An intensive multilocation temporal dataset of fungal and bacterial communities in the root and rhizosphere of Brassica napus.
Ontology highlight
ABSTRACT:
SUBMITTER: Bazghaleh N
PROVIDER: S-EPMC7486468 | biostudies-literature |
REPOSITORIES: biostudies-literature
Similar Datasets
Project description:The plant microbiome has been recently recognized as a plant phenotype to help in the food security of the future population. However, global plant microbiome datasets are insufficient to be used effectively for breeding this new generation of crop plants. We surveyed the diversity and temporal composition of fungal communities in the root and rhizosphere of Brassica napus, the world's second largest oilseed crop, weekly in eight diverse lines at one site and every three weeks in sixteen lines, at three sites in 2016 and 2017 in the Canadian Prairies. 14,944 unique amplicon sequence variants (ASV) were detected based on the internal transcribed spacer region, with an average of 43 ASVs per root and 105 ASVs per rhizosphere sample. Temporal, site-to-site, and line-driven variability were key determinants of fungal community structure. This dataset is a valuable resource to systematically extract information on the belowground microbiome of diverse B. napus lines in different environments, at different times in the growing season, in order to adapt effective varieties for sustainable crop production systems.
| S-EPMC7182712 | biostudies-literature
Project description:Plant roots show morphological plasticity and play a substantial role in tolerance to various edaphic stresses. The aim of this study was to explore salinity-induced morphogenic responses of root traits and root hairs of two rapeseed varieties, BARI Sarisha-8 and Binasarisha-5, at the reproductive stage and perceive the effects on their reproductive growth. The experiment was conducted in a hydroponic culture. Two treatments, 0 mM NaCl as control and 100 mM NaCl, were imposed 55 d after germination. Plants exposed to 100 mM NaCl for seven days displayed greater damage in the leaves, flowers, and siliquae compared to control. Length of root hairs on first-order and third-order lateral roots, density of root hairs on first-order lateral roots, and length of third-order lateral roots were significantly greater by 91%, 22%, 29%, and 48%, respectively, in the treated condition compared to the control. An increase in estimated root surface area by 20% under salt stress conditions indicated that the spontaneous responses of plants to uptake more water and nutrients allowed a plant to cope with stressful conditions. The results of this study suggest that any future stress breeding programs should consider plasticity of root traits intensively.
| S-EPMC6681291 | biostudies-literature
Project description:The application of organic amendments to saline-alkaline soil has been recommended as an agricultural strategy to improve crop productivity and soil health. However, there has been limited research on how organic soil amendment strategies affect the health of oats and their associated rhizosphere fungal communities in saline-alkaline conditions. Thus, the objectives of this study were to understand the effects of oat cultivars with contrasting saline-alkaline tolerances and different amendments on plant morphologies, root exudates (soluble sugars and organic acids), and rhizosphere fungal communities in a saline-alkaline environment. Experiments were conducted on a saline-alkaline tolerant cultivar, Baiyan2, and a saline-alkaline sensitive cultivar, Caoyou1, under four different organic amendment strategies: 1. control (no amendment application), 2. bio-fertilizer application, 3. rotten straw application, and 4. a co-application of bio-fertilizer and rotten straw. Results showed that plant morphological characters of Baiyan2 were better than Caoyou1, and that soluble sugar and organic acid levels in the rhizosphere of Baiyan2 were significantly lower than Caoyou1. Compared to the control, oat root and plant development was significantly improved by the combined bio-fertilizer and rotten straw amendment. Bio-fertilizer application promoted malic and citric acid levels, contributing to a higher total organic acid level, and significantly increased the abundance of Rhizopus arrhizus and decreased the abundance of the fungal pathogens Alternaria, Cladosporium, Sarocladium and Heydenia of Ascomycota in both oat cultivars. All amendment treatments containing rotten straw, except the combined amendment in Baiyan2, significantly increased the relative abundance of Ascomycota (specifically Gibberella, Talaromyces, Fusarium, and Bipolaris) and decreased the relative abundance of R. arrhizus by reducing soluble sugar and organic acid levels. For the combined amendment in Baiyan2, there were no significant changes in Gibberella and Rhizopus between the control and amendment treatment. Our results suggest that co-application of bio-fertilizer and rotten straw, combined with a tolerant oat cultivar, is an effective method to increase crop productivity and enhance soil health in a saline-alkaline environment.
