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The huge variety The huge variety of life in soilsof life in soils
WimWim
van van derder
PuttenPutten
Netherlands Institute of EcologyNetherlands Institute of Ecology
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Huge varietyof life in soils:
So what?
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Soil biodiversityis all aboutto eat….and to be eaten
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First microscope by Antonie van Leeuwenhoek showing bacterial cells + 1670
In spite of this long standing knowledge on lifein soil, we still consider soil as dirt, filling up material or whatsoever non-biotic
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1 square meter of soil contains1-50 plant species5,000-10,000 microbial taxaHundreds of species of nematodesCollembola, mites, earthworms, etc.
1 square meter of water columncontains minimally a hundred-fold less biodiversity than soil
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When and where
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Bacterial feeding nematodes Plant feeders Omnivore
Carnivore
Fungal feeding nematodesNematode sample collected from soil (photos Hans Helder, Hanny van Meegen)
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Gregor Yeates Tom Bongers
Many nematode experts are 60+!
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Single worm – classical identification & series digital pictures
DNA extraction
DNA amplification
Cloning in vector
DNA sequencing
Wageningen molecular nematode identification projectFrom: Hans Helder
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GTGGTAAACTTCATCTAAGACTTAATATTGCCACGAGGCCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTGAGGTG Cl 1129+1626+1627 GTGGTAAACTTCATCTAAGACTTAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTAAGGTG Cl 1109+1622+1743 GTGGTAAACTTCATCTAAGACCTAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACATTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTAAGGTG clone1586+1587+1588 GTGGTAAACTTCATCTAAGACTCAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTGAGGTG clone1589+1590+1591 GTGGTAAACTTCATCTAAGACTTAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTAAGGTG clone1592+1593+1594 GTGGTAAACTTCATCTAAGACTTAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTAAGGTG clone1595+1596+159 GTGGTAAACTTCATCTAAGACTCAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGATAGAGTTAAAGAGGACGTGAAACCGGAGAGGTG clone1598+1599+1600 GTGGTAAACTTCATCTAAGACTTAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTAAGGTG clone1601+1602+1603 GTGGTAAACTTCATCTAAGACTTAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTAAGGTG clone1607+1608+16 GTGGTAAACTTCATCTAAGACTTAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGTAAGGTG Cl 1610+1611+1612 GTGGTAAACTTCATCTAAGACTCAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAAGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGAGAGGTG Cl 1613+1614+1615 GTGGTAAACTTCATCTAAGACTCAATATTGCCACGAGACCGATAGCAAACAAGTACTGTGAAGGAAGGTTGCAAAGCACTTTGAAGAGAGAGTTAAAGAGGACGTGAAACCGGAGAGGTG
From: Hans Helder
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Towards a nematode community analysis tool –Qualitative and quantitative characterization of nematode communitiesfor e.g. soil quality assessment
DNA extraction Q-PCR: each sigmoid curverepresents a nematode taxon
From: Hans Helder
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The future: take a hand full of soil, get all DNA out, determinediversity of soil life quantitatively and assess ecosystems services?!?
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Whatever you eat, wear or breath: it has passed and will pass the soil biota over and over again
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Contribute tobiodiversity
Fight/suppress pests (IPM)
Build soil structure
Remove pesticides and nutrients in buffer strips
Support plant and animals viamutualism
Control and cycle plant nutrients
How soil organisms contribute to agricultural ecosystem services (From: Kate Scow)
Source/sink of GHG
Biodegrade pesticides in field
Breakdown wastes, make compost
Develop antibiotic resistence (or not)
Fix nitrogen
Build soil organic matter
Contaminate food (or not)
Sequestercarbon
Support farmer’s digestion and immunity
Control parasitic nematodes
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root
feeding fauna
mycorrhiza
pathogens
direct pathway to plants indirect pathway to plants
detritus
foodweb
?
Wardle et al Science 2004
Focus on direct and indirect belowground interactions!
