BRIO

1. 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

2. Laboratory of Microbiology (LM-UGent), Faculty of Sciences, Ghent University Department of Biochemistry and Microbiology K. L. Ledeganckstraat 35 http://www.lm.ugent.be/

3. Laboratory of Microbiology • 65 staff members, including • 3 permanent senior scientists (P. De Vos, A. Willems & P. Vandamme) • 10 postdoctoral fellows • 12 PhD students

4. 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. Patent and Safe deposits Distribution of public strains Analysis of strains for third parties Stock of over 200.000 ampoules Extended range of methods BCCM/LMG main services

6. Research interests: • Microbial diversity, evolution, ecology and function • Medical, food, agricultural & environmental microbiology

7. 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 analysesand a liquid handler (Genesis Workstation RSP 200/8, Tecan, Switzerland)

8. 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

9. 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

10. Research interests: • Environmental microbiology • Antarctic bacteria • Microbiology of intertidal sediments • Methanotrophic bacteria • Denitrification

11. Research interests: Plant – bacteria interactions Plantpathogens Xanthomonas fragariae angular leaf spot on strawberry Pseudomonas chicorii midrib rot in lettuce isolation of phytopathogenic strains pectinolysis of potatoe slice infection of chicory leaves characterization FAME SDS-PAGE BOX-PCR gene sequencing

12. 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

13. Research interests: Plant – bacteria interactions Beneficial interactions Endosymbionts in green algae Plant Growth Promoting Rhizobacteria (PGPR) of potatoe (VALORAM project) Burkholderia in biocontrol

14. 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

15. 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

16. WP1 – Extensive stock review Leader: UCL Start: mo. 1 / End: mo. 36 Objectives: To organise expertiseon rhizosphere micro-organisms (MO) that provide nutrients to plants = biofertilisers. To organise the holdings of rhizosphere MO used as biofertilisers.

17. 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

18. 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

19. 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.)

20. WP2 – Biofertilizers Leader: UGent Start: mo. 14 / End: mo. 36 Objectives: To organise expertiseon rhizosphere micro-organisms (MO) that provide nutrients to plants = biofertilisers. To organise the holdings of rhizosphere MO used as biofertilisers.

21. WP2 – Biofertilizers Participants: all scientific teams

22. 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 ?

23. 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

24. 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

25. 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.

26. 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.

27. 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.

28. 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

29. WP2 – Biofertilizers Deliverables: D2.1 Specialists inFrankia, rhizobia, azospirilla, AMF and saprotrophic fungi. Besides the experts from the teams, externalspecialists will be invited active preferably in their region. The group will have access to the projectintranet. D2.2 This database subset will compile the materialselected from the individual participants' holdings inventories (Deliverable 1.2) plus the additions madeaccording to the enhancement plan set at Meeting in mo. 18.

30. WP2 – Biofertilizers Milestones: