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Ruff, S Emil; Ramette, Alban; Boetius, Antje (2016): Metadata und statistic analysis of archaeal and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (all habitats). PANGAEA, https://doi.org/10.1594/PANGAEA.861873, In supplement to: Ruff, S Emil; Felden, Janine; Gruber-Vodicka, Harald R; Marcon, Yann; Knittel, Katrin; Ramette, Alban; Boetius, Antje (2018): In situ development of a methanotrophic microbiome in deep-sea sediments. The ISME Journal, https://doi.org/10.1038/s41396-018-0263-1

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Abstract:
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.
Related to:
Ruff, S Emil; Felden, Janine; Gruber-Vodicka, Harald R; Marcon, Yann; Knittel, Katrin; Ramette, Alban; Boetius, Antje (2014): Metagenom sequences of Archaea and Bacteria from sediment samples of the Haakon Mosby mud volcano. European Nucleotide Archive (ENA), insdc:PRJNA248084
Further details:
Ruff, S Emil; Boetius, Antje (2018): Archaea from the Håkon Mosby mud volcano used in Ruff et al., 2018. Ruff_et_al_HMMV_All_OTU_Archaea.zip
Ruff, S Emil; Boetius, Antje (2018): Bacterias from the Håkon Mosby mud volcano used in Ruff et al., 2018. Ruff_et_al_HMMV_All_OTU_Bacteria.zip
Ruff, S Emil; Boetius, Antje (2018): Gene families from the Håkon Mosby mud volcano used in Ruff et al., 2018. Ruff_et_al_HMMV_Table_of_Gene_Families.zip
Ruff, S Emil; Boetius, Antje (2018): Key populations from the Håkon Mosby mud volcano used in Ruff et al., 2018. Ruff_et_al_HMMV_OTU_Key_Populations.zip
Funding:
Seventh Framework Programme (FP7), grant/award no. 226354: Hotspot Ecosystem Research and Mans Impact On European Seas
Sixth Framework Programme (FP6), grant/award no. 36851: European Seafloor Observatory Network
Coverage:
Median Latitude: 72.003821 * Median Longitude: 14.727859 * South-bound Latitude: 72.000300 * West-bound Longitude: 14.702167 * North-bound Latitude: 72.006660 * East-bound Longitude: 14.747660
Date/Time Start: 2003-06-28T10:02:00 * Date/Time End: 2010-10-04T13:01:00
Minimum DEPTH, sediment/rock: 0.05 m * Maximum DEPTH, sediment/rock: 4.58 m
Event(s):
MSM16/2_809-1 * Latitude: 72.006660 * Longitude: 14.747660 * Date/Time: 2010-09-26T08:23:00 * Elevation: -1257.4 m * Location: North Atlantic * Campaign: MSM16/2 (LOOME) * Basis: Maria S. Merian * Method/Device: MultiCorer (MUC) * Comment: Action: at sea bottom; ship position
MSM16/2_823-1 * Latitude: 72.002700 * Longitude: 14.732467 * Date/Time: 2010-09-28T09:54:00 * Elevation: -1261.5 m * Location: Håkon Mosby Mud Volcano * Campaign: MSM16/2 (LOOME) * Basis: Maria S. Merian * Method/Device: MultiCorer (MUC) * Comment: Action: at sea bottom; Position sensor: Gear-mounted USBL transponder (Ixsea Posidonia); Comment: rope length max. 1267 m
MSM16/2_838-1 * Latitude: 72.004796 * Longitude: 14.726150 * Date/Time: 2010-10-01T09:13:00 * Elevation: -1258.5 m * Location: Håkon Mosby Mud Volcano * Campaign: MSM16/2 (LOOME) * Basis: Maria S. Merian * Method/Device: MultiCorer (MUC) * Comment: Action: at sea bottom; Position sensor: Gear-mounted USBL transponder (Ixsea Posidonia); Comment: rope length max. 1258 m
Parameter(s):
#NameShort NameUnitPrincipal InvestigatorMethod/DeviceComment
1Event labelEventRuff, S Emil
2Sample code/labelSample labelRuff, S Emil
3HabitatHabitatRuff, S Emil
4DEPTH, sediment/rockDepthmRuff, S EmilGeocode
5MethaneCH4µmol/kgRuff, S Emil
6Methane oxidation rateMOXmmol/m2/dayRuff, S EmilRadioactive tracer injectiondepth integrated 0-0.1 m bsf
7Sulfate reduction rate, depth integrated, sedimentSRR int sedmmol/m2/dayRuff, S EmilRadioactive tracer injectiondepth integrated 0-0.1 m bsf
8Deoxyribonucleic acid per volumeDNAµg/mlRuff, S Emil
9Accession number, geneticsAccess no genRuff, S EmilSequence Read Archive; Archaea
10Accession number, geneticsAccess no genRuff, S EmilSequence Read Archive; Bacteria
11Accession number, geneticsAccess no genRuff, S EmilSequence Read Archive; metagenomic
12Chao 1 richnessChao1 richRuff, S Emilof Archaea
13Inverse Simpson indexInv Simpson IRuff, S Emilof Archaea
14Archaea, operational taxonomic unitA OTU#Ruff, S Emilsub
15Archaea, operational taxonomic unitA OTU#Ruff, S Emilof Archaea
16Chao 1 richnessChao1 richRuff, S Emilof Bacteria
17Inverse Simpson indexInv Simpson IRuff, S Emilof Bacteria
18Bacteria, operational taxonomic unitB OTU#Ruff, S Emilsub
19Bacteria, operational taxonomic unitB OTU#Ruff, S Emil
Size:
251 data points

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