Rhizosphere Microbial Communities Research Articles

Trichoderma harzianum prevents red kidney bean root rot by increasing plant antioxidant enzyme activity and regulating the rhizosphere microbial community.

Root rot is one of the main reasons for yield losses of red kidney bean (Phaseolus vulgaris) production. Pre-inoculation with Trichoderma harzianum can effectively lower the incidence of red kidney bean root rot. In this study, four treatments including CK (control), Fu13 (Fusarium oxysporum), T891 (T. harzianum) and T891 + Fu13 (T. harzianum + F. oxysporum) were arranged in a pot experiment to investigate how T891 affected the incidence and severity of root rot, plant growth, and changes of defense enzyme activity in red kidney bean plants. Community composition and diversity of the rhizosphere microbiota was evaluated through high-throughput sequencing, and co-occurrence network was analyzed. The results showed that when compared to the Fu13 treatment, pre-inoculation with T891 reduced the incidence and severity of red kidney bean root rot by 40.62 and 68.03% (p < 0.05), increased the root length, shoot length, total dry biomass by 48.63, 97.72, 122.17%. Upregulated activity of super-oxide dismutase (SOD), peroxidase (POD), catalase (CAT) by 7.32, 38.48, 98.31% (p < 0.05), and reduced malondialdehyde (MDA) by 23.70% (p < 0.05), respectively. Microbiological analyses also showed that F. oxysporum reduced alpha diversity resulting in alteration the composition of the rhizosphere microbial community in red kidney bean. T891 significantly reduced abundance of F. oxysporum, allowing the enrichment of potentially beneficial bacteria Porphyrobacter (ASV 46), Lysobacter (ASV 85), Microbacteriaceae (ASV 105), and Gemmatimonas (ASV 107), resulting in a more stable structure of the microbial network. The results of random forest analysis further revealed that ASV 46 (Porphyrobacter) was the primary influencing factor for the incidence of root rot after inoculation with T891, while ASV 85 (Lysobacter) was the primary influencing factor for the biomass of red kidney bean. In conclusion, T. harzianum promotes the growth of red kidney bean and inhibits root rot by improving plant antioxidant enzyme activity and regulating the rhizosphere microbial community.

Magnesium oxide nanoparticles reduce clubroot by regulating plant defense response and rhizosphere microbial community of tumorous stem mustard (Brassica juncea var. tumida).

Clubroot, caused by Plasmodiophora brassicae, is a major disease that significantly impairs the yield of cruciferous crops and causes significant economic losses across the globe. The prevention of clubroot, especially in tumorous stem mustard (without resistant varieties), are is limited and primarily relies on fungicides. Engineered nanoparticles have opened up new avenues for the management of plant diseases, but there is no report on their application in the prevention of clubroot. The results showed that the control efficacy of 500 mg/L MgO NPs against clubroot was 54.92%. However, when the concentration was increased to 1,500 and 2,500 mg/L, there was no significant change in the control effect. Compared with CK, the average fresh and dry weight of the aerial part of plants treated with MgO NPs increased by 392.83 and 240.81%, respectively. Compared with the F1000 treatment, increases were observed in the content of soil available phosphorus (+16.72%), potassium (+9.82%), exchangeable magnesium (+24.20%), and water-soluble magnesium (+20.64%) in the 1,500 mg/L MgO NPs treatment. The enzyme-linked immune sorbent assay (ELISA) results showed that the application of MgO NPs significantly increased soil peroxidase (POD, +52.69%), alkaline protease (AP, +41.21%), alkaline phosphatase (ALP, +79.26%), urease (+52.69%), and sucrase (+56.88%) activities; And also increased plant L-phenylalanine ammonla-lyase (PAL, +70.49%), polyphenol oxidase (PPO, +36.77%), POD (+38.30%), guaiacol peroxidase (POX, +55.46%) activities and salicylic acid (SA, +59.86%) content. However, soil and plant catalase (CAT, -27.22 and - 19.89%, respectively), and plant super oxidase dismutase (SOD, -36.33%) activities were significantly decreased after the application of MgO NPs. The metagenomic sequencing analysis showed that the MgO NPs treatments significantly improved the α-diversity of the rhizosphere soil microbial community. The relative abundance of beneficial bacteria genera in the rhizosphere soil, including Pseudomonas, Sphingopyxis, Acidovorax, Variovorax, and Bosea, was significantly increased. Soil metabolic functions, such as oxidative phosphorylation (ko00190), carbon fixation pathways in prokaryotes (ko00720), indole alkaloid biosynthesis (ko00901), and biosynthesis of various antibiotics (ko00998) were significantly enriched. These results suggested that MgO NPs might control clubroot by promoting the transformation and utilization of soil nutrients, stimulating plant defense responses, and enriching soil beneficial bacteria.

