Rhizosphere Bacterial Communities Research Articles

Root Traits and Soil Bacterial Composition Explain the Rhizosphere Effects along a Chronosequence of Rubber Plantations

Rubber tree plantations (Hevea brasiliensis) are expanding into the tropical regions of southwest China to ensure production to meet the growing demand for latex. The effects of long-term plantations on soil carbon processes are still unclear. Also, the effects of the plant’s rhizosphere on the decomposition of soil organic matter (SOM) play a crucial role in predicting soil carbon dynamics. The rhizosphere and soils corresponding to a chronosequence of ages (4, 15 and 30 years) of rubber plantations were collected and incubated to determine the effect of the rhizosphere (RE) on SOM decomposition. We also examined the soil physicochemical properties; bacterial community structure; and root morphological, chemical, and physiological traits to further explore the underlying mechanisms of the RE on SOM decomposition. The REs on SOM decomposition varied significantly in the different age classes of the rubber plantations, and the higher the REs on SOM decomposition in an older plantation might limit the accumulation of organic carbon in the soil. Root traits, including the specific root length, root nitrogen content, and root carbon/nitrogen ratio, varied significantly in response to the plantation age and explained more of the variance in the RE on SOM decomposition than the soil and microbial properties. Due to the changing root morphological and chemical traits along the age chronosequence, the rhizosphere bacterial community composition tended to shift the carbon utilisation strategy and the bulk soil nitrogen content decreased. These variations also affected the RE on SOM decomposition. Our results indicate that the development of rubber plantations would prevent soil carbon accumulation, especially in the rhizosphere, by increasing the RE on SOM decomposition, which would be predicated by root morphological and chemical traits.

Rare and abundant bacterial communities in poplar rhizosphere soils respond differently to genetic effects

Interactions between plants and soil microbes are important to plant hybrid breeding under global change. However, the relationship between host plants and rhizosphere soil microorganisms has not been fully elucidated. Understanding the rhizosphere microbial structure of parents and progenies would provide a deeper insight into how genetic effects modulate the relationship between plants and soil. In this study, two family groups of poplar trees (A: parents and their two progenies; B: parents and their one progeny) with different genetic backgrounds (including seven genotypes) were selected from a common garden, and their rhizobacterial communities were analyzed to explore parent-progeny relationships. Our results showed significant differences in phylogenetic diversity, the number of 16S genes and the structure of rhizosphere bacterial communities (Adonis: R2 = 0.166, P < 0.01) between different family groups. Rhizosphere bacterial community structure was significantly dominated by genetic effects. Compared with abundant taxa, genetic effects were more powerful drivers of rare taxa. In addition, bacterial communities of hybrid progenies were all significantly more similar to their parents compared to the other group of parents, especially among rare taxa. The two poplar family groups exhibited differences between their rhizosphere bacterial co-occurrence networks. Group B had a relatively complex network with 2380 edges and 468 nodes, while group A had 1829 edges and 304 nodes. Soil organic carbon and carbon to nitrogen ratio (C/N) also influenced the rhizosphere bacterial community assembly. This was especially true for soil C/N, which explained 23 % of the β-nearest taxon index (βNTI) variation in rare taxa. Our results reveal the relationship of rhizosphere microorganisms between parents and progenies. This can help facilitate an understanding of the combination of plant breeding with microbes resource utilization and provide a theoretical basis for scientific advancement to support the development of forestry industry.

Agronomic strategies to enhance the early vigor and yield of maize. Part I: the role of seed applied biostimulant, hybrid and starter fertilization on rhizosphere bacteria profile and diversity.

