Analysis of eDNA Experimental data

TITLE: Analysis of eDNA Experimental data

ACAN:

The purpose of this Advance Contract Award Notice (ACAN) is to signal the government’s intention to award a contract for these services to Maelle Sevellec, Thorigné-Fouillard, France. 

Before awarding a contract, however, the government would like to provide other suppliers with the opportunity to demonstrate that they are capable of satisfying the requirements set out in this Notice, by submitting a statement of capabilities during the ACAN posting period.

If other potential suppliers submit a statement of capabilities during this ACAN posting period that meets the requirements set out in the ACAN, the government will proceed to a full tendering process on either GETS or through traditional means, in order to award the contract.

If no other supplier submits, on or before the closing date, a statement of capabilities meeting the requirements set out in the ACAN, a contract will be awarded to the pre-selected supplier.

INTRODUCTION:

The Department of Fisheries and Oceans (DFO) has been conducting research to support the development genomic tools including environmental DNA (eDNA) which can be utilized for community-based coastal biodiversity monitoring program in the Canadian Arctic. This research will address the DFO Results Framework under the Aquatic Ecosystems core responsibility to conserve and protect Canada’s oceans and other aquatic ecosystems and species from human impact and invasive species.

BACKGROUND:

Environmental DNA (eDNA) has the ability to allow researchers to monitor and collect baseline biodiversity data on a large spatial and temporal scale in remote regions where data collection and monitoring is often limited. Although eDNA is a powerful tool for the biomonitoring of Arctic ecosystems, a better understanding of factors influencing eDNA variability is needed to improve the standardization of this method. DFO has conducted experimental work in several regions of the Arctic to examine the ecology of eDNA in Arctic marine coastal environments with respect to DNA recovery and species detection from water samples. Samples were previously collected in various locations and have been sequenced with taxonomic assignments.

OBJECTIVES:

DFO requires a contractor to conduct analyses of the eDNA data, write up data analysis methods, provide interpretation of results, and conduct background literature reviews/ write associated summaries on selected topic areas as outlined below.

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WORK REQUIREMENT:

The contractor will conduct analyses of the data, write up data analysis methods and interpretation of results, and conduct background literature reviews/ write associated summaries related to the following experiments: 

1. Contrasting efficiency between zooplankton bulk metabarcoding versus water eDNA metabarcoding;
2. Interannual variation in eDNA-based biodiversity indices across coastal locations;
3. Evaluating water sample size versus volume effects on coastal eDNA-based estimates of coastal biodiversity; and
4. eDNA-based evaluation of diversity in ship hull biofouling assemblages. This information will be important in improving the standardization of eDNA for coastal biodiversity sampling and development of community-based monitoring protocols

TASKS AND DELIVERABLES:

Experiment 1: Contrasting efficiency between zooplankton bulk metabarcoding versus water eDNA metabarcoding;

1. Literature review/summary
   1. Conduct literature review on evaluating eDNA efficiency to monitor zooplankton and write up summary for inclusion in draft manuscript introduction and discussion sections
2. Data preparation/cleaning with Barque pipeline:
   1. Select taxonomic groups of interest (aquatic metazoans).
   2. Removal of species or genera for cases where the number of sequence in the negative controls is calculated to be greater than 2% of the total number of sample sequences.
   3. Treatment of sequences with multiple hits following approach outlined in Lacoursiere et al. 2018.
3. Data analyses:
   1. Conduct multivariate analyses (including canonical correspondence analyses and diversity analyses) and develop saturation curves to compare paired bulk zooplankton and eDNA water sample based biodiversity for CO1 and 18S primers.
4. Writing of analysis methods and results:
   1. Write up a description of above data analysis methods for inclusion in a draft manuscript.
   2. Write up above results for inclusion in a draft manuscript.

Experiment 2: Interannual variation in eDNA-based biodiversity indices across coastal locations

1. Data preparation/cleaning with Barque pipeline:
   1. Select taxonomic groups of interest (aquatic metazoans).
   2. Removal of species or genera for cases where the number of sequence in the negative controls is calculated to be greater than 2% of the total number of sample sequences.
   3. Treatment of sequences with multiple hits following approach outlined in Lacoursiere et al. 2018.
2. Data analyses:
   1. Conduct multivariate analyses (including canonical correspondence analyses and diversity analyses) and develop saturation curves to compare metazoan biodiversity with CO1 and 18S primers based on eDNA coastal water samples across 4 ports over 3 years.
3. Writing of analysis methods and results:
   1. Write up a description of above data analysis methods for inclusion in a draft manuscript.
   2. Write up above results for inclusion in a draft manuscript.