Response of antioxidant activity, active constituent and rhizosphere microorganisms of Salvia miltiorrhiza to combined application of microbial inoculant, microalgae and biochar under Cu stress

Salvia miltiorrhiza, a widely used medicinal herb renowned for its properties in promoting blood circulation, removing blood stasis and alleviating pain, is currently facing quality degradation due to excessive heavy metal levels, posing a threat to medication safety. In order to investigate the effects of microbial inoculant, microalgae and biochar on the growth of Salvia miltiorrhiza under copper (Cu) stress, as well as its Cu absorption, antioxidant activity, active component contents and rhizosphere microbial community, a pot experiment was conducted. Salvia miltiorrhiza plants were cultivated in the soil containing 400 mg/kg of Cu for six months and treated with microbial inoculant, microalgae and biochar, either individually or in combination. Almost all soil amendment treatments led to an increase in root biomass. Notably, co-application of microbial inoculant and microalgae had the optimal effect with a 63.07 % increase compared to the group treated solely with Cu. Moreover, when microbial inoculant was applied alone or in combination with microalgae, the Cu content in plant roots was reduced by 19.29 % and 25.37 %, respectively, whereas other treatments failed to show a decreasing trend. Intriguingly, Cu stress increased the active component contents in plant roots, and they could also be enhanced beyond non-stress levels when microbial inoculant and microalgae were applied together or in combination with biochar. Analyses of plant antioxidant activity, soil properties and rhizosphere microorganisms indicated that these amendments may alleviate Cu stress by enhancing peroxidase activity, facilitating plant nutrient absorption, and enriching beneficial microorganisms capable of promoting plant growth and mitigating heavy metal-induced damage. This study suggests that the combined application of microbial inoculant and microalgae can reduce Cu levels in Salvia miltiorrhiza while enhancing its quality under Cu stress.

Impact of Inoculation Practices on Microbiota Assembly and Community Stability in a Fabricated Ecosystem

Studying plant–microbe–soil interactions is challenging due to their high complexity and variability in natural ecosystems. While fabricated ecosystems provide opportunities to recapitulate aspects of these systems in reduced complexity and controlled environments, inoculation can be a significant source of variation. To tackle this, we evaluated how different bacterial inoculation practices and plant harvesting time points affect the reproducibility of a synthetic microbial community (SynCom) in association with the model grass Brachypodium distachyon. We tested three microbial inoculation practices, seed inoculation, transplant inoculation, and seedling inoculation, and two harvesting points, early (14-day-old plants) and late (21 days postinoculation). We grew our plants and bacterial strains in sterile devices (EcoFABs) and characterized the microbial community from root, rhizosphere, and sand using 16S ribosomal RNA gene sequencing. The results showed that inoculation practices significantly affected the rhizosphere microbial community when harvesting at an early time point but not at the late time point. As the SynCom showed a persistent association with B. distachyon at 21 days postinoculation regardless of inoculation practices, we assessed the reproducibility of each inoculation method and found that transplant inoculation showed the highest reproducibility. Moreover, plant biomass was not adversely affected by transplant inoculation treatment. We concluded that bacterial inoculation while transplanting coupled with a later harvesting time point gives the most reproducible microbial community in the EcoFAB− B. distachyon−SynCom fabricated ecosystem. We recommend this method as a standardized protocol for use with fabricated ecosystem experimental systems. [Formula: see text] This manuscript has been authored by an author at Lawrence Berkeley National Laboratory under Contract number DE-AC02-05CH11231 with the U.S. Department of Energy. The U.S. Government retains, and the publisher, by accepting the article for publication, acknowledges, that the U.S. Government retains a non-exclusive, paid-up, irrevocable, world-wide license to publish or reproduce the published form of this manuscript, or allow others to do so, for U.S. Government purposes. This is an open access article distributed under the CC BY-NC-ND 4.0 International license .

