Rhizosphere Microbial Diversity Research Articles

Microbial communities in crop phyllosphere and root endosphere are more resistant than soil microbiota to fertilization

Crop harbors diverse microbial communities that profoundly influence host health and agricultural productivity. Crop habitat is a dynamic and heterogeneous environment, and thus crop microbiota may display spatial organization across different compartments. However, impacts of long-term fertilization, as a common agricultural practice, on the assembly of crop microbiota and their relationships with crop yield and quality remain largely unresolved. Here, we collected sorghum roots and leaves, and rhizosphere and bulk soils, from an eight-year field experiment with multiple fertilization regimes, and characterized sorghum-associated microbiomes by amplicon sequencing of bacterial 16S rRNA gene and fungal ITS region. Rhizosphere and bulk soils harbored significantly higher diversity of bacteria and fungi than phyllosphere and root endophytes, and the microbial community composition significantly differed across the four compartments. Fertilization significantly influenced the diversity and compositions of sorghum-associated microbial communities, but had more pronounced effects on rhizosphere and bulk soil microbiomes through altering the relative abundances of some major microbial biomarkers. Bacterial genera Lysobacter, Acidibacter, Steroidobacter, RB41, and Blastococcus, and fungal genera Fusarium and Guehomyces were the dominant microbial predictors of sorghum yield and protein content. Structural equation models revealed that fertilization had a positive and indirect effect on sorghum yield and protein content through influencing the microbial diversity in rhizosphere and bulk soils. We provide novel evidence that microbial communities in sorghum phyllosphere and root endosphere are more resistant than soil microbiota to long-term fertilization, and soil microbiota are important predictors of sorghum yield and protein content.

Intercropping Alters the Soil Microbial Diversity and Community to Facilitate Nitrogen Assimilation: A Potential Mechanism for Increasing Proso Millet Grain Yield.

Intercropping of cereals and legumes has been used in modern agricultural systems, and the soil microorganisms associated with legumes play a vital role in organic matter decomposition and nitrogen (N) fixation. This study investigated the effect of intercropping on the rhizosphere soil microbial composition and structure and how this interaction affects N absorption and utilization by plants to improve crop productivity. Experiments were conducted to analyze the rhizosphere soil microbial diversity and the relationship between microbial composition and N assimilation by proso millet (Panicum miliaceum L.) and mung bean (Vigna radiata L.) from 2017 to 2019. Four different intercropping row arrangements were evaluated, and individual plantings of proso millet and mung bean were used as controls. Microbial diversity and community composition were determined through Illumina sequencing of 16S rRNA and internal transcribed spacer (ITS) genes. The results indicated that intercropping increased N levels in the soil–plant system and this alteration was strongly dependent on changes in the microbial (bacterial and fungal) diversities and communities. The increase in bacterial alpha diversity and changes in unique operational taxonomic unit (OTU) numbers increased the soil N availability and plant N accumulation. Certain bacterial taxa (such as Proteobacteria) and fungal taxa (such as Ascomycota) were significantly altered under intercropping and showed positive responses to increased N assimilation. The average grain yield of intercropped proso millet increased by 13.9–50.1% compared to that of monoculture proso millet. Our data clearly showed that intercropping proso millet with mung bean altered the rhizosphere soil microbial diversity and community composition; thus, this intercropping system represents a potential mechanism for promoting N assimilation and increasing grain yield.

Changes in rhizosphere microbial diversity and composition due to NaCl addition to the soil modify the outcome of maize-weed interactions

Increases in salt concentration in the soil may occur as a consequence of manure and fertilizer application. We have hypothesized that changes in the structure of rizhosphere microbial communities, caused by increased salt, lead to distinct outcomes of crop-weed ecological interactions. Here, we have evaluated the outcomes of Zea mays-weed coexistence as a function of changes in the structure of the rhizosphere microbial communities due to NaCl addition to the soil. The growth of two weed species, Amaranthus viridis and Bidens pilosa, and the crop Z. mays, was evaluated in the greenhouse under two management conditions, monoculture and plant coexistence, with and without NaCl addition to the soil. Total DNA from the microbial populations in the rhizosphere soil was extracted, followed by PCR amplification and sequencing using the Illumina MiSeq platform. NaCl addition caused significant changes in bacterial diversity and in the structure and composition of bacterial and fungal taxa. These changes were associated to the outcome of maize-weed interactions. The rhizosphere soil microbiota was more sensitive to NaCl addition than the plants. For the interaction between maize and B. pilosa, the ecological interaction changed from competition to facilitation after NaCl addition. This could be attributed to the changes in the rhizosphere microbial community structure rather than to increases in soil electrical conductivity (EC) since this variable did not affect plant growth. Thus, the influence of rhizosphere microbial communities on plant-plant interactions should be taken into account for the development of integrated weed management practices.

