Land uses
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA407787 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR6050560_1.fastq.gz | Fastqsanger.gz | |||
| SRR6050560_2.fastq.gz | Fastqsanger.gz | |||
| SRR6050570_1.fastq.gz | Fastqsanger.gz | |||
| SRR6050570_2.fastq.gz | Fastqsanger.gz | |||
| SRR6050580_1.fastq.gz | Fastqsanger.gz |
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Project description:Different land uses soil Microbe Raw sequence reads
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Project description:BackgroundPrimary biodiversity records (PBR) are essential in many areas of scientific research as they document the biodiversity through time and space. However, concerns about PBR quality and fitness-for-use have grown, especially as derived from taxonomical, geographical and sampling effort biases. Nonetheless, the temporal bias stemming from data ageing has received less attention. We examine the effect of changes in land use in the information currentness, and therefore data obsolescence, in biodiversity databases.MethodsWe created maps of land use changes for three periods (1956-1985, 1985-2000 and 2000-2012) at 5-kilometres resolution. For each cell we calculated the percentage of land use change within each period. We then overlaid distribution data about small mammals, and classified each data as 'non-obsolete or 'obsolete,' depending on both the amount of land use changes in the cell, and whether changes occurred at or after the data sampling's date.ResultsA total of 14,528 records out of the initial 59,677 turned out to be non-obsolete after taking into account the changes in the land uses in Navarra. These obsolete data existed in 115 of the 156 cells analysed. Furthermore, more than one half of the remaining cells holding non-obsolete records had not been visited at least for the last fifteen years.ConclusionLand use changes challenge the actual information obtainable from biodiversity datasets and therefore its potential uses. With the passage of time, one can expect a steady increase in the availability and use of biological records-but not without them becoming older and likely to be obsolete by land uses changes. Therefore, it becomes necessary to assess records' obsolescence, as it may jeopardize the knowledge and perception of biodiversity patterns.
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Project description:In this study, we use DNA affinity purification sequencing to identiy genome-wide binding of LFY transcription factor, a master regulator of flower development in Arabidopsis. We generated two sets of data, one using genomic DNA from plant tissue, thus retain DNA methylation, as probe for DNA affinity purification (DAP-seq dataset), and the other using PCR amplified genomic DNA (without DNA methylation; AmpDAP-seq dataset).
2021-03-25 | GSE160013 | GEO
Project description:A genomewide association study for bronchopulmonary dysplasia using DNA pooling
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Project description:16S rRNA amplicon sequences (V3-V4) from land use soils and rainforest of the Bukit region, Indonesia
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Project description:Land use change alters the structure and composition of microbial communities. However, the links between environmental factors and microbial functions are not well understood. Here we interrogated the functional structure of soil microbial communities across different land uses. In a multivariate regression tree analysis of soil physicochemical properties and genes detected by functional microarrays, the main factor that explained the different microbial community functional structures was C : N ratio. C : N ratio showed a significant positive correlation with clay and soil pH. Fields with low C : N ratio had an overrepresentation of genes for carbon degradation, carbon fixation, metal reductase, and organic remediation categories, while fields with high C : N ratio had an overrepresentation of genes encoding dissimilatory sulfate reductase, methane oxidation, nitrification, and nitrogen fixation. The most abundant genes related to carbon degradation comprised bacterial and fungal cellulases; bacterial and fungal chitinases; fungal laccases; and bacterial, fungal, and oomycete polygalacturonases. The high number of genes related to organic remediation was probably driven by high phosphate content, while the high number of genes for nitrification was probably explained by high total nitrogen content. The functional gene diversity found in different soils did not group the sites accordingly to land management. Rather, the soil factors, C : N ratio, phosphate, and total N, were the main factors driving the differences in functional genes across the fields examined.
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Project description:Antioxidants (AOX) in soils originate mainly from secondary plant metabolites and are pivotal in many redox processes in environment, maintaining soil quality. Still, little is known about the influence of land uses on their accumulation in soil. The aim of the paper was to determine the content of these redox-active compounds in the extracts of A horizons of abandoned fallows, arable and woodland soils. Total antioxidant capacity (TAC) of soils under various uses and vegetation was evaluated in different soil extracts using Folin-Ciocâlteu method. The contribution of humic acids to TAC was determined and antioxidant profiles estimated using the chromatographic GC-MS method. Forest soils exhibited the highest TAC (15.5 mg g-1) and AOX contents (4.34 mg g-1), which were positively correlated with soil organic carbon content. It was estimated that humic acids contribute to over 50% of TAC in soils. The main phenolics in woodland A horizons were isovanillic and p-hydroxybenzoic acid (p-HA), while esculetin and p-HA predominated in the abandoned fallows due to the prevalence of herbaceous vegetation. Cultivated soils were the most abundant in p-HA (56.42%). In the studied topsoils, there were considerable amounts of aliphatic organic matter, which role in redox processes should be further evaluated.
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