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Faculty of Mathematics and Natural SciencesInstitute of Zoology - AG Bonkowski

2024

  • Albracht C, Solbach MD, Hennecke J, Bassi L, van der Ploeg GR, Eisenhauer N, Weigelt A, Buscot F, Heintz-Buschart A (2024) Common soil history is more important than plant history for arbuscular mycorrhizal community assembly in an experimental grassland diversity gradient. Biol Fertil Soils 60, 547–562. doi: https://doi.org/10.1007/s00374-024-01821-0
  • Fiore-Donno AM, Freudenthal J, Dahl MB, Rixen C, Urich T, Bonkowski M (2024) Biotic interactions explain seasonal dynamics of the alpine soil microbiome. ISME Communications 4. doi: 10.1093/ismeco/ycae028
  • Qiao M, Sun R, Wang Z, Dumack K, Xie X, Dai C, Wang E, Zhou J, Sun B, Peng X, Bonkowski M, Chen Y (2024) Legume rhizodeposition promotes nitrogen fixation by soil microbiota under crop diversification. Nature Communications 15: 2924. doi: 10.1038/s41467-024-47159-x.
  • Schlüter S, Lucas M, Grosz B, Ippisch O, Zawallich J, He H, Dechow R, Kraus D, Blagodatsky S, Senbayram M, Kravchenko A, Vogel H-J, Well R (2024) The anaerobic soil volume as a controlling factor of denitrification: a review. Biology and Fertility of Soils. doi: 10.1007/s00374-024-01819-8.
  • Niedeggen D, Rüger L, Oburger E, Santangeli M, Mutez A, Vetterlein D, Blagodatsky S, Bonkowski M (2024) Microbial utilisation of maize rhizodeposits applied to an agricultural soil at a range of concentrations bioRxiv preprint doi: https://doi.org/10.1101/2024.03.15.585161
  • Clayton J, Lemanski K, Solbach MD, Temperton VM, Bonkowski M (2024) Two-way NxP fertilisation experiment on barley (Hordeum vulgare) reveals shift from additive to synergistic N-P interactions at critical phosphorus fertilisation level. Frontiers in Plant Science 15: 1346729. doi: 10.3389/fpls.2024.1346729.
  • Vogel HJ, Amelung W, Baum C, Bonkowski M, Blagodatsky S, Grosch R, Herbst M, Kiese R, Koch S, Kuhwald M, König S, Leinweber P, Lennartz B, Müller CW, Pagel H, Rillig MC, Rüschhoff J, Russell D, Schnepf A, Schulz S, Siebers N, Vetterlein D, Wachendorf C, Weller U, Wollschläger U (2024) How to adequately represent biological processes in modeling multifunctionality of arable soils. Biology and Fertility of Soils. 60: 263–306, doi: 10.1007/s00374-024-01802-3.
  • Zhu L, Chen Y, Sun R, Zhang J, Hale L, Dumack K, Geisen S, Deng Y, Duan Y, Zhu B (2023) Resource availability affects how underground microbes band together to support plant life. Researchsquare.com.
  • Kästner M, Maskow T, Miltner A, Lorenz M, Thiele-Bruhn S, Bölscher T, Blagodatsky S, Streck T, Pagel H, Blagodatskaya E (2024) Gibbs energy or enthalpy—What is relevant for microbial C‐turnover in soils? Global Change Biology 30: e17183.
  • Kumar A, Kuznetsova O, Gschwendtner S, Chen H, Alonso‐Crespo IM, Yusuf M, Schulz S, Bonkowski M, Schloter M, Temperton V (2024) Implications of domestication syndrome in barley for above-and belowground plant traits and microbial interactions. Plants, People, Planet (subm. 14.12.23)
  • Ferlian O, Goldmann K, Bonkowski M, Dumack K, Wubet T, Eisenhauer N (2024) Invasive earthworms shift soil microbial community structure in northern North American forest ecosystems. iScience 27. doi: 10.1016/j.isci.2024.108889.
  • Dumack K, Lara E, Duckert C, Ermolaeva E, Siemensma F, Singer D, Krashevska V, Lamentowicz M, Mitchell EAD (2024) It's time to consider the Arcellinida shell as a weapon. European Journal of Protistology 92: 126051. doi: https://doi.org/10.1016/j.ejop.2024.126051.
  • Hennecke J, Bassi L, Mommer L, Albracht C, Bergmann J, Eisenhauer N, Guerra CA, Heintz-Buschart A, Kuyper TW, Lange M, Solbach MD, Weigelt A (2023) Responses of rhizosphere fungi to the root economics space in grassland monocultures of different age. New Phytologist 240: 2035-2049. https://doi.org/10.1111/nph.19261.
  • Bassi L, Hennecke J, Albracht C, Bröcher M, Solbach MD, Schaller J, Doan VC, Wagner H, Eisenhauer N, Ebeling A, Meyer ST, van Dam NM, Weigelt (2024) A Uncovering the secrets of monoculture yield decline: trade-offs between leaf and root chemical and physical defence traits in a grassland experiment. Oikos e10061. doi: 10.1111/oik.10061.
  • Laub M, Blagodatsky S, Van de Broek M, Schlichenmaier S, Kunlanit B, Six J, Vityakon P, Cadisch G (2024) SAMM version 1.0: a numerical model for microbial- mediated soil aggregate formation. Geosci Model Dev 17: 931-956. doi: 10.5194/gmd-17-931-2024.            
  • Pingthaisong W, Blagodatsky S, Vityakon P, Cadisch G (2024) Mixing plant residues of different quality reduces priming effect and contributes to soil carbon retention. Soil Biology and Biochemistry 188: 109242. doi: https://doi.org/10.1016/j.soilbio.2023.109242.
  • Neyret M, Le Provost G, Boesing AL, Schneider FD, Baulechner D, Bergmann J, de Vries FT, Fiore-Donno AM, Geisen S, Goldmann K, Merges A, Saifutdinov RA, Simons NK, Tobias JA, Zaitsev AS, Gossner MM, Jung K, Kandeler E, Krauss J, Penone C, Schloter M, Schulz S, Staab M, Wolters V, Apostolakis A, Birkhofer K, Boch S, Boeddinghaus RS, Bolliger R, Bonkowski M, Buscot F, Dumack K, Fischer M, Gan HY, Heinze J, Hölzel N, John K, Klaus VH, Kleinebecker T, Marhan S, Müller J, Renner SC, Rillig MC, Schenk NV, Schöning I, Schrumpf M, Seibold S, Socher SA, Solly EF, Teuscher M, van Kleunen M, Wubet T, Manning P (2024) A slow-fast trait continuum at the whole community level in relation to land-use intensification. Nature Communications 15: 1251. doi: 10.1038/s41467-024-45113-5.