The sustainable intensification of maize-based systems may reduce greenhouse-gas emissions and the excessive use of non-renewable inputs. Considering the key role that the microbiological fertility has on crop growth and resilience, it is worth of interest studying the role of cropping system on the rhizosphere bacterial communities, that affect soil health and biological soil fertility. In this work we monitored and characterized the diversity and composition of native rhizosphere bacterial communities during the early growth phases of two maize genotypes of different early vigor, using a nitrogen (N)-phosphorus (P) starter fertilization and a biostimulant seed treatment, in a growth chamber experiment, by polymerase chain reaction-denaturing gradient gel electrophoresis of partial 16S rRNA gene and amplicon sequencing. Cluster analyses showed that the biostimulant treatment affected the rhizosphere bacterial microbiota of the ordinary hybrid more than that of the early vigor, both at plant emergence and at the 5-leaf stage. Moreover, the diversity indices calculated from the community profiles, revealed significant effects of NP fertilization on richness and the estimated effective number of species (H2) in both maize genotypes, while the biostimulant had a positive effect on plant growth promoting community of the ordinary hybrid, both at the plant emergence and at the fifth leaf stage. Our data showed that maize genotype was the major factor shaping rhizosphere bacterial community composition suggesting that the root system of the two maize hybrids recruited a different microbiota. Moreover, for the first time, we identified at the species and genus level the predominant native bacteria associated with two maize hybrids differing for vigor. These results pave the way for further studies to be performed on the effects of cropping system and specific crop practices, considering also the application of biostimulants, on beneficial rhizosphere microorganisms.

Tetracycline inhibits the nitrogen fixation ability of soybean (Glycine max (L.) Merr.) nodules in black soil by altering the root and rhizosphere bacterial communities

Tetracycline is a widely used antibiotic and may thus also be an environmental contaminant with an influence on plant growth. The aim of this study was to investigate the inhibition mechanisms of tetracycline in relation to soybean growth and ecological networks in the roots and rhizosphere. To this end, we conducted a pot experiment in which soybean seedlings were grown in soil treated with 0, 10, or 25 mg/kg tetracycline. The effects of tetracycline pollution on growth, productivity, oxidative stress, and nitrogenase activity were evaluated. We further identified the changes in microbial taxa composition and structure at the genus and species levels by sequencing the 16S rRNA gene region. The results showed that tetracycline activates the antioxidant defense system in soybeans, which reduces the abundance of Bradyrhizobiaceae, inhibits the nitrogen-fixing ability, and decreases the nitrogen content in the root system. Tetracycline was also found to suppress the formation of the rhizospheric environment and decrease the complexity and stability of bacterial networks. Beta diversity analysis showed that the community structure of the root was markedly changed by the addition of tetracycline, which predominantly affected stochastic processes. These findings demonstrate that the influence of tetracycline on soybean roots could be attributed to the decreased stability of the bacterial community structure, which limits the number of rhizobium nodules and inhibits the nitrogen-fixing capacity. This exploration of the inhibitory mechanisms of tetracycline in relation to soybean root development emphasises the potential risks of tetracycline pollution to plant growth in an agricultural setting. Furthermore, this study provides a theoretical foundation from which to improve our understanding of the physiological toxicity of antibiotics in farmland.

Foliar Spraying of Chlorpyrifos Triggers Plant Production of Linolenic Acid Recruiting Rhizosphere Bacterial Sphingomonas sp.

Plants have developed an adaptive strategy for coping with biotic or abiotic stress by recruiting specific microorganisms from the soil pool. Recent studies have shown that the foliar spraying of pesticides causes oxidative stress in plants and leads to changes in the rhizosphere microbiota, but the mechanisms by which these microbiota change and rebuild remain unclear. Herein, we provide for the first-time concrete evidence that rice plants respond to the stress of application of the insecticide chlorpyrifos (CP) by enhancing the release of amino acids, lipids, and nucleotides in root exudates, leading to a shift in rhizosphere bacterial community composition and a strong enrichment of the genus Sphingomonas sp. In order to investigate the underlying mechanisms, we isolated a Sphingomonas representative isolate and demonstrated that it is both attracted by and able to consume linolenic acid, one of the root exudates overproduced after pesticide application. We further show that this strain selectively colonizes roots of treated plants and alleviates pesticide stress by degrading CP and releasing plant-beneficial metabolites. These results indicate a feedback loop between plants and their associated microbiota allowing to respond to pesticide-induced stress.

