SPECIAL NOTICE
B -- DNA MARKER GENE ANALYSIS Sole Source
- Notice Date
- 5/5/2020 5:34:15 PM
- Notice Type
- Special Notice
- NAICS
- 541380
— Testing Laboratories
- Contracting Office
- OFFICE OF ACQUISITON GRANTS SACRAMENTO CA 95819 USA
- ZIP Code
- 95819
- Solicitation Number
- 140G0320Q0098
- Archive Date
- 05/30/2020
- Point of Contact
- Ciccarelli, Cheryl
- E-Mail Address
-
cciccarelli@usgs.gov
(cciccarelli@usgs.gov)
- Awardee
- null
- Description
- Notice of Intent This is a notice of intent to solicit from a single source. The U.S. Geological Survey (USGS), intends to negotiate a purchase order, with the University of Delaware for DNA market gene analysis on Methane derived authigenic carbonate rocks collected from the Cascadia Margin. The Statement of Work is attached herein. Award will be made in accordance with Federal Acquisition Regulation (FAR) 13.106-1(b) and the procedures at FAR Part 12 entitled, Acquisition of Commercial Items and FAR Part 13 entitled, Simplified Acquisition Procedures. The University of Delaware has the necessary equipment, staff, expertise and to process all authigenic carbonate samples and can provide results from analysis on the desired timeline. The USGS and University of Delaware have collaborated on a gene sequencing project on methane derived authigenic carbonates, the first ever study from the United States Atlantic Margin (USAM). The prior study produced microbial phylogeny from two USAM seep sites. We now have additional samples from more seeps sites along the USAM as well as new seeps along the Pacific Margin. These additional samples along the USAM and the Pacific Margin will help us answer questions about the heterogeneous nature of cold seep ecosystems. Specifically, we need to compare this first study with new results to fill spatial gaps in our understanding of what archaeal bacterial consortia are involved in anaerobic oxidation of methane along both margins and this requires project continuity. The purpose of this notice is to satisfy the requirements of FAR Subpart 5.2. This notice of intent is not a request for competitive quotes. However, all responsible parties may submit a quotation by the closing date of this announcement which shall be considered by the agency. No solicitation will be issued. A determination not to compete this action based upon responses received is in the sole discretion of the Government. The NAICS code for this action is 541380 Testing Laboratories and associated size standard is $16.5 million apply to this announcement. Responses or inquiries shall only be accepted through electronic mail addressed to Cheryl Ciccarelli, cciccarelli@usgs.gov and must be uploaded and received in their entirety no later than May 12, 2020. Responses submitted by hardcopy or the FedConnect web portal or the FedConnect Message Center shall not be accepted or considered. STATEMENT OF WORK I. GENERAL INFORMATION A. Introduction: The U.S. Geological Survey, Geology, Pacific Coastal and Marine Science (PCMSC) has identified a need for DNA marker gene analysis on methane derived authigenic carbonate rocks collected from the Cascadia Margin. B. Background: Seafloor methane seeps serve as hotspots for the exogenic carbon cycle, introducing into the mobile carbon cycle mostly fossil (14C�dead) carbon that has been sequestered for thousands to millions of years. Anaerobic oxidation of methane (AOM), mediated by methanotrophic archaea and sulfate reducing bacteria (SRB), sequester carbon via AOM-induced carbonate precipitation, representing a major carbon sink. As a consequence of AOM, methane derived authigenic carbonates (MDAC) are precipitated from the localized oversaturation of bicarbonate ions in pore water (according to the reaction CH4 + SO4-2 HS- + HCO3- + H2O) and can incorporate diagnostic biomarkers that reflect their microbial origins. Removal of methane by both anaerobic and aerobic oxidation of methane in the marine setting plays a key role in the marine carbon cycle. Therefore, identifying where AOM occurs and which communities are driving AOM is important for marine carbon processes at both modern and dormant seep sites. Consortia of methane-oxidizing archaea (i.e., methanotrophs) and sulfate reducing bacteria (SRB) have been identified as carrying out AOM. Diagnostic biomarkers preserved in MDACs can therefore serve as fingerprints to archaeal bacterial consortia involved in sulfate-dependent AOM and provide insight into the ancient environments favoring the growth of one consortium over another. C. Definitions/Applicable Documents: n/a D. The high stability of archaeal lipids and reduced degradation under anoxic conditions suggests that archaeal lipid variability is well preserved in fossil environments (e.g., MDACs) and not affected by differential degradation of archaeal biomass types. Therefore, the molecular fingerprint preserved in the carbonates yields important information on the microbial origin of MDACs and the conditions under which they form, providing a diagnostic for methane oxidizing archaea carrying out AOM. Three distinct methanotrophic archaea (ANME) clusters (ANME-1, -2, and -3) have been identified in association with sulfate reducing bacterial partners of the Desulfosarcina/Desulfococcus and Desulfobulbus branches. However, it is difficult to differentiate between the different ANME clades based solely on organic geochemical data given that ANME are closely related to methanogenic archaea (e.g., Methanosarcinales and Methanomicrobiales) and recent investigations suggest that AOM is an enzymatic reversal of bicarbonate methanogenesis. Therefore including phylogenetic data is needed to further identify the methanotrophic consortia driving AOM II. WORK REQUIREMENTS A. Technical Requirements. 1. The contractor must have an extensive background in microbial community analyses via DNA marker gene analysis. In addition, the contractor must have specific knowledge and experience with extracting DNA from authigenic carbonates and PCR amplification and statistical analysis of 16S rRNA gene sequences using Nonmetric multidimensional scaling. This includes 2. Contractor's compliance will be measured by producing QA/QC results from gene sequencing. B. Deliverables. 1. Deliverables include producing table of relative abundance of microbial abundances according to 16S rRNA gene sequencing in carbonate samples from seep sites; and results from MDS analysis to USGS Point of Contact electronically as a .csv or excel file. USGS Point of Contact: TBD 2. Delivery dates for work/product is 6 months from receiving physical samples or at a later date agreed upon by the USGS POC. III. SUPPORTING INFORMATION B. The period of performance will commence May 2020, and will continue until May 2021 with the possibility of additional samples added from ongoing research along the US Pacific margin and options for funds to be added during the second through fourth year options. 100 samples will be submitted. 22 additional samples will be submitted for each option periods, Options 1-3, May 2021 through May 2024. C. Government Furnished Property (GFP): 100 authigenic carbonate samples D. Special Considerations. 1. Key personnel qualifications biochemistry and molecular biology and experience with DNA marker gene analysis in authigenic carbaonets ) 2. Data Rights, Safety, Environment: follow proper lab safety protocols 3. Security/Privacy issues : n/a 4. If there is archived sample remaining, then these samples should be shipped back or kept if replicated are needed for additional analysis.
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