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Predacious arthropods
Bacteria
Enchytraeids
Earthworms
Detritivorousarthropods
ProtozoaBacterivorousnematodes
Omnivorous nematodes
Fungi
Mycorrhizalfungi
Herbivorous nematodes
Herbivorous arthropods
Colembola
OribatidaFungivorousnematodes
Carnivorous nematodes
Uropodina
Gamasina& Prostigmata
Soil organic matter Root
Relative biomass of different components in the soil food web Bez
emer
et a
l. E
colo
gy 2
010
(in p
ress
)
Direct interactions
Indirectinteractions
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Effects of root pathogens, root herbivores and symbionts on plant biodiversity:relatively little contribution of these soil biota to soil biomass, but profound effectson plant community composition.
- Soil biota + Soil biota
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When and where
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Lourens Baas Becking (1930’s):"Everything is everywhere, but the environment selects”
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100 2000Distance (km)
1
0
Jaccardsimilarity index
Nematodes
Bacteria
Chalk grasslands in southern UK: nematode and bacteria similarity decline with distance(source: the EU-TLinks project)
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0.2
0.3
0.4
0.5
0.6
same plant species, same plant communitysame plant species, different plant community
different plant species, same plant communitydifferent plant species, different plant community
Holcus Anthox. Leucanth. Plantago Tanacetum Vicia LotusNem
atod
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unity
sim
ilarit
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2 in
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dual
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Grass G G F F F L L
Soil organisms can also differ at very local scales:
-Strong effects bacterivores and predators
-No effects for plant feeders
-No effects of plant functional groups
Festuca ovina
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0.2
0.3
0.4
0.5
0.6
same plant species, same plant communitysame plant species, different plant community
different plant species, same plant communitydifferent plant species, different plant community
Festuca Holcus Anthox. Leucanth. Plantago Tanacetum Vicia LotusNem
atod
e co
mm
unity
sim
ilarit
y of
2 in
divi
dual
pla
nts
Grass G G Forb F F Legume L
Nematode community composition is determined by plant species, as well as by where these plant species grow
Bezemer et al. Ecology 2010 (in press)
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Van de Voorde et al. New Phytol. (2010)
0
1
2
3
4
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
Plant community heterogeneity
0
1
2
3
4
0 0.1 0.2 0.3 0.4 0.5 0.6 0.7
Arb
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Heterogeneity arbuscular
mycorrhizal
fungi depends on plant community heterogeneity
Arbuscular mycorrhizalfungi on Jacobaea vulgaris
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Currently, existing theories, such as island biography and other ecological concepts, are tested for soil biota
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Exotic invaders: Prunus serotina is native in the U.S. and an exotic invader in the EU
EU USA
- +- -
Seedling mortalityin soil in greenhouse
Packer and Clay Nature 2000
Reinhart et al. 2003 Ecology Letters
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% o
f see
dlin
gs w
ith ro
ot ro
t
0
10
20
30
40
50
60
70
native rangenon-native range
Origin of isolates***
***
Seed sourceUSA Eu
% m
orta
lity
of se
edlin
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0
10
20
30
40
50
60
**
***
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Reinhart et al. New Phytologist 2010
Prunus serotina native range :aggressive and mild soil pathogens
Prunus serotina non-native rangemild soil pathogens only:
USA NW-Europe
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Before warming After warming
Herbivore
Carnivore
Herbivore
Carnivore
Herbivore
C
B
D
A
Before warming After warming
Herbivore
Carnivore
Herbivore
Carnivore
Herbivore
Before warming After warming
Herbivore
Carnivore
Herbivore
Carnivore
Herbivore
C
B
D
A
Van der Putten et al. Phil. Trans. 2010
The same principle of enemy releasealso applies to climate warming
Only plants move: invasive potential
All move: no invasive potential
Plants and herbivores move: no invasive potential
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European Commission DG ENV ENVNVTREN
Soil biodiversity: functions, threats and
tools for policy makers [Contract 07.0307/2008/517444/ETU/B1]
Draft final report
25th of November 2009
Soil Biodiversity synthesis report February 2010http://ec.europa.eu/environment/soil/biodiversity.htm
Report for theEurpean CommissionDG Environment
Authors:
Anne TurbéArianna De ToniPatricia BenitoPatrick LavellePerrine LavelleNuria Ruiz Wim H. Van der Putten Shailendra Mudgal
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Variety in undergroundis crucial for sustainability; it
provides food, clean water and air, fibers, and it promotes variety
aboveground!