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Mathematisch-Naturwissenschaftliche FakultätInstitut für Zoologie - AG Bonkowski

Main research interests

1. Ecology of soil protists using metagenomics/metatranscriptomics

Protists are a heterogeneous assemblage of single-cell eukaryotes encompassing a huge diversity of forms and life cycles. They play critical roles in soils, mainly as bacterial and fungal grazers, stimulating the rates of organic matter decomposition and shaping bacterial communities. Our current understanding of soil protistan diversity and their function in soil is limited by our ability to precisely identify and quantify free-living species. Although environmental sequencing offered potential new insights into biodiversity, it is still challenging to apply it to protists - the genetic divergence observed between and within major protistan groups greatly exceeds that between animals, plants and fungi. This has the direct and unfortunate consequence that we are unable to get a global picture of the extant diversity, since current studies are strongly biased towards only a few lineages.

Currently, I am participating in several projects aiming at deciphering the diversity of targeted groups of protists. In these projects, physico-chemical soil characteristics have been recorded, as well as metagenomics/metatranscriptomics data for prokaryotes/fungi/plants/microfauna. We aim at identifying the main factors - abiotic and biotic - driving spatio-temporal changes in community structures and the main groups interacting with each other, thus enabling a better understanding of the soil dynamics.

2. Molecular evolution, phylogeny and the early evolution of protists

In the past years, I have participated in establishing large-scale, multigene phylogenies of protists in general and Amoebozoa in particular. My main contribution has been to reconstruct the evolutionary history of Myxomycetes (also called plasmodial slime-moulds or Myxogastria), a widespread group of soil amoebae, one of the largest in the phylum Amoebozoa (941 species listed). I have established the first phylogenies of Myxomycetes and allied taxa, drawing strength from a combined molecular and morphological approach, identifying novel evolutionary trends and providing an extensive SSU rRNA database for environmental sampling and barcoding – and, as a bonus, some of the weirdest ribosomal sequences of all eukaryotes, showing an unusually high rate of evolution.

Current projects

Climate change, snow cover and microbial diversity in mountain soils: critical processes during snowmelt (Snowmelt, DFG FI 1686/2-1|RI 2834/1-1)

We are investigating the soil microbial biodiversity (including, for the first time, protists) and its functions before, during and after snowmelt, the modalities of the microbial turnover during snowmelt and how it is affected by warming. Our study has been carried out on three mountains in the Alps (Davos, Switzerland), at three different altitudes and in three seasons, with a collection of 160 soil samples. In addition, we have mimiced the effects of climate warming by experimentally modifying the snow cover - compacting and removing the snow to compare with control sites. One of the most innovative aspects of this study is the use of metatranscriptomics to obtain information on both composition and function of the soil communities. To our knowledge, metatranscriptomics have to date not been used on such a large scale. Our study will contribute to the fundamental understanding of spring soil microbial dynamics in the mountains responsible of soil organic matter mineralization at thaw and the biogeochemical cycles contributing to greenhouse gas emissions as a result of climate warming. The multiple qualifications assembled in our German-Swiss collaborative project will ensure a successful completion of the project. Our project will thus make a significant contribution to understanding the functioning of alpine and subalpine ecosystems.
 

UNIEUK - Universal taxonomic framework and integrated reference gene databases for Eukaryotic biology, ecology, and evolution

With the current deluge of eukaryotic meta-omics data, we urgently need to build up a universal eukaryotic taxonomy bridging the protist -omics age to the fragile, centuries-old body of classical knowledge that has effectively linked protist taxa to morphological, physiological, and ecological information ( http://unieuk.org/project/). Since November 2016, I was invited to join the curation effort of the EukRef - building an 18S rDNA database for improved identification of environmental sequences, as an expert of Myxogastria. Work is still in progress.

