Effect of climate change and management
on plant-associated microbial communities
Gabriele Berg
Environmental Biotechnology
INTRODUCTION: Impact of climate change
Bogs
Impact on global cycles
• carbon cycle
• nitrogen cycle
1
Introduction: Plant
Plant--microbe interaction
Disease
Soil-borne
pathogens
Plant
Induced resistance
Root exudation
Biocontrol
Plants form a unique
habitat in terrestrial
ecosystem.
Plant growth
promotion
Hormomal
stimulation
Competition
Manyfold interactions/interplays take place.
Change of composition
The balance of structure and functions is important
for plant growth and health.
Plant-associated
microorganisms
2
INTRODUCTION: Impact of climate change
Multiple Interactions
Host
Pathogen
Temperature (warming)
Moisture (Heavy rains
Storms)
Drought
Elevated CO2
Changing conditions
Climate
change
Vectors
INTRODUCTION: Impact
Up to 422,000 species
Pittmann & Jørgensen Science 2002
Plant species
Animals
Grazers
Human activities
Pathogens
Plant-associated
communities
Geography
Treatments
Climate
Annual
[Smalla et al. AEM 2001]
[Berg et al. AEM 2002]
[Berg et al. AEM 2005]
[Opelt et al. The ISME J. 2007]
Soil quality
cycle
3
INTRODUCTION: Impact of climate change
Impact on plant pathogens
Temperature:
bigger areal, higher aggressiveness/virulence
More HGT, new pathogens
Changing conditions:
More niches: Multi-species infections
More host plants
Storms:
Better distribution
INTRODUCTION: Impact of climate change
Impact on soil
Salinisation
Drought
Impact on plant beneficial bacteria
Better performance
-> rev. by Compant et al. 2010 FEMS
4
I. Impact on plant
pathogens and biocontrol?
1. Example: Soil
Soil--borne pathogens: Verticillium dahliae
Verticillium dahliae
Serratia plymuthica
HRO C48
Strawberry, rape
olives
5
INTRODUCTION: Target pathogens
Yield losses caused by soil-borne pathogens worldwide: 4 billion $
1st target pathogen:
Verticillium dahliae Kleb.
cause Verticillium wilt on a broad host range
Methyl bromide was used – banned
HIGH RISK PATHOGEN
No possibility to suppress the pathogen
Model--organism: Serratia plymuthica HRO
Model
HRO--C48 (RhizoStar)
RHIZOSTAR® Serratia plymuthica
HRO-C48
• Isolated from the rhizosphere of rape
• European Patent 98124694.5
• No risk for human health and environment
(risk group 1)
Solution:
Biocontrol by naturally
occurring bacteria
Serratia
Adaptation to new host plants
Rape and Olives
6
Model--organism: Serratia plymuthica HRO
Model
HRO--C48 (RhizoStar)
Influence of Quorum Sensing (QS) on the interaction
of S. plymuthica on the interaction with eucaryotes
Plants
Serratia plymuthica HRO-C48
Rhizosphere
competence
QS
QS
Biofilms
IAA production
QS
QS
QS
Fungi
Proteases
Chitinases
Pyrrolnitrin
[Müller et al. FEMS Microb. Ecol. 2009]
7
Model--organism: Serratia plymuthica HRO
Model
HRO--C48 (RhizoStar)
VOC´s
200 l of Serratia
plymuthica HROC48 Suspension
Control
Serratia
Examples for VOCs produced by Serratia plymuthica:
2-Heptanon, Di-Methylpyrazin, 2-Nonanon, 2phenylethanol, Benzylnitril, Undecanon
Impact on rhizosphere communities: microbial fingerprints
5 weeks
10 weeks
15 weeks
Bacterial
communities:
Strawberry
+
Potato
rhizosphere
only short-term changes in the composition of
bacterial and fungal communities
8
Impact on rhizosphere communities: microbial fingerprints
5.0
4.0
3.0
-1
log10 CFU g root fresh weight
6.0
2.0
1.0
0.0
Non-infested soil
V. longisporum-infested soil
Bacterial
communities:
Soil treatment
Non-inoculated
V.l.
Ctrl.
Serratia plymuthica-inoculated
V.l.
Ctrl.
V.l.
Ctrl.
V.l.
Ctrl.
