Microbial Diversity In Rhizosphere Soil Research Articles

Analysis of Physicochemical Properties, Enzyme Activity, Microbial Diversity in Rhizosphere Soil of Coconut (Cocos nucifera L.) Under Organic and Chemical Fertilizers, Irrigation Conditions

The application of chemical fertilizers and organic fertilizers, as well as irrigation, is an important agricultural practice that can increase crop yields and affect soil biogeochemical cycles. This study conducted coconut field experiments to investigate the effects of conventional fertilization (NCF), optimized fertilization (MCF), conventional fertilization + organic fertilizer (NOF), optimized fertilization + organic fertilizer (MOF), conventional fertilization + organic fertilizer + irrigation (NOFW), and optimized fertilization + organic fertilizer + irrigation (MOFW) treatments on soil physicochemical properties, soil enzyme activity, bacterial and fungal community structure and diversity, and compared the controls (CK, non-fertilizer and non-irrigation). The results showed that MOFW significantly increased soil electrical conductivity (EC), organic matter (OM), alkaline nitrogen (AN), available phosphorus (AP), available potassium (AK), available calcium (ACa), and available magnesium (AMg) levels. At the same time, it also significantly enhanced the activities of soil catalase (CE), polyphenol oxidase (POE), sucrase (SE), urease (UE), acid protease (APE), and acid phosphatase (APPE) (p < 0.05). The PCA analysis of soil microorganisms in the coconut rhizosphere soil showed indicated significant changes in bacteria and fungi community structure under fertilization treatments. The fertilization application leaded to an increase in the relative abundance and diversity of bacteria, but a decrease in fungi. Acidobacteriota, Proteobacteria, and Actinobacterota were the dominant bacterial phyla, and Ascomycota, Basidiomycota, Rozellomycota, and Mortierellomycota were the significant fungal phyla. Compared with CK, MOFW significantly increased the abundance of Acidobacteriota, Proteobacteria, Basidiomycota, and Mortierellomycota. Redundancy analysis (CCA) and Mantel test further revealed that pH, EC, OM, and AP were the main soil fertility factors driving changes in microbial communities. CE, SE, UE, APE, APPE were significantly correlated with microbial communities. Compared with NOFW, MOFW has a lower proportion of N, P, and K fertilizers in its fertilizer composition. The results indicated that MOFW can better improve the nutrient and enzyme status of the soil, which is a promising method for maintaining the balance of soil microorganisms in coconut orchards, and accordingly, reducing chemical fertilizers within a certain range can not only ensure consistency with conventional fertilizers, but also effectively improve soil conditions.

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

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

Altitude Distribution Patterns and Driving Factors of Rhizosphere Soil Microbial Diversity in the Mountainous and Hilly Region of Southwest, China

The distribution characteristics of the microbial community in rhizosphere soils of different altitudinal gradients were explored to uncover ecological factors affecting microbial community composition. In this study, the community variations of bacteria and fungi in the rhizosphere soil of Chrysanthemum indicum L. were analyzed. Samples were distributed along an altitudinal gradient of 300–1500 m above sea level in the Fuling watershed of the Three Gorges Reservoir area, China. The analysis was conducted using Illumina MiSeq high-throughput sequencing and bioinformatics analyses. Through correlation analysis with ecological factors, the altitude distribution pattern and driving factors of soil microbial diversity in the mountainous and hilly region of Chongqing were explored. According to the results, the richness and diversity of rhizosphere soil bacteria increased with altitude, while fungi were the richest and most diverse at an altitude of 900 m. The composition of the microbial community differed among different altitudes. Actinobacteria, Proteobacteria, Acidobacteriota, Chloroflexi, Bacteroidota, Ascomycota, unclassified_k_Fungi, Basidiomycota, and Mortierellomycota dominated the microbial community in rhizosphere soil. Correlation analysis showed that the distribution of rhizosphere soil microbial communities correlated with soil ecological factors at different altitudes. Moisture, pH, total nitrogen, total potassium, available potassium, urease, and catalase were significantly positively correlated with rhizosphere soil bacterial α-diversity, while their correlations with fungi were not significant. Variation partition analysis showed that the combined effects of soil physical and chemical factors, enzyme activity, and microbial quantity regulated bacterial community structure and composition. Their combined contributions (19.21%) were lower than the individual effects of soil physical and chemical factors (48.49%), enzyme activity (53.24%), and microbial quantity (60.38%). The effects of ecological factors on fungal communities differed: While the soil physical and chemical factors (44.43%) alone had a clear effect on fungal community structures, their combined contributions had no apparent effect. The results of this study not only contribute to a deeper understanding of the impact mechanism of altitude gradient on the diversity of rhizosphere soil microbial communities, but also provide a scientific basis for the protection and management of mountainous and hilly ecosystems. It lays a foundation for the future exploration of the relationship between microbial communities and plant–soil interactions.