Professional career

  • Sep. 2019 – Aug. 2022 Principal Investigator. Climate change, snow cover and microbial diversity in mountain soils: critical processes during snowmelt. German Research Foundation grant, in cooperation with C. Rixen, T. Urich and M. Bonkowski. University of Cologne, DE.
  • Apr. 2017 – Aug. 2018: Research assistant. Factors driving the distribution and diversity of protistan plant pathogens in grasslands and forests of the Biodiversity Exploratories. Prof. M. Bonkowski, University of Cologne, DE.
  • Dec. 2014 – Jan.2017: Research assistant. Assessing protists diversity in soils by Illumina sequencing: developing primers, optimizing protocols and bioinformatic pipelines. Prof. M. Bonkowski, University of Cologne, DE.
  • Jan. 2013 – Nov.2014: Research assistant, German Research Foundation grant. Nanofauna (flagellates, amoebae) diversity in relation to land use and ecosystem functioning. Prof. M. Bonkowski, University of Cologne, DE.
  • Dec. 2009 – Nov.2012: Postdoctoral research assistant, 3 years German Research Foundation grant. Reproductive systems of Myxomycetes: How does evolution shape the relative proportion of sexual and asexual reproduction in species that are able to do both? Prof. M. Schnittler, University of Greifswald, DE.
  • Oct. 2006 – June 2009: Postdoctoral Research Fellow, Leverhulme Trust Foundation, grant R1008101. Molecular phylogeny of Amoebozoa and the early evolution of eukaryotes. Oxford University, UK.
  • Aug. 2007 – Sep. 2009: The Royal Society, International Joint Project Grant. Molecular phylogenetic analysis of nivicolous Myxomycetes and diversity in soils. Oxford University, UK & Hokkaido University, JP.
  • Oct. 2005 – Sep. 2006: Postdoctoral Research Fellow, Swiss National Science Foundation PBSKA-110567. A molecular phylogeny of the Mycetozoa (Dictyostelia, Protostelia, Myxogastria) and related amoebae. York University, UK.
  • Sep. 2002 – Aug. 2005: Scientific guest. E. & L. Schmidheiny Foundation grant. Continuation of research in Myxogastria and Mycetozoa phylogeny. University of Geneva, CH.
  • June – Aug. 2002: Postdoctoral internship (short stay.) Royal Society grant. A molecular phylogeny of the myxogastrid slime molds. York University, UK.
  • Jan. 1999 – Feb. 2001: Graduate assistant for teaching and research, PhD project. Institute of Ecology, University of Lausanne, CH.
  • Nov. 1994 – Oct. 1995: Research assistant, project : Lichens Red List (BUWAL). Geneva Botanical Garden, CH.

Education

  • 1997-2001: Ph.D. in Mycology, Université Henri-Poincaré Nancy-I, France. Forest microbiological biodiversity: spatiotemporal variations of the genetic structure of selected species of ectomycorrhizal fungi. Co-Supervisors: Dr. F. Martin, Nancy, FR and Prof. H. Clémençon, Lausanne, CH.
  • 1990-1997: Bachelor and Masters in Biology, University of Geneva, CH.
  • 1978-1981: Occupational therapist diploma, Ecole d'Ergothérapie, Lausanne, CH.

