Final Sources Sought.pdf

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Pre-solicitation Notice (P) X Sources Sought (R) Modification &

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Award Notice (A) Special Notice (S) Combined Synopsis/Sol. (K)

Complete All:

Solicitation Number: NFFR7400-20-02229 NAICS Code: 541380 - Testing

Laboratories

Title: Assessing Biodiversity using environmental DNA (eDNA)

Classification Code:

B -- Special studies and analysis - not R&D

Pre-Sol Issue Date: Estimated Mid-June Quote Due Date:

Mid-late July

Contract Specialist: Carina Topasna

Contract Support Staff to Receive E-mail of Response: Carina Topasna

Text:

The Department of Commerce, National Oceanic and Atmospheric Administration (NOAA), National Marine Fisheries Service (NMFS), Pacific Islands Fisheries Science Center (PFSC), Ecosystem Sciences Division (ESD), conducts field research activities range from near-shore island ecosystems like coral reefs to open ocean ecosystems on the high seas. They use numerical ecosystem models to analyze the current structure and dynamics of marine environments, as well as to examine potential projections of future conditions, such as those resulting from climate change impacts surveys.

The ESD is tracking marine life with invisible clues through DNA. As animals swim, they shed scales, tissue, and waste, leaving traces of DNA in the water. Scientists collect a water sample and analyze the DNA found in it, identifying the species that left it behind without capturing a single animal. Environmental DNA (eDNA) refers to all genetic material that is recovered from environmental substrates such as water or sediment. eDNA is a by-product of metabolic processes and is derived from sources such as feces, urine, skin, hair or decomposing organisms. This preserved, but often degraded, genetic material provides a means to audit species composition and communities at a given location. Metabarcoding is a technique that allows the amplification of multiple taxonomic groups simultaneously. This can be used to generate a biodiversity audit from an environmental sample containing multiple species. When combined with high-throughput DNA sequencing technologies, eDNA can provide a wealth of information for biodiversity studies of the detection of species in a rapid, cost-effective and non-destructive manner.

The PIFSC does not possess the equipment needed to process and sequence eDNA samples.

Therefore, there is a need to contract with an external commercial laboratory to process and sequence these samples. PIFSC will provide samples so that eDNA can be extracted, amplified using a combination of universal and taxa-specific assays, and then sequenced. The combination of multiple high-throughput assays can reveal greater diversity of species and finer taxonomic resolution.

The Scope of Work:

Contractor Laboratory Workflow Overview DNA is extracted from incoming samples by a hybrid manual/automated method using commercially supported reagents.

The Contractor shall use the metabarcoding assays noted below to target a wide diversity of marine species of relevance to this study.

(i) a nuclear rRNA 18S assay; invertebrate taxa

(ii) an assay to detect the mitochondrial cytochrome c oxidase 1 (CO1);

(iii) a fish mtDNA 16S assay.

(iv) an assay targeting the 12S rRNA known as MiFish.

Options for:

(v) an assay targeting the 23S rRNA for detection of algae.

(vi) coral ITS2 assays – for detection of hard and soft corals, worms, anemones, jellyfish.

We anticipate requesting processing between 115 to 800 eDNA water filter samples to be sequenced at 2-6 assays per sample.

• We anticipate on average processing 4 assays per sample, but may adjust between 2 and 6 assays per sample.

Analysis of sequence data Sequence data shall be demultiplexed by the Contractor and provided to the client who shall analyze data against their database to identify present taxa.

Tasks:

All laboratory benchwork shall be conducted according to the Contractor’s preferred standard operations and procedures, but shall include the following processes:

(1) DNA extraction from water filters;

(2) DNA quantification

(3) Fusion tagging PCR (i.e., amplification and sequencing index adapter ligation)

(4) Minipooling and Quantification (post-PCR)

(5) Library blending and Purification

(6) Sequencing

(7) Demultiplexing (Post-sequencing bioinformatics) of raw sequencing reads then provided to

PIFSC.

The contractor shall provide PIFSC the following:

• Sequencing data shall be returned in FastQ format in clean (i.e., passing Illumina’s instrument quality assessment pipeline) de-multiplexed form.

• Basic facts of methods used shall be disclosed, as would be expected for inclusion of sequencing data in the peer-reviewed literature (e.g., instrument/kit used).

• All libraries shall be performed using the same techniques/kits, and all libraries shall be sequenced on the same platform, unless negotiated with and approved by the PIFSC Point of Contact.

Applicable Standards:

• Assays are prepared with the use of isolated purpose-built ‘Ultra-Clean’ rooms. Massively parallel sequencing (also known as Next Generation Sequencing, or NGS) will be applied on the prepared metabarcoding assays. This innovative technique enables all amplified sample organisms from the collected sample to be represented in the assay result.

• This method is very sensitive to external contamination at all stages of the methodology.

Multiple negative controls are included throughout the laboratory handling workflows. Work is done in dedicated purpose-built clean rooms and eDNA dedicated equipment under strict logistical protocols.

