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SRX2058448: Metagenomic sequencing of Phillipines serpentinizing spring gDNA
1 ILLUMINA (Illumina HiSeq 1000) run: 16M spots, 1.8G bases, 674.6Mb downloads

Design: Metagenomic shotgun sequencing (Hiseq): We use Picogreen (Invitrogen) to quantitate genomic DNA samples. DNA is sheared using a Covaris and libraries were constructed with the Nugen Ovation Ultralow Library protocol. We aim for an insert size of 175bp to enable read merging. Amplified libraries are visualized on an Agilent DNA1000 chip or Caliper HiSens Bioanalyzer assay, pooled at equimolar concentrations based on these results, and size selected using a Sage PippinPrep 2% cassette. The library pool is quantified using a Kapa Biosystems qPCR library quantification kit, then sequenced on the Illumina HiSeq1000 in a 2x100 paired-end sequencing run using dedicated read indexing. The samples are demultiplexed with CASAVA 1.8.2.
Submitted by: Marine Biological Laboratory
Study: Manleluag Spring National Park Metagenome
show Abstracthide Abstract
Manleluag Spring National Park (the Philippines) hosts several continental serpentinizing fluid springs in a tropical, densely vegetated environment. The spring fluids originate in the Acoje block of the Zambales ophiolite range, and are ultra-basic (pH ~10.9) and oligotrophic. Uranium-thorium radiometric dating indicates that the Zambales ophiolite complex is approximately 40 Myr old, placing formation of the oceanic crust in a nascent island arc during Eocene seafloor spreading (Abrajano et al., 1988; Hawkins and Evans, 1983). Fluid and sediment samples were collected for metagenomic analysis to characterize the deep subsurface microbial community originating in these springs. Samples were collected in two ways: a) by pumping approximately 20 liters of spring fluid through 0.22 µm Millipore® Sterivex™ filter units (Merck KGaA, Darmstadt, Germany) via peristaltic pump, and b) by collection of sediment from spring pools in Whirl-Pak® sampling bags (Nasco, Fort Atkinson, WI, USA). Previously conducted 16S rRNA gene amplicon sequencing analysis indicated that the springs hosted microbial consortia primarily consisting of Bacteroidetes, Deinococcus-Thermi, Proteobacteria, Firmicutes, and Euryarchaeota (Woycheese et al., 2015). Geochemical parameters observed in Manleluag springs indicated that methanogenesis/methanotrophy, hydrogen oxidation, iron cycling, sulfur cycling, and ammonia oxidation were all feasible based on bioenergetic yield calculations (Cardace et al., 2015). The results of this analysis provide further insight into the taxonomic diversity and metabolic capacity of microbial communities in oligotrophic, deeply-sourced tropical serpentinizing fluid springs.References:Abrajano, T.A., et al., (1988). Methane-hydrogen gas seeps, Zambales ophiolite, Philippines: Deep or shallow origin? Chem. Geol. 71(1-3): 211-222. doi: 10.1016/0009-2541(88)90116-7.Hawkins, J. W., and Evans, C. A. (1983). Geology of the Zambales Range, Luzon, Philippine Islands: Ophiolite Derived from an Island Arc-Back Arc Basin Pair, in The Tectonic and Geologic Evolution of Southeast Asian Seas and Islands: Part 2 (ed. D. E. Hayes), American Geophysical Union, Washington, D. C. doi: 10.1029/GM027p0095.Cardace, D., et al., (2015). Feasible metabolisms in high pH springs of the Philippines. Front. Microbiol. 6:10. doi:10.3389/fmicb.2015.00010.Woycheese, K., et al., (2015). Out of the dark: transitional subsurface-to-surface microbial diversity in a terrestrial serpentinizing seep (Manleluag, Pangasinan, the Philippines). Front. Microbiol. 6(44): 1-12. doi: 10.3389/fmicb.2015.00044.
Sample:
SAMN05712279 • SRS1650432 • All experiments • All runs
Library:
Name: Sample_121018_ML2_sterivex_filter
Instrument: Illumina HiSeq 1000
Strategy: WGS
Source: METAGENOMIC
Selection: RANDOM
Layout: PAIRED
Runs: 1 run, 16M spots, 1.8G bases, 674.6Mb
Run# of Spots# of BasesSizePublished
SRR407197516,000,0001.8G674.6Mb2016-08-30

ID:
3052634

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