Enrichment of Burkholderia in the Rhizosphere by Autotoxic Ginsenosides to Alleviate Negative Plant-Soil Feedback

Analysis and Functional Prediction of Core Bacteria in the Arabidopsis Rhizosphere Microbiome under Drought Stress

The effects of global warming, population growth, and economic development are increasing the frequency of extreme weather events, such as drought. Among abiotic stresses, drought has the greatest impact on soil biological activity and crop yields. The rhizosphere microbiota, which represents a second gene pool for plants, may help alleviate the effects of drought on crops. In order to investigate the structure and diversity of the bacterial communities on drought stress, this study analyzed the differences in the bacterial communities by high-throughput sequencing and bioinformatical analyses in the rhizosphere of Arabidopsis thaliana under normal and drought conditions. Based on analysis of α and β diversity, the results showed that drought stress had no significant effect on species diversity between groups, but affected species composition. Difference analysis of the treatments showed that the bacteria with positive responses to drought stress were Burkholderia-Caballeronia-Paraburkholderia (BCP) and Streptomyces. Drought stress reduced the complexity of the rhizosphere bacterial co-occurrence network. Streptomyces was at the core of the network in both the control and drought treatments, whereas the enrichment of BCP under drought conditions was likely due to a decrease in competitors. Functional prediction showed that the core bacteria metabolized a wide range of carbohydrates, such as pentose, glycans, and aromatic compounds. Our results provide a scientific and theoretical basis for the use of rhizosphere microbial communities to alleviate plant drought stress and the further exploration of rhizosphere microbial interactions under drought stress.

Soil microbiome of shiro reveals the symbiotic relationship between Tricholoma bakamatsutake and Quercus mongolica

Tricholoma bakamatsutake is a delicious and nutritious ectomycorrhizal fungus. However, its cultivation is hindered owing to limited studies on its symbiotic relationships. The symbiotic relationship between T. bakamatsutake and its host is closely related to the shiro, a complex network composed of mycelium, mycorrhizal roots, and surrounding soil. To explore the symbiotic relationship between T. bakamatsutake and its host, soil samples were collected from T. bakamatsutake shiro (Tb) and corresponding Q. mongolica rhizosphere (CK) in four cities in Liaoning Province, China. The physicochemical properties of all the soil samples were then analyzed, along with the composition and function of the fungal and bacterial communities. The results revealed a significant increase in total potassium, available nitrogen, and sand in Tb soil compared to those in CK soil, while there was a significant decrease in pH, total nitrogen, total phosphorus, available phosphorus, and silt. The fungal community diversity in shiro was diminished, and T. bakamatsutake altered the community structure of its shiro by suppressing other fungi, such as Russula (ectomycorrhizal fungus) and Penicillium (phytopathogenic fungus). The bacterial community diversity in shiro increased, with the aggregation of mycorrhizal-helper bacteria, such as Paenibacillus and Bacillus, and plant growth-promoting bacteria, such as Solirubrobacter and Streptomyces, facilitated by T. bakamatsutake. Microbial functional predictions revealed a significant increase in pathways associated with sugar and fat catabolism within the fungal and bacterial communities of shiro. The relative genetic abundance of carboxylesterase and gibberellin 2-beta-dioxygenase in the fungal community was significantly increased, which suggested a potential symbiotic relationship between T. bakamatsutake and Q. mongolica. These findings elucidate the microbial community and relevant symbiotic environment to better understand the relationship between T. bakamatsutake and Q. mongolica.

Effects of simulated acid rain on hydrochemical factors and microbial community structure in red soil aquifers