Effects of γ-polyglutamic acid supplementation on alfalfa growth and rhizosphere soil microorganisms in sandy soil

This study aimed at exploring the effects of γ-polyglutamic acid on the growth of desert alfalfa and the soil microorganisms in the rhizosphere. The study examined the effects of varying concentrations of γ-polyglutamic acid (0%-CK, 2%-G1, 4%-G2, 6%-G3) on sandy soil, the research investigated its impact on the growth characteristics of alfalfa, nutrient content in the rhizosphere soil, and the composition of bacterial communities. The results indicated that there were no significant differences in soil organic matter, total nitrogen, total phosphorus, total potassium, and available phosphorus content among the G1, G2, and G3 treatments. Compared to CK, the soil nutrient content in the G2 treatment increased by 14.81–186.67%, showing the highest enhancement. In terms of alfalfa growth, the G2 treatment demonstrated the best performance, significantly increasing plant height, chlorophyll content, above-ground biomass, and underground biomass by 54.91–154.84%. Compared to the CK treatment, the number of OTUs (operational taxonomic units) in the G1, G2, and G3 treatments increased by 14.54%, 8.27%, and 6.84%, respectively. The application of γ-polyglutamic acid altered the composition and structure of the bacterial community, with Actinobacteriota, Proteobacteria, Chloroflexi, Acidobacteriota, and Gemmatimonadota accounting for 84.14–87.89% of the total bacterial community. The G2 treatment significantly enhanced the diversity and evenness of soil bacteria in the rhizosphere. Redundancy analysis revealed that organic matter, total nitrogen, total potassium, moisture content, and pH were the primary factors influencing the structure of bacterial phyla. At the genus level, moisture content emerged as the most influential factor on the bacterial community. Notably, moisture content exhibited a strong positive correlation with Acidobacteriota, which in turn was positively associated with indicators of alfalfa growth. In summary, the application of γ-polyglutamic acid at a 4% ratio has the potential for improving sandy soil quality, promoting plant growth, and regulating the rhizosphere microbial community.

Fulvic Acid Promotes Legume-Rhizobium Symbiosis by Stimulating Endogenous Flavonoids Synthesis and Secretion.

Fulvic acid (FA) promotes symbiosis between legumes and rhizobia. To elucidate from the aspect of symbiosis, the effects of root irrigation of water-soluble humic materials (WSHM) or foliar spraying of its highly active component, FA, on soybean root exudates and on rhizosphere microorganisms were investigated. As a result, WSHM/FA treatments significantly altered root exudate metabolite composition, and isoflavonoids were identified as key contributors in both treatments compared to the control. Increased expression of genes related to the isoflavonoid biosynthesis were validated by RT-qPCR in both treatments, which notably elevated the synthesis of symbiotic signals genistein, daidzin, coumestrol, and biochanin A. Moreover, the WSHM/FA treatments induced a change in rhizosphere microbial community, coupled with an increase in the relative abundance of rhizobia. Our findings showed that WSHM/FA promotes symbiosis by stimulating the endogenous flavonoid synthesis and leads to rhizobia accumulation in the rhizosphere. This study provides new insights into mechanisms underlying the FA-mediated promotion of symbiosis.

The Effects of Salinity and Genotype on the Rhizospheric Mycobiomes in Date Palm Seedlings.