2023

  • Rüger L, Feng K, Chen Y, Sun R, Sun B, Deng Y, Vetterlein D, Bonkowski M (2023) Responses of root architecture and the rhizosphere microbiome assembly of maize (Zea mays L.) to a soil texture gradient. Soil Biology and Biochemistry: 109026. doi: https://doi.org/10.1016/j.soilbio.2023.109026.
  • Rocha U, Coelho Kasmanas J, Kallies R, Saraiva JP, Toscan RB, Štefanič P, Bicalho MF, Borim Correa F, Baştürk MN, Fousekis E, Viana Barbosa LM, Plewka J, Probst AJ, Baldrian P, Stadler PF, CLUE-TERRA Consortium... M. Bonkowski, ... A.M. Fiore-Donno, ... (2024) MuDoGeR: Multi-Domain Genome recovery from metagenomes made easy. Molecular Ecology Resources 24: e13904. doi: https://doi.org/10.1111/1755-0998.13904.
  • Nguyen TB-A, Bonkowski M, Dumack K, Chen Q-L, He J-Z, Hu H-W (2023) Protistan predation selects for antibiotic resistance in soil bacterial communities. The ISME Journal. doi: 10.1038/s41396-023-01524-8.
  • Estermann AH, Teixeira Pereira Bassiaridis J, Loos A, Solbach MD, Bonkowski M, Hess S, Dumack K (2023) Fungivorous protists in the rhizosphere of Arabidopsis thaliana – Diversity, functions, and publicly available cultures for experimental exploration. Soil Biology and Biochemistry: 109206. doi: https://doi.org/10.1016/j.soilbio.2023.109206.
  • Hu J, Hassi U, Gebremikael MT, Dumack K, De Swaef T, Wesemael W, Sleutel S, De Neve S (2023) Root Traits Explain Multitrophic Interactions of Belowground Microfauna on Soil Nitrogen Mineralization and Plant Productivity. Available at SSRN 4341051.
  • Heck N, Freudenthal J, Dumack K (2023) Microeukaryotic predators shape the wastewater microbiome. bioRxiv: 2023.2004.2004.535543. doi: https://doi.org/10.1101/2023.04.04.535543
  • Sushko S, Ovsepyan L, Gavrichkova O, Yevdokimov I, Komarova A, Zhuravleva A, Blagodatsky S, Kadulin M, Ivashchenko K (2023) Contribution of microbial activity and vegetation cover to the spatial distribution of soil respiration in mountains. Frontiers in Microbiology 14. doi: https://doi.org/10.3389/fmicb.2023.1165045
  • Rüger L, Ganther M, Freudenthal J, Jansa J, Heintz-Buschart A, Tarkka MT, Bonkowski M (2023) Root cap is an important determinant of rhizosphere microbiome assembly. New Phytologist. doi: https://doi.org/10.1111/nph.19002
  • Rosinger C, Rousk J, Bonkowski M, Rethemeyer J, Jaeschke A (2023) Rewetting the hyper-arid Atacama Desert soil reactivates a carbon-starved microbial decomposer community and also triggers archaeal metabolism. Science of The Total Environment 892: 164785. doi: https://doi.org/10.1016/j.scitotenv.2023.164785
  • Phiwdaeng N, Kaewpradit W, Blagodatsky S, Rasche F (2023) Temporal soil carbon and nitrogen accumulation after land use change from paddy rice to upland sugarcane cropping in Thailand. Geoderma Regional 33: e00656. doi: https://doi.org/10.1016/j.geodrs.2023.e00656
  • Zhu L, Chen Y, Sun R, Zhang J, Hale L, Dumack K, Geisen S, Deng Y, Duan Y, Zhu B, Li Y, Liu W, Wang X, Griffiths BS, Bonkowski M, Zhou J, Sun B (2023) Resource-dependent biodiversity and potential multi-trophic interactions determine belowground functional trait stability. Microbiome 11: 95. doi: https://doi.org/10.1186/s40168-023-01539-5
  • Martens J, Mueller C, Joshi P, Rosinger C, Maisch M, Kappler A, Bonkowski M, Schwamborn G, Schirrmeister L, Rethemeyer J (2023) Stabilization of mineral-associated organic carbon in Pleistocene permafrost. Nature Communications 14:2120. doi: https://doi.org/10.1038/s41467-023-37766-5
  • Chen H, Rosinger Ch, Blagodatsky S, Reichel R, Li B, Kumar A, Rothardt S, Luo J, Brüggemann N, Kage H, Bonkowski M (2023) Straw amendment and nitrification inhibitor controlling N losses and immobilization in a soil cooling-warming experiment. Science of the Total Environment 870: 162007. doi: https://doi.org/10.1016/j.scitotenv.2023.162007
  • Rindt O, Rosinger C, Bonkowski M, Rixen C, Brüggemann N, Urich T, Fiore-Donno AM (2023) Biogeochemical dynamics during snowmelt and in summer in the Alps. Biogeochemistry. 162: 257–266. doi: https://doi.org/10.1007/s10533-022-01005-8

