Kenyak yeye: UK-Australian Global Soil Meta-omic Programme
Lead Research Organisation:
Rothamsted Research
Department Name: Sustainable Agriculture Sciences-H
Abstract
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Organisations
People |
ORCID iD |
| John Crawford (Principal Investigator) | |
| Andrew Neal (Co-Investigator) |
| Description | Through analysis of the global soil metagenome (the sum of all DNA extracted from a soil in a given location, collected from a diverse range of locations around the world), we have discovered patterns that are consistent with the hypothesis that a core set of functions exists everywhere in soil, but that specialist functions are transferred between species through a process of horizontal gene transfer. This hints at the critical importance of mobile genetic elements in conferring functional resilience to soil, and agues against descriptions of soil biological diversity purely in terms of species or taxonomic groups (since functional genes are shared across these domains). This work has been extended in collaboration with colleagues in Madrid to explore a universal theoretical framework for linking community structure to dynamics and function. A national conference was established to study how human, animal and soil microbiomes might be understood collectively and how we could extract added value from collaboration. Our conclusion is tat we need an integrative theory that would provide the scaffolding, in terms of precise and quantitative hypotheses, that could be tested. |
| Exploitation Route | We have initiated a collaboration with IBM to use the unique complexities and purpose of the data set to develop new analytic tools that will be relevant to any study of metagenome-scale data where complexity is to be related to functional consequence (e.g. the gut and rumen microbiomes). A new collaboration with gut and wastewater microbiome scientists at Glasgow University has been established to take the integrative science forward |
| Sectors | Agriculture Food and Drink Digital/Communication/Information Technologies (including Software) Environment Healthcare |
| Description | The findings from this work are now being developed as part of a new collaboration between IBM Research (UK) to develop new visualisation and analytic tools that will feed in to the computational biology pipeline that IBM are developing as part of their product portfolio. This will have impacts beyond the current project including potential societal impacts should the tools be deployed in wider environmental and biomedical applications. This work has led to a new collaboration in 2019 with mathematicians at the Technical University in Madrid to develop a generic theoretical model for the microbiome. A joint publication has been submitted. The work has led to a new collaboration with microbiome scientists in engineering and medicine at the University of Glasgow. A joint proposal is being drafted. |
| First Year Of Impact | 2019 |
| Sector | Agriculture, Food and Drink,Digital/Communication/Information Technologies (including Software),Environment,Healthcare,Pharmaceuticals and Medical Biotechnology |
| Impact Types | Societal Economic |
| Description | Soil Health discussion with DEFRA |
| Geographic Reach | National |
| Policy Influence Type | Participation in a guidance/advisory committee |
| Title | BASE metagenomes |
| Description | We have incorporated soil microbiomes generated from sites across Australia into Rothamsted's collection of global soil metagneomes |
| Type Of Material | Database/Collection of data |
| Year Produced | 2017 |
| Provided To Others? | Yes |
| Impact | the database is allowing partners to study soil microbiome diversity at a global scale and comparing the effects of agricultural management upon contrasting soil from the UK and Australia |
| Description | BASE partnership |
| Organisation | Bioplatforms Australia |
| Country | Australia |
| PI Contribution | We have coordinated monthly video-conferences between academic partners. Two Rothamsted team members visited partners in Melbourne to discuss project and presented soil metagenomics work at the Annual Meeting of the Australian Society for Microbiology in Hobart, Tasmania. We also provided training to PhD students at LaTrobe University |
| Collaborator Contribution | Partners have provided intellectual input and expertise in soil microbiology and provided access to soil metagenome sequences collected across Australia. Partners are providing on-going input to the development of manuscript and the design of future work |
| Impact | None to date. The collaboration is multi-disciplinary, incorporating microbiology, soil science and bioinformatics |
| Start Year | 2017 |
| Description | BASE partnership |
| Organisation | Commonwealth Scientific and Industrial Research Organisation |
| Department | Agriculture and Food |
| Country | Australia |
| Sector | Public |