Salinity severely affects the health and productivity of plants, with root-associated microbes, including fungi, potentially playing a crucial role in mitigating this effect and promoting plant health. This study employed metagenomics to investigate differences in the structures of the epiphyte mycobiomes in the rhizospheres of seedlings of two distinct date palm cultivars with contrasting salinity tolerances, the susceptible cultivar, 'Zabad', and the tolerant cultivar, 'Umsila'. Next-generation sequencing (NGS) of the internal transcribed spacer (ITS) rRNA was utilized as a DNA barcoding tool. The sequencing of 12 mycobiome libraries yielded 905,198 raw sequences of 268,829 high-quality reads that coded for 135 unique and annotatable operational taxonomic units (OTUs). An OTU analysis revealed differences in the rhizofungal community structures between the treatments regardless of genotype, and non-metric dimensional scaling (N-MDS) analyses demonstrated distinct separations between the cultivars under saline stress. However, these differences were not detected under the control environmental conditions, i.e., no salinity. The rhizospheric fungal community included four phyla (Ascomycota, Basidiomycota, Chytridiomycota, and Mucoromycota), with differences in the abundances of Aspergillus, Clonostachys, and Fusarium genera in response to salinity, regardless of the genotype. Differential pairwise comparisons showed that Fusarium falciforme-solani and Aspergillus sydowii-versicolor increased in abundance under saline conditions, providing potential future in vitro isolation guidelines for plant growth-promoting fungi. This study highlights the intricate dynamics of the rhizosphere microbial communities in date palms and their responses to salt stress. Additionally, we found no support for the hypothesis that indigenous epiphytic fungal communities are significantly involved in salinity tolerance in date palms.

The proliferation of beneficial bacteria influences the soil C, N, and P cycling in the soybean-maize intercropping system.

Soybean-maize intercropping system can improve the utilization rate of farmland and the sustainability of crop production systems. However, there is a significant gap in understanding the interaction mechanisms between soil carbon (C), nitrogen (N), and phosphorus (P) cycling functional genes, rhizosphere microorganisms, and nutrient availability. To reveal the key microorganisms associated with soil nutrient utilization and C, N, and P cycling function in the soybean-maize intercropping system, we investigated the changes in soil properties, microbial community structure, and abundance of functional genes for C, N, and P cycling under soybean-maize intercropping and monocropping at different fertility stages in a pot experiment. We found that there was no significant difference in the rhizosphere microbial community between soybean-maize intercropping and monocropping at the seeding stage. As the reproductive period progressed, differences in microbial community structure between intercropping and monocropping gradually became significant, manifesting the advantages of intercropping. During the intercropping process of soybean and maize, the relative abundance of beneficial bacteria in soil rhizosphere significantly increased, particularly Streptomycetaceae and Pseudomonadaceae. Moreover, the abundances of C, N, and P cycling functional genes, such as abfA, mnp, rbcL, pmoA (C cycling), nifH, nirS-3, nosZ-2, amoB (N cycling), phoD, and ppx (P cycling), also increased significantly. Redundancy analysis and correlation analysis showed that Streptomycetaceae and Pseudomonadaceae were significantly correlated with soil properties and C, N, and P cycling functional genes. In brief, soybean and maize intercropping can change the structure of microbial community and promote the proliferation of beneficial bacteria in the soil rhizosphere. The accumulation of these beneficial bacteria increased the abundance of C, N, and P cycling functional genes in soil and enhanced the ability of plants to fully utilize environmental nutrients and promoted growth.

Synergistic effects of rhizosphere effect and combined organic and chemical fertilizers application on soil bacterial diversity and community structure in oilseed rape cultivation.

The combined application of chemical and organic fertilizers has been recognized to enhance soil fertility and foster the soil microbial ecosystem. However, the optimal ratio of chemical and organic fertilizers in oilseed rape cultivation is still uncertain, and the role of rhizosphere effect is still unclear. Thus, this study aimed to elucidate the impacts of varying ratios of chemical and organic fertilizers on the structure and potential functionalities of rhizosphere and non-rhizosphere soil microbial communities. The interplay of microbial communities with soil properties and oilseed rape root exudates was investigated in controlled pot cultivations receiving varying ratios of chemical and organic fertilizers. Results indicated clear segregation in the soil bacterial community, influenced by both fertilization treatments and rhizosphere effects. The bacterial community structure significantly correlated with nitrate nitrogen, organic acids, and dissolved organic carbon (DOC) content. Rhizosphere effects led to increased bacteria abundance, reduced diversity, and decreased network stability. Notably, F3 treatment receiving 25% chemical and 75% organic fertilizers showed a significantly higher abundance at 1.43 × 1011 copies g-1 dry soil, accompanied by increased species and genetic diversity, and ecological network complexity. This treatment also yielded the highest aboveground biomass of oilseed rape. However, the application of organic fertilizers also increased the risk of plant pathogenicity. This study reveals the impact of fertilizers and rhizosphere effects on soil microbial community structure and function, shedding light on the establishment of more effective fertilization schemes for oilseed rape agriculture.

