Unravelling the Soil Microbial Metagenome:
assessing the effects of change on biodiversity and ecosystem function
Catriona Macdonald, Ian Clark, Steve McGrath, Penny Hirsch
Centre for Soils and Ecosystem Function, Rothamsted Research, AL5 2JQ, UK. Email: [email protected]
High-throughput sequencing and microarrays in conjunction with conventional methodologies will for the
first time reveal the relationship between microbial community function and phylogenetic diversity,
providing greater insight into the consequences of environmental change on ecosystem function.
1. Park Grass
2. Broadbalk
3. Highfield
4. LtSE
1. Park Grass
At Rothamsted a series
of long-term experiments
are providing a valuable
resource to answer key
ecosystems questions
relating to sustainable
land practices.
Approaches
Soil physical properties
(structure)
Soil chemical properties
(est. 1856)
Investigating the long term effects of fertilisers and soil pH on plant species diversity,
productivity and soil functions in a permanent grassland.
Metasoil/TerraGenome: an international consortium; http://www.terragenome.org/
•Sequencing all microorganisms in a reference soil.
•Sequence data and clones will be available to give an inventory of bacterial function and
to improve understanding of adaptation and evolution.
BBSRC Underwood Fellow at Rothamsted; Li-You Wu, University of Oklahoma
 
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• Microarray and 454 sequencing to determine the effect of pH on the distribution and
diversity of microbial functional genes and the relationship between above ground and
below ground diversity.
(e.g. pH, C, N)
2. Broadbalk
Broad scale microbial
measures
Investigating the effects of inorganic and organic fertilisers on wheat yields,
maintained >160 years.

(e.g. Biomass, C-utilisation)
Specific microbial
function
(e.g. Nitrification,

denitrification, methane
oxidation).
Community Structure:
bacteria, fungi and
archaea

(e.g. DGGE, t-RFLP, PLFA)
Quantitative assessment    
of structure and function
(qPCR of specific target
genes e.g. amoA, nifH, nodD,
nirS & K, nosZ).
Microarrays
• Phylochip - diversity array
with 15,000 species specific
probes
• GeoChip3 > 37,700 genes,
290 gene families (e.g.C, N, P
and S cycling, metal
reduction & resistance and
degradation pathways)
Omics’:
Transcriptomics,
Metabolomics.
USDA Funded Project: Eric Triplett, University of Florida
•Collaborative metagenomic research project
investigating how bacterial and archaeal
diversity, abundance and function are
regulated by different agro-ecosystems.
•Results to date
•Significant impacts of fertiliser and
treatment on bacterial community structure.
•260 million sequences to date.
3. Highfield
(est. 1949/1959)
Reversion
(est. 2008)
Investigating the effects of different cropping systems, including bare-fallow (BF)
on soil organic matter & yields.
Results to date: Dramatic reduction in soil organic carbon, loss of soil structure,
meso & microfauna abundance greatly reduced in BF but high microbial diversity
maintained.
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

 
High throughput
sequencing
•454: 1 Million at ~400bp
•SOLiD: >250Million at 50bp
•Illumina:20 Million at 200bp
(est. 1843)
•In 2008 a reversion experiment was set up to monitor changes in SOM, soil physical
& chemical properties, mesofauna /flora, microbial communities and functional assays
due to reversion of previous treatments.
•Deep Soil (International consortium) will use metagenomics, transcriptomics &
metabolomics to assess the impact of starving the soil for 50 years of plant inputs
(BF plots) on microbial diversity and function.
4. Long-term sludge experiment



(est. 1994)
A series of 9 experimental sites investigating the long-term impacts of sludgederived metal contamination in soil microbial community structure and function.
 

Other Resources:
Meteorological data, Environmental Change
Network), Archived soils, Crop yield data,
Soil fauna data
Treatments:
No Sludge Control
Sludge Control
Zn treatments
Results to date:
All Sites:
Bacteria
*
Woburn
Control
Sludge C
Zn 250
Zn 350
Zn 450
7
8
1
4
(150, 250, 350 + 450 mg kg-1)
5
93
6
2
Cu treatments
(50, 100, 150 +200 mg kg-1)
•Residual impacts of Zn and Cu on
bacterial and fungal community
structure (T-RFLP).
•Decreased potential nitrification
rates under metal (Zn and Cu)
contamination.
Outcomes and Beyond
•Understanding how microbial community structure and function are influenced by pH, fertiliser inputs, metal
contamination, land management & plant cover in the long-term.
•Access to historical metadata (meterological, yield data, soil/plant archive) provides an additional resource.
•Metagenomics is also a discovery technology for new taxa, biochemical pathways and a range of novel compounds
of industrial and pharmaceutical importance from soil, the most diverse ecosystem in the world.
Collaborators
Metasoil
Tim Vogel & Tom Demont
Laboratoire Ampere
Ecole Centrale de Lyon .
France
United States Department
of agriculture
Joe Zhou & Li-You Wu
Institute for
Environmental Genomics
University of Oklahoma
Deep Soil
Janet Jansson
Lawrence Berkeley
National Laboratory