2022

  • ​​​Yim B, Ibrahim Z, Rüger L, Ganther M, Maccario L, Sørensen SJ, Heintz-Buschart A, Tarkka MT, Vetterlein D, Bonkowski M, Blagodatskaya E, Smalla K (2022) Soil texture is a stronger driver of the maize rhizosphere microbiome and extracellular enzyme activities than soil depth or the presence of root hairs. Plant and Soil 478, 229–251. https://doi.org/10.1007/s11104-022-05618-8
  • Dumack K, Feng K, Flues S, Sapp M, Schreiter S, Grosch R, Rose L, Deng Y, Smalla K, Bonkowski M (2022) What Drives the Assembly of Plant-associated Protist Microbiomes? Investigating the Effects of Crop Species, Soil Type and Bacterial Microbiomes. Protist 173: 125913. doi: https://doi.org/10.1016/j.protis.2022.125913
  • Hense J, Schittek K, Forbriger M, Mächtle B, Schäbitz F, Bonkowski M (2022) The oribatid mite (acari: oribatida) community of a high-andean cushion peatland in southern Peru. Acarologia 62(4): 879-891. doi: https://doi.org/10.24349/idxe-mfsx
  • Roy J, Mazel F, Dumack K, Bonkowski M, Rillig MC (2022) Hierarchical phylogenetic community assembly of soil protists in a temperate agricultural field. Environmental Microbiology, doi: https://doi.org/10.1111/1462-2920.16134
  • 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. Philos Trans R Soc Lond B Biol Sci 377: 20210387. doi: 10.1098/rstb.2021.0387.
  • Sun, D., Ardestani, M. M., Pohořelý, M., Moško, J., Winding, A., Bonkowski, M., Zhao, Y. & Frouz, J. (2022) Does micro-sized pyrogenic carbon made in lab affect earthworm mortality in restrained water content? Applied Soil Ecology, 177, 104540. doi.org/10.1016/j.apsoil.2022.104540
  • Schingen M, Barthel LMF, Pham DTK, Pham CT, Nguyen TQ, Ziegler T, Bonkowski M (2022) Will climatic changes affect the Vietnamese crocodile lizard? Seasonal variation in microclimate and activity pattern of Shinisaurus crocodilurus vietnamensis. Amphibia Reptilia doi:10.1163/15685381-bja10089
  • Fiore-Donno, A. M., Human, Z. R., Štursová, M., Mundra, S., Morgado, L., 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 Biology and Biochemistry, 168, 108628. doi.org/10.1016/j.soilbio.2022.108628
  • Schnepf A, Carminati A, Ahmed MA, Ani M, Benard P, Bentz J, Bonkowski M, Knott M, Diehl D, Duddek P, Kröner E, Javaux M, Landl M, Lehndorff E, Lippold E, Lieu A, Mueller CW, Oburger E, Otten W, Portell X, Phalempin M, Prechtel A, Schulz R, Vanderborght J, Vetterlein D (2022) Linking rhizosphere processes across scales: Opinion. Plant and Soil. doi: 10.1007/s11104-022-05306-7.
  • Freudenthal J, Ju F, Bürgmann H, Dumack K (2022) Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal. Microbiome 10. doi: 10.1186/s40168-022-01225-y.
  • Hu J, Gebremikael MT, Tytgat B, Dumack K, Hassi U, Salehi Hosseini P, Sleutel S, Verleyen E, De Neve S (2022) Combined selective gamma irradiation and pulverized soil inoculation for ecologically relevant soil microfauna studies. Applied Soil Ecology 169: 104223. doi: https://doi.org/10.1016/j.apsoil.2021.104223.
  • Dumack, K., Ferlian, O., Morselli Gysi, D., Degrune, F., Jauss, R.-T., Walden, S., Öztoprak, H., Wubet, T., Bonkowski, M., Eisenhauer, N. (2022): Contrasting protist communities (Cercozoa: Rhizaria) in pristine and earthworm-invaded North American deciduous forests. Biological Invasions. doi:10.1007/s10530-021-02726-x..
  • Rosinger C, Clayton J, Baron K, Bonkowski M (2022) Soil freezing-thawing induces immediate shifts in microbial and resource stoichiometry in Luvisol soils along a postmining agricultural chronosequence in Western Germany. Geoderma 408. doi: 10.1016/j.geoderma.2021.115596.