Chetoui Olive Cultivar Rhizosphere: Potential Reservoir for Exoenzymes and Exopolysaccharides Producing Bacteria

Rhizospheric soils from cultivated olive (Olea europaea) trees of Chemlali, Chetoui, Quaissi, and Djalat cultivars were assessed for their bacterial abundance and diversity and were further screened for production of exopolysaccharides and exoenzymes (cellulase, chitinase, amylase, protease, lipase, and peroxidase). The results of the present study indicate that Chetoui cultivar revealed higher diversity, followed by Chemlali > Quaissi > Djalat, wherein, bacilli, enteric bacteria, and pseudomonads were abundantly present as specific bacterial groups associated with the Chetoui rhizosphere. Moreover, the exopolysaccharide (EPS)-producing bacteria of Chetoui cultivar (68.4%) presented the highest efficiency, followed by Djalat (23.5%) > Chemlali (7 %) > Quaissi (1%). These results revealed that the Chetoui cultivar presented highest enzyme activities, followed by Chemlali > Djalat > Quaissi, with a distinct abundance of peroxidase- and chitinase-producing bacteria, which may play a pivotal role in adapting olives to the environmental stresses. From this preliminary study, we confirmed that olive rhizosphere microbial diversity is essentially driven by the geographical origin and genotype of olive cultivars. Furthermore, we recommended the Chetoui olive cultivar rhizosphere as a potential reservoir for exoenzyme- and EPS-producing bacteria useful for future biotechnological applications.

Diminished rhizosphere and bulk soil microbial abundance and diversity across succession stages in Karst area, southwest China

Soil microorganisms are important for plant nutrients and health. However, our understanding of soil microbial communities in the rhziosphere and bulk soils as plant succession stages increased in the Karst area remains unclear. Here, we evaluated how the bacterial and fungal communities of rhizosphere and bulk soils respond to different vegetation succession stages: grassland (GR), shrubland (SH), secondary forest (SF), and primary forest (PF). The abundance and composition of bacteria and fungi were determined by qPCR and MiSeq high-throughput sequencing methods, respectively. The results showed that the abundance and diversity in rhizosphere and bulk soils were diminished among vegetation succession stages. We found that SOC led to high microbial abundance in GR and SH during the period of primary succession stages, while AP potentially led to low abundance of microbes in the PF and SF of subsequent succession stages. Additionally, the OTUs shared by four succession stages (common OTUs) comprised approximately 87.61 ‐ 98.90% of the total relative abundance of bacteria and fungi in the rhizosphere and bulk soils, which indicated that the composition of fungi and bacteria in these environments were similar across different succession stages. pH might be an important driving factor involved in the similarity of bacterial and fungal compositions among different succession stages. However, the relative abundance of bacterial and fungal phyla across the four vegetation stages was different, and also determined by multiple soil properties. pH was the main factor determining bacterial community structure in rhizosphere soils, whereas SOC was the principal determinant of the same parameter for bacteria in bulk soils, and in both the rhizosphere and bulk soils for fungi. Overall, our results suggested that bacterial and fungal communities in the rhizosphere and bulk soils diminished with vegetation stages, which may provide evidence that mechanisms underlying the soil microbe-driven vegetation succession in the Karst area of southwest China.

Hydrological and soil physiochemical variables determine the rhizospheric microbiota in subtropical lakeshore areas.

