Dr. Paolina Garbeva
ResearcherMicrobial Ecology |
Research expertisegenome mining microbe-microbe interactions microbial chemical ecology microbial volatiles plant-microbe interactions
Page last updated: 10-07-2018
Current research
The focus of my current research is to understand the fundamental mechanisms of microbial chemical interactions and communication. Secondary metabolites (both volatile and water-soluble) play an important role in microbial interactions, e.g. as signalling compounds for communication or as suppressive agents in interference competition.
Using omics-based tools, advanced analytical chemistry and novel imaging techniques, my research aims to decipher, explore and exploit the so far unknown belowground microbe-microbe and plant-microbe chemical interactions and communication. Understanding the belowground inter-kingdom (bacteria, protists, fungi, plants) interactions is crucial for assessing the functioning of soil ecosystems, which underpins soil and plant health.
Previous positions:
January 2013- January 2015: Tenure track position within the Department of Microbial Ecology, NIOO-KNAW
VIDI personal grant (NWO); Project title: The secrets of success: the best bacterial competitive strategies in the rhizosphere.
April 2010 – April 2014: Postdoctoral researcher within the Department of Microbial Ecology, NIOO- KNAW
MEERVOUD personal grant (NWO); Project title: Bacterial interactions in soil: the role of volatiles as infochemical and competitive tools.
July 2006 – April 2010: Postdoctoral position within the group of Terrestrial Microbial Ecology, NIOO-KNAW
VENI personal grant (NWO); Project title: Suppression of plant-pathogenic fungi as a result of inter-specific bacterial interactions.
August 2005- June 2006: Postdoctoral position in the School of Biological Sciences, University of Aberdeen, UK
Project title: Contribution of nitrifier denitrification to N2O and N2 emissions from soils.
August 2004- August 2005: Postdoctoral position Department Microbial Ecology, Groningen University
EU project METACONTROL: Soil metagenomics to identify novel mechanisms of antagonism and antifungal activity for the improved control of phytopathogens.
PhD degree: obtained 21/06/2005, Leiden University, the Netherlands
PhD project “The significance of microbial diversity in agricultural soil for disease suppressiveness”
Editorial board member of:
- FEMS Microbiology Letters since May 2009-present
- Frontiers in Microbiology since September 2014-present
- Journal of Plant Interactions since June 2016-present
Fellowships and awards:
- Aspasia (NWO) personal grant, obtained in 2013
- VIDI (NWO) personal grant, obtained in 2012
- MEERVOUD personal grant (NWO), obtained in November 2010
- VENI (NWO) personal grant, obtained in 2006
- IAC grant, The Netherlands, obtained in 2000
Current supervision :
PhD students:
- Kristin Schulz (VIDI project, NWO),
- Adam Ossowiscki (NWO-Groen project)
- Yueling Qi (China Scholarship Council)
Post-docs:
- Olaf Tyc (VIDI project, NWO),
- Purva Kulkarni (NIOO-strategic funds)
- Lara Martin-Sanchez (NWO-Open).
Previous supervision:
PhD students:
- Ruth Schmidt (VIDI project, NWO)
- Olaf Tyc (BE-Basic project)
Post-doc:
- Chunxu Song (Aspasia, NWO)
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2013- March 2018 (VIDI-NWO) “The secrets of success: the best bacterial competitive strategies in the rhizosphere”
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2016- September 2021 (NWO- Groen) “Harnessing the soil microbiome for improved stress tolerance in crop plants”
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2017- July 2018 (NIOO Strategic funds) “Developing bioinformatics tools for future metabolomics data analysis”
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2017- January 2020 (NWO- Open) “Unravelling the ecological role of bacterial terpenes”
