Rhizosphere Microbial Community Structure Research Articles

Linking Nitrogen Load to the Structure and Function of Wetland Soil and Rhizosphere Microbial Communities.

Wetland ecosystems are important reservoirs of biodiversity and significantly contribute to emissions of the greenhouse gases CO2, N2O, and CH4. High anthropogenic nitrogen (N) inputs from agriculture and fossil fuel combustion have been recognized as a severe threat to biodiversity and ecosystem functioning, such as control of greenhouse gas emissions. Therefore, it is important to understand how increased N input into pristine wetlands affects the composition and activity of microorganisms, especially in interaction with dominant wetland plants. In a series of incubations analyzed over 90days, we disentangled the effects of N fertilization on the microbial community in bulk soil and the rhizosphere of Juncus acutiflorus, a common and abundant graminoid wetland plant. We observed an increase in greenhouse gas emissions when N is increased in incubations with J.acutiflorus, changing the system from a greenhouse gas sink to a source. Using 16S rRNA gene amplicon sequencing, we determined that the bacterial orders Opitutales, subgroup 6 Acidobacteria, and Sphingobacteriales significantly responded to high N availability. Based on metagenomic data, we hypothesize that these groups are contributing to the increased greenhouse gas emissions. These results indicated that increased N input leads to shifts in microbial activity within the rhizosphere, altering N cycling dynamics. Our study provides a framework for connecting environmental conditions of wetland bulk and rhizosphere soil to the structure and metabolic output of microbial communities. IMPORTANCE Microorganisms living within the rhizospheres of wetland plants significantly contribute to greenhouse gas emissions. Understanding how microbes produce these gases under conditions that have been imposed by human activities (i.e., nitrogen pollution) is important to the development of future management strategies. Our results illustrate that within the rhizosphere of the wetland plant Juncus acutiflorus, physiological differences associated with nitrogen availability can influence microbial activity linked to greenhouse gas production. By pairing taxonomic information and environmental conditions like nitrogen availability with functional outputs of a system such as greenhouse gas fluxes, we present a framework to link certain taxa to both nitrogen load and greenhouse gas production. We view this type of combined information as essential in moving forward in our understanding of complex systems such as rhizosphere microbial communities.

Microorganisms reveal what plants do not: wheat growth and rhizosphere microbial communities after Azospirillum brasilense inoculation and nitrogen fertilization under field conditions

Azospirillum brasilense is one of plant growth promoting bacteria used to improve plant growth and grain yield of cereal crops. The level of inoculation response is defined by complex plant-microorganism interactions, many of them still unknown. Thus, we evaluated both agronomic response and microbial ecology of wheat crop under A. brasilense inoculation and nitrogen fertilization at field conditions in order to improve inoculation efficiency. Treatments were: control, nitrogen fertilization and inoculation with 40M and 42M strains. Functional and structural diversity of rhizosphere bacterial communities were evaluated by community-level physiological and terminal restriction fragment length polymorphism profiles. Besides, aerial biomass, grain yield and counts of microaerophilic diazotrophic rhizobacteria were determined. Plant ontogeny modified the number of culturable microaerophilic diazotrophic rhizobacteria. Although agronomic response did not show differences, plant ontogeny and the agricultural practices modified both physiology and genetic structure of rhizosphere microbial communities. Interestingly, these differences due to the treatments were observed at jointing stage but not at grain-filling stage of wheat. Our results demonstrate how different management decisions can change plant- microorganism relationships. While wheat could not show differences between some agricultural treatments, under the soil surface microbial communities could show them.

