professor jim harris department of natural ser europe...

The role of soil microbiology in restoration

Professor Jim HarrisDepartment of Natural Resources

SER EuropeSummer School

September 2007

The MillenniumEcosystem Assessment

The Millennium Ecosystem Assessment

• 60% of world ecosystem services have been degraded

• Of 24 evaluated ecosystem types, 15 are being damaged

• About a quarter of the Earth's land surface is now cultivated.

Soil-dependentecosystem services

OverburdenOverburdenSubSub --soilsoilTopsoilTopsoil

Nine attributes of a restored ecosystem

1. Reference ecosystem, characteristic assemblages

2. Indigenous species, some exceptions 3. Functional groups present or available

4. Physical environment appropriate

5. Ecosystem functions normally for successional stage6. Landscape integration, biotic and abiotic interactions

7. Potential threats eliminated8. Resilience and integrity

9. Self-sustaining

Criteria for ecological indicators

• Easily measured• Sensitive

• Respond predictably to stress• Anticipatory• Allow for adaptive management intervention

• Integrative• Have known responses to stress, disturbances

and time• Low variability in response

Derived from Dale and Beyeler 2001

A QUICK PRIMER ON LIFE IN EARTH

SERVICES PROVIDED BY SOILS

• Primary productivity• food and fibre production

• diverse habitats

• Environmental services

• filtering

• buffering

• transforming

• Biological habitat and biodiversity reserve

• Platform functions

• Landscape and heritage

• Source of raw materials

THE SOIL HABITAT

5 cm 5 mm

SOIL BIOMASS

• Handful of arable soil(c. 200g)…..

• .…approximately0.5 g of fresh biomass (mainly ‘microbial’)

5 t ha-1

equivalent to 100 sheep per hectare

grassland – 20 times greater = 2000 sheep per hectare

DISTRIBUTION WITHIN SOIL PROFILE

POPLAR PLANTATION (2-YEARS OLD)

0

5

10

15

20

25

30

35

0 - 25 25 - 60 60 -100

Depth (cm)

t ha

-1

TOTAL C

0

50

100

150

200

250

300

0 - 25 25 - 60 60 -100Depth (cm)

MIC

RO

BE

, kg

/ ha

0

200

400

600

800

1000

1200

1400

RO

OT

, kg

/ ha

Fungal CBacterial CRoot C

BIOLOGICAL C

(Horwath , 1993, adapted from Paul and Clark, 1996)

SOIL BIODIVERSITY

µm

cm

mm

MAMMALS

PROTOZOANEMATODES

INSECTSARACHNIDSMOLLUSCSWORMS

BACTERIAFUNGIALGAE

SOILBIOMASS

PLANT ROOTS

TENS OF THOUSANDS spp.

HUNDREDS

HUNDREDS

FEW

TENS

20 µm50 µm

10-100 µm

0.1 - 2 mm

2-20 mm

MAP OF Armillaria bulbosa in Michigan forest

CLONE A

CLONE B

N

100 m

CLONE A

CLONE B

N

100 m

CLONE A

CLONE B

N

100 m

CLONE A

CLONE B

N

100 m

BlueWhale

ARBUSCULAR MYCORRHIZAE

NEMATODE-TRAPPING FUNGI

Arthrobotrys anchonia

EXAMPLE OF SOIL FOOD WEB IN ARABLE SOIL

de Ruiter, Moore et al. 1993; Journal of Applied Ecology 30, 95-106

What can we measure?

•Size•Composition •Activity

Community Size andGross Activity

0

200

400

600

800

1000

1200

1400

0 50 100 150 200 250

Time (Years)

Mic

robi

al B

iom

ass-

C (µ

g/g)

BareVegetated

Change in BiomassChange in Biomass--C with timeC with time

(redrawn from Insam and Domsch, 1989)

Microbial Community Size and Activity

Scatterplot (Spreadsheet2 in Tom Hill data 3v*12c)

Dune 5 yr

Dune 17 yrDune 30 yr

Dune 50 yrDune 80 yr

Dune 100 yr

56 104 177 239 277

Biomass-C

-50

0

50

100

150

200

250

300

350

400

450

500

DH

A

Adapted from Hill, 1995

1000 metres

Location of Sutton Courtenay landfill site.