Acid rain can lower the pH of groundwater and affect its hydrogeochemistry and microbial ecology. However, the effects of acid rain on the hydrogeochemistry and microbial ecology of red soil groundwater systems in southern China are poorly understood. Previous research had mainly investigated the sources and patterns of groundwater acidification, but not the microbial mechanisms that contribute to this process and their associations with hydrochemical factors. To address this knowledge gap, we conducted a soil column experiment to simulate the infiltration of acid rain through various filter materials (coarse, medium, and fine sand) and to examine the hydrochemical and microbial features of the infiltrate, which can reveal how simulated acid rain (pH 3.5-7.0) alters the hydrochemistry and microbial community composition in red soil aquifers. The results showed that the pH of the leachate decreased due to simulated acid rain, and that the leaching efficiency of nitrogen and metal ions was influenced by the particle size of the filter media. Illumina 16S rRNA gene sequencing revealed that the leachate was dominated by Proteobacteria, Patescibacteria, Actinobacteria, and Acidobacteria, with Proteobacteria accounting for 67.04-74.69% of the bacterial community and containing a high proportion of nitrifying and denitrifying bacteria. Additionally, several genera with heavy metal tolerance, such as Burkholderia-Caballeronia-Paraburkholderia, Delftia, Methylversatilis, Aquicella, and Ralstonia, were widely distributed in the leachate, indicating the strong adaptive capacity of the microbial population. A correlation analysis between the hydrochemical factors and the microbial community structure revealed that pH was the most influential factor, followed by NO2--N, Fe, Al, Cu, Mn, and others. These results indicate that acidification modifies the hydrochemical conditions of the aquifer, creating an environment that is unfavorable for microbial growth and survival. However, some microorganisms may acquire resistance genes to cope with environmental changes.

Diversity of Endophytes of Actinidia arguta in Different Seasons

The seasonal changes in environmental conditions can alter the growth states of host plants, thereby affecting the living environment of endophytes and forming different endophytic communities. This study employs Illumina MiSeq next-generation sequencing to analyze the 16SrRNA and ITS rDNA of endophytes in 24 samples of Actinidia arguta stem tissues across different seasons. The results revealed a high richness and diversity of endophytes in Actinidia arguta, with significant seasonal variations in microbial community richness. This study identified 897 genera across 36 phyla for bacteria and 251 genera across 8 phyla for fungi. Notably, 69 bacterial genera and 19 fungal genera significantly contributed to the differences in community structure across seasons. A distinctive feature of coexistence in the endophytic community, both specific and conservative across different seasons, was observed. The bacterial community in winter demonstrated significantly higher richness and diversity compared to the other seasons. Environmental factors likely influence the optimal timing for endophyte colonization. Solar radiation, temperature, precipitation, and relative humidity significantly impact the diversity of endophytic bacteria and fungi. In addition, seasonal variations show significant differences in the nutritional modes of fungal endophytes and the degradation, ligninolysis, and ureolysis functions of bacterial endophytes. This study elucidates the potential role of endophytes in assisting Actinidia arguta in adapting to seasonal changes and provides a theoretical basis for further exploration of functional microbial strains.

Diversity and correlation analysis of different root exudates on the regulation of microbial structure and function in soil planted with Panax notoginseng

Introduction

Specific interactions between root exudates and soil microorganisms has been proposed as one of the reasons accounting for the continuous cropping obstacle (CCO) of Panax notoginseng. However, rotation of other crops on soils planted with P. notoginseng (SPP) did not show CCO, suggesting that root exudates of different crops differentially regulate soil microorganisms in SPP.

Methods

Here, we investigated the microbial community structure and specific interaction mechanisms of the root exudates of the four plant species, P. notoginseng (Pn), Zea mays (Zm), Nicotiana tabacum (Nt) and Perilla frutescens (Pf), in SPP by static soil culture experiment.

Results

The results showed that the chemical diversity of root exudates varied significantly among the four plant species. Pn had the highest number of unique root exudates, followed by Nt, Zm and Pf. Terpenoids, flavonoids, alkaloids and phenolic acids were the most abundant differentially accumulated metabolites (DAMs) in Pn, Nt, Zm and Pf, respectively. However, lipids were the most abundant common DAMs among Zm Nt and Pf. Pn root exudates decreased the relative abundance of bacteria, but increased that of fungi. While specific DAMs in Pn enriched Phenylobacterium_zucineum, Sphingobium_yanoikuyae, Ophiostoma_ulmi and functional pathways of Nucleotide excision repair, Streptomycin biosynthesis, Cell cycle-Caulobacter and Glycolysis/Gluconeogenesis, it inhibited Paraburkholderia _caledonica and Ralstonia_pickettii. However, common DAMs in Zm, Nt and Pf had opposite effects. Moreover, common DAMs in Zm, Nt and Pf enriched Ralstonia_pseudosolanacearum and functional pathway of Xylene degradation; unique DAMs in Zm enriched Talaromyces_purcureogeneus, while inhibiting Fusarium_tricinctum and functional pathways of Nucleotide excision repair and Alanine, aspartate and glutamate metabolism; unique DAMs in Pf enriched Synchytrium_taraxaci.