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2017- January 2020 (China Scholarship Council) “Microplastics in terrestrial ecosystem: effect on plant growth and rhizosphere community”
2018-2021 (ITN-H2020) "Impact of microbial inoculums on microbiome composition and resistance-induction of host plants against insect pest"
Previous projects
- 2010 – April 2014 (MEERVOUD -NWO) “Bacterial interactions in soil: the role of volatiles as infochemical and competitive tools”
- 2006 – April 2010 (VENI-NWO) “Suppression of plant-pathogenic fungi as a result of inter-specific bacterial interactions”
- 2012-2016 (BE-Basic) “Mining into interspecific bacterial interactions for discovery of novel antimicrobial compounds”
- 2016-2017 (NIOO Strategic funds) “Scents in the dark: exploring volatile emission in the rhizosphere”
- Garbeva, P., & Weisskopf, L. (2020). Airborne medicine - Bacterial volatiles and their influence on plant health: Transley review. New Phytologist, 226(1), 32-43. https://doi.org/10.1111/nph.16282
- Qi, Y., Ossowicki, A., Yang, X., Huerta Lwanga, E., Dini-Andreote, F., Geissen, V., & Garbeva, P. (2020). Effects of plastic mulch film residues on wheat rhizosphere and soil properties. Journal of Hazardous Materials, 387, [121711]. https://doi.org/10.1016/j.jhazmat.2019.121711
- Ossowicki, A., Tracanna, V., Petrus, M. L. C., van Wezel, G., Raaijmakers, J. M., Medema, M. H., & Garbeva, P. (2020). Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat. Proceedings of the Royal Society B-Biological Sciences, 287(1921), [ 20192527.]. https://doi.org/10.1098/rspb.2019.2527
- Avalos, M., Garbeva, P., Raaijmakers, J. M., & van Wezel, G. P. (2020). Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces. ISME Journal, 14, 568-583. https://doi.org/10.1101/450833, https://doi.org/10.1038/s41396-019-0537-2
- Tyc, O., Putra, R., Gols, R., Harvey, J. A., & Garbeva, P. (2020). The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom. MicrobiologyOpen, 9(1), [e00954]. https://doi.org/10.1002/mbo3.954
- Li, X. G., Garbeva, P., Liu, X., Klein Gunnewiek, P. J. A., Clocchiatti, A., Hundscheid, M. P. J., Wang, X., & De Boer, W. (2020). Volatile-mediated antagonism of soil bacterial communities against fungi. Environmental Microbiology, 22(3), 1025-1035. https://doi.org/10.1111/1462-2920.14808
- Janssens, T. K. S., Tyc, O., Besselink, H., De Boer, W., & Garbeva, P. V. (2019). Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine. FEMS Microbiology Letters, [fnz023]. https://doi.org/10.1093/femsle/fnz023
- Schmidt, R. L., Ulanova, D., Wick, L. Y., Bode, H. B., & Garbeva, P. V. (2019). Microbe-driven chemical ecology – past, present and future. ISME Journal, 13, 2656-2663. https://doi.org/10.1038/s41396-019-0469-x
- De Boer, W., Li, X. G., Meisner, A., & Garbeva, P. V. (2019). Pathogen suppression by microbial volatile organic compounds in soils. FEMS Microbiology Ecology, 95(8), [fiz105]. https://doi.org/10.1093/femsec/fiz105
- Martín-Sánchez, L., Saurabh Singh, K., Avalos Garcia, M., van Wezel, G. P., Dickschat, J. S., & Garbeva, P. V. (2019). Phylogenomic analyses and distribution of terpene synthases among Streptomyces. Beilstein Journal of Organic Chemistry, 15, 1181–1193. https://doi.org/10.3762/bjoc.15.115
- Wilschut, R. A., van der Putten, W. H., Garbeva, P. V., Harkes, P., Konings, W., Kulkarni, P., Martens, H. J., & Geisen, S. (2019). Root traits and belowground herbivores relate to plant-soil feedback variation among congeners. Nature Communications, 10, [1564(2019)]. https://doi.org/10.1038/s41467-019-09615-x
- Schulz-Bohm, K., Gerards, S., Hundscheid, M. P. J., Melenhorst, J., De Boer, W., & Garbeva, P. V. (2018). Calling from distance: Attraction of soil bacteria by plant root volatiles. ISME Journal, 12. https://doi.org/10.1038/s41396-017-0035-3