Biomass, activity and structure of rhizosphere soil microbial community under different metallophytes in a mining site

Microbial properties are often used to assess the recovery of soil health during phytoremediation. A field survey was conducted to test the effects of different plant metallophytes (excluder and hyperaccumulator) on soil microbial characteristics. Microbial properties in the rhizosphere of four metallophytes (Sedum alfredii, Rubus hunanensis, Lysimachia christinae and Clinopodium gracile) growing naturally on highly Cd-, Zn- and Pb-contaminated soils were investigated. Microbial biomass carbon, basal respiration, enzyme activities and phospholipid fatty acids were analyzed to study microbial community function and composition. The total microbial biomass, bacterial, actinomycete, fungal, and protozoan PLFAs, basal respiration and enzyme activities in the rhizosphere of metallophytes were significantly higher than in bulk soil. Moreover, the largest increases were found in the rhizosphere of the hyperaccumulator S. alfredii. The microbial community composition in the rhizosphere of S. alfredii was significantly different from the other 3 plants. Redundancy analysis showed that soil physico-chemical properties such as metal concentrations, labile carbon and pH explained most of the variation in microbial community biomass, activity and structure. Metallophytes using different strategies to adapt to metal-rich soils induced different effects on soil microbial properties, which were also influenced by physico-chemical characteristics.

Shifts in soil microbial community, soil enzymes and crop yield under peanut/maize intercropping with reduced nitrogen levels

A field experiment with five nitrogen (N) application rates (120, 140, 160, 180, 200kghm−2) under peanut/maize intercropping regime was conducted to evaluate cropping patterns and N application rates on yield, soil enzyme activities, and rhizosphere microbial community structure. The field experiment showed that the land equivalent ratio (LER) in maize/peanut intercropping system was not decreased as compared with the monoculture pattern, though the total N supply was approximately reduced by 20%. Terminal restriction fragment length polymorphism (T-RFLP) results showed that the treatments of intercropping (IMP100%, IMP80% and IMP60%) increased the abundance of Rhizobium hainanense, Rhizobium leguminosarum and Frankia which are associated with nitrogen fixation as compared to monoculture pattern (M100% and P100%). The qPCR results revealed that the copy number of nifH was significantly higher in the treatments of intercropping than in monoculture pattern. The result was also consistent with the T-RFLP analysis. In conclusion, peanut and maize under the condition of intercropping can promote the population of microorganisms associated with nitrogen-fixing in the rhizospheric soil. Our results provide a theoretical basis and technical support to soil N utilization, development of low carbon agriculture and protection of farmland ecological environment.

Variance of microbial composition and structure and relation with soil properties in rhizospheric and non-rhizospheric soil of a flooded paddy

Soil microbial structure and nutrient properties varied with fertilization and plant growth simultaneously in the rhizosphere. However, the relationships between rhizospheric microbial community structure and soil characteristics were still unclear. This study aimed to explore the impact of nitrogen (N) fertilizer and rice growth on microbial community structure and their relation with soil physiochemical properties. A pot experiment for rice-planting with two levels of N fertilization was conducted in a flooded paddy soil. At tillering and ripening stages, both rhizospheric and non-rhizospheric soils were sampled separately for physiochemical analysis, real-time quantitative PCR assay and terminal restriction fragment length polymorphism (T-RFLP) analysis. The results showed that both N addition and growth stage of rice could affect physiochemical properties of rhizosphere and non-rhizosphere soil simultaneously. At tillering stage, no significant difference of bacterial and archaeal gene abundance was observed, but rhizospheric abundance of microorganisms was significantly different with non-rhizosphere at ripening stage. One-way ANOVA analysis indicated that N addition has greater effect on microbial structure diversity of bacteria rather than archaea, non-rhizosphere than rhizosphere, respectively. Non-metric multidimensional scaling analysis showed two groups of bacterial community both in rhizospheric and in non-rhizospheric soils at tillering stage differing much, but similar at ripening stage. Redundancy analysis showed that the microbial community compositions at tillering stage were most correlated with NH4 +, total N (TN), pH, microbial biomass N (Nmic) and microbial biomass carbon (Cmir) whereas at ripening stage were more or less lined with Olsen-P, C/N ratio, total C (TC) and available K. Our research suggested that the N addition has more influence on community composition diversity of bacteria and non-rhizosphere. The growth stage might be the main factor affecting bacterial community structure both in rhizospheric and in non-rhizospheric soils affected by different soil parameters.

The plant circadian clock influences rhizosphere community structure and function.

