Fungal community profiles in agricultural soils of a long-term field trial under different tillage, fertilization and crop rotation conditions analyzed by high-throughput ITS-amplicon sequencing
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB19896 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR1876250_1.fastq.gz | Fastqsanger.gz | |||
| ERR1876250_2.fastq.gz | Fastqsanger.gz | |||
| ERR1876251_1.fastq.gz | Fastqsanger.gz | |||
| ERR1876251_2.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 4 of 4 |
Similar Datasets
Project description:Fungal communities in agricultural soils are assumed to be affected by soil and crop management. Our intention was to investigate the impact of different tillage and fertilization practices on fungal communities in a long-term crop rotation field trial established in 1992 in Central Germany. Two winter wheat fields in replicated strip-tillage design, comprising conventional vs. conservation tillage, intensive vs. extensive fertilization and different pre-crops (maize vs. rapeseed) were analyzed by a metabarcoding approach applying Illumina paired-end sequencing of amplicons generated by two recently developed primer pairs targeting the two fungal Internal Transcribed Spacer regions (ITS1, ITS2). Analysis of 5.1 million high-quality sequence reads uncovered a diverse fungal community in the two fields, composed of 296 fungal genera including 3,398 Operational Taxonomic Units (OTUs) at the 97% sequence similarity threshold. Both primer pairs detected the same fungal phyla (Basidio-, Asco-, Zygo-, Glomero- and Chytridiomycota), but in different relative abundances. OTU richness was higher in the ITS1 dataset, while ITS2 data were more diverse and of higher evenness. Effects of farming practice on fungal community structures were revealed. Almost two-thirds of the fungal genera were represented in all different soil treatments, whereas the remaining genera clearly responded to farming practice. Principal Component Analysis revealed four distinct clusters according to tillage practice and pre-crop. Analysis of Variance (ANOVA) substantiated the results and proved significant influences of tillage and pre-crop, while fertilization had the smallest and non-significant effect. In-depth analysis of putative phytopathogenic and plant beneficial fungal groups indicated distinct responses; for example Fusarium was significantly enriched in the intensively fertilized conservation tillage variants with the pre-crop maize, while Phoma displayed significant association with conventional tillage and pre-crop rapeseed. Many putative plant beneficial fungi also reacted differentially to farming practice with the most distinct responders identified among the Glomeromycota (arbuscular mycorrhizal fungi, AMF).
| S-EPMC5886558 | biostudies-literature
Project description:The changes in soil organic matter composition induced by anthropogenic factors is a topic of great interest for the soil scientists. The objective of this work was to identify possible structural changes in humic molecules caused by a 2-year rotation of durum wheat with faba bean, lasted for a decade, and conducted with different agricultural practices in a Mediterranean soil. Humic acids (HA) were extracted at three depths (0-30, 30-60 and 60-90 cm) from a Mediterranean soil subjected to different tillage (no tillage, minimum tillage and conventional tillage), crops (faba bean and wheat), and fertilization. The changes in HA quality were assessed by several chemical (ash, yield and elemental analysis) and spectroscopic techniques (solid-state 13C nuclear magnetic resonance, Fourier transform infrared and fluorescence). The results suggest that the different agronomic practices strongly affected the quality of HA. Smaller but more aromatic molecules were observed with depth, while the fertilization induced the formation of simpler and less aromatic molecules due to the enhanced decomposition processes. Under no tillage, more stable humic molecules were observed due to the less soil aeration, while under conventional tillage larger and more aromatic molecules were obtained. Compared to wheat, more aromatic and more oxidized but less complex molecules were observed after faba bean crop. The inorganic fertilization accelerates the decomposition of organic substances rather than their stabilization. At the end of each crop cycle, humic matter of different quality was isolated and this confirms the importance of the rotation practice to guarantee a diversification of the soil organic matter with time. Finally, no tillage induces the formation of more stable humic matter.
