Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Phylotype diversity of forest, grassland soils and enrichment cultures

ABSTRACT: Phylotype diversity of forest and grassland soils as well as of the corresponding enrichments

PROVIDER: PRJEB9137 | ENA |

REPOSITORIES: ENA

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	ERR863468_1.fastq.gz	Fastqsanger.gz
	ERR863468_2.fastq.gz	Fastqsanger.gz
	ERR863469_1.fastq.gz	Fastqsanger.gz
	ERR863469_2.fastq.gz	Fastqsanger.gz
	ERR863470_1.fastq.gz	Fastqsanger.gz

Items per page:

1 - 5 of 42

Similar Datasets

forest and grassland soils fungi sequencing

Project description:forest and grassland soils fungi sequencing Raw sequence reads

| PRJNA799875 | ENA

forest and grassland soils bacteria sequencing

Project description:forest and grassland soils bacteria sequencing Raw sequence reads

| PRJNA877445 | ENA

grassland soils

Project description:Uruguayan grassland soil microbiota communities

| PRJNA643923 | ENA

Forest and grassland samples

Project description:Estonian forest and grassland topsoil samples

| PRJEB24121 | ENA

Identifying Hidden Viable Bacterial Taxa in Tropical Forest Soils Using Amplicon Sequencing of Enrichment Cultures.

Project description:This study aims to estimate the proportion and diversity of soil bacteria derived from eDNA-based and culture-based methods. Specifically, we used Illumina Miseq to sequence and characterize the bacterial communities from (i) DNA extracted directly from forest soil and (ii) DNA extracted from a mixture of bacterial colonies obtained by enrichment cultures on agar plates of the same forest soil samples. The amplicon sequencing of enrichment cultures allowed us to rapidly screen a culturable community in an environmental sample. In comparison with an eDNA community (based on a 97% sequence similarity threshold), the fact that enrichment cultures could capture both rare and abundant bacterial taxa in forest soil samples was demonstrated. Enrichment culture and eDNA communities shared 2% of OTUs detected in total community, whereas 88% of enrichment cultures community (15% of total community) could not be detected by eDNA. The enrichment culture-based methods observed 17% of the bacteria in total community. FAPROTAX functional prediction showed that the rare and unique taxa, which were detected with the enrichment cultures, have potential to perform important functions in soil systems. We suggest that enrichment culture-based amplicon sequencing could be a beneficial approach to evaluate a cultured bacterial community. Combining this approach together with the eDNA method could provide more comprehensive information of a bacterial community. We expected that more unique cultured taxa could be detected if further studies used both selective and non-selective culture media to enrich bacteria at the first step.

| S-EPMC8301126 | biostudies-literature

Detailed global modelling of soil organic carbon in cropland, grassland and forest soils.

Project description:Assessments of the global carbon (C) cycle typically rely on simplified models which consider large areas as homogeneous in terms of the response of soils to land use or consider very broad land classes. For example, "cropland" is typically modelled as an aggregation of distinct practices and individual crops over large regions. Here, we use the process-based Rothamsted soil Carbon Model (RothC model), which has a history of being successfully applied at a global scale, to calculate attainable SOC stocks and C mineralization rates for each of c. 17,000 regions (combination of soil type and texture, climate type, initial land use and country) in the World, under near-past climate conditions. We considered 28 individual crops and, for each, multiple production practices, plus 16 forest types and 1 grassland class (total of 80 classes). We find that conversion to cropland can result in SOC increases, particularly when the soil remains covered with crop residues (an average gain of 12 t C/ha) or using irrigation (4 t C/ha), which are mutually reinforcing effects. Attainable SOC stocks vary significantly depending on the land use class, particularly for cropland. Common aggregations in global modelling of a single agricultural class would be inaccurate representations of these results. Attainable SOC stocks obtained here were compared to long-term experiment data and are well aligned with the literature. Our results provide a regional and detailed understanding of C sequestration that will also enable better greenhouse gas reporting at national level as alternatives to IPCC tier 2 defaults.

| S-EPMC6752864 | biostudies-literature

Mediterranean grassland soil C-N compound turnover is mediated by genomically novel organisms, depth stratified, and rainfall dependent

Project description:integrated soil metagenomics and metaproteomics to study grassland soil microbial communities

2019-03-27 | PXD013110 | Pride

Environmental factors affect Acidobacterial communities below the subgroup level in grassland and forest soils.

Project description:In soil, Acidobacteria constitute on average 20% of all bacteria, are highly diverse, and are physiologically active in situ. However, their individual functions and interactions with higher taxa in soil are still unknown. Here, potential effects of land use, soil properties, plant diversity, and soil nanofauna on acidobacterial community composition were studied by cultivation-independent methods in grassland and forest soils from three different regions in Germany. The analysis of 16S rRNA gene clone libraries representing all studied soils revealed that grassland soils were dominated by subgroup Gp6 and forest soils by subgroup Gp1 Acidobacteria. The analysis of a large number of sites (n = 57) by 16S rRNA gene fingerprinting methods (terminal restriction fragment length polymorphism [T-RFLP] and denaturing gradient gel electrophoresis [DGGE]) showed that Acidobacteria diversities differed between grassland and forest soils but also among the three different regions. Edaphic properties, such as pH, organic carbon, total nitrogen, C/N ratio, phosphorus, nitrate, ammonium, soil moisture, soil temperature, and soil respiration, had an impact on community composition as assessed by fingerprinting. However, interrelations with environmental parameters among subgroup terminal restriction fragments (T-RFs) differed significantly, e.g., different Gp1 T-RFs correlated positively or negatively with nitrogen content. Novel significant correlations of Acidobacteria subpopulations (i.e., individual populations within subgroups) with soil nanofauna and vascular plant diversity were revealed only by analysis of clone sequences. Thus, for detecting novel interrelations of environmental parameters with Acidobacteria, individual populations within subgroups have to be considered.

| S-EPMC3457104 | biostudies-literature

Effect of elevated CO2, warming, added rainfall and added nitrogen on Geranium dissectum growing in a natural grassland

Project description:We used microarrays to discern patterns of gene expression in response to global climate change factors on leaf tissue of an annual dicot, Geranium dissectum, growing in a natural grassland. Keywords: multifactorial global change treatments

2007-06-01 | GSE6597 | GEO

grassland metagenome

Project description:grassland metagenome Raw sequence reads

| PRJNA888229 | ENA