2021

  • Tarkka MT, Bonkowski M, Ge T, Knief C, Razavi BS, Vetterlein D (2021) Editorial: Rhizosphere Spatiotemporal Organisation. Frontiers in Plant Science 12. doi: 10.3389/fpls.2021.795136.
  • Wang H, Weil M, Dumack K, Zak D, Münch D, Günther A, Jurasinski G, Blume-Werry G, Kreyling J, Urich T (2021) Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands. FEMS Microbiology Ecology 97. doi: 10.1093/femsec/fiab121.
  • Dumack K, Siemensma F, Clauß S (2021) Transfer of the thecate amoebae Lecythium spinosum and Pamphagus armatus to Rhizaspis (Thecofilosea, Cercozoa, Rhizaria). European Journal of Protistology: 125843. doi: https://doi.org/10.1016/j.ejop.2021.125843.
  • Wang H, Weil M, Dumack K, Zak D, Münch D, Günther A, Jurasinski G, Blume-Werry G, Kreyling J, Urich T (2021) Eukaryotic rather than prokaryotic microbiomes change over seasons in rewetted fen peatlands. FEMS Microbiology Ecology 97. doi: 10.1093/femsec/fiab121.
  • Siemensma F, Holzmann M, Apothéloz-Perret-Gentil L, Clauß S, Voelcker E, Bettighofer W, Roshan SK, Walden S, Dumack K, Pawlowski J (2021) Broad sampling of monothalamids (Rhizaria, Foraminifera) gives further insight into diversity of non-marine Foraminifera. European Journal of Protistology 77: 125744. doi: https://doi.org/10.1016/j.ejop.2020.125744.
  • Huang X, Wang J, Dumack K, Liu W, Zhang Q, He Y, Di H, Bonkowski M, Xu J, Li Y (2021) Protists modulate fungal community assembly in paddy soils across climatic zones at the continental scale. Soil Biology and Biochemistry 160. doi: 10.1016/j.soilbio.2021.108358. Editors’ Choice: https://www.journals.elsevier.com/soil-biology-and-biochemistry/editors-choice/september-2021-editors-picks-soil-biology-and-biochemistry; Faculty Opinions - special significance in its field: https://facultyopinions.com
  • Pohl N, Solbach MD, Dumack K (2021) The wastewater protist Rhogostoma minus (Thecofilosea, Rhizaria) is abundant, widespread, and hosts Legionellales. Water Research 203: 117566. doi: https://doi.org/10.1016/j.watres.2021.117566.
  • Le Provost G, Thiele J, Westphal C, Penone C, Allan E, Neyret M, van der Plas F, Ayasse M, Bardgett RD, Birkhofer K, Boch S, Bonkowski M, Buscot F, Feldhaar H, Gaulton R, Goldmann K, Gossner MM, Klaus VH, Kleinebecker T, Krauss J, Renner S, Scherreiks P, Sikorski J, Baulechner D, Blüthgen N, Bolliger R, Börschig C, Busch V, Chisté M, Fiore-Donno AM, Fischer M, Arndt H, Hoelzel N, John K, Jung K, Lange M, Marzini C, Overmann J, Paŝalić E, Perović DJ, Prati D, Schäfer D, Schöning I, Schrumpf M, Sonnemann I, Steffan-Dewenter I, Tschapka M, Türke M, Vogt J, Wehner K, Weiner C, Weisser W, Wells K, Werner M, Wolters V, Wubet T, Wurst S, Zaitsev AS, Manning P (2021) Contrasting responses of above- and belowground diversity to multiple components of land-use intensity. Nature Communications 12: 3918. doi: 10.1038/s41467-021-23931-1.
  • Kumar A, Rosinger C, Chen H, Protic S, Bonkowski M, Temperton VM (2021) Gone and forgotten: facilitative effects of intercropping combinations did not carry over to affect barley performance in a follow-up crop rotation. Plant and Soil. doi: 10.1007/s11104-021-05104-7.
  • Rosinger C, Bonkowski M (2021) Soil age and soil organic carbon content shape biochemical responses to multiple freeze–thaw events in soils along a postmining agricultural chronosequence. Biogeochemistry 155: 113-125. doi: 10.1007/s10533-021-00816-5.
  • Walden S, Jauss RT, 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 Microbiology Ecology 97. doi: 10.1093/femsec/fiab081. (Editor's Choice: https://academic.oup.com/femsec/pages/editors-choice])
  • Jauss, R.-T., Walden, S., Fiore-Donno, A.M., Schaffer, S., Wolf, R., Feng, K., Bonkowski, M., Schlegel, M. (2021) A parasite’s paradise: biotrophic species prevail Oomycete community composition in tree canopies. Frontiers in Forests and Global Change, 4, 668895. doi: 10.3389/ffgc.2021.668895.
  • Jauss, R.-T., Nowack, A., Walden, S., Wolf, R., Schaffer, S., Schellbach, B., Bonkowski, M., Schlegel, M. (2021) To the canopy and beyond: Air samples reveal wind dispersal as a driver of ubiquitous protistan pathogen assembly in tree canopies. European Journal of Protistology 80. doi: 10.1016/j.ejop.2021.125805
  • Mayer M, Rewald B, Matthews B, Sanden H, Rosinger C, Katzensteiner K, Gorfer M, Berger H, Tallian C, Berger TW, Godbold DL (2021) Soil fertility relates to fungal-mediated decomposition and organic matter turnover in a temperate mountain forest. New Phytol. doi: 10.1111/nph.17421.
  • Dumack, K., Sapp, M., von Steimker, T., Mänz, A.T., Rose, L.E., Bonkowski, M. (2021) A call for research: A resource of core microbial symbionts of the Arabidopsis thaliana microbiome ready and awaiting experimental exploration. Phytobiomes Journal, 0: PBIOMES-11-20-0080-A. doi: 10.1094/pbiomes-11-20-0080-a.
  • Bonkowski, M., Tarkka, M., Razavi, B.S., Schmidt, H., Blagodatskaya, E., Koller, R., Yu P, Knief C, Hochholdinger F, Vetterlein D (2021). Spatiotemporal Dynamics of Maize (Zea mays L.) Root Growth and Its Potential Consequences for the Assembly of the Rhizosphere Microbiota. Frontiers in Microbiology 12(461). doi: 10.3389/fmicb.2021.619499
  • Rüger L, Feng K, Dumack K, Freudenthal J, Chen Y, Sun R, Wilson M, Yu P, Sun B, Deng Y, Hochholdinger F, Vetterlein D, Bonkowski M (2021) Assembly patterns of the rhizosphere microbiome along the longitudinal root axis of maize (Zea mays L.). Frontiers in Microbiology 12(237) doi: 10.3389/fmicb.2021.614501
  • Khanipour Roshan, S., Dumack, K., Bonkowski, M., Leinweber, P., Karsten, U. & Glaser, K. (2021) Taxonomic and Functional Diversity of Heterotrophic Protists (Cercozoa and Endomyxa) from Biological Soil Crusts. Microorganisms, 9, 205. doi: 10.3390/microorganisms9020205.
  • Clayton J, Lemanski K, Bonkowski M (2021) Shifts in soil microbial stoichiometry and metabolic quotient provide evidence for a critical tipping point at 1% soil organic carbon in an agricultural post-mining chronosequence. Biology and Fertility of Soils 57(3): 435-446. doi: 10.1007/s00374-020-01532-2.
  • Fiore-Donno AM, Bonkowski M (2021) Different community compositions between obligate and facultative oomycete plant parasites in a landscape-scale metabarcoding survey. Biology and Fertility of Soils, 57, 245-256. doi: 10.1007/s00374-020-01519-z.
  • Solbach MD, Bonkowski M, Dumack K (2021) Novel endosymbionts in rhizarian amoebae imply universal infection of unrelated free-living amoebae by Legionellales. Frontiers in Cellular and Infection Microbiology 11: 117. doi: 10.3389/fcimb.2021.642216.
  • Dumack, K., Duckert, C., Meinhardt, R., Lara, E., Bonkowski, M. (2021) Description of Phaeobola aeris gen. nov., sp. nov (Rhizaria, Cercozoa, Euglyphida) sheds light on Euglyphida’s dark matter. Journal of Eukaryotic Microbiology 68(2), e12835. doi: https://doi.org/10.1111/jeu.12835.
  • Dumack, K., Bonkowski, M. (2021) "Protists in the Plant Microbiome: An Untapped Field of Research," in The Plant Microbiome. Methods in Molecular Biology, eds. L.C. Carvalhais & P.G. Dennis. (New York, NY: Humana), 77-84.

