Rhizosphere Microbiome Research Articles

The Role of Phosphate-Solubilizing Microbial Interactions in Phosphorus Activation and Utilization in Plant-Soil Systems: A Review.

To address the issue of phosphorus limitation in agricultural and forestry production and to identify green and economical alternatives to chemical phosphorus fertilizers, this paper reviews the utilization of phosphorus in plant-soil systems and explores the considerable potential for exploiting endogenous phosphorus resources. The application of phosphate-solubilizing microorganisms (PSMs) is emphasized for their role in phosphorus activation and plant growth promotion. A focus is placed on microbial interactions as an entry point to regulate the functional rhizosphere microbiome, introducing the concept of synthetic communities. This approach aims to deepen the understanding of PSM interactions across plant root, soil, and microbial interfaces, providing a theoretical foundation for the development and application of biological regulation technologies to enhance phosphorus utilization efficiency.

Paenibacillus polymyxa J2-4 induces cucumber to enrich rhizospheric Pseudomonas and contributes to Meloidogyne incognita management under field conditions.

Root knot nematodes (RKNs) pose a great threat to agricultural production worldwide. The bacterial nematocides have received increasing attention due to their safe and efficient control against RKNs. Here, we investigated the biocontrol efficacy of Paenibacillus polymyxa J2-4 against Meloidogyne incognita in the field and analyzed the rhizosphere microbiome of cucumber under nematode infection after application of the J2-4 strain. Furthermore, a biomarker strain of Pseudomonas spp. was isolated from the J2-4-inoculated rhizosphere soil, and its nematocidal activity and growth-promoting effect on host plants were determined. In addition, chemotaxis assay of P. fluroescens ZJ5 toward root exudates was carried out. The field experiment demonstrated that P. polymyxa J2-4 could effectively suppressed gall formation in cucumber plants, with the galling index reduced by 67.63% in 2022 and 65.50% in 2023, respectively, compared with controls. Meanwhile, plant height and yield were significantly increased in J2-4 treated plants compared with controls. Metagenomic analysis indicated that J2-4 altered the rhizosphere microbial communities. The relative abundance of Pseudomonas spp. was notably enhanced in the J2-4 group, which was consistent with Linear discriminant analysis Effect Size results that Pseudomonas was determined as one of the biomarkers in the J2-4 group. Furthermore, the ZJ5 strain, one of the biomarker Pseudomonas strains, was isolated from the J2-4-inoculated rhizosphere soil and was identified as Pseudomonas fluorescens. In addition, P. fluorescens ZJ5 exhibited high nematicidal activity in vitro and in vivo, with 99.20% of the mortality rate of M. incognita at 24 h and 69.75% of gall index reduction. The biocontrol efficiency of the synthetic community of ZJ5 plus J2-4 was superior to that of any other single bacteria against M. incognita. Additionally, ZJ5 exhibited great chemotaxis ability toward root exudates inoculated with J2-4. Paenibacillus polymyxa J2-4 has good potential in the biological control against M. incognita under field conditions. Enrichment of the beneficial bacteria Pseudomonas fluorescens ZJ5 in the J2-4-inoculated rhizosphere soil contributes to M. incognita management. © 2024 Society of Chemical Industry.

Features of the isolation of yeast from the root microbiome of winter wheat (Triticum aestivum L.)

Aim. Development of approaches for isolating yeast symbionts from the rhizosphere of various varieties of winter wheat for their further taxonomic identification, as well as studying the influence of yeast species on the growth and development of wheat plants. Methods. Isolation and identification of yeast from the root microbiome of selected wheat varieties was carried out using microbiological and microscopic research methods. Results. As a result of the investigation, conditions were selected, isolation and primary identification of yeast from the root microbiome of winter wheat varieties in different growing periods was carried out. The following yeast species were identified: Saccharomyces serevisiae, Hanseniaspora uvarum, Papiliotrema terrestris, Pichia fementans, Candida subhashii, Torulaspora delbruecki and Candida sp. Conclusions. The difference in the species composition of yeast-symbionts in different periods of development of winter wheat varieties Lisova Pisnya, Pereyaslivka, Bohdana, Smuglyanka, Podolyanka, Kolonia, Reform and Rebel was noted. The obtained data emphasize the importance of studying the rhizosphere microbiome, in particular the functional role of yeast, for understanding the mechanisms of interaction between the plant and the soil, as well as for the development of effective agronomic strategies in the cultivation of wheat and other crops.

