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Salt marshes sediment microhabitats Metagenome

Dataset homepage

Citation

MGnify (2019). Salt marshes sediment microhabitats Metagenome. Sampling event dataset https://doi.org/10.15468/iqcnpl accessed via GBIF.org on 2023-01-31.

Description

In the present study, microbial communities of bulk and rhizosphere sediments were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of bulk sediment and two plant species inhabiting salt marsh systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences after demultiplexing thus without a chimera check and other quality filtering. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences.

Sampling Description

Sampling

In the present study, microbial communities of bulk and rhizosphere sediments were investigated using barcoded pyrosequencing of 16S rRNA gene amplicons. Our main goals were to compare the bacterial richness and composition of bulk sediment and two plant species inhabiting salt marsh systems. FLX 454 titanium pyrosequencing study. Note that the sequences submitted are raw sequences after demultiplexing thus without a chimera check and other quality filtering. These will need to be filtered out using, e.g., using qiime scripts such as split_libraries and pick_otus with the usearch_ref argument, which will provide a chimera check and filter out poor quality sequences.

Method steps

  1. Pipeline used: https://www.ebi.ac.uk/metagenomics/pipelines/4.1

Taxonomic Coverages

Geographic Coverages

Bibliographic Citations

Contacts

originator
University of Aveiro
metadata author
University of Aveiro
administrative point of contact
University of Aveiro
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