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NERC Environmental Omics Facility (NEOF)

Lead Research Organisation: University of Liverpool
Department Name: Institute of Integrative Biology

Abstract

New 'omic' technologies have transformed biology by allowing scientists to read genomes (genomics) and to measure the amount of proteins (proteomics) or other chemicals (metabolomics) within living cells and organisms. Tiny amounts of DNA can be collected from the environment (environmental DNA, eDNA) to measure biodiversity and monitor the health of our soils, rivers and seas. This creates a tremendous opportunity to understand the diversity of different individuals and species within the natural environment, their evolution, and the diversity of different characters and forms that allow them to live within their environment. Understanding biodiversity is more pressing than ever, given the rate at which it is being lost from the planet and the central role that it plays in allowing species and ecosystems to respond to, and survive, climate change.

Scientists wanting to use omic technologies in their research face significant hurdles: the equipment required costs millions of pounds and few labs can afford it; the expertise to apply these techniques is rare, particularly to species from the natural environment; and there is a lack of the specialist skills present within the environmental science community to design studies using omic technology and to then analyse the resulting data. To overcome these hurdles and equip scientists with the tools and skills they need to address their research questions using omics, we will provide the NERC Environmental Omics Facility (NEOF). NEOF will be a unique capability within the UK that has the expertise and equipment to train scientists in omic methods, help them to understand the potential of the technology and design studies to use it, provide the means to test adventurous ideas, and to support larger-scale NERC research projects. NEOF will be run by a team of scientists who are world-leading experts and are able to cover a broad range of omics methods, with experience of applying these to questions in environmental sciences. We will use this expertise to train early-stage scientists and to upskill scientists at any stage of their career. We will empower the community of NERC scientists to engage with new technologies and approaches and to then use them to address questions using omics that were previously impossible to answer in environmental science. We also have extensive equipment and space that we will use to support omic analysis for NERC scientists.

NEOF will be excellent value for NERC. We are able to provide £20m of existing equipment and >£2m of previous refurbishment so that NERC does not need to buy this for us. Our Universities will provide further refurbishment, space and support towards this proposal. Our team has >10 years' experience of delivering a highly effective facility to NERC, with a host of processes in place to ensure that projects are managed quickly and to budget. Because of this, we will be able to hit the ground running and provide this facility immediately to NERC scientists.

Publications

10 25 50
 
Description Our users have used capability at NEOF to deliver a mixture of fundamental and applied research. We have supported researchers from Phd students to established professors. We introduced a pilot for early career researchers to access the facility, which has helped their ability to apply for fellowships or first permanent position. Our facility has helped to deliver highest quality publications and increased NERC international visibility through our users ability to access collaborators and field-sites across the world. We have supported >100 projects across the range of NERC's remt related to biology.

We have provided training as project-based and workshop based training for ~1000 students, helping to empower the next generation of environmental scientists with omics skills in demand in academia, industry and government.

We have reduced the carbon footprint of the facility and achieved Laboratory Environment Assessment Framework (LEAF) silver award, by reducing plastic waste and shipping costs.

During the COVID pandemic, unique capability at NEOF in environmental omics was able to develop a novel method to sequence SARS-CoV-2 genomes from wastewater, thereby enabling wastewater based epidemiology of new variants. Initial work, which detected the rise of the Alpha lineage in London sewage samples, was reported to the Chief Medical Officer, and consequently formed part of public health decision-making in the run up to Christmas 2020. DHSC then invested £7.9m into a consortium of labs, led by NEOF director Paterson, which provided real-time insight into SARS-CoV-2 variants for central government and local health teams, and subsequently detected the rise of Delta and Omicron variants.
Exploitation Route We enhance the skills base of the UK, particularly through training of post-graduate researchers.
New methods, such as environmental DNA, provide new tools to monitor biodiversity and pathogen threats.
Sectors Environment

URL https://neof.org.uk/case-studies/
 
Description Work has been used to monitor SARS-CoV2 variants in wastewater in support of the pandemic resonse.
First Year Of Impact 2020
Sector Healthcare
 
Description Evaluation the Public Health Risks of Urban Flooding Events
Amount £0 (GBP)
Funding ID 2544261 
Organisation Engineering and Physical Sciences Research Council (EPSRC) 
Sector Public
Country United Kingdom
Start 09/2020 
End 04/2024
 
