raw bacterial amplicon sequencing data  (Biotechnology Information)

Journal: Frontiers in Microbiology

Article Title: Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

doi: 10.3389/fmicb.2016.01638

Figure Lengend Snippet: Abundances of bacterial and archaeal 16S rRNA genes and archaeal and bacterial amoA genes (AOA- amoA , AOB- amoA ) per gram soil in savanna soil samples taken from 5 cm depth at different locations along the granitic (GI-GIV) and the basaltic (BI-BIII) catena . Bars represent mean abundances of replicate samples, each measured in triplicate qPCR reactions, and respective standard deviations. Abundances of bacterial amoA genes were below the quantification limit (50 genes per qPCR reaction) in all samples except BII and maximum estimates based on this limit are shown.

Article Snippet: Bacterial and archaeal 16S rRNA amplicon Illumina sequencing raw data were deposited in the European Nucleotide Archive database under the study accession number PRJEB13568 .

Techniques:

Journal: Frontiers in Microbiology

Article Title: Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

doi: 10.3389/fmicb.2016.01638

Figure Lengend Snippet: Phlyum-level taxonomic classification of sequences obtained from bacterial 16S rRNA gene-targeted Illumina sequencing of savanna soil samples taken from 5 cm depth at different locations along the granitic (GI-GIV) and the basaltic (BI-BIII) catena . Cand. Div., Candidate Division. For some samples, replicates had to be excluded from further analysis of the normalized data set due to low read numbers. Results based on the non-normalized sequence data, including more soil replicates, are presented in Supplementary Figure .

Article Snippet: Bacterial and archaeal 16S rRNA amplicon Illumina sequencing raw data were deposited in the European Nucleotide Archive database under the study accession number PRJEB13568 .

Techniques: Illumina Sequencing, Sequencing

Journal: Frontiers in Microbiology

Article Title: Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

doi: 10.3389/fmicb.2016.01638

Figure Lengend Snippet: Correlations (Spearman's rank correlation coefficients) between abundances of archaeal amoA (AOA- amoA ), archaeal and bacterial 16S rRNA genes, soil chemical parameters (soil pH, ammonium and nitrate concentrations, total C and N content) and respiration-based parameters (BAS, basal respiration; C mic , microbial biomass) along the granitic and basaltic catena .

Article Snippet: Bacterial and archaeal 16S rRNA amplicon Illumina sequencing raw data were deposited in the European Nucleotide Archive database under the study accession number PRJEB13568 .

Techniques:

Journal: Frontiers in Microbiology

Article Title: Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

doi: 10.3389/fmicb.2016.01638

Figure Lengend Snippet: Biplot from canonical correspondence analysis (CCA) of five measured environmental variables (ammonium concentration, nitrate concentration, total C, total N, soil pH) and the bacterial 16S rRNA gene-based community structure in soil samples from two catenas, detected as average read numbers of OTUs determined at 97% sequence identity on nucleic acid-level per sampling location . For this purpose, samples were normalized to the same number of total reads prior to analysis. Samples from the granitic and the basaltic catena are shown as filled circles (GI-GIV) and open squares (BI-BIII), respectively.

Article Snippet: Bacterial and archaeal 16S rRNA amplicon Illumina sequencing raw data were deposited in the European Nucleotide Archive database under the study accession number PRJEB13568 .

Techniques: Concentration Assay, Sequencing, Sampling

Journal: Frontiers in Microbiology

Article Title: Community Composition and Abundance of Bacterial, Archaeal and Nitrifying Populations in Savanna Soils on Contrasting Bedrock Material in Kruger National Park, South Africa

doi: 10.3389/fmicb.2016.01638

Figure Lengend Snippet: Classification of sequences obtained from archaeal 16S rRNA gene-targeted Illumina sequencing of savanna soil samples taken from 5 cm depth at different locations along the granitic (GI-GIV) and the basaltic (BI-BIII) catena . Eur, Euryarchaeota; RC, Rice Cluster; Woes, Woesearchaeota; DHVE, Deep Sea Hydrothermal Vent Euryarchaeota Group; Thaum, Thaumarchaeota; uncl, unclassified; (F)SCG, (Forest) Soil Creanarchaeota Group. For some samples, replicates had to be excluded from further analysis of the normalized data set due to low read numbers. Results based on the non-normalized sequence data, including more soil replicates, are presented in Supplementary Figure .

Article Snippet: Bacterial and archaeal 16S rRNA amplicon Illumina sequencing raw data were deposited in the European Nucleotide Archive database under the study accession number PRJEB13568 .

Techniques: Illumina Sequencing, Sequencing