Development of metaproteomics for in situ investigation of microbial activity both in vivo and in soil and faeces

Lead Research Organisation: University of Warwick
Department Name: Biological Sciences

Abstract

Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
 
Description New developments in analysis of gene clusters online; novel method of extracting proteins from communities in faeces and soil.
Soil microorganisms play a crucial role in the degradation of recalcitrant polymers in the soil. Colonisation and subsequent degradation is achieved by a diversity of secreted proteins for adhesion to substrates and subsequent enzymatic degradation which liberates products suitable for uptake. These proteins play a key role in nutrient cycling and the presence of some of them has long been used as an indicator of biological activity state and soil health. With the progress in environmental metagenomics and diversity analysis of key soil enzymes a unique opportunity exists to unite traditional soil analysis of total soil enzyme activities with molecular approaches to establish which proteins are secreted and begin to identify their origins. This combination has the potential to impact on all aspects of soil microbiology and in addition provide an improved understanding of the microbial populations contributing to the 'soil enzyme pool'. Enzymes have been extracted from soil for many decades to define soil biological activity but such assays can not differentiate fungal or bacterial origin nor determine diversity of functional groups. We aimed to examine, compare and discuss methodological approaches for extracting environmental protein from soil targeting the secretome. We considered the methods developed in different labs, appraised the analytics aspects and challenges and the prospects for future developments. Examples were given of applications to key studies of soil microbiology and other environments and a special roundtable was organized over consecutive meetings of the International Symposium of Microbial Ecology in Seattle in 2010. This was a culmination of the extensive meetings with key US experts: a workshop was for all microbial community scientists at Warwick University interested to study metaproteomics of natural habitats. This workshop will be led by Dr. Nathan C. VerBerkmoes (Organic and Biological Mass Spectrometry Group, Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA). This visit was funded by a University North American Travel Fund and BBSRC Metagenomics Network ComMet awards to Prof. Liz Wellington.


Relevance:
This roundtable session has relevance for a wide range of ISME sessions including climate change, ecology of cold habitats, and ecology of recalcitrant compounds, forest soil ecology and metagenomics. It fits well with the range of terrestrial ecological processes being discussed at ISME as part of understanding impacts of key processes such as climate change and pollution on soil and nutrient cycling. It will allow expertise in areas such as metaproteomics in the gut and key extreme environments to be discussed in the context of the problems of extraction from soil. All speakers have direct expertise in the extraction of proteins from soil.
Exploitation Route Professor Wellington has established an international reputation for the study of microbiomes in the environment and her work on soil, plant and riverine microbiomes is well known but in addition she has been recognized for her efforts to promote this area of research by disseminating methods to establish environmental microbiome research in particular running partnering award on community metagenomics sponsored by BBSRC and community metaproteomics partnering award with USA which was used to invite key experts from USA to attend workshops organized at Warwick University and open to the academic community. Further to these efforts she is Editor in Chief of the prestigious journal Microbiome impact factor 10 and setting up two sister journals Environmental Microbiome and Animal Microbiome. These journals are attracting research from the International community of scientists who has been inspired by our efforts.
Sectors Agriculture, Food and Drink,Environment,Healthcare

URL http://metagenomics.uk
 
Description New method published in ISMEJ 2014 and now available for use. Citations for our methods paper are evidence that the metaexoproteomics technique is being used and we used the support and interest of the scientific community to further develop networks for knowledge dissemination and started a new network ComMet in 2014 and website to host environmental omic advances and hold more indepth workshops. The website www.metagenomics.uk was set up and was continued via funds gained from a network grant "The exploitation of metagenomics and meta-omics approaches in life science research. Community network in metagenomics, ComMet. BBSRC BB/L027801/1 2014-2017 £100,000", We have now continued this work with recent success in another series of workshops specifically focused on the constraints and bottlenecks fro the community in exploiting metaproteomics. This resulted in partnering grant with Sheffield University and Dr Jags Pandal the funding "New approaches to resolving community metaproteomes: ComProt. PI co-I Chris Quince, WMS and Jags Pandal University of Sheffield. NERC NE/S013539/1 2018-2019 £50,000" will support two workshops which we will join forces with Jags and showcase new methods in analysis of metaproteomes and also discuss approaches to extraction.
First Year Of Impact 2014
Sector Agriculture, Food and Drink,Environment
Impact Types Economic