Oilseed rape
Presence of the pathogen enhance the abundance of
the antagonist
S. plymuthica HROC48
Impact on rhizosphere communities: microbial fingerprints
Similarity of microbial communities
Climate change?
community
field site
growth stage
treatment
bacteria
60
66-75
78-100
pseudomonads
62
70-78
82-100
fungi
59
70-72
69-79
Compared to the growth stage and the field site, the
treatments showed only negligible, short-term effects
the composition of microbial communities
[Scherwinski et al. Biocontrol 2005; FEMS Microb. Ecol. 2009]
9
2. Example: Soil
Soil--borne pathogens: Rhizoctonia solani
Rhizoctonia solani
Serratia plymuthica
Pseudomonas trivialis
Trichoderma gamsii
Sugar beet
BIOTECHNOLOGY: Biocontrol of Rhizoctonia solani
*
* Formulation into the pill of the
sugar beet seed
Colonization of the rhizosphere
Protection against Rhizoctonia solani
10
BIOTECHNOLOGY: Biocontrol of Rhizoctonia solani
[Zachow et al. FEMS Microb. Ecol. 2010]
BIOTECHNOLOGY: Biocontrol of Rhizoctonia solani
11
Serratia plymuthica and Trichoderma gamsii
in the sugar beet rhizosphere
BIOTECHNOLOGY: Biocontrol of Rhizoctonia solani
Parcel field trial Tabertshausen-Kasten (TAK) 2009
120
RI in relation to Std
BERETTA
n beets in relation to Std
BERETTA
100
80
60
40
20
0
A cocktail of antagonistic microorganisms is much
more effective than a treatment using single BCA.
12
Impact on rhizosphere communities: microbial fingerprints
Endophytic
communities:
Lettuce
rhizosphere
Compared to the sampling time and site effects, the
treatments showed only negligible, short-term effects
the composition of microbial communities
[Grosch et al. Mycol Res 2006]
3. Example: Multi
Multi--species infections
?
?
Oil seed pumpkin
13
Biocontrol of pumpkin diseases
High yield losses of the Styrian oilseed pumpkin
caused by :
Climate (Temperature, Moisture ) and thunder storms – hail
a complex of pathogens:
Didymella bryoniae Fuckel, (1870) (anamorph : Phoma
cucurbitacearum)
Biocontrol of pumpkin diseases
High yield losses of the Styrian oilseed pumpkin
•Erwinia carotovora
cucurbitae
Pseudomonas spp.
Xanthomonas
14
Biocontrol of pumpkin diseases
Isolation and identification of D. bryoniae strains from
different fields used for infection studies
I. Characterization of isolates
Isolation from
infected pumpkins
Morphological
characterization
Sequenz
analysis/identification
II. Establishment of a pathosystem
14 days old plant
D. bryoniae on QPDA
plate
Conidia suspension
injected
in the leaf stalk
were
Biocontrol of pumpkin diseases
Interaction between D. bryoniae and bacterial pathogens
Bacteria use the fungal hyphae as highway
15
Biocontrol of pumpkin diseases
Development of a biocontrol strategy
Isolation of pumpkin
pumpkin--associated
microorganisms (bacteria and fungi)
In vitro screening for their antagonistic
potential against D. bryoniae and bacteria
Ad planta experiments with BCA strains
Effective antagonists - biological product and
evaluation under field conditions
Biocontrol of pumpkin diseases
Development of a biocontrol strategy
Gleisdorfer Gleisdorfer Gleisdorfer
Ölkürbis
Diamant
Maximal
roots
9x104
2.2x104
6.5x104
blossoms
1.1x107
1.2x107
1.6x107
pulps of fruits
2.0x104
9.6x103
3.1x104
Altogether, 2.321 isolates
43 with a broad-spectrum antagonistic potential
6 were chosen for further experiments
Greenhouse and field trials
16
Biocontrol of pumpkin diseases
Development of a biocontrol strategy
Greenhouse
experiments
+ and – infection
Field experiments
Gleisdorf: - infection
Stadl-Paura: + and - infection
II. New pathogens from the
rhizosphere?
17
Biosafety: Pathogens from the rhizosphere?
Facultatively human pathogenic bacteria
• USA: 85.000 patients die per year
• EU: infection rate on intensive care units: 46%
• Germany: 1 Million nosocomial infections per year
• Bacillus spp.