0

200

400

600

800

1000

1200

R4 R13G R20G R35 CON

Field

Mic

rob

ial

Bio

mas

s,

g.g

dry

so

il

Microbial Biomass results from each sample area. The bars show standard error (n=3).

50 100 150 200 250 300 350 400 450 500 550

ATP

0

100

200

300

400

500

600

>2m

m a

gg s

tab

(g/k

g)11 Years

6 years

5 years6 years

Compacted

6 yearswaterlogged

CHARACTERISING BIODIVERSITY

GENOTYPIC

• fundamental information – the blueprint

FUNCTIONAL• processes – the working engine

PHENOTYPIC• expressed information – the parts

CHARACTERISING BIODIVERSITY

GENOTYPIC

• fundamental information – the blueprint

Environmental Sample

Purification

Polymerase chain reaction

Diversity measures :SequencingDGGE, TGGE, ARDRA-RFLP,G+C contents,Disassociation-reassociation curves

Enumeration:Real time PCR,Probes, G+C contents

Activities:Real time PCR-mRNA

ExtractionActivities:Microscopy•Reporter genes•STARFISH

Enumeration:Probes

BROAD-SCALE GENETIC ANALYSIS

• %G+C profiling of soil community DNA in UK upland grasslands

-5

-4

-3

-2

-1

0

1

2

3

4

5

-6 -4 -2 0 2 4 6 8

CV1

CV

2

Unimproved

Semi-improved

Improved

-5

-4

-3

-2

-1

0

1

2

3

4

5

-6 -4 -2 0 2 4 6 8

CV1

CV

2

Unimproved

Semi-improved

Improved

Unimproved

Semi-improved

Improved

CHARACTERISING BIODIVERSITY

PHENOTYPIC• expressed information – the parts

Microbe

Cell MembraneCell Membrane

PHOSPHOLIPID FATTY ACIDS

PLFA Profile from a mixed woodlandPLFA Profile from a mixed woodland

PLFA profiles: Microbial groupsPLFA profiles: Microbial groups

PLFA PHENOTYPIC PROFILING

• Appropriateness in context of biodiversity ?• relationship to taxonomy is rather loose• relationship to environmental context is

apparently quite high• are number of PLFA’s a measure of ‘diversity’

0.0

0.2

0.4

0.6

0.8

1.0

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

0.0

0.2

0.4

0.6

0.8

1.0

1.2

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30

Community 1

Community 2

Pro

port

ion

Abbots Hall Farm EssexAbbots Hall Farm Essex

SSOO

FF

FrFrYY

-5

-4

-3

-2

-1

0

1

2

3

-7 -5 -3 -1 1 3 5

SaltmarshFarmlandFarmland (former marsh)Restored Marsh (1995 flood)Restored Marsh (2002)

SaltmarshSaltmarsh

FarmlandFarmland

Reclaimed Farmland (300yr)Reclaimed Farmland (300yr)

20022002 RestorationRestoration

1995 Restoration1995 Restoration

CHARACTERISING BIODIVERSITY

FUNCTIONAL

• processes – the working engine

FUNCTIONAL PROFILING

• High-throughput systems:• enzyme profiling

• fluorimetric systems (umbelliferones, MUF)

• substrate utilisation profiling

Carbon is the currency of the soil economy

Multiple Substrate Induced Respiration

96-channel respirometers:

RABIT MicroRespTM

MSIR OUTPUT: RATE CURVES

CTA

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

MNL

0

20

40

60

80

100

0 5 10 1 5 20

ERY

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

GLT

0

20

40

60

80

100

0 5 10 1 5 20

PHN

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

QNA

0

20

40

60

80

100

0 5 10 1 5 20

URE

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

MGL

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

BSA

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

CLB

0

20

40

60

80

100

0 5 10 15 20

CDX

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

GLC

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 2 0

MLA

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

MNS

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

GLA

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

GLY

0

20

40

60

80

100

0 5 10 15 20

ARG

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

A SC

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 2 0

A SP

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

GLM

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

HST

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

LY S

0

20

40

60

80

100

0 5 10 15 20

SER

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

MAL

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 2 0

PNT

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

STC

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

SNC

0

2 0

4 0

6 0

8 0

10 0

0 5 10 15 20

TWN

0

20

40

60

80

100

0 5 10 15 20

WA T XYL

0

2 0

4 0

6 0

8 0

10 0

0 2 4 6 8 10 12 14 16 18

KBA

0

2 0

4 0

6 0

8 0

10 0

0 2 4 6 8 10 12 14 16 18

KGA

0

20

40

60

80

100

0 2 4 6 8 10 12 14 16 18

Subtract respiration from water controls

FUNCTIONAL PROFILING:FUNCTIONAL PROFILING:Multiple substrate SIRMultiple substrate SIR