Discussion

The core strains identified that interact with different root exudates will provide key clues for regulation of soil microorganisms in P. notoginseng cultivation to alleviate CCO.

Integrated microbiology and metabolomics analysis reveal responses of cotton rhizosphere microbiome and metabolite spectrum to conventional seed coating agents

Fludioxonil (FL) and metalaxyl-M·fludioxonil·azoxystrobin (MFA) are conventional seed coating agents for controlling cotton seedling diseases. However, their effects on seed endophytic and rhizosphere microecology are still poorly understood. This study aimed to assess the effects of FL and MFA on cotton seed endophytes, rhizosphere soil enzymatic activities, microbiome and metabolites. Both seed coating agents significantly changed seed endophytic bacterial and fungal communities. Growing coated seeds in the soils originating from the Alar (AL) and Shihezi (SH) region inhibited soil catalase activity and decreased both bacterial and fungal biomass. Seed coating agents increased rhizosphere bacterial alpha diversity for the first 21 days but decreased fungal alpha diversity after day 21 in the AL soil. Seed coating reduced the abundance of a number of beneficial microorganisms but enriched some potential pollutant-degrading microorganisms. Seed coating agents may have affected the complexity of the co-occurrence network of the microbiome in the AL soil, reducing connectivity, opposite to what was observed in the SH soil. MFA had more pronounced effects on soil metabolic activities than FL. Furthermore, there were strong links between soil microbial communities, metabolites and enzymatic activities. These findings provide valuable information for future research and development on application of seed coatings for disease management.

Diversity Analysis and Function Prediction of Bacterial Communities in the Different Colored Pericarp of Citrus reticulata cv. 'Shatangju' Due to 'Candidatus Liberibacter asiaticus' Infection

Huanglongbing (HLB), caused by the Candidatus Liberibacter spp., is the most devastating disease in the citrus industry. HLB significantly affects and alters the microbial community structure or potential function of the microbial community of leaves and roots. However, it is unknown how the microbial community structure of the pericarp with different pigments is affected by Candidatus Liberibacter asiaticus (CLas). This study identified the enriched taxa of the microbial community in the citrus pericarp with normal or abnormal pigment and determine the effects of HLB on the pericarp microbial community using 16S rRNA-seq. The alpha and beta diversity and composition of microbial communities were significantly different between normal and abnormal pigment pericarp tissues of ripe fruits infected by CLas. Firmicutes, Actinobacteriota, Bacteroidota, Acidobacteriota, and Desulfobacterota dominated the pericarp microbiota composition in WDYFs (whole dark yellow fruits) samples. The relative abundance of most genera in WDYFs was higher than 1%, such as Burkholderia, and Pelomonas. However, with the exception of the HLB pathogen, the relative abundance of most genera in the abnormal-colored pericarp samples was less than 1%. CLas decreased the relative abundance of pericarp taxonomic. The predicted function of microbial was more plentiful and functional properties in the WDYF sample, such as translation, ribosomal structure and biogenesis, amino acid transport and metabolism, energy production and conversion, and some other clusters of orthologous groups (COG) except for cell motility. The results of this study offer novel insights into understanding the composition of microbial communities of the CLas-affected citrus pericarps and contribute to the development of biological control strategies for citrus against Huanglongbing.

Waterlogging stress alters the structure of sugar beet rhizosphere microbial community structure and recruiting potentially beneficial bacterial

