Workgroup Terrestrial Ecology
Prof. Dr. Michael Bonkowski
Dr. Anna Maria Fiore-Donno

Dr. Anna Maria Fiore-Donno


room: -1.807
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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

1.1 Diversity of Cercozoa and their response to increasing aridity in desert soil crusts

In collaboration with: Fernando Maestre (Uni Rey Juan Carlos, Mostoles, Spain), Michael Bonkowski.

In a global field study conducted across 80 dryland sites from all continents the diversity and abundance of soil bacteria and fungi was reduced as aridity increased (Maestre et al. 2015, PNAS, doi:10.1073/pnas.1516684112). From these same samples, I have obtained a wide variety of Cercozoa. Cercozoa are among the most common amoebae and flagellates in soils and probably play a major role in nutrient cycling as bacterial feeders. I developed specific primers targeting the V4 variable region of the small subunit of the ribosomal RNA gene for Illumina high-throughput sequencing. All 80 soil samples gave positive results (average number of sequences/sample: average 74,077) - rarefaction curves show that saturation is reached, and preliminary results show that the 2,992 OTUs are not evenly distributed. Multivariate analyses are in progress to see how the composition and diversity of Cercozoa vary across the sites depending on soil, vegetation and climatic conditions and their links with bacteria, fungi and plants. We will explore how the diversity of Cercozoa influences ecosystem functioning, as it has already been published for bacteria and fungi from the same dataset (Delgado-Baquerizo, Maestre et al. 2016, Nat Commun, doi:10.1038/ncomms10541).

1.2 BACK TO THE ROOTS - how do plants select for beneficial microbes in the rhizosphere and the role of protists (Cercozoa and Myxomycetes).

In collaboration with: Mendes Rodrigo (Lab of Env Microbiol, Embrapa Environment, Jaguariuna, Brazil), De Magalhaes Rosa Artur Jordao (Brazilian Agricultural Research Corporation) and Jos Raaijmakers (Department of Microbial Ecology, Netherlands Institute of Ecology, Wageningen), Michael Bonkowski, University of Cologne.

Plant breeding using modern agricultural practices, which include fertilization and pesticides, possibly led to a selection against plant traits that are essential for the establishment of beneficial microbes in the rhizosphere. This study compares the rhizosphere microbiome of modern and ancient cultivars to that of wild strains of wheat (Triticum aestivum). Next-generation sequencing of 16S rRNA (bacterial community) and 18S rRNA (fungal community) has been conducted on 96 plants, revealing different communities in wild and modern stains of wheat. Metagenomics of soil protists (Cercozoa and Myxomycetes) are conducted to infer the role of bacterivores and fungivores on nutrient cycling and plant growth.
We have obtained Illumina sequencing results targeting Cercozoa (Myxomycetes still in progress) from 96 rhizosphere samples as described above. I am currently supervising a PhD student, Kenneth Dumack, on the bioinformatic pipeline and the basic statistics.

1.3 SCALEMIC - spatio-temporal diversity of Cercozoa in a grassland soil

In collaboration with: Ellen Kandeler and Sven Marhan( University of Hohenheim), Michael Bonkowski, University of Cologne.

In the framework of the priority program "Exploratorien zur funktionellen Biodiversitätsforschung" of the DFG, subproject "SCALEMIC" I investigated the spatial and temporal distribution of the Cercozoa in an unfertilized grassland soil in the Swabian Alps. From 180 soil samples, collected six times from April to November 2011 in a 10 m2 plot, I obtained ~10 millions good quality reads, of which ~5.5 millions were unique. The primers were highly specific: 91% of the reads were assigned to Cercozoa. Sequences from the whole phylum were obtained, spanning from the basal plant parasites Plasmodiophorida (Endomyxa), to the filosean Sarcomonadea, Cryomonadida, the testate amoebae Euglyphida and the very abundant - in environmental sampling - Glissomonadida. The spatial variability of soil bacterial community structure, plant diversity, and soil properties have been already published and possible correlations between those traits and cercozoan distribution are currently investigated.

Professional career

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. 2005Scientific 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.


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.


Fiore-Donno AM, Rixen C, Rippin M, Glaser K, Samolov E, Karsten U, Becker B & Bonkowski M. 2017. Efficient retrieval of cercozoan sequences in next-generation environmental diversity surveys, with emphasis on worldwide biological soil crusts. Mol Ecol Res, in review, MER-17-0056

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.<7p>

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.