2020

  • Jauss, R.-T., Walden, S., Fiore-Donno, A. M., 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. Frontiers in Microbiology 11: 3364.
  • Chen, Y., Bonkowski, M., Shen, Y., Griffiths, B.S., Jiang, Y., Wang, X. & Sun, B. (2020) Root ethylene mediates rhizosphere microbial community reconstruction when chemically detecting cyanide produced by neighbouring plants. Microbiome, 8, 4.
  • Dumack, K., Pundt, J., Bonkowski, M. (2020) Transfer of the Thecate Amoeba Lecythium mutabilis to a Novel Genus Omnivora (Fiscullidae, Thecofilosea, Cercozoa). Journal of Eukaryotic Microbiology, 67, 245-251.
  • Siemensma F, Dumack K (2020) SSU rDNA Phylogeny Indicates the Scale-lacking Trivalvulariida ord. nov. as a sister group to the Euglyphida (Cercozoa, Rhizaria). Protist 171: 125701.
  • Dumack K, Siemensma F (2020) Shell colour in Cercozoa; a simple trait to distinguish Thecofilosea from Imbricatea? Protist: 171(2): 125718.
  • Rossmann M, Pérez-Jaramillo J, Kavamura V, Chiaramonte J, Dumack K, Fiore-Donno AM, Mendes LW, Ferreira M, Bonkowski M, Raaijmakers J, Mauchline T, Mendes R (2020) Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiology Ecology 96 (4) fiaa032. doi: 10.1093/femsec/fiaa032.
  • Felipe-Lucia MR, Soliveres S, Penone C, Fischer M, Ammer C, Boch S, Boeddinghaus RS, Bonkowski M, Buscot F, Fiore-Donno AM, Frank K, Goldmann K, Gossner MM, Hölzel 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, Weisser WW, Wilcke W, Wubet T, Allan E (2020) Land-use intensity alters networks between biodiversity, ecosystem functions, and services. Proceedings of the National Academy of Sciences: 117(45): 28140-28149.
  • Khanipour Roshan S, Dumack K, Bonkowski M, Karsten U, Glaser K (2020) Stramenopiles and Cercozoa dominate the heterotrophic protist community of biological soil crusts irrespective of edaphic factors. Pedobiologia 83: 150673. doi: https://doi.org/10.1016/j.pedobi.2020.150673.
  • Jiang L, Bonkowski M, Luo L, Kardol P, Zhang Y, Chen X, Li D, Xiao Z, Hu F, Liu M (2020) Combined addition of chemical and organic amendments enhances plant resistance to aboveground herbivores through increasing microbial abundance and diversity. Biology and Fertility of Soils 56: 1007–1022
  • Jiang Y, Luan L, Hu K, Liu M, Chen Z, Geisen S, Chen X, Li H, Xu Q, Bonkowski M, Sun B (2020) Trophic interactions as determinants of the arbuscular mycorrhizal fungal community with cascading plant-promoting consequences. Microbiome 8: 142. doi: 10.1186/s40168-020-00918-6.
  • Lara E, Dumack K, García-Martín JM, Kudryavtsev A, Kosakyan A (2020) Amoeboid protist systematics: A report on the “Systematics of amoeboid protists” symposium at the VIIIth ECOP/ISOP meeting in Rome, 2019. European Journal of Protistology 76: 125727.
  • Siemensma F, Holzmann M, Apothéloz-Perret-Gentil L, Clauß S, Voelcker E, Bettighofer W, Khanipour Roshan S, Walden S, Dumack K, Pawlowski J (2020) Broad sampling of monothalamids (Rhizaria, Foraminifera) gives further insight into diversity of non-marine Foraminifera. European Journal of Protistology: 125744. doi: https://doi.org/10.1016/j.ejop.2020.125744..
  • 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 in Microbiology 11: 1823. doi: 10.3389/fmicb.2020.01823. Terrestrial Microbiology Editor’s Pick 2021: https://www.frontiersin.org/research-topics/23055/terrestrial-microbiology-editors-pick-2021#articles
  • Bernardes M, Le MD, Nguyen TQ, Pham CT, Pham AV, Nguyen TT, Rödder D, Bonkowski M, Ziegler T (2020) Integrative taxonomy reveals three new taxa within the Tylototriton asperrimus complex (Caudata, Salamandridae) from Vietnam. ZooKeys 935: 121-164. doi: 10.3897/zookeys.935.37138.
  • Miralles A, Bruy T, Wolcott C, Scherz MD, Begerow D, Beszter B, Bonkowski M, Felden J, Gemeinholzer -B, Glaw F, Glöckner FO, Hawlitscheck O, Kostadinov I, Nattkemper TW, Printzen C, Renz J, Rybalka N, Stadler M, Weibulat T, Wilke T, Renner SS, Vences M (2020) Repositories for taxonomic data: Where we are and what is missing. Systematic Biology doi: 10.1093/sysbio/syaa026.
  • Öztoprak H, Walden S, Heger T, Bonkowski M, Dumack K (2020) What drives the diversity of the most abundant cercozoan taxon (Rhogostomidae, Cercozoa, Rhizaria) in terrestrial habitats? Microorganisms 8: 1123
  • Zheng Y, Chen X, Gong X, Bonkowski M, Wang S, Griffiths B, Hu F, Liu M (2020) The geophagous earthworm Metaphire guillelmi effects on rhizosphere microbial community structure and functioning vary with plant species. Geoderma 379: 114647. doi: https://doi.org/10.1016/j.geoderma.2020.114647.
  • Cainelli R, de Haan M, Meyer M, Bonkowski M, Fiore-Donno AM (2020) Phylogeny of Physarida (Amoebozoa, Myxogastria) based on the small-subunit ribosomal RNA gene, redefinition of P. pusillum s. str. and reinstatement of P. gravidum Morgan. The Journal of Eukaryotic Microbiology 67: 327-336. doi: 10.1111/jeu.12783
  • Dumack, K, Görzen D, González-Miguéns R, Siemensma F, Lahr DJG, Lara E, Bonkowski M (2020) Molecular investigation of Phryganella acropodia Hertwig et Lesser, 1874 (Arcellinida, Amoebozoa). European Journal of Protistology 75: 125707. doi: https://doi.org/10.1016/j.ejop.2020.125707.
  • Bui VB, Ziegler T, Bonkowski M (2020) Checklist of beetles in the subgenus Copris (Paracopris) Balthasar from Asia with description of a new species, and redescription of Copris (Paracopris) punctulatus Wiedemann (Coleoptera: Scarabaeidae: Scarabaeinae). Zootaxa 4712(1), 51-64. doi: 10.11646/zootaxa.4712.1.3.
  • Bui VB, Ziegler T, Bonkowski M (2020) Morphological traits reflect dung beetle response to land use changes in tropical karst ecosystems of Vietnam. Ecological Indicators 108:105697. doi: 10.1016/j.ecolind.2019.105697.
  • 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. Systematics and Biodiversity 18:3, 228-236.

