16S rRNA of agricultural soils under soybean cultivation
Ontology highlight
ABSTRACT:
PROVIDER: PRJEB30887 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| ERR3089100_1.fastq.gz | Fastqsanger.gz | |||
| ERR3089100_2.fastq.gz | Fastqsanger.gz | |||
| ERR3089110_1.fastq.gz | Fastqsanger.gz | |||
| ERR3089110_2.fastq.gz | Fastqsanger.gz | |||
| ERR3089101_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 28 |
Similar Datasets
Project description:IntroductionBiological communities present in soil are essential to sustainable and productive agricultural practices; however, an accurate determination of the ecological status of agricultural soils remains to date an elusive task. An ideal indicator should be pervasive, play a relevant role in the ecosystem, show a rapid and proportional answer to external perturbations and be easily and economically measurable. Rhizobacteria play a major role in determining soil properties, becoming an attractive candidate for the detection of ecological indicators. The application of massive sequencing technologies to metagenomic analysis is providing an increasingly more precise view of the structure and composition of soil communities. In this work, we analyse soil rhizobacterial composition under various stress levels to search for potential ecological indicators.General biodiversity indicatorsOur results suggest that the Shannon index requires observation of a relatively large number of individuals to be representative of the true population diversity, and that the Simpson index may underestimate rare taxa in rhizobacterial environments.Taxonomical classification methodsDetection of indicator taxa requires comparison of taxonomical classification of sequences. We have compared RDP classifier, RTAX and similarity-based taxonomical classification and selected the latter for taxonomical assignment because it provides larger detail.Taxonomy-based ecological indicatorsThe study of significant variations in common, clearly identified, taxa, using paired datasets allows minimization of non-treatment effects and avoidance of false positives. We have identified taxa associated to specific perturbations as well as taxa generally affected in treated soils. Changes in these taxa, or combinations of them, may be used as ecological indicators of soil health. The overall number and magnitude of changes detected in taxonomic groups does also increase with stress. These changes constitute an alternative indicator to measuring specific taxa, although their determination requires large sample sizes, better obtained by massive sequencing.SummaryThe main ecological indicators available are the Shannon index, OTU counts and estimators, overall detection of the number and proportion of changes, and changes of specific indicator taxa. Massive sequencing remains the most accurate tool to measure rhizobacterial ecological indicators. When massive sequencing is not an option, various cultivable taxonomic groups, such as specific groups in the Actinobacteria tree, are attractive as potential indicators of large disruptions to the rhizobiome.
| S-EPMC5079562 | biostudies-literature
Project description:Techniques based on amplification of 16S rRNA genes for comparing bacterial communities are now widely used in microbial ecology, but calibration of these techniques with traditional tools, such as cultivation, has been conspicuously absent. In this study, we compared levels of bacterial community diversity in two pinyon rhizosphere soil samples and two between-tree (interspace) soil samples by analyzing 179 cultivated bacterial isolates and 801 16S rRNA genes amplified from extracted soil DNA. Phylotypes were defined by performing a restriction fragment length polymorphism analysis of 16S rRNA gene sequences with the enzymes RsaI and BstUI. The average level of 16S rRNA gene sequence similarity of members of a phylotype was 86.6% based on an analysis of partial sequences. A total of 498 phylotypes were identified among the 16S ribosomal DNA (rDNA) clones, while 34 phylotypes occurred among the cultivated isolates. Analysis of sequences from a subset of the phylotypes showed that at least seven bacterial divisions were represented in the clone libraries, whereas the isolates represented only three. The phylotype richness, frequency distribution (evenness), and composition of the four culture collections and the four clone libraries were investigated by using a variety of diversity indices. Although cultivation and 16S rRNA cloning analyses gave contradictory descriptions of the relative phylotype richness for one of the four environments, the two methods identified qualitatively consistent relationships when levels of evenness were compared. The levels of phylotype similarity between communities were uniformly low (15 to 31%). Both methods consistently indicated that one environment was distinct from the other three. Our data illustrate that while 16S rDNA cloning and cultivation generally describe similar relationships between soil microbial communities, significant discrepancies can occur.
