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
Laine VN
(2023)
Whole-genome Analysis Reveals Contrasting Relationships Among Nuclear and Mitochondrial Genomes Between Three Sympatric Bat Species.
in Genome biology and evolution
Taylor CH
(2023)
Living with chronic infection: Persistent immunomodulation during avirulent haemoparasitic infection in a wild rodent.
in Molecular ecology
DAY George
(2023)
The population genetics and breeding biology of the European nightjar
Dawson Pell F
(2023)
Dispersal behaviour and settlement in an invasive bird: dispersers prefer their natal habitat
in Animal Behaviour
Bates S
(2023)
Meiotic drive does not impede success in sperm competition in the stalk-eyed fly, Teleopsis dalmanni
in Evolution
Wainwright J
(2023)
Multiple axes of visual system diversity in Ithomiini, an ecologically diverse tribe of mimetic butterflies
in Journal of Experimental Biology
Cicconardi F
(2023)
Evolutionary dynamics of genome size and content during the adaptive radiation of Heliconiini butterflies
in Nature Communications
Recknagel H
(2023)
Common lizard microhabitat selection varies by sex, parity mode, and colouration.
in BMC ecology and evolution
Barão-Nóbrega J
(2023)
Characterising a genetic stronghold amidst pervasive admixture: Morelet's crocodiles (Crocodylus moreletii) in central Yucatan
in Conservation Genetics
Lawson Michael
(2023)
An integrative approach to studying speciation in a recent adaptive radiation
Ransome E
(2023)
Evaluating the transmission risk of SARS-CoV-2 from sewage pollution.
in The Science of the total environment
Lam D
(2023)
Both selection and drift drive the spatial pattern of adaptive genetic variation in a wild mammal
in Evolution
Couto A
(2023)
Rapid expansion and visual specialisation of learning and memory centres in the brains of Heliconiini butterflies.
in Nature communications
Tan CCS
(2023)
Genomic screening of 16 UK native bat species through conservationist networks uncovers coronaviruses with zoonotic potential.
in Nature communications
Browett SS
(2023)
Resource competition drives an invasion-replacement event among shrew species on an island.
in The Journal of animal ecology
Dunn JC
(2023)
Evidence for strain-specific virulence of Trichomonas gallinae in African columbiformes.
in Parasitology
Young R
(2023)
Investigating the association between diet and infection with Trichomonas gallinae in the European turtle dove ( Streptopelia turtur )
in Environmental DNA
Ellis EE
(2023)
Negative effects of urbanisation on diurnal and nocturnal pollen-transport networks.
in Ecology letters
Nadal-Jimenez P
(2023)
Isolation, culture and characterization of Arsenophonus symbionts from two insect species reveal loss of infectious transmission and extended host range.
in Frontiers in microbiology
Wanelik KM
(2023)
Maternal transmission gives way to social transmission during gut microbiota assembly in wild mice.
in Animal microbiome
Morland F
(2023)
Early-life telomere length predicts life-history strategy and reproductive senescence in a threatened wild songbird.
in Molecular ecology
Field J
(2023)
Brood Parasites That Care: Alternative Nesting Tactics in a Subsocial Wasp.
in The American naturalist
Collins DH
(2023)
Costs of reproduction are present but latent in eusocial bumblebee queens.
in BMC biology
Hanski E
(2023)
Gut microbiota of the critically endangered Saiga antelope across two wild populations in a year without mass mortality.
in Scientific reports
Fisher AM
(2023)
The ecology of viruses in urban rodents with a focus on SARS-CoV-2.
in Emerging microbes & infections
San-Jose LM
(2023)
Investigating the genetic basis of vertebrate dispersal combining RNA-seq, RAD-seq and quantitative genetics.
in Molecular ecology
De Jong M
(2023)
Rapid evolution of novel biotic interactions in the UK Brown Argus butterfly uses genomic variation from across its geographical range.
in Molecular ecology
Dittrich C
(2024)
Genome Assembly of the Dyeing Poison Frog Provides Insights into the Dynamics of Transposable Element and Genome-Size Evolution
in Genome Biology and Evolution
Allingham S
(2024)
Effects of burning on vegetation, soil physicochemistry and prokaryotic microbial communities in surface and subsurface peat
in Science of The Total Environment
Worsley S
(2024)
Longitudinal gut microbiome dynamics in relation to age and senescence in a wild animal population
in Molecular Ecology
Dawson Pell F
(2024)
Social associations are predicted by nest proximity but not kinship in a free-living social parrot
in Biological Journal of the Linnean Society
Scutt S
(2024)
Evaluating the Public Health Risks of Urban Flooding Events
Mable B
(2024)
History of molecular biology work in the Graham Kerr Building (1996-2024)
in The Glasgow Naturalist
Whiting-Fawcett F
(2024)
Across the Atlantic: Searching for the origins of disease tolerance in three Myotis bats
| 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 |