AMF influences the bacterial composition and functional diversity through 16 S rRNA gene sequencing and non-targeted metabolomics analysis in the rhizosphere of aluminum-sensitive soybean that were inoculated with pathogenic fungus Nigrospora oryzae and phosphorus-solubilizing fungus Talaromyces verruculosus in an acidic soil.ResultsThe inoculation of R. intraradices, N. oryzae and T. verruculosus didn’t have a significant influence on the levels of soil C, N, and P, or various plant characteristics such as seed weight, crude fat and protein content. However, their inoculation affected the structure, function and nutrient dynamics of the resident bacterial community. The co-inoculation of T. verruculosus and R. intraradices increased the relative abundance of Pseudomonas psychrotolerans, which was capable of N-fixing and was related to cry-for-help theory (plants signal for beneficial microbes when under stress), within the rhizosphere. R. intraradices increased the expression of metabolic pathways associated with the synthesis of unsaturated fatty acids, which was known to enhance plant resistance under adverse environmental conditions. The inoculation of N. oryzae stimulated the stress response inside the soil environment by enriching the polyene macrolide antifungal antibiotic-producing bacterial genus Streptomyces in the root endosphere and upregulating two antibacterial activity metabolic pathways associated with steroid biosynthesis pathways in the rhizosphere. Although inoculation of pathogenic fungus N. oryzae enriched Bradyrhizobium and increased soil urease activity, it had no significant effects on biomass and N content of soybean. Lastly, the host niches exhibited differences in the composition of the bacterial community, with most N-fixing bacteria accumulating in the endosphere and Rhizobium vallis only detected in the endosphere.ConclusionsOur findings demonstrate that intricate interactions between AMF, associated core fungi, and the soybean root-associated ecological niches co-mediate the regulation of soybean growth, the dynamics of rhizosphere soil nutrients, and the composition, function, and metabolisms of the root-associated microbiome in an acidic soil.

Adaptation of rhizobacterial and endophytic communities in Citrus Grandis Exocarpium to long-term organic and chemical fertilization.

Organic fertilizers (OF) are crucial for enhancing soil quality and fostering plant growth, offering a more eco-friendly and enduring solution compared to chemical fertilizers (CF). However, few studies have systematically analyzed the effects of OF/CF on root microbiome of medicinal plants, especially in combination with active ingredients. In this study, we investigated the composition and function of bacteria and fungi in the rhizosphere or within the root of traditional Chinese medicinal plants, Citri Grandis Exocarpium (Huajuhong), which were treated with OF or CF over 1, 3, and 5 years (starting from 2018). Additionally, we conducted metabolome analysis to evaluate the effects of different fertilizers on the medicinal properties of Huajuhong. The results indicated that extended fertilization could enhance the microbial population and function in plant roots. Notably, OF demonstrated a stronger influence on bacteria, whereas CF enhanced the cohesion of fungal networks and the number of fungal functional enzymes, and even potentially reduced the proliferation of harmful rhizosphere pathogens. By adopting distancebased redundancy analysis, we identified the key physicochemical characteristics that significantly influence the distribution of endophytes, particularly in the case of OF. In contrast, CF was found to exert a more pronounced impact on the composition of the rhizosphere microbiome. Although the application of OF resulted in a broader spectrum of compounds in Huajuhong peel, CF proved to be more efficacious in elevating the concentrations of flavonoids and polysaccharides in the fruit. Consequently, the effects of long-term application of OF or CF on medicinal plants is different in many ways. This research provides a guide for OF/CF selection from the perspective of soil microecology and aids us to critically assess and understand the effects of both fertilizers on the soil environment, and promotes sustainable development of organic agriculture.

Effects of Grafting on the Structure and Function of Coffee Rhizosphere Microbiome

Heterologous double-root grafting represents an effective strategy to mitigate challenges associated with continuous coffee cropping and reduce soil-borne diseases. However, its specific regulatory mechanism remains unclear. Therefore, a field experiment was conducted including six different grafting combinations for C. canephora cv. Robusta (Robusta) and Coffea Liberica (Liberica): Robusta scion with a homologous double root (R/RR), Liberica scion with a homologous double root (L/LL), Robusta scion with a heterologous double root (R/RL and L/RL), and Liberica scion with a heterologous double root (L/LR and R/LR); these combinations were conducted to clarify the effects of heterologous double-root grafting combinations on the root exudates and soil microbial diversity, structure, and function of Robusta and Liberica. The results demonstrated notable differences in root exudates, rhizosphere microbial structure, and function between Robusta and Liberica. Despite Liberica having lower diversity in its rhizosphere microbial communities and relatively higher levels of potential pathogenic bacteria, it showed stronger resistance to diseases. Roots of Robusta in heterologous double-root coffee seedlings significantly enhanced the secretion of resistance compounds, increased the relative abundance of potentially beneficial bacteria, and reduced the relative abundance of potential pathogenic fungi. This enhances the rhizosphere immunity of Robusta against soil-borne diseases. The results indicated that grafting onto Liberica roots can strengthen resistance mechanisms and enhance the rhizosphere immunity of Robusta, thereby mitigating challenges associated with continuous cropping.

