Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
Biological Soil Mapping
BioSoM
Programme plan 2009-2012
1
Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
Overall program objectives
The aim is to provide a scientific background and to design the operations for a mapping
routine of soil-borne pathogens useful to optimize crop rotation under Swedish condition. The
objectives are:
 Development and validation of PCR-based detection methods for soil-borne
pathogens
 Development of samplings methods and routines for presentation of infestation,
distribution and correlation with soil characteristics
 Increased knowledge about pathogen biology, forecast of effects of pathogens and
effect of plant management on pathogens
 Initiate implementation of integrated soil mapping of pathogens in collaboration
with stakeholder
Background
BioSoM (Biological Soil Mapping) is a thematic research program, aiming to give scientific
support towards a new service to farmers detecting soil borne pathogens and advising in crop
management to optimize production in Sweden.
Soil-borne pathogens use the soil to survive until next possibility to act as a pathogen. Today,
the practical uses of analysis of presence of soil borne pathogens are restricted to some bioassay testing for a few pathogens. Many of them have some sort of resting spores such as
sclerotia or chlamdyspores, or are spread with mycelium, infect the roots and continue to
grow inside the plant, which makes it difficult to observe colonization. The life-time of
resting spores is often long 10-20 years and the time of survival depending on soil conditions,
crop rotation etc. The possible long duration makes it profitable and relevant to develop
mapping of present infestations status for many soil-borne pathogens. In Sweden we have
considerable problems with pathogens such as club-rot and Verticillium wilt in Brassica crops
and rot root in pea and with different rots in clover.
In the future agriculture with high expectations of increasing yields with a good quality
(www.fao.org) and a changing climate, the level of infestation of pathogens must be
effectively monitored to employ adequate crop management routines. New technologies used
in Precision Agriculture such as Global Positions System (GPS) and Geographic Information
Systems (GIS) makes it possible to keep track of and present infestations levels in a
pedagogic way. New detections methods based on DNA–technologies makes it possible to
specific estimate infestations levels of many organism in soil and the rapidly growing
possibilities to map the genome of organism and to connect to functions in pathogen and plant
opens for new ways of control of /manipulations/management of crop and soil to reduce
effects of pathogens.
The aim of this research program is to establish the scientific foundation for a in practice
useful biological soil mapping of soil-borne pathogens (BioSoM) to be used by farmers to
optimize crop production. This should be done by:
- developing and validate DNA-base PCR-methods for specific and quantitative
detection of soil-borne pathogens in Swedish soils.
- The development and validation of standard operation procedures (SOP) for field
sampling and handling as well as for detection presentation and implementation of
results of detection of infections.
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
-
-
enhancing the understanding of correlation between level of infections level and soil
characteristics such as pH-value as clay content as well as macro- and micro nutrients
increasing the knowledge of the biology of sclerotia using genomics to better
understand formation, survival and infection during different soil and field conditions.
monitoring changes in soil pathogen populations caused by crop management such as
choice of crop or cultivar or different fertilization strategies or different soil
treatment (e.g. non-tilling practice)
development and validation of SOP for presentation of soil borne pathogens using
Geographic Information Systems (GIS) to present presence or predicted damage of a
pathogen for use in practice by advisers and farmers.
The program is funded by the Faculty of Natural resources and Agricultural Sciences, SLU
(50 % of the funding), the Swedish farmers Research Foundation (SLF) and the SSO, VL and
SL research foundations, the companies Eurofins Food Agro AB, HS Konsult AB, Findus
R&D, SW and Scanbi Diagnostics AB
.
The BioSoM research team is composed of researcher from agronomy, plant breeding, plant
pathology, molecular microbiology/biology and bio/chemistry working within six major work
pages (WP):
1) Sampling and detection of soil borne pathogens
2) Forecast - based on bio-assay and field trials
3) Pathogen biology – resting structures and applied genomics
4) Soil characteristics and infestation of pathogens
5) Implementation and use in R&D and practice
Programme structure
Research within BioSoM is organized as three types of activities:
I)
Development of detection methods using molecular methods
II)
Scientific in-depth studies of pathogen biology, effect of dose of pathogen and
interactions with soil parameters
III)
Development and use of preliminary SOP for soil mapping in on-going R&Dprojects and the establishment of a “de facto” standard
Programme management
A Steering Committee is appointed to ensure that the Program is carried out in accordance
with the intentions in the Program Plan and the policy guidelines for NL-faculty thematic
program. The NL-faculty and each external contributor are entitled to appoint one Committee
member each. The faculty will also provide the secretary for the meetings. The membership in
the steering committee includes the right to leave the committee or substitute the appointed
member. The Steering Committee meets regularly, at present four meeting per year are
scheduled. The Steering Committee has appointed a Program Director Dr. Anders Jonsson,
responsible for directing work within the Program. The Program Director has appointed a
Program Management Group, responsible for assisting in managing the program. This group
consists of key researchers within BioSoM, presently it includes Prof. Christina Dixelius and
Dr. A-C Wallenhammar, all are in association with Dr. Fredrik Heyman and Assoc. Prof.
