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.
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.
Organisations
Publications
Calero Preciado C
(2021)
Implications of Climate Change: How Does Increased Water Temperature Influence Biofilm and Water Quality of Chlorinated Drinking Water Distribution Systems?
in Frontiers in microbiology
Sparks A
(2022)
Sex-dependent effects of parental age on offspring fitness in a cooperatively breeding bird
in Evolution Letters
Harvey HJ
(2022)
Application of microfluidic systems in modelling impacts of environmental structure on stress-sensing by individual microbial cells.
in Computational and structural biotechnology journal
Brunner FS
(2022)
City-wide wastewater genomic surveillance through the successive emergence of SARS-CoV-2 Alpha and Delta variants.
in Water research
Precioso M
(2022)
Effects of long-term ethanol storage of blood samples on the estimation of telomere length
in Evolutionary Ecology
Lemos Barão-Nóbrega JA
(2022)
N-mixture models provide informative crocodile (Crocodylus moreletii) abundance estimates in dynamic environments.
in PeerJ
Veltsos P
(2022)
Experimental sexual selection reveals rapid evolutionary divergence in sex-specific transcriptomes and their interactions following mating.
in Molecular ecology
Sparks AM
(2022)
Telomere heritability and parental age at conception effects in a wild avian population.
in Molecular ecology
Davies CS
(2022)
Immunogenetic variation shapes the gut microbiome in a natural vertebrate population.
in Microbiome
Thomas R
(2022)
Successful storage of Trichomonas gallinae on Whatman FTA cards following culture
in Conservation Genetics Resources
Dimitriu T
(2022)
Bacteriostatic antibiotics promote CRISPR-Cas adaptive immunity by enabling increased spacer acquisition
in Cell Host & Microbe
Roper M
(2022)
Individual variation explains ageing patterns in a cooperatively breeding bird, the long-tailed tit Aegithalos caudatus.
in The Journal of animal ecology
Choo SW
(2022)
A collective statement in support of saving pangolins.
in The Science of the total environment
Marsh KJ
(2022)
Synchronous Seasonality in the Gut Microbiota of Wild Mouse Populations.
in Frontiers in microbiology
Lima C
(2022)
Simultaneous Raman and Infrared Spectroscopy of Stable Isotope Labelled Escherichia coli.
in Sensors (Basel, Switzerland)
Gómez P
(2022)
Rapid decline of adaptation of Pseudomonas fluorescens to soil biotic environment.
in Biology letters
Hanski
(2022)
Host-microbiota interactions in mammals
Pepper Jake
(2022)
Evolutionary genomics of the zebra finch Z chromosome inversion polymorphism
Lima C
(2022)
Simultaneous Raman and infrared spectroscopy: a novel combination for studying bacterial infections at the single cell level.
in Chemical science
Giraldo-Deck LM
(2022)
Intralocus conflicts associated with a supergene.
in Nature communications
Van Lieshout SHJ
(2022)
Early-life seasonal, weather and social effects on telomere length in a wild mammal.
in Molecular ecology
Tew Nick E.
(2022)
Floral resources and insect pollinator populations in urban landscapes
Hillary LS
(2022)
RNA-viromics reveals diverse communities of soil RNA viruses with the potential to affect grassland ecosystems across multiple trophic levels.
in ISME communications
Tercel MPTG
(2022)
DNA metabarcoding reveals introduced species predominate in the diet of a threatened endemic omnivore, Telfair's skink (Leiolopisma telfairii).
in Ecology and evolution
Fish KE
(2022)
Author Correction: Uncharted waters: the unintended impacts of residual chlorine on water quality and biofilms.
in NPJ biofilms and microbiomes
Price T
(2022)
Sisters doing it for themselves: extensive reproductive plasticity in workers of a primitively eusocial bee
in Behavioral Ecology and Sociobiology
Brown TJ
(2022)
Causes and consequences of telomere lengthening in a wild vertebrate population.
in Molecular ecology
Price PD
(2022)
Detecting signatures of selection on gene expression.
in Nature ecology & evolution
Mayberry Jillian
(2022)
Biodiversity: Testing new approaches to study and monitor arthropod diversity
Jones S
(2022)
Testing bats in rehabilitation for SARS-CoV-2 before release into the wild.
in Conservation science and practice
Calero Preciado C
(2022)
Climate change and management of biofilms within drinking water distribution systems
in Frontiers in Environmental Science
Dulias K
(2022)
Ancient DNA at the edge of the world: Continental immigration and the persistence of Neolithic male lineages in Bronze Age Orkney.
in Proceedings of the National Academy of Sciences of the United States of America
Halliwell C
(2022)
Coordination of care by breeders and helpers in the cooperatively breeding long-tailed tit
in Behavioral Ecology
Sturrock N
(2022)
Who to help? Helping decisions in a cooperatively breeding bird with redirected care
in Behavioral Ecology and Sociobiology
Braga LPP
(2022)
Viruses direct carbon cycling in lake sediments under global change.
in Proceedings of the National Academy of Sciences of the United States of America
Busana M
(2022)
Structural equation modeling reveals determinants of fitness in a cooperatively breeding bird.
in Behavioral ecology : official journal of the International Society for Behavioral Ecology
Worsley SF
(2022)
Assessing the causes and consequences of gut mycobiome variation in a wild population of the Seychelles warbler.
in Microbiome
Jackson HA
(2022)
Genomic erosion in a demographically recovered bird species during conservation rescue.
in Conservation biology : the journal of the Society for Conservation Biology
Montejo-Kovacevich G
(2022)
Repeated genetic adaptation to altitude in two tropical butterflies.
in Nature communications
Figueras Jimenez Javier
(2022)
Investigating the regulation and evolution of tartan during Drosophila male genital diversification
Busana M
(2022)
Population level consequences of facultatively cooperative behaviour in a stochastic environment.
in The Journal of animal ecology
Monaghan Josie
(2022)
Hybridisation and genetic structure of woodland specialist ants in fragmented habitat
Aase-Remedios ME
(2023)
Evolution of the Spider Homeobox Gene Repertoire by Tandem and Whole Genome Duplication.
in Molecular biology and evolution
| 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 |