| S-EPMC6597113 | biostudies-literature
Project description:Fungi communities in crop rotation soils
| PRJEB66214 | ENA
Project description:Crop Rotation Fungal Community Raw sequence reads
| PRJNA447943 | ENA
Project description:Massive sequencing of fungal communities showed that climatic factors, followed by edaphic and spatial variables, are feasible predictors of fungal richness and community composition. This study, based on a long-term field experiment with tillage and no-tillage management since 1995 and with a crop rotation introduced in 2009, confirmed that tillage practices shape soil properties and impact soil fungal communities. Results highlighted higher biodiversity of saprotrophic fungi in soil sites with low disturbance and an inverse correlation between the biodiversity of ectomycorrhizal and saprotrophic fungi. We speculated how their mutual exclusion could be due to a substrate-mediated niche partitioning or by space segregation. Moreover, where the soil was ploughed, the species were evenly distributed. There was higher spatial variability in the absence of ploughing, with fungal taxa distributed according to a small-scale pattern, corresponding to micro-niches that probably remained undisturbed and heterogeneously distributed. Many differentially represented OTUs in all the conditions investigated were unidentified species or OTUs matching at high taxa level (i.e., phylum, class, order). Among the fungi with key roles in all the investigated conditions, there were several yeast species known to have pronounced endemism in soil and are also largely unidentified. In addition to yeasts, other fungal species emerged as either indicator of a kind of management or as strongly associated with a specific condition. Plant residues played a substantial role in defining the assortment of species.
| S-EPMC8247931 | biostudies-literature
Project description:Microbiota of soil crop rotation (tomato, lettuce, cauliflower)
| PRJNA900046 | ENA
Project description:We used high-throughput sequencing to study the rotation effect on soil bacteria
| PRJEB16323 | ENA
Project description:Soil rotational tillage is an effective measure to overcome the problems caused by long-term of a single tillage, but the effect of the interval time of rotational tillage practices is not very well understood. Therefore, we conducted a 3-year field study in a wheat-maize cropping system to evaluate the effects of rotary tillage (RT) in rotation with plowing tillage (PT) on soil properties in northern China. Four practices were designed as follows: 3 years of RT to a depth of 10-15 cm (3RT), 3 years of PT to a depth of 30-35 cm (3PT), 1 year of PT followed by 2 years of RT (PT+2RT), and 2 years of PT followed by 1 year of RT (2PT+RT). Within 20 cm of the surface soil, the 3RT treatment significantly increased the soil quality index (SQI) by 6.0%, 8.8% and 13.1%, respectively, relative to the PT+2RT, 2PT+RT and 3PT treatments. The improvement was closely related to the significant increase in the soil organic carbon (SOC) and available nutrients concentrations in the 0-20 cm depths and the improvement of soil invertase, urease, alkaline phosphatase and catalase activities in the topsoil (0-10 cm). However, the opposite effects were observed in the subsoil (20-40 cm). Compared with the 3RT treatment, the 3PT, 2PT+RT and PT+2RT treatments decreased soil bulk density, and significantly enhanced enzyme activities, resulting in an increase in SQI of 32.6%, 24.4% and 0.7%, respectively, especially in the 3PT and 2PT+RT treatments, the difference was significant. When averaged across to all soil depths, the SQI under the 3RT and 2PT+RT treatments was much higher than that under the other treatments. The yields of wheat and maize under the 2PT+RT treatment were 15.0% and 14.3% higher than those under the 3RT treatment, respectively. The 2PT+RT treatment was the most effective tillage practice. These results suggest that RT in rotation with PT could improve soil quality in the soil profile whilst enhancing crop yield after continuous RT, and the benefits were enhanced with an interval time of one year. Therefore, the 2PT+RT treatment could act as an effective method for both soil quality and crop yield improvement in a wheat-maize cropping system under straw incorporation conditions.
| S-EPMC6002108 | biostudies-literature
Project description:Effects of long term crop rotation and tillage on agricultural soil oomycetes communities
| PRJNA833903 | ENA
Project description:The acreage planted in corn and soybean crops is vast, and these crops contribute substantially to the world economy. The agricultural practices employed for farming these crops have major effects on ecosystem health at a worldwide scale. The microbial communities living in agricultural soils significantly contribute to nutrient uptake and cycling and can have both positive and negative impacts on the crops growing with them. In this study, we examined the impact of the crop planted and soil tillage on nutrient levels, microbial communities, and the biochemical pathways present in the soil. We found that farming practice, that is conventional tillage versus no-till, had a much greater impact on nearly everything measured compared to the crop planted. No-till fields tended to have higher nutrient levels and distinct microbial communities. Moreover, no-till fields had more DNA sequences associated with key nitrogen cycle processes, suggesting that the microbial communities were more active in cycling nitrogen. Our results indicate that tilling of agricultural soil may magnify the degree of nutrient waste and runoff by altering nutrient cycles through changes to microbial communities. Currently, a minority of acreage is maintained without tillage despite clear benefits to soil nutrient levels, and a decrease in nutrient runoff-both of which have ecosystem-level effects and both direct and indirect effects on humans and other organisms.
| S-EPMC5108259 | biostudies-literature