BackgroundDue to intensive sluice construction and other human disturbances, lakeshore vegetation has been destroyed and ecosystems greatly changed. Rhizospheric microbiota constitute a key part of a functioning rhizosphere ecosystem. Maintaining rhizosphere microbial diversity is a central, critical issue for sustaining these rhizospheric microbiota functions and associated ecosystem services. However, the community composition and abiotic factors influencing rhizospheric microbiota in lakeshore remain largely understudied.MethodsThe spatiotemporal composition of lakeshore rhizospheric microbiota and the factors shaping them were seasonally investigated in three subtropical floodplain lakes (Lake Chaohu, Lake Wuchang, and Lake Dahuchi) along the Yangtze River in China through 16S rRNA amplicon high-throughput sequencing.ResultsOur results showed that four archaeal and 21 bacterial phyla (97.04 ± 0.25% of total sequences) dominated the rhizospheric microbiota communities of three lakeshore areas. Moreover, we uncovered significant differences among rhizospheric microbiota among the lakes, seasons, and average submerged depths. The Acidobacteria, Actinobacteria, Bacteroidetes, Bathyarchaeota, Gemmatimonadetes, and Proteobacteria differed significantly among the three lakes, with more than half of these dominant phyla showing significant changes in abundance between seasons, while the DHVEG-6, Ignavibacteriae, Nitrospirae, Spirochaetes, and Zixibacteria varied considerably across the average submerged depths (n = 58 sites in total). Canonical correspondence analyses revealed that the fluctuation range of water level and pH were the most important factors influencing the microbial communities and their dominant microbiota, followed by total nitrogen, moisture, and total phosphorus in soil. These results suggest a suite of hydrological and soil physiochemical variables together governed the differential structuring of rhizospheric microbiota composition among different lakes, seasons, and sampling sites. This work thus provides valuable ecological information to better manage rhizospheric microbiota and protect the vegetation of subtropical lakeshore areas.

Contrasting Responses of Rhizosphere Bacteria, Fungi and Arbuscular Mycorrhizal Fungi Along an Elevational Gradient in a Temperate Montane Forest of China.

Elevational gradients strongly affect microbial biodiversity in bulk soil through altering plant and soil properties, but the effects on rhizosphere microbial patterns remain unclear, especially at large spatial scales. We therefore designed an elevational gradient experiment to examine rhizosphere microbial (bacteria, fungi and arbuscular mycorrhizal fungi) diversity and composition using Illumina sequencing of the 16S rRNA and ITS genes for comparison to plant and soil properties. Our results showed that bacterial and fungal alpha diversity was significantly higher at mid-elevation, while AMF alpha diversity decreased monotonically. The beta diversities of the three groups were significantly affected by elevational gradients, but the effect on bacterial beta diversity was larger than on fungal and AMF beta diversity. Proteobacteria, the dominant phyla of bacteria, was significantly higher at the mid-elevation, while Acidobacteria and Actinobacteria significantly decreased as elevation increased. The main fungal taxa, Basidiomycota, significantly decreased with elevation, and Ascomycota significantly increased with elevation. Glomeromycota, the dominant AMF phyla, responded insignificantly to the elevational gradients. The responses of bacterial and fungal alpha diversity were mostly associated with tree diversity and organic carbon, whereas AMF alpha diversity mainly depended on litter N and P. Changes in bacterial community composition along the elevational gradient were explained primarily by litter N and P, and litter P was the main driver of fungal and AMF community composition. Overall, our results suggest that plant litter, particularly litter N and P, were the main source of external carbon input and drove the observed differences in rhizosphere microbial diversity and community composition. Our results highlight the importance of litter nutrition in structuring rhizosphere microbial communities in mountain ecosystems.

Inoculations with Pseudomonas fluorescens and Bacillus cereus affect the soil enzyme activity, growth and rhizosphere microbial diversity of Taxus chinensis var. mairei