Dicranopteris dichotoma rhizosphere-derived Bacillus sp. MQB12 acts as an enhancer of plant growth via increasing phosphorus utilization, hormone synthesis, and rhizosphere microbial abundance

In recent years, microbial inoculants have showed a great potential to replace chemical fertilizers as a new generation of soil amendment agents, however, the understanding of their effects on nutrient cycling within plants and rhizosphere microbial diversity are still limited. In this study, the rhizosphere growth-promoting bacteria MQB12 was used to inoculate Vigna radiata to evaluate the effects of external inoculants on plant transcriptomics and rhizosphere soil microbial diversity. Enrichment analysis using GO and KEGG revealed significant enrichment in DNA-binding transcription factor activity, transcriptional regulatory factor activity, and phenylpropanoid biosynthesis among the differentially expressed genes. MQB12 inoculation positively responded to phosphorus starvation response, increased the expression of phosphorus starvation response genes (PHT/PAP), enhanced the synthesis of ethylene and salicylic acid to cope with external stress, and improved the expression of plant disease resistance genes to strengthen the disease resistance of plants to pathogens. At the same time, microbial diversity analysis further revealed the positive effect of MQB12 inoculum. MQB12 inoculum enriched beneficial flora, improved flora abundance, changed the structure and diversity of V. radiata rhizosphere microbial community, enhanced the interconnections between the flora, and positively promoted growth. MQB12 was found to adjust the microflora of the rhizosphere, which subsequently changed the environment for plant colonization. This change led to the enrichment of beneficial bacteria and removal of pathogenic bacteria, which positively affected the internal pathways of plants. Additionally, changes in gene expression levels of plants resulted in the formation of different phenotypes and various metabolites, further influencing the formation of rhizosphere microbial communities through close contact between roots and soil. This study provides new insights into the effects of microbial agents on plant growth and root environment construction and is conducive to the further development and application of microbial agents.Graphical

Combined effects of border irrigation and super-absorbent polymers on enzyme activity and microbial diversity of poplar rhizosphere soil.

Fast-growing poplar plantations are considered a great benefit to timber production, but water availability is a key factor limiting their growth and development, especially in arid and semi-arid ecosystems. Super-absorbent polymers facilitate more water retention in soil after rain or irrigation, and they are able to release water gradually during plant growth. This study aimed to examine the effects of reduced irrigation (60% and 30% of conventional border irrigation) co-applied with super-absorbent polymers (0, 40 kg/ha) on root exudates, enzyme activities, microbial functional diversity in rhizosphere soil, and volume increments in poplar (Populus euramericana cv. 'Neva'). The results showed that 60% border irrigation co-applied with super-absorbent polymers significantly increased the content of organic acids, amino acids and total sugars in the root exudates, and the activities of invertase, urease, dehydrogenase, and catalase in the rhizosphere soil in comparison to conventional border irrigation without super-absorbent polymers. Meanwhile, this treatment also enhanced the average well-color development, Shannon index, and McIntosh index, but decreased the Simpson index. Additionally, the average volume growth rate and relative water content of leaves reached their maximum using 60% irrigation with super-absorbent polymers, which was significantly higher than other treatments. However, using 30% irrigation with super-absorbent polymers, had a smaller effect on rhizosphere soil and volume growth than 60% irrigation with super-absorbent polymers. Therefore, using an appropriate water-saving irrigation measure (60% conventional border irrigation with super-absorbent polymers) can help to improve enzyme activities and microbial diversity in the rhizosphere soil while promoting the growth of poplar trees.