 
Description BBSRC Networks
Amount £100,000 (GBP)
Funding ID BB/L010852/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 02/2014 
End 01/2017
 
Description BBSRC SARISA
Amount £860,445 (GBP)
Funding ID BB/L026074/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Department Soil and rhizosphere interactions for sustainable agri-ecosystems
Sector Academic/University
Country United Kingdom
Start 01/2015 
End 12/2019
 
Description Defra bovine TB research programme
Amount £380,000 (GBP)
Funding ID SE3280 
Organisation Animal Health And Veterinary Laboratories Agency (AHVLA) 
Sector Public
Country United Kingdom
Start 04/2012 
End 01/2014
 
Description KTP No 3356
Amount £250,000 (GBP)
Funding ID KTP No 3356 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2013 
End 06/2016
 
Title Metaexoproteomics 
Description New way to extract proteins from soil involving a series of extractions steps 
Type Of Material Technology assay or reagent 
Year Produced 2014 
Provided To Others? Yes  
Impact Acquired new funding from BBSRC 
 
Title Novel enzymes 
Description Novel enzyme assay and enzyme activity relating to phosphate solubilisation 
Type Of Material Physiological assessment or outcome measure 
Year Produced 2017 
Provided To Others? No  
Impact Important for commercial exploitation of bacteria in the rhizosphere of plant for improved supply of inorganic phosphate 
 
Title Novel use of minION for diagnostics 
Description Novel approach to diagnostics for typing pathogens in faecal samples directly 
Type Of Material Technology assay or reagent 
Year Produced 2017 
Provided To Others? No  
Impact New approach for direct typing of a pathovar or spoligotype directly from cells in a faecal or other samples for example soil, blood, tissue. This will allow rapid identification of pathogens in the environment and help track dissemination pathways. 
 
Description Environmental reservoirs of microbial pathogens 
Organisation National University of Sciences and Technology
Department Institute of Environmental Sciences and Engineering (IESE)
Country Pakistan 
Sector Academic/University 
PI Contribution Working on developing bids for GCRF and other funding agencies to halt the spread of microbial pathogens and AMR in the environment
Collaborator Contribution Hosted a workshop and paid our team's expenses to visit and work in a collaborative pilot study in addition to talks and visits to field sites
Impact The collaboration resulted in the analysis of field sites to consider the environmental reservoirs of microbial pathogens and understanding transmission pathways through water and food chain routes.
Start Year 2019
 
Description Environmental reservoirs of microbial pathogens 
Organisation University College of Islamabad
Country Pakistan 
Sector Academic/University 
PI Contribution Working on developing bids for GCRF and other funding agencies to halt the spread of microbial pathogens and AMR in the environment
Collaborator Contribution Hosted a workshop and paid our team's expenses to visit and work in a collaborative pilot study in addition to talks and visits to field sites
Impact The collaboration resulted in the analysis of field sites to consider the environmental reservoirs of microbial pathogens and understanding transmission pathways through water and food chain routes.
Start Year 2019
 
Description Public Science Evening 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Presentation given at an evening event on the Microbiome event to inform the public about the importance of bacteria in the human gut, in the soil and in the bioremediation of polluted environments.
Year(s) Of Engagement Activity 2017
 
Description Used method for part of a workshop on metagenomics network sponsored by BBSRC 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Postgraduate students
Results and Impact Training in methods needed for metagenomics and this included how analysis of habitat or sample total DNA, RNA and protein can be analysed for community functional studies. The primary focus was on bacteria and fungi but as proteins were analysed data was presented on total sample components including proteins from plants and animals. Purpose was to inform participants of the benefits of protein analysis and pitfalls when trying to identify proteins. Many attendees were motivated to try these new approaches.
Year(s) Of Engagement Activity 2009,2015,2016
URL http://www.metagenomics.uk