Description Genomics of Host-Parasite Coevolution: A Test of Arms Race and Red Queen Dynamics in a Wild Insect System
Amount £153,085 (GBP)
Funding ID NE/W001519/1 
Organisation United Kingdom Research and Innovation 
Sector Public
Country United Kingdom
Start 01/2022 
End 01/2025
 
Description Genomics of Host-Parasite Coevolution: A Test of Arms Race and Red Queen Dynamics in a Wild Insect System
Amount £395,422 (GBP)
Funding ID NE/W001616/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 07/2022 
End 01/2025
 
Description Identifying the genetic targets of sexual selection
Amount £497,744 (GBP)
Funding ID NE/V001566/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 11/2020 
End 10/2024
 
Description NERC Environmental Omics Facility
Amount £15,820,000 (GBP)
Funding ID NE/Y005430/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 03/2024 
End 03/2031
 
Description NSFDEB-NERC The blueprint for marine biomineralization in a changing climate
Amount £566,464 (GBP)
Funding ID NE/W005115/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 07/2022 
End 01/2026
 
Description Sex-specific fitness landscapes in the evolution of egg-laying vs live-birth
Amount £803,730 (GBP)
Funding ID NE/Y001672/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 04/2024 
End 04/2028
 
Description Uncharacterised microbial pathways are key to understanding large fluxes of biogenic reactive nitrogen gases from agronomic soils
Amount £558,663 (GBP)
Funding ID BB/X002187/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2023 
End 04/2026
 
Description Understanding the eco-evolutionary drivers of emerging antifungal resistance
Amount £1,074,166 (GBP)
Funding ID NE/X00547X/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 12/2022 
End 11/2026
 
Title Costs of reproduction and their effect on age-related gene expression in Bombus terrestris queens 
Description We used mRNA-seq to identify the RNA profiles in three tissue types (brain, fat body and ovary) in two time points (after 10% cohort death (TP1) and 60% cohort death (TP2)) for two treatments (egg removal (R) and egg removal and replacement (C)), with up to six biological replicates per tissue/time point/treatment combination. Each sample was sequenced on two lanes (L1 and L2) of the sequencing machine in order to generate sufficient numbers of reads while controlling for between lane variability. Illumina TruSeq stranded mRNA-seq libraries were constructed (from submitted RNA) and sequenced by Edinburgh Genomics (Edinburgh, UK) using 100 base pair paired-end reads. Quality of raw reads was assessed using FastQC v0.11.9 and aligning/pseudoaligning the reads to the Bombus terrestris genome/transcriptome (Bombus_terrestris.Bter_1.0.dna.toplevel.fa/ Bombus_terrestris.Bter_1.0.cdna.all.fa) using HISAT2 v2.1.0 and Kallisto v0.46.1, respectively. Bombus GEO dataset; accession number GSE172422 NBAF1153 outputs (from NERC project NE/R000875/1) 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? No  
Impact None to date. 
 
Title The effect of larval diet on the fecundity-longevity relationship and age-related gene expression in Drosophila melanogaster 
Description We used mRNA-seq to identify the RNA profiles in three tissue types (fat body, head and ovary) in two time points (after 10% cohort death (RNA-1) and 60% cohort death (RNA-2)) for two treatments (medium-quality larval diet (M) and high-quality larval diet (H)), with three biological replicates per tissue/time point/treatment combination. Illumina TruSeq stranded mRNA-seq libraries were constructed (from submitted RNA) and sequenced by Edinburgh Genomics (Edinburgh, UK) using 100 base pair paired-end reads. Quality of raw reads was assessed using FastQC v0.11.9 and aligning/pseudoaligning the reads to the Drosophila melanogaster genome/transcriptome (Drosophila_melanogaster.BDGP6.22.dna.toplevel.fa / Drosophila_melanogaster.BDGP6.22.cdna.all.fa) using HISAT2 v2.1.0 and Kallisto v0.46.1, respectively. Drosophila GEO dataset: accession number GSE175623 NBAF1153 outputs (from NERC project NE/R000875/1) 
Type Of Material Database/Collection of data 
Year Produced 2021 
Provided To Others? No  
Impact None to date. 
 
Description Natural England eDNA workshop 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact ~20 Scientists and policymakers from Natural England attended a training workshop on use of environmental DNA in biodiversity monitoring.
Year(s) Of Engagement Activity 2022