Taxus chinensis var. mairei is a rare tree endemic to China. Pseudomonas fluorescens CLW17 and Bacillus cereus CLY07 were isolated from the T. chinensis var. mairei rhizosphere and the two strains were efficient phosphate-solubilizing bacteria. We investigated the effect of inoculation with P. fluorescens CLW17 and B. cereus CLY07 on soil enzyme activity, growth and the rhizosphere microbial diversity of Taxus chinensis var. mairei over different time periods. The plant biomass, seedling height, stem diameter and root vitality were measured, so that the inoculation effects of the two bacterial strains on T. chinensis var. mairei seedlings could be evaluated. Three types of soil enzymes (alkaline phosphatase, invertase and dehydrogenase) were identified. The soil microbial community composition and diversity were determined by high-throughput pyrosequencing analysis. Inoculation with P. fluorescens CLW17 and B. cereus CLY07 significantly increased plant biomass, seedling height, stem diameter and root vitality, and improved soil enzyme activities (alkaline phosphatase, invertase and dehydrogenase) (P < 0.05) in T. chinensis var. mairei. High-throughput pyrosequencing of 16S and 18S rRNA genes revealed minor changes in the diversity, relative abundance, and composition of the microbial community in the T. chinensis var. mairei rhizosphere after inoculation. Inoculation with P. fluorescens CLW17 and B. cereus CLY07 promoted T. chinensis var. mairei growth and improved the soil enzyme activity with a small change in rhizosphere microbial diversity. This study provides necessary insight for developing effective, cheap and safe inoculants of strains P. fluorescens CLW17 and B. cereus CLY07 for T. chinensis var. mairei.

Increasing methane (CH4) emissions and altering rhizosphere microbial diversity in paddy soil by combining Chinese milk vetch and rice straw.

BackgroundChinese milk vetch (Astragalus sinicus L.) can improve paddy soil fertility and ecology through nitrogen fixation, but it can also increase greenhouse gas emissions. Our primary objective was to investigate how Chinese milk vetch, rice straw, and nitrogen fertilization affect the methane and microbial components of the rice rhizosphere.MethodsWe examined the rhizosphere’s methane emissions and microbial abundance and diversity after incorporating Chinese milk vetch and rice straw into paddy soil. We used high-throughput sequencing of the 16s rRNA and ITS1 genes to study changes in the bacterial and fungal communities, respectively. Over the course of our experiment, we applied seven different treatments to the paddy soil: conventional fertilization (the control treatment) for winter fallow crops, three levels of nitrogen in Chinese milk vetch, and three levels of nitrogen in Chinese milk vetch combined with rice straw.ResultsRice yield and methane emissions increased during cultivation when the soil was treated with Chinese milk vetch with and without added straw. The nitrogen application also affected the methane fluxes. Alpha diversity measurements showed that Chinese milk vetch increased the diversity of the soil fungal community but did not significantly affect the bacterial community. Chinese milk vetch affected the rhizosphere microorganism communities by increasing the number of Methanomicrobia.

Effects of inorganic and organic treatments on the microbial community of maize rhizosphere by a shotgun metagenomics approach

PurposeThe main drivers of biogeochemical cycling of nutrients, plant growth promotion, and disease suppression are microbes. Organic manure increases soil quality and plant productivity; the same is true of inorganic fertilizer. In this study, we explored shotgun metagenomics study to investigate how maize (Zea mays everta) rhizosphere microbial community diversity is shaped following the application of both compost manure and inorganic fertilizer.MethodsWe used high throughput next-generation sequencing—metagenomics studies to examine the rhizosphere microbial community of maize plants grown in an organic compost manure (8 tons/ha and 4 tons/ha) and inorganic (120 kg/ha NPK and 60 kg/ha NPK chemical) fertilized soils. An unfertilized soil was used as a control.ResultsThe taxonomic analysis of the soil revealed that regardless of the fertilization regimes, Proteobacteria and Bacteroidetes are distributed across all the samples, but in varying populations. Higher quantities of organic manure (8 tons/ha) and lower (60 kg/ha) nitrogen fertilizer, as well as the untreated control, supports the selection and enrichment of Proteobacteria and Actinobacteria, while lower quantities of organic compost (4 tons/ha) manure boost the population of Bacteroidetes. Firmicutes, on the other hand, were most abundant in low organic manure (4 tons/ha) and higher inorganic (120 kg/ha) fertilized soil. Fungi were selected and enriched by higher (8 tons/ha) and lower (4 tons/ha) compost manure, while archaea were mostly supported by higher doses of inorganic fertilizers (120 kg/ha) and high compost manure (8 tons/ha) treatments.ConclusionTherefore, comprehending the effects of compost and chemical fertilizers (NPK—20% nitrogen, 7% phosphorus, 3% potassium) on the community structure, dynamics, and abundance of rhizosphere microbiome will help in the manipulation of soil microbial community to increase microbial diversity in the agroecosystem.

