Diazotroph community succession during the VAHINE mesocosm experiment... - SRA

SRX1394281: Diazotroph community succession during the VAHINE mesocosm experiment (New Caledonia Lagoon)
1 ILLUMINA (Illumina MiSeq) run: 77,725 spots, 46.8M bases, 25.9Mb downloads

Design: Partial nifH fragments (ca. 360 base pairs) were amplified using a nested PCR assay and universal nifH primers nifH1-4, as described in Turk-Kubo et al., (2014). Two lagoon samples (day 1 and day 22), and three samples from each mesocosm (day 3, day 23, and the day where UCYN-C abundances were beginning to increase, i.e. days 11-15, see discussion below) were chosen for analysis. For each sample, triplicate PCR reactions were pooled. Internal primers were modified 5’ common sequence (CS) linkers (CS1_nifH1F: 5’-ACACTGACGACATGGTTCTACATGYGAYCCNAARGCNGA, CS2_nifH2R: 5’-TACGGTAGCAGAGACTTGGTCTADNGCCATCATYTCNCC) to facilitate library preparation at the DNA Services (DNAS) Facility at the University of Illinois, Chicago, using the targeted amplicons sequencing (TAS) approach described in Green et al. (2015). These libraries were pooled with other libraries to achieve a target depth of ca. 40,000 sequences per sample. Sequencing of paired end reads was performed at the W.M. Keck Center for Comparative and Functional Genomics at the University of Illinois at Urbana-Champaign using Illumina MiSeq technology.

Submitted by: University of California Santa Cruz

Study: Marine photic zone, New Caledonia Lagoon raw sequence reads, nitrogenase amplicons

PRJNA300416 • SRP065439 • All experiments • All runs

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The VAHINE mesocosm experiment, conducted in the low-nutrient low-chlorophyll waters of the Noumea Lagoon (coastal New Caledonia) was designed to trace the incorporation of nitrogen (N) fixed by diazotrophs into the food web, using large volume (50 m3) mesocosms. This experiment provided a unique opportunity to study the succession of N2-fixing microorganisms (diazotrophs) and calculate in situ net growth and mortality rates in response to fertilization with dissolved inorganic phosphate (DIP) over a 23-day period, using both polymerase chain reaction (PCR) amplification of nitrogenase genes (nifH) and quantitative PCR (qPCR) assays targeting known marine diazotroph lineages.

Sample: Mesocosm2, day13

SAMN04202530 • SRS1138800 • All experiments • All runs

Organism: marine metagenome

Library:

Name: 60351

Instrument: Illumina MiSeq

Strategy: AMPLICON

Source: METAGENOMIC

Selection: PCR

Layout: PAIRED

Spot descriptor:

1 forward251 reverse

Runs: 1 run, 77,725 spots, 46.8M bases, 25.9Mb

Run	# of Spots	# of Bases	Size	Published
SRR2849339	77,725	46.8M	25.9Mb	2016-10-28

ID:: 1980040

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