| S-EPMC7714365 | biostudies-literature
Project description:Hazelnut has gained economic value in China in recent years, but its large-scale planting and research started later than other countries. Conducting basic research on hazelnut trees requires studying their related microorganisms. Here, we used high-throughput DNA sequencing to quantify the fungal communities in the root endospheres and rhizosphere soil of four hazelnut species. Fungal diversity in the rhizosphere soil was significantly higher than that in the root endospheres. Rhizosphere soil had more Mortierellomycota, and the fungal community compositions differed among the four hazelnut species. The root endospheres, especially those of the Ping'ou (Corylus heterophylla × Corylus avellana) trees, contained more ectomycorrhizal fungi. The co-occurrence networks in the rhizosphere soil were more sophisticated and stable than those in the root endospheres, even when the root endospheres had higher modularity, because the structural differentiation of the root endospheres differed from that of the rhizosphere soil. Two-factor correlation network analysis and linear regression analysis showed that the total organic carbon was the main environmental factor affecting the fungal communities. Our study revealed the community compositions, functional predictions, and co-occurrence network structural characteristics of fungi in hazelnut root endospheres and rhizosphere soil. We also examined the potential keystone taxa, and analyzed the environmental factors of the dominant fungal community compositions. This study provides guidance for the growth of hazelnut and the management of hazelnut garden, and provides an insight for future development of fungal inoculants to be used in hazelnut root.
| S-EPMC8692873 | biostudies-literature
Project description: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.
| S-EPMC5524829 | biostudies-other
Project description:Canola (oilseed rape, Brassica napus L.) is susceptible to infection by the biotrophic protist Plasmodiophora brassicae, the causal agent of clubroot. To understand the roles of microRNAs (miRNAs) during the post-transcriptional regulation of disease initiation and progression, we have characterized the changes in miRNA expression profiles in canola roots during clubroot disease development and have compared these to uninfected roots. Two different stages of clubroot development were targeted in this miRNA profiling study: an early time of 10-dpi for disease initiation and a later 20-dpi, by which time the pathogen had colonized the roots (as evident by visible gall formation and histological observations). P. brassicae responsive miRNAs were identified and validated by qRT-PCR of miRNAs and the subsequent validation of the target mRNAs through starBase degradome analysis, and through 5' RLM-RACE. This study identifies putative miRNA-regulated genes with roles during clubroot disease initiation and development. Putative target genes identified in this study included: transcription factors (TFs), hormone-related genes, as well as genes associated with plant stress response regulation such as cytokinin, auxin/ethylene response elements. The results of our study may assist in elucidating the role of miRNAs in post-transcriptional regulation of target genes during disease development and may contribute to the development of strategies to engineer durable resistance to this important phytopathogen.
| S-EPMC3909011 | biostudies-literature
Project description:The temporal dynamics of rhizosphere and root microbiota composition was compared between healthy and infected Chinese cabbage plants by the pathogen Plasmodiophora brassicae. When inoculated with P. brassicae, disease was measured at five sampling dates from early root hair infection to late gall development. The first symptoms of clubroot disease appeared 14 days after inoculation (DAI) and increased drastically between 14 and 35 DAI. The structure of microbial communities associated to rhizosphere soil and root from healthy and inoculated plants was characterized through high-throughput DNA sequencing of bacterial (16S) and fungal (18S) molecular markers and compared at each sampling date. In healthy plants, Proteobacteria and Bacteroidetes bacterial phyla dominated the rhizosphere and root microbiota of Chinese cabbage. Rhizosphere bacterial communities contained higher abundances of Actinobacteria and Firmicutes compared to the roots. Moreover, a drastic shift of fungal communities of healthy plants occurred between the two last sampling dates, especially in plant roots, where most of Ascomycota fungi dominated until they were replaced by a fungus assigned to the Chytridiomycota phylum. Parasitic invasion by P. brassicae disrupted the rhizosphere and root-associated community assembly at a late step during the root secondary cortical infection stage of clubroot disease. At this stage, Flavisolibacter and Streptomyces in the rhizosphere, and Bacillus in the roots, were drastically less abundant upon parasite invasion. Rhizosphere of plants colonized by P. brassicae was significantly more invaded by the Chytridiomycota fungus, which could reflect a mutualistic relationship in this compartment between these two microorganisms.
| S-EPMC6388920 | biostudies-literature
Project description:Fungi play important roles as decomposers, plant symbionts and pathogens in soils. The structure of fungal communities in the rhizosphere is the result of complex interactions among selection factors that may favour beneficial or detrimental relationships. Using culture-independent fungal community profiling, we have investigated the effects of nitrogen fertilizer dosage on fungal communities in soil and rhizosphere of field-grown sugarcane. The results show that the concentration of nitrogen fertilizer strongly modifies the composition but not the taxon richness of fungal communities in soil and rhizosphere. Increased nitrogen fertilizer dosage has a potential negative impact on carbon cycling in soil and promotes fungal genera with known pathogenic traits, uncovering a negative effect of intensive fertilization.
| S-EPMC5155403 | biostudies-literature
Project description:Soil fungi are key players in nutrient cycles as decomposers, mutualists and pathogens, but the impact of tropical rain forest transformation into rubber or oil palm plantations on fungal community structures and their ecological functions are unknown. We hypothesized that increasing land use intensity and habitat loss due to the replacement of the hyperdiverse forest flora by nonendemic cash crops drives a drastic loss of diversity of soil fungal taxa and impairs the ecological soil functions. Unexpectedly, rain forest conversion was not associated with strong diversity loss but with massive shifts in soil fungal community composition. Fungal communities clustered according to land use system and loss of plant species. Network analysis revealed characteristic fungal genera significantly associated with different land use systems. Shifts in soil fungal community structure were particularly distinct among different trophic groups, with substantial decreases in symbiotrophic fungi and increases in saprotrophic and pathotrophic fungi in oil palm and rubber plantations in comparison with rain forests. In conclusion, conversion of rain forests and current land use systems restructure soil fungal communities towards enhanced pathogen pressure and, thus, threaten ecosystem health functions.
| S-EPMC6399230 | biostudies-literature
Project description:Plant root-associated microbiomes play critical roles in promoting plant health, productivity, and tolerance to biotic/abiotic stresses. Blueberry (Vaccinium spp.) is adapted to acidic soils, while the interactions of the root-associated microbiomes in this specific habitat under various root microenvironments remain elusive. Here, we investigated the diversity and community composition of bacterial and fungal communities in various blueberry root niches (bulk soil, rhizosphere soil, and root endosphere). The results showed that blueberry root niches significantly affected root-associated microbiome diversity and community composition compared to those of the three host cultivars. Deterministic processes gradually increased along the soil-rhizosphere-root continuum in both bacterial and fungal communities. The co-occurrence network topological features showed that both bacterial and fungal community complexity and intensive interactions decreased along the soil-rhizosphere-root continuum. Different compartment niches clearly influenced bacterial-fungal interkingdom interactions, which were significantly higher in the rhizosphere, and positive interactions gradually dominated the co-occurrence networks from the bulk soil to the endosphere. The functional predictions showed that rhizosphere bacterial and fungal communities may have higher cellulolysis and saprotrophy capacities, respectively. Collectively, the root niches not only affected microbial diversity and community composition but also enhanced the positive interkingdom interactions between bacterial and fungal communities along the soil-rhizosphere-root continuum. This provides an essential basis for manipulating synthetic microbial communities for sustainable agriculture. IMPORTANCE The blueberry root-associated microbiome plays an essential role in its adaptation to acidic soils and in limiting the uptake of soil nutrients by its poor root system. Studies on the interactions of the root-associated microbiome in the various root niches may deepen our understanding of the beneficial effects in this particular habitat. Our study extended the research on the diversity and composition of microbial communities in different blueberry root compartment niches. Root niches dominated the root-associated microbiome compared to that of the host cultivar, and deterministic processes increased from the bulk soil to the endosphere. In addition, bacterial-fungal interkingdom interactions were significantly higher in the rhizosphere, and those positive interactions progressively dominated the co-occurrence network along the soil-rhizosphere-root continuum. Collectively, root niches dominantly affected the root-associated microbiome and the positive interkingdom interactions increased, potentially providing benefits for the blueberry.
| S-EPMC10269492 | biostudies-literature