Waterlogging has been shown to have a significant inhibitory effect on plant growth. However, the response mechanisms of the soil environment of sugar beet seedlings under waterlogging conditions still need to be fully understood. This study aimed to investigate the effects of waterlogging treatments on the content of effective nutrients and the microbial communities in the rhizosphere and non-rhizosphere using high-throughput sequencing. We set up waterlogging and non-waterlogging treatments, sampled sugar beet seedlings after 10 days of waterlogging, determined the effective soil nutrients in the rhizosphere and non-rhizosphere of the plants, and analyzed the differences in microbial diversity at ten days of waterlogging. The results showed that waterlogging significantly affected available potassium (AK) content. The Ak content of waterlogged soil was significantly higher than that of non-waterlogged soil. Waterlogging caused no significant difference in available nitrogen (AN) content and pH. Moreover, the plant growth-promoting bacteria Pseudomonas was significantly enriched in sugar beet waterlogged rhizospheres compared with the non-waterlogged ones. Similarly, the harmful fungi Gibellulopsis and Alternaria were enriched in sugar beet non-waterlogged rhizosphere. The network analysis revealed that waterlogging built a less complex root-microbial network than non-waterlogging. These findings implied that sugar beets subjected to waterlogging stress were enriched with beneficial microorganisms in the rhizosphere, potentially alleviating the stress.

Comparative Genomics and Physiological Investigations Supported Multifaceted Plant Growth-Promoting Activities in Two Hypericum perforatum L.-Associated Plant Growth-Promoting Rhizobacteria for Microbe-Assisted Cultivation

Plants are no longer considered standalone entities; instead, they harbor a diverse community of plant growth-promoting rhizobacteria (PGPR) that aid them in nutrient acquisition and can also deliver resilience. Host plants recognize PGPR in a strain-specific manner; therefore, introducing untargeted PGPR might produce unsatisfactory crop yields. Consequently, to develop a microbe-assisted Hypericum perforatum L. cultivation technique, 31 rhizobacteria were isolated from the plant's high-altitude Indian western Himalayan natural habitat and in vitro characterized for multiple plant growth-promoting attributes. Among 31 rhizobacterial isolates, 26 produced 0.59 to 85.29 μg mL-1 indole-3-acetic acid and solubilized 15.77 to 71.43 μg mL-1 inorganic phosphate; 21 produced 63.12 to 99.92% siderophore units, and 15 exhibited 103.60 to 1,296.42 nmol α-ketobutyrate mg-1 protein h-1 1-aminocyclopropane-1-carboxylate deaminase (ACCD) activity. Based on superior plant growth-promoting attributes, eight statistically significant multifarious PGPR were further evaluated for an in planta plant growth-promotion assay under poly greenhouse conditions. Plants treated with Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18 showed, by significant amounts, the highest photosynthetic pigments and performance, eventually leading to the highest biomass accumulation. Comparative genome analysis and comprehensive genome mining unraveled their unique genetic features, such as adaptation to the host plant's immune system and specialized metabolites. Moreover, the strains harbor several functional genes regulating direct and indirect plant growth-promotion mechanisms through nutrient acquisition, phytohormone production, and stress alleviation. In essence, the current study endorsed strains HypNH10 and HypNH18 as cogent candidates for microbe-assisted H. perforatum cultivation by highlighting their exclusive genomic signatures, which suggest their unison, compatibility, and multifaceted beneficial interactions with their host and support the excellent plant growth-promotion performance observed in the greenhouse trial. IMPORTANCE Hypericum perforatum L. (St. John's wort) herbal preparations are among the top-selling products to treat depression worldwide. A significant portion of the overall Hypericum supply is sourced through wild collection, prompting a rapid decline in their natural stands. Crop cultivation seems lucrative, although cultivable land and its existing rhizomicrobiome are well suited for traditional crops, and its sudden introduction can create soil microbiome dysbiosis. Also, the conventional plant domestication procedures with increased reliance on agrochemicals can reduce the diversity of the associated rhizomicrobiome and plants' ability to interact with plant growth-promoting microorganisms, leading to unsatisfactory crop production alongside harmful environmental effects. Cultivating H. perforatum with crop-associated beneficial rhizobacteria can reconcile such concerns. Based on a combinatorial in vitro, in vivo plant growth-promotion assay and in silico prediction of plant growth-promoting traits, here we recommend two H. perforatum-associated PGPR, Kosakonia cowanii HypNH10 and Rahnella variigena HypNH18, to extrapolate as functional bioinoculants for H. perforatum sustainable cultivation.

