Trialling Benthic eDNA Sampling Methods for Monitoring Marine Biodiversity

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    "description": "JNCC is undertaking an offshore survey to collect data to assist in monitoring the effectiveness of proposed fisheries management measures covering 42 English Marine Protected Areas (MPAs) including North-West of Jones Bank (NWJB) Marine Conservation Zone (MCZ). This survey is being utilised as an opportunity to investigate the effectiveness of various benthic environmental DNA (eDNA) sampling techniques for monitoring marine biodiversity, and to assess the performance of each method relative to the others to inform future monitoring methodology.\nJNCC wishes to commission a contract to undertake an analysis of marine taxa eDNA present in sediment and water samples to be collected at the seafloor on the TC25035 survey of North-West of Jones Bank MCZ. JNCC plan to trial three benthic eDNA collection methods within the survey area.\n3.\tProject Background\nThe RV Tom Crean will depart from Cork for the TC25035 survey on 9 September 2025 and return on 25 September 2025. Seventeen days of sampling will be carried out as part of the survey, focusing on data collection to support the assessment of potential fisheries management measures. The survey will gather data on the effects of reduced fishing pressure on the recovery of subtidal mud habitats, as well as of sea-pen and burrowing megafauna communities.\nNorth-West of Jones Bank MCZ is situated approximately 165 km offshore from the South-West of England. The site covers 399.14 km2 of continental shelf, and it contributes one of the largest areas of subtidal mud to the MPA network of all designated MCZs. For more information regarding NWJB MCZ please see https://jncc.gov.uk/our-work/north-west-of-jones-bank-mpa/.\nDNA and eDNA are increasingly utilised, cost-effective tools for monitoring biodiversity. Traces of DNA (e.g. from scales, faeces, skin, blood) left in the environment (e.g. water and sediments), called environmental DNA, are left behind by all organisms. Using molecular methods, such as eDNA metabarcoding, we can detect an organism\u0027s presence in the environment without directly observing it. eDNA techniques can provide high-resolution pictures of biodiversity from micro to macro scales and inform on assemblage composition and biological processes at reduced costs and time. Niskin bottles, metaprobes and sediment samples have been increasingly used in recent years to collect DNA from inshore marine waters, complementing existing traditional survey methods. However, application of these methods in offshore waters has been more limited.\n4.\tProject Objectives\nAs part of the offshore survey to North-West of Jones Bank MCZ, the primary research and development objective will be to trial three eDNA sampling techniques to fill significant knowledge gaps on the use of eDNA in offshore environments.\nTo achieve this objective, the following research questions to be answered are:\n1.\tWhich benthic eDNA sampling methods are recommended for sampling offshore marine organisms based on the following factors?\na.\tQuantity of DNA collected\nb.\tQuality of DNA collected\n2.\tHow do the following parameters compare among the benthic eDNA sampling methods?\na.\tSpecies detected\nb.\tSpecies of conservation interest detected\nc.\tSpecies richness\nTo answer these questions, JNCC plan to collect four eDNA samples using each of the three methods below, at four stations within the survey area. This will result in up to 48 eDNA samples plus six controls.\neDNA source\teDNA collection method\tStorage\tSampling methods\nWater\tSterivex filter \t99% ethanol (volume tbc)\tNiskin bottles attached to a CTD from a depth 3 metres above the seafloor\nWater including sediment particles \tGauze \t50ml 99% ethanol \tMetaprobes attached to a towed camera sledge for 30 mins\nSediment\tSediment sample \tFrozen\tSediment samples collected from a Day grab\nJNCC wishes to commission a contract to undertake this analysis of marine taxa eDNA in water and sediment samples collected on the TC25035 survey of NWJB. JNCC plan to collect a total of 54 samples. However, please note that the resulting sample number will depend on successful sampling delivery, which could be affected by factors such as weather.\nJNCC would like to use primers to test samples for the presence of marine vertebrates, fishes, invertebrates, meiofauna and bacteria.\nThe successful contractor will undertake the analysis as set out below (Section 5) adhering to common standards.\n5.