Publications

  • Pescador DS, Delgado-Baquerizo M, Fiore-Donno AM, Singh BK, Bonkowski M & Maestre FT (2022) Ecological clusters of soil taxa within bipartite networks are highly sensitive to climatic conditions in global drylands. Phil Trans R Soc B, 377:0387. doi:10.1098/rstb.2021.0387
  • Starke R, Fiore-Donno AM, White III R A , Parente Fernandes M L, Martinovic T, Bastida F, Delgado-Baquerizo M, Jehmlich N (2022) Biomarker metaproteomics for relative taxa abundances across soil organisms. Soil Biol Biochem, 175:108861. doi:10.1016/j.soilbio.2022.108861
  • Fiore-Donno AM, Human ZR, Štursová M, Mundra S, Morgado LN, Kauserud H, Baldrian P & Bonkowski M (2022) Soil compartments (bulk soil, litter, root and rhizosphere) as main drivers of soil protistan communities distribution in forests with different nitrogen deposition. Soil Biol Biochem, 168:108628. doi:10.1016/j.soilbio.2022.108628
  • Le Provost G, Thiele J, Westphal C, Penone C, Allan E, Neyret M, van der Plas F, Ayasse M, Bardgett R, Birkhofer K, Boch S, Bonkowski M, .... & Manning P (2021) Contrasting responses of above- and belowground diversity to multiple components of land-use intensity. Nat Commun, 12:3918. doi:10.1038/s41467-021-23931-1
  • Walden S, Jauss R-T, Feng K, Fiore-Donno AM, Dumack K, Schaffer S, Wolf R, Schlegel M & Bonkowski M (2021) On the phenology of protists: Recurrent patterns reveal seasonal variation of protistan (Rhizaria: Cercozoa, Endomyxa) communities in tree canopies. FEMS Microbiol Ecol, 97:fiab081. doi:10.1093/femsec/fiab081
  • Jauss R-T, Walden S, Fiore-Donno AM, Schaffer S, Wolf R, Feng K, Bonkowski M & Schlegel M (2021) A parasite’s paradise: Biotrophic species prevail oomycete community composition in tree canopies. Front For Glob Change. 2021;4:668895
  • Felipe-Lucia MR, Soliveres S, Penone C, Fischer M, Ammer C, Boch S, Boeddinghaus R, Bonkowski M, Buscot F, Fiore-Donno AM, Frank K, Goldmann K, Gossner MM, Hölzel1 N, Jochum M, Kandeler E, Klaus VH, Kleinebecker T, Leimer S, Manning P, Oelmann Y, Saiz H, Schall P, Schloter M,  Schöning I, Schrumpf M, Solly EF, Stempfhuber B, Weiser WW, Wilcke W, Wubet T & Allan E (2020) Land-use intensity alters networks between biodiversity, ecosystem functions, and services. PNAS. 117:28140-28149. doi: 10.1073/pnas.2016210117
  • Fiore-Donno AM & Bonkowski M (2021) Different community compositions between obligate and facultative oomycete plant parasites in a landscape-scale metabarcoding survey. Biol Fertil Soils. 57:245-256. doi: 10.1007/s00374-020-01519-z
  • Jauss R-T, Walden S, Fiore-Donno AM, Dumack K, Schaffer S, Wolf R, Schlegel M & Bonkowski M (2020) From forest soil to the canopy: Increased habitat diversity does not increase species richness of Cercozoa and Oomycota in tree canopies. Front Microbio, 11:592189. doi:10.3389/fmicb.2020.592189
  • Fiore-Donno AM, Richter-Heitmann T & Bonkowski M (2020) Contrasting responses of protistan plant parasites and phagotrophs to ecosystems, land management and soil properties. Frontiers Microbiol. 11:1823. doi: 10.3389/fmicb.2020.01823
  • Rossmann M, Pérez-Jaramillo JE, Kavamura VN, Chiaramonte JB, Dumack K, Fiore-Donno AM, Mendes LW, Ferreira MMC, Bonkowski M, Raaijmakers JM, Mauchline TH & Mendes R (2020) Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiol Ecol 96:fiaa032. doi:10.1093/femsec/fiaa032
  • Strelow D, de Haan M, Bonkowski M & Fiore-Donno AM (2020) New insights into the phylogeny of the dark-spored Myxomycetes (Amoebozoa: Conosa: Myxogastria: Fuscisporidia) and polyphyly of the genus Stemonitis. Syst Biodivers 18:228-236. doi: 10.1080/14772000.2020.1733128
  • Cainelli R, de Haan M, Meyer M, Bonkowski M & Fiore-Donno AM (2020) Phylogeny of Physarida (Amoebozoa, Myxogastria), redefinition of Physarum pusillum s. str. and reinstatement of P. gravidum Morgan. J Eukar Microbiol. 67:327-336. doi: 10.1111/jeu.12783.
  • Dumack K, Fiore-Donno AM, Bass D & Bonkowski M. 2019. Making sense of environmental sequencing data: ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria). Mol Ecol Res. 20:398-403. doi:10.1111/1755-0998.13112.
  • Bondarenko N, Smirnov A, Nassonova E, Glotova A & Fiore-Donno AM. 2019. Mitochondrial genomes of Amoebozoa. Protistology. 13:179-191. doi:10.21685/1680-0826-2019-13-4-1.
  • Voss C, Fiore-Donno AM, Guerreiro MA, Peršoh D & Bonkowski M (2019) Metatranscriptomics reaveal unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage. FEMS Microbiol Ecol. In press. doi:10.1093/femsec/fiz142.
  • Fiore-Donno AM, Richter-Heitmann T, Degrune F, Dumack K, Regan KM, Marhan S, Boeddinghaus R S, Rillig M, Friedrich MW, Kandeler E, Bonkowski M (2019) Functional traits and spatio-temporal structure of a major group of soil protists (Rhizaria: Cercozoa) in a temperate grassland. Frontiers Microbiol, 10:1332. doi:10.3389/fmicb.2019.01332.
  • Degrune F, Dumack K, Fiore-Donno AM, Bonkowski M, Sosa-Hernández M, Schloter M, Kautz T, Fischer D, Rillig M (2019) Distinct communities of Cercozoa at different soil depths in a temperate agricultural field. FEMS Microbiol Ecol, 95:4. doi:10.1093/femsec/fiz041.
  • Bonkowski M, Dumack K & Fiore-Donno AM (2019) The protists in soil – a token of untold eukaryotic diversity. In: Modern Soil Microbiology, Eds: van Elsas JD, Trevors JT, Soares Rosado A & Nannipieri P. Pp. 125-140. doi:10.1201/9780429059186-8.
  • Fiore-Donno AM, Tice AK & Brown MW (2018) A non-flagellated member of the Myxogastria and expansion of the Echinosteliida. J Euk Microbiol. 66:538-544. doi:10.1111/jeu.12694
  • Fiore-Donno AM, Rixen C, Rippin M, Glaser K, Samolov E, Karsten U, Becker B & Bonkowski M (2018) New barcoded primers for efficient retrieval of cercozoan sequences in high-throughput environmental diversity surveys, with emphasis on worldwide biological soil crusts. Mol Ecol Res, 18:229-239. doi:10.1111/1755-0998.12729.
  • Sapp M, Ploch S, Fiore-Donno AM, Bonkowski M & Rose LE (2018) Protists are an integral part of the Arabidopsis thaliana microbiome. Environ Microbiol, 20:30-43. doi:10.1111/1462-2920.13941.
  • Geisen S, Mitchell EAD, Wilkinson DM, Adl SM, Bonkowski M, Brown MW, Fiore-Donno AM et al. (2017) Soil protistology rebooted: 30 fundamental questions to start with. Soil Biol Biochem, 111:94-103.
  • Shang Y, Sikorski J, Bonkowski M, Fiore-Donno AM, Kandeler E, Marhan S, Boeddinghaus RS, Solly EF, Schrumpf M, Schöning I, Wubet T, Buscot F & Overmann J (2017) Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters. PLoS ONE, 12:e0173765.
  • Tice AK, Shadwick L, Fiore-Donno AM, Geisen S, Kang S, Schuler GA, Spiegel FW, Wilkinson KA, Bonkowski M, Dumack K, Lahr DJG, Voelcker E, Clauß S, Zhang J, Brown MW (2016). Expansion of the molecular and morphological diversity of Acanthamoebidae (Centramoebida, Amoebozoa) and identification of a novel life cycle type within the group. Biol Dir 11:69.
  • Fiore-Donno AM, Weinert J, Wubet T, Bonkowski M (2016). Metacommunity analysis of amoeboid protists in grassland soils. Sci Rep6:19068.
  • Kretzschmar M, Kuhnt A, Bonkowski M & Fiore-Donno AM(2016) Phylogeny of the highly divergent Echinosteliales (Amoebozoa). J Euk Microbiol63:453-459.
  • Cavalier-Smith T, Fiore-Donno AM, Chao EE, Kudryavtsev A, Berney C, Snell EA & Lewis R (2016) Multigene phylogeny resolves deep branching of Amoebozoa. Mol Phyl Evol 83:293-304.
  • Fiore-Donno AM, Clissmann F, Meyer M, Schnittler M, Cavalier-Smith T (2013) Two-gene Phylogeny of Bright-Spored Myxomycetes (Slime Moulds, Superorder Lucisporidia). PLoS ONE 8(5): e62586.
  • Cavalier-Smith T, Chao EE, Snell EA, Berney C, Fiore-Donno AM& Lewis R (2014) Multigene eukaryote phylogeny reveals the likely protozoan ancestors of opisthokonts (animals, fungi, choanozoans) and Amoebozoa. Mol Phyl Evol 81:71-85.
  • Geisen S, Fiore-Donno AM, Walochnik J & Bonkowski M (2014) Acanthamoeba everywhere: high diversity of Acanthamoeba in soils. Paras Res 113:3151-3158.
  • Aguilar M, Fiore-Donno AM& Cavalier-Smith T (2014) Using environmental niche models to test the ‘everything is everywhere’ hypothesis for Badhamia. ISME J8:737-745.
  • Fiore-Donno AM, Clissmann F, Meyer M, Schnittler M & Cavalier-Smith T (2013) Two-gene phylogeny of bright-spored myxomycetes (slime moulds, superorder Lucisporidia). PLoS ONE8:e62586.
  • Kamono A, Meyer M, Cavalier-Smith T, Fukui M, Fiore-Donno AM (2013) Exploring slime mould diversity in high-altitude forests and grasslands by environmental RNA analysis. FEMS Microbiology Ecology, 94:98-109
  • Pawlowski J, Adl SM, Audic S, Bass D, Belbahri L, Berney C, Bowser S, Cepicka I, Decelle J, Dunthorn M, Fiore-Donno AM, Gile G, Holzmann M, Jahn R, Jirků M, Keeling PJ, Kostka M, Kudryavtsev A, Lara E, Lukeš J et al. (2012) CBOL Protist Working Group: Barcoding eukaryotic richness beyond the animal, plant and fungal kingdoms. PloS Biology 10: e1001419.
  • Fiore-Donno AM, Kamono A, Meyer M, Schnittler M, Fukui M, Cavalier-Smith T (2012) 18S rDNA phylogeny of Lamproderma and allied genera (Stemonitales, Myxomycetes, Amoebozoa). PLoS ONE 7: e35359.
  • Fiore-Donno AM, Novozhilov Y., Meyer M, Schnittler M (2011) Genetic structure of two protist species (Myxogastria, Amoebozoa) suggests asexual reproduction in sexual amoebae. PLoS ONE 6: e22872.
  • Stephenson SE, Fiore-Donno AM, Schnittler M (2011) Myxomycetes in soil. Soil Biology and Biochemistry 43, 2237-2242.
  • Fiore-Donno AM, Nikolaev SI, Nelson M, Pawlowski J, Cavalier-Smith T, Baldauf SL (2010) Deep phylogeny and evolution of slime moulds (Mycetozoa). Protist 161, 55-70.
  • Fiore-Donno AM, Meyer M., Baldauf SL, Pawlowski J (2008) Evolution of dark-spored Myxomycetes (slime-molds): molecules versus morphology. Molecular Phylogenetics and Evolution 46, 878-889.
  • Fiore-Donno AM, Berney C, Pawlowski J, Baldauf SL (2005) Higher-order phylogeny of plasmodial slime molds (Myxogastria) based on EF1A and SSU rRNA sequences. Journal of Eukaryotic Microbiology 52, 201-210.
  • Fiore-Donno AM, Martin F (2001) Populations of ectomycorrhizal Laccaria amethystina and Xerocomus spp. show contrasting colonization patterns in a mixed forest. New Phytologist 152, 533-542.