Computational protocol: Near-Bottom Hypoxia Impacts Dynamics of Bacterioplankton Assemblage throughout Water Column of the Gulf of Finland (Baltic Sea)

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Protocol publication

[…] Reads with low quality (Q<30) and shorter than 225 bp (basepairs) were removed from the dataset. Operational taxonomic unit (OTU) was defined using the average neighbor-clustering algorithm of MOTHUR 1.34.4 [] with 97% similarity threshold. Reference sequences were selected from the SILVA ribosomal RNA database release 102 []. The UCHIME algorithm was used to remove chimeric DNA sequences caused by PCR errors []. Taxonomic assignments were processed by the Ribosomal Database Project (RDP) naïve Bayesian Classifier [] and BLAST [] searched against a NCBI (National Center for Biotechnology Information) nucleotide database (release 206, http://www.ncbi.nlm.nih.gov/). Sequences matching eukaryotic DNA were discarded from the dataset. Statistical analyses were carried out with program R version 3.1.2 (http://www.r-project.org), ACE (Abundance-based Coverage Estimation) [] and Chao1 [] richness estimates were calculated using VEGAN package []. The same package was used to carry out the non-metric multidimensional scaling (NMDS) analyses. Week number was used as an independent variable for time. For data visualizations ggplot2 package was used []. All sequences are uploaded to the GenBank and are available under accession numbers KT855220–KT860044. […]

Pipeline specifications

Software tools mothur, UCHIME, vegan, Ggplot2
Applications Miscellaneous, 16S rRNA-seq analysis
Organisms Bacteria