Linking function to process: developing methods to explore the link between microbial function and biogeochemical cycling in soils

Lead Research Organisation: Rothamsted Research
Department Name: Unlisted

Abstract

Many important biogeochemical cycling processes in soils are mediated by soil microorganisms, but only recently have techniques become available to identify some of the key organisms in the soil microbial community. In particular, molecular methods are now sufficiently developed to enable their use in the DNA- and organic chemical-rich environment of soils. We will test existing, and develop new, molecular and other methods to identify key soil microorganisms and their function and link these to the biogeochemical cycling processes that they mediate. We will begin with nitrogen cycling because (1) nitrogen is the main yield-determining nutrient in crop-based systems and the loss of nitrogen from cropping systems represents an economic loss to the farmer and pollutes air and water; (2) we have made excellent process in developing molecular techniques to study nitrifying organisms and want to extend this to denitrifying organisms.

The main objectives of this project are:
1) To validate DNA/RNA based methods for profiling microorganisms involved in key biogeochemical cycling processes, beginning with microbial species involved in nitrogen cycling processes, specifically denitrification.
2) To investigate the relationship between process and function, beginning with the link between N2O fluxes and functional gene expression.

Publications


10 25 50
 
Description The key finding from this project was a better understanding of the microbial basis of nitrogen cycling in soils, especially the process of denitrification. The project developed methods to extract the DNA of the soil organisms that mediate (i.e. cause) the various stages of the process of denitrification: nitrate to nitrite to nitric oxide, nitrous oxide and finally dinitrogen gas (N2). Using these methods we have been able to study the factors that control the process and, especially, those that determine how much of the greenhouse gas nitrous oxide is produced. We can then suggest management options for reducing nitrous oxide emissions.



We also explored novel mathematical methods of studying the variation of nitrous oxide emissions across the landscape at scales of 1 m to 7 km. This showed that different factors seems to control emissions at different scales, e.g. soil nitrate content at up to 1 m but clay content and pH at larger scales, e.g. 1 km. This warns against the simple 'scaling up' of results from the laboratory or field plot to the field or landscape.



The research is ongoing, continuing in a current project. To date it appears not to be possible to manage the microorganisms other than through maintaining good soil structure (maintaining adequate soil organic matter, avoding compaction and waterlogging) and avoiding applying excess nitrogen as fertiliser or manure.
Exploitation Route As well as being used to formulate advice to farmers and growers, the research formed part of the exhibit 'Journey to the Centre of the Earth, the first 23 cm' presented at the Royal Society's Summer Exhibition in 2010. This attracted thousands of public visitors. Exploitation routes are via presentations and discussions with farmers and advisors and the formulation of advice in the UK 'Fertiliser Manual (RB209)', the revision of which in 2010 was led by Rothamsted. The aim is to guide on the more effieicnt use of nitrogen fertilisers, manures and other 'biosolids' for optimum crop production but minimal environmental impact.
Sectors Agriculture, Food and Drink,Environment
URL http://www.rothamsted.ac.uk/agec/mme_front.php
 
Description We have used molecular biology to study the factors that control the nitrogen cycling processes of nitrification and denitrification, especially the factors that determine how much of the greenhouse gas nitrous oxide is produced by these processes. There are simple farm management options that can limit emissions, either by stopping or slowing nitrification or by encouraging denitrification through to its end product dinitrogen gas (N2), thus closing the nitrogen cycle begun by nitrogen fixation. These are 'win'wins' in that they are appropriate to general good soil management and include maintaining soil organic matter levels and good soil structure, avoiding compaction and waterlogging and applying fertilisers and manures at appropriate times and rates. We also explored novel mathematical methods of studying the variation of nitrous oxide emissions across the landscape at scales of 1 m to 7 km. This showed that different factors seems to control emissions at different scales, e.g. soil nitrate content at up to 1 m but clay content and pH at larger scales, e.g. 1 km. This warns against the simple 'scaling up' of results from the laboratory or field plot to the field or landscape. The research is ongoing, continuing in a current project. To date it appears not to be possible to manage the microorganisms other than through maintaining good soil structure (maintaining adequate soil organic matter, avoding compaction and waterlogging) and avoiding applying excess nitrogen as fertiliser or manure.
First Year Of Impact 2011
Sector Agriculture, Food and Drink,Environment
Impact Types Economic,Policy & public services
 
Description BBSRC New Investigator Grant
Amount £350,000 (GBP)
Funding ID BB/K001051/1 ? ?Elucidating the importance of the pools of nitrate in soils on denitrification 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 03/2013 
End 02/2016
 
Description Newton Fund - Virtual Joint Centres in N Agronomy
Amount £2,438,488 (GBP)
Funding ID BB/N013468/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom of Great Britain & Northern Ireland (UK)
Start 01/2016 
End 12/2019
 
Title eRA 
Description A new version of the Electronic Rothamsted Archive (eRA) has been launched: http://www3.rothamsted.ac.uk/cdera/extract/pages/data_extraction_prototype6.html. It includes: data from the North Wyke Farm Platform; open access data on yields for the Broadbalk and Hoosfield long-term (>150 years) experiments; plant species data for Park Grass; soil organic carbon trends; meteorological data; 3300 reports, maps and plans, which will be given DOIs and made publically available. 
Type Of Material Database/Collection of data 
Year Produced 2014 
Provided To Others? Yes  
Impact eRA has been delivering data to enquirers for many years with a steadily increasing demand: 73 users in 2010/11 and 120 users in 2015/15. The new version of eRA was launched in 2014. 
URL http://www3.rothamsted.ac.uk/cdera/extract/pages/data_extraction_prototype6.html
 
Description International Year of Soils 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact The Sample Archive and soil cores from the long-term experiments were exhibited as part the activities at the Rothamsted International Year of Soils event on May 17-18, 2015. Positive comments about the event were received from visitors, including Professor Sir Martyn Poliakoff CBE FRS, Vice President of the Royal Society.
Year(s) Of Engagement Activity 2015
 
Description Royal Society Summer Exhibition: 'Journey to the centre of the Earth. The first 23 cm' 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? Yes
Geographic Reach local
Primary Audience Public/other audiences
Results and Impact Multimedia display about soil biodiversity at the Royal Society's Summer Exhibition in June and July 2010, with closed presentations to Royal Society fellows and then a week's presentation to the public. Held at the Southbank Centre in London. Computer displays. Handouts. Games.

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
 
Description The importance of soil biology/biodiversity 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Type Of Presentation keynote/invited speaker
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Informal discussion with farmers at a Natural England soil biology workshop and farm walk Presentations by Matthew Shepherd and I to the farmer group and then a farm walk, discussing soil biodiversity at several locations around the farm None

Increased farmer interest in soil biology and soil management.
Year(s) Of Engagement Activity 2011