Nitrogen fertilization practices alter microbial communities driven by clonal integration in Moso bamboo

Nitrogen (N) fertilization is crucial for maintaining plant productivity. Clonal plants can share resources between connected ramets through clonal integration influencing microbial communities and regulating soil biogeochemical cycling, especially in the rhizosphere. However, the effect of various N fertilization practices on microbial communities in the rhizosphere of clonal ramets remain unknown. In this study, clonal fragments of Moso bamboo (Phyllostachys edulis), consisting of a parent ramet, an offspring ramet, and an interconnecting rhizome, were established in the field. NH4NO3 solution was applied to the parent, offspring ramets or rhizomes to investigate the effect of fertilization practices on the structure and function of rhizosphere microbial communities. The differences in N availability, microbial biomass and community composition, and abundance of nitrifying genes among rhizosphere soils of ramets gradually decreased during the rapid growth of Moso bamboo, irrespective of fertilization practice. The soil N availability variation, particularly in NO3−, caused by fertilization practices altered the rhizosphere microbial community. Soil N availability and stable microbial biomass N in parent fertilization were the highest, being 9.0 % and 18.7 %, as well as 60.8 % and 90.4 % higher than rhizome and offspring fertilizations, respectively. The microbial network nodes and links in rhizome fertilization were 1.8 and 7.5 times higher than in parent and offspring fertilization, respectively. However, the diversity of bacterial community and abundance of nitrifying and denitrifying genes were the highest in offspring fertilization among three practices, which may be associated with increased N loss. Collectively, the rhizosphere microbial community characteristics depended on fertilization practices by altering the clonal integration of N in Moso bamboo. Parent and rhizome fertilization were favorable for N retention in plant-soil system and resulted in more stable microbial functions than offspring fertilization. Our findings provide new insights into precision fertilization for the sustainable Moso bamboo forest management.

Consecutive Fertilization-Promoted Soil Nutrient Availability and Altered Rhizosphere Bacterial and Bulk Fungal Community Composition

Fertilization is an important measure to quickly supplement the soil nutrients required for plantation productivity. However, the response patterns of the microbial community and functional taxa in Larix plantation root, rhizosphere, and bulk soil to short-term and consecutive fertilization have rarely been reported. In this study, we assessed Larix root, rhizosphere, and bulk soil microbial community on days 0, 5, 15, and 30 after the first inorganic fertilization and after three consecutive years of fertilization. The bacterial 16S and fungal ITS high-throughput sequencing technology were used to monitor changes in microbial community composition and potential functional groups, as well as changes in soil nutrient content and enzyme activity to evaluate the status of plantation soil productivity. Consecutive fertilization treatment significantly increased the available nitrogen, phosphorus, and potassium (NPK) content and soil enzyme activity. The nonmetric multidimensional scaling (NMDS) and analysis of similarities (ANOSIM) results showed that there were significant differences in microbial community composition in root samples, rhizosphere soil, and bulk soil samples. The dominant microbial taxa were different between root and soil microbial community composition. Consecutive fertilization treatment had little effect on endophytic microbial community but significantly increased the abundance of Gaiellales in rhizosphere soil and Mortierella in bulk soil. The redundancy analysis (RDA) and co-occurrence network analyses showed that Gaiellales and Mortierellales had significant positive correlations with soil nutrient content and enzyme activity. The fungal functional group compositions were significantly affected by consecutive fertilization treatment and the proportions of ectomycorrhizal and saprotroph significantly decreased, but the proportion of endophyte significantly increased in bulk soil samples. Our results suggested that consecutive fertilization may promote soil nutrient availability by increasing the abundance of Gaiellales and Mortierella. Consecutive fertilization maintained the balance of the soil microbiota under Larix plantation and had a positive effect on promoting soil nutrient availability. This study provided a theoretical basis for consecutive fertilization to promote soil nutrient availability through specific microbial groups.