Plants alter chemical and physical properties of soil, and thereby influence rhizosphere microbial community structure. The structure of microbial communities may in turn affect plant performance. Yet, outside of simple systems with pairwise interacting partners, the plant genetic pathways that influence microbial community structure remain largely unknown, as are the performance feedbacks of microbial communities selected by the host plant genotype. We investigated the role of the plant circadian clock in shaping rhizosphere community structure and function. We performed 16S ribosomal RNA gene sequencing to characterize rhizosphere bacterial communities of Arabidopsis thaliana between day and night time points, and tested for differences in community structure between wild-type (Ws) vs clock mutant (toc1-21, ztl-30) genotypes. We then characterized microbial community function, by growing wild-type plants in soils with an overstory history of Ws, toc1-21 or ztl-30 and measuring plant performance. We observed that rhizosphere community structure varied between day and night time points, and clock misfunction significantly altered rhizosphere communities. Finally, wild-type plants germinated earlier and were larger when inoculated with soils having an overstory history of wild-type in comparison with clock mutant genotypes. Our findings suggest the circadian clock of the plant host influences rhizosphere community structure and function.

Rhizosphere Microbial Diversity in Different Wetland Microcosms

To investigate the rhizosphere microbial community structure characteristics in varying combinations of plants and filter materials in the process of aquaculture pond water treatment, six types of wetland microcosms were established using two kinds of plants (Zizania latifolia Turcz. and Sagittaria graminea) and two types of filter materials (garnet and magnetite). High-throughput sequencing technology was used to analyze the microbial structural features and composition diversity of the wetland rhizosphere. The results were as follows. The microorganisms recovered belonged to 52 phyla, 118 classes, 455 families, 905 genera, and 1426 species. Based on the Shannon index, Zizania latifolia Turcz. (average value: 5.77) had a higher capacity than Sagittaria graminea(average value: 5.29) in terms of microbial enrichment. However, the rate of Proteobacteria in the rhizosphere microorganism communities of the Sagittaria graminea and Zizania latifolia Turcz. microcosms were 61.97% and 51.78%, respectively, further showing that the roots of Sagittaria graminea in the wetland microcosms better enriched the Proteobacteria during the experimental period. The major bacterial groups of different plant roots were enriched with β-Proteobacteria in the experiment. The results of this study provide a theoretical basis for species optimization in artificial wetland systems and best combination of wetland construction that will be useful for future investigations.

Impact of Transgenic Brassica napus Harboring the Antifungal Synthetic Chitinase (NiC) Gene on Rhizosphere Microbial Diversity and Enzyme Activities.

Transgenic Brassica napus harboring the synthetic chitinase (NiC) gene exhibits broad-spectrum antifungal resistance. As the rhizosphere microorganisms play an important role in element cycling and nutrient transformation, therefore, biosafety assessment of NiC containing transgenic plants on soil ecosystem is a regulatory requirement. The current study is designed to evaluate the impact of NiC gene on the rhizosphere enzyme activities and microbial community structure. The transgenic lines with the synthetic chitinase gene (NiC) showed resistance to Alternaria brassicicola, a common disease causing fungal pathogen. The rhizosphere enzyme analysis showed no significant difference in the activities of fivesoil enzymes: alkalyine phosphomonoestarase, arylsulphatase, β-glucosidase, urease and sucrase between the transgenic and non-transgenic lines of B. napus varieties, Durr-e-NIFA (DN) and Abasyne-95 (AB-95). However, varietal differences were observed based on the analysis of molecular variance. Some individual enzymes were significantly different in the transgenic lines from those of non-transgenic but the results were not reproducible in the second trail and thus were considered as environmental effect. Genotypic diversity of soil microbes through 16S–23S rRNA intergenic spacer region amplification was conducted to evaluate the potential impact of the transgene. No significant diversity (4% for bacteria and 12% for fungal) between soil microbes of NiC B. napus and the non-transgenic lines was found. However, significant varietal differences were observed between DN and AB-95 with 79% for bacterial and 54% for fungal diversity. We conclude that the NiC B. napus lines may not affect the microbial enzyme activities and community structure of the rhizosphere soil. Varietal differences might be responsible for minor changes in the tested parameters.