Niclas Gyllenstrand.
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
External financing and in kind from stakeholders
The external financing from stakeholders have been handled through a number of agreements
as specified below.
Contributor/ Stakeholder
NL-SLU,
Contribution
Financing
Type
Agreement
Date
2009-05
SLF-Fältförsök & Metodik
- Växtodling
- Växtodling FH
Financing
Financing
Financing
Contract
Contract
Contract
2009-03
2008-12
2008-12
VL-Stiftelsen
SL-Stiftelsen
SSO
Financing
Financing
Financing
Contract
Contract
Contract
2009-03
2007-11
2008-12
Eurofins Food & Agro
Scanbi Diagnostic AB
Findus R&D
HS Konsult AB
SW
In kind
In kind
In kind
In kind
In kind
Agreement
Agreement
Agreement
Agreement
Agreement
2009-04
2009-04
2009-05
2009-04
2009-09
Potential intellectual properties rights (IPR) issues in the program will be handled based on
Swedish law, a “first right of refusal” for the stakeholders and for granted patents a licensefee based on commercial value. SLU Holding may become a partner for IPR management. All
results from the programme work will be published eventually maximal delayed three months
for a patent application.
Communication plan
BioSoM maintains a close direct communication with program stakeholders representing
broad areas of the Swedish agricultural sector. The programme also aims for an efficient
communication through standard scientific procedures, e.g. conference presentations and
peer-reviewed journal publications, as well as more general national presentations and a
home-page targeting a broader audience (http://www.biosom.slu.se).
Communication activities - resources and deliverables 2010-2012
1. External communication
Deliverables
Year:Q
 Web-page maintenance
 Hits
10:1
 Lecture and poster preparations, incl. presentations
 International
Presentations (10)
10:2 / 12:2
▪ Approved plan
09:4
▪ Publications (6)
10:2 – 12:2
▪ Minutes
09:4 – 12:2
▪ Press reports
10:2
 Program plan for 2009 -2012
 Writing of publications
 Meetings with stakeholders
 Interviews and popular science
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
2. Internal communication
Deliverables
Year:Q
▪ Monthly programme meetings
Minutes
09:4-12:2
▪ Internal seminars
Hand-outs
09:4 – 12:2
▪ Preparation of presentations for Steering Comm.
Reports
09:4 -12:
BioSoM programme deliverables
The programme as such, has a number of overall deliverables, some in common with the
individual project areas, WP 1-6.
Programme Level – Work-packages, tasks, and deliverables
1. Staffing, management and infra structure
Deliverables
▪
Formation of key scientist team
Report to SC
Year:Q
09:3
▪
Program management group formed
Report to SC
09:3
▪
Recruitment of lab tech./
Hiring
9:3
▪
Recruitment of post-docs
First working day
10:1
▪
Recruitment of PhD students
Official SLU registration
10:1
2. Communication
Deliverables
▪
BioSoM homepage
First external log-in
▪
▪
General program poster – public communication
General program poster – scientific communication
First presentation
First presentation
09:4
09:4
▪
▪
Press releases and newspaper interviews
Oral presentations for stakeholders
(politicians, farmers, industrialists etc)
Newspaper articles (5)
Presentations (10)
09:209:3-
▪
Scientific presentations at international symposia
10:4 -
▪
Scientific publications
Oral presentations (5)
Posters (5)
Scientific publications (4-6)
Year:Q
09:4
12:4
1
3. Education
Deliverables
*
▪
▪
MSc theses (4)
PhD theses (1)
Course 2 days
Year:Q
10:4 13:3
12:2
4. Innovation and development
Deliverables
Year:Q
▪
Analysis of soil-borne pathogen
Commercial available analysis- first
▪
SOP for Biological soil mapping
Service to farmers
- 3 pathogens
- >6 pathogens
MSc projects
PhD projects
Biological soil mapping for advisers / researchers
10:1
11:2
12:3
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
Project workpage WP 1-5
WP 1. Sampling and detection
Project team
Charlotta Almquist (PhD-student)
Åsa Fransson (Lab. tech)
Mattias Myråsen (Lab tech )
Anna Nyberg
Fredrik Heyman
Anders Jonsson
2009/10
5 mFTE
4 mFTE
1 mFTE
2 mFTE
3 mFTE
2 mFTE
1
Resource
Resources available to WP 1 in month FTE (FTE= Full Time Equivalent):
09/10 (17 mFTE), 10/11 (15 mFTE) ; 11/12(15 mFTE
Objective
Develop a sampling and a detection protocol for soil borne pathogens; a protocol suitable for
use in practice for sampling in connection with ordinary chemical soil mapping. Investigate
the possibilities to use multiplex qPCR methods.