Experiment 3: Evaluating water sample size versus volume effects on coastal eDNA-based estimates of coastal biodiversity;

1. Literature review/summary
   1. Conduct literature review on potential factors affecting evaluating eDNA capture from water samples and write up summary for inclusion in draft manuscript introduction and discussion sections
2. Data preparation/cleaning with Barque pipeline:
   1. Select taxonomic groups of interest (aquatic metazoans).
   2. Removal of species or genera for cases where the number of sequence in the negative controls is calculated to be greater than 2% of the total number of sample sequences.
   3. Treatment of sequences with multiple hits following approach outlined in Lacoursiere et al. 2018.
3. Data analyses:
   1. Conduct multivariate analyses (including canonical correspondence analyses and diversity analyses) and develop saturation curves to compare metazoan biodiversity with CO1 and 18S primers based on various combinations of volume and sample size of eDNA coastal water samples.
4. Writing of analysis methods and results:
   1. Write up a description of above data analysis methods for inclusion in a draft manuscript.
   2. Write up above results for inclusion in a draft manuscript.

      Experiment 4: eDNA-based evaluation of diversity in ship hull biofouling assemblages.

1. Data preparation/cleaning with Barque pipeline:
   1. Select taxonomic groups of interest (aquatic metazoans).
   2. Removal of species or genera for cases where the number of sequence in the negative controls is calculated to be greater than 2% of the total number of sample sequences.
   3. Treatment of sequences with multiple hits following approach outlined in Lacoursiere et al. 2018.
2. Data analyses:
   1. Conduct multivariate analyses (including canonical correspondence analyses and diversity analyses) and develop saturation curves to compare metazoan biodiversity with CO1 and 18S primers based on eDNA coastal water samples across 4 ports over 3 years.
3. Writing of analysis methods and results:
   1. Write up a description of above data analysis methods for inclusion in a draft manuscript.
   2. Write up above results for inclusion in a draft manuscript.

      RESOURCES AND LEVEL OF EFFORT

      One resource is required to conduct all the tasks and deliverables. The estimated LOE is 1800 hours.

      MANDATORY CRITERIA:

      Official Language Requirement

• English Essential

Education:

• Graduation with an acceptable doctoral degree from a recognized post-secondary institution in a field of pure, natural and applied sciences with a specialization related to:

• Biology-environmental
• Biostatistics
• Biotechnology

Experience:

• Experience in planning and conducting research
• Experience in bioinformatics
• Experience in the study of Arctic marine communities
• Experience in metagenomics and eDNA
• Experience in statistical analysis of DNA data
• Experience in the preparation and publication of manuscripts on metagenomics, eDNA and arctic marine communities,

• Must have at least 5 publications (first or co-authored) on metagenomics/eDNA, two of which are related to Arctic marine communities

ESTIMATED VALUE

The total value of the contract shall not exceed $90,000.00 excluding all applicable taxes for the firm period from contract award to 31 March 2022 with 1 option year, each of 1 year duration. Initial Contract period is estimated at $45,000.00; Option Year 1 is estimated at $45,000.00.

SECURITY REQUIREMENT

There is no security requirement.

TRADE AGREEMENTS APPLICABILITY OR OTHER OBLIGATIONS:

No Trade Agreements apply.

GOVERNMENT CONTRACTS REGULATIONS EXCEPTION AND LIMITED TENDERING REASONS:

The following policy requirements are applicable to this ACAN process:

Applicable Exceptions to Soliciting Bids under the Government Contracting Regulations (GCRs) (Section 6):

Section 10.2.1 Section 6 (d) only one person or firm is capable of performing the work applies to this ACAN for the following reasons:

• There are no known alternative sources of supply. It is feasible and affordable to compete the requirement.

CONTRACT PERIOD:

The period of the contract is from contract award to 31 March 2022 inclusive. The contract will include 1 optional year, to be exercised at the discretion of DFO.

Firm Period: Contract award to 31 March 2022

Option Year 1: 1 April 2022 to 31 March 2023

SUPPLIER’S RIGHT TO SUBMIT A STATEMENT OF CAPABILITIES:

Suppliers who consider themselves fully qualified and available to provide the services described herein, must submit a Statement of Capabilities in writing to the Contracting Officer identified in this Notice on or before closing date. The Statement of Capabilities must clearly demonstrate how the supplier meets the advertised requirements.

CLOSING DATE FOR SUBMITTING STATEMENT OF CAPABILITIES:

23 December 2021 at 2:00 p.m. (AST)

Inquiries and statements of capabilities are to be directed to:

Hannah State

Senior Procurement Officer

Procurement Hub – Fredericton

Telephone: (506) 429-2622

Email: DFOtenders-soumissionsMPO@dfo-mpo.gc.ca