Inactive

Special Notice of Intent to Award a Sole Source Procurement THIS IS NOTICE OF INTENT IS NOT A REQUEST FOR COMPETITIVE PROPOSALS; HOWEVER, ALL RESPONSIBLE SORCES MAY SUBMIT A CAPABILITY STATEMENT WHICH... Special Notice of Intent to Award a Sole Source Procurement THIS IS NOTICE OF INTENT IS NOT A REQUEST FOR COMPETITIVE PROPOSALS; HOWEVER, ALL RESPONSIBLE SORCES MAY SUBMIT A CAPABILITY STATEMENT WHICH SHALL BE CONSIDERED BY THE AGENCY. This Notice is to announce that the U.S. Department of the Interior (DOI), U.S. Geological Survey (USGS), is proposing to negotiate a contract with the University of Colorado CWEST to conduct specialized analysis of algae samples from rivers and lakes across the country. Services will include We are working to develop a protocol that can be implemented broadly by the USGS and other agencies. The approach is based on our success in developing methods for 1) consistent taxonomic identification of algae in the laboratory, 2) evaluation of sample analysis protocols directed at water quality assessment, 3) providing web-based tools for species identification. The current project follows our approach to establish a strong analytical basis and expands upon our work with diatoms and soft algae to address streamlined protocols directed at HABS. Our work depends on continuity with existing USGS long-term databases, such as USGS BioData and Diatoms of North America (diatoms.org). We follow upon the CWEST/INSTAAR cooperative agreement with USGS that supported development of a "bioinformatics pipeline" for algal sequence data in federal programs. This pipeline is basically a series of steps to insure that algal genomic sequences are processed for assessment in a consistent manner. This statement of work is intended to apply those steps to HABS molecular sequence data in the Delaware River Watershed, with the ability to further scale up to for additional large watersheds. One of the limitations for molecular sequence data is that reference libraries that link a particular algal species with DNA sequence within a specific region have not been developed. Thus, algal sequence data is dependent upon the integrity of the bioinformatics pipeline, and the clear expression of decision points along the way. The success of this project is dependent upon using a publically accessible, transparent bioinformatics processing of sequence data. Requiring program office is the Water Mission Area, Earth Systems Process Division, Water Resources Assessment Branch. The proposed action is for services for which the Government intends to solicit and negotiate with only one source under the authority FAR 13.106-1(b)(1). The reason justifying this sole source procurement is that the Government believes only one responsible source can provide the services that will satisfy the agency's requirement. The following services are provided: Services, non-personal, to provide all plant equipment, labor, travel, and materials including replacement parts (unless otherwise provided herein) necessary for the analysis of integrated treatment and analysis of algae samples to produce high quality data as described in the following Work Requirements and Standards. The requirement is for integrated treatment and analysis of algae samples, particularly harmful algal blooms (HABS). Services will include 1) receiving of shipments, secure storage, and login of preserved and low temperature (-20°C) samples; 2) extraction of frozen samples for eDNA; 3) quantitative subsampling of DNA and preparation for sequencing; 4) bioinformatics processing of DNA data using standardized protocols; and 5) identification of cyanobacteria using a specific protocol and taxonomic system. Work Requirements and Standards: The scope of work includes two primary sets of sample analysis: 1) environmental DNA samples (eDNA) for sequencing, and 2) algal samples for microscopic identification based on morphology. The first set of samples will be collected by USGS staff, placed on dry ice, and submitted to the laboratory for a series of processes, all taking place at -20°C to prevent degradation of DNA. Samples will be accessioned, tracked based on USGS identifiers, and extracted. The laboratory will be responsible for submitting quantified amounts of extracted DNA for Illumina sequencing. Then, the laboratory will run the sequence data through established R scripts (the bioinformatics pipeline) to produce final data. The second set of samples will also be collected by USGS staff, preserved in the field, and submitted to the laboratory. These samples will be identified to the genus level based on morphological features, using the Utermohl method of inverted light microscopy. Data will be reported in formats specified to match existing USGS R scripts. We expect to submit a total of 50 samples for each set of analysis in 2019 and 50 samples for each set of analysis in 2020. A. Technical Requirements. 1. Description. Description: 1) Environmental DNA samples (eDNA) for sequencing Genomic DNA will be shipped frozen on dry ice to the laboratory. The laboratory will be notified prior to shipment to confirm that laboratory staff are available for receipt of samples. On the same day of shipment arrival, staff will place samples in a -20°C freezer. Within 1 month of arrival at the laboratory, staff will enter samples into database and assign an internal lab tracking number. Samples will be properly labeled with the tracking number. Extractions will be completed by a laboratory technician trained in use of micropipettes, and skill demonstrated to a laboratory manager. DNA extraction will be conducted in a lab dedicated to clean DNA methods, following the DNeasy PowerSoil Kit Handbook (2017). Each round of DNA extraction will be documented in a laboratory notebook. When all of the project DNA samples have been extracted, quantitative subsamples will be removed and submitted for Illumina sequencing. The remaining extracted DNA will be stored at -20°C for a period of 5 years. Sequence data will be processed following the bioinformatics pipeline of Schulte (in prep.). Algal data will be reported as raw sequences and as the lowest taxonomic unit following USGS BioData. Criteria for acceptance of Service. Data will be provided in Tidy format accompanied by a metadata file including USGS sample identifiers, internal lab tracking numbers, number of reads, read quality scores, sample blanks, and lowest taxonomic unit. Description: 2) Algal samples for microscopic identification Samples for microscopic analysis will be preserved in the field with 10% formalin and shipped to the laboratory. Within 1 month of arrival at the laboratory, staff will enter samples into database and assign an internal lab tracking number. Samples will be properly labeled with the tracking number. Sample analysis will follow Lund et al. (1958), using Utermohl chambers and an inverted microscope. A voucher flora will be produced for cyanobacteria following Tyree et al. (2020). The method will be modified to report the identity of cyanobacterial cells and colonies, based on genus level identifications (USGS BioData). Criteria for acceptance of Service. Data will be provided in Tidy format accompanied by a metadata file including USGS sample identifiers, internal lab tracking numbers, the presence of cyanobacterial genera in each sample, sample preservation notes, and lowest taxonomic unit. An image voucher flora will be provided as a pdf. B. Deliverables. 1. Characteristics for service identified by name and quantity. ¿ Approximately 50 samples per year (2019 and 2020) for Bacteria/Archaea 16S library prep and sequencing ¿ Approximately 50 samples per year (2019 and 2020) for Eukaryotic 18S library prep and sequencing ¿ Approximately 50 samples per year (2019 and 2020) for Eukaryotic rblc library prep and sequencing ¿ Provide raw sequencing data for all data. ¿ Meta data file USGS sample identifiers, internal lab tracking numbers, number of reads, read quality scores, sample blanks, and lowest taxonomic unit. ¿ Accompanying documents describing methods used for processes including library preparation through sequencing and details on reagents, kits, and equipment used. 2. Delivery dates for work/product to be completed and point of delivery. ¿ Data and accompany methods are to be delivered no later than 60 business days following receipt of samples for library prep. The contractor shall provide the USGS with access to and FTP server or other secure server for downloading sequencing data. ¿ All corresponding quality control information including barcodes (tags), library prep kit information, and primers (as appropriate) should be accompanied with data delivery. ¿ Provide access to data for downloading for at minimum 60 days following receipt of sequencing data. ¿ Submit all files and documentation no later than December 30, 2020