Effects of different long-term fertilization on rhizosphere soil nitrogen mineralization and microbial community composition under the double-cropping rice field

ABSTRACT Soil extracellular enzymes play an important role in regulating nitrogen (N) mineralization processes in paddy fields. Therefore, in this work, we determine the influence of a long-term fertilizer regime on rhizosphere soil N fertilization rates, soil enzymes, soil microbial community (bacterial ureolytic community (ureC), bacterial chitinolytic community (chiA)) under the double-cropping rice field in southern of China. The field experiment included the following fertilizer regimes: inorganic fertilizer alone (IF), rice straw and inorganic fertilizer (RF), 30% organic manure and 70% inorganic fertilizer (OM), without any fertilizer input as a control (CK). The results showed that rhizosphere soil N transformation rates in the paddy fields with OM and RF treatments were increased, compared with IF and CK treatments. Soil urease, β-glucosaminidase and arginase activities were significantly increased under OM and RF treatments. This result indicated that functional gene abundances of sub, npr and chiA were significantly greater under RF and OM treatments compared to IF and CK treatments. Soil bacterial ureolytic and chitinolytic communities were significantly changed by the different fertilization strategies. The practice of applying rice straw and organic manure seems beneficial for increasing rhizosphere soil N mineralization rates and microbial community diversity in the double-cropping rice fields.

Analysis on metabolic functions of rhizosphere microbial communities of Pinus massoniana provenances with different carbon storage by Biolog Eco microplates.

Rhizosphere microorganisms are influenced by vegetation. Meanwhile, they respond to vegetation through their own changes, developing an interactive feedback system between microorganisms and vegetation. However, it is still unclear whether the functional diversity of rhizosphere soil microorganisms varies with different carbon storage levels and what factors affect the functional diversity of rhizosphere soil microorganisms. In this study, the Biolog-Eco microplate technique was used to analyze the metabolic diversity of carbon source of rhizosphere soil microorganisms from 6 Pinus massoniana provenances with three levels of high, medium and low carbon storage. The results showed that the average well color development(AWCD) value of rhizosphere microorganisms was significantly positive correlated with carbon storage level of Pinus massoniana (p < 0.05). The AWCD value, Simpson and Shannon diversity of high carbon sequestrance provenances were 1.40 (144h incubation) 0.96 and 3.24, respectively, which were significantly higher (p < 0.05) than those of other P. massoniana provenances. The rhizosphere microbial AWCD, Shannon and Simpson diversity of the 6 provenances showed the same variation trend (SM>AY>QJ>SX>HF>SW). Similarly, microbial biomass carbon (MBC) content was positively correlated with carbon storage level, and there were significant differences among high, medium and low carbon storage provenances. The PCA results showed that the differences in the carbon source metabolism of rhizosphere microorganisms were mainly reflected in the utilization of amino acids, carboxylic acids and carbohydrates. Pearson correlation analysis showed that soil organic carbon (SOC), total nitrogen (TN) and pH were significantly correlated with rhizosphere AWCD (p < 0.05). Soil properties are important factors affecting rhizosphere microbial carbon source metabolism. The study confirmed that the microorganisms of high carbon storage provenances had relatively high carbon metabolic activity. Among them, the carbon metabolic activity of rhizosphere microorganisms of SM provenance was the highest, which was the preferred provenances in effective ecological service function.

Exceptional anti-toxic growth of water spinach in arsenic and cadmium co-contaminated soil remediated using biochar loaded with Bacillus aryabhattai