Analysis of Microbial Diversity in Rhizosphere Soil of Panax notoginseng under Different Water and Microbial Fertilizer Conditions

Panax notoginseng is a highly regarded medicinal plant that has obstacles associated with continuous cropping. Understanding soil microorganisms is crucial, as they play a major role in this regard. However, soil microorganisms are affected by multiple factors; therefore, we need to conduct more in-depth research. This study investigated the combined effects of irrigation and microbial fertilizer treatments (J1F1, J1F2, J2F1, J2F2, J3F1, J3F2, and CK) on the diversity of bacterial and fungal microbial communities in the rhizosphere of Panax notoginseng. The bacterial 16S rRNA genes and fungal internal transcribed spacer (ITS) sequences were sequenced using Illumina HiSeq. The results showed that, without microbial fertilizer (CK), the microbial community abundance and diversity were significantly lower than in the other treatments; moreover, among the microbial fertilizer treatments, the microbial abundance in F1 was higher than that in F2. Under the same microbial fertilizer application, the incidence rate of Panax notoginseng root rot was J2 > J1 > J3, and the yield of Panax notoginseng was J3 > J2 > J1. Under the same irrigation conditions, the incidence rate of Panax notoginseng root rot was F1 > F2, and the yield of Panax notoginseng was F2 > F1. This study provides important guidance for Panax notoginseng plant microbiota and sustainable agriculture.

Fertility and microbial diversity in rhizosphere soil of Camellia oleifera under different intercropping systems

Fertility and microbial diversity in rhizosphere soil of Camellia oleifera under different intercropping systems

Response of the rhizosphere soil microbial diversity to different nitrogen and phosphorus application rates in a hulless barley and pea mixed-cropping system

The mixed-cropping mode of hulless barley (Hordeum vulgare L) and peas (Pisum sativum L) can optimize the planting system, effectively enhancing crop nitrogen and phosphorus utilization and increasing yield. This mode has been widely applied in Qinghai Province, China. In this study, a split-plot experimental design was employed to investigate the bacterial and fungal communities in the rhizosphere soil of monocropping and mixed-cropping treatments under different fertilization levels. The Illumina MiSeq sequencing technology was used for the research, and the physicochemical properties of the soil were measured. The results indicated that with the increase in the application of nitrogen and phosphorus, the bacterial α-diversity in the rhizosphere of the mixed-cropping system initially increased and then decreased after reaching a peak. The α-diversity index of soil bacteria was higher under the mixed-cropping mode than under the monocropping mode. For the rhizosphere soil fungi in the mixed-cropping system, the Shannon index initially increased and then decreased, while the Chao1 and ACE indices decreased initially and then increased. Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium, Sphingomonas, and Pseudomonas comprised the predominant bacterial genera in the rhizosphere soil of the hulless barley–pea intercropping treatment, whereas Fusarium, Metarhizium, and Cladosporium dominated among the fungal genera across the 12 treatments. Under the same fertilization levels, the relative abundances of Allorhizobium-Neorhizobium-Pararhizobium-Rhizobium in the rhizosphere soil of the mixed-cropping treatment increased by 8.4 %, 7.1 %, 5.7 %, and 5.6 %, respectively, compared to the monoculture of hulless barley, with a decreasing trend as nitrogen and phosphorus levels increased. Compared to the monoculture of hulless barley, the relative abundance of Fusarium in the mixed-cropping treatment decreased by 37.3 %, 43.8 %, 56.8 %, and 40.3 %, respectively. Redundancy and correlation analyses suggested that the variation in bacterial and fungal diversity and community composition in the mixed-cropping zone due to the interaction between hulless barley and peas under different nitrogen and phosphorus fertilizer application levels was significantly correlated with changes in soil organic matter, available phosphorus, and alkaline hydrolyzable nitrogen.

Analysis of rhizosphere soil microbial diversity and its functions between Dahongpao mother tree and cutting Dahongpao.

