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

DOI

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 scripts. Operational taxonomic units at 98% sequence identity (OTU0.03) that occurred only once in the whole dataset were termed absolute single sequence OTUs (SSOabs; doi:10.1038/ismej.2011.132). OTU0.03 sequences that occurred only once in at least one sample, but may occur more often in other samples were termed relative single sequence OTUs (SSOrel). SSOrel are particularly interesting for community ecology, since they comprise rare organisms that might become abundant when conditions change.16S rRNA amplicons and metagenomic reads have been stored in the sequence read archive under SRA project accession number SRP042162.

Identifier
DOI https://doi.org/10.1594/PANGAEA.861873
Related Identifier https://doi.org/10.1594/PANGAEA.861266
Related Identifier https://doi.org/10.1038/s41396-018-0263-1
Related Identifier https://store.pangaea.de/Publications/Ruff-etal_2016/Ruff_et_al_HMMV_All_OTU_Archaea.zip
Related Identifier https://store.pangaea.de/Publications/Ruff-etal_2016/Ruff_et_al_HMMV_All_OTU_Bacteria.zip
Related Identifier https://store.pangaea.de/Publications/Ruff-etal_2016/Ruff_et_al_HMMV_Table_of_Gene_Families.zip
Related Identifier https://store.pangaea.de/Publications/Ruff-etal_2016/Ruff_et_al_HMMV_OTU_Key_Populations.zip
Metadata Access https://ws.pangaea.de/oai/provider?verb=GetRecord&metadataPrefix=datacite4&identifier=oai:pangaea.de:doi:10.1594/PANGAEA.861873
Provenance
Creator Ruff, S Emil ORCID logo; Ramette, Alban ORCID logo; Boetius, Antje ORCID logo
Publisher PANGAEA
Publication Year 2016
Funding Reference Seventh Framework Programme https://doi.org/10.13039/100011102 Crossref Funder ID 226354 https://cordis.europa.eu/project/id/226354 Hotspot Ecosystem Research and Mans Impact On European Seas; Sixth Framework Programme https://doi.org/10.13039/100011103 Crossref Funder ID 36851 https://cordis.europa.eu/project/id/36851 European Seafloor Observatory Network
Rights Creative Commons Attribution 3.0 Unported; https://creativecommons.org/licenses/by/3.0/
OpenAccess true
Representation
Resource Type Dataset
Format text/tab-separated-values
Size 251 data points
Discipline Earth System Research
Spatial Coverage (14.702W, 72.000S, 14.748E, 72.007N); North Atlantic; Håkon Mosby Mud Volcano; Norwegian Sea
Temporal Coverage Begin 2003-06-28T10:02:00Z
Temporal Coverage End 2010-10-04T13:01:00Z