High-Throughput Sequencing Reveals the Diversity and Community Structure in Rhizosphere Soils of Three Endangered Plants in Western Ordos, China.

China's western Ordos is a distribution area for the extremely precious remnants of ancient Asian environments, which in endangered plant species and complex ecosystems. Accordingly, in this study, we collect three endangered plants belonging to the Zygophyllaceae family, namely Tetraena mongolica, Sarcozygium xanthoxylon, and Nitraria tangutorum Bobr. High-throughput sequencing technology was applied to study microbial diversity in these plant rhizosphere soils. Analysis of species composition abundance, Alpha diversity, Beta diversity and microbial structure are analyzed. 2428 bacterial OTUs and 1256 fungal OTUs are obtained from the rhizosphere soils, and the bacterial and fungal sequencing coverage is above 99%. Bacilli are the most abundant (86.91%) in the bacterial community. The fungal community has significant differences in three plants. The abundances of the genus Dothideomycetes in the rhizosphere soils of Tetraenamongolica and Sarcozygium xanthoxylon plants are the highest, which are 44.57% and 37.69%, respectively. Thus, Dothideomycetes is the dominant bacteria in the community. The genus Sordariomycetes in the rhizosphere soil is the dominant fungi with a relative abundance of 41.04%. Redundancy analysis revealed that microbial communities were closely related to environmental factors. Overall, this study bring new insights into the relationship between rhizosphere soils microbial diversity and environment to improving the adaptability of theendangered plants in survival environment.

Functional diversity of rhizosphere soil microbial communities in response to different tillage and crop residue retention in a double-cropping rice field.

Microbial community functional diversity is a sensitive indicator of soil quality, soil management such as tillage and crop residue which can affect the microbial community functional diversity of paddy field. However, there is still limited information about the influence of different tillage and crop residue management on rhizosphere soil microbial community functional diversity in a double-cropping rice (Oryza sativa L.) field. Therefore, four tillage treatments were set up in paddy field, tillage treatments were included: conventional tillage with residue incorporation (CT), rotary tillage with residue incorporation (RT), no-tillage with residue retention (NT), and rotary tillage with residue removed as control (RTO). And the effects of CT, RT, NT, and RTO treatments on the average well color development (AWCD), genetic diversity indices and carbon source utilization of rhizosphere soil were studied in the present paper. The results showed that the values of AWCD with CT, RT and NT treatments were higher than that of RTO treatment. It was implied that application of crop residue management resulted in the variation of the carbon utilization efficiency of rhizosphere soil microbial communities. At maturity stages of early and late rice, the Richness indices, Shannon indices and McIntosh indices with CT treatment were significantly higher than that of RTO treatment, and with the order as CT>RT>NT>RTO. Principal component analysis (PCA) results indicated that there were significant differences in carbon substrate utilization patterns among different tillage treatments. Carbohydrates and amino acids were the main carbon resources utilized by rhizosphere soil microbes. Therefore, the combined application of tillage with crop residue management could significantly increase the rhizosphere soil microbial community functional diversity in the double-cropping paddy field of southern China.

Simultaneous reduction of arsenic and cadmium bioavailability in agriculture soil and their accumulation in Brassica chinensis L. by using minerals.

In situ immobilization of heavy metal cations in contaminated soil using natural minerals is an attractive remediation technique. However, little research has focused on the remediation of arsenic (As) and cadmium (Cd) co-contaminated. In this work, three different crystal structures and chemical compositions minerals, zeolite; bentonite; and dolomite, were applied to simultaneously reduce the uptake of As and Cd in Brassica chinensis L., and the mechanism on reducing As and Cd bioavailability in soil were also investigated. The results showed that the three minerals decreased the bioavailability of As and Cd and restrained their uptake by Brassica chinensis L. with the order followed bentonite>zeolite>dolomite. Particularly, bentonite decreased the exchangeable As and Cd by 4.05% and 32.5% and the concentrations of As and Cd in shoots of Brassica chinensis L. by 36.2% and 64.6%, as compared with the controls. Moreover, with the addition of minerals increased, the dry biomass of Brassica chinensis L. and the rhizosphere microbial functional diversity increased significantly, and the highest biomass increased by 289% at 4.0% addition of bentonite. Correlation analysis indicated that the uptake of As and Cd was positive with the available Cd and As in soil, and was negative with soil pH and available N. Furthermore, the Scanning Electron Microscopy-Energy Dispersive Spectroscopy and Fourier Transform Infrared Spectroscopy analysis illustrated the interaction between minerals and Cd mainly involved ion-exchange and adsorption, while As was mainly immobilized by calcium and magnesium through forming precipitation. In conclusion, this present study implied that the bentonite can be recommended as the more effective amendment to immobilize metal (loid)s in soil and thereby reduce the exposure risk of metal (loid)s associated with grains consumption.