Dahongpao mother tree (Camellia sinensis (L.) O. Ktze) is a representative of Wuyi rock tea. Whether there is a difference in rhizosphere soil microbial diversity and function between asexually propagated cuttings of Dahongpao (PD) and the parent Dahongpao mother tree (MD) has not been reported. In this study, high throughput sequencing technology was used to analyze rhizosphere soil microbial diversity, functions and their relationship with soil available nutrients and enzyme activities in MD and PD. The results showed that available nitrogen, phosphorus and potassium contents and urease, protease, acid phosphatase and sucrase activities of rhizosphere soils in MD were significantly higher than those in PD. Both bacterial and fungal diversity were higher in rhizosphere soils in MD than in PD, and secondly, the bacterial community structure was less stable while the fungal community structure was more stable in PD compared to MD. There were significant differences between MD and PD tea tree rhizosphere soils in 6 genera of characteristic bacteria and 4 genera of characteristic fungi. The results of function and interaction effect analysis showed that the rhizosphere soil available nutrient content and enzyme activities in MD were significantly higher than those in PD, and their contributions mainly originated from Pirellula and Acidisphaera of characteristic bacteria and Alatospora of characteristic fungi. Secondly, MD maybe had a stronger ability to inhibit soil pathogens than PD, with the main contribution coming from Scopulariopsis and Tolypocladium of characteristic fungi. Overall, compared with PD, soil texture in MD was relatively better, and its soil nutrient cycling-related enzyme activities were stronger, which was more favorable to soil nutrient cycling and increased the available nutrient content of the soil, which in turn promoted the growth of tea trees. This study provides an important reference for the planting and management of tea tree cuttings and microbial regulation of tea tree growth.

Divergent rhizosphere and non-rhizosphere soil microbial structure and function in long-term warmed steppe due to altered root exudation.

While there is an extensive body of research on the influence of climate warming on total soil microbial communities, our understanding of how rhizosphere and non-rhizosphere soil microorganisms respond to warming remains limited. To address this knowledge gap, we investigated the impact of 4 years of soil warming on the diversity and composition of microbial communities in the rhizosphere and non-rhizosphere soil of a temperate steppe, focusing on changes in root exudation rates and exudate compositions. We used open top chambers to simulate warming conditions, resulting in an average soil temperature increase of 1.1°C over a span of 4 years. Our results showed that, in the non-rhizosphere soil, warming had no significant impact on dissolved organic carbon concentrations, compositions, or the abundance of soil microbial functional genes related to carbon and nitrogen cycling. Moreover, soil microbial diversity and community composition remained largely unaffected, although warming resulted in increased complexity of soil bacteria and fungi in the non-rhizosphere soil. In contrast, warming resulted in a substantial decrease in root exudate carbon (by 19%) and nitrogen (by 12%) concentrations and induced changes in root exudate compositions, primarily characterized by a reduction in the abundance in alcohols, coenzymes and vitamins, and phenylpropanoids and polyketides. These changes in root exudation rates and exudate compositions resulted in significant shifts in rhizosphere soil microbial diversity and community composition, ultimately leading to a reduction in the complexity of rhizosphere bacterial and fungal community networks. Altered root exudation and rhizosphere microbial community composition therefore decreased the expression of functional genes related to soil carbon and nitrogen cycling. Interestingly, we found that changes in soil carbon-related genes were primarily driven by the fungal communities and their responses to warming, both in the rhizosphere and non-rhizosphere soil. The study of soil microbial structure and function in rhizosphere and non-rhizosphere soil provides an ideal setting for understanding mechanisms for governing rhizosphere and non-rhizosphere soil carbon and nitrogen cycles. Our results highlight the distinctly varied responses of soil microorganisms in the rhizosphere and non-rhizosphere soil to climate warming. This suggests the need for models to address these processes individually, enabling more accurate predictions of the impacts of climate change on terrestrial carbon cycling.