Soil amendment with insect frass and exuviae affects rhizosphere bacterial community, shoot growth and carbon/nitrogen ratio of a brassicaceous plant

AimsIn terrestrial ecosystems, deposition of insect frass and cadavers in the soil influences soil characteristics, including microbial community composition, with consequences for plant growth and development. Insect frass and exuviae are also a major residual stream from insect production for food and feed, that may be used as soil amendment. However, only few studies have thoroughly examined the effect of soil amendment with insect frass and exuviae on rhizosphere microbial communities and plant growth.MethodsWe studied the effects of soil amendment with frass and/or exuviae originating from three insect species, Tenebrio molitor, Acheta domesticus, and Hermetia illucens, at three different concentrations, compared to synthetic fertiliser. At several time points we analysed the rhizosphere bacterial community and assessed multiple plant-growth parameters of a brassicaceous plant.ResultsSoil amendment with frass and/or exuviae improved plant growth at least as well as synthetic fertiliser, A. domesticus exuviae having the strongest impact. The origin (insect species), type (frass or exuviae) and concentration of soil amendment influenced the effects on plant traits. The rhizosphere bacterial community differed between amended and unamended soil. Bacterial genera that contain plant growth-promoting species were more abundant in the rhizosphere of plants grown in amended soil.ConclusionsAddition of insect frass and/or exuviae to the soil differentially affects the bacterial rhizosphere community and promotes plant growth in these soils, underlining their unique roles in the aboveground-belowground feedback loop, and their potential use as soil amendment in circular agriculture.

Simulated phytoremediation by root exudates of Sudan grass of soil organochlorine pesticides: impact on the rhizosphere microbial community.

The present work aims to study the efficiency of root exudates of Sudan grass on the degradation of organochlorine pesticides (OCPs) and the consequent impact on the microbial and ecological characteristics of the soil, including population composition, quantity dynamics, and community structure. Pot experiments were carried out to study the effect of root exudates on the degradation of OCPs at initial concentrations ranging from 66.67 to 343.61mg/kg. In addition, the influence of root exudates on the rhizosphere microbial growth and their community structure was studied by monitoring the microbial biomass carbon, microbial biomass nitrogen, and phospholipid fatty acids (PLFAs) in the soils. In the range of OCP content (66.67 ~ 343.61mg/kg), the soil-microbial system mediated by root exudates significantly promoted the removal of OCP pollutants. The removal rate of OCPs in the rhizosphere soil (TR2) was as high as 79.32%, 36.86% higher than that in the OCP-contaminated group (TR1) and 60.63% higher than that in the sterilized treatment group (CK). Under the same treatment conditions (pollution level and additive dose), the enhanced removal rate of HCHs, toxaphene, HCB, aldrin, and γ-chlordane by root exudates was much higher than the total amount of OCPs, while the extent of enhanced dissipation of DDTs, mirex, endosulfanI, dieldrin, and heptachlor epoxide was always lower than that in the corresponding soils. During the experiment, the phospholipid fatty acid content of bacteria was dominant, followed by that of fungi, and their variation trend was consistent with the degradation characteristics of OCPs in soil. Root exudates of Sudan grass might change the rhizosphere bacterial and fungal community structure during the process of phytoremediation, leading to enhanced OCP degradation.

The Composition and Function of the Rhizosphere Bacterial Community of Paeonia lactiflora Varies with the Cultivar.

The composition and diversity of the rhizosphere microbial community maintain the stability of the root microclimate, and several studies have focused on this aspect of rhizosphere microorganisms. However, how these communities vary with cultivars of a species is not completely understood. Paeonia lactiflora-a perennial herb species of the family Paeoniaceae-includes a wide variety of cultivars, with rich rhizosphere microbial resources. Hence, we studied the differences in rhizosphere bacterial communities associated with eight P. lactiflora cultivars. We noted that Actinobacteria, Proteobacteria, Acidobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia, Planctomycetes and Chloroflexi were the dominant phyla associated with the cultivars. The composition of rhizosphere bacterial community of different cultivars was highly similar at taxonomic levels, but there were slightly differences in the relative abundance. LEfSe analysis showed that the cultivars "Sheng Tao Hua" and "Zi Lou Xian Jin" exhibited the most biomarkers. Differential ASV analysis revealed the maximum difference in ASV abundance between "Lian Tai" and "Zi Hong Zheng Hui", as well as between "Sheng Tao Hua" and "Tao Hua Fei Xue", and the maximum similarity between "Duo Ye Zi" and "Xue Feng". Co-occurrence network analysis revealed that rhizosphere bacteria in most cultivars maintain homeostasis by cooperation, wherein Actinobacteria and Proteobacteria played a vital role. In addition, microbial resources related to cultivars like bioremediation, organic degradation and resistance to diseases are found. This study revealed the structures of the rhizosphere bacterial communities associated with different cultivars of P. lactiflora and explored their stress resistance potential, which can be used to guide future agricultural practices.

