The Diversity of Dirt
What is the role of the soil microbial
community in ecosystem functioning?
Dr Martina Girvan
June 2012
Talk Structure
•How Diverse is Soil? Back to the
Classroom!
•Exploitation of Genetic Diversity and how
if relates to Functional Diversity
•Research Case Study
•Why it matters
June 2012
Common View of Biodiversity
Soil Microbial Diversity and Function
July 9, 2012
Page 3
Traditional Taxonomists View of Biodiversity
• “the biological heterogeneity of a
system, it encompasses species
richness and distribution”
• Animalia
Eukaryota
• Plantae
• Fungi
• Protista
Prokaryota
• Monera
Soil Microbial Diversity and Function
July 9, 2012
Page 4
Current Taxonomic View of Biodiversity
• Animalia
• Plantae
• Chromista
• Fungi
• Protozoa
• Archaezoa etc.
Bacteria • Bacteria (many kingdoms)
Archaea • Archaebacteria (many kingdoms)
Soil Microbial Diversity and Function
July 9, 2012
Page 5
Bacteria
Archaea
Methanosarcina
Proteobacteria
Cyanobacteria
Gram
positives
Slime moulds
Entamoebae
Thermoproteus
Green
Non-sulphur
Bacteria
July 9, 2012
Animals
Plants
Ciliates
Flagellates
Trichomonads
Microsporidia
Diplomonads
LUCA
Soil Microbial Diversity and Function
Fungi
Methanococcus
Pyrodictium
Thermatogales
Halophiles
Methanobacterium
Thermococcus
Flavobacteria
Eucarya
Page 6
Different Phenotypes Same Metabolic Pathway/ Same
Phenotype Different Metabolic Pathway
Methanocella paludicola
Methanogenesis:
4H2 + CO2 → CH4 + 2H2O
Nitrosotalea devanaterra
Autotrophic Ammonia oxidation:
NH3 + O2
NO2- + H2O
CO2
organic C
Desulfopila aestuarii
Sulphate reduction with acetate:
Oxygen-respiration with glucose:
C6H12O6 + 6O2 → 6CO2 + 6H2O
Soil Microbial Diversity and Function
July 9, 2012
CH3COO- + SO42- → 2CO2 + HS- + 2H2O
Page 7
Soil Diversity
• Eukaryotic diversity on Earth was estimated to be approx.
8.7 million (8.7 x 106) species in total1
• One individual sample of 10g soil was estimated to contain
8.3 million (8.3 x 106) microbial species2
Soil Microbial Diversity and Function
July 9, 2012
Page 8
Why Such Diversity?: Heterogeneity and spatial
structure of soil microbial communities
Variability in physicochemical properties
e.g. water content, oxygen availability and pH
high
Aerobes
(e.g. pseudomonads)
O2
availability
high
pH
low
low
Soil Microbial Diversity and Function
July 9, 2012
Anaerobes
(e.g. fermentative bacteria (organic acids)
methanogenic archaea (methane))
Page 9
Why Such Diversity?: Heterogeneity and spatial
structure of soil microbial communities
Variability in soil structure e.g. avoidance of predation
Fast-growing organisms
Protozoa
Slow-growing organisms
Soil Microbial Diversity and Function
July 9, 2012
Page 10
Why Such Diversity?: Heterogeneity and spatial
structure of soil microbial communities
Variability in carbon sources e.g. root exudates
Plant root
Low molecular
weight compounds
- Sugars
- Amino acids
- Carboxylic acids
Soil Microbial Diversity and Function
July 9, 2012
Root exudates
Page 11
hy Such Diversity?: Heterogeneity and spatial structure
of soil microbial communities
Variability in energy sources e.g. light
Phototrophs
(e.g. cyanobacteria)
Chemoheterotrophs
(e.g. Bacillus sp.
Pseudomonas sp.)
Soil Microbial Diversity and Function
July 9, 2012
Page 12
Soil Microbial Diversity Summary
• Bacterial and Archaea are more different from each
other than we are from nematodes or indeed Bacteria,
both in taxonomic and functional terms
• Soil represents a huge range of different habitats for
soil microbes
• Different microbes have evolved to take advantage of
specific ecological niches
• Therefore, thousands of habitats = thousands of
species
Soil Microbial Diversity and Function
July 9, 2012
Page 13
Talk Structure
•How Diverse?