The mechanism effects of root exudate on microbial community of rhizosphere soil of tree, shrub, and grass in forest ecosystem under N deposition

Forests are composed of various plant species, and rhizosphere soil microbes are driven by root exudates. However, the interplay between root exudates, microbial communities in the rhizosphere soil of canopy trees, understory shrubs, grasses, and their responses to nitrogen (N) deposition remains unclear. Pinus tabulaeformis, Rosa xanthina, and Carex lancifolia were used to investigate root exudates, rhizosphere soil microbial communities, and their responses to N application in forest ecosystem. Root exudate abundances of P. tabulaeformis were significantly higher than that of R. xanthina and C. lancifolia, with carbohydrates dominating P. tabulaeformis and R. xanthina root exudates, fatty acids prevailing in C. lancifolia root exudates. Following N application, root exudate abundances of P. tabulaeformis and R. xanthina initially increased before decreasing, whereas those of C. lancifolia decreased. Microbial number of rhizosphere soil of C. lancifolia was higher than that of P. tabulaeformis and R. xanthina, but there was insignificant variation of rhizosphere soil microbial diversity among plant species. N application exerted promotional and inhibitory impacts on bacterial and fungal numbers, respectively, while bacterial and fungal diversities were increased by N application. Overall, N application had negative effects on root exudates of P. tabulaeformis, inhibiting rhizosphere soil microbial populations. N application suppressed rhizosphere soil microbial populations by increasing root exudates of R. xanthina. Conversely, N application elevated nutrient content in the rhizosphere soil of C. lancifolia, reducing root exudates and minimally promoting microbial populations. This study highlights the importance of understory vegetation in shaping soil microbial communities within forests under N deposition.

A biological product of Bacillus amyloliquefaciens QST713 strain for promoting banana plant growth and modifying rhizosphere soil microbial diversity and community composition.

Bananas are not only an important food crop for developing countries but also a major trading fruit for tropical and semitropical regions, maintaining a huge trade volume. Fusarium wilt of banana (FWB) caused by Fusarium oxysporum f. sp. cubense is becoming a serious challenge to the banana industry globally. Biological control has the potential to offer both effective and sustainable measures for this soil-borne disease. In order to explore the biocontrol effects of the biological agent Bacillus amyloliquefaciens QST713 strain on banana plants, two cultivars, Brazilian and Yunjiao No. 1, with varied resistance to FWB, were used in greenhouse pot experiments. Results showed that the plant height and pseudostem diameter of banana-susceptible cultivar Brazilian increased by 11.68% and 11.94%, respectively, after QST713 application, while the plant height and pseudostem diameter of resistant cultivar Yunjiao No. 1 increased by 14.87% and 12.51%, respectively. The fresh weight of the two cultivars increased by 20.66% and 36.68%, respectively, indicating that this biological agent has potential effects on plant growth. Analysis of the rhizosphere soil microbial communities of two different cultivars of banana plants showed that TR4 infection and B. amyloliquefaciens QST713 strain application significantly affected the bacterial and fungal diversity of Yunjiao No. 1, but not in the cultivar Brazilian. In addition, TR4 infection and QST713 application changed the bacterial community composition of both banana cultivars, and the fungal community composition of Yunjiao No. 1 also changed significantly. Relevance analysis indicated that the relative richness of Bacillus and Pseudomonas in the rhizosphere of both cultivars increased significantly after QST713 application, which had a good positive correlation with plant height, pseudostem girth, aboveground fresh weight, leaf length, and leaf width. Therefore, the outcome of this study suggests that the biological agent QST713 strain has potential application in banana production for promoting plant growth and modification of soil microbial communities, particularly in the TR4-infected field.

Changes in Bulk and Rhizosphere Soil Microbial Diversity Communities of Native Quinoa Due to the Monocropping in the Peruvian Central Andes.

Quinoa (Chenopodium quinoa) is a highly nutritious crop that is resistant to adverse conditions. Due to the considerable increase in its commercial production in Andean soils, the plant is suffering the negative effects of monocropping, which reduces its yield. We used for the first time a high-throughput Illumina MiSeq sequencing approach to explore the composition, diversity, and functions of fungal and bacterial communities of the bulk and rhizosphere in soils of native C. quinoa affected by monocropping in the central Andes of Peru. The results showed that the bacterial and fungal community structure among the treatments was significantly changed by the monocropping and the types of soil (rhizosphere and bulk). Also, in soils subjected to monocropping, there was an increase in Actinobacteria and a decrease in Proteobacteria, and the reduction in the presence of Ascomycota and the increase in Basidiomycota. By alpha-diversity indices, lower values of bacteria and fungi were observed in the monoculture option compared to the soil not affected by monocropping, and sometimes significant differences were found between both. We detected differentially abundant phytopathogenic fungi and bacteria with growth-stimulating effects on plants. Also, we denoted a decrease in the abundance of the functional predictions in bacteria in the monocropped soils. This research will serve as a starting point to explore the importance and effects of microorganisms in degraded soils and their impact on the growth and quality of quinoa crops.