Effects of nanoscale zinc oxide treatment on growth, rhizosphere microbiota, and metabolism of Aconitum carmichaelii.

Trace elements play a crucial role in the growth and bioactive substance content of medicinal plants, but their utilization efficiency in soil is often low. In this study, soil and Aconitum carmichaelii samples were collected and measured from 22 different locations, followed by an analysis of the relationship between trace elements and the yield and alkaloid content of the plants. The results indicated a significant positive correlation between zinc, trace elements in the soil, and the yield and alkaloid content of A. carmichaelii. Subsequent treatment of A. carmichaelii with both bulk zinc oxide (ZnO) and zinc oxide nanoparticles (ZnO NPs) demonstrated that the use of ZnO NPs significantly enhanced plant growth and monoester-type alkaloid content. To elucidate the underlying mechanisms responsible for these effects, metabolomic analysis was performed, resulting in the identification of 38 differentially expressed metabolites in eight metabolic pathways between the two treatments. Additionally, significant differences were observed in the rhizosphere bacterial communities, with Bacteroidota and Actinobacteriota identified as valuable biomarkers for ZnO NP treatment. Covariation analysis further revealed significant correlations between specific microbial communities and metabolite expression levels. These findings provide compelling evidence that nanoscale zinc exhibits much higher utilization efficiency compared to traditional zinc fertilizer.

Rice bacterial leaf blight drives rhizosphere microbial assembly and function adaptation.

Our results suggest that rhizosphere bacteria are more sensitive to bacterial leaf blight (BLB) than fungi. BLB infection decreased the diversity of the rhizosphere bacterial community but increased the complexity and size of the rhizosphere microbial community co-occurrence networks. In addition, the relative abundance of the genera Streptomyces, Chitinophaga, Sphingomonas, and Bacillus increased significantly. Finally, these findings contribute to the understanding of plant-microbiome interactions by providing critical insight into the ecological mechanisms by which rhizosphere microbes respond to phyllosphere diseases. In addition, it also lays the foundation and provides data to support the use of plant microbes to promote plant health in sustainable agriculture, providing critical insight into ecological mechanisms.

Enhancing nutrient recovery from food waste anaerobic digestate

The study synthesised the raw liquid fraction of digestate into a nutrient rich solid digestate through acidification whilst preventing nitrogen loss through ammonium volatilisation during evaporation. To stabilise ammonium in the digestate, it was acidified with sulphuric, nitric, and phosphoric acid to produce solid digestate with ammonium sulphate, ammonium nitrate and ammonium phosphate, respectively. These treatments were compared against urea ammonium nitrate, raw digestate, and unacidified solid digestate. To evaluate the effect of these transformed digestate products in soil, a plant growth experiment (Kikuyu; Cenchrus clandestinus) was conducted, and characterised, plant growth, soil chemistry, and rhizosphere bacterial communities. Plant growth was enhanced by all digestate treatments compared to control and urea ammonium nitrate. Ammonium phosphate solid digestate plant growth was significantly higher than all other acidified treatments due to the high P content. Moreover, digestate-amended soil had elevated Proteobacteria and putative denitrification genes.

Mechanism and Association between Microbial Nitrogen Transformation in Rhizosphere and Accumulation of Ciprofloxacin in Choysum (Brassica parachinensis).

Rhizosphere microbiota are an important factor impacting plant uptake of pollutants. However, little is known about how microbial nitrogen (N) transformation in the rhizosphere affects the uptake and accumulation of antibiotics in plants. Here, we determined recruitment of N transformation functional bacteria upon ciprofloxacin (CIP) exposure, by comparing differences in assembly processes of both rhizospheric bacterial communities and N transformation between two choysum (Brassica parachinensis) varieties differing in CIP accumulation. The low accumulation variety (LAV) of CIP recruited more host bacteria (e.g., Nitrospiria and Nitrolancea) carrying nitrification genes (mainly nxrA) but fewer host bacteria carrying denitrification genes, especially narG, relative to the high accumulation variety (HAV) of CIP. The nxrA and narG abundance in the LAV rhizosphere were, respectively, 1.6-7.8 fold higher and 1.4-3.4 fold lower than those in the HAV rhizosphere. Considering that nitrate can decrease CIP uptake into choysum through competing for the proton motive force and energy, such specific bacteria recruitment in LAV favored the production and utilization of nitrate in its rhizosphere, thus limiting its CIP accumulation with 1.6-2.4 fold lower than the HAV. The findings give insight into the mechanism underlying low pollutant accumulation, filling the knowledge gap regarding the profound effects of rhizosphere microflora and N transformation processes on antibiotic accumulation in crops.