Harnessing Belowground Interaction: Re-analyzing the Role of Rhizosphere Microbiome in Plant–Pathogen Interaction Under Water Stress

Harnessing Belowground Interaction: Re-analyzing the Role of Rhizosphere Microbiome in Plant–Pathogen Interaction Under Water Stress

Changes in enzyme activity, structure and growth strategies of the rhizosphere microbiome influenced by elevated temperature and CO2

The impacts of global warming and increased CO2 levels on soil processes and crop growth are concerning. Soil enzymes in the rhizosphere, produced mainly by microbes, play a vital role in nutrients mobilization for plants. Nevertheless, a comprehensive understanding of how microbial communities in the rhizosphere respond to increased temperatures and CO2 levels, particularly in relation to nutrient acquisition, is still lacking. Addressing this problem, we grew soybeans under elevated temperature (ET, +2 °C) and CO2 levels (eCO2, +300 ppm), both individually and in combination (eCO2 + eT), in rhizobox mesocosms. Enzyme activity and microbial communities in soybean rhizospheres were investigated using soil zymography. eCO2 increased enzyme activity by 2.5 % to 8.7 %, while eT expanded the hotspot area from 1.8 % to 3.3 %. The combined factors amplified both the hotspot area by 5.3 % to 10.1 % and enzyme activity by 35.4 % to 67.3 %. Compared to ambient conditions, rhizosphere communities under eCO2 were predominantly comprised of r-strategist keystone taxa, including Acidobacteria, Proteobacteria, and Ascomycota. On the contrary, eT induced a shift in the microbial community towards K-selected taxa, characterized by an increased relative abundance of Basidiomycota and Actinobacteria. Furthermore, the combination of eCO2 and eT led to an increase in the relative abundance of key bacterial species (Acidobacteria, Proteobacteria, and Actinobacteria) as well as fungi (Ascomycota and Basidiomycota). These findings indicate the potential significance of enzyme hotspots in modulating responses to climate change. Changes in enzyme activity and hotspot area could indicate the alteration in microbial growth strategies. The treatments exhibited distinct changes in the composition of microbial communities, in network organization, and in the proportion of species designated as r or K-strategists. Overall, these findings highlight the combined effects of global change factors on bacterial and fungal communities, providing insights into their growth strategies and nutrient mobilization under climate change scenarios.

Optimal Irrigation and Fertilization Enhanced Tomato Yield and Water and Nitrogen Productivities by Increasing Rhizosphere Microbial Nitrogen Fixation

Irrigation and nitrogen application rates have significant effects on greenhouse tomato yields, as well as water and nitrogen use efficiencies, but little is known regarding how these rates affect plant–microbiome interactions and how the associated changes might impact tomato yields. In this greenhouse study conducted over two years, the effects of three irrigation levels (moderate deficit with 65–75% water holding capacity threshold, slight deficit with 75–85%, and sufficient irrigation with 85–95%) and four nitrogen application levels (60, 120, 240, and 360 kg ha−1) on tomato growth, yield, water and nitrogen productivities, and rhizosphere microbial diversities and functions were investigated. The results demonstrated that the highest tomato leaf area, dry biomass, yield, and water and nitrogen productivities were obtained under the treatment with sufficient irrigation. With increasing nitrogen application, the tomato leaf area, dry biomass, yield, and water and nitrogen productivities showed a trend of first increasing and then decreasing. Overall, the treatment (N2W3) with sufficient irrigation and 240 kg ha−1 N was associated with the highest tomato growth, yield, and water and nitrogen productivities. Moreover, optimal irrigation and nitrogen application obviously altered the structures of rhizosphere bacterial and fungal communities, particularly recruiting microbiota conferring benefits to tomato growth and nitrogen fixation—namely, Lysobacter and Bradyrhizobium. Ultimately, optimal irrigation and nitrogen application significantly increased the relative abundances of functions related to carbon, sulfur, and nitrogen metabolism, especially nitrogen fixation. In summary, optimal irrigation and fertilization enhanced tomato yield, as well as water and nitrogen productivities by increasing the nitrogen fixation functions of the rhizosphere microbiome. Our results provide significant implications for tomato cultivation in greenhouses, in terms of optimized irrigation and fertilization.

Biological Decline of Alfalfa Is Accompanied by Negative Succession of Rhizosphere Soil Microbial Communities.

The growth and biological decline of alfalfa may be linked to the rhizosphere microbiome. However, plant-microbe interactions in the rhizosphere of alfalfa and associated microbial community variations with stand age remain elusive. This study explored the successional pattern of rhizosphere microbial communities across different aged alfalfa stands and its relationship with alfalfa decline. Rhizosphere soils were collected from 2- and 6-year-old alfalfa stands. Control soils were collected from interspaces between alfalfa plants in the same stands. Soil bacterial and fungal communities were characterized by 16S and ITS rRNA gene sequencing, respectively. Specific microbial taxa colonized the rhizosphere soils, but not the control soils. The rhizosphere-specific taxa mainly included potentially beneficial genera (e.g., Dechloromonas, Verrucomicrobium) in the young stand and harmful genera (e.g., Peziza, Campylocarpon) in the old stand. Alfalfa roots regulated soil microbial communities by selective promotion or inhibition of distinct taxa. The majority of time-enriched taxa were reported as harmful fungi, whose relative abundances were negatively correlated with plant traits. Time-depleted taxa were mostly known as beneficial bacteria, which had relative abundances positively correlated with plant traits. The relative abundances of functional bacterial genes associated with vancomycin biosynthesis, zeatin biosynthesis, and amino acid metabolism trended lower in rhizosphere soils from the old stand. An upward trend was observed for fungal pathogens and wood saprotrophs with increasing stand age. The results suggest that root activity drives the negative succession of rhizosphere microbial communities during alfalfa decline in old stands.

Auxin-Mediated Modulation of Maize Rhizosphere Microbiome: Insights from Azospirillum Inoculation and Indole-3-Acetic Acid Treatment

Auxin-Mediated Modulation of Maize Rhizosphere Microbiome: Insights from Azospirillum Inoculation and Indole-3-Acetic Acid Treatment

Dry season irrigation promotes nutrient cycling by reorganizing Eucalyptus rhizosphere microbiome

In southern China, seasonal droughts and low soil phosphorus content constrain the productivity of Eucalyptus trees. To understand the rhizosphere microbiome response to the dry season, metagenomic sequencing analysis was used to investigate the 6-year-old Eucalyptus rhizosphere microbiome under four different irrigation and fertilization treatments. The results showed that irrigation and fertilization during the dry season significantly altered the composition of microbiome in the rhizosphere soil of Eucalyptus plantations. The soil physicochemical properties and enzyme activity explained 30.73 % and 29.75 % of the changes in bacterial and fungal community structure in Eucalyptus rhizosphere soil, respectively. Irrigation and fertilization during the dry season significantly altered the physicochemical properties of rhizosphere soil. Compared with the seasonal drought without fertilizer treatment (CK), the dry season irrigation with fertilizer treatment (WF) significantly increased the content of total nitrogen (46.34 %), available nitrogen (37.72 %), available phosphorus (440.9 %), and organic matter (35.34 %). Soil organic matter (OM), pH, and available phosphorus (AP) were key environmental factors influencing the microbial community composition. Moreover, irrigation and fertilization promoted carbon fixation and nitrogen and phosphorus mineralization, increasing soil OM content and the availability of inorganic nitrogen and phosphorus. Meanwhile, compared to the CK, the increase of acid phosphatase (16.81 %), invertase (146.89 %)and urease (59.45 %) in rhizosphere soil under irrigation (W) treatment further proves that dry season irrigation promote the soil carbon, nitrogen and phosphorus cycles. Irrigation and fertilization treatment alleviated the constraints of low phosphorus in southern China's soil, which promoted Eucalyptus productivity. In conclusion, we suggest implementing reasonable irrigation and fertilization strategies in the production practice of Eucalyptus and utilizing microbial resources to improve soil fertility and Eucalyptus productivity.