Autotoxic Ginsenoside Stress Induces Changes in Root Exudates to Recruit the Beneficial Burkholderia Strain B36 as Revealed by Transcriptomic and Metabolomic Approaches

Plants can recruit beneficial microbes to help improve their fitness under abiotic or biotic stress. Our previous studies found that Panax notoginseng could enrich beneficial Burkholderia sp. B36 in the rhizosphere soil under autotoxic ginsenoside stress. Here, we clarified that ginsenoside stress activated the phenylpropanoid biosynthesis and α-linolenic acid metabolism pathways of roots to increase the secretion of cinnamic acid, 2-dodecenoic acid, and 12-oxo-phytodienoic acid. These metabolites could promote the growth of B36. Importantly, cinnamic acid could simultaneously promote the chemotaxis and growth of B36, enhance the colonization of B36 in the rhizosphere, and eventually increase the survival rate of P. notoginseng. Overall, the plants could promote the growth and colonization of beneficial bacteria through key metabolites in root exudates under autotoxin stress. This finding will facilitate the practical application of beneficial bacteria in agricultural production and lead to successful and reproducible biocontrol efficacy by the exogenous addition of key metabolites.

Foliar Pathogen Infection Manipulates Soil Health through Root Exudate-Modified Rhizosphere Microbiome

Negative plant-soil feedback (NPSF) due to the buildup of soilborne pathogens in soil is a major obstacle in sustainable agricultural systems. Beneficial rhizosphere microfloras are recruited by plants, and mediating this has become a strategic priority to manipulate plant health. Here, we found that foliar infection of Panax notoginseng by Alternaria panax changed plant-soil feedback from negative to positive. Foliar infection modified the rhizosphere soil microbial community and reversed the direction of the buildup of the soilborne pathogen Ilyonectria destructans and beneficial microbes, including Trichoderma, Bacillus, and Streptomyces, in rhizosphere soil. These beneficial microbes not only showed antagonistic ability against the pathogen I. destructans but also enhanced the resistance of plants to A. panax. Foliar infection enhanced the exudation of short- and long-chain organic acids, sugars, and amino acids from roots. In vitro and in vivo experiments validated that short- and long-chain organic acids and sugars play dual roles in simultaneously suppressing pathogens but enriching beneficial microbes. In summary, foliar infection could change root secretion to drive shifts in the rhizosphere microbial community to enhance soil health, providing a new strategy to alleviate belowground disease in plants through aboveground inducement. IMPORTANCE Belowground soilborne disease is the main factor limiting sustainable agricultural production and is difficult to manage due to the complexity of the soil environment. Here, we found that aboveground parts of plants infected by foliar pathogens could enhance the secretion of organic acids, sugars, and amino acids in root exudates to suppress soilborne pathogens and enrich beneficial microbes, eventually changing the plant and soil feedback from negative to positive and alleviating belowground soilborne disease. This is an exciting strategy by which to achieve belowground soilborne disease management by manipulating the aboveground state through aboveground stimulation.

Microbiota Modulation in Blueberry Rhizosphere by Biocontrol Bacteria

Microbial interactions in agricultural soils can play important roles in the control of soil-borne phytopathogenic diseases. Yields from blueberry plantations from southern Spain have been impacted by the pathogenic fungus, Macrophomina phaseolina. The use of chemical fungicides has been the common method for preventing fungal infections, but due to their high environmental impact, legislation is increasingly restricting its use. Biocontrol alternatives based on the use of microorganisms is becoming increasingly important. Using the metabarcoding technique, fungi and bacteria were characterized (via 16S and ITS regions, respectively) from rhizosphere soils of healthy and dead blueberry plants infected by M. phaseolina, and which had undergone three different treatments: two biocontrol strategies—one of them a mix of Pseudomonas aeruginosa and Bacillus velezensis and the other one with Bacillus amyloliquefaciens—and a third treatment consisting of the application of a nutrient solution. The treatments produced changes in the bacterial microbiota and, to a lesser extent, in the fungi. The abundance of Fusarium was correlated with dead plants, likely favoring the infection by M. phaseolina. The presence of other microorganisms in the soil, such as the fungi Archaeorhizomyces or the bacteria Actinospica, were correlated with healthy plants and could promote their survival. The different genera detected between dead and healthy plants opens the possibility of studying new targets that can act against infection and identify potential microorganisms that can be used in biocontrol strategies.

