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

Huge varietyof life in soils:

So what?

Soil biodiversityis all aboutto eat….and to be eaten

http://soils.usda.gov/sqi/concepts/soil_biology/images/Campbell1Lo.jpg

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

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

When and where

Bacterial feeding nematodes Plant feeders Omnivore

Carnivore

Fungal feeding nematodesNematode sample collected from soil (photos Hans Helder, Hanny van Meegen)

Gregor Yeates Tom Bongers

Many nematode experts are 60+!

Single worm – classical identification & series digital pictures

DNA extraction

DNA amplification

Cloning in vector

DNA sequencing

Wageningen molecular nematode identification projectFrom: Hans Helder

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

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

The future: take a hand full of soil, get all DNA out, determinediversity of soil life quantitatively and assess ecosystems services?!?

Whatever you eat, wear or breath: it has passed and will pass the soil biota over and over again

http

://im

ages

.goo

gle.

com

/imgr

es?i

mgu

rl =ht

tp://

ww

w.s

are.

org/

publ

ica

tions

/exp

lore

/imag

es/s

cene

wid

e2.jp

g

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

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!

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

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

When and where

Lourens Baas Becking (1930’s):"Everything is everywhere, but the environment selects”

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)

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

e co

mm

unity

sim

ilarit

y of

2 in

divi

dual

pla

nts

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

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)

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

uscu

lar

myc

orrh

izae

com

mun

ity h

eter

ogen

eity

Heterogeneity arbuscular

mycorrhizal

fungi depends on plant community heterogeneity

Arbuscular mycorrhizalfungi on Jacobaea vulgaris

Currently, existing theories, such as island biography and other ecological concepts, are tested for soil biota

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

% 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

gs

0

10

20

30

40

50

60

**

***

b

a

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

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

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

Variety in undergroundis crucial for sustainability; it

provides food, clean water and air, fibers, and it promotes variety

aboveground!