Long-term impacts of heavy metals on soil microbial diversity numbers and function

Lead Research Organisation: Rothamsted Research
Department Name: Sustainable Soils and Grassland Systems

Abstract

Soil not only supports plant growth, but also is crucial for the cycling of nutrients. Soil microorganisms play an absolutely essential role in these processes. Their populations are large and diverse but some groups of bacteria and fungi, as well as some specific processes are sensitive to environmental changes such as the build up of toxic metals. These metals are an example of a factor that could strongly affect the sustainable future use of soils. However, the current EU risk assessments of toxic metals in soils rely exclusively on short-term laboratory tests, which may not reflect the long-term effects of metals in the environment. Also many investigations on the impact of toxic metals in the environment use heavily polluted sites where plant growth is severely decreased due to acute metal toxicity, rather than considering the long-term accumulation of toxic metals that normally build up slowly and cause chronic pollution. The role of biodiversity within soil microbial groups plays in maintaining soil functions is not well understood, although it is assumed that a factor known as soil resilience (the ability to continue to perform functions in the presence of stress, e.g. metal pollution) relies on the presence of diverse individuals within the soil microbial population. This resilience to stress (from chemical, physical or biological factors) may be compromised if microbial diversity is reduced as a result of toxic metal accumulation. The proposal aims to evaluate the effects of zinc, a common pollutant of soil present in sewage sludge and galvanised (zinc coated) metal, and copper which is also present in sludge and animal manures, on the tolerance of microbial communities, key microbial processes, and the genetic diversity of key groups responsible for soil functions. Soils from long-term sewage-sludge experiments set up six years ago on different soil types in the UK, and soil with decreasing concentrations of zinc at increasing distances away from galvanised structures, will provide unique experimental materials to tackle these issues. A range of microbial parameters will be measured using both physiological and molecular biological assays. The results will be related to soil chemical measurements to establish the exact chemical conditions that induce toxicity to soil microbes. This information can be used by legislators to apply to other situations and help to increase the sustainable use of land by preventing critical accumulations from building up in the future.

Technical Summary

Soil microbes are responsible for providing essential ecosystem services and they are one of the most sensitive groups that influence soil protection legislation to guard against unsustainable metal accumulations in soil. We will focus on three contrasting bacterial groups which have important functions in soils and determine the relationships between their population size, diversity and functions, and environmental exposure. We will use a range of recent molecular (q-PCR, 16S rRNA, DGGE, specific functional gene primers, BrdU incorporation for native population analyses) and conventional techniques to quantify the numbers, diversity and function of these groups across gradients of chronic Zn and Cu exposure, derived from unique field experiments. Chemical measurements of soils and soil solutions and the latest speciation modelling methods will be employed to determine the environmental exposure associated with the microbiological changes. Our results will be used to provide a scientific basis for national and European agricultural and environmental policies related to protection of ecosystem services and sustainable practices.
 
Description Developed molecular probes that specifically target Rhizobium leguminosarum bv. trifolii and bv. viciae. This will greatly advance our ability to monitor the effects of land management, pollutants etc. on these agronomically important species.

We generated 374,443 partial gene sequences of bacterial , rhizobial, fungal, archeal and functional genes have been generated
Exploitation Route Gene sequences will be logged on the NCBI and EBI public databases. http://www.ncbi.nlm.nih.gov/; http://www.ebi.ac.uk



Results will be used to provide a scientific basis for national and European agricultural and environmental policies realted to protection of ecosystem services and sustainable practices.
Sectors Agriculture, Food and Drink,Environment

 
Description Long term impacts of heavy metals on soil microbial diversity, numbers and function
Geographic Reach Asia 
Policy Influence Type Participation in a national consultation
Impact Our results will be used to provide a scientific basis for national and European agricultural and environmental policies related to protection of ecosystem services and sustainable practices.
 
Description Soil Screening Values for Priority Contaminants
Geographic Reach National 
Policy Influence Type Participation in advisory committee
Impact Draft Environment Agency Documents
 
Title Gene Sequences 
Description We have generated 374,443 partial gene sequences of bacterial (16S, 209,420), rhizobial (16S, 6,976), fungal (ITS, 56,944), archaeal (16S, 52,908) as well as functional (amoA, 48,195) genes using next generation (GS FLX 454) sequencing. This provides an in-depth sequence profile of the effect of Zn and Cu on these microbial groups as well as providing a resource for future data mining. Sequences are logged on the NCBI (National Centre for Biotechnology Information) and EBI (European Bioinformatics Institute) public databases. 
Type Of Material Cell line 
Year Produced 2010 
Provided To Others? Yes  
Impact UNKNOWN 
 