Ecological guild and enzyme activities of rhizosphere soil microbial communities associated with Bt-maize cultivation under field conditions in North West Province of South Africa.

Insecticidal proteins expressed by genetically modified Bt maize may alter the enzymatic and microbial communities associated with rhizosphere soil. This study investigated the structure and enzymatic activity of rhizosphere soil microbial communities associated with field grown Bt and non-Bt maize. Rhizosphere soil samples were collected from Bt and non-Bt fields under dryland and irrigated conditions. Samples were subjected to chemical tests, enzyme analyses, and next generation sequencing. Results showed that nitrate and phosphorus concentrations were significantly higher in non-Bt maize dryland soils, while organic carbon was significantly higher in non-Bt maize irrigated field soil. Acid phosphatase and β-glucosidase activities were significantly reduced in soils under Bt maize cultivation. The species diversity differed between fields and Bt and non-Bt maize soils. Results revealed that Actinobacteria, Proteobacteria, and Acidobacteria were the dominant phyla present in these soils. Redundancy analyses indicated that some chemical properties and enzyme activities could explain differences in bacterial community structures. Variances existed in microbial community structures between Bt and non-Bt maize fields. There were also differences between the chemical and biochemical properties of rhizosphere soils under Bt and non-Bt maize cultivation. These differences could be related to agricultural practices and cultivar type.

Crop rhizospheric microbial community structure and functional diversity as affected by maize and potato intercropping

ABSTRACTField trials were conducted to evaluate the effects of different cropping patterns (maize monocropping, maize and potato intercropping, potato monocropping) on microbial abundance, community structure, and microbial functional diversity using plate culture and Biolog technique. Results showed that compared with monocropping, intercropping increased the abundance of soil bacteria, fungi, and actinomyces in rhizosphere surrounding maize and potato. The average well color development (AWCD) and Shannon index (H) were higher in intercropping soil than that found in monocropping soil. The ability of rhizospheric soil microorganisms in utilizing six types of carbon sources had definite differences, and the most dominant community structure was the carbohydrates metabolic groups. Principal component analysis demonstrated that intercropping changed significantly soil microbial community functional diversity depending mainly on carbohydrates and carboxylic acids. Our findings suggested that maize–potato intercropping has positive effects on the improvement of soil microbial abundances, activity, and functional diversity.

Long-Term Rock Phosphate Fertilization Impacts the Microbial Communities of Maize Rhizosphere.

Phosphate fertilization is a common practice in agriculture worldwide, and several commercial products are widely used. Triple superphosphate (TSP) is an excellent soluble phosphorus (P) source. However, its high cost of production makes the long-term use of crude rock phosphate (RP) a more attractive alternative in developing countries, albeit its influence on plant-associated microbiota remains unclear. Here, we compared long-term effects of TSP and RP fertilization on the structure of maize rhizosphere microbial community using next generation sequencing. Proteobacteria were dominant in all conditions, whereas Oxalobacteraceae (mainly Massilia and Herbaspirillum) was enriched in the RP-amended soil. Klebsiella was the second most abundant taxon in the RP-treated soil. Burkholderia sp. and Bacillus sp. were enriched in the RP-amended soil when compared to the TSP-treated soil. Regarding fungi, Glomeromycota showed highest abundance in RP-amended soils, and the main genera were Scutellospora and Racocetra. These taxa are already described as important for P solubilization/acquisition in RP-fertilized soil. Maize grown on TSP and RP-treated soil presented similar productivity, and a positive correlation was detected for P content and the microbial community of the soils. The results suggest changes of the microbial community composition associated to the type of phosphate fertilization. Whilst it is not possible to establish causality relations, our data highlights a few candidate taxa that could be involved in RP solubilization and plant growth promotion. Moreover, this can represent a shorter path for further studies aiming the isolation and validation of the taxa described here concerning P release on the soil plant system and their use as bioinoculants.

Ecotoxicological assessment of pesticides and their combination on rhizospheric microbial community structure and function of Vigna radiata.