Responses of Brassica napus to soil cadmium under elevated CO2 concentration based on rhizosphere microbiome, root transcriptome and metabolome

Rising atmospheric carbon dioxide (CO2) and soil heavy metal pollution affect crop safety and production. Exposure to elevated CO2 (ECO2) increases cadmium (Cd) uptake in some crops like wheat and rice, however, it remains unclear how ECO2 affects Cd uptake by Brassica napus. Here, we investigated the responses of B. napus seedlings exposed to ECO2 and Cd through analyses of physiology, transcriptome, metabolome, and rhizosphere microbes. Compared with Cd-stress alone (Cd50_ACO2), ECO2 boosted the uptake of Cd by B. napus roots by 38.78% under coupled stresses (Cd50_ECO2). The biomass and leaf chlorophyll a content increased by 38.49% and 79.66% respectively in Cd50_ECO2 relative to Cd50_ACO2. Activities of superoxide dismutase (SOD) and peroxidase (POD) enhanced by 8.42% and 185.01%, respectively, while glutathione (GSH) and ascorbic acid (AsA) contents increased by 16.44% and 52.48%, and abundances of rhizosphere microbes changed significantly under coupled stresses (Cd50_ECO2) relative to Cd-stress alone (Cd50_ACO2). Also, the upregulation of glutathione, glutathione transferase genes, and heavy metal ATPase expression promoted the detoxification effect of rapeseed on Cd. Changes in the expression of transcription factors like MAPK, WRKY, BAK1 and PR1, as well as changes in metabolic pathways like β-alanine, may be involved in the regulatory mechanism of stress response. These findings provide new insights for studying the regulatory mechanism of rapeseed under ECO2 on soil Cd stress, and also provide a basis for further research on Cd tolerant rapeseed varieties in the future climate context.

Rhizosphere microbiomes derived from vermicompost alter gene expression and regulatory pathways in tomato (Solanum lycopersicum, L.).

The gut microbiome of worms from composting facilities potentially harbors organisms that are beneficial to plant growth and development. In this experiment, we sought to examine the potential impacts of rhizosphere microbiomes derived from Eisenia fetida worm castings (i.e. vermicompost) on tomato (Solanum lycopersicum, L.) plant growth and physiology. Our experiment consisted of a greenhouse trial lasting 17weeks total in which tomato plants were grown with one of three inoculant treatments: a microbial inoculant created from vermicompost (V), a microbial inoculant created from sterilized vermicompost (SV), and a no-compost control inoculant (C). We hypothesized that living microbiomes from the vermicompost inoculant treatment would enhance host plant growth and gene expression profiles compared to plants grown in sterile and control treatments. Our data showed that bacterial community composition was significantly altered in tomato rhizospheres, but fungal community composition was highly variable in each treatment. Plant phenotypes that were significantly enhanced in the vermicompost and sterile vermicompost treatments, compared to the control, included aboveground biomass and foliar δ15N nitrogen. RNA sequencing revealed distinct gene expression changes in the vermicompost treatment, including upregulation of nutrient transporter genes such as Solyc06g074995 (high affinity nitrate transporter), which exhibited a 250.2-fold increase in expression in the vermicompost treatment compared to both the sterile vermicompost and control treatments. The plant transcriptome data suggest that rhizosphere microbiomes derived from vermicompost can influence tomato gene expression and growth-related regulatory pathways, which highlights the value of RNA sequencing in uncovering molecular responses in plant microbiome studies.

Apple-Based Farming Systems Improve Production and Rhizosphere Microbiome in The North-West Himalayan Region's Dry Temperate Environment

Apple-Based Farming Systems Improve Production and Rhizosphere Microbiome in The North-West Himalayan Region's Dry Temperate Environment

Profiling sorghum-microbe interactions with a specialized photoaffinity probe identifies key sorgoleone binders in Acinetobacter pittii.