Improvement effect of biochar on soil microbial community structure and metabolites of decline disease bayberry.

Decline disease is a new disease that has recently caused severe damage in bayberry industry. The effect of biochar on decline disease was determined by investigating the changes in the vegetative growth and fruit quality of bayberry trees as well as soil physical and chemical properties, microbial community structure, and metabolites. Results indicated that the application of biochar could improve the vigor and fruit quality of diseased trees, and rhizosphere soil microbial diversity at the levels of phyla, orders, and genera. The relative abundance of Mycobacterium, Crossiella, Geminibasidium, and Fusarium were significantly increased, while Acidothermus, Bryobacter, Acidibacter, Cladophialophora, Mycena, and Rickenella were significantly decreased by biochar in rhizosphere soil of decline diseased bayberry. Analysis of redundancies (RDA) of microbial communities and soil characteristics revealed that the composition of bacterial and fungal communities was significantly affected by the pH, organic matter, alkali hydrolyzable nitrogen, available phosphorus, available potassium, exchangeable calcium and exchangeable magnesium in bayberry rhizosphere soil, and the contribution rates to fungi were larger than those to bacteria at the genus level. Biochar greatly influenced the metabolomics distribution of rhizosphere soils of decline disease bayberry. One hundred and nine different metabolites from both the presence and absence of biochar, mainly include acid, alcohol, ester, amine, amino acid, sterol, sugar, and other secondary metabolites, of which the contents of 52 metabolites were increased significantly such as aconitic acid, threonic acid, pimelic acid, epicatechin, and lyxose. The contents of 57 metabolites decreased significantly, such as conduritol β-expoxide, zymosterol, palatinitol, quinic acid, and isohexoic acid. There was a great difference between the absence and presence of biochar in 10 metabolic pathways, including thiamine metabolism, arginine and proline metabolism, glutathione metabolism, ATP-binding cassette (ABC) transporters, butanoate metabolism, cyanoamino acid metabolism, tyrosine metabolism, phenylalanine metabolism, phosphotransferase system (pts), and lysine degradation. There was a significant correlation between the relative content of microbial species and the content of secondary metabolites in rhizosphere soil at the levels of bacterial and fungal phyla, order, and genus. Overall, this study highlighted the significant influence of biochar in decline disease by regulating soil microbial community, physical and chemical properties, and secondary metabolites in rhizosphere soil, which provided a novel strategy for managing bayberry decline disease.

Exogenous application of Bradyrhizobium japonicum AC20 enhances soybean tolerance to atrazine via regulating rhizosphere soil microbial community and amino acid, carbohydrate metabolism related genes expression

Atrazine is used to control broad-leaved weeds in farmland and has negative impacts on soybean growth. Legume-rhizobium symbiosis plays an important role in regulating abiotic stress tolerance of plants, however, the mechanisms of rhizobia regulate the tolerance of soybean to atrazine based on the biochemical responses of the plant-soil system are limited. In this experiment, Glycine max (L.) Merr. Dongnong 252, planted in 20 mg kg−1 of atrazine-contaminated soil, was inoculated with Bradyrhizobium japonicum AC20, and the plant growth, rhizosphere soil microbial diversity and the expression of the genes related to soybean carbon and nitrogen metabolism were assessed. The results indicated that strain AC20 inoculation alleviated atrazine-induced growth inhibition via increasing the contents of leghemoglobin and total nitrogen in soybean seedlings. The psbA gene expression level of the soybean seedlings that inoculated strain AC20 was 1.4 times than that of no rhizobium inoculating treatments. Moreover, the inoculated AC20 increased the abundance of Acidobacteria and Actinobacteria in soybean rhizosphere. Transcriptome analysis demonstrated that strain AC20 regulated the genes expression of amino acid metabolism and carbohydrate metabolism of soybean seedlings. Correlation analysis between 16S rRNA and transcriptome showed that strain AC20 reduced Planctomycetes abundance so as to down-regulated the expression of genes Glyma. 13G087800, Glyma. 12G005100 and Glyma.12G098900 involved in starch synthesis pathway of soybean leaves. These results provide available information for the rhizobia application to enhance the atrazine tolerate in soybean seedlings.