Specific goals.
SOP (Standard Operations Procedure) for: sampling soil in the field, handling and preparation
of soil extraction of DNA from soil, detection and quantification of soil-borne pathogens
given priority in the program (Figure 1).
TEMA-Program: Pathogen and activities & new knowledge
Pathogen
Biologica
l
¨Basic
Science”
DNA
Detection
Bio
Assay
Field Trials
Validation
P. brassicae
Club root





V. longisporum
Verticillium wilt





S. sclerotiorum
Sclerotina stem rot





Phytophthora sp.
New rot i Pea





A. euteiches
Rot root of Pea










 




G. graminis
Take all
F. avenaceum
P . exigua
C. destructans
Clover root rot
BioSoM Map,
Farm Service
using GIS
 = Knowledge status  = knowledge blanks to fill in the project
Figure 1. Pathogens given priority in the BioSoM project and including some important pathogens (in yellow)
waiting for funding.
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
Project strategy and Scientfic approach and realization
The aim is to initially focus on the P. brassicae, V. longisporum and S. sclerortiorum
pathogens on Brassica crops, take all (Gaeumannomyces gramnis) in wheat and on pea A.
euteiches together with the new identified Phytophthora species (Figure1). Preliminary
knowledge is aviable for these organisms including specific PCR and real-time qPCR. (Zhou
et al. 2006; Heymans 2008, Almquist et al. 2009).
This part of the programme has its emphasis on optimizing soil sampling including number of
sub-samples to be included in the “main-sample”, how they are covering the field of interest,
handling of samples from different field to avoid contamination, appropriate storage, grinding
procedures and DNA extractions. This work may need a number of pilot studies in order to
optimize the routines. For example samples with sclerotia which are problematic to grind,
resulting in underestimated levels of DNA. Other troublesome factors may be various soil
components (clay, high humus levels etc). When the procedures are optimised, archive soil
samples from well-characterized fields will be analysed to generate valuable background data
but most importantly in order to generate hypothesis on cause and effect factors that could be
assessed in the next phase of the work.
Work-packages, tasks, resources and deliverables
1. Soil sampling and handling (2009/10)
▪
Preliminary instructions for soil sampling
▪
▪
Testing of sample density using geostatistics (GIS)
▪
▪
Testing of contamination in soil, milling and handling
Deliverables
Year:Q
Preliminary instructions for soil
sampling
09:3
Variograms for pathogen
10:1
(Scientfic article)
9:4
SOP sampling and handling
Alternative milling and sample reduction,
▪
▪
10:1
Soil and DNA-archive
10:2
SOP for enrichment of low frequent
pathogen
10:4
Routines for storage of soil samples
▪
▪
Methods for reduction of sample
size
Enrichment of pathogen – flotation, centrifugation etc
2. Soil sample – DNA extraction and preparation (2009-10)
Deliverables
Year:Q
SOP for extraction
▪
Validation of general extraction routines
▪
Routines for storage of soil DNA–extracts
▪
Development of soil dependent cleaning etc
DNA-archive
First version
10:2
10:2
10:1
3. Detection of pathogen (2009-2012)
Deliverables
▪
PCR–routines for P. brassicae and A. euteiches
SOP for A.e and P .b.
▪
PCR-method for V. longisporum/dahliae
SOP for V. l/d
▪
PCR method for Guannomyces spp and Phytophthora sp
SOP / report /
▪
PCR Sclerotina sclerotiorum
SOP
▪
Development for more cost effective SOP, ie duplex, array
SOP and publications
Year:Q
09:3
10:1
10:2
10:1
10:4
7
Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
▪
Refinement of SOP for soil analysis of soilborne pathogens
Up-dated protocols
12:1
12:4
WP 2 Forecast - based on bio-assay and field trials
Project team
A-C Wallenhammar*
Mattias Myråsen/Lab techn
Post doc / Lab techn
2009/10
4 mFTE
4 mFTE
8 mFTE
Objective
The aim is to generate predictions and risk assessments based on the quantification of the
pathogens and chemical conditions in the field
Resources
Resources available to WP2: 09/10 (16 mFTE), 10/11 (16 mFTE) ; 11/12 (16 mFTE).
* To be decided by faculty
Specific goals
- Bio-assay for evaluation of potential damage of the different amounts of a pathogen
- Correlations between bio-assays and damage in field and field trials
- Patho-typing of pathogens starting with P. brassicae and V. longisporum
- Risks assessments in connection to predictions of future levels of pathogens
Project strategy
It is of importance to validate presence of pathogens, their imposed yield and quality
reduction. To do so dose-response data need to be generated that link such parameters
together and provide a basis for future prognosis and advice to farmers. Besides established
DNA quantifications, field assessment data and various biotest confirmations must be
performed and form foundations of reliable models.
Scientific approach and realisation
The research tools will be the bio-assays for P. brassicae (Wallenhammar 1999 and A. euteiches ( at
Findus R&D) and new development of bioassay methods for Verticillium rot and take-all. Alternative
methods to bioassay might also be considered (Wallenhammar, et al 2008). Initially the aim is to use
already established and accessible field trials to check presence of infestation and grading
and measurement of effect on crop and yield (www.ffe.slu.se) There is also possibilities to use so
called long-term field trials with documentation of crop rotation, yield and archived soil samples (
pers comm.. L. Mattsson, Department of Soil and Environment, SLU). Next step will be to establish
validation trials on field with known infestations levels and follow them during some years. To
identify suitable research sites field will be screened for pathogens. The DNA-extraction will be kept
in an archive and tested for other pathogens as new methods made available in WP1.
An important research field will be development of field trials with a minimal number of
repetitions and treatments to useful for evaluation of dose-response for pathogens and
validation of forecast. This work will done in close co-work with the statisticians at FFE,
SLU.
For the P. brassicae with a bioassay and an established risk assessment the scientific focus will be to
improve knowledge of patho-types in Sweden. A selection of cultivars of Brassica will adopted based
on earlier systems for patho-typing ( Some et al 1996, Buczacki etal 1975, Williams 1966 ) with the
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
addition of modern cultivars from the company Syngenta with a pathotype specific resistance to
clubroot. For A. euteiches also with a established bio-assay the R&D focus will be on risk assessment
at low levels of infestation and correlation with crop management.
Work packages WP 2 , tasks and deliverables
1. Clubroot
Deliverables
▪
Sampling in field and field trials 2009/10/11
Level of presence of pathogen
▪
Testing of patho-types
Pathotype distribution
▪
Quantification long-term trials
▪
Correlation between bioassay and field effect
Interactions with cropraotation and
infestation
Validation of prediction/prognosis
2.
Verticillium longisporum
Deliverables
▪
Sampling in field and field trials 2009/10/11
Level of presence of pathogen
Bio-assay
Dose-respons - potential
10:2
Quantification in long-term field- trial
Level of infestation and crop
rotation
Validation of forecast
10:4
▪
Field trials, different levels of infestation
3.
Aphnomyces euteiches
Deliverables
▪
Sampling in field and field trials 2009/10/11
Report and soil in archive
▪
Bio-aasay, low frequence testing at Findus
Report low frequency
4.
Phytophthora sp
Deliverables
▪
Sampling in field and field trials 2009/10/11
Level of presence of pathogen
▪
Development of bio-assay ?
potential dose -response
.
Screening of infestation in field
Level of site specific variation
Year:Q
9:4/10:4
10:4
12:4
Year:Q
9:4-
12:4-
Year:Q
9:4
10:2-
Year:Q
10:4
12:4
5. G graminis
Deliverables
▪
Sampling in field and field trials 2010/11
Level of presence of pathogen
10:4-
▪
Development of bio-aasay ?
Bio-assay established – potential dos
response
Validation of forecast
11:4
Field trials at different levels of infestation
Year:Q
12:4-
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
WP3 Pathogen biology – resting structures and applied genomics
Project team/ resources 2009/10
Christina Dixelius
Niclas Gyllenstrand
Mattias M (Lab tech)
8 FTE
Post-doc/researcher
4 FTE
Objective
Our main task is to increase knowledge about formation, survival and germinations of
sclerotia aiming for new ways of controlling sclerotia-forming pathogens using different types
of crops, improved resistance breeding and crop management.
Our second but more long-term aim is sequencing the genome of P. brassicae since genome
comparisons allows identification of races, gene clusters important for disease linked genes,
and effector genomics and defence allele mining are effective new tools to improve
breeding/cultivation practices.
Resources
Resources available to WP3: 09/10 (12 FTE), 10/11 (16 FTE) ; 11/12 (16 FTE).
Brief background
Verticillium wilt and stem rot cause significant crop losses particularly in Brassica oil seed
crops. Both S. sclerotiorum and Verticillium dahliae/longisporum are broad host range
pathogens, producing pigmented, multi-hyphal sclerotia that are capable of long-term survival
in soil. Verticillium and Sclerotinia have much in common as plant fungal pathogen but their
biology as organisms differs significantly (Hegedus & Rimmer 2005; Fradin & Thomma
2006; Bolton et al. 2006). Soilborne sclerotia-producing fungi are difficult to control since the
sclerotia are long-lived in soil, the germination induction is unclear and that the fungi infect
the roots and spread in the vascular tissue, making fungicide treatments and phenotypic
evaluations difficult in an early infection stage.
Specific goals
1) To identify metabolic pathways and genes involved taking part in sclerotia development.
This will initially be done by a comparative genomic approach.
2) Function of candidate genes will be assessed via gene knockout technology utilising the
homologous recombination capacity of the fungal species.
3) Since incitement of a plant disease is tightly linked to responses in the plant host such
signals will be looked for.
4. To generate molecular tools to monitor important pathogen-associated genes and plant
defence responses
5) To link our data with field observations generated under WP2
6) To generate data on the Plasmodiophora brassicae genome in order to generate
informative tools for pathological understanding, plant protection as well as for the breeding
side. This undertaking is a long-term goal in WP3 but has capacity to generate new and novel
data useful for future detection of club-rot races.
Project strategy
The strategy is to generate more applied data, new information and tools based on the
indicated work tasks i.e. integrating new genomic and bioinformatic tools that can be used in
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
near future integrative disease management strategies together with improved plant variety
assortment.
Scientific approach
There is now a wealth of fungal sequence data mainly due to enormous technical
advancement made on new sequencing technologies. More than 40 completed genomes are
public available and over 300 are in progress. This source provides a rich opportunity to
enhance our understanding of plant pathogens. Fungal genomes have generally a size of 30-40
Mb, comprising roughly 10,000 genes. Our initial approach to identify important metabolic
pathways and candidate genes are via applying new bioinformatic tools where different fungal
genomes can be compared. (Bioinformatics = conceptualizing biology in terms of molecules
and applying “informatics” techniques derived from statistics, computer science, mathematics
to organise and understand the information associated with these molecules on a large scale).
Here we can choose to compare sclerotia vs. non-sclerotia, plant vs. non-plant pathogens etc.
The aim here is to identify <100 genes of high importance. Instead of making advanced
metabolomic or transcriptomic analysis the approach initially is to focus on secreted proteins
and on plant mutations in known candidate genes from other patho-systems. The task at the
end will be to generate new molecular tools that can be used in various contexts but
importantly for BioSoM to link our data with prognosis and modelling developed in WP2.
Furthermore, very little sequence information is present today on the clubroot pathogen P.
brassicae making e.g. rapid race differentiation based on molecular markers instead of a set of
host plants difficult. On the other hand, the breeders need tools to facilitate their resistance
breeding work. The genome of P. brassicae is small 20 Mb (Siemens et al. 2009). Thus, we
would like to run genome sequencing utilizing the 454/Roche GS FLX Titanium sequencing
platform at the CMS node at KTH, which is well suited for de novo sequencing due to its read
length (400-500 bp. This information can then be used in different ways e.g. to identify P.
brassicae races via PCR detection as being done on the other soilborne pathogens in BioSoM,
genes important for host interactions and disease development can be revealed but the data
can also be turned into effector genomic related studies in order to identify new plant defence
alleles.
Work-package 3, tasks, resources and deliverables
1.
Sclerotia biology
Deliverables


Candidate genes identified
Gene function studies initiated
10:2
10:3




Sclerotia-related genes identified.
Confirmation of candidate genes.
Evaluation of sclerotia – germination/toxic substances
Linking genetic data to field observations
Preliminary gene list
Complementation
procedures
developed
Functional gene list
Fungal genes short-listed
List of important substances
Improvement of prognosis/models
12:03
Deliverables
Year:Q
2. Plasmodiophora brassicae genomics



The P. bassicae obligate system under “lab-control”
Spores from Swedish clubroot generated for sequencing
Genomic sequencing data generated
Comparative genomic data generated
Lab. protocol
Lab. protocol
Sequencing raw files
Comparative
genomic
files
available. Gene list available
Target
Year:Q
10:4/11:1
11:02/03
11:04
10:02
10:02
10:03/04
11:01
11:02/03
12
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
WP 4. Soil characteristics and infestation of pathogen
Project team / resources 2009/10
Anders Jonsson (PL)
3 FTE
Mattias M (lab. techn)
4 FTE
Postdoc ( Dr X 10:2)
4 FTE
Mats Söderström (EM 38) 1 FTE
Objective
Improve understanding of correlations between soil characteristics and presence, distribution
and pathogenicity of soil-borne pathogens.
Resources
Resources available to WP4: 09/10 (12 FTE), 10/11 (16 FTE) ; 11/12 (16 FTE).
Specific goals
- description of in-field correlations between pathogens and soil characteristics
- possibilities to use chemical characterizations, electromagnetic inductance ( EM 38)
and the Soil Mole ” as co-factors for improvement of description of presences and risk
assessments of pathogens ( WP 5)
- correlation between NPK fertilization and presence and development of important
pathogens e.g. P. brassicae
- Effect of micro-nutrients and fitness of pathogens in soil
Project strategy and background
The aim is to evaluate how characterization of soil can support and improve the mapping of
soil-borne pathogens and improve the prediction of effect of infestation. It is well known that
soil conditions such as soil-type, water and level mineral nutrients may affect the
development and effect of soil-borne pathogens. The result from field screening and test in
bioassays will also enable a better precision in the following measures and treatments of soils
to reduce infestations of soil borne pathogens using fertilization (Datnoff et al. 2007).
A strategy is to study effects of these changes in nutrient supply on some pathogens
To be able to better understand the spread of a pathogen and propose practical
countermeasures it is important not only to understand the effect of different crops and but
also how the fertilization might affect the pathogens ability to infect and increase. For
example Ca addition is reported to reduce effect of P. brassicae and many other pathogens
(Heyman 2008). K-fertilization reduced A. euteiches in pea but also reported to increase P
brassicae as well as addition of phosphate does. The form of N is reported to affects
pathogens e.g. P brassicae is increased by ammonia (Datnoff et al. 2007). During the last 1520 years the Swedish supply with mineral nutrients has changed. The use of CaNO3 has
decreased and been replaced with ammonium nitrate. The S-fertilization has been established
and the level of P-addition has been reduced in many crops. The supply of Mn has change
from a Mn-sulfate to a Mn-chelat.
Scientific approach and realisation
The work will include assessing impact of various major nutrient forms of N, P, K etc on soil
born pathogen survival and their ability to colonise plant in bio-assays. Measurement of infield variation of pathogens and soil characteristic will be used to improve knowledge about
12
Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
correlation between soil factors and infestations. Mapping will be improve by using
conductivity measurement (EM 38) and the Soil Mole (measurement of radioactive isotope of
K etc) . To study the effect of changes in supply of macro (and micro nutrients) the
established bio-aassays for pathogens will be used and adopted for manipulation of nutrient
supply. New methods for grading of disease severity will be evaluated image analysis, DNAexpression etc. Data from field trials will be analyzed and correlated to disease severity as
well as field trials will established to confirm observations in bio-assay.
Work-package 4, tasks and deliverables
1. Soil characterization – presence and distribution of
Deliverables
Year:Q
pathogen
Measurement of soil condition in field with variation in pathogens
infestations P.brassica, A.euteiches
Correlations between pathogen and
chemical / physical properties (
EM38) Publication.
10:3
Measurement of soil condition in field with variation in pathogens
infestations V. longisporum and S. sclerotiorum
Correlations between pathogen and
chemical / physical properties ( EM
38 and/or the Mole). Publication
11:3
2. Interactions pathogen and soil chemistry / fertilizer
Deliverables
▪
Recruitment of postdoc
▪
Effect of fertilizer on development of pathogens in bio-assays
Postdoc in work
of P. brassicae (A. euteiches)
▪
Evaluation of available field trials
▪
▪
Field trials – effect of nutrient supply on development of
pathogen
Reports on effect of nutrient status
on disease severity of P. brassicae
Report from field observations,
each year
Publications of interaction with
nutrients – greenhouse and field
Year:Q
10:2
10:4
11:4
10:4.
11:4
12:4
WP 5. Implementation and use in R&D and practice
Project team
Mats Söderström (PL)
A-C Wallenhammar*
Anders Jonsson
2009/10
1 m FTE
0,5 m FTE
0,5 mFTE
Resources
Resources available to WP 5: 09/10 ( 2,0* FTE), 10/11 ( 2,5 FTE) ; 11/12( 3,5 FTE).
Objective
The general aim is a root disease risk management routine available to farmers for optimizing
crop production. This includes soil sampling, number of samples and identification of cofactors for mapping and routines that are economical interesting for laboratories and farmer
and still on a solid scientific ground.
The aim is to in close collaboration with stakeholders design an economically feasible system
for soil screening of soil-borne pathogens. It will be based on adoptions from the scientific
work done in the program with sampling, sample point density, extraction and quantifications
13
Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
Specific goals
- Routines for presentation of infestation and prediction of pathogen infection
- Maps presenting variation in presentations of pathogens in a way easy to understand
- “Maps” presenting the risk for yield reduction
- “de facto” SOPs for mapping of interest for researcher in and outside of universities
- Commercially well functioning and interesting products from laboratories for use by
advisers and farmers
Project strategy
Close co-work with stakeholders, i.e. laboratories and advisor services and use of GISprograms for presentation of results and predictions on maps. In co-work with stakeholder and
other researcher at SLU rapidly establish routines for practical use of analysis of “new”
important pathogens. And as soon as the basic knowledge is evaluated state and present a “de
facto” SOP for the most important pathogens and for handling of soil samples and to decide
the density of sampling point.
In co-work with stakeholders and researcher at universities in Sweden identify “new”
interesting organism and soil factors to be included in BioSoM of soil-borne pathogens.
Scientific approach and realisation
Development of different ways of presentations of quantity of pathogen and predictions, ie
limits, number classes, colours, combinations with chemical characteristics etc using
different GIS –approaches and evaluate the responses to different methods.
In close co-work with development of sampling and evaluate the possibilities to use co-factors
to improve precision in description of field/in-field variation (McBratney et al 2000,
Rosenbaum and Söderström 2006). Test reductions of number of samples/ha based on the
possibility to use co-factors such as soil conductivity (i.e. EM 38 or NIR) (Wetterlind 2009).
The adjustment will be done in co-work with the GIS-specialist and agronomist and based on
biology of pathogens and geo-statistical considerations.
The development of risk maps/index will be done in close co-work with the WP 2
dose/response and with the different stakeholder in the program.
A further aim is also to increase this WP 5 and include specialist in communication and
advice service during the first 3 years period with the objective to use BioSoM as a case
working with interactive learning process (Ljung 2001).
Work-package 5, tasks and deliverables
1. Presentation of pathogens in soil and predictions of risks
Deliverables
▪
Development of a “first routine” for presentation of pathogens
on map
Preliminary SOP for presentation to
“Markkarteringsrådet*”
▪
Geo-statistical work with pathogens i.e. clubroot, including
sampling density , in field variation, use of chemical co-factors
for the first pathogen i.e. clubroot
Report on variogram and
improvement using cofactors
10:2
▪
Presentation of in-field variation using different presentations
possibilities and cofactors i.e. soil conductivity, soil type
Reports and Scientific article
10:4
▪
Development of routines for presentations of risk of yield
reduction for two pathogens. PhD-student**
11:2
▪
Reports and Scientific article
PhD-student**
Up-dated routine for presentation of pathogen infection and
risks assessment to farmers
SOP for BioSoM v.1.0 for farmers
12: 2
Year:Q
10:2
14
Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
*Markkarteringsrådet is a working group in Sweden that discuss and propose the SOP for “ good soil mapping practice” .
The group includes representatives from Swedish Board of Agriculture (SJV), advisory services such as the different
Agricultural Societies (HS), laboratories ie AgriLab AB and Eurofins Food & Agri and fertilize suppliers such as YARA and
Lantmännen.
** Presently not financed
Publications and implementation of results
We expect to make several joint BioSoM but also group/subject specific publications, all to be
submitted to international referee journals with good reputation. There will be high
probability for at least 5 such papers. We also intend to present our results in Svensk
Frötidning, Lantmannen and similar Swedish journals and publications.
An important way to reach the advice services is presentations at the regional and local yearly
meetings such at the in Uddevalla, Växjö and Linköping, At these meeting the last year’s
results are presented from field experiments with cultivars, fertilization and plant protection.
The work by SARDI in Australia (Ophel-Keller et al 2008) is a sort of road-model for the
work in BioSoM aiming for practical use and the our results will be amalgamated with the
experiences from down under.
Future perspectives – beyond 2013
The major transmission phase will be 2013-2016 i.e. the second phase of the TEMA-program,
bringing basic fundamental knowledge into applied tools/tentative products and further
evaluations of new control strategies.
Our present project plan 2009-2012 is ambitious and a majority of results will most likely be
generated and/or based on further evaluations be shown to be of significance year 3 and later
in the programme. We have initially stated that all this work needs more than 3 years
particularly if we want to evaluate new data and tools as well introduce new cultivation
practices etc to improve disease control and to measures in new field trials. This is certainly
true if we are looking for breeding improvements. However, since for example parallel
projects on biology of the pathogenic organisms and the defence to V. longisproum, L.
maculans and Phytophthora infestans are ongoing in the group of Dixelius We already
foresee possibilities of fruitful joint efforts and collaboration to generate interesting results.
Similar possibilities exist also with other research groups at example for take all in wheat and
the research group at Department of Forest Mycology and Pathology. Much international
work is ongoing on Phytophthora species particularly on the genomic side which has links to
the pea rot caused by Phytophthora. Particularly oospore biology will in this case be in focus.
However, we estimate that these studies will take place year 4-6 but some molecular tools
may be generated earlier.
We foresee similar synergism with other areas such as nutrition supply. Implementation of
potential new analytic tools and knowledge for plant protection, plant breeding and plant
management foreseen for the period 4-6 year
 Addition of detection methods for other important soil born plant pathogens such as fungi,
nematodes etc in sugar beet, potatoes and cereals
 Implementation of biological mapping in practice for the “hardest” pathogens
 Validation of crop management to reduce infection such as macro/micro fertilization, crop
rotation
 P. brassicae genome and molecular detection tools public available
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012


Important plant-sclerotia signals identified and impact on sclerotia germination or
initiation detected.