Community structures of mangrove endophytic and rhizosphere bacteria in Zhangjiangkou National Mangrove Nature Reserve

Bacterial communities play an important role in mangrove ecosystems. In order to gain information on the bacterial communities in mangrove species and rhizospheres grown in Zhangjiangkou National Mangrove Nature Reserve, this study collected root, branch, and leaf samples from five mangrove species as well as rhizosphere and non-rhizosphere samples and analyzed the community structure of endophytic bacteria and bacteria in rhizosphere and non-rhizosphere using Illumina high-throughput sequencing technique. Bacteria in 52 phyla, 64 classes, 152 orders, 295 families, and 794 genera were identified, which mainly belonged to Proteobacteria, Cyanobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Fusobacteria, and Nitrospirota. At each taxonomic level, the community structure of the rhizosphere bacteria varied slightly with mangrove species, but endophytic bacteria differed greatly with plant species. The diversity indices of endophytic bacteria in branch and leaf samples of Acanthus ilicifolius were significantly lower, and endophytic bacteria in the plant tissues had higher abundance in the replication/repair and translation Clusters of Orthologous Genes functional categories but lower abundance in the carbohydrate metabolism category. This study helps to understand the community structure and diversity characteristics of endophytic and rhizosphere bacteria in different mangrove plants. Provide a theoretical basis for in-depth research on the functions of mangrove ecosystems.

Effects of Pruning on Growth, Rhizosphere Soil Physicochemical Indexes and Bacterial Community Structure of Tea Tree and Their Interaction

Pruning is an agronomic practice that contributes to tea tree yield during cultivation, but little is known about how pruning improves yield through shifting bacterial communities in rhizosphere soil. Therefore, Meizhan tea (Camellia sinensis) was used as the research object to analyze the effect of unpruning and pruning on the growth and rhizosphere soil physicochemical indexes of the tea tree, and sequencing technology was used to obtain the diversity of soil bacterial communities. The results showed that leaf area, hundred bud weight and yield of pruned tea trees increased by 1.32, 1.40, and 1.84 times, respectively, and pH and available N, available P, and available K contents increased by 1.10, 1.07, 1.30, and 1.07 times, respectively, compared with unpruned treatment, while total N, total P, and total K contents decreased by 1.20, 1.37, and 1.13 times, respectively. Analysis of the bacterial community structure showed that the key differential bacteria between pruned and unpruned tea trees were Candidatus Solibacter, Acidibacter, Rhizomicrobium, Bryobacter, Solanum torvum, Mizugakiibacter, Nitrospira, Sphingomonas, and Granulicella. Among them, the bacterial abundance of Candidatus Solibacter, Bryobacter, and Nitrospira showed an upward trend and the rest showed a downward trend after pruned treatment. Interaction network analysis showed that the correlation between the total key genera of microorganisms and organic matter, total N, total K, and total P content in rhizosphere soil did not reach a significant level, whereas the correlation with soil available N, available K, available P, pH, and tea tree growth indexes were all positively and significantly correlated. It can be seen that pruning changed the structure of the rhizosphere soil microbial community of tea trees, promoted soil nutrient transformation, increased the content of soil available nutrients, and promoted the growth of tea tree.