Low Nitrogen Fertilization Alter Rhizosphere Microorganism Community and Improve Sweetpotato Yield in a Nitrogen-Deficient Rocky Soil.

Sweetpotato can be cultivated in the reclaimed rocky soil in Sichuan Basin, China, which benefits from the release of mineral nutrients in the rocky soil by microorganisms. Shortage of nitrogen (N) in the rocky soil limits sweetpotato yield, which can be compensated through N fertilization. Whereas high N fertilization inhibits biological N fixation and induces unintended environmental consequences. However, the effect of low N fertilization on microorganism community and sweetpotato yield in the N-deficient rocky soil is still unclear. We added a low level of 1.5 g urea/m2 to a rocky soil cultivated with sweetpotato, and measured rocky soil physiological and biochemical properties, rhizosphere microbial diversity, sweetpotato physiological properties and transcriptome. When cultivating sweetpotato in the rocky soil, low N fertilization (1.5 g urea/m2) not only improved total N (TN) and available N (AN) in the rocky soil, but also increased available phosphorus (AP), available potassium (AK), and nitrogenase and urease activity. Interestingly, although low N fertilization could reduce bacterial diversity through affecting sweetpotato root exudates and rocky soil properties, the relative abundance of P and K-solubilizing bacteria, N-fixing and urease-producing bacteria increased under low N fertilization, and the relative abundance of plant pathogens decreased. Furthermore, low N fertilization increased the phytohormones, such as zeatin riboside, abscisic acid, and methyl jasmonate contents in sweetpotato root. Those increases were consistent with our transcriptome findings: the inhibition of the lignin synthesis, the promotion of the starch synthesis, and the upregulated expression of Expansin, thus resulting in promoting the formation of tuberous roots and further increasing the sweetpotato yield by half, up to 3.3 kg/m2. This study indicated that low N fertilization in the N-deficient rocky soil improved this soil quality through affecting microorganism community, and further increased sweetpotato yield under regulation of phytohormones pathway.

Effect of rhizospheric inoculation of isolated arsenic (As) tolerant strains on growth, As-uptake and bacterial communities in association with Adiantum capillus-veneris.

Two arsenic (As) hyper-tolerant bacterial strains NM01 Paracoccus versutus and NM04 Aeromonas caviae were isolated from As polluted site of West Bengal, India. The strains not only possess the potential to tolerate up to 20,000mgl-1 As(V) and 10,000mgl-1 As(III) but also possess plant growth promoting (PGP) traits like phosphate solubilization, siderophore production, IAA production. Greenhouse pot experiments were conducted to assess the effect of rhizospheric inoculation of both the strains individually and in consortia in As accumulation by Adiantum capillus-veneries. It was observed that the microbial inoculation significantly (p<0.05) increased the synthesis of thiolic compounds and thus, enhanced As accumulation with translocation factor (TF)>1. The strains regulated endogenous phytohormone up to 90% and 77.9% increase in auxin of consortia inoculated root and shoot, respectively. Interestingly, inoculation of the isolated strains augmented rhizospheric microbial diversity which was negatively affected by heavy metal. The results of high-throughput Illumina MiSeq sequencing technique to observe the composition of the bacterial community revealed 11,536 unique bacterial operational taxonomic units (OTUs) from As+S (non-inoculated), whereas 11,884 from Consortia As+S (inoculated) rhizospheric soil samples. Inoculated soil displayed higher bacterial diversity indices (ACE and Chao 1) with the dominant bacterial phyla Proteobacteria, Actinobacteria and Firmicutes. Our results highlight the innate PGP abilities of the strains and its potential to facilitate phytoextraction by enhancing As accumulation in the shoot.

