Metagenomic analysis of cellulose degrading communities

Lead Research Organisation: University of Liverpool
Department Name: Sch of Biological Sciences

Abstract

The carbon cycle in freshwater lake systems comprises two main phases: primary production (photosynthesis) and biodegradation. Sediments and the lower regions of the water column are often anoxic, particularly in summer, and here anaerobic microorganisms degrade the cellulosic phytoplankton biomass, principally to carbon dioxide and methane. In the environment, microorganisms function as communities or consortia from which the isolation and cultivation of individual species is both difficult and a poor representation of the inherent complexity, particularly for anaerobes. In landfill sites, cellulosic waste is the principal source of carbon that is ultimately converted again to carbon dioxide and methane, and in this managed environment it is the activity of anaerobic microorganisms that is entirely responsible for the stabilisation of waste. Cellulose is the principal component of biomass on earth and its degradation and recycling is an important driver of the carbon cycle. Yet the number of species known to be capable of colonising and degrading native crystalline cellulose is limited, and due at least in part to the inadequacies of conventional microbiological methods that rely on the isolation of strains and their cultivation in the laboratory. One alternative is to analyse DNA and RNA extracted directly from environmental samples, and we have applied this molecular ecological approach to the cellulose-degrading community of freshwater lakes and landfill sites. Our strategy has been to suspend cotton (cellulose) baits directly in lakes and in validated landfill leachate microcosms, to enrich and specifically target microorganisms that truly colonise and degrade cellulose in situ. We have indeed been able to publish evidence for the presence of novel species implicated in cellulose degradation in both environments, and more importantly, demonstrate that their occurrence and distribution is quantitatively significant. We now want to exploit the recent advances in high throughput affordable DNA sequencing technology (pyrosequencing) to analyse the metagenomes (total gene content) of cellulose colonised in, and subsequently retrieved from, the environment. We will primarily use RNA as our template, both for identification of the species present and to focus on genes that are actually being expressed in the biofilm and responsible for degradation of the cellulose substrate. This first description of the colonised cellulose expressed gene pool will enable us to design the tools that we will then apply to the identification of larger genetic fragments containing the combinations of ordered genes responsible for adsorption to and degradation of cellulose, and enabling the identification of any entities that are truly novel. In some cases, it may be possible to express these genes and overproduce cellulases for characterisation but in tandem we will also attempt to isolate and cultivate the species responsible for their production in the envrionment. It remains inconceivable that our knowledge of the species responsible for cellulose degradation in the natural aquatic and managed landfill environments is so superficial, but in addition to redressing this imbalance, we hope to identify new sources of cellulases with commercial potential, particularly in the field of second generation biofuel production.
 
Description We have participated in the development of new methods for directly analysing the DNA of living microorganisms that recycle organic matter in environments where there is no oxygen - lake sediments and landfill sites. We have produced evidence for the existence of novel species in these communities as well as genes encoding potentially new enzymes for biotechnological exploitation.
Exploitation Route We have used these findings in research grant applications aimed at using our metatranscriptomic approach to novel gene discovery, but as yet these have not been successful.
Sectors Agriculture, Food and Drink,Energy,Environment

 
Description Findings not used in an impact context
 
Description Anaerobic fungi
Amount £2,000 (GBP)
Organisation British Mycological Society 
Sector Learned Society
Country United Kingdom
Start 06/2011 
End 08/2011
 
Description Anaerobic fungi
Amount £2,000 (GBP)
Organisation British Mycological Society 
Sector Learned Society
Country United Kingdom
Start 06/2011 
End 08/2011
 
Description Analysis of a microbial biofilm metagenome
Amount £200 (GBP)
Organisation Society for Applied Microbiology 
Sector Learned Society
Country United Kingdom
Start 07/2011 
End 09/2013
 
Description Analysis of a microbial biofilm metagenome
Amount £200 (GBP)
Organisation Society for Applied Microbiology 
Sector Learned Society
Country United Kingdom
Start 07/2011 
End 09/2013
 
Description Cloning and over expression of a microbiaI endoglucanase identified in an environmental metagenomic library.
Amount £1,480 (GBP)
Funding ID VS12/105 
Organisation Society of General Microbiology 
Sector Charity/Non Profit
Country European Union (EU)
Start 07/2012 
End 08/2012
 
Description Cloning and over expression of a microbiaI endoglucanase identified in an environmental metagenomic library.
Amount £1,480 (GBP)
Funding ID VS12/105 
Organisation Society of General Microbiology 
Sector Charity/Non Profit
Country European Union (EU)
Start 07/2012 
End 08/2012
 