- Huerta Lwanga, E., Thapa, B., Yang, X., Gertsen, H., Salánki, T., Geissen, V., & Garbeva, P. V. (2018). Decay of low-density polyethylene by bacteria extracted from earthworm’s guts: a potential for soil restoration. Science of the Total Environment, 624, 753-757. https://doi.org/10.1016/j.scitotenv.2017.12.144
- Schmidt, R. L., Durling, M., de Jager, V. C. L., Menezes, R. C., Nordkvist, E., Svatos, A., Dubey, M., Lauterbach, L., Dikschat, J. S., Karlsson, M., & Garbeva, P. V. (2018). Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum. FEMS Microbiology Ecology, 94(6), [fiy078]. https://doi.org/10.1093/femsec/fiy078
- Geesink, P., Tyc, O., Küsel, K., Taubert, M., van de Velde, C., Kumar, S., & Garbeva, P. V. (2018). Growth Promotion and Inhibition Induced by Interactions of Groundwater Bacteria. FEMS Microbiology Ecology, 94(11), [fiy164]. https://doi.org/10.1093/femsec/fiy164
- Avalos Garcia, M., van Wezel, G. P., Raaijmakers, J. M., & Garbeva, P. V. (2018). Healthy scents: microbial volatiles as new frontier in antibiotic research? Current Opinion in Microbiology, 45(October), 84-91. https://doi.org/10.1016/j.mib.2018.02.011
- Kulkarni, P., A. Wilschut, R., J.F. Verhoeven, K., H. van der Putten, W., & Garbeva, P. (2018). LAESI mass spectrometry imaging as a tool to differentiate the root metabolome of native and range-expanding plant species. Planta, 248(December), 1515-1523. https://doi.org/10.1101/322867, https://doi.org/10.1007/s00425-018-2989-4
- Veraart, A. J., Garbeva, P. V., van Beersum, F., Ho, A., Hordijk, C. A., Meima-Franke, M., Zweers, A. J., & Bodelier, P. L. E. (2018). Living apart together – Bacterial volatiles influence methanotrophic growth and activity. ISME Journal, 12, 1163-1166. https://doi.org/10.1038/s41396-018-0055-7
- Qi, Y., Yang, X., Pelaez, A. M., Huerta Lwanga, E., Beriot, N., Gertsen, H., Garbeva, P. V., & Geissen, V. (2018). Macro- and micro- plastics in soil-plant system: effects of plastic mulch film residues on wheat (Triticum aestivum) growth. Science of the Total Environment, 645(15 december 2018), 1048-1056. https://doi.org/10.1016/j.scitotenv.2018.07.229
- Molinaro, F., Tyc, O., Beekwilder, J., Cankar, K., Bertea, C. M., Negre, M., & Garbeva, P. V. (2018). The effect of isabelin, a sesquiterpene lactone from Ambrosia artemisiifolia on soil microorganisms and human pathogens. FEMS Microbiology Letters, 365(4), [fny001]. https://doi.org/10.1093/femsle/fny001
- Wilschut, R. A., Silva, J. C. P., Garbeva, P. V., & van der Putten, W. H. (2017). Belowground plant-herbivore interactions vary among climate-driven range-expanding plant species with different degrees of novel chemistry. Frontiers in Plant Science, 8, [fpls.2017.01861]. https://doi.org/10.3389/fpls.2017.01861
- Tyc, O., de Jager, V. C. L., Van den Berg, M., Gerards, S., Janssens, T., Zaagman, N., Kai, M., Svatos, A., Zweers, A. J., Hordijk, C. A., Besselink, H., De Boer, W., & Garbeva, P. V. (2017). Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds. Microbial Biotechnology, 10(4), 910-925. https://doi.org/10.1111/1751-7915.12735
- Schmidt, R. L., de Jager, V. C. L., Zühlke, D., Wolff, C., Bernhardt, J., Cankar, K., Beekwilder, J., van Ijcken, W., Sleutels, F., De Boer, W., Riedel, K., & Garbeva, P. V. (2017). Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. Scientific Reports, 7, [862 ]. https://doi.org/10.1038/s41598-017-00893-3
- Schulz-Bohm, K., Tyc, O., De Boer, W., Peereboom, N., Debets, F., Zaagman, N., Janssens, T. K. S., & Garbeva, P. (2017). Fungus-associated bacteriome in charge of their host behaviour. Fungal Genetics and Biology, 102, 38-48. https://doi.org/10.1016/j.fgb.2016.07.011
- Schulz-Bohm, K., Martín-Sánchez, L., & Garbeva, P. V. (2017). Microbial volatiles: Small molecules with an important role in intra- and inter-kingdom interactions. Frontiers in Microbiology, 8, [02484]. https://doi.org/10.3389/fmicb.2017.02484
- Ossowicki, A., Jafra, S., & Garbeva, P. V. (2017). The Antimicrobial Volatile Power of the Rhizospheric Isolate Pseudomonas donghuensis P482. PLoS One, 12(3), [174362]. https://doi.org/10.1371/journal.pone.0174362
