PD Dr. Mika Tarkka

Contact / Address


PD Dr. Mika Tarkka
Senior Scientist

Department of Soil Ecology
Helmholtz Centre for Environmental Research - UFZ
Theodor-Lieser-Strasse 4 | D-06120 Halle/Saale
Germany

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Fax:
Email:

+49 345 5585 414
+49 345 5585 449
mika.tarkka@ufz.de

Mika Tarkka

Research interest

Plant beneficial micro-organisms

My scientific work is devoted to answering the question how soil microorganisms affect plant growth and stress resistance, and whether these interactions can be used to benefit plant health. In particular, my colleagues and I work with micro-organisms associated with pedunculate oak, and our models of biotic interactions include streptomycetes, fungal mutualists and pathogens. Our current work on ectomycorrhizal symbiosis assesses the physiology and molecular interactions from both the host plant’s and the symbiotic fungus’ point of view. While much of the current work focusses on genome regulation, my colleagues and I have also performed analyses on soil bacterial communities influencing plant and fungal resistance against parasites, and playing out in decomposition and nutrient mobilisation. My main motivation in this research field is to contribute to the assessment of the overall impact of microorganisms on plant health, and to assess the existing uses of microbes for improved plant production. Overall, I believe that combination of model systems with field work pave the way for a novel, more dynamic view on plant-microbe interactions.


Current position

since 2007

Senior Scientist in Molecular Plant-Microbe Interactions, Department of Soil Ecology, Helmholtz Centre for Environmental Research - UFZ

Curriculum Vitae

2001-2007

Research Associate at the University of Tübingen, Dept. of Physiological Ecology of Plants.
Projects: Modulation of fungal virulence and symbiosis with soil bacteria (with R. Hampp).
Horizontal gene transfer in ectomycorrhiza and Biological safety of transgenic poplars overproducing glutathione (with U. Nehls)

2001

Ph. D. thesis: Developmentally regulated proteins in Scots pine roots and ectomycorrhiza. Supervisor: Marjatta Raudaskoski

1995

M. Sc. Major subject plant physiology, minor subjects biochemistry and general chemistry.


Projects

TrophinOak

The TrophinOak project investigates the interactions between endogenous rhythmic growth and biotic interactions at the levels of resource allocation and gene expression.

Attached Project

"Increasing the stress resistance of agricultural ecosystems through plant growth promoting rhizobacteria (PGPR) using winter wheat (Triticum L.) production as a case study"
Funded by DBU (20015/391) | Project term: 2016 - 2019 | PhD Student: Claudia Breitkreuz
Supervision by Dr. Mika Tarkka and Dr. Thomas Reitz


Research platforms

PhytOakMeter

The PhytOakMeter platform was created by planting pedunculate oak DF159 trees along a geographic gradient in Europe. It used to investigate the adaptation of the oak trees and the associated organisms to different climates, soils, and land use types.

Global Change Experimental Facility (GCEF)

The GCEF is a field experiment at the UFZ research station Bad Lauchstädt, used for the investigation of the impacts of climate change and land use scenarios on ecosystem processes.


Selected publications

Maboreke, H.R., Feldhahn, L., Bönn, M., Tarkka, M.T., Buscot, F., Herrmann, S., Menzel, R., Ruess, L. (2016):
Transcriptome analysis in oak uncovers a strong impact of endogenous rhythmic growth on the interaction with plant-parasitic nematodes.
BMC Genomics 17 , art. 627   Journal

Complete lists of publications

Inhalt:

Artikel in ISI-gelisteten Zeitschriften (30)
Artikel in anderen Zeitschriften (nicht ISI gelistet) (3)
Buchkapitel (4)

Weiterführende Recherchen können Sie in unserem Publikationsverzeichnis durchführen.