Special Requirements:

• The Contractor shall possess Illumina sequencing equipment, equipment for quality and quantity assessment as appropriate for library preparation from DNA and sequencing, and equipment for library construction.

• Contractor will provide personnel experienced in DNA extraction, library preparation, and sequencing.

• The Contractor shall be able to process samples (including all steps for conversion of total DNA sample into sequence data) at an average rate of 100 samples/3 months or faster.

Deliverables Schedule:

Date Range Deliverable Activities Estimated Number of Samples

September 1, 2020

– August 31, 2021

Samples shipped to Contractor who will process according to applicable standards and procedures as outlined in this SOW

115 - 800

September 1, 2021

– August 31, 2022

Samples shipped to Contractor who will process according to applicable standards and procedures as outlined in this SOW

115 - 800

September 1, 2022

– August 31, 2023

Samples shipped to Contractor who will process according to applicable standards and procedures as outlined in this SOW

115 - 800

September 1, 2023

– August 31, 2024

Samples shipped to Contractor who will process according to applicable standards and procedures as outlined in this SOW

115 - 800

The Contractor shall provide the following:

1. Sequence data from each provided sample in FastQ format, in demultiplexed form, returned on average within 90 days of receipt of samples or faster, and in no case more than 6 months of sample receipt.

2. Overview of methods used in contractor format, as would be expected for inclusion of library preparation and sequence methods in the peer-reviewed literature for publications presenting the sequencing results. This includes names of the sequencing instrument and main kits used for library construction, cleaning/demultiplexing protocol, and statement of the number of samples sequenced per lane.

The intent of this acquisition is to obtain a firm fixed price contract, which includes a 12 month base period and three 12 month option periods.

The period of performance is:

Base Period: September 1, 2020 – August 31, 2021 Option Period 1: September 1, 2021 – August 31, 2022 Option Period 2: September 1, 2022 – August 31, 2023 Option Period 3: September 1, 2023 – August 31, 2024

The place of performance shall be at the contractor’s facility. The contractor’s facility needs to be a commercial molecular laboratory with separate dedicated purpose-built clean rooms for each stage of eDNA genetic processing procedures (DNA extraction, PCR, and post-PCR processes) in order to minimize the risk of sample cross-contamination. In addition, the facility shall possess dedicated and up-to-date eDNA equipment and access to an Illumina sequencer (e.g., MiSeq). The facility shall be able to receive and store sensitive eDNA samples.

PIFSC will collect and filter water samples using polyethersulfone membranes (PES, filters) with a vacuum pump to capture eDNA present in the water. Filters will be frozen shortly after collection and kept frozen until and during shipping to Contractor’s location via overnight shipment on dry-ice.

The contractor shall process and sequence each sample as per Contractor’s standard operating procedures. Processing includes extracting DNA from water filters, quantifying DNA, PCR amplification and indexed adapter ligation, library blending and purification, Illumina sequencing, and de-multiplexing raw sequencing reads.

A comprehensive list of actual requirements will be included in the Statement of Work within the solicitation package document.

The Contractor shall furnish all necessary personnel, equipment, required for performance of the statement of work/specifications which will be provided in the RFQ.

The Government is conducting market research to identify entities that have the capabilities and facilities needed to accomplish this scope. Accepting capabilities from all companies and universities, but if a small business concern please indicate that on your capability statement. The NAICS code for this procurement is 541380 and the business size standard for this requirement is $15 million dollars.

It is highly encouraged that any vendor meeting this size standard and desiring to be considered for award be registered in the System for Award Management (SAM) using this NAICS code or a NAICS code with an equivalent size standard. For additional information and to register in SAM, please access the following web site: www.sam.gov. In order to register with the SAM, all offerors must also have a Dun & Bradstreet Number. A Dun & Bradstreet number may be acquired free of charge by contacting Dun & Bradstreet on-line at https://iupdate.dnb.com/iUpdate/ viewiUpdateHome.htm or by phone at (866) 969-8491. It is also preferred that offerors to complete the electronic representations and certifications at the SAM website.

Any resulting contract will be awarded as a firm-fixed price type contract. Solicitation documents will be made available for download on or about late June 2020 at sam.beta.gov. Paper copies of this solicitation will not be issued. Interested parties should use the Sam.Beta.Gov [Add to Watchlist] and [Add Me to Interested Vendors] features which provide a notification when the Request for Quote (RFQ) becomes available for download as well as all postings of information associated with this solicitation thereafter. Each potential offeror is responsible for checking the Sam.beta.gov website to gain all current information related to the solicitation. The solicitation and any further announcements regarding the solicitation will be posted only at sam.beta.gov. The date offers are due will be stated within the solicitation documents and will be adjusted based upon the actual release date of the solicitation. All questions of any nature regarding this procurement should be sent in writing to the Contracting Specialist Carina Topasna at carina.topasna@noaa.gov.

(End of Document) http://www.fbo.gov/ http://www.fbo.gov/ mailto:carina.topasna@noaa.gov