India is one of the leading countries in production and indiscriminate consumption of pesticides. Owing to their xenobiotic nature, pesticides affect soil microorganisms that serve as mediators in plant growth promotion. Our study aimed to deliver a comprehensive picture, by comparing the effects of synthetic pesticides (chlorpyriphos, cypermethrin, and a combination of both) with a biopesticide (azadirachtin) at their recommended field application level (L), and three times the recommended dosage (H) on structure and function of microbial community in rhizosphere of Vigna radiata. Effect on culturable fraction was assessed by enumeration on selective media, while PCR-denaturing gradient gel electrophoresis (DGGE) was employed to capture total bacterial community diversity. This was followed by a metabolic sketch using community-level physiological profiling (CLPP), to obtain a broader picture of the non-target effects on rhizospheric microbial community. Although plant parameters were not significantly affected by pesticide application, the microbial community structure experienced an undesirable impact as compared to control devoid of pesticide treatment. Examination of DGGE banding patterns through cluster analysis revealed that microbial community structure of pesticide-treated soils had only 70% resemblance to control rhizospheric soil even at 45days post application. Drastic changes in the metabolic profiles of pesticide-treated soils were also detected in terms of substrate utilization, rhizospheric diversity, and evenness. It is noteworthy that the effects exacerbated by biopesticide were comparable to that of synthetic pesticides, thus emphasizing the significance of ecotoxicological assessments before tagging biopesticides as "safe alternatives."

The rhizospheric microbial community structure and diversity of deciduous and evergreen forests in Taihu Lake area, China.

Soil bacteria are important drivers of biogeochemical cycles and participate in many nutrient transformations in the soil. Meanwhile, bacterial diversity and community composition are related to soil physic-chemical properties and vegetation factors. However, how the soil and vegetation factors affect the diversity and community composition of bacteria is poorly understood, especially for bacteria associated with evergreen and deciduous trees in subtropical forest ecosystems. In the present paper, the microbial communities of rhizospheric soils associated with different types of trees were analyzed by Illumina MiSeq sequencing the V3-V4 region of the 16S rRNA gene. A total of 121,219 effective 16S rRNA gene sequences were obtained, which were classified into 29 bacterial phyla and 2 archaeal phyla. The dominant phyla across all samples (>5% of good-quality sequences in each sample) were Proteobacteria, Acidobacteria, Firmicutes and Bacteroidetes. The bacterial community composition and diversity were largely affected by both soil pH and tree species. The soil pH was the key factor influencing bacterial diversity, with lower pH associated with less diverse communities. Meanwhile, the contents of NO3− were higher in evergreen tree soils than those associated with deciduous trees, while less NH4+ than those associated with deciduous trees, leading to a lower pH and indirectly influencing the diversity and composition of the bacteria. The co-occurrence patterns were assessed by network analysis. A total of 415 pairs of significant and robust correlations (co-occurrence and negative) were identified from 89 genera. Sixteen hubs of co-occurrence patterns, mainly under the phyla Acidobacteria, Proteobacteria, Firmicutes and Bacteroidetes, may play important roles in sustaining the stability of the rhizospheric microbial communities. In general, our results suggested that local environmental conditions and soil pH were important in shaping the bacterial community of the Taihu Lake zone in east China.

Linking the Belowground Microbial Composition, Diversity and Activity to Soilborne Disease Suppression and Growth Promotion of Tomato Amended with Biochar

Biochar, in addition to sequestering carbon, ameliorating soil, and improving plant performance, can impact foliar and soilborne plant diseases. Nevertheless, the mechanisms associated with suppression of soilborne diseases and improved plant performances are not well understood. This study is designed to establish the relationships between biochar-induced changes in rhizosphere microbial community structure, taxonomic and functional diversity, and activity with soilborne disease suppression and enhanced plant performance in a comprehensive fashion. Biochar suppressed Fusarium crown and root-rot of tomato and simultaneously improved tomato plant growth and physiological parameters. Furthermore, biochar reduced Fusarium root colonization and survival in soil, and increased the culturable counts of several biocontrol and plant growth promoting microorganisms. Illumina sequencing analyses of 16S rRNA gene revealed substantial differences in rhizosphere bacterial taxonomical composition between biochar-amended and non-amended treatments. Moreover, biochar amendment caused a significant increase in microbial taxonomic and functional diversity, microbial activities and an overall shift in carbon-source utilization. High microbial taxonomic and functional diversity and activity in the rhizosphere has been previously associated with suppression of diseases caused by soilborne pathogens and with plant growth promotion, and may collectively explain the significant reduction of disease and improvement in plant performance observed in the presence of biochar.