Effect of Biochar on Rhizosphere Soil Microbial Diversity and Metabolism in Tobacco-Growing Soil

In this study, four different biochar application rates and a control were set up using indoor potted tobacco, to study the effects of biochar on the microbial diversity and metabolism of tobacco-growing soil. The five treatments were as follows: control—0% biochar (w/w) + 26 g fertilizer/pot; biochar treatments—1% biochar (w/w) + 26 g fertilizer/pot, 2% biochar (w/w) + 26 g fertilizer/pot, 3% biochar (w/w) + 26 g fertilizer/pot, and 4% biochar (w/w) + 26 g fertilizer/pot. We found that biochar increases the microbial diversity of soils and simultaneously changes the microbial community structure. Under the influence of biochar, soil urease activity increased by 18%, invertase activity increased by 23.40%, polyphenol oxidase activity increased by 59.50%, and catalase activity increased by 30.92%. Biochar also significantly increased the microbial biomass carbon and nitrogen content of the soil. Soil microbial biomass nitrogen had a positive correlation on bacterial diversity, with the highest coefficient, while soil microbial biomass carbon had a positive correlation on fungal diversity, with the highest coefficient. The microbial diversity and metabolic capacity of soil are improved under the influence of biochar, and soil enzyme activity and microbial biomass carbon and nitrogen have positive impacts on soil microbial diversity.

Novel liquid organic fertilizer: A potential way to effectively recycle spent mushroom substrate

A novel liquid organic fertilizer (LOF) was made from spent mushroom substrate (SMS) and then the resultant fertilizer (SMS-LOF) was applied on Pak-choi in this study. Results showed that SMS-LOF could enhance the production of Pak-choi by approximately 30% and improve the nutrients level of soil. The application of SMS-LOF also changed the microbial diversity of rhizosphere soil. At genus level, the microbial community was predominated by Bacillus (9.5%), RB41 (6.81%) and Sphingomonas (4.07%) for unfertilized soil, whereas they separately took up 8.65%, 5.27% and 4.81% under fertilized condition. The mechanisms exploration indicated that a plant hormone (indole-3-acetic acid, IAA) was synthesized probably through Pseudomonas and tryptophan during the anaerobic fermentation of liquid SMS, which together with macronutrients and microelements promoted the plant growth. On the whole, SMS-LOF can serve as an appropriate liquid organic fertilizer, most likely a potential way to effectively recycle spent mushroom substrate.

Changes in Microbial Diversity, Soil Function, and Plant Biomass of Cotton Rhizosphere Soil Under the Influence of Chlorpyrifos

Chlorpyrifos (CPF), a common organophosphorus pesticide, is extensively used in agricultural practices. However, we lack sound evidence for the linkage between soil microbial diversity, soil function, and plant biomass under the influence of CPF, which prevents us from assessing the actual impact of CPF on agricultural production. In this study, we used high-throughput sequencing to test the effects of CPF on soil microbial diversity, soil function, and cotton biomass in indoor pot experiments. The use of CPF leads to a significant reduction in cotton biomass until the concentration of CPF used reaches 15mgkg-1, and the cotton biomass is no longer significantly reduced. Compared with the original soil, the alpha-diversity of bacteria, which was significantly linearly related to cotton biomass, was significantly decreased when the soil was treated with 15mgkg-1 CPF. Affected by CPF, the overall soil microbial composition has changed significantly. Acidobacteria, Nitrospirae, Planctomycetes, and Actinobacteria were significantly regulated after CPF treatment. Correspondingly, key soil functions, including nitrogen metabolism and iron (III) transporter, have been significantly down-regulated. The reduction of nitrogen and Fe3+ should deprive the cotton of essential nutrients during the short crop cycle and thus affect cotton biomass. Our study provides experimental evidence that CPF affects cotton rhizosphere soil microbial diversity, the relative content of key bacterial genera, and soil function, which shows that it has an important impact on plant biomass, and provides a reference for studying the actual impact of CPF on the environment and agricultural production.

