Attachment_A_-_PWS.pdf

Attachment A – PWS 140G0225Q0009

PERFORMANCE-BASED WORK STATEMENT (PWS)

Analysis of Environmental DNA (eDNA) Services

GENERAL INFORMATION

Introduction – The Department of the Interior (DOI) United States Geological Survey (USGS) Kansas Water Science Center (KS WSC), 1217 Biltmore Drive, LAWRENCE KS 66049 USA, requires services for analysis of environmental DNA (eDNA) samples for macroinvertebrate community assemblages via metabarcoding and fecal source tracking via quantitative PCR (qPCR).

Background – The USGS is conducting a study focused on a comprehensive assessment of macroinvertebrate communities as integrated indicators of overall Johnson County, KS stream health. The results from this assessment will be compared with similar data collected during 2003 through 2010. Availability of current macroinvertebrate community assemblages via metabarcoding and fecal source tracking via qPCR will help identify stream locations least and most affected by environmental stressors and habitat factors that may be affecting those conditions. The USGS will collect eDNA samples to be analyzed for macroinvertebrate community assemblages via metabarcoding and fecal source tracking samples via qPCR at 6 different stream locations in Johnson County, KS.

For quality-control purposes, eDNA samples to be analyzed for macroinvertebrate community assemblages via metabarcoding will be collected in triplicate with a field blank sample at each stream location. Additionally, there will be at least one replicate collected during the fecal source tracking samples analyzed via qPCR.

All samples will be collected between February and April 2025, resulting in an estimated 24 eDNA samples to be analyzed for macroinvertebrate community assemblages via metabarcoding (triplicate samples and one blank collected at 6 stream locations) and 7 eDNA samples to be analyzed for fecal source trackers via qPCR (6 samples and one replicate). eDNA samples to be analyzed for macroinvertebrate community assemblages via metabarcoding will be collected and filtered in the field using a Smith-Root eDNA sampler following the methods described in Laramie and others, 2015. eDNA samples to be analyzed for fecal source trackers via qPCR will be collected, filtered, and preserved in the field using laboratory-supplied sample collection kits. The analytical laboratory will quantify the composition of the aquatic macroinvertebrate community assemblage using metabarcoding of eDNA. Additionally, the analytical laboratory will search the water samples and quantify eDNA associated with fecal matter for the following species:

E. coli, human, dog, swine, sheep, poultry, bovine, goose, and deer. The project has potential to collect additional samples depending on findings, scope, and continuation of funding.

Definitions/Applicable documents – USGS Environmental DNA sampling protocol -filtering water to capture DNA from aquatic organisms (https://doi.org/10.3133/tm2A13).

Scope – Services, non-personal, to provide all equipment, labor, travel, supervision, and materials (unless otherwise provided herein) necessary for analysis of eDNA samples for macroinvertebrate community assemblages via metabarcoding and fecal source tracking via quantitative qPCR for E. coli, human, dog, swine, sheep, poultry, bovine, goose, and deer.

TECHNICAL REQUIREMENTS

Task 1 – The contractor shall receive and monitor samples to the following quality standards:

Chains-of-custody for all laboratory operations, and analyses for each sample, shall be fully documented.

Samples shall be received by the Contractor Monday through Friday.

The contractor shall report sample receipt records to the USGS Technical Liaison.

Task 2 – The contractor shall analyze samples to the following quality standards:

Task 2.1 – When ordered by the Government, the contractor shall perform analysis of eDNA samples for macroinvertebrate community assemblages via metabarcoding conducted by a trained expert analyst who has experience with benthic macroinvertebrate communities in Kansas using the most current references, keys, and publications.

The organisms shall be identified to the lowest practical level, generally family or genus level, which should be sufficient for bioassessment purposes.

The contractor shall provide 10-point quality control, full bioinformatics, and 1-year storage of raw data.

All data entry shall be double checked for accuracy and validated by the laboratory manager.

Anticipated number of samples submitted for Task 2.1:

o 24 eDNA samples to be analyzed for macroinvertebrate community assemblages via metabarcoding (triplicate samples and one blank collected at 6 stream locations).

Task 2.2 – When ordered by the Government, the contractor shall perform fecal source tracking analysis of eDNA samples via quantitative qPCR for E. coli, human, dog, swine, sheep, poultry, bovine, goose, and deer. Fecal source tracking shall be conducted by a trained expert analyst.

The contracted laboratory shall provide the eDNA sampling kit, including a barcoded sample cup, desiccant, syringe, and filter. The filter will be preserved and shipped back to the contracted laboratory after collection.

The contracted laboratory shall extract and analyze the eDNA to quantify the number of copies of mitochondrial DNA from potential hosts (E. coli, human, dog, swine, sheep, poultry, bovine, goose, and deer) using qPCR.

Anticipated number of samples submitted for Task 2.2:

o 7 eDNA samples to be analyzed for fecal source trackers via qPCR (6 samples and one replicate).

Deliverables: The contractor shall submit all results electronically. These deliverables shall include:

Results of macroinvertebrate community assemblages via metabarcoding electronically.

Full qPCR report that includes detections of each of the host organisms (E.

coli, human, dog, swine, sheep, poultry, bovine, goose, and deer), detailed methods, and 5-point standard curve.

The contractor shall provide a Quality Control Plan (QCP) with its proposal and adhere to the QCP when performing the services. A chain of custody for each sample shall be maintained and documented.

I. SUPPORTING INFORMATION

1. Place of Performance – Location of Contractor’s facility.

2. Periods of Performance: 02/10/2025 through 02/09/2030 (estimated)

3. Government Furnished Property (GFP) – N/A

4. Special Considerations. – N/A

QUALITY ASSURANCE SURVEILLANCE PLAN

The contractor is responsible for laboratory quality control (QC) and shall adhere to its QC Plan.

The Government is responsible for quality assurance (QA) and will monitor the contractor’s performance to assure that the performance quality standards and time standards are met or exceeded by the contractor for the PWS tasks by taking the following efforts:

Task 1 – Sample Reception. The Technical Liaison (TL) will review the data for completeness and ensure all required deliverables are provided in acceptable digital formats.

Task 2 – Sample Analysis. The Technical Liaison (TL) may submit blind samples, including the analysis of replicates, and will evaluate their consistency using known published analytical results. Replicate data and lab QC data shall be compiled into a Lab Evaluation Plan that will be updated biennially after initial compilation (usually within first 1-2 years depending on volume of submitted samples). Should it be deemed necessary, a USGS scientist will be permitted to visit the laboratory facility to view the materials handling and measurement workflow of the contracting lab.