Request for Proposals: Census of Deep Life Sequencing Opportunities

Since 2011, the Deep Carbon Observatory’s Deep Life Community has sponsored the Census of Deep Life (CoDL), which has supported surveys of the diversity of microbes present in several deep continental and subseafloor environments. The first surveys (2011-2012) were conducted using 454 pyrosequencing and subsequently (2013) Illumina sequencing strategies were adopted. Through this initiative, the Deep Life Community has allowed the characterization of the diversity of subsurface microbial communities at numerous sites worldwide, including the subseafloor and deep continental locations from a range of geologic settings (e.g., large igneous provinces, subglacial lakes, methane hydrate-rich sediments, cratons). The Illumina platform provides increased numbers of reads for more samples at reduced cost. For DNA samples submitted to the CoDL for sequencing, proponents have the option of obtaining 400-450 nt sequences that span the V4V5 region of Bacterial and Archaeal rRNA coding regions or a greater number of reads for V6 regions that through complete overlap of forward and reverse reads allows detection of lower abundance taxa with reduced stochastic error rates. Shotgun metagenomic DNA sequencing for key samples also can be performed.

This call for proposals aims to support sequencing that represents expanded analyses from ongoing Deep Life Community projects or projects that represent sites and investigators new to the DCO’s Deep Life Community. Two independent options, each of which use the Illumina sequencing platform, are available:

  • Option 1: This option offers the opportunity to submit up to 24 samples for 16S rDNA amplicon sequencing (as described above for Bacterial and Archaeal sequences). Note: sequencing of Bacteria AND Archaea in a single sample counts as two samples; therefore a maximum of 12 samples for paired analysis of both Archaea and Bacteria would be acceptable. On a case-by-case basis, sequencing of a reasonable number of additional samples (more than the specified 24) may be requested and justified in the proposal and will be considered by reviewers. Control experiments are important and strongly encouraged in subsurface systems where biomass is low.  For this reason investigators may submit control blanks (at the expense of the allocated number of samples for analysis) that combine the reagents used to prepare their libraries. Successful applicants must be able to provide high-quality DNA samples to the Marine Biological Laboratory at Woods Hole for Illumina sequencing before November 1, 2018.
  • Option 2: This option offers the opportunity to submit up to three select samples from subsurface environments for shotgun metagenomic sequencing. Ideal samples for the metagenomic surveys will have evidence of limited microbial diversity as a result of the prior microbial rDNA community analyses. Successful applicants must be able to provide high-quality DNA samples before October 1, 2018. Note: Within the context of the shotgun metagenomic option, we will also consider requests for draft genome sequencing of individual genomes either from cultivars or from single-cell genomic preparations.

Download the full RFP (.docx)

15 July 2018
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