- Tyc, O., Song, C., Dickschat, J., Vos, M., & Garbeva, P. V. (2017). The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria. Trends in Microbiology, 25(4), 280-292. https://doi.org/10.1016/j.tim.2016.12.002
- Schulz-Bohm, K., Geisen, S., Wubs, E. R. J., Song, C., De Boer, W., & Garbeva, P. V. (2017). The prey’s scent – volatile organic compound mediated interactions between soil bacteria and their protist predators. ISME Journal, 11, 817-820. https://doi.org/10.1038/ismej.2016.144
- van Dam, N. M., Weinhold, A., & Garbeva, P. V. (2016). Calling in the Dark: the Role of Volatiles for Communication in the Rhizosphere. In Deciphering Chemical language of Plant Communication (pp. 175-210). (Signaling and Communication in Plants). Springer. https://doi.org/10.1007/978-3-319-33498-1_8
- Rinkel, J., Rabe, P., Garbeva, P. V., & Dickschat, J. (2016). Lessons from 1,3-Hydride Shifts in Sesquiterpene Cyclizations. Angewandte Chemie, 55(43), 13593-13596. https://doi.org/10.1002/anie.201608042
- Schmidt, R., Etalo, D. N., de Jager, V. C. L., Gerards, S., Zweers, H., De Boer, W., & Garbeva, P. V. (2016). Microbial small talk: volatiles in fungal-bacterial interactions. Frontiers in Microbiology, 6, [01495]. https://doi.org/10.3389/fmicb.2015.01495
- Weisskopf, L., Garbeva, P. V., Ryu, C-M., & Raaijmakers, J. M. (2016). Smelly fumes: volatile-mediated communication between bacteria and other organisms. Frontiers in Microbiology, 7, [2031]. https://doi.org/10.3389/fmicb.2016.02031
- Tyc, O., Tomás-Menor, L., Garbeva, P. V., Barrajón-Catalán, E., & Micol, V. (2016). Validation of the AlamarBlue® assay as a fast screening method to determine the antimicrobial activity of botanical extracts. PLoS One, 11(12), [e0169090]. https://doi.org/10.1371/journal.pone.0169090
- Schulz-Bohm, K., Zweers, H., De Boer, W., & Garbeva, P. (2015). A fragrant neighborhood: Volatile mediated bacterial interactions in soil. Frontiers in Microbiology, 6, [01212]. https://doi.org/10.3389/fmicb.2015.01212
- Song, C., Schmidt, R. L., de Jager, V. C. L., Krzyzanowska, D., Jongedijk, E., Cankar, K., Beekwilder, J., van Veen, A., De Boer, W., van Veen, J. A., & Garbeva, P. V. (2015). Exploring the genomic traits of fungus-feeding bacterial genus Collimonas. BMC Genomics, 16, [1103]. https://doi.org/10.1186/s12864-015-2289-3
- Hol, G., Garbeva, P., Hordijk, C., Hundscheid, M. P. J., Klein Gunnewiek, P. J. A., Van Agtmaal, M., Kuramae, E. E., & De Boer, W. (2015). Non-random species loss in bacterial communities reduces antifungal volatile production. Ecology, 96(8), 2042-2048. https://doi.org/10.1890/14-2359.1
- Tyc, O., Wolf, A., & Garbeva, P. (2015). The effect of phylogenetically different bacteria on the fitness of Pseudomonas fluorescens in sand microcosms. PLoS One, 10(3), [e0119838]. https://doi.org/10.1371/journal.pone.0119838
- Schmidt, R., Cordovez, V., De Boer, W., Raaijmakers, J., & Garbeva, P. (2015). Volatile affairs in microbial interactions. ISME Journal, 9, 2329-2335. https://doi.org/10.1038/ismej.2015.42
- Tyc, O., Zweers, H., De Boer, W., & Garbeva, P. V. (2015). Volatiles in inter-specific bacterial interactions. Frontiers in Microbiology, 6, [2015.01412]. https://doi.org/10.3389/fmicb.2015.01412
- Bitzer, A. S., Garbeva, P. V., & Silby, M. W. (2014). Draft Genome Sequence of Pedobacter sp. Strain V48, Isolated from a Coastal Sand Dune in the Netherlands. Genome Announcements, 2(1), [e00094-14]. https://doi.org/10.1128/genomeA.00094-14
- Tyc, O., Van den Berg, M., Gerards, S., Van Veen, J. A., Raaijmakers, J., De Boer, W., & Garbeva, P. (2014). Impact of interspecific interactions on antimicrobial activity among soil bacteria. Frontiers in Microbiology, 5, [567]. https://doi.org/10.3389/fmicb.2014.00567