• Burkholderia cepacia
• Pseudomonas aeruginosa
• Serratia marcescens
• Staphylococcus spp.
• Stenotrophomonas maltophilia
Stenotrophomonas – a pathogen from the root?
Ecosystem functioning: Stenotrophomonas plays an
important ecological role in the nitrogen and sulphur cycle
Pathogen defence: biological control of several soil-borne
plant pathogens
Plant growth promotion: strawberries, Brassicaceae
Plant stress protection: salinated conditions
Bio- & phytoremediation: xenobiotics, RDX, cocaine...
18
Stenotrophomonas – a pathogen from the root?
control
S. rhizophila
DSM14405T
Stenotrophomonas – a pathogen from the root?
S. maltophilia is also an emerging human pathogen
S. maltophilia has been associated with bacteremia and
pneumonia infections of immunocompromised patients,
these infections have a very high rate of mortality
Is it possible to differentiate between clinical
and environmental strains?
19
Stenotrophomonas – a pathogen from the root?
I. Differentiation between S. maltophilia – S. rhizophila
ARDRA: Restriction of the 16S rRNA gene using Pst I
S. rhizophila
DSM
14405
S. maltophilia
DSM
50170
II. Differentiation between S. maltophilia – S. rhizophila
Key enzyme of osmolyt synthesis (Glucosylglycerol = GG)
Only S. rhizophila isolates produce GG
II. What turn Stenotrophomonas strains into
Multidrug
efflux pumppathogens?
opportunistic
Only S. maltophilia isolates have the efflux pump
[Ribbeck-Busch et al, Environ Microb 2005]
Biosafety: Pathogens from the rhizosphere?
Plant
Humans
Adherence
Antibiosis/Toxicity
Resistance against antibiotics
Biofilm formation
and minerals (siderophores)
Production of hydrolytic enzymes
Fitness
rhizobacteria
Competition for nutrients
Osmotolerance
Versatility
Facultative pathogens
Pathogenicity
Recognition
Induced resistance in plants
Production of phytohormons Growth at 37°C
[Berg et al. Environ Microb 2005]
20
Stenotrophomonas – a pathogen from the root?
Endophytic colonisation of S. maltophilia
Three-dimensional reconstruction of a CLSM-stack based on isosurfaces and dots showing
Stenotrophomonas cells colonizing a new coming root hair of tomato (red: bacteria; beige:
tomato root). Panel a shows the full dataset, panel b and c show a 3D-crop along the X-axes
(orthogonal cut) and the Z-axes (oblique cut), respectively
Stenotrophomonas – a pathogen from the root?
Mutation frequencies
Low mutation frequencies were particularly frequent among
environmental S. maltophilia strains (58.3%), whereas
hypermutators were only found among clinical isolates.
[Turrientes et al. AEM 2010]
CONCLUSIONS
S. rhizophila is a promising Biological control and Stress
protecting agent.
S. maltophilia should be excluded from direct
biotechnological applications.
These results indicate that clinical environments might
select bacterial populations with high mutation frequencies.
21
CONCLUSIONS, COOPERATIONS AND THANKS
Prof. Dr. Kornelia Smalla (BBA Braunschweig)
Dr. Arne Peters
Prof. Dr. Leo Eberl (Uni Zürich)
E-nema GmbH
Prof. Rafael Imenez Diaz (Uni Cordoba)
Robert Dahl
Dr. Rita Grosch (IGZ Großbeeren)
Erdbeerhof Rövershagen
Prof. Leda Mendoça-Hagler (Uni Rio de Janeiro)
Dr. Ralf Tilcher
Prof.Plants
Ben Lugtenberg
(Uni
Leiden) habitat in terrestrial ecosystem.
form a
unique
KWS Saat AG
Dr. Dilfuza Egamberdiyeva (Uni Taschkent)
Dr.
Wolfgang
Vogt
take
place.
Prof.Manyfold
Martin Grubeinteractions/interplays
(Uni Graz)
Sourcon-Padena AG
Prof. Erich Leitner (TU Graz)
The balance of structure and functions is important
for plant growth and health. This balance will be
influenced by climate change.
Plant-associated microorganisms are an important
factor influencing the response of plants to climate
change.
22