� Effect of agricultural management regimes

So

urc

e: D

ege

ns &

Ha

rris

19

97: S

oil

Bio

lBio

chem

29

:13

09

-132

0

-1

-0.9

-0.8

-0.7

-0.6

-0.5

-0.4

-0.3

-0.2

-1.2 -1 -0.8 -0.6 -0.4 -0.2 0 0.2 0.4

PC1

PC

2

Continuous pastureArable2y pasture leyReseeded pasture

MONITORING: TRAINING LOADS

• BIOLOGICAL STATUS OF SOILS• microbes provide sensitive indicator• Approach pioneered in USA

EFFECT OF MILITARY TRAFFICKING UPON SOIL MICROBIAL BIOMASS

0

5

10

15

20

25

30

35

40

45

Reference Light Moderate Heavy Remediated

PLF

A p

mol

g-1

So

urc

e: P

ea

cock

et a

l. (2

001

) E

colo

gic

al In

dic

ato

rs 1

:11

3-1

21

TRAINING LOAD

BIO

MA

SS

EFFECT OF MILITARY TRAFFICKING UPON SOIL MICROBIAL BIOMASS

0

5

10

15

20

25

30

35

40

45

Reference Light Moderate Heavy Remediated

PLF

A p

mol

g-1

So

urc

e: P

ea

cock

et a

l. (2

001

) E

colo

gic

al In

dic

ato

rs 1

:11

3-1

21

TRAINING LOAD

BIO

MA

SS

Salisbury Plain Training Area

BACKGROUND

• Covering approx. 14,000 ha, ATE SP has by far the largest extent of chalk grassland in the UK, and indeed, in north-west Europe

• Chalk grassland is one of the most ecologically diverse wildlife habitats to be found in Britain

• Site of Special Scientific Interest (SSSI) and Special Protection Area (SPA) for birds

• Historical and current land-use of SPTA have resulted in landscapes and wildlife almost unique in the UK

EFFECT OF DISTURBANCE UPON SOIL COMMUNITIES

• Cranfield University Development Project• Case study @ Salisbury Plain

• SOILS SAMPLED FROM FIVE CATEGORIES [March 04]

Arable field (cereal)X

SevereE

HeavyD

MediumC

LightB

NoneA

DISTURBANCE CATEGORYCODE

PROPERTIES MEASURED

• How much is life is there ?• microbial biomass

• Who is there ?• community structure

• Soil chemical properties

SAMPLING LOCATIONS

E D C

BA

X

A

B

C

E

D

MICROBIAL BIOMASS

DISTURBANCE CATEGORY

µg

C g

dry

soi

l-1

0

250

500

750

1000

A B C D E X

ANALYSIS OF MULTI-VARIATE DATA

• Principal component analysis• reduces large data sets to a few numbers

(Principal Components, PCs) that essentially capture the same information as is contained within the full data set

• quantify the extent to which the PCs ‘represent’the entire data set

• identify which of the properties are most responsible for discriminating between samples

E

D

C

B

A

-3

-2

-1

0

1

2

3

4

5

-6 -4 -2 0 2 4 6

PC1 (55%)

PC

2 (1

7%)

PRINCIPAL COMPONENT ANALYSIS

X

A

B

X

D

E

C

PLOT OF FIRST THREE PRINCIPAL COMPONENTS

Discrimination mainly due to one

PLFA

A

B

X

D

E

C

PLOT OF FIRST THREE PRINCIPAL COMPONENTS

Discrimination mainly due to one

PLFA

FUNGAL:BACTERIAL RATIO

DISTURBANCE CATEGORY

0.00

0.02

0.04

0.06

0.08

0.10

0.12

0.14

A B C D E X

“STRESS” RATIO

DISTURBANCE CATEGORY

0.4

0.6

0.8

A B C D E X

SALISBURY PLAIN CASE STUDY

• Training load influences microbial biomass in a consistent manner

• greater disturbance � smaller biomass

• Microbial community structure shows distinct trajectory in relation to training load

• relatively few PLFAs lead to discrimination

• Sample site C – why different ?