2019

  • van den Hoogen J, Geisen S, Routh D, Ferris H, Traunspurger W, Wardle DA, de Goede RGM, Adams BJ, Ahmad W, Andriuzzi WS, Bardgett RD, Bonkowski M, Campos-Herrera R, Cares JE, Caruso T, de Brito Caixeta L, Chen X, Costa SR, Creamer R, Mauro da Cunha Castro J, Dam M, Djigal D, Escuer M, Griffiths BS, Gutierrez C, Hohberg K, Kalinkina D, Kardol P, Kergunteuil A, Korthals G, Krashevska V, Kudrin AA, Li Q, Liang W, Magilton M, Marais M, Martin JAR, Matveeva E, Mayad EH, Mulder C, Mullin P, Neilson R, Nguyen TAD, Nielsen UN, Okada H, Rius JEP, Pan K, Peneva V, Pellissier L, Carlos Pereira da Silva J, Pitteloud C, Powers TO, Powers K, Quist CW, Rasmann S, Moreno SS, Scheu S, Setala H, Sushchuk A, Tiunov AV, Trap J, van der Putten W, Vestergard M, Villenave C, Waeyenberge L, Wall DH, Wilschut R, Wright DG, Yang JI, Crowther TW (2019) Soil nematode abundance and functional group composition at a global scale. Nature 572: 194-198. doi: 10.1038/s41586-019-1418-6.
  • van den Hoogen J, Geisen S, Routh D, Ferris H, Traunspurger W, Wardle DA, de Goede RGM, Adams BJ, Ahmad W, Andriuzzi WS Bardgett RD, Bonkowski M, Campos-Herrera R, Cares JE, Caruso T, de Brito Caixeta L, Chen X, Costa SR, Creamer R da Cunha Castro JM, Dam M, Djigal D, Escuer M, Griffiths BS, Gutiérrez C, Hohberg K, Kalinkina D, Kardol P, Kergunteuil A, Korthals G, Krashevska V, Kudrin AA, Li Q, Liang W, Magilton M, Marais M, Martín JAR, Matveeva E, Mayad EH, Mulder C Mullin P, Neilson R, Nguyen TAD, Nielsen UN, Okada H, Rius JEP, Pan K, Peneva V, Pellissier L, Pereira da Silva JC, Pitteloud C, Powers TO, Powers K, Quist C W, Rasmann S, Sánchez Moreno S, Scheu S,Setälä H, Sushchuk A, Tiunov AV, Trap J, van der Putten WH, Vestergård M, Villenave C, Waeyenberge L, Wall DH, Wilschut R, Wright DG, Yang J, Schmidt O, Keith A, Crowther TW (2019) A global database of soil nematode abundance and functional group composition" Scientific Data (reference number: SDATA-19-00909).
  • Hünninghaus M, Dibbern D, Kramer S, Koller R, Pausch J, Schloter-Hai B, Urich T, Kandeler E, Bonkowski M, Lueders T (2018) Disentangling microbial carbon flows across microbial kingdoms in rhizosphere of maize. Soil Biology & Biochemistry 134: 122-130. doi: 10.1016/j.soilbio.2019.03.007.
  • Dumack K, Fiore-Donno A M, Bass D, Bonkowski M (2019) Making sense of environmental sequencing data: ecologically important functional traits of the protistan groups Cercozoa and Endomyxa (Rhizaria). Molecular Ecology Resources 20:2, 398-403. doi: 10.1111/1755-0998.13112.
  • Fiore-Donno AM, Richter-Heitmann T, Degrune F, Dumack K, Regan KM, Mahran S, Boeddinghaus RS, Rillig MC, 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 in Microbiology 10: 1332. doi: 10.3389/fmicb.2019.01332.
  • Lemanski K, Armbruster M, Bonkowski M (2019) Linking soil microbial nutrient limitation to fertilizer regime and sugar beet yield. Plant and Soil 441: 253-259. doi: 10.1007/s11104-019-04114-w.
  • Dumack K, Siemsma F (2019) Transfer of the thecate amoeba Lecythium mutabilis to a novel genus Omnivora (Fiscullidae, Thecofilosea, Cercozoa. Journal of Eukaryotic Microbiology 67:2, 245-251. doi: 10.1111/jeu.12778.
  • Eisenhauer N, Bonkowski M, Brose U, Buscot F, Durka W, Ebeling A, Fischer M, Gleixner G, Heintz-Buschart A, Hines J, Jesch A, Lange M, Meyer S, Roscher C, Scheu S, Schielzeth H, Schloter M, Schulz S, Unsicker S, van Dam NM, Weigelt A, Weisser WW, Wirth C, Wolf J, Schmid B (2019) Biotic interactions, community assembly, and eco-evolutionary dynamics as drivers of long-term biodiversity–ecosystem functioning relationships. Research Ideas and Outcomes 5: e47042.
  • Liu T, Chen X, Gong X, Jiang Y, Feng W, Li X, Whalen JK, Griffiths B, Hu F, Bonkowski M, Liu M (2019) Earthworms coordinate soil biota to improve multiple ecosystem functions. Current Biology 29: 3420-3429. doi: 10.1016/j.cub.2019.08.045. See commentary: Hines J (2019) Ecosystem Functioning: How much system is needed to explain function? Current Biology 29: R1072-R1074
  • Sapp M, Tyborski N, Linstädter A, López Sánchez A, Mansfeldt T, Waldhoff G, Bareth G, Bonkowski M, Rose LE (2019) Site-specific distribution of oak rhizosphere-associated oomycetes revealed by cytochrome c oxidase subunit II metabarcoding. Ecology and Evolution 9: 10567– 10581. doi: 10.1002/ece3.5577.
  • Voss C, Fiore-Donno AM, Guerreiro M, Peršoh D, Bonkowski M (2019) Metatranscriptomics reveals unsuspected protistan diversity in leaf litter across temperate beech forests, with Amoebozoa the dominating lineage. FEMS Microbiology Ecology 95: fiz142. doi: 10.1093/femsec/fiz142.
  • Bui, V.B., Ziegler, T., Bonkowski, M. (2019) Checklist of beetles in the subgenus Copris (Paracopris) Balthasar from Asia with description of a new species, and redescription of Copris (Paracopris) punctulatus Wiedemann (Coleoptera: Scarabaeidae: Scarabaeinae). Zootaxa, 4712, 51-64.
  • 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 Microbiology Ecology 95: fiz041. doi: 10.1093/femsec/fiz041.
  • Dumack K, Pundt J, Bonkowski M (2019) Food choice experiments indicate selective fungivorous predation in Fisculla terrestris (Thecofilosea, Cercozoa). Journal of Eukaryotic Microbiology 66: 525-527. doi: 10.1111/jeu.12680.
  • Dumack K, Kahlich C, Lahr D, Bonkowski M (2019) Reinvestigation of Phryganella paradoxa (Arcellinida, Amoebozoa) Penard, 1902. Journal of Eukaryotic Microbiology 66: 232-243. doi: 10.1111/jeu.12665.
  • Ardestani, M.M., Jílková, V., Bonkowski, M., and Frouz, J. (2019). The effect of arbuscular mycorrhizal fungi Rhizophagus intraradices and soil microbial community on a model plant community in a post-mining soil. Plant Ecology 220: 789-800. doi: 10.1007/s11258-019-00953-w.
  • Bondarenko N, Smirnov A, Nassonova E, Glotova A, Fiore-Donno AM (2019) Mitochondrial genomes of Amoebozoa. Protistology 13:4, 179–191
  • Bonkowski M, Dumack K, Fiore-Donno AM (2019) Chapter 8 – Protists in soil - the untold eukaryotic diversity. Modern Soil Microbiology (3rd edition), van Elsas JD, Trevors JT, Soares Rosado A, Nannipieri P (eds.), CRC Press, Boca Raton, USA, pp 125-140.
  • Bonkowski M (2019) Microcosm approaches to investigate multitrophic interactions between bacteria, protists, symbiotic fungi and their host plants. In: Sharma AK, Reinhard, D (eds) Methods in Rhizosphere Biology Research. Springer, New York, pp 255-270.
  • Ntakou, E., Siemensma, F., Bonkowski, M., Dumack, K. (2019). The dancing star: reinvestigation of Artodiscus saltans (Variosea, Amoebozoa) Penard 1890. Protist 170, 349-357. https://doi.org/10.1016/j.protis.2019.06.002.
  • Sarkar D, Rovenich H, Jeena G, Nizam S, Tissier A, Balcke G, Mahdi L, Bonkowski M, Langen G, Zuccaro A (2019) The inconspicuous gatekeeper: endophytic Serendipita vermifera acts as extended plant protection barrier in the rhizosphere. New Phytologist 224: 886-901. doi: 10.1111/nph.15904.
  • Siebert J, Eisenhauer N, Poll C, Marhan S, Bonkowski M, Hines J, Koller R, Ruess L, Thakur M (2019) Earthworms modulate the effects of climate warming on soil the taxon richness of soil meso- and macrofauna in an agricultural system. Agriculture, Ecosystems and Environment 278: 72-80. doi: 10.1016/j.agee.2019.03.004.

