Transcript BCCM/LMG Bacteria Collection

BRIO
Banking rhizosphere micro-organisms. EuropeanRussian initiative to set up a network of rhizosphere
microbiological resources
Partner 3 – Lab. Microbiology, Ghent University
- contribution to all WPs
- leader of WP2 Biofertilizers
Anne WILLEMS
BRIO meeting, September 9-13, Perm, Russia
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Laboratory of Microbiology (LM-UGent), Faculty of
Sciences, Ghent University
Department of Biochemistry and Microbiology
K. L. Ledeganckstraat 35
http://www.lm.ugent.be/
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Laboratory of Microbiology
• 65 staff members, including
– 3 permanent senior scientists (P. De Vos,
A. Willems & P. Vandamme)
– 10 postdoctoral fellows
– 12 PhD students
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BCCM/LMG Bacteria Collection
• LM-UGent holds the bacterial branch of the
BCCM/LMG Bacteria Collection
(http://bccm.belspo.be) maintaining currently
over 24,000 strains (500 genera, 3400 sp.)
• Second largest non-medical collection in Europe
• LM-UGent also holds an additional non-public
research collection of about 40,000 bacterial
isolates
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BCCM/LMG main services
Patent and Safe deposits
Distribution of
public strains
Stock of over 200.000 ampoules
Analysis of strains for
third parties
Extended range of methods
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Research interests:
• Microbial diversity, evolution, ecology
and function
• Medical, food, agricultural &
environmental microbiology
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Culture dependent analysis of
microbial communities
• Traditional culture based approaches followed
by dereplication and identification of isolates by
means of polyphasic approaches
• Development of high throughput technology by
means of colony picker coupled with MALDI
TOF/TOF MS (Applied Biosystems 4800 Plus), a
Synapt™ High Definition Mass Spectrometer for
electrospray analyses and a liquid handler
(Genesis Workstation RSP 200/8, Tecan,
Switzerland)
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Culture independent analysis of
microbial communities
• Tagged pyrosequencing to produce 16S rRNA
gene inventory of samples
• Real-time PCR
– Bifidobacteria in probiotic products and faecal
samples
– Bacillus contaminants during gelatine production
• MALDI TOF and electrospray MS
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Research interests:
Medical and food microbiology
• Intestinal microbiome
composition in health and
disease (ulcerative colitis,
cystic fibrosis, asthma)
• Epidemiology and diagnosis
of unusual food borne
pathogens
• Diversity and role of lactic
acid and acetic acid bacteria
in traditional fermented
foods
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Research interests:
Environmental microbiology
• Antarctic bacteria
• Microbiology of intertidal
sediments
• Methanotrophic bacteria
• Denitrification
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Research interests:
Plant – bacteria interactions
Plantpathogens
Xanthomonas fragariae angular
leaf spot on strawberry
Pseudomonas chicorii
midrib rot in lettuce
pectinolysis of
potatoe slice
isolation of
phytopathogenic
strains
infection of
chicory leaves
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FAME
SDS-PAGE
-PCR
characterization
BOX-PCR
gene sequencing
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Research interests:
Plant – bacteria interactions
Rhizobia
Isolation and polyphasic
identification of strains
Identification using housekeeping
genes:
- Bradyrhizobium
- Sinorhizobium
- Mesorhizobium
- Rhizobium
- non-traditional rhizobia
Collection of reference rhizobia
Collection of local isolates
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Research interests:
Plant – bacteria interactions
Beneficial interactions
Endosymbionts in
green algae
Plant Growth Promoting Rhizobacteria
(PGPR) of potatoe (VALORAM project)
Burkholderia
in biocontrol
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BRIO
Banking rhizosphere micro-organisms. EuropeanRussian initiative to set up a network of rhizosphere
microbiological resources
Partner 3 – Lab. Microbiology, Ghent University
- contribution to all WPs
- leader of WP2 Biofertilizers
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WP1: Extensive stock review
WP2: Biofertilizers
WP3: Biopesticides and disease prevention
WP4: Bioremediation
WP5: Network
WP6: Database
WP7: Regulations and IPR
WP8: Project management and dissemination
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WP1 – Extensive stock review
Leader: UCL
Start: mo. 1 / End: mo. 36
Objectives:
To organise expertise on rhizosphere micro-organisms
(MO) that provide nutrients to plants = biofertilisers.
To organise the holdings of rhizosphere MO used as
biofertilisers.
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WP1 – Extensive stock review
Contribution to Task 1.1 by UGent:
Inventory for BRIO of the BCCM/LMG bacteria
collection:
General collection with over 30.000 cultures (+800
genera, +4000 species) >> work in phases to
document applications
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WP1 – Extensive stock review
Contribution to Task 1.1 by UGent:
First phase: for each genus: verify reports of use as
biofertilizers, in biocontrol or bioremediation
applications. For some genera this is well known, but
for the majority this had to be assessed by means of
literature searches.
→ 868 genera verified: 198 bacterial genera positive
64 genera plant growth promotion
87 genera biocontrol
158 genera bioremediation
→ Elimination of non-soil genera: 148 genera remaining
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WP1 – Extensive stock review
Contribution to Task 1.1 by UGent:
Last phase: verify of the 148 remaining genera which
strains (and species) are documented specifically for
biofertilization, biocontrol or bioremediation
applications. This work is ongoing; in total, this involves
8.878 strains.
→ When positive, these strains (or a selection) will be
marked for inclusion in the BRIO catalogue.