Artikel in ISI-gelisteten Zeitschriften (30)

  • Herrmann, S., Grams, T.E.E., Tarkka, M.T., Angay, O., Bacht, M., Bönn, M., Feldhahn, L., Graf, M., Kurth, F., Maboreke, H., Mailander, S., Recht, S., Fleischmann, F., Ruess, L., Schädler, M., Scheu, S., Schrey, S., Buscot, F., (2016):
    Endogenous rhythmic growth, a trait suitable for the study of interplays between multitrophic interactions and tree development
    Perspect. Plant Ecol. Evol. Syst. 19 , 40 - 48
    Volltext (URL)
  • Maboreke, H.R., Feldhahn, L., Bönn, M., Tarkka, M.T., Buscot, F., Herrmann, S., Menzel, R., Ruess, L., (2016):
    Transcriptome analysis in oak uncovers a strong impact of endogenous rhythmic growth on the interaction with plant-parasitic nematodes
    BMC Genomics 17 , art. 627
    Volltext (URL)
  • Caravaca, F., Maboreke, H., Kurth, F., Herrmann, S., Tarkka, M.T., Ruess, L., (2015):
    Synergists and antagonists in the rhizosphere modulate microbial communities and growth of Quercus robur L.
    Soil Biol. Biochem. 82 , 65 - 73
    Volltext (URL)
  • Herrmann, S., Recht, S., Boenn, M., Feldhahn, L., Angay, O., Fleischmann, F., Tarkka, M.T., Grams, T.E.E., Buscot, F., (2015):
    Endogenous rhythmic growth in oak trees is regulated by internal clocks rather than resource availability
    J. Exp. Bot. 66 (22), 7113 - 7127
    Volltext (URL)
  • Kohler, A., Kuo, A., Nagy, L.G., Morin, E., Barry, K.W., Buscot, F., Canbäck, B., Choi, C., Cichocki, N., Clum, A., Colpaert, J., Copeland, A., Costa, M.D., Doré, J., Floudas, D., Gay, D., Girlanda, M., Henrissat, B., Herrmann, S., Hess, J., Högberg, N., Johansson, T., Khouja, H.-R., La Butti, K., Lahrmann, U., Levasseur, A., Lindquist, E.A., Lipzen, A., Marmeisse, R., Martino, E., Murat, C., Chew, Y., Ngan, C.Y., Nehls, U., Plett, J.M., Pringle, A., Ohm, R.A., Perotto, S.P., Riley, R., Rineau, F., Ruytinx, J., Salamov, A., Shah, F., Sun, H., Tarkka, M., Tritt, A., Veneault-Fourrey, C., Zuccaro, A., Tunlid, A., Grigoriev, I.V., Hibbett, D.S., Martin, F., (2015):
    Convergent losses of decay mechanisms and rapid turnover of symbiosis genes in mycorrhizal mutualists
    Nature Genet. 47 , 410 - 415
    Volltext (URL)
  • Kurth, F., Feldhahn, L., Bönn, M., Herrmann, S., Buscot, F., Tarkka, M.T., (2015):
    Large scale transcriptome analysis reveals interplay between development of forest trees and a beneficial mycorrhiza helper bacterium
    BMC Genomics 16 , art. 658
    Volltext (URL)
  • Lesur, I., Le Provost, G., Bento, P., Da Silva, C., Leplé, J.-C., Murat, F., Ueno, S., Bartholomé, J., Lalanne, C., Ehrenmann, F., Noirot, C., Burban, C., Léger, V., Amselem, J., Belser, C., Quesneville, H., Stierschneider, M., Fluch, S., Feldhahn, L., Tarkka, M., Herrmann, S., Buscot, F., Klopp, C., Kremer, A., Salse, J., Aury, J.-M., Plomion, C., (2015):
    The oak gene expression atlas: insights into Fagaceae genome evolution and the discovery of genes regulated during bud dormancy release
    BMC Genomics 16 , art. 112
    Volltext (URL)
  • Goris, T., Schubert, T., Gadkari, J., Wubet, T., Tarkka, M., Buscot, F., Adrian, L., Diekert, G., (2014):