Interactions between plants and soil microbial communities that benefit plant growth and enhance nutrient acquisition are driven by the selective release of metabolites from plant roots, or root exudation. To investigate these plant-microbe interactions, we developed a photoaffinity probe based on sorgoleone (sorgoleone diazirine alkyne for photoaffinity labeling, SoDA-PAL), a hydrophobic secondary metabolite and allelochemical produced in Sorghum bicolor root exudates. We applied SoDA-PAL to the identification of sorgoleone-binding proteins in Acinetobacter pittii SO1, a potential plant growth-promoting microbe isolated from sorghum rhizosphere soil. Competitive photoaffinity labeling of A. pittii whole cell lysates with SoDA-PAL identified 137 statistically enriched proteins, including putative transporters, transcriptional regulators, and a subset of proteins with predicted enzymatic functions. We performed computational protein modeling and docking with sorgoleone to prioritize candidates for experimental validation and then confirmed binding of sorgoleone to four of these proteins in vitro: the α/β fold hydrolase SrgB (OH685_09420), a fumarylacetoacetase (OH685_02300), a lysophospholipase (OH685_14215), and an unannotated hypothetical protein (OH685_18625). Our application of this specialized sorgoleone-based probe coupled with structural bioinformatics streamlines the identification of microbial proteins involved in metabolite recognition, metabolism, and toxicity, widening our understanding of the range of cellular pathways that can be affected by a plant secondary metabolite.IMPORTANCEHere, we demonstrate that a photoaffinity-based chemical probe modeled after sorgoleone, an important secondary metabolite released by sorghum roots, can be used to identify microbial proteins that directly interact with sorgoleone. We applied this probe to the sorghum-associated bacterium Acinetobacter pittii and showed that probe labeling is dose-dependent and sensitive to competition with purified sorgoleone. Coupling the probe with proteomics and computational analysis facilitated the identification of putative sorgoleone binders, including a protein implicated in a conserved pathway essential for sorgoleone catabolism. We anticipate that discoveries seeded by this workflow will expand our understanding of the molecular mechanisms by which specific metabolites in root exudates shape the sorghum rhizosphere microbiome.

Exploring microbial diversity in the rhizosphere: a comprehensive review of metagenomic approaches and their applications.

The rhizosphere, the soil region influenced by plant roots, represents a dynamic microenvironment where intricate interactions between plants and microorganisms shape soil health, nutrient cycling, and plant growth. Soil microorganisms are integral players in the transformation of materials, the dynamics of energy flows, and the intricate cycles of biogeochemistry. Considerable research has been dedicated to investigating the abundance, diversity, and intricacies of interactions among different microbes, as well as the relationships between plants and microbes present in the rhizosphere. Metagenomics, a powerful suite of techniques, has emerged as a transformative tool for dissecting the genetic repertoire of complex microbial communities inhabiting the rhizosphere. The review systematically navigates through various metagenomic approaches, ranging from shotgun metagenomics, enabling unbiased analysis of entire microbial genomes, to targeted sequencing of the 16S rRNA gene for taxonomic profiling. Each approach's strengths and limitations are critically evaluated, providing researchers with a nuanced understanding of their applicability in different research contexts. A central focus of the review lies in the practical applications of rhizosphere metagenomics in various fields including agriculture. By decoding the genomic content of rhizospheric microbes, researchers gain insights into their functional roles in nutrient acquisition, disease suppression, and overall plant health. The review also addresses the broader implications of metagenomic studies in advancing our understanding of microbial diversity and community dynamics in the rhizosphere. It serves as a comprehensive guide for researchers, agronomists, and policymakers, offering a roadmap for harnessing metagenomic approaches to unlock the full potential of the rhizosphere microbiome in promoting sustainable agriculture.

Diversification of crops and intensification of canola impact the diversity, community structure, and productivity in successive crop systems: A study on arbuscular mycorrhizal fungal communities in roots and rhizosphere

The widespread cultivation of canola, conventionally still considered a non-host plant for AM fungi, coupled with its increasing frequency in crop rotations, raises concerns about its impacts on soil microbial diversity and overall crop productivity. The main objective of this study is to assess the influence of different crop succession systems, incorporating canola, on AM fungal diversity and community structure in both the roots and in the rhizosphere, as well as on productivity of each crop present within the succession. Doubling the frequency of canola occurrence in a 4-year crop succession did not reduce the productivity of the other crops in the succession, nor did it result in a decrease in AM fungal biodiversity in the roots or rhizosphere of these crops. Interestingly, the diversity of AM fungi was higher in canola roots compared to wheat roots, indicating that canola might serve as a rudimentary host of AM fungi. The succession systems did, however, alter the AM fungal community structure in both roots and rhizosphere environments, exhibiting positive or negative correlations with crop productivity. This suggests that a simple modification of the cropping system could potentially be employed to manipulate root or rhizosphere microbiomes. Results of this study add to the growing body of evidences that plants that were thought to be non-AM fungi host, such as plants from the Brassicaceae family, could in fact interact with AM fungi.