Striking alterations in the soil bacterial community structure and functioning of the biological N cycle induced by Pennisetum setaceum invasion in a semiarid environment

The objective of this study was to determine whether native and invasive plants harbor different bacterial communities in their rhizospheres and whether there are bacterial indicator species associated with the invasive rhizosphere. Additionally, physico-chemical, biochemical, and biological properties have been determined in the native and invasive rhizospheres in order to ascertain the relationships between these soil properties and the rhizosphere bacterial communities. We carried out a study in five independent locations under Mediterranean semiarid conditions, where the native Hyparrhenia hirta is being displaced by Pennisetum setaceum. Partial 16S rRNA genes of the rhizosphere bacterial communities were amplified and 454-pyrosequenced. Principal coordinate analysis revealed differences in the composition and structure of the rhizosphere bacterial communities between native and invasive plants, the values of the richness index being higher in the invasive microbial community. Rhizosphere microbial community structure was also influenced by invaded location. The indicator species analysis showed a higher number of indicators for the invasive community at all the taxonomic levels studied, the genus Ohtaekwangia being the most abundant indicator. As shown by canonical correspondence analysis, the protease and dehydrogenase activities and soil respiration were related to the rhizosphere bacterial community of invasive plant. However, only protease activity was significantly affected by the plant type, being higher in the invasive plant rhizosphere. Our results show that P. setaceum invasion has produced an intense interaction with the soil bacterial community, shifting its structure, composition, and protease activity related to N cycling, which may be altering the function of the invaded ecosystem.

不同连作年限怀牛膝根际土壤理化性质及微生物多样性

PDF HTML阅读 XML下载 导出引用 引用提醒 不同连作年限怀牛膝根际土壤理化性质及微生物多样性 DOI: 10.5846/stxb201606071097 作者: 作者单位: 作者简介: 通讯作者: 中图分类号: 基金项目: 国家自然科学基金（81303170，81573530，31401950，U1205021）；闽台作物特色种质创制与绿色栽培协同创新中心（2015-75） Analysis of physicochemical properties and microbial diversity in rhizosphere soil of Achyranthes bidentata under different cropping years Author: Affiliation: Fund Project: 摘要 | 图/表 | 访问统计 | 参考文献 | 相似文献 | 引证文献 | 资源附件 | 文章评论 摘要:以不同连作年限怀牛膝根际土壤为材料，采用土壤农化分析技术和磷脂脂肪酸生物标记法，对土壤理化性质以及根际微生物群落结构进行分析。结果表明：怀牛膝连作会使大部分大量元素（全磷、碱解氮、速效磷和速效钾）含量上升，而全氮、全钾的变化并无明显趋势。全量钙、全量镁、全量锰和有效锌的含量也会随着连作年限的增加而增加。研究发现，怀牛膝连作1a的土壤与对照相比，根际土壤微生物群落结构差别不大，但是与连作10a和30a的土壤相比微生物多样性却发生了明显变化。土壤中总PLFAs、细菌、革兰氏阴性菌Gram（-）及真菌含量都随连作年限增加而明显上升，微生物多样性增加，且革兰氏阳性菌Gram（+）/革兰氏阴性菌Gram（-）的比值随着连作年限的增加而下降。此外，土壤中一些嗜热解氢杆菌和真菌等参与土壤物质循环和木质素降解的微生物类群数量明显增加，假单胞菌等有益微生物类群也显著增多，这是牛膝连作促进作用的生物学基础。研究用药用植物怀牛膝证明了植物根际微生物结构和功能多样性对植物连作促进或连作抑制作用的产生与控制的生态学意义。 Abstract:In this study, the rhizosphere soils of Achyranthes bidentata, which was grown in a monoculture for multiple years, were investigated for analyzing the major elements, trace elements and rhizosphere microbial community structure by means of agricultural chemistry and phospholipid fatty acid (PLFA) analysis techniques. The results showed that consecutive monocultures of A. bidentata increased the contents of major elements (total phosphorus, alkaline hydrolysis nitrogen, available phosphorus, and available potassium). However, the ability of consecutive monocultures to change the total nitrogen content and total potassium was not obvious. In addition, total calcium, total magnesium, total manganese, and available zinc contents also increased with the increasing years of monoculture. Further analysis of PLFA profiles showed that there were no obvious differences in the rhizosphere microbial community structures between the control and newly planted A. bidentata. Besides, different results were depicted by 10 years and 30 years of consecutive monoculture, which showed that the total PLFA, bacteria (especially G-), and fungal content increased significantly, and the G+/G- ratio decreased with increasing years of monoculture. Moreover, some microbes involved in material cycling and lignin degradation, such as Hydrogenobacter, fungi (PLFA18:2ω6,9), and some beneficial bacteria including Pseudomonas increased significantly with increasing years of monoculture. These results suggest the important biological basis for the promotion mechanism of A. bidentata under a monoculture system. The case study exemplifies the ecological significance of rhizosphere microbial structure and its functional diversity in monoculture promotion or monoculture inhibition. 参考文献 相似文献 引证文献