Description Metatranscriptomic analysis of microbial communities degrading cellulose in landfill
Amount £60,000 (GBP)
Organisation Research Councils UK (RCUK) 
Sector Public
Country United Kingdom
Start 10/2011 
End 03/2015
 
Description Metatranscriptomic analysis of microbial communities degrading cellulose in landfill
Amount £60,000 (GBP)
Organisation Research Councils UK (RCUK) 
Sector Public
Country United Kingdom
Start 10/2011 
End 03/2015
 
Description Microbial Assimilation of phosphorous in the subtropical Atlantic Ocean: a molecular approach
Amount £64,915 (GBP)
Funding ID NE/J013676/1 
Organisation Natural Environment Research Council 
Sector Public
Country United Kingdom
Start 01/2013 
End 09/2013
 
Description Research Grant
Amount £14,904 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 09/2011 
End 04/2013
 
Description Research Grant
Amount £14,904 (GBP)
Organisation The Royal Society 
Sector Academic/University
Country United Kingdom
Start 09/2011 
End 04/2013
 
Description Research fund grant
Amount £806 (GBP)
Organisation Systematics Association 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2011 
End 09/2011
 
Description Research fund grant
Amount £806 (GBP)
Organisation Systematics Association 
Sector Charity/Non Profit
Country United Kingdom
Start 05/2011 
End 09/2011
 
Description Microbial community RNA as a resource to facilitate the utilisation and exploitation of marine macroalgae. 
Organisation Scottish Association For Marine Science
Country United Kingdom 
Sector Charity/Non Profit 
PI Contribution Application for NERC/BBSRC co-funding
Collaborator Contribution Lead PI on metatranscriptomics grant applications
Impact none
Start Year 2012
 
Description Mining metagenomic data for new cellulases and oxidases 
Organisation Croda International
Country United Kingdom 
Sector Private 
PI Contribution Collaborative meetings to discuss funding opportunities
Start Year 2012
 
Description The impact of the alkaline disturbed zone (ADZ) on the transport of key radionuclides from a geological disposal facility (GDF) for radioactive waste (AD-TRANS). 
Organisation University of Huddersfield
Department School of Applied Sciences Huddersfield
Country United Kingdom 
Sector Academic/University 
PI Contribution NERC RATE consortium proposal based on the methodologies developed in this grant
Collaborator Contribution Provision of molecular biological expertise and facilities
Impact A manuscript submitted for publication
Start Year 2013
 
Description University of Georgia (UGA) 
Organisation University of Georgia
Department Department of Genetics
Country United States 
Sector Academic/University 
PI Contribution Preparation of U.S./U.K. postgraduate training applications in metagenomics
Collaborator Contribution Preparation of U.S./U.K. postgraduate training applications in metagenomics
Impact Unfunded applications to date
Start Year 2013
 
Description Christmas lectures for 6th formers 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Primary Audience Schools
Results and Impact Christmas lectures for 6th formers
Year(s) Of Engagement Activity 2010
 
Description DNA extraction 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Primary Audience Public/other audiences
Results and Impact EcoScience Day at the Bangor Science Festival

Oganisation and delivery of sessions on DNA extraction at Ecoscience Day as part of the Bangor Science Festival on three successive years
Year(s) Of Engagement Activity 2010
 
Description Energ lecture 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Primary Audience
Results and Impact Lecture on Renewable Energy at West Kirby Grammar School

Lecture to sixth formers on renewable energy
Year(s) Of Engagement Activity 2012
 
Description National Science Week 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Primary Audience Schools
Results and Impact Annual visit to Balshaws School

National Science Week activity outreach
Year(s) Of Engagement Activity 2008
 
Description Oral Presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Primary Audience Participants in your research or patient groups
Results and Impact Northwest Microbiology Group Annual Meeting

Talk at the Annual Meeting of the Northwest Microbiology Group at the University of Liverpool
Year(s) Of Engagement Activity 2012
 
Description Oral presentation 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research or patient groups
Results and Impact Research talk

Talk at the Annual Meeting of the Molecular Microbial Ecology Group at the University of East Anglia
Year(s) Of Engagement Activity 2012
 
Description Public lecture 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? Yes
Primary Audience Public/other audiences
Results and Impact Lecture for families at the Bangor Science Festival

Marvellous Microbes. Public lecture at the Bangor Science Festival Hidden Worlds Exhibition
Year(s) Of Engagement Activity 2013
 
Description Radio interview 
Form Of Engagement Activity A press release, press conference or response to a media enquiry/interview
Part Of Official Scheme? Yes
Primary Audience Public/other audiences
Results and Impact BBC Radio Wales preview of the Hidden Worlds Exhibition

Interview to preview the Hidden Worlds Exhibition at the Bangor Science Festival
Year(s) Of Engagement Activity 2013