Effects of Chlortetracycline on the Growth of Eggplant and Associated Rhizosphere Bacterial Communities

The widespread use of tetracycline antibiotics in the poultry and cattle sectors endangers both human health and the terrestrial ecosystem. Chlortetracyclines (CTCs), in particular, have been proven to affect soil microorganisms in addition to plants in the terrestrial ecosystem. In order to assess the effects of CTC on soil properties, eggplant growth, and soil microorganisms, a potted experiment was carried out in this study. CTC significantly reduced the levels of ammonium nitrogen (NH4+–N) and nitrite nitrogen (NO2−–N) in soil. Meanwhile, the eggplant’s growth was clearly hampered. CTC dramatically and dose-dependently lowered the fluorescence parameters except the quantum yield of non-regulated energy dissipation (ΦNO). Rhodoplanes and Cupriavidus, which were involved in N cycle, were enriched by 10 mg/kg CTC, according to results about different microorganisms at the genus level. Flavisolibacter was reduced by 10 and 50 mg/kg CTC, while Methylosinus and Actinocorallia were enriched by 250 mg/kg CTC. Redundancy analysis highlighted the profound impact of CTC on the soil microbial community, where strong correlations were observed with soil potential of hydrogen (pH), nitrate nitrogen (NO3−–N), and NO2−–N. These findings demonstrated the interdependence between the microbial community and soil characteristics, with CTC primarily affecting the microbes responsible for nitrogen cycling. Consequently, chlortetracycline poses potential hazards to both eggplant plants and the soil microbes in eggplant cultivation soil.

Maize straw application reduced cadmium and increased arsenic uptake in wheat and enhanced the rhizospheric bacterial communities in alkaline-contaminated soil

Many fields where wheat is grown in northern China are co-polluted by arsenic (As) and cadmium (Cd). Thus, remediation of As and Cd-contaminated alkaline soils is crucial for safe wheat production. In this study, a pot experiment was carried out to investigate the impact of 1% and 2% maize straw (MS) incorporation on As and Cd bioavailability, binding forms, uptake by winter wheat (Triticum aestivum L.), and bacterial communities in smelter (SS) and irrigation (IS) alkaline contaminated soils. The results indicated that 2% MS incorporation significantly (p < 0.05) increased bioavailable-As by 37% (SS) and 39% (IS) with no significant change in the bioavailable-Cd in SS2% (31.95%) from 31.95% (SSCK) and IS2% (33.33%) from 32.82% (ISCK). Incorporation of 2% MS increased the grain As concentration from 0.22 mg kg−1 (SSCK) to 0.51 mg kg−1 (SS2%) and from 0.59 mg kg−1 (ISCK) to 0.84 mg kg−1 (IS2%) which is above the acceptable standard of 0.5 mg kg−1 (GB2726-2017). In contrast, the Cd content in grains was maintained at 0.09 (SS1%), 0.04 (SS2%) and 0.03 (IS1%), 0.02 (IS2%) below the acceptable standard of 0.10 mg kg−1 (GB2762–2017). The amendment through dissolved organic carbon mediated As desorption enhanced As transfer to wheat grain, decreasing DTPA-Cd in the soils and its consequent translocation to wheat leaves and grain. The 2% MS incorporation increased the active As fractions, reduced mobile Cd into immobile fractions, and promoted the abundance of Actinobacteria, Bacteroidetes, and Firmicutes in the two soils. These attributes of MS in decreasing the accumulation of Cd in wheat leaves and grains signified its potential as a suitable ingredient for Cd sequestration and food safety in Cd-contaminated soils.

Impact of Rhizobacterial Inoculants and Organic Amendment on Bacterial Communities of Jerusalem artichoke Tissue and Rhizosphere by using Denaturing Gradient Gel Electrophoresis

The application of organic amendments can improve soil quality and influence bacterial communities, contributing to enhanced soil health in agricultural systems. This study investigated the effect of using rain tree leaf, corn husk, and peat moss as soil amendments, supplemented with plant growth promoting rhizobacteria on communities of bacteria in the tissue and rhizosphere of Jerusalem artichoke. The plants were observed for 120 days after transplanting. Polymerase chain reaction-denaturing gradient gel electrophoresis (DGGE) technique was used to investigate the impact of both organic amendments and bacterial consortium with comparative profiles. Comparison DGGE profile by clustering analysis did not clearly separate each organic amendment and bacterial inoculation, but principal component analysis (PCA) revealed that plant age had an influence on tissue and rhizosphere bacterial communities. The results indicated that soil amendments and bacterial inoculation had no effect on bacterial community shifts. Interestingly, the genera of bacteria able to most colonize in the tissue and rhizosphere were the uncultured bacteria. Thus, we provide promising data for boosting Jerusalem artichoke growth and soil quality with potential organic amendments to improve soil with sustainable strategies.