Functionalized biochars are crucial for simultaneous soil remediation and safe agricultural production. However, a comprehensive understanding of the remediation mechanism and crop safety is imperative. In this work, the all-in-one biochars loaded with a Bacillus aryabhattai (B10) were developed via physisorption (BBC) and sodium alginate embedding (EBC) for simultaneous toxic As and Cd stabilization in soil. The bacteria-loaded biochar composites significantly decreased exchangeable As and Cd fractions in co-contaminated soil, with enhanced residual fractions. Heavy metal bioavailability analysis showed a maximum CaCl2-As concentration decline of 63.51% and a CaCl2-Cd decline of 50.96%. At a 3% dosage of composite, rhizosphere soil showed improved organic matter, cation exchange capacity, and enzyme activity. The aboveground portion of water spinach grown in pots was edible, with final As and Cd contents (0.347 and 0.075 mg·kg⁻¹, respectively) meeting food safety standards. Microbial analysis revealed the composite's influence on the rhizosphere microbial community, favoring beneficial bacteria and reducing plant pathogenic fungi. Additionally, it increased functional microorganisms with heavy metal-resistant genes, limiting metal migration in plants and favoring its growth. Our research highlights an effective strategy for simultaneous As and Cd immobilization in soil and inhibition of heavy metal accumulation in vegetables.

Deciphering Microbial Community and Nitrogen Fixation in the Legume Rhizosphere.

Nitrogen is the most limiting factor in crop production. Legumes establish a symbiotic relationship with rhizobia and enhance nitrogen fixation. We analyzed 1,624 rhizosphere 16S rRNA gene samples and 113 rhizosphere metagenomic samples from three typical legumes and three non-legumes. The rhizosphere microbial community of the legumes had low diversity and was enriched with nitrogen-cycling bacteria (Sphingomonadaceae, Xanthobacteraceae, Rhizobiaceae, and Bacillaceae). Furthermore, the rhizosphere microbiota of legumes exhibited a high abundance of nitrogen-fixing genes, reflecting a stronger nitrogen-fixing potential, and Streptomycetaceae and Nocardioidaceae were the predominant nitrogen-fixing bacteria. We also identified helper bacteria and confirmed through metadata analysis and a pot experiment that the synthesis of riboflavin by helper bacteria is the key factor in promoting nitrogen fixation. Our study emphasizes that the construction of synthetic communities of nitrogen-fixing bacteria and helper bacteria is crucial for the development of efficient nitrogen-fixing microbial fertilizers.

Foliar Application of Iron Nutrition Not Only Improves Root Activity but Also Significantly Affects Rhizosphere Microbial Community of Brassica Chinensis on Karst Calcareous Soil

Foliar Application of Iron Nutrition Not Only Improves Root Activity but Also Significantly Affects Rhizosphere Microbial Community of Brassica Chinensis on Karst Calcareous Soil

Ancient bayberry increased stress resistance by enriching tissue-specific microbiome and metabolites.

The ancient bayberry demonstrates superior resistance to both biotic and abiotic stresses compared to cultivated bayberry, yet the underlying mechanisms remain largely unexplored. This study investigates whether long-term bayberry cultivation enhances stress resistance through modulation of tissue-specific microbes and metabolites. Employing microbiome amplicon sequencing alongside untargeted mass spectrometry analysis, we scrutinize the role of endosphere and rhizosphere microbial communities and metabolites in shaping the differential resistance observed between ancient and cultivated bayberry trees. Our findings highlight the presence of core microbiome and metabolites across various bayberry tissues, suggesting that the heightened resistance of ancient bayberry may stem from alterations in rhizosphere and endosphere microbial communities and secondary metabolites. Specifically, enrichment of Bacillus in roots and stems, Pseudomonas in leaves, and Mortierella in rhizosphere soil of ancient bayberry was noted. Furthermore, correlation analysis underscores the significance of enriched microbial species in enhancing ancient bayberry's resistance to stresses, with elevated levels of resistance-associated metabolites such as beta-myrcene, benzothiazole, L-glutamic acid, and gamma-aminobutyric acid identified through GC-MS metabolomics analysis. The beneficial role of these resistance-associated metabolites was further elucidated through assessment of their promotive and allelopathic effects, as well as their phytostatic and antioxidant functions in lettuce plants. Ultimately, our study delves into the intrinsic reasons behind the greater resistance of ancient bayberry to biotic and abiotic stresses by evaluating the impact of long-term planting on the microbial community and metabolites in the bayberry endosphere and rhizosphere, shedding light on the complex dynamics of host-microbial interactions.