•Exploitation of Genetic Diversity
and how if relates to Functional
Diversity
•Research Case Study
•Why it matters
June 2012
Bio-prospecting for Genetic Resources
5
Please let the
Pseudomonads be
ready!
3
Soil Microbial Diversity and Function
July 9, 2012
4
5
Page 15
Functional Resources
• Mineralisation of Organic and Inorganic Substrates
– E.g. Leaf litter decomposition, sulphur oxidation and
reduction, ammonification, nitrogen fixation,
methanogenesis and methane oxidation
– Bacteria and Archaea exploit inorganic compounds for
energy and so complete chemical pathways , therefore
major biogeochemical cycles such as carbon, nitrogen,
sulphur, phosphorus are inextricably linked to soil microbes
• Water Purification
– Reedbed sewage purification and other mainstream sewage
treatment plants by aerobic digestion
• Carbon Sequestration
– Peatbogs only 3% land surface but contain nearly a third of
the worlds soil organic carbon6
Soil Microbial Diversity and Function
July 9, 2012
Page 16
Biodiversity of DNA and Function Combine to Create
Functional Soil Ecosystems
• Genetic diversity within and between
species
– Provide novel genes and the ability to adapt
• Functional diversity
– Different species with different genetic
components may provide similar functions
within an Ecosystem
• Ecosystem
– It is the functional elements and interrelation of
these species which comprise an Ecosystem
Soil Microbial Diversity and Function
July 9, 2012
Page 17
Why unfamiliar to mainstream ecology?
• Not visible
• Not accessible to natural historians
• 99.9% of bacteria cannot be cultured so not accessible
to traditional microbiologists
• Advances in study became possible due to complex
DNA amplification techniques, Metagenomics
• Difficult and expensive (also just a tad unglamorous,
NOT like CSI or the X Files)
Soil Microbial Diversity and Function
July 9, 2012
Page 18
Talk Structure
•How Diverse?
•Exploitation of Genetic Diversity
and how if relates to Functional
Diversity
•Research Case Study
•Why it matters
Soil Genetic Diversity7
soil
DNA extraction insitu/ cell separation
Calculate diversity of community profile
mechanical cell lysis
buffer variations
DNA purification
chemical cell lysis
humic inhibitors
sephedex columns
caesium chloride gradient
agarose gel purification
PEG/ethanol precipitation
PCR
functional gene
16/18S DNA
full length sequence
Partial sequence
clone analysis
fragment length heterogeneity
DGGE analysis
more diverse
Soil Microbial Diversity and Function
July 9, 2012
Page 20
less diverse
Different Measurable Components of Soil
DNA
RNA
Culturable
Present
Active
Traditionally Visible
Soil Microbial Diversity and Function
July 9, 2012
Page 21
Microcosm experiment with copper and benzene applied at time 0
control
copper
benzene
16S rDNA analysis
Analysis of 16S rDNA
sequences showed the
diversity of both the copper
and benzene contaminated
communities to be significantly
reduced by week 9
weeks 0
1
4
9
0
1
4
9
0
1
4
9
Shannon index of diversity
3.5
Soil Microbial Diversity and Function
3
control
copper
2.5
benzene
2
1.5
July 9, 2012
week 0
week 1
Page 22
week 4
week 9
Microcosm experiment with copper and benzene applied at time 0
16S rRNA analysis
control
copper
benzene
Analysis of 16S rRNA
sequences again showed a
significant reduction in diversity
of both the copper and benzene
contaminated communities by
week 9
Shannon index of diversity
weeks 0
Soil Microbial Diversity and Function
1
4
9
0
1
4
9
0
1
4
9
3.5
3
control
copper
2.5
benzene
2
1.5
July 9, 2012
week 0
week 1
Page 23
week 4
week 9
14C
mineralisation assays showing functional
community capacity
Wheat shoot (broad niche) mineralisation measured by 14C
0.25
% Mineralisation
Although genetic
diversity was
significantly reduced
in benzene and copper
contaminated soil by
week 9 wheat shoot
mineralisation was
unaffected
0.30
0.20
0.15
0.10
0.05
control
copper
benzene
0
18
2,4, DCP (narrow niche) mineralisation measured by 14C
week 1
week 4
week 9
week 1
week 4
week 9
However 2,4 DCP
mineralisation was
severely inhibited until
recovery by week 9
% Mineralisation
1.5
1.4
1.2
1.0
0.8
0.6
0.4
0.2
0
Soil Microbial Diversity and Function
July 9, 2012
Page 24
Summary of Research Findings
• Soil is genetically resistant
• Soil also shows functional resilience
• Some functional redundancy for broad scale niche
utilisation
• BUT narrow niche function was impaired
• Overall genetic diversity confers the ability for soil to
recover functionally
• We do not know enough about soil processes to risk
it!