Changes and Correlation Between Physiological Characteristics of Rhododendron simsii and Soil Microbial Communities Under Heat Stress

The relationship between Rhododendron simsii and its soil microbial community under heat stress was not clear. In this study, the effects of heat stress on the physiological characteristics, soil physicochemical properties and soil microbial community structure of R. simsii were investigated. The experimental control (CK) was set as day/night (14/10 h) 25/20°C and experimental treatments were set as light heat stress (LHS) 35/30°C and high heat stress (HHS) 40/35°C. Our results showed that, compared with CK, LHS treatment significantly increased malondialdehyde, hydrogen peroxide, proline and soluble sugar contents, as well as catalase and peroxidase activities, while HHS treatment significantly increased ascorbate peroxidase activity and decreased chlorophyll content. Compared with CK, LHS treatment significantly reduced soil ammonium-nitrogen and nitrate-nitrogen content, while HHS significantly increased soil ammonium-nitrogen content. Compared with CK, both treatments changed the soil microbial community structure. For bacterial community, LHS and HHS treatment resulting in the significant enrichment of Burkholderia-Caballeronia-Paraburkholderia and Occallatibacte, respectively. For fungal community, LHS treatment resulting in the significant enrichment of Candida, Mortierella and Boothiomyces. The redundancy analysis showed that plant physiological characteristics, soil ammonium-nitrogen content were significantly correlated with the soil microbial community. Therefore, heat stress altered the soil microbial community structure, and affected the availability of soil available nitrogen, which in turn affected the physiological characteristics of R. simsii. We suggest that soil microbial community may play an important role in plant resistance to heat stress, and its mechanism deserves further study.

Multiomics Reveals the Effect of Root Rot on Polygonati Rhizome and Identifies Pathogens and Biocontrol Strain

Root (rhizome) rot of Polygonatum plants has received substantial attention because it threatens yield and sustainable utilization in the polygonati rhizome industry. However, the potential pathogens that cause rhizome rot as well as the direct and indirect (via root-associated microbes) strategies by which Polygonatum defends against pathogens remain largely unknown. Herein, we used integrated multiomics of plant-targeted metabolomics and transcriptomics, microbiome, and culture-based methods to systematically investigate the interactions between the Polygonatum cyrtonema Hua root-associated microbiota and pathogens. We found that root rot inhibited P. cyrtonema rhizome growth and that the fresh weight significantly decreased (P < 0.001). The transcriptomic and metabonomic results showed that the expression of differentially expressed genes (DEGs) related to specialized metabolic and systemic resistance pathways, such as glycolysis/gluconeogenesis and flavonoid biosynthesis, cycloartenol synthase activity (related to saponin synthesis), mitogen-activated protein kinase (MAPK) signaling, and plant hormone signal transduction, was particularly increased in diseased rhizomes. Consistently, the contents of lactose, d-fructose, sarsasapogenin, asperulosidic acid, botulin, myricadoil, and other saponins, which are functional medicinal compounds present in P. cyrtonema rhizomes, were also increased in diseased plants infected with rhizome rot. The microbiome sequencing and culture results showed that root rot disrupted the P. cyrtonema bacterial and fungal communities and reduced the microbial diversity in the rhizomes and rhizosphere soil. We further found that a clear enrichment of Streptomyces violascens XTBG45 (HJB-XTBG45) in the healthy rhizosphere could control the root rot caused by Fusarium oxysporum and Colletotrichum spaethianum. Taken together, our results indicate that P. cyrtonema can modulate the plant immune system and metabolic processes and enrich beneficial root microbiota to defend against pathogens. IMPORTANCE Root (rhizome or tuber) reproduction is the main method for the agricultural cultivation of many important cash crops, and infected crop plants rot, exhibit retarded growth, and experience yield losses. While many studies have investigated medicinal plants and their functional medicinal compounds, the occurrence of root (rhizome) rot of plant and soil microbiota has received little attention. Therefore, we used integrated multiomics and culture-based methods to systematically study rhizome rot on the famous Chinese medicine Polygonatum cyrtonema and identify pathogens and beneficial microbiota of rhizome rot. Rhizome rot disrupted the Polygonatum-associated microbiota and reduced microbial diversity, and rhizome transcription and metabolic processes significantly changed. Our work provides evidence that rhizome rot not only changes rhizome transcription and functional metabolite contents but also impacts the microbial community diversity, assembly, and function of the rhizome and rhizosphere. This study provides a new friendly strategy for medicinal plant breeding and agricultural utilization.