Metadata und statistic analysis of archaeal and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (all habitats)

• Main Authors: Ruff, S Emil, Ramette, Alban, Boetius, Antje
• Format: Dataset
• Language: English
• Published: PANGAEA 2016
• Subjects: Accession number; genetics; Archaea; operational taxonomic unit; ARK-XIX/3b; ARK-XXIV/2; Bacteria; Chao 1 richness; Deoxyribonucleic acid per volume; DEPTH; sediment/rock; ESONET; European Seafloor Observatory Network; Event label; GC; Gravity corer; Habitat; Håkon Mosby Mud Volcano; HERMIONE; Hotspot Ecosystem Research and Mans Impact On European Seas; Inverse Simpson index of diversity; LOOME; Maria S. Merian; Methane; Methane oxidation rate; MSM16/2; MSM16/2_809-1; MSM16/2_823-1; MSM16/2_838-1; MSM16/2_847-1; MSM16/2_855-1; MUC; MultiCorer; Multicorer with television; North Atlantic; Norwegian Sea; Polarstern; PS64; PS64/312-1; PS64/317_PUC-17; PS64/326_PUC-12; PS64/332-1; PS64/336-1; PS64/371-1; PS64/372-1; PS64/373-1; PS74; PS74/168-1; PS74/169-1_PUC-3; Bray
• Online Access: https://doi.pangaea.de/10.1594/PANGAEA.861873; https://doi.org/10.1594/PANGAEA.861873

DNA extraction was carried out as described on the MICROBIS project pages (http://icomm.mbl.edu/microbis ) using a commercially available extraction kit. We amplified the hypervariable regions V4-V6 of archaeal and bacterial 16S rRNA genes using PCR and several sets of forward and reverse primers (http://vamps.mbl.edu/resources/primers.php). Massively parallel tag sequencing of the PCR products was carried out on a 454 Life Sciences GS FLX sequencer at Marine Biological Laboratory, Woods Hole, MA, following the same experimental conditions for all samples. Sequence reads were submitted to a rigorous quality control procedure based on mothur v30 (doi:10.1128/AEM.01541-09) including denoising of the flow grams using an algorithm based on PyroNoise (doi:10.1038/nmeth.1361), removal of PCR errors and a chimera check using uchime (doi:10.1093/bioinformatics/btr381). The reads were taxonomically assigned according to the SILVA taxonomy (SSURef v119, 07-2014; doi:10.1093/nar/gks1219) implemented in mothur and clustered at 98% ribosomal RNA gene V4-V6 sequence identity. V4-V6 amplicon sequence abundance tables were standardized to account for unequal sampling effort using 1000 (Archaea) and 2300 (Bacteria) randomly chosen sequences without replacement using mothur and then used to calculate inverse Simpson diversity indices and Chao1 richness (doi:10.2307/4615964). Bray-Curtis dissimilarities (doi:10.2307/1942268) between all samples were calculated and used for 2-dimensional non metric multidimensional scaling (NMDS) ordinations with 20 random starts (doi:10.1007/BF02289694). Stress values below 0.2 indicated that the multidimensional dataset was well represented by the 2D ordination. NMDS ordinations were compared and tested using Procrustes correlation analysis (doi:10.1007/BF02291478). All analyses were carried out with the R statistical environment and the packages vegan (available at: http://cran.r-project.org/package=vegan), labdsv (available at: http://cran.r-project.org/package=labdsv), as well as with custom R ...