Unravelling the microbiome of wild flowering plants: a comparative study of leaves and flowers in alpine ecosystems

BackgroundWhile substantial research has explored rhizosphere and phyllosphere microbiomes, knowledge on flower microbiome, particularly in wild plants remains limited. This study explores into the diversity, abundance, and composition of bacterial and fungal communities on leaves and flowers of wild flowering plants in their natural alpine habitat, considering the influence of environmental factors.MethodsWe investigated 50 wild flowering plants representing 22 families across seven locations in Austria. Sampling sites encompassed varied soil types (carbonate/silicate) and altitudes (450–2760 m). Amplicon sequencing to characterize bacterial and fungal communities and quantitative PCR to assess microbial abundance was applied, and the influence of biotic and abiotic factors assessed.ResultsOur study revealed distinct bacterial and fungal communities on leaves and flowers, with higher diversity and richness on leaves (228 fungal and 91 bacterial ASVs) than on flowers (163 fungal and 55 bacterial ASVs). In addition, Gammaproteobacteria on flowers and Alphaproteobacteria on leaves suggests niche specialization for plant compartments. Location significantly shaped both community composition and fungal diversity on both plant parts. Notably, soil type influenced community composition but not diversity. Altitude was associated with increased fungal species diversity on leaves and flowers. Furthermore, significant effects of plant family identity emerged within a subset of seven families, impacting bacterial and fungal abundance, fungal Shannon diversity, and bacterial species richness, particularly on flowers.ConclusionThis study provides novel insights into the specific microbiome of wild flowering plants, highlighting adaptations to local environments and plant–microbe coevolution. The observed specificity indicates a potential role in plant health and resilience, which is crucial for predicting how microbiomes respond to changing environments, ultimately aiding in the conservation of natural ecosystems facing climate change pressures.

Thiophanate-methyl and its major metabolite carbendazim weaken rhizobacteria-mediated defense responses in cucumbers against Fusarium wilt

AbstractThe effect of fungicides on the plant-rhizosphere microbiome is a subject of ongoing debate, but whether any alteration in the rhizosphere microbiome could affect plant health is an issue that has not been thoroughly investigated. To address this deficiency, we analyzed the rhizosphere microbiome of wilt disease—resistant and disease-susceptible cucumber cultivars to determine whether (and which) plant-associated microorganisms have a role in disease resistance. We further assessed whether the fungicides thiophanate-methyl and carbendazim affect the rhizosphere microbiome, which may contribute to the plant’s immune response. Based on results acquired with both radicle-inoculation and soil-inoculation methods, cultivars Longyuanxiuchun (LYXC) and Shuyan2 (SY2) were identified as being disease resistant, whereas Zhongnong6 (ZN6) and Zhongnong38 (ZN38) were susceptible. The microbiome structure differed substantially between the resistant and susceptible plants, with LYXC and SY2 each having a significantly greater Shannon index than Zhongnong38. These results revealed that the disease-resistant cucumber cultivars recruited more beneficial bacteria, i.e., Bacillus, in their rhizosphere soil; as such, Bacillus was identified as a keystone genus in the microbial co-occurrence network. Thus, the presence of Bacillus may help cucumbers defend against fungal pathogens within the rhizosphere. Bacillus subtilis strain LD15, which was isolated from LYXC rhizosphere soil, could suppress pathogen growth, in vitro, and reduce disease severity in pot assays. Moreover, evidence also confirmed the accumulation of LD1 in the rhizosphere soil of resistant cucumber cultivars. For LYXC, application of thiophanate-methyl or carbendazim altered the microbiome structure, decreased bacterial diversity, and reduced the abundance of Bacillus species. Finally, pot assays verified that fungicide application decreased the proportion of LD15 in rhizosphere soil. From a microbial perspective, thiophanate-methyl and carbendazim may weaken the rhizobacteria-mediated defense response of cucumbers against cucumber Fusarium wilt disease. Our findings reveal a role for the rhizosphere microbiome in protecting plants from pathogens and constitute a reference for assessing the ecotoxicological risk of pesticides to non-target soil microorganisms.