Effect of Organic and Chemical Fertilizer on the Diversity of Rhizosphere and Leaf Microbial Composition in Sunflower Plant.

Applying organic manure to crops positively impacts the soil microbial community which is negatively impacted when chemical fertilizers are used. Organic manures also add new microbes to the soil in addition to influencing the growth of native ones. Metagenomic analysis of different organic manures, soil, and pot culture experiments conducted under various fertilizer conditions constitute the primary methodologies employed in this study. We compared the effect of two organic manure combinations and an inorganic fertilizer combination on microbial community of rhizosphere soil and leaves of sunflower plants. Metagenomic sequencing data analysis revealed that the diversity of bacteria and fungi is higher in organic manure than in chemical fertilizers. Each organic manure combination selectively increased population of some specific microbes and supported new microbes. Application of chemical fertilizer hurts many plant beneficial fungi and bacteria. In summary, our study points out the superiority of organic manure combinations in enhancing microbial diversity and supporting beneficial microbes. These findings enhance the profound influence of fertilizer types on sunflower microbial communities, shedding light on the intricate dynamics within the rhizosphere and leaf microbiome. Bacterial genera such as Bacillus, Serratia, Sphingomonas, Pseudomonas, Methylobacterium, Acinetobacter, Stenotrophomonas, and fungal genera such as Wallemia, Aspergillus, Cladosporium, and Penicillium constitute the key microbes of sunflower plants.

Genes to specialized metabolites: accumulation of scopoletin, umbelliferone and their glycosides in natural populations of Arabidopsis thaliana

BackgroundScopoletin and umbelliferone belong to coumarins, which are plant specialized metabolites with potent and wide biological activities, the accumulation of which is induced by various environmental stresses. Coumarins have been detected in various plant species, including medicinal plants and the model organism Arabidopsis thaliana. In recent years, key role of coumarins in maintaining iron (Fe) homeostasis in plants has been demonstrated, as well as their significant impact on the rhizosphere microbiome through exudates secreted into the soil environment. Several mechanisms underlying these processes require clarification. Previously, we demonstrated that Arabidopsis is an excellent model for studying genetic variation and molecular basis of coumarin accumulation in plants.ResultsHere, through targeted metabolic profiling and gene expression analysis, the gene-metabolite network of scopoletin and umbelliferone accumulation was examined in more detail in selected Arabidopsis accessions (Col-0, Est-1, Tsu-1) undergoing different culture conditions and characterized by variation in coumarin content. The highest accumulation of coumarins was detected in roots grown in vitro liquid culture. The expression of 10 phenylpropanoid genes (4CL1, 4CL2, 4CL3, CCoAOMT1, C3’H, HCT, F6’H1, F6’H2,CCR1 and CCR2) was assessed by qPCR in three genetic backgrounds, cultured in vitro and in soil, and in two types of tissues (leaves and roots). We not only detected the expected variability in gene expression and coumarin accumulation among Arabidopsis accessions, but also found interesting polymorphisms in the coding sequences of the selected genes through in silico analysis and resequencing.ConclusionsTo the best of our knowledge, this is the first study comparing accumulation of simple coumarins and expression of phenylpropanoid-related genes in Arabidopsis accessions grown in soil and in liquid cultures. The large variations we detected in the content of coumarins and gene expression are genetically determined, but also tissue and culture dependent. It is particularly important considering that growing plants in liquid media is a widely used technology that provides a large amount of root tissue suitable for metabolomics. Research on differential accumulation of coumarins and related gene expression will be useful in future studies aimed at better understanding the physiological role of coumarins in roots and the surrounding environments.

Plant growth-promoting rhizobacteria enhance active ingredient accumulation in medicinal plants at elevated CO2 and are associated with indigenous microbiome.

