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    BRIO Banking 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 University Department of Biochemistry and Microbiology K. 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

  • 5 Stock 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 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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    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

    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 interactions Plantpathogens

    Research interests:

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    Plant – bacteria interactions Rhizobia

    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)

    Burkholderia in biocontrol

    Plant – bacteria interactions Beneficial interactions

    Research interests:

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    BRIO Banking 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 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

    → Elimina on 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 First name Institution/Company Position in Company Roumiantseva Marina All Russia Res Inst Agr

    Microbiol, St. Petersburg Senior researcher

    Lindström Kristina Univ Helsinki, Dept Food & Environm Sci

    Professor

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

    Murdoch University Postdoctoral 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  ag