Possible candidate substance for pre-commercialization and/or mol marker tools
References
Almquist, C., Wallenhammar, A-C. och Jonsson, A. 2008. Quantitative PCR- detection for mapping
in-field variation of Plasmodiophora brassicae and Aphanomyces eutheiches. Journal of Plant
Pathology (2008), 90, S2.398.
Bolton MD, Thomma BPHJ, Nelson BD 2006. Sclerotinia sclerotiorum (Lib.) de Bary:
biology and molecular traits of a cosmopolitan pathogen. Mol Plant Pathol. 7:1-16.
Buczacki, S.T., Toxopeus H., Mattusch P., Johnston T.D., Dixon G.R. Hobolth L.A., 1975.
Study of physiologic specialization in P. brassicae: Proposal for attempted rationalization
through an international approach. Trans. Br. Mycol soc. 65,2, 295-303
Datnoff L.E, Elmer W.H and Huber D.M.(ed). 2007. Mineral nutrition and plant disease,
APS Press, The American Phytopathological Society. St Paul, Minnesota. USA, pp 278.
Dixon GR 2009. The occurrence and economic impact of Plasmodiophora brassicae and
clubroot disease. J. Plant Growth Regul 28:194-202
Dobinson KF, Grant SJ, Kang S 2004. Cloning and targeted disruption, via Agrobacterium
tumefaciens-mediated transformation, of a trypsin protease gene from the vascular wilt
fungus Verticillium dahliae. Curr Genet 45:104-110.
Fradin EF, Thomma BPHJ 2006. Physiology and molecular aspects of Verticillium wilt
diseases caused by V. dahliae and V. albo-atrum. Mol Plant Pathol 7:71-86
Hegedus DD, Rimmer SR 2005. Sclerotinia sclerotiorum: When “to be or not to be” a
pathogen? FEMS Microb. Lett 251:177-184.
Heyman F 2008. Root rot of Pea caused by Aphanomyces euteiches. Dissertation, Swedish University
of Agricultural Sciences. Acta Universitatis Agriculturae Suecia, Agraria, 2008:24
Hogenhout SA, van der Hoorn RA, Terauchi R, Kamoun S 2009. Emerging concepts in
effector biology of plant-associated organisms. Mol Plant-Microbe Int 22:115-122
Ljung M, 2001.Collaborative learning for sustainable development of agri-food systems.
Doktorsavhandling. Agraria 308, SLU. (ISSN 1401-6249. ISBN 91-576-5827-7)
Levy M, Erental A, Yarden O 2008. Efficient gene replacement and direct hyphal
transformation in Sclerotinia sclerotiorum. Mol Plant Pathol 9:719-725
McBratney, A. B., Odeh, I. O. A., Bishop, T. F. A., Dunbar, M. S., & Shatar, T. M., 2000. An
overview of pedometric techniques for use in soil survey. Geoderma, 97, 293–327.
Ophel-Keller K, McKay A. Hartley D, Herdina, Curran J, 2008. Development of routine
DNA-based testing service for soilborne diseases in Australia. Australasian Plant
Pathology 37, 243-253.
Rosenbaum, M. S. & Söderström, M., 1996. Cokriging of heavy metals as an aid to
biogeochemical mapping. ACTA Agric. Scand., Sect. B, Soil and Plant Sci., 46, 1-8.
Siemens J, Bulman S, Rehn F, Sundelin T 2009. Molecular biology of Plasmodiophora
brassicae. J Plant Growth Regul 28:245-251
Some A, Manazanares M.J., Laurens F., Baron F., Thomas G., Rouxel F. 1996. Variation for
virulence on B. napus L. amongst P. brassicae collections from France and derived singlespores isolates. Plant Pathology 45,432-439,
Wallenhammar 1999, Monitoring and control P. brassicae I nspring brassicae crops Dissertation:
Swedish Uniersity of Agricultural Sciences. Acta Univertsitatis agriculturae Sueciae Agrarian 183.
Wallenhammar, A-C, Almqvist, C., Redner, A. och Sjöberg, A. 2008. Improved risk assessment of
Sclerotinia Stem Rot in Oilseed Rape by quantitative PCR-assay. Applied Aspects of Aerobiology,
89, 37-42.
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Tema-forskningsprogram Biological Soil Mapping, BioSoM
Programme plan 2009-2012
Wetterlind J 2009. Improved Farm Soil Mapping Using Near Infrared Reflexion
Spectroscopy. Doctoral Thesis No. 2009:68 Faculty of Natural resources and Agricultural
Sciences, SLU, Uppsala
Williams P.H. 1966 a system for determination of races of P. brassicae that infect cabbage
and rutabaga. Phytopathology 56, 6.624.
Zhou L, Hu Q, Johansson A, Dixelius C 2006. Verticillium longisporum and V. dahliae:
infection and disease in Brassica napus. Plant Pathol. 55:137-144.
(Zhou et al. 2006; Heymans 2008, Almquist et al. 2009).
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