气候变化领域集成服务门户(CCPortal): Metadata und statistic analysis of archaeal and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (all habitats)

CCPortal

DOI	https://doi.org/10.1594/PANGAEA.861873
	Metadata und statistic analysis of archaeal and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (all habitats)
	Ruff; S Emil; Ramette; Alban; Boetius; Antje
发布日期	2016-06-20
数据集类型	dataset
英文简介	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.
空间范围	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
时间范围	2003-06-28T10:02:00 - 2010-10-04T13:01:00
语种	英语
国家	国际
学科大类	气候变化
学科子类	气候变化
文献类型	数据集
条目标识符	http://gcip.llas.ac.cn/handle/2XKMVOVA/219316
推荐引用方式 GB/T 7714	Ruff,S Emil,Ramette,et al. Metadata und statistic analysis of archaeal and bacterial sequences originating from sediments of the Håkon Mosby mud volcano (all habitats).2016-06-20.https://doi.org/10.1594/PANGAEA.861873.