| S-EPMC91235 | biostudies-literature
Project description:Agricultural soils Microbe Raw sequence reads
| PRJNA785286 | ENA
Project description:Illinois Agricultural Soils Targeted loci environmental
| PRJNA529017 | ENA
Project description:The objective of this data in brief article is to represent the associated data set regarding our published paper in Plant Science Nadeem et al., 2019. Data set represent soil acid phosphatase activity, association of individual molecular species of four major lipid classes with soybean forage quality indices when cultivated in boreal podzolic soils under cool climatic conditions. Phosphatidylcholine (PC), phosphatidylethanolamine (PE), phosphatidic acid (PA) and acylated glucosyl betasitosterol ester (AGIcSiE) molecular species grouped the soybean forage quality indices in different quadrants on principal component analyses. Furthermore, the total lipid profile and correlation of major lipid species with forage quality indices are included in this data in brief article. This data set support the main findings described in Nadeem et al., 2019.
| S-EPMC6557726 | biostudies-literature
Project description:Clubroot is a damaging disease of oilseed rape and vegetable brassicas worldwide, caused by the soil-borne protist Plasmodiophora brassicae Wor. Due to the long life of resting spores, the assessment of the pathogen abundance in agricultural fields can serve as a guideline for disease control at the country-wide level or the regional scale. Between 2013 and 2019, we collected 431 soil samples from fields cultivated with Brassicaceae crops throughout 16 provinces of Poland. The samples were subjected to qPCR based analysis of P. brassicae DNA concentration. From these data, the spore loads and gene copies g-1 soil were calculated and used to produce an assessment of the current clubroot risk potential at a country-wide and regional scale. The country-wide map, showing the spread of the pathogen in agricultural soils, was made using ArcGis software package implementing the interpolation with the Inverse Distance Weight method. The calculation of gene copies specific to P. brassicae helped to formulate the recommendations for farmers in respect to the cultivation guidelines. It showed a high risk of yield losses in defined regions of north, south-west and central Poland and an urgent need to undertake intensive preventative measures.
| S-EPMC7766057 | biostudies-literature
Project description:Phosphorus (P) is an essential element in terrestrial ecosystems. Knowledge on the role of dust in the biogeochemical cycling of phosphorus is very limited with no quantitative information on aeolian (by wind) P fluxes from soils. The aim of this study is to focus on P cycling via dust emissions under common land-use practices in an arid environment by integration of sample analyses and aeolian experiments. The experiments indicate significant P fluxes by PM10 dust due to agricultural land use. Even in a single wind-dust event at moderate velocity (7.0 m s(-1)), P flux in conventional agricultural fields can reach 1.83 kg km(-2), that accumulates to a considerable amount per year at a regional scale. The results highlight a negative yearly balance in P content (up to hundreds kg km(-2)) in all agricultural soils, and thus more P nutrition is required to maintain efficient yield production. In grazing areas where no P nutrition is applied, the soil degradation process can lead to desertification. Emission of P from soil dust sources has significant implications for soil nutrient resources and management strategies in agricultural regions as well as for loading to the atmosphere and global biogeochemical cycles.
| S-EPMC4837371 | biostudies-other
Project description:We analyzed the communities of soil basidiomycetes in agroecosystems that differ in tillage history at the Kellogg Biological Station Long-Term Ecological Research site near Battle Creek, Michigan. The approach combined soil DNA extraction through a bead-beating method modified to increase recovery of fungal DNA, PCR amplification with basidiomycete-specific primers, cloning and restriction fragment length polymorphism screening of mixed PCR products, and sequencing of unique clones. Much greater diversity was detected than was anticipated in this habitat on the basis of culture-based methods or surveys of fruiting bodies. With "species" defined as organisms yielding PCR products with > or =99% identity in the 5' 650 bases of the nuclear large-subunit ribosomal DNA, 241 "species" were detected among 409 unique basidiomycete sequences recovered. Almost all major clades of basidiomycetes from basidiomycetous yeasts and other heterobasidiomycetes through polypores and euagarics (gilled mushrooms and relatives) were represented, with a majority from the latter clade. Only 24 of 241 "species" had 99% or greater sequence similarity to named reference sequences in GenBank, and several clades with multiple "species" could not be identified at the genus level by phylogenetic comparisons with named sequences. The total estimated "species" richness for this 11.2-ha site was 367 "species" of basidiomycetes. Since >99% of the study area has not been sampled, the accuracy of our diversity estimate is uncertain. Replication in time and space is required to detect additional diversity and the underlying community structure.
| S-EPMC1636180 | biostudies-literature
Project description:Rewetted Dutch agricultural soils 16S rRNA gene amplicon sequencing Raw sequence reads
| PRJNA562618 | ENA