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.
Organisations
- Rothamsted Research (Lead Research Organisation)
- Southwest University (Collaboration)
- Chinese Academy of Sciences (Collaboration)
- WRc (Collaboration)
- James Hutton Institute (Collaboration)
- Newcastle University (Collaboration)
- Agricultural Development Advisory Service (United Kingdom) (Collaboration)
- North West Agriculture and Forestry University (Collaboration)
- University of Plymouth (Collaboration)
- University of Natural Resources and Life Sciences (Collaboration)
- Fujian Academy of Agricultural Science (Collaboration)
Publications
Macdonald CA
(2011)
Development of a real-time PCR assay for detection and quantification of Rhizobium leguminosarum bacteria and discrimination between different biovars in zinc-contaminated soil.
in Applied and environmental microbiology
Macdonald C
(2011)
Long-term impacts of zinc and copper enriched sewage sludge additions on bacterial, archaeal and fungal communities in arable and grassland soils
in Soil Biology and Biochemistry
Gregory A
(2015)
A review of the impacts of degradation threats on soil properties in the UK
in Soil Use and Management
Charlton A
(2016)
Long-term Impact of Sewage Sludge Application on biovar : An Evaluation Using Meta-Analysis.
in Journal of environmental quality
Stroud J
(2016)
Population collapse of Lumbricus terrestris in conventional arable cultivations and response to straw applications
in Applied Soil Ecology
Xie WY
(2016)
Long-Term Impact of Field Applications of Sewage Sludge on Soil Antibiotic Resistome.
in Environmental science & technology
Charlton A
(2016)
Long-term impact of sewage sludge application on soil microbial biomass: An evaluation using meta-analysis.
in Environmental pollution (Barking, Essex : 1987)
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 | Contribution to a national consultation/review |
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 a guidance/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 Life Sciences |
Country | Austria |
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 |
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 |
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 |
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 |
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 | Newcastle University |
Country | United Kingdom |
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 |
Country | United Kingdom |
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 |
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 | Chinese Academy of Sciences |
Department | Research Center for Eco-environmental Sciences |
Country | China |
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 |
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 |
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 |
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 |
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 |
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 |
Country | United Kingdom |
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 |
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 |
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 |
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 |
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 | 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 | 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 | 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/ |