Plant growth-promoting rhizobacteria (PGPR) and elevated CO2 (eCO2) have demonstrated their individual potential to enhance plant yield and quality through close interaction with rhizosphere microorganisms and plant growth. However, the efficacy of PGPR under eCO2 on rhizosphere microbiome and, ultimately, plant yield and active ingredient accumulation are not yet fully understood. This study investigated how the medicinal plant Pseudostellaria heterophylla (P. heterophylla) and its rhizosphere microbes respond to PGPR (Bacillus subtilis and Pseudomonas fluorescens) at eCO2 (1,000 ppm). It was found that the yield and active ingredient polysaccharides accumulation in the tuber of P. heterophylla were significantly increased by 38 and 253%, respectively. This promotion has been associated with increased root development and changes in the indigenous microbial community. Metagenomics analysis revealed a significant reduction in pathogenic Fusarium abundance in the rhizosphere. Potential biocontrol bacteria Actinobacteria and Proteobacteria were enriched, especially the genera Bradyrhizobium and Rhodanobacter. The reshaping of the rhizosphere microbiome was accompanied by the upregulation of biological pathways related to metabolite biosynthesis in the rhizosphere. These modifications were related to the promotion of the growth and productivity of P. heterophylla. Our findings highlighted the significant role played by PGPR in medicinal plant yield and active ingredient accumulation when exposed to eCO2.

Rhizosphere Microbiome Co-Occurrence Network Analysis across a Tomato Domestication Gradient.

When plant-available phosphorus (P) is lost from a soil solution, it often accumulates in the soil as a pool of unavailable legacy P. To acquire legacy P, plants employ recovery strategies, such as forming associations with soil microbes. However, the degree to which plants rely on microbial associations for this purpose varies with crop domestication and subsequent breeding. Here, by generating microbial co-occurrence networks, we sought to explore rhizosphere bacterial interactions in low-P conditions and how they change with tomato domestication and breeding. We grew wild tomato, traditional tomato (developed circa 1900), and modern tomato (developed circa 2020) in high-P and low-P soil throughout their vegetative developmental stage. Co-occurrence network analysis revealed that as the tomatoes progressed along the stages of domestication, the rhizosphere microbiome increased in complexity in a P deficit. However, with the addition of P fertilizer, the wild tomato group became more complex, surpassing the complexity of traditional and modern tomato, suggesting a high degree of responsiveness in the rhizosphere microbiome to P fertilizer by wild tomato relatives. By illustrating these changing patterns of network complexity in the tomato rhizosphere microbiome, we can further understand how plant domestication and breeding have shaped plant-microbe interactions.

Metabolism of isodecyl diphenyl phosphate in rice and microbiome system: Differential metabolic pathways and underlying mechanisms

Isodecyl diphenyl phosphate (IDDP) is among the emerging aromatic organophosphate esters (aryl-OPEs) that pose risks to both human beings and other organisms. This study aims to investigate the translocation and biotransformation behavior of IDDP in rice and the rhizosphere microbiome through hydroponic exposure (the duration of hydroponic exposure was 10 days). The rhizosphere microbiome 9-FY was found to efficiently eliminate IDDP, thereby reducing its uptake in rice tissues and mitigating the negative impact of IDDP on rice growth. Furthermore, this study proposed the first-ever transformation pathways of IDDP, identifying hydrolysis, hydroxylation, methylation, methoxylation, carboxylation, and glucuronidation products. Notably, the methylation and glycosylation pathways were exclusively observed in rice, indicating that the transformation of IDDP in rice may be more complex than in microbiome 9-FY. Additionally, the presence of the product COOH-IDDP in rice suggested that there might be an exchange of degradation products between rice and rhizobacteria, implying their potential interaction. This finding highlights the significance of rhizobacteria's role which cannot be overlooked in the accumulation and transformation of organic pollutants in grain crops. The study revealed active members in 9-FY during IDDP degradation, and metagenomic analysis indicated that most of the active populations contained IDDP-degrading genes. Moreover, transcriptome sequencing showed that cytochrome P450, acid phosphatase, glucosyltransferase, and methyltransferases genes in rice were up-regulated, which was further confirmed by RT-qPCR. This provides insight into the intermediate products identified in rice, such as hydrolysis, hydroxylated, glycosylated, and methylated products. These results significantly contribute to our understanding of the translocation and transformation of organophosphate esters (OPEs) in plants and the rhizosphere microbiome, and reveal the fate of OPEs in rice and microbiome system to ensure the paddy yield and rice safety.