Biotransformation of the herbicide nicosulfuron residues in soil and seven sulfonylurea herbicides by Bacillus subtilis YB1: A climate chamber study

Bacillus subtilis YB1 is a strain that can efficiently transform nicosulfuron. In order to study its remediation ability and effects on other microorganisms in the soil, indoor biological remediation experiments and rhizosphere microbial diversity analysis were performed. B. subtilis YB1 granules were prepared and applied to the nicosulfuron contaminated soil. The concentration of nicosulfuron was detected by ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) and changes in the physiological indicators of wheat were measured. At the same time, the changes in the rhizosphere soil microbial diversity were determined by 16S RNA sequencing. Results showed that the YB1 granules made a contribution to the transformation of nicosulfuron (0.05 mg kg−1) in the soil within 55 days. The physiological indicators of wheat also showed consistent result about nicosulfuron transformation. Rhizosphere soil microbial diversity results indicated the relative abundance of Firmicutes decreased (3.0%–0.35%) and Acidobacteria first decreased (25.82%–22.38%) and then increased (22.3%–26.1%) with nicosulfuron added (N group). The relative abundance of Acidobacteria first decreased (25.8%–15.3%) and then increased (15.3%–21.7%) while Proteobacteria increased (26.5%–38.08%). At the same time, Firmicutes first increased (2.6%–12.3%) and then decreased to original level (12.3%–0.7%) in the N group with YB1 granules (NYB1 group). Members of the genus Bacillus initially increased and then decreased to the original level as the Control group, therefore, they did not become dominant in the rhizosphere soil. Alpha diversity analyses showed no obvious differences in species diversity among the N, NYB1 and Control groups. So YB1 did not have obvious influence on the rhizosphere microbial community structure during nicosulfuron transformation, which only had some effect on species abundance. This study revealed the successful indoor bioremediation of nicosulfuron in the soil, providing a potential strategy for solving the problem of nicosulfuron contamination.

Rhizosphere microbial diversity and community dynamics during potato cultivation

In order to understand the dynamic changes of in the rhizosphere microbiome during potato cultivation, we studied the rhizosphere microbial diversity and soil physical-chemical properties during the growth of potato plants in soil that had been under continuous cultivation for five years. The V3–V4 region from chromosomal prokaryotic 16S rRNA and the fungal ITS1-ITS2 region were sequenced by Illumina MiSeq technology. Both the bacterial and fungal communities were clearly different at the seedling stage compared with the first stage of potato pre-planting, and it stabilized at the flowering stage and then experienced relatively small changes until the potato crop matured. The relative abundance of Acidobacteria and Saccharibacteria in the bacterial community increased (p < 0.05) at the harvesting stage compared with the planting stage. At the seedling stage, the abundance of Bacteroidetes increased (p < 0.05), and that of Chloroflexi significantly decreased (p < 0.05). In the fungal community, the abundance of Ascomycota increased (p < 0.05) at the seedling stage, while the abundance of Basidiomycota decreased (p < 0.05). Soil pH and soil electrical conductivity declined over the course of potato cultivation, and the total salt levels decreased. Soil enzyme activities also differed at each potato growth stage. The growth and development period of potato was the main factor affecting the composition of rhizosphere microbial communities.

Research Advances of Beneficial Microbiota Associated with Crop Plants.

Plants are associated with hundreds of thousands of microbes that are present outside on the surfaces or colonizing inside plant organs, such as leaves and roots. Plant-associated microbiota plays a vital role in regulating various biological processes and affects a wide range of traits involved in plant growth and development, as well as plant responses to adverse environmental conditions. An increasing number of studies have illustrated the important role of microbiota in crop plant growth and environmental stress resistance, which overall assists agricultural sustainability. Beneficial bacteria and fungi have been isolated and applied, which show potential applications in the improvement of agricultural technologies, as well as plant growth promotion and stress resistance, which all lead to enhanced crop yields. The symbioses of arbuscular mycorrhizal fungi, rhizobia and Frankia species with their host plants have been intensively studied to provide mechanistic insights into the mutual beneficial relationship of plant–microbe interactions. With the advances in second generation sequencing and omic technologies, a number of important mechanisms underlying plant–microbe interactions have been unraveled. However, the associations of microbes with their host plants are more complicated than expected, and many questions remain without proper answers. These include the influence of microbiota on the allelochemical effect caused by one plant upon another via the production of chemical compounds, or how the monoculture of crops influences their rhizosphere microbial community and diversity, which in turn affects the crop growth and responses to environmental stresses. In this review, first, we systematically illustrate the impacts of beneficial microbiota, particularly beneficial bacteria and fungi on crop plant growth and development and, then, discuss the correlations between the beneficial microbiota and their host plants. Finally, we provide some perspectives for future studies on plant–microbe interactions.