| PI Contribution | We have coordinated monthly video-conferences between academic partners. Two Rothamsted team members visited partners in Melbourne to discuss project and presented soil metagenomics work at the Annual Meeting of the Australian Society for Microbiology in Hobart, Tasmania. We also provided training to PhD students at LaTrobe University |
| Collaborator Contribution | Partners have provided intellectual input and expertise in soil microbiology and provided access to soil metagenome sequences collected across Australia. Partners are providing on-going input to the development of manuscript and the design of future work |
| Impact | None to date. The collaboration is multi-disciplinary, incorporating microbiology, soil science and bioinformatics |
| Start Year | 2017 |
| Description | BASE partnership |
| Organisation | Commonwealth Scientific and Industrial Research Organisation |
| Department | CSIRO Hobart |
| Country | Australia |
| Sector | Public |
| PI Contribution | We have coordinated monthly video-conferences between academic partners. Two Rothamsted team members visited partners in Melbourne to discuss project and presented soil metagenomics work at the Annual Meeting of the Australian Society for Microbiology in Hobart, Tasmania. We also provided training to PhD students at LaTrobe University |
| Collaborator Contribution | Partners have provided intellectual input and expertise in soil microbiology and provided access to soil metagenome sequences collected across Australia. Partners are providing on-going input to the development of manuscript and the design of future work |
| Impact | None to date. The collaboration is multi-disciplinary, incorporating microbiology, soil science and bioinformatics |
| Start Year | 2017 |
| Description | BASE partnership |
| Organisation | Commonwealth Scientific and Industrial Research Organisation |
| Country | Australia |
| Sector | Public |
| PI Contribution | We have coordinated monthly video-conferences between academic partners. Two Rothamsted team members visited partners in Melbourne to discuss project and presented soil metagenomics work at the Annual Meeting of the Australian Society for Microbiology in Hobart, Tasmania. We also provided training to PhD students at LaTrobe University |
| Collaborator Contribution | Partners have provided intellectual input and expertise in soil microbiology and provided access to soil metagenome sequences collected across Australia. Partners are providing on-going input to the development of manuscript and the design of future work |
| Impact | None to date. The collaboration is multi-disciplinary, incorporating microbiology, soil science and bioinformatics |
| Start Year | 2017 |
| Description | BASE partnership |
| Organisation | State Government of Victoria |
| Country | Australia |
| Sector | Public |
| PI Contribution | We have coordinated monthly video-conferences between academic partners. Two Rothamsted team members visited partners in Melbourne to discuss project and presented soil metagenomics work at the Annual Meeting of the Australian Society for Microbiology in Hobart, Tasmania. We also provided training to PhD students at LaTrobe University |
| Collaborator Contribution | Partners have provided intellectual input and expertise in soil microbiology and provided access to soil metagenome sequences collected across Australia. Partners are providing on-going input to the development of manuscript and the design of future work |
| Impact | None to date. The collaboration is multi-disciplinary, incorporating microbiology, soil science and bioinformatics |
| Start Year | 2017 |
| Description | Informatics and network analysis of deep metagenomic sequences from the global soil metagenome project |
| Organisation | IBM |
| Department | IBM UK Labs Ltd |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Based on the preliminary analysis of the global soil metagenomes that are the subject of this collaboration, we recognised patterns that would benefit from deeper analyses. We approached IBM Research (UK) to discuss collaboration with the Computational Life Science programme and established a joint programme with the team led by Dr Ritesh Krishna. We provided the scientific questions, the biological knowledge and all of the data. |
| Collaborator Contribution | IBM have brought new analysis tools and high performance computer hardware to the project which means we can undertake analysis of the metagenomes in minutes compared with days and weeks on the Rothamsted cluster. They are also working with us on the development of new algorithms and on the interpretation of the results |
| Impact | This collaboration is highly multidisciplinary and brings together computer science, bioinformatics, mathematics, microbiology and genetics. the results include new tools for identifying differences in metagenomic sequences between treatments. The innovation is that the analysis is multi-scale and focused on functions that relate to critical soil properties including water storage, greenhouse gas emission and nutrient efficiency |
| Start Year | 2018 |