Soil nutrient management influences diversity, community association and functional structure of rhizosphere bacteriome under vegetable crop production.

Rhizosphere bacterial communities play a crucial role in promoting plant and soil ecosystem health and productivity. They also have great potential as key indicators of soil health in agroecosystems. Various environmental factors affect soil parameters, which have been demonstrated to influence soil microbial growth and activities. Thus, this study investigated how rhizosphere bacterial community structure and functions are affected by agronomic practices such as organic and conventional fertiliser application and plant species types. Rhizosphere soil of vegetable crops cultivated under organic and conventional fertilisers in different farms was analysed using high-throughput sequencing of the 16S rRNA gene and co-occurrence network pattern among bacterial species. The functional structure was analysed with PICRUSt2 pipeline. Overall, rhizosphere bacterial communities varied in response to fertiliser type, with soil physicochemical parameters, including NH4, PO4, pH and moisture content largely driving the variations across the farms. Organic farms had a higher diversity richness and more unique amplicon sequence variants than conventional farms. Bacterial community structure in multivariate space was highly differentiated across the farms and between organic and conventional farms. Co-occurrence network patterns showed community segmentation for both farms, with keystone taxa more prevalent in organic than conventional farms. Module hub composition and identity varied, signifying differences in keystone taxa across the farms and positive correlations between changes in microbial composition and ecosystem functions. The organic farms comprised functionally versatile communities characterised by plant growth-promoting keystone genera, such as Agromyces, Bacillus and Nocardioides. The results revealed that organic fertilisers support high functional diversity and stronger interactions within the rhizosphere bacterial community. This study provided useful information about the overall changes in soil microbial dynamics and how the changes influence ecosystem functioning under different soil nutrient management and agronomic practices.

The Influence of the Genotype and Planting Density on the Structure and Composition of Root and Rhizosphere Microbial Communities in Maize.

Maize has the largest cultivation area of any crop in the world and plays an important role in ensuring food security. High-density planting is essential for maintaining high maize yields in modern intensive agriculture. Nonetheless, how high-density planting and the tolerance of individual genotypes to such planting shape the root-associated microbiome of maize is still unknown. In this study, we analyzed the root and rhizosphere bacterial communities of two maize accessions with contrasting shoot architectures grown under high- and low-density planting conditions. Our results suggested that maize hosted specific, distinct bacterial communities in the root endocompartment and that the maize genotype had a significant effect on the selection of specific microbes from the rhizosphere. High-density planting also had significant effects on root-associated bacterial communities. Specifically, genotype and high-density planting coordinated to shape the structure, composition, and function of root and rhizosphere bacterial communities. Taken together, our results provide insights into how aboveground plant architecture and density may alter the belowground bacterial community in root-associated compartments of maize.

Root chemistry and microbe interactions contribute to metal(loid) tolerance of an aromatic plant – Vetiver grass

Aromatic plants, such as vetiver grass (Chrysopogon zizanioides), possess strong abilities to resist environmental stresses. However, whether such abilities stem from the interaction between specific chemical characteristics and the associated microbes in roots and rhizosphere remains unclear. We conducted pot experiments to analyze stress-tolerant parameters, organic compounds, and bacterial communities in roots and rhizosphere of vetiver under typical metal(loid) stress [cadmium (Cd), arsenic (As), or Cd + As] over time. The results showed that the vetiver displayed limited toxic symptoms in terms of oxidative stress-antioxidant balance and chlorophyll content. The root low-molecular-weight organic acids (LMWOAs), fatty acids, and sterols were highly sensitive to growth stage (increased from the 4-month to the 8-month stage), and less sensitive to metal(loid) stress. The sugar contents in the rhizosphere soils also notably increased over time. Such endo and rhizosphere chemical changes strongly correlated with and enriched the functional bacteria including Streptomyces, which can resist stress and promote plant growth. The compound-bacteria interaction highly depended on growth stage. Vetiver demonstrated a progressive adaptation to stresses through metabolite modulation and cellular defense reinforcement. Our study evidenced that vetiver shapes the interaction between organic compounds and bacterial community in the root-soil interface and provides notable stress-resistant functions.