CURRENT STATUS: 1250 strains checked
 57 retained with documented uses to be included
in BRIO catalogue (32 biofert. / 1 biocontr. / 29 biodegr.)
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WP2 – Biofertilizers
Leader: UGent
Start: mo. 14 / End: mo. 36
Objectives:
To organise expertise on rhizosphere micro-organisms
(MO) that provide nutrients to plants = biofertilisers.
To organise the holdings of rhizosphere MO used as
biofertilisers.
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WP2 – Biofertilizers
Participants: all scientific teams
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WP2 – Biofertilizers
Tasks:
2.1 Organize collections
Linking resource centres to enable research on optimal combinations of
biofertilisers, plant of agricultural interest and soil conditions >> Access to
human expertise and microbial resources → Will be achieved by the
creation of the virtual BRIO catalogue and the web presence
CURRENT STATUS: ongoing
Private companies will be invited to collaborate. These companies already
collaborate with some Russian partners >> Field applications → input
from Russian partners needed to provide feedback in work package
report
CURRENT STATUS: to be done / ongoing ?
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WP2 – Biofertilizers
Tasks:
2.1 Organize collections
Organize a multidisciplinary group of biofertilizers experts >> consider
capacity building needs and check for solutions/available training in e.g.
taxonomy, meeting in mo. 18. → Discussion needed on: activating the
network, disseminate activities, information …
CURRENT STATUS: experts contacted
Name
Roumiantseva
First name
Marina
Institution/Company
All Russia Res Inst Agr
Microbiol, St. Petersburg
Position in Company
Senior researcher
Lindström
Kristina
Univ Helsinki, Dept Food &
Environm Sci
Professor
Willems
Anne
Lab. Microbiology, UGent
Professor
De Meyer
Sofie
Centre for Rhizobium Studies, Postdoctoral researcher
Murdoch University
Vereecke
Claudine
BCCM/LMG
Curator BCCM/LMG public collection
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WP2 – Biofertilizers
Tasks:
2.2 Enhancement of specific collections (~ WP1)
Frankia: N2-fixing actinomycete symbionts of diverse non-leguminous
(actinorhizal) plants. VKM maintains +50 strains
Rhizobia: N2-fixing symbionts of legumes. UGent has expertise in
isolation and identification and holds a rich representation of rhizobial
reference strains in the BCCM/LMG bacteria collection that is hosted by
UGent
Azospirilla: nitrogen-fixing plant-growth-promoting rhizobacteria that
dwell under various soil-climatic conditions. IBPPM maintains the largest
Russian collection of Azospirillum, including isolates that degrade various
classes of hydrocarbons
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WP2 – Biofertilizers
Tasks:
2.2 Enhancement of specific collections (~ WP1)
Arbuscular mycorrhizal fungi:
UCL hosts MUCL, the world largest collection of AMF (the Glomeromycota
Phylum). Strains originate from temperate to tropical ecosystems and a
number have been evaluated for improved nutrition and growth of
agricultural important crops (e.g. banana, potato) and for in vitro
cultivation (biotization) of plants.
ART has a collection of 100 strains of AMF. Strains originate from arable
land and grassland in Middle Europe and recently also from new habitats or
niches (e.g. deeper soil layers, or AMF strains with a very long life cycle).
The ART AMF collection complements the collection at MUCL in that the
isolates originate from Middle Europe and its strong focus on the functional
diversity of AMF.
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WP2 – Biofertilizers
Tasks:
2.2 Enhancement of specific collections (~ WP1)
Saprotrophic fungi: UNITO has a big collection (about 1000 strains) of
fungi isolated from the rhizosphere, the rhizoplane and inside the roots of
many herbaceous and woody plants. These will be further characterized for
important features to be exploited as biofertilisers.
→ The partners will continue to enhance their collections and feed
this into the BRIO catalogue.
CURRENT STATUS: For rhizobia we have deposited 42 new strains of
Belgian rhizobia in the LMG collection that will be included in BRIO
→ Input from the partners is needed to provide feedback in the work
package report on specific achievements related to the different
biofertilizer groups.
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WP2 – Biofertilizers
Tasks:
2.3 Taxonomic and functional characterization
Functional characterization of the selected strains of the above microbial
groups will feed the catalogue with data related to their properties, and
their suitability for specific uses for agro-environmental applications.
CURRENT STATUS: For rhizobia we have checked the identity of the
42 new strains of Belgian rhizobia that will be included in BRIO
→ Input from the partners is needed to provide feedback in the work
package report on specific achievements related to the different
selected biofertilizer groups.
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WP2 – Biofertilizers
Tasks:
2.4 Capacity building
According to needs of participants >> fact sheets, training sessions in
particular techniques. → To be discussed
Based on stock review >> exchanges of strains, reciprocal laboratory work
visits at participants’ facilities. → To be discussed
2.5 Metagenomic data
Existing metagenomic data available from the participants will be loaded in
the general database. The data pertaining to metagenomes recovered in
environmental samples collected in the context of biofertilisers survey will
be handled in the Work package 6 and added to the databank consolidating
all data. → To be discussed
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WP2 – Biofertilizers
Deliverables:
D2.1 Specialists in Frankia, rhizobia, azospirilla, AMF and saprotrophic fungi.
Besides the experts from the teams, external specialists will be invited active
preferably in their region. The group will have access to the project intranet.
D2.2 This database subset will compile the material selected from the
individual participants' holdings inventories (Deliverable 1.2) plus the
additions made according to the enhancement plan set at Meeting in mo. 18.
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WP2 – Biofertilizers
Milestones:
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