The impact of arbuscular mycorrhizal fungi and endophytic bacteria on peanuts under the combined pollution of cadmium and microplastics

It remains unclear how symbiotic microbes impact the growth of peanuts when they are exposed to the pollutants cadmium (Cd) and microplastics (MPs) simultaneously. This study aimed to investigate the effects of endophytic bacteria Bacillus velezens SC60 and arbuscular mycorrhizal fungus Rhizophagus irregularis on peanut growth and rhizosphere microbial communities in the presence of Cd at 40 (Cd40) or 80 (Cd80) mg kg−1 combined without MP or the presence of low-density polyethylene (LDPE) and poly butyleneadipate-co-terephthalate (PBAT). This study assessed soil indicators, plant parameters, and Cd accumulation indicators. Results showed that the application of R. irregularis and B. velezens significantly enhanced soil organic carbon and increased Cd content under the conditions of Cd80 and MPs co-pollution. R. irregularis and B. velezens treatment increased peanut absorption and the enrichment coefficient for Cd, with predominate concentrations localized in the peanut roots, especially under combined pollution by Cd and MPs. Under treatments with Cd40 and Cd80 combined with PBAT pollution, soil microbes Proteobacteria exhibited a higher relative abundance, while Actinobacteria showed a higher relative abundance under treatments with Cd40 and Cd80 combined with LDPE pollution. In conclusion, under the combined pollution conditions of MPs and Cd, the co-treatment of R. irregularis and B. velezens effectively immobilized Cd in peanut roots, impeding its translocation to the shoot.

Maize functional requirements drive the selection of rhizobacteria under long-term fertilization practices.

Rhizosphere microbiomes are pivotal for crop fitness, but the principles underlying microbial assembly during root-soil interactions across soils with different nutrient statuses remain elusive. We examined the microbiomes in the rhizosphere and bulk soils of maize plants grown under six long-term (≥ 29 yr) fertilization experiments in three soil types across middle temperate to subtropical zones. The assembly of rhizosphere microbial communities was primarily driven by deterministic processes. Plant selection interacted with soil types and fertilization regimes to shape the structure and function of rhizosphere microbiomes. Predictive functional profiling showed that, to adapt to nutrient-deficient conditions, maize recruited more rhizobacteria involved in nutrient availability from bulk soil, although these functions were performed by different species. Metagenomic analyses confirmed that the number of significantly enriched Kyoto Encyclopedia of Genes and Genomes Orthology functional categories in the rhizosphere microbial community was significantly higher without fertilization than with fertilization. Notably, some key genes involved in carbon, nitrogen, and phosphorus cycling and purine metabolism were dominantly enriched in the rhizosphere soil without fertilizer input. In conclusion, our results show that maize selects microbes at the root-soil interface based on microbial functional traits beneficial to its own performance, rather than selecting particular species.

Rhizosphere-Associated Anammox Bacterial Diversity and Abundance of Nitrogen Cycle-Related Functional Genes of Emergent Macrophytes in Eutrophic Wetlands.

Rhizospheric microbial community of emergent macrophytes plays an important role in nitrogen removal, especially in the eutrophic wetlands. The objective of this study was to identify the differences in anammox bacterial community composition among different emergent macrophytes and investigate revealed the the main factors affecting on the composition, diversity, and abundance of anammox bacterial community. Results showed that the composition, diversity, and abundance of the anammox community were significantly different between the vegetated sediments of three emergent macrophytes and unvegetated sediment. The composition of the anammox bacterial community was different in the vegetated sediments of different emergent macrophytes. Also, the abundance of nitrogen cycle-related functional genes in the vegetated sediments was found to be higher than that in the unvegetated sediment. Canonical correspondence analysis (CCA) and structural equation models analysis (SEM) showed that salinity and pH were the main environmental factors influencing the composition and diversity of the anammox bacterial community and NO2--N indirectly affected anammox bacterial community diversity by affecting TOC. nirK-type denitrifying bacteria abundance had significant effects on the bacterial community composition, diversity, and abundance of anammox bacteria. The community composition of anammox bacteria varies with emergent macrophyte species. The rhizosphere of emergent macrophytes provides a favorable environment and promotes the growth of nitrogen cycling-related microorganisms that likely accelerate nitrogen removal in eutrophic wetlands.