Title Molecular probe 
Description Molecular probes that specifically target Rhizobium leguminosarum bv. trifolii and bv. viciae have been developed that allow the quantification of these species in environmental samples. Previously this had only been possible through time consuming trap plant assays. This developed methodology will greatly advance our ability to monitor the effects of land management, pollutants etc. on these agronomically important species. 
Type Of Material Model of mechanisms or symptoms - in vitro 
Year Produced 2010 
Provided To Others? Yes  
Impact UNKNOWN 
 
Title Gene Sequences 
Description We have generated 374,443 partial gene sequences of bacterial (16S, 209,420), rhizobial (16S, 6,976), fungal (ITS, 56,944), archaeal (16S, 52,908) as well as functional (amoA, 48,195) genes using next generation (GS FLX 454) sequencing. This provides an in-depth sequence profile of the effect of Zn and Cu on these microbial groups as well as providing a resource for future data mining. Sequences are logged on the NCBI (National Centre for Biotechnology Information) and EBI (European Bioinformatics Institute) public databases. 
Type Of Material Database/Collection of data 
Year Produced 2010 
Provided To Others? Yes  
Impact UNKNOWN 
 
Title Generation of partial gene-sequences 
Description Generated 374,443 partial gene sequences of bacterial (16S, 209,420), rhizobial (16S, 6,976), fungal (ITS, 56,944), archaeal (16S, 52,908) as well as functional (amoA, 48,195) genes using next generation (GS FLX 454) sequencing. This provides an in-depth sequence profile of the effect of Zn and Cu on these microbial groups as well as providing a resource for future data mining. Sequences will be logged on the NCBI (National Centre for Biotechnology Information) and EBI (European Bioinformatics Institute) public databases. 
Type Of Material Database/Collection of data 
Year Produced 2010 
Provided To Others? Yes  
Impact UNKNOWN 
 
Description Appropriate measures of bioavailable metals for microbes 
Organisation University of Natural Resources and Applied Life Sciences
Country Austria, Republic of 
Sector Academic/University 
PI Contribution Some of this work has been included in the paper ?Development of real-time PCR assay for detection and quantification of Rhizobium leguminosarum and discrimination between different biovars in soil?.
Start Year 2009
 
Description Impacts of heavy metals on soil microbial diversity 
Organisation North West Agriculture and Forestry University
Country China, People's Republic of 
Sector Academic/University 
PI Contribution Relative impact of soil, metal source and metal concentration on bacterial community structure and community tolerance
Start Year 2007
 
Description InvestigatIon into the effects of Cu-sludge addition on methane oxidising communities 
Organisation Newcastle University
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Paper in Soil Biology and Biochemistry
Start Year 2007
 
Description Long term impacts of heavy metals on soil microbial diversity, numbers and function 
Organisation ADAS
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Sharing samples and data from all the of long-term sludge experimental sites
Start Year 2007
 
Description Long term impacts of heavy metals on soil microbial diversity, numbers and function 
Organisation Macaulay Land Use Research Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Charity/Non Profit 
PI Contribution Investigate the effects of Cu-sludge addition on methane oxidising communities.
Start Year 2007
 
Description Long term impacts of heavy metals on soil microbial diversity, numbers and function 
Organisation Newcastle University
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution investigate the effects of Cu-sludge addition on methane oxidising communities.
Start Year 2007
 
Description Long term impacts of heavy metals on soil microbial diversity, numbers and function 
Organisation WRc plc
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Sharing samples and data from all the of long-term sludge experimental sites. An MSc project has recently been formulated in collaboration with WRC that has directly stemmed from observations made on this project.
Start Year 2007
 
Description Long term impacts of zinc and copper enriched sludge additions on bacterial, archael and fungal communities across seven agricultural soils 
Organisation Macaulay Land Use Research Institute
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Charity/Non Profit 
PI Contribution Paper in Soil Biology and Biochemistry
Start Year 2007
 
Description Long-term impacts of heavy metals on soil microbial diversity numbers and function 
Organisation Chinese Academy of Sciences
Department Research Center for Eco-environmental Sciences
Country China, People's Republic of 
Sector Academic/University 
PI Contribution To quantify the relative abundance of bacterial and archaeal amoA genes in an upland Zn-contaminated grassland soil
Start Year 2007
 
Description Low biodegradability of fluoxetine HCl, diazepam and their human metabolites in sewage sludge-amended soil 
Organisation Newcastle University
Department School of Civil Engineering and Geosciences
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Resulting in a paper in a refereed journal
Start Year 2007
 