Arsenic-enrichment enhanced root exudates and altered rhizosphere microbial communities and activities in hyperaccumulator Pteris vittata

Phytoremediation of arsenic (As)-contaminated soil by hyperaccumulator Pteris vittata is promising. A better understanding of the rhizosphere microbial dynamics that regulate As availability and plant growth is important to optimize the phytoremediation process. In this study, Illumina sequencing of 16S rRNA genes was applied to assess the rhizosphere microbial community structure of P. vittata. Microbial functionality was monitored by soil enzyme activities and MPN-PCR targeting genes of interest. Arsenic (100mgkg−1 AsV) addition to soil significantly increased DOC, root exudates, As and P uptake and the frond biomass of P. vittata. Moreover, As-enrichment significantly increased soil enzyme activities involved in N, P and S cycling and the gene abundance of As transforming bacteria, Fe- and S-reducing bacteria and N and C fixing bacteria in the rhizosphere of P. vittata. Together, the results revealed that the combined selective pressure of As and rhizosphere resulted in stimulation of microbial community, which most likely has a role in reductive dissolution of Fe and S, As and P mobilization, C degradation and fixation, and N fixation. These changes appeared to have a role in mitigation of As toxicity and to promote growth and the As uptake ability of P. vittata under As-enriched conditions.

Seasonal induced changes in spinach rhizosphere microbial community structure with varying salinity and drought.

Salinity is a common problem under irrigated agriculture, especially in low rainfall and high evaporative demand areas of southwestern United States and other semi-arid regions around the world. However, studies on salinity effects on soil microbial communities are relatively few while the effects of irrigation-induced salinity on soil chemical and physical properties and plant growth are well documented. In this study, we examined the effects of salinity, temperature, and temporal variability on soil and rhizosphere microbial communities in sand tanks irrigated with prepared solutions designed to simulate saline wastewater. Three sets of experiments with spinach (Spinacia oleracea L., cv. Racoon) were conducted under saline water during different time periods (early winter, late spring, and early summer). Bacterial 16S V4 rDNA region was amplified utilizing fusion primers designed against the surrounding conserved regions using MiSeq® Illumina sequencing platform. Across the two sample types, bacteria were relatively dominant among three phyla-the Proteobacteria, Cyanobacteria, and Bacteroidetes-accounted for 77.1% of taxa detected in the rhizosphere, while Proteobacteria, Bacteroidetes, and Actinobacteria accounted for 55.1% of taxa detected in soil. The results were analyzed using UniFrac coupled with principal coordinate analysis (PCoA) to compare diversity, abundance, community structure, and specific bacterial groups in soil and rhizosphere samples. Permutational analysis of variance (PERMANOVA) analysis showed that soil temperature (P=0.001), rhizosphere temperature (P=0.001), rhizosphere salinity (P=0.032), and evapotranspiration (P=0.002) significantly affected beta diversity of soil and rhizosphere microbial communities. Furthermore, salinity had marginal effects (P=0.078) on soil beta diversity. However, temporal variability differentially affected rhizosphere microbial communities irrigated with saline wastewater. Therefore, microbial communities in soils impacted by saline irrigation water respond differently to irrigation water quality and season of application due to temporal effects associated with temperature.