Soil Microbial Diversity and Function
July 9, 2012
Page 25
Talk Structure
•How Diverse?
•Exploitation of Genetic Diversity
and how if relates to Functional
Diversity
•Research Case Study
•Why it matters
June 2012
Summary
•
•
•
•
•
•
Bacterial and Archaeal Soil microbial diversity is vast
equalling the whole of the Eukaryotes in the world in
just 10g of soil
This diversity is caused by heterogeneity in structure ,
energy sources and oxygen gradients etc.
The functional elements of soil are vital to life on earth
but poorly studied due to technical difficulties
There is much functional redundancy among microbial
populations. Therefore using macro-ecological
measurements of diversity may not apply
Functional diversity may be more realistic means of
measuring the “health” of microbial communities
Although molecular techniques are important we can
only achieve a comprehensive analysis of functional
diversity if we increase the culturability of soil
microorganisms
Soil Microbial Diversity and Function
July 9, 2012
Page 27
Have We Got It Right?
Us
of
Herbivores
Pe
rce
p
tio
n
Invertebrates
Plants
Invertebrates
Soil
Soil Microbial Diversity and Function
July 9, 2012
Page 28
ty?
ali
Re
im
po
rta
nc
e
Carnivores
Tom Curtis8
(2006) Microbial ecologists: it's time to 'go large' Nature Reviews
Microbiology 4, 488
“For if the last blue whale choked to death on the last
panda, it would be disastrous but not the end of the
world.
But if we accidentally poisoned the last two species
of ammonia oxidisers, that would be another matter.”
Soil Microbial Diversity and Function
July 9, 2012
Page 29
References
1. Mora C, Tittensor DP, Adl S, Simpson AGB, Worm B (2011) How Many Species
Are There on Earth and in the Ocean? PLoS Biol 9(8): e1001127.
doi:10.1371/journal.pbio.1001127
2. Gans J, Murray Wolinsky, and John Dunbar (2005) Computational
Improvements Reveal Great Bacterial Diversity and High Metal Toxicity in Soil
Science : 309 (5739), 1387-1390.
3. Rolf Daniel (2005) The metagenomics of soil Nature Reviews Microbiology 3,
470-478
4. Knowles, B. H. & Ellar, D. J. (1988) Differential specificity of 2 insecticidal toxins
from Bacillus thurinigensis var aizawai. Molecular Microbiology, 2, 153-157.
5. Meikle, A., Killham, K., Prosser, J. I. & Glover, L. A. (1992) Luminometric
measurement of population activity of genetically modified Pseudomonas
fluorescens in the soil. FEMS Microbiology Letters, 99(2-3), 217-220.
6. Koehler, A K, Sottocornola, M And Kiely, G. Global Change Biology (2011) 17:
309–319
7. Girvan M. S., L.A. Glover, K. Killham, C. Campbell, J.I. Prosser. 2005. Bacterial
Diversity Promotes Community Stability and Functional Resilience after
Perturbation. Environmental Microbiology. 7: 301–313
Soil Microbial Diversity and Function
July 9, 2012
Page 30
Thank You for Listening
Thanks to Dr Graeme Nicol of Aberdeen University for all his
help and advice, a great lab partner
Thanks to the AECOM ecology team for listening!
Please do contact me for further information
[email protected]
June 2012