Effects of nitrogen application after abrupt drought-flood alternation on rice root nitrogen uptake and rhizosphere soil microbial diversity

Abrupt drought-flood alternation is a frequent meteorological disaster that occurs during the summer in southern China. This study sought to clarify the composition of the bacterial community in the rhizosphere soil of rice under nitrogen (N) application after abrupt drought-flood alternation and to provide more basic data for understanding N absorption by the roots system under N application after abrupt drought-flood alternation. The activity of N metabolism enzymes and the N content and N accumulation in various organs improved under N application after abrupt drought-flood alternation. Between the T1_N and T1 comparison groups, 1758 differentially expressed genes were identified, including 1027 upregulated and 731 downregulated genes. Transcriptomic GO and KEGG analyses indicated that nitrate assimilation, response to bacterium, defence response to bacterium, and N compound metabolic processes were enriched. At the phylum level, Proteobacteria, Acidobacteria, Nitrospirota, and Gemmatimonadota were the dominant flora. The root glutamine synthetase activity was significantly negatively correlated with Nitrospirota. Nitrospirota is a key taxon regulating rice root N absorption under N application after abrupt drought-flood alternation. N application after abrupt drought-flood alternation promoted the rapid recovery ability of plants and improved the microbial environment in rice. This study preliminarily clarified the role of microorganisms in the root uptake of rice under N application after abrupt drought-flood alternation. • This study was subjected to RNA-seq and 16S rRNA gene technology. • Abrupt drought-flood alternation changed rice rhizosphere soil microbial environment. • The nitrospirota of T1_N is the dominant flora at the phylum level. • Response to bacterium, nitrogen compound metabolic processes were enriched between T1_N and T1.

Network Analysis Reveals the Combination of Controlled-Release and Regular Urea Enhances Microbial Interactions and Improves Maize Yields.

Increased complexity of microbial networks can contribute to increased biodiversity and multifunctionality and thus crop productivity. However, it is not clear which combination ratio of regular and controlled-release urea will increase the soil microbial community complexity and improve maize yield in the North China Plain. To address this knowledge gap, a 2-year field experiment was conducted to explore the effects of the combination of regular (U) and controlled release (S) urea ratios [no fertilizer control (CT), regular urea alone (U), controlled-release urea alone (S), controlled-release urea mixed with regular urea 3:7 (SU3), controlled-release urea mixed with regular urea 5:5 (SU5), and controlled-release urea mixed with regular urea 7:3 (SU7)] on XianYu 688 yield and its rhizosphere and bulk soil microbial community composition and network complexity at different fertility stages. The combination of controlled-release and regular urea increased the N agronomic efficiency, N partial factors productivity, maize yield, and grain number per spike, with the maximum maize yield (9,186 kg ha–1) being achieved when the ratio of controlled-release urea to regular urea was 3:7 (SU3, p < 0.05). Maize yield increased by 13% in the SU3 treatment compared to the CT treatment. Rhizosphere soil microbial diversity remained stable at the silking stage of maize while increased at the physiological maturity stage of maize, with the increasing controlled-release to regular N fertilizer ratios (from 3:7 to 7:3, p < 0.05). This result suggests that a combination of regular and controlled-release N fertilizer can still substantially increase soil microbial diversity in the later stages of maize growth. The combination of controlled-release and regular urea is more effective in improving microbial network total links and average degree, and N agronomic efficiency (R2 = 0.79, p < 0.01), N partial factor productivity (R2 = 0.79, p < 0.01), spikes per unit area (R2 = 0.54, p < 0.05), and maize yield (R2 = 0.42, p < 0.05) increased with the microbial network complexity. This result indicates that the higher microbial network complexity is strongly associated with the higher N agronomic efficiency and N partial factors productivity and maize yield. In conclusion, the ratio of controlled-release to regular urea at SU3 not only increases the yield of maize and N agronomic efficiency but also enhances microbial diversity and network complexity in the North China Plain.