Behavior of selected organophosphate flame retardants (OPFRs) and their influence on rhizospheric microorganisms after short-term exposure in integrated vertical-flow constructed wetlands (IVCWs)

Considering its ubiquitous occurrence and potential adverse effects of organophosphorus flame retardant (OPFR), it is urgent to explore the efficient treatment for OPFRs wastewater. Thus, integrated vertical-flow constructed wetlands (IVCWs) were set up to comparatively evaluate their nitrogen removal capacity under tidal flow operations and to investigate environmental behavior and rhizosphere microbial responses after short-term exposure to three OPFRs. The results show that IVCWs have an excellent TN removal rate (628.13 ± 110.63 mg m−2 d−1) and moderate mitigation efficiencies (48.37 ± 9.52 to 82.28 ± 7.48%) for target OPFRs when treating low-C/N ratio wastewater. Moreover, the sorption of selected OPFRs to soil (28.85–308.41 ng g−1, dry weight (dw)), igneous rock (659.85–970.80 ng g−1 dw) and zeolite (1045.60–1351.70 ng g−1 dw) and accumulation in tissues of C. alternifolius (0–289.68 ng g−1 dw) and P. australis (0.56–108.22 ng g−1 dw) showed a hydrophobicity-specific feature. Namely, the highly hydrophobic compound tricresyl phosphate (TCrP) partitioned preferentially to sediment, and the chlorinated analytes were more easily taken up and then translocated into the plant body. Simultaneously, further mass balance analysis revealed the fate of OPFRs in IVCW components. A total of 53.25% of the highly hydrophobic TCrP inflow mass settled in sediment, while tris (2-chloroethyl) phosphate (TCEP) and tris (1-chloro-2-propyl) phosphate (TCPP) were more liable to discharge (35.33–50.89%) and other pathways (38.77–39.87%). Furthermore, the abundance of aerobic denitrifying bacteria (AD) in rhizosphere soil (2.25–5.12%), jointly with the prevalence of nitrobacteria (NOBs, 1.84–13.60%) and denitrifying bacteria (DNBs, 5.84–7.89%) in sublayer matrices, was responsible for superior TN removal. Additionally, the rhizosphere microbial richness, diversity and nitrogen-related microorganisms were clearly influenced by the presence of OPFRs. Notably, the genera Pseudomonas and Sphingobium might be the functional microorganisms for mixture OPFRs biodegradation.

Effect of vermicompost tea on rooibos (Aspalathus linearis) growth and rhizosphere microbial diversity under field conditions

Increasing demand for rooibos tea (Aspalathus linearis) requires producers to increase production in a sustainable manner. The aim of the study was to examine the effect of applying vermicompost tea (VCT) (100 and 500 L ha–1 month–1) and tap water drenches on one-year old rooibos nutrient uptake, and tea yields and rhizosphere microbial diversity under field conditions in the Nieuwoudtville region. The application of VCT solutions had no significant effect on rooibos survival or tea yields compared to the same volume of tap water. The application of tap water with or without VCT resulted in significant increases in plant survival (23–31% higher), resulting in lower tea yields (38–66% lower) likely due to increased plant competition. The application of VCT drench applied at 5 times the supplier’s recommendations (500 L ha–1 month–1) significantly enhanced foliar P and Fe and reduced foliar Al, attributed to the organic acids in VCT. VCT application at 100 L ha–1 significantly enhanced bacterial species diversity and decreased dominance. Further research is needed to identify which bacterial species are increasing with addition of vermicompost tea. Application of compost tea with higher mineral N content would likely be more beneficial for enhancing yields.