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BRIOBanking rhizosphere micro-organisms. European-

Russian 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 UniversityDepartment of Biochemistry and MicrobiologyK. L. Ledeganckstraat 35

http://www.lm.ugent.be/

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• 65 staff members, including– 3 permanent senior scientists (P. De Vos,

A. Willems & P. Vandamme)– 10 postdoctoral fellows– 12 PhD students

Laboratory of Microbiology

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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

5Stock of over 200.000 ampoules

Distribution of public strains Analysis of strains for

third parties

Extended range of methods

Patent and Safe deposits

BCCM/LMG main services

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• Microbial diversity, evolution, ecology and function

• Medical, food, agricultural & environmental microbiology

Research interests:

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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 rRNAgene 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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Medical and food microbiology

• Intestinal microbiomecomposition 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

Research interests:

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Research interests:Environmental microbiology

• Antarctic bacteria

• Microbiology of intertidal sediments

• Methanotrophic bacteria

• Denitrification

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Pseudomonas chicorii midrib rot in lettuce

isolation of phytopathogenic

strainspectinolysis of potatoe slice

infection of chicory leaves

characterization

FAME SDS-PAGE BOX-PCR gene sequencing

Xanthomonas fragariae angular leaf spot on strawberry

Plant – bacteria interactionsPlantpathogens

Research interests:

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Plant – bacteria interactionsRhizobia

Research interests:

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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Endosymbionts in green algae

Plant Growth Promoting Rhizobacteria (PGPR) of potatoe (VALORAM project)

Burkholderiain biocontrol

Plant – bacteria interactionsBeneficial interactions

Research interests:

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BRIOBanking rhizosphere micro-organisms. European-

Russian 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 reviewLeader: 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 reviewContribution 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 reviewContribution 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 promotion87 genera biocontrol158 genera bioremediation

→ Elimina on of non‐soil genera: 148 genera remaining

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WP1 – Extensive stock reviewContribution 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 checked57 retained with documented uses to be included

in BRIO catalogue (32 biofert. / 1 biocontr. / 29 biodegr.)

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WP2 – BiofertilizersLeader: 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 – BiofertilizersParticipants: 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 First name Institution/Company Position in CompanyRoumiantseva Marina All Russia Res Inst Agr

Microbiol, St. PetersburgSenior researcher

Lindström Kristina Univ Helsinki, Dept Food & Environm Sci

Professor

Willems Anne Lab. Microbiology, UGent ProfessorDe Meyer Sofie Centre for Rhizobium Studies,

Murdoch UniversityPostdoctoral researcher

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 vitrocultivation (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: