Metatranscriptomes from Prairie Pothole Wetland Sediments - SRA

SRX5089122: Metatranscriptomes from Prairie Pothole Wetland Sediments
1 ABI_SOLID (AB 5500xl Genetic Analyzer) run: 857.6M spots, 42.9G bases, 32Gb downloads

Design: For RNA-Seq, RNA was extracted using Qiagen RNeasy mini kit (cat74104), followed by genomic DNA removal and cleaning using Qiagen RNase-Free DNase Set kit (cat#79254) and Qiagen Mini RNeasy kit (cat#74104). Integrity of the RNA samples was assessed using the Alegient 2100 Bioanalyzer. RNA samples having RNA Integrity Number between 9 10 were used in this work. Ribo-Zero rRNA removal Kit (cat#MRZPL1224) was used for enrichment of transcripts. The SOLiD Total RNA-Seq Kit (cat#4445374) was used to construct template cDNA for RNA-Seq following the protocol recommended by Applied Biosystems. Briefly, mRNA was fragmented using chemical hydrolysis followed by ligation with strand specific adapters and reverse transcript to generate cDNA. The cDNA fragments, 150 to 250 bp in size, were isolated and amplified through 15 amplification cycles to produce the required number of templates for the SOLiD EZ Bead system, which was used to generate the template bead library for ligation base sequencing by 5500xl SOLiD instrument (LifeTechnologies).

Submitted by: Pacific Northwest National Laboratory

Study: Carbon and Sulfur Cycling in Prairie Pothole Wetland Sediments

PRJNA330672 • SRP079905 • All experiments • All runs

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This study aimed to provide the first information on coupled geochemistry and microbial communities in wetland sediments from the largest wetland ecosystem in the US, the Prairie Pothole Region (PPR). Wetlands in this region contain one of the highest concentrations of dissolved organic carbon (DOC) ever measured in freshwater systems and abundant sulfur (~ 20 mM sulfate, 6mM sulfide, and other sulfur species). The two analyzed wetlands are involved in massive methane fluxes (up to 162 mg methane/m2/hour in P7) and sustain sulfate reduction rates up to 22 umol sulfate/cm3/day. We used these 16S rRNA gene data to infer key microbial players in carbon and sulfur processing and to investigate why such active sulfate reduction did not inhibit methanogenesis. Abundant DOC and putative methanogens that utilize non-competitive substrates provide distinct mechanisms for bypassing thermodynamic inhibition. This work suggested that the PPR might play a unrecognized role in carbon mineralization and methane emissions, characterizing this wetlands as biogeochemical hotspots.

Sample: Please see the papers https://doi.org/10.1111/gcb.13633 and https://doi.org/10.1186/s40168-018-0522-4

SAMN10506008 • SRS4100945 • All experiments • All runs

Organism: sediment metagenome

Library:

Name: P8_1012_Sept

Instrument: AB 5500xl Genetic Analyzer

Strategy: RNA-Seq

Source: METATRANSCRIPTOMIC

Selection: cDNA

Layout: SINGLE

Runs: 1 run, 857.6M spots, 42.9G bases, 32Gb

Run	# of Spots	# of Bases	Size	Published
SRR8272512	857,575,339	42.9G	32Gb	2018-12-03

ID:: 6865545

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