- Garbeva, P. V., Hordijk, C. A., Gerards, S., & De Boer, W. (2014). Volatile-mediated interactions between phylogenetically different soil bacteria. Frontiers in Microbiology, 5, 289. https://doi.org/10.3389/fmicb.2014.00289
- Garbeva, P. V., Hordijk, C. A., Gerards, S., & De Boer, W. (2014). Volatiles produced by the mycophagous soil bacterium Collimonas. FEMS Microbiology Ecology, 87(3), 639-649. https://doi.org/10.1111/1574-6941.12252
- Mendes, R., Garbeva, P. V., & Raaijmakers, J. M. (2013). The rhizosphere microbiome: significance of plant beneficial, plant pathogenic, and human pathogenic microorganisms. FEMS Microbiology Reviews, 37(5), 634-663. https://doi.org/10.1111/1574-6976.12028
- Garbeva, P. V., Van Elsas, J. D., & De Boer, W. (2012). Draft Genome Sequence of the Antagonistic Rhizosphere Bacterium Serratia plymuthica Strain PRI-2C. Journal of Bacteriology, 194(15), 4119-4120. https://doi.org/10.1128/JB.00679-12
- Garbeva, P. V., Hol, W. H. G., Termorshuizen, A. J., Kowalchuk, G. A., & De Boer, W. (2011). Fungistasis and general soil biostasis - A new synthesis. Soil Biology & Biochemistry, 43(3), 469-477. https://doi.org/10.1016/j.soilbio.2010.11.020
- Garbeva, P. V., Tyc, O., Remus-Emsermann, M. N. P., Van der Wal, A., Vos, M., Silby, M. W., & De Boer, W. (2011). No apparent costs for facultative antibiotic production by the soil bacterium Pseudomonas fluorescens Pf0-1. PLoS One, 6(11), [e27266]. https://doi.org/10.1371/journal.pone.0027266
- Garbeva, P. V., Silby, M. W., Raaijmakers, J. M., Levy, S., & De Boer, W. (2011). Transcriptional and antagonistic responses of Pseudomonas fluorescens Pf0-1 to phylogenetically different bacterial competitors. ISME Journal, 5(6), 973-985. https://doi.org/10.1038/ismej.2010.196
- Garbeva, P. V., & De Boer, W. (2009). Inter-specific interactions between carbon-limited soil bacteria affect behavior and gene expression. Microbial Ecology, 58(1), 36-46. https://doi.org/10.1007/s00248-009-9502-3
- Garbeva, P. V., van Elsas, J. D., & Van Veen, J. A. (2008). Rhizosphere microbial community and its response to plant species and soil history. Plant and Soil, 302(1-2), 19-32. https://doi.org/10.1007/s11104-007-9432-0
- Garbeva, P. V., Postma, J., Van Veen, J. A., & van Elsas, J. D. (2006). Effect of above-ground plant species on soil microbial community structure and its impact on suppression of Rhizoctonia solani AG3. Environmental Microbiology, 8(2), 233-246. https://doi.org/10.1111/j.1462-2920.2005.00888.x
- Garbeva, P. V. (2005). The significance of microbial diversity in agricultural soil for disease suppressiveness (PhD Thesis).
- Garbeva, P. V., Van Veen, J. A., & van Elsas, J. D. (2004). Assessment of the diversity, and antagonism towards Rhizoctonia solani AG3, of Pseudomonas species in soil from different agricultural regimes. FEMS Microbiology Ecology, 47(1), 51-64. https://doi.org/10.1016/S0168-6496(03)00234-4
- Garbeva, P. V., Van Veen, J. A., & van Elsas, J. D. (2004). Microbail diversity in soil: selection of microbial populations by plant and soil type and implications for disease suppressiveness. Annual Review of Phytopathology, 42, 243-270. https://doi.org/10.1146/annurev.phyto.42.012604.135455
- Garbeva, P. V., Voesenek, K., & van Elsas, J. D. (2004). Quantitative detection and diversity of the pyrrolnitrin biosynthetic locus in soil under different treatments. Soil Biology & Biochemistry, 36(9), 1453-1463. https://doi.org/10.1016/j.soilbio.2004.03.009
- Garbeva, P. V., Van Veen, J. A., & Van Elsas, J. D. (2003). Predominant Bacillus spp. in agricultural soil under different management regimes detected via PCR-DGGE. Microbial Ecology, 45(3), 302-316. https://doi.org/10.1007/s00248-002-2034-8
- Van Elsas, J. D., Garbeva, P. V., & Salles, J. (2002). Effects of agronomical measures on the microbial deversity of soils as related to the suppression of soil-borne plant pathogens. Biodegradation, 13(1), 29-40. https://doi.org/10.1023/A:1016393915414