    Insights into organohalide respiration and the versatile catabolism of Sulfurospirillum multivorans gained from comparative genomics and physiological studies
    Environ. Microbiol. 16 (11), 3562 - 3580
    Volltext (URL)
  • Kurth, F., Mailänder, S., Bönn, M., Feldhahn, L., Herrmann, S., Große, I., Buscot, F., Schrey, S.D., Tarkka, M.T., (2014):
    Streptomyces-induced resistance against oak powdery mildew involves host plant responses in defense, photosynthesis, and secondary metabolism pathways
    Mol. Plant-Microbe Interact. 27 (9), 891 - 900
    Volltext (URL)
  • Kurth, F., Zeitler, K., Feldhahn, L., Neu, T.R., Weber, T., Krištůfek, V., Wubet, T., Herrmann, S., Buscot, F., Tarkka, M.T., (2013):
    Detection and quantification of a mycorrhization helper bacterium and a mycorrhizal fungus in plant-soil microcosms at different levels of complexity
    BMC Microbiol. 13 , art. 205
    Volltext (URL)
  • Pavic, A., Stanković, S., Saljnikov, E., Krüger, D., Buscot, F., Tarkka, M., Marjanović, Z., (2013):
    Actinobacteria may influence white truffle (Tuber magnatum Pico) nutrition, ascocarp degradation and interactions with other soil fungi
    Fungal Ecol. 6 (6), 527 - 538
    Volltext (URL)
  • Pöritz, M., Goris, T., Wubet, T., Tarkka, M.T., Buscot, F., Nijenhuis, I., Lechner, U., Adrian, L., (2013):
    Genome sequences of two dehalogenation specialists - Dehalococcoides mccartyi strains BTF08 and DCMB5 enriched from the highly polluted Bitterfeld region
    FEMS Microbiol. Lett. 343 (2), 101 - 104
    Volltext (URL)
  • Tarkka, M.T., Herrmann, S., Wubet, T., Feldhahn, L., Recht, S., Kurth, F., Mailänder, S., Bönn, M., Neef, M., Angay, O., Bacht, M., Graf, M., Maboreke, H., Fleischmann, F., Grams, T.E.E., Ruess, L., Schädler, M., Brandl, R., Scheu, S., Schrey, S.D., Grosse, I., Buscot, F., (2013):
    OakContigDF159.1, a reference library for studying differential gene expression in Quercus robur during controlled biotic interactions: use for quantitative transcriptomic profiling of oak roots in ectomycorrhizal symbiosis
    New Phytol. 199 (2), 529 - 540
    Volltext (URL)
  • Schrey, S.D., Erkenbrack, E., Früh, E., Fengler, S., Hommel, K., Horlacher, N., Schulz, D., Ecke, M., Kulik, A., Fiedler, H.P., Hampp, R., Tarkka, M.T., (2012):
    Production of fungal and bacterial growth modulating secondary metabolites is widespread among mycorrhiza-associated streptomycetes
    BMC Microbiol. 12 , art. 164
    Volltext (URL)
  • Taubert, M., Vogt, C., Wubet, T., Kleinsteuber, S., Tarkka, M.T., Harms, H., Buscot, F., Richnow, H.-H., von Bergen, M., Seifert, J., (2012):
    Protein-SIP enables time-resolved analysis of the carbon flux in a sulfate-reducing, benzene-degrading microbial consortium
    ISME J. 6 (12), 2291 - 2301
    Volltext (URL)
  • Yurkov, A., Krüger, D., Begerow, D., Arnold, N., Tarkka, M.T., (2012):
    Basidiomycetous yeasts from Boletales fruiting bodies and their interactions with the mycoparasite Sepedonium chrysospermum and the host fungus Paxillus
    Microb. Ecol. 63 (2), 295 - 303
    Volltext (URL)
  • Frey-Klett, P., Burlinson, P., Deveau, A., Barret, M., Tarkka, M., Sarniguet, A., (2011):
    Bacterial-fungal interactions: hyphens between agricultural, clinical, environmental, and food microbiologists
    Microbiol. Mol. Biol. Rev. 75 (4), 583 - 609
    Volltext (URL)
  • Lehr, N.A., Adomas, A., Asiegbu, F.O., Hamp, R., Tarkka, M.T., (2009):
    WS-5995 B, an antifungal agent inducing differential gene expression in the conifer pathogen Heterobasidion annosum but not in Heterobasidion abietinum
    Appl. Microbiol. Biotechnol. 85 (2), 347 - 358
    Volltext (URL)
  • Tarkka, M.T., Sarniguet, A., Frey-Klett, P., (2009):
    Inter-kingdom encounters: recent advances in molecular bacterium-fungus interactions
    Curr. Genet. 55 (3), 233 - 243
    Volltext (URL)
  • Lehr, N.A., Schrey, S.D., Hampp, R., Tarkka, M.T., (2008):
    Root inoculation with a forest soil streptomycete leads to locally and systemically increased resistance against phytopathogens in Norway spruce
    New Phytol. 177 (4), 965 - 976
    Volltext (URL)
  • Schrey, S.D., Tarkka, M.T., (2008):
    Friends and foes: streptomycetes as modulators of plant disease and symbiosis
    Antonie Van Leeuwenhoek 94 (1), 11 - 19
    Volltext (URL)
  • Frey-Klett, P., Garbaye, J., Tarkka, M., (2007):
    The mycorrhiza helper bacteria revisited
    New Phytol. 176 (1), 22 - 36
    Volltext (URL)
  • Lehr, N.A., Schrey, S.D., Bauer, R., Hampp, R., Tarkka, M.T., (2007):
    Suppression of plant defence response by a mycorrhiza helper bacterium
    New Phytol. 174 (4), 892 - 903
    Volltext (URL)
  • Schrey, S.D., Salo, V., Raudaskoski, M., Hampp, R., Nehls, U., Tarkka, M.T., (2007):
    Interaction with mycorrhiza helper bacterium Streptomyces sp. AcH 505 modifies organisation of actin cytoskeleton in the ectomycorrhizal fungus Amanita muscaria (fly agaric)
    Curr. Genet. 52 (2), 77 - 85
    Volltext (URL)
  • Tarkka, M.T., Piechulla, B., (2007):
    Aromatic weapons: truffles attack plants by the production of volatiles
    New Phytol. 175 (3), 381 - 383
    Volltext (URL)
  • Riedlinger, J., Schrey, S.D., Tarkka, M.T., Hampp, R., Kapur, M., Fiedler, H.P., (2006):
    Auxofuran, a novel metabolite that stimulates the growth of fly agaric, is produced by the mycorrhiza helper bacterium Streptomyces strain AcH 505
    Appl. Environ. Microb. 72 (5), 3550 - 3557
    Volltext (URL)
  • Tarkka, M.T., Schrey, S., Nehls, U., (2006):
    The α-tubulin gene AmTuba1: a marker for rapid mycelial growth in the ectomycorrhizal basidiomycete Amanita muscaria
    Curr. Genet. 49 (5), 294 - 301
    Volltext (URL)
  • Juuti, J.T., Jokela, S., Tarkka, M.T., Paulin, L., Lahdensalo, J., (2005):
    Two phylogenetically highly distinct β-tubulin genes of the basidiomycete Suillus bovinus
    Curr. Genet. 47 (4), 253 - 263
    Volltext (URL)
  • Schrey, S.D., Schellhammer, M., Ecke, M., Hampp, R., Tarkka, M.T., (2005):
    Mycorrhiza helper bacterium Streptomyces AcH 505 induces differential gene expression in the ectomycorrhizal fungus Amanita muscaria
    New Phytol. 168 (1), 205 - 216
    Volltext (URL)
  • Saarma, K., Tarkka, M.T., Itavaara, M., Fagerstedt, K.V., (2003):
    Heat shock protein synthesis is induced by diethyl phthalate but not by di(2-ethylhexyl) phthalate in radish (Raphanus sativus)
    J. Plant Physiol. 160 (9), 1001 - 1010
    Volltext (URL)
zum Inhalt

Artikel in anderen Zeitschriften (nicht ISI gelistet) (3)

  • Tarkka, M.T., Feldhahn, L., Buscot, F., Wubet, T., (2015):
    Genome sequence of the mycorrhiza helper bacterium Streptomyces sp. strain AcH 505
    Genome Announc. 3 (2), e01386-14
    Volltext (URL)
  • Tarkka, M.T., Feldhahn, L., Krüger, D., Arnold, N., Buscot, F., Wubet, T., (2015):
    Draft genome sequence of Streptomyces sp. Strain 150FB, a mushroom mycoparasite antagonist
    Genome Announc. 3 (2), e01441-14
    Volltext (URL)
  • Tarkka, M.T., Lehr, N.A., Hampp, R., Schrey, S.D., (2008):
    Plant behavior upon contact with streptomycetes
    Plant Signaling & Behavior 3 (11), 1 - 3
    Volltext (URL)
zum Inhalt

Buchkapitel (4)

  • Hampp, R., Tarkka, M.T., (2009):
    Interaction with soil microorganisms
    In: Varma, A., Kharkwal, A.C., (eds.)
    Symbiotic fungi. Principles and practice
    Soil Biology 18
    Springer, Berlin, Heidelberg, p. 197 - 210
    Volltext (URL)
  • Tarkka, M., Hampp, R., (2008):
    Secondary metabolites of soil streptomycetes in biotic interactions
    In: Karlovsky, P., (ed.)
    Secondary metabolites in soil ecology
    Soil Biology 14
    Springer, Berlin, Heidelberg, p. 107 - 126
    Volltext (URL)
  • Tarkka, M., Schrey, S.D., Hampp, R., (2008):
    Plant associated soil micro-organisms
    In: Nautiyal, C.S., Dion, P., (eds.)
    Molecular mechanisms of plant and microbe coexistence
    Soil Biology 15
    Springer, Berlin, Heidelberg, p. 3 - 51
    Volltext (URL)
  • Tarkka, M.T., Frey-Klett, P., (2008):
    Mycorrhiza helper bacteria
    In: Varma, A., (ed.)
    Mycorrhiza. State of the art, genetics and molecular biology, eco-function, biotechnology, eco-physiology, structure and systematics
    Springer, Berlin, Heidelberg, p. 113 - 132
    Volltext (URL)
zum Inhalt

Peer-reviewed publications

Riedlinger J., Schrey S.D., Tarkka M.T., Hampp R., Kapur M., Fiedler H.P. (2006)
Auxofuran, a novel substance stimulating growth of fly agaric, produced by the mycorrhiza helper bacterium Streptomyces AcH 505.
Applied and Environmental Microbiology 72, 3550-3557. download

Tarkka M.T., Schrey S., Nehls U . (2006)
The alpha-tubulin gene AmTuba1: A marker for rapid mycelial growth in the ectomycorrhizal basidiomycete Amanita muscaria.
Current Genetics 49, 294-301. download

Schrey S.D., Schellhammer M., Ecke M., Hampp R., Tarkka M.T. (2005)
Mycorrhization helper bacterium Streptomyces AcH 505 induces differential gene expression in the ectomycorrhizal fungus Amanita muscaria.
New Phytologist 168, 205-216. download

Juuti J.T., Jokela S., Tarkka M.T., Paulin L., Lahdensalo J. (2005)
Two phylogenetically highly distinct beta-tubulin genes of the basidiomycete Suillus bovinus.
Current Genetics 47, 253-263.

Saarma K., Tarkka M.T., Itavaara M., Fagerstedt K.V. (2003)
Heat shock protein synthesis is induced by diethyl phthalate but not by di(2-ethylhexyl) phthalate in radish (Raphanus sativus).
Journal of Plant Physiology 160, 1001-1010.

Gorfer M., Tarkka M.T., Hanif M., Pardo A.G., Laitiainen E., Raudaskoski M. (2001)
Characterization of small GTPases Cdc42 and Rac and the relationship between Cdc42 and actin cytoskeleton in vegetative and ectomycorrhizal hyphae of Suillus bovinus.
Molecular Plant-Microbe Interactions 14, 135-144.

Tarkka M.T., Nyman T.A., Kalkkinen N., Raudaskoski M. (2001)
Scots pine expresses short root-specific peroxidases during development.
European Journal of Biochemistry 268, 86-92.

Tarkka M.T., Vasara R., Gorfer M., Raudaskoski M. (2000)
Molecular characterization of actin genes from homobasidiomycetes: two different actin genes from Schizophyllum commune and Suillus bovinus.
Gene 251, 27-35.

Tarkka M., Niini S.S., Raudaskoski M. (1998)
Developmentally regulated proteins during differentiation of root system and ectomycorrhiza in Scots pine (Pinus sylvestris) with Suillus bovinus.
Physiologia Plantarum 104, 449-455.

Niini S.S., Tarkka M.T., Raudaskoski M. (1996)
Tubulin and actin protein patterns in Scots pine (Pinus sylvestris) roots and developing ectomycorrhiza with Suillus bovinus.
Physiologia Plantarum 96, 186-192.


Book Chapters

Nehls U., Zhang C., Tarkka M., Hampp R., Fladung M. (2006)
Investigation of horizontal gene transfer from transgenic aspen to ectomycorrhizal fungi.
In: Recent developments in tree transgenesis, Fladung M, Ewald D (eds), pp 323-333. Springer-Verlag

Tarkka M.T., Nehls U., Hampp R. (2005)
Physiology of Ectomycorrhiza (ECM).
Progress in Botany 66, 220-247.

Raudaskoski M., Tarkka M.T., Niini S.S. (2004)
Mycorrhizal development and cytoskeleton.
In: Plant Surface Microbiology, pp. 293-330. Springer-Verlag.

Raudaskoski M., Pardo A., Tarkka M., et al. (2001)
Small GTPases, cytoskeleton and signal transduction in filamentous homobasidiomycetes.
NATO Science Series I: 328, 123-136