Evolution of the amino acid fingerprint in the unsterilized rhizosphere of a legume in relation to plant maturity

The exudation of low-molecular-weight compounds, such as amino acids, contributes to the structure of rhizospheric microbial communities and plays a crucial role in nutrient mobility throughout the vegetative cycle of the plant. Due to their low concentration and their constant removal by microorganisms, the study of amino acids is difficult in unsterilized rhizospheric soil. Our aim was to investigate the dynamics of amino acids in unsterilized soil.Since there was currently no available method to estimate accurately amino acid exudation in soil, a methodology was developed to assess amino-acid fingerprints in the rhizosphere. This proved a viable approach for understanding the dynamics of amino-acid release into the rhizosphere. The method was tested on Medicago truncatula, with the hypothesis that the fingerprint of amino acids in the rhizosphere should reflects amino acid exudation from leguminous plants, subject to the influence of microbiological components of the soil, and should be correlated with the stage of plant growth. M. truncatula plants were grown in either unsterilized or sterilized substrate. Amino acids in the substrate samples were identified and quantified by gas chromatography-mass spectrometry (GC-MS) and microbial biomass in the soil samples was also assessed.The total content of amino acids in the sterilized rhizospheric substrate increased substantially during plant growth with the highest content observed at the end of the vegetative stage. Despite the probable continual removal of amino acids by microorganisms, we also observed a significant quantitative and qualitative plant-dependent effect on the amino acid fingerprint in unsterilized soil. A clear chronological differentiation of this fingerprint in the rhizosphere of unsterilized and sterilized substrate was revealed by principal component analysis. We observed predominantly serine and glycine in the sterilized rhizosphere, whereas asparagine became prominent before flowering in the unsterilized rhizosphere soil. Root amino acid metabolic pathways and exudation appear to differ in unsterilized soil compared to in sterilized substrate, indicating an adaption to the rhizospheric environment.The established method could be used in other applications, for example, for future ecophysiological studies aiming at following root exudation of amino acids in response to changing environmental conditions.

Comparison on the structure and function of the rhizosphere microbial community between healthy and root-rot Panax notoginseng

Root-rot disease, the main catastrophic disease of Panax notoginseng (Burk.) F.H. Chen, causes yield reduction and serious economic losses. However, knowledge of the relationship between rhizosphere microbial community and root-rot disease is limited. Therefore, the objective of this study was to evaluate the changes in the rhizosphere microbial community following the occurrence of P. notoginseng root-rot disease using three different techniques: phospholipid fatty acid (PLFA) profiling, 16S rRNA gene sequencing and functional-inference-based approaches (PICRUSt: phylogenetic investigation of communities by reconstruction of unobserved states). With paired comparison design, we studied the rhizosphere microbial community structure of healthy and root-rot P. notoginseng plants in Wenshan region of Yunnan province, southwest China. Microbial PLFA profiles showed that the abundance of total microbes, bacteria, fungi and the proportion of gram-negative bacteria in the rhizosphere soil of diseased plants were significantly higher than those of healthy plants. Furthermore, the proportion of gram-positive bacterial, actinomycetal and arbuscular mycorrhizal fungal PLFAs were significantly lower in the rhizosphere soil of diseased plants, and Proteobacteria was identified to be the marker phylum in rhizosphere soil of diseased P. notoginseng. By PICRUSt analysis, bacterial community function was predicted based on 16S rRNA sequencing. It was found that the potential function of microbial community from rhizosphere soil of diseased P. notoginseng differed significantly from that of healthy plants. Moreover, soil variables including soil texture and soil organic carbon significantly correlated with PLFA profiles, and were identified as important abiotic factors in shaping microbial communities.