\tProject Objectives: Detailed Tasks\nThe tenderers should provide a quote broken down into the following elements:\n\u2022\tTransport of 54 samples (48 eDNA samples plus six controls) from Cork, Ireland to the laboratory\n\u2022\tSample preparation and DNA extraction of 54 samples (48 eDNA samples plus six controls)\n\u2022\tThe per-sample analysis of:\no\t16 x niskin bottle eDNA samples plus two controls\no\t16 x metaprobe eDNA samples plus two controls\no\t16 x sediment eDNA samples plus two controls\nUsing universal primers to target a full range of marine biodiversity such as:\no\tBacteria and archaea (e.g. marker 16S rRNA)\no\tMeiofauna invertebrates (e.g. marker 18SSSU)\no\tInvertebrates (e.g. marker CO1LB)\no\tFish (e.g. marker 12STele)\no\tVertebrates (e.g. marker 16SMV3)\n\u2022\tDelivery of a final report, to include:\no\tIntroduction and aims\no\tMethods\no\tResults\no\tDiscussion\no\tRecommendations for future offshore monitoring\nThe methods section of the report should share sufficient detail for the study to be repeated. It should cover:\n\u2022\tClear field protocol detailing eDNA sampling and storage for method comparison and validation.\n\u2022\tDNA extraction methods - including the names of kits if used. State how the DNA was quantified and discuss the quality of DNA extracted.\n\u2022\tPCR amplification - specify the primers, PCR cycle conditions and reagents used.\n\u2022\tSequencing - detail how the DNA products were prepared for sequencing including reagents, primers and conditions. State how the DNA was quantified, and the model of the sequencing machine used. In addition, the methods should allow the reader to understand the confidence in the sequences obtained.\n\u2022\tBio-informatic processing: State in detail how the bio-informatic processing was completed, by specifying the steps taken. State any programs that were used.\n\u2022\tState any reference libraries used, and if a custom database was created the rules used.\n\u2022\tWhere sequences are being used for taxonomic assignment, please explain the methods used to assign a species and why any reads may have been discarded.\nThe results and discussion sections of the report should include the following:\n\u2022\tThe efficiency of DNA extraction and correct amplification of expected PCR products at each stage.\n\u2022\tA discussion of any problems and how they were resolved, such as issues with PCR leading to a change of reagents or amplification conditions.\n\u2022\tA detailed discussion explaining the results and confidence levels of the bioinformatic processing.\n\u2022\tDetailed results, including statistical analysis of data, to address Questions 1 and 2 above.\n\u2022\tTo answer Question 2b, the results should include tables on species of interest, detected using each method. The list (to be provided by JNCC) includes UK BAP Priority Species, OSPAR Threatened and/or Declining Species, Annex II species, Species listed as Features of Conservation Interest (FOCI), and invasive non-native species.\nTenderers are invited to provide a description of how these requirements will be met.\nPlease ensure you provide a quote per sample.\nPlease also include details of internal quality assurance processes to ensure quality is assured in the project outputs. For example, this could include inclusion of negative control DNA extraction samples, quantification and purity checks to assess DNA yield and quality, and review of the project report by multiple experts.\n6.\tOutputs\nAny products or outputs submitted to JNCC should adhere to JNCC\u0027s house-style and should be produced in an accessible format (see product specification for more information).\nOutput / Deliverable\tFormat\nSpreadsheet listing the species identified (Latin and common names)\nthe fragment of DNA extracted as part of the study identified as that species,\nand the reference library and sequence ID used to identify the species\tMS Excel spreadsheet (.xlsx)\n(proforma to be provided by JNCC)\nAll raw sequence data generated \tFASTQ format\nFinal report\tMS Word document (.docx) and\nAdobe PDF (.pdf)\n7.\tProduct Specification\nJNCC is committed to making its publicly available resources and documents accessible, in accordance with the Public Sector Bodies (Websites and Mobile Applications) (No. 2) Accessibility Regulations 2018.\nMaking material accessible means making sure it can be used by as many people as possible.  This includes those with:\n\uf0a7\timpaired vision\n\uf0a7\tmotor difficulties\n\uf0a7\tcognitive impairments or learning disabilities\n\uf0a7\tdeafness or impaired hearing\nThe outputs and material that JNCC publishes should be compliant with the Web Content Accessibility Guidelines version 2.1 AA standard.\nTo meet this standard, all reports and other documentation which are to be made publicly available must adhere to JNCC\u0027s house-style (to be provided) and be produced using a JNCC template (to be provided), unless otherwise stated. All reports (draft and final) should be provided electronically via email both as a Microsoft Word document and an Adobe PDF.\nCopies of documentation associated with case studies should be provided in electronic format with an associated reference catalogue.\nFor any other outputs or products which are to be made publicly available through JNCC, evidence regarding how the accessibility standard will be reached should be included.",
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