DECISION TREE ANALYSIS

• Formulate model using decision tree

• Which are key drivers that discriminate between samples ?

• Showed significance of

• microbial biomass

• certain key PLFA compounds

• Predict to 93% accuracy to which disturbance level a soil sample corresponds

Putting it all together

3D Scatterplot (Spreadsheet1 in Workbook3 4v*12c)

Floodmeadow 1

Restored Grass 5 yr

Floodmeadow 2

Restored Woodland 1

Rough Grassland

Restored Grass 10 yr

Restored Woodland 2

Breckland

Woodland 1

Chalk Grassland

Woodland 2Woodland 3

3D Scatterplot (Spreadsheet1 in Workbook3 4v*12c)

Floodmeadow 1

Restored Grass 5 yr

Floodmeadow 2

Restored Woodland 1

Rough Grassland

Restored Grass 10 yr

Restored Woodland 2

Breckland

Woodland 1

Chalk Grassland

Woodland 2Woodland 3

3D Scatterplot (Spreadsheet1 in Workbook3 4v*12c)

Floodmeadow 1

Restored Grass 5 yr

Floodmeadow 2

Restored Woodland 1

Rough Grassland

Restored Grass 10 yr

Restored Woodland 2

Breckland

Woodland 1

Chalk Grassland

Woodland 2Woodland 3

SOIL MICROBIAL PROPERTIES AS ECOLOGICAL INDICATORSSOIL MICROBIAL PROPERTIES AS ECOLOGICAL INDICATORS

TOTAL TOTAL BIOMASSBIOMASS

Community Community compositioncomposition

GROSS ACTIVITYGROSS ACTIVITY

Late Grass

Mid Grass

5 Year Restored

Early Grass

Scrub

Stored Soil

Pioneer

Forest

Bare

COMMUNITY TRAJECTORIESCOMMUNITY TRAJECTORIES……

TOTAL TOTAL BIOMASSBIOMASS

GROSS ACTIVITYGROSS ACTIVITY

Late Grass

Mid Grass

5 Year Restored

Early Grass

Scrub

Stored Soil

Pioneer

Forest

Bare

Community Community compositioncomposition

CONCLUSIONS: BIOLOGICAL STATUS OF SOILS

• Microbes provide sensitive indicator of ecological status / ecosystem health

• assessment of degree of disturbance• assessment of current status in relation to

management of degraded and restored ecosystems

• quantify where the system ‘is’ and where it is ‘going’

• Restoration context• assess potential for restoration and status of such

management (target setting)

Facilitators or Followers?

• Facilitation by modifying soil conditions• Facilitation by symbionts• Inhibition by symbionts• Facilitation by pathogens and herbivores

• Inhibition by pathogens and herbivores• Maintenance of stability in late-successional

assemblages

Principal research gaps

• How much genotypic and functional diversity is required to facilitate plant community function?

• What community players, other than symbionts, are essential for facilitation or inhibition?

• Do shifts from bacterial to fungal dominated communities result in ecosystem stability?

• A large scale survey of restoration and reference sites

• What are the feedbacks between the soil biological community and soil structural formation and stability?

Nine attributes of a restored ecosystem

1. Reference ecosystem, characteristic assemblages

2. Indigenous species, some exceptions 3. Functional groups present or available

4. Physical environment appropriate

5. Ecosystem functions normally for successional stage6. Landscape integration, biotic and abiotic interactions

7. Potential threats eliminated8. Resilience and integrity

9. Self-sustaining

Nine attributes of a restored ecosystem

1. Reference ecosystem, characteristic assemblages

2. Indigenous species, some exceptions 3. Functional groups present or available

4. Physical environment appropriate

5. Ecosystem functions normally for successional stage6. Landscape integration, biotic and abiotic interactions

7. Potential threats eliminated8. Resilience and integrity

9. Self-sustaining

Conclusions

• The soil biological community is a a key component of the soil ecosystem, crucial in supplying ecosystem goods and services

• Understanding it is critical to provide successful outcomes in restoration programmes

• It may be use to indicate objectively the progress, or lack of it, in such programmes