Description Low biodegradability of fluoxetine HCl, diazepam and their human metabolites in sewage sludge-amended soil 
Organisation Newcastle University
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Publication in an international journal; We provided access to our field experiments
Start Year 2007
 
Description Low biodegradability of fluoxetine HCl, diazepam and their human metabolites in sewage sludge-amended soil 
Organisation University of Plymouth
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution Papers in refereed journals
Start Year 2007
 
Description Low biodegradability of fluoxetine HCl, diazepam and their human metabolites in sewage sludge-amended soil 
Organisation University of Plymouth
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Academic/University 
PI Contribution We provided access to the field experiments as a resource
Start Year 2007
 
Description Relative impact on soil, metal source and metal concentration on bacterial community structure and community tolerance 
Organisation Southwest University
Department College of Resources and Environment
Country China, People's Republic of 
Sector Academic/University 
PI Contribution Paper in Soil Biology and Biochemistry
Start Year 2008
 
Description Sharing samples and data from long term sludge experiments 
Organisation WRc plc
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Sharing samples and data from long term sludge experiments
Start Year 2007
 
Description Sharing samples and data from the Long term sludge experiments 
Organisation ADAS
Country United Kingdom of Great Britain & Northern Ireland (UK) 
Sector Private 
PI Contribution Sharing samples and data from Long term sludge experiments
Start Year 2007
 
Description The importance of soil pH in determining the impacts of Zn on soil microbial communities 
Organisation Chinese Academy of Sciences
Department Research Center for Eco-environmental Sciences
Country China, People's Republic of 
Sector Academic/University 
PI Contribution A visit to China resulted in a publication from the work The importance of soil pH in determining the impacts of Zn on soil microbial communities
Start Year 2007
 
Description The importance of soil pH in determining the impacts of Zn on soil microbial communities 
Organisation Chinese Academy of Sciences
Country China, People's Republic of 
Sector Public 
PI Contribution The importance of soil pH in determining the impacts of Zn on soil microbial communities
Start Year 2007
 
Description To quantify the relative abundance of bacterial and archaeal amoA genes in an upland Zn-contaminated grassland soil 
Organisation Fujian Academy of Agricultural Science
Country China, People's Republic of 
Sector Academic/University 
PI Contribution The relative abundance of bacterial and archaeal amoA genes in an upland Zn-contaminated grassland soil in determining the impacts of Zn on soil microbial communities
Start Year 2007
 
Description Bioavailability and ecotoxicity of metals in soils 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? Yes
Type Of Presentation paper presentation
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Talk sparked questions and discussions afterwards

unknown
Year(s) Of Engagement Activity 2011
 
Description International Year of Soils 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? Yes
Geographic Reach Local
Primary Audience Public/other audiences
Results and Impact Received lots of positive feedback from the public

unknown
Year(s) Of Engagement Activity 2015
 
Description Journey to centre of the Earth: the first 23cm 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact The Royal Society Summer Science Exhibition- This work was included as part of a larger exhibition highlighting the importance of biodiversity in soil http://www.seefurtherfestival.org/exhibition/view/journey-centre-earth-first-23cm.

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
URL http://www.seefurtherfestival.org/exhibition/view/journey-centre-earth-first-23cm.
 
Description Long term impacts of heavy metals on soil microbial diversity, numbers and function 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact This work was discussed in the wider context of the significance of heavy metal contamination in agricultural practice.

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
 
Description Long term impacts of heavy metals on soil microbial diversity, numbers and function 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Public/other audiences
Results and Impact This work was discussed in the wider context of the significance of heavy metal contamination in agricultural practice.

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
 
Description RRES Open Weekend. 
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 UNKNOWN
Year(s) Of Engagement Activity 2010
 
Description Rothamsted Open Weekend 
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 This work was discussed in the wider context of the significance of heavy metal contamination in agricultural practice. Attendance was 170 secondary school students and 7000 members of the public

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
 
Description Soil Bio Interactions and Engineering 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Participants in your research and patient groups
Results and Impact Workshop

no actual impacts realised to date
Year(s) Of Engagement Activity 2007
 
Description The Royal Society Summer Science Exhibition 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact This work was included as part of a larger exhibition highlighting the importance of biodiversity in soil: http://www.seefurtherfestival.org/exhibition/view/journey-centre-earth-first-23cm. http://royalsociety.org/summer-science/2010/journey-to-centre-of-earth/

no actual impacts realised to date
Year(s) Of Engagement Activity 2010
URL http://royalsociety.org/summer-science/2010/journey-to-centre-of-earth/