2018

  • Flues S, Blokker M, Dumack K, Bonkowski M (2018) Diversity of cercomonad species in the phyllosphere and rhizosphere of different plant species with a description of Neocercomonas epiphylla (Cercozoa, Rhizaria) a leaf-associated protist. Journal of Eukaryotic Microbiology 65: 587-599. doi: 10.1111/jeu.12503.
  • Bui VB, Bonkowski M (2018) Synapsis puluongensis sp. nov. and new data on the poorly known species Synapsis horaki (Coleoptera: Scarabaeidae) from Vietnam with a key to Vietnamese species. Acta Entomologica Musei Nationalis Pragae. 58:407-418. doi: 10.14411/eje.2018.016.
  • Henkes, G.J., Kandeler, E., Marhan, S., Scheu, S., Bonkowski, M. (2018). Interactions of mycorrhiza and protists in the rhizosphere systemically alter microbial community composition, plant shoot-to-root ratio and within-root system nitrogen allocation Frontiers in Environmental Science 6: 117. doi: 10.3389/fenvs.2018.00117.
  • Zheng, Y., Wang, S., Bonkowski, M., Chen, X., Griffiths, B., Hu, F., et al. (2018). Litter chemistry influences earthworm effects on soil carbon loss and microbial carbon acquisition. Soil Biology and Biochemistry 123: 105-114. https://doi.org/10.1016/j.soilbio.2018.05.012.
  • Luu VQ, Bonkowski M, Nguyen TQ, Le MD, Calame T, Ziegler T (2018) A new species of Lycodon Boie, 1826 (Serpentes: Colubridae) from central Laos. Revue Suisse de Zoologie 125: 263-276. https://doi.org/10.5281/zenodo.1414221
  • Valencia E, Gross N, Quero JL, Carmona CP, Ochoa V, Gozalo B, Delgado-Baquerizo M, Dumack K, Hamonts K, Singh BK, Bonkowski M, Maestre FT (2018) Cascading effects from plants to soil microorganisms explain how plant species richness and simulated climate change affect soil multifunctionality. Global Change Biology 24: 5642-5654. doi: 10.1111/gcb.14440.
  • Pausch J, Hünninghaus M, Kramer S, Scharroba A, Scheunemann N, Butenschoen O, Marhan S, Bonkowski M, Kandeler E, Scheu E, Kuzyakov Y, Ruess L (2018) Carbon budgets of top- and subsoil food webs in an arable system. Pedobiologia 69: 29-33 https://doi.org/10.1016/j.pedobi.2018.06.002.
  • Rillig MC, Bonkowski M (2018) Microplastics and soil protists: a call for research. Environmental Pollution 241: 1128-1131. doi: 10.1016/j.envpol.2018.04.147
  • Bui VB, Dumack K, Bonkowski M (2018) Two new species and one new record of the genus Copris (Coleoptera: Scarabaeidae: Scarabaeinae) from Vietnam with a key to Vietnamese species. European Journal of Entomology 115: 167-191. doi: 10.14411/eje.2018.016.
  • Bukovská P, Bonkowski M, Konvalinková T, Beskid O, Hujslová M, Püschel D, Řezáčová V, Semiramis Gutiérrez-Núñez M, Gryndler M, Jansa J (2018) Utilization of organic nitrogen by arbuscular mycorrhizal fungi – is there a specific role for protists and ammonia oxidizers? Mycorrhiza 28: 269-283. doi: 10.1007/s00572-018-0825-0.
  • Geisen S, Mitchell EAD., Adl S, Bonkowski M, Dunthorn M, Ekelund F, Fernández L, Jousset A, Krashevska V, Singer D, Spiegel F, Walochnik J, Lara E (2018) Soil protists: a fertile frontier in soil biology research. FEMS Microbiolog Reviews 42: 293-323. doi: 10.1093/femsre/fuy006. Among 5 top-rated FEMS papers 2018: https://academic.oup.com/femsre/pages/articles_making_impact
  • Sorkau E, Boch S, Boeddinghaus R, Bonkowski M, Kandeler E, Marhan S, Prati D, Schöning I, Schrumpf M, Weinert J, Oelmann Y (2018) The role of soil chemical properties, land use and plant diversity for microbial phosphorus in forest and grassland soils. Journal of Plant Nutrition and Soil Science 181: 185-197. doi: 10.1002/jpln.201700082.
  • Miclu A, Puga-Freitas R, Ellison A, Blouin M, Scheu S, Freschet G, Rose L, Barot S, Cesarz S, Eisenhauer N, Girin T, Assandri D, Bonkowski M, Buchmann N, Butenschoen O, Devidal S, Gleixner G, Gessler A, Gigon A, Greiner A, Grignani C, Hansart A, Kayler Z, Lange M, Lata J C, Le Galliard J-F, Lukac M, Mannerheim N, Müller M E H, Pando A, Rotter P, Scherer-Lorenzen M, Seyhun R, Urban-Mead K, Weigelt A, Zavattaro L, Roy J (2018) Genotypic variability enhances the reproducibility of an ecological study. Nature Ecology & Evolution: 2: 279-287. doi: 10.1038/s41559-017-0434-x.
  • Geisen S & Bonkowski M (2018) Methodological advances to study the diversity of soil protists and their functioning in soil food webs. Applied Soil Ecology 123: 328-333. https://doi.org/10.1016/j.apsoil.2017.05.021.
  • Dumack K, Siemensma F, Bonkowski M (2018) Rediscovery of the testate amoeba genus Penardeugenia (Thaumatomonadida, Imbricatea). Protist 169: 29-42. https://doi.org/10.1016/j.protis.2017.12.002.
  • Dumack K, Bonkowski M, Clauß S, Völcker E (2018) Phylogeny and redescription of the testate amoeba Diaphoropodon archeri (Chlamydophryidae, Thecofilosea, Cercozoa), De Saedeleer 1934, and Annotations on the polyphyly of testate amoebae with agglutinated tests in the Cercozoa. Journal of Eukaryotic Microbiology 65: 308-314. doi: doi:10.1111/jeu.12474.
  • 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. Molecular Ecology Resources 18: 229-239. doi:10.1111/1755-0998.12729.

