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SRX4515996: 16S amplicon sequencing of ME3 Time 0 near bottom water
1 ILLUMINA (Illumina MiSeq) run: 26,840 spots, 8M bases, 3.5Mb downloads

Design: The 16S rRNA gene V4 variable region PCR primers 515/806 with barcode on the forward primer were used in a 28 cycle PCR using the HotStarTaq Plus Master Mix Kit (Qiagen, USA) under the following conditions: 94C for 3 minutes, followed by 28 cycles of 94C for 30 seconds, 53C for 40 seconds and 72C for 1 minute, after which a final elongation step at 72C for 5 minutes was performed. After amplification, PCR products are checked in 2% agarose gel to determine the success of amplification and the relative intensity of bands. Multiple samples are pooled together in equal proportions based on their molecular weight and DNA concentrations. Pooled samples are purified using calibrated Ampure XP beads. Then the pooled and purified PCR product is used to prepare illumina DNA library. Sequencing was performed at MR DNA (www.mrdnalab.com, Shallowater, TX, USA) on a MiSeq following the manufacturers guidelines.
Submitted by: Ocean University of China
Study: Bacterial dimethylsulfoniopropionate biosynthesis in the East China Sea Raw sequence reads
show Abstracthide Abstract
Dimethylsulfoniopropionate (DMSP), is one of the Earth's most abundant organosulfur molecules, and the major precursor for gaseous dimethyl sulfide (DMS). DMSP and DMS have important roles in global sulfur cycling and atmospheric chemistry. It was thought that only eukaryotes produce significant amounts of DMSP, but many marine heterotrophic bacteria also produce DMSP and contain the dsyB or mmtN reporter genes for DMSP synthesis. Here we present the first depth profiled case study of bacterial DMSP production in one marine environment — the East China Sea (ECS). The concentrations of total DMSP (DMSPt) decreased with the depth from surface water (10.23–88.42 nM, SW) to near bottom water (3.22–11.45 nM, NBW), while the percentage of particulate DMSP likely apportioned mainly to bacterial origin (DMSPp 0.22–3 µm) increased with the depth, from 7.7% ± 2.9% in the surface to 13.4% ± 3.0% in the near bottom water. Furthermore, high level of DMSPt (16.29 ± 1.07 nmol·g-1) was detected in the oxic seabed sediment (OSS) and was mainly apportioned to be in the bacteria-dominant particulate form (14.19 ± 1.70 nmol·g-1, 86.9% ± 5.3%). Meanwhile, the genetic potential for DMSP synthesis via the bacterial dsyB/mmtN-dependent pathway was prominent in the ECS samples , with the proporition in total bacteria increased from SW to BW water and then to OSS samples. Microbial enrichment for DMSP-producing bacteria identified many different taxonomic groups of DMSP-producing bacteria with their intracellular DMSP concentrations ranging from 0.7 mM to 63.1 mM. These bacteria were likely producing DMSP in the original ECS environment since dsyBs and mmtNs found in some of these bacteria were present in the natural metagenomic data and representatives were able to produce DMSP in the seawater incubation experiment. This study supports the hypotheses that heterotrophic bacteria may have a significant role in marine DMSP production and that bacterial contribution to total DMSP increases with the depth, especially in the oxic sediment.
Sample:
SAMN09767639 • SRS3634443 • All experiments • All runs
Library:
Name: ME3_NBW_T0_16S_amplicon-2
Instrument: Illumina MiSeq
Strategy: AMPLICON
Source: GENOMIC
Selection: PCR
Layout: SINGLE
Runs: 1 run, 26,840 spots, 8M bases, 3.5Mb
Run# of Spots# of BasesSizePublished
SRR765355226,8408M3.5Mb2019-08-01

ID:
6118653

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