2017

  • Hu Z, Zhu C, Chen X, Bonkowski M, Griffiths B, Chen F, Zhu J, Hu S, Hu F, Liu M (2017) Responses of rice paddy micro-food webs to elevated CO2 are modulated by nitrogen fertilization and crop cultivars. Soil Biology and Biochemistry 114: 104-113. https://doi.org/10.1016/j.soilbio.2017.07.008.
  • Flues S, Bass D & Bonkowski M (2017) Grazing of Cercomonads (Protists: Rhizaria: Cercozoa) structures bacterial phyllosphere communities and function. Environmental Microbiology 19: 3297-3309. doi: 10.1111/1462-2920.13824.
  • Sapp M, Ploch S, Fiore-Donno AM, Bonkowski M, Rose L (2017) Protists are an integral part of the Arabidopsis thaliana microbiome. Environmental Microbiology 20: 30-43. doi: 10.1111/1462-2920.13941.
  • Hünninghaus M, Koller R, Kramer S, Marhan S, Kandeler E & Bonkowski M (2017) Changes in bacterial community composition and soil respiration indicate rapid successions of protist grazers during mineralization of maize crop residues. Pedobiologia 62: 1-8. http://dx.doi.org/10.1016/j.pedobi.2017.03.002.
  • Morrien E, Hannula SE, Snoek LB, Helmsing NR, Zweers H, de Hollander M, Soto RL, Bouffaud ML, Buee M, Dimmers W, Duyts H, Geisen S, Girlanda M, Griffiths RI, Jorgensen HB, Jensen J, Plassart P, Redecker D, Schmelz RM, Schmidt O, Thomson BC, Tisserant E, Uroz S, Winding A, Bailey MJ, Bonkowski M, Faber JH, Martin F, Lemanceau P, de Boer W, van Veen JA, van der Putten WH (2017) Soil networks become more connected and take up more carbon as nature restoration progresses. Nature Communications 8:14349. doi: 10.1038/ncomms14349.
  • Geisen S, Mitchell EAD, Wilkinson DM, Adl S, Bonkowski M, Brown MW, Fiore-Donno AM, Heger TJ, Jassey VEJ, Krashevska V, Lahr DJG, Marcisz K, Mulot M, Payne R, Singer D, Anderson OR, Charman DJ, Ekelund F, Griffiths BS, Rønn R, Smirnov A, Bass D, Belbahri L, Berney C, Blandenier Q, Chatzinotas A, Clarholm M, Dunthorn M, Feest A, Fernández LD, Foissner W, Fournier B, Gentekaki E, Hájek M, Helder J, Jousset A, Koller R, Kumar S, La Terza A, Lamentowicz M, Mazei Y, Santos SS, Seppey CVW, Spiegel FW, Walochnik J, Winding A, Lara E (2017) Soil protistology rebooted: 30 fundamental questions to start with. Soil Biology and Biochemistry 111:94-103. https://doi.org/10.1016/j.soilbio.2017.04.001.
  • Van Hoesel W, Tiefenbacher A, König N, Dorn VM, Hagenguth JF, Prah U, Widhalm T, Wiklicky V, Koller R, Bonkowski M, Lagerlöf J, Ratzenböck A, Zaller JG (2017) Single and combined effects of pesticide seed dressings and herbicides on earthworms, soil microorganisms, and litter decomposition. Frontiers in Plant Science 8:215. https://doi.org/10.3389/fpls.2017.00215
  • Shang Y, Sikorski J, Bonkowski M, Fiore-Donno AM, Kandeler E, Marhan S, Boeddinghaus R, Solly EF, Schrumpf M, Schöning I, Wubet T, Buscot F, Overmann J (2016) Inferring interactions in complex microbial communities from nucleotide sequence data and environmental parameters. PLOS ONE 12 (3):e0173765.
  • Nguyen TAD, Abolafia J, Dumack K, Bonkowski M, Peña-Santiago R (2016) Two known species of Aporcelinus Andrássy, 2009 (Dorylaimida, Aporcelaimidae) from Vietnam, with the first molecular study of the genus. Nematology 19: 853-868.
  • Bonkowski M, Kappes H (2017) Niche partitioning and indication of ontogenetic niche shifts in forest slugs according to stable isotopes. Journal of Molluscan Studies 84: 11-112.
  • Luu VQ, Nguyev TQ, Le MD, Bonkowski M, Ziegler T (2017) A new karst dwelling species of the Gekko japonicus group (Squamata: Gekkonidae) from central Laos. Zootaxa 4263 (1):179-193.
  • Smirnov A, Nassonova E, Geisen S, Bonkowski M, Kudryavtsev A, Berney C, Glotova A, Bondarenko N, Dykova I, Mrva M, Fahrni J, Pawlowski J (2017) Phylogeny and systematics of leptomyxid amoebae (Amoebozoa, Tubulinea, Leptomyxida). Protist 168: 220-252 https://doi.org/10.1016/j.protis.2016.10.006
  • Tice AK, Shadwick LL, 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. Biology Direct 11 (1):69.
  • Dumack K, Flues S, Hermanns K, Bonkowski M (2017) Rhogostomidae (Cercozoa) from soils, roots and plant leaves (Arabidopsis thaliana): Description of Rhogostoma epiphylla and R. cylindrica sp. nov. European Journal of Protistology 60: 76-86.
  • Dumack K, Mylnikov AP, Bonkowski M (2017) Evolutionary relationship of the scale-bearing Kraken (incertae sedis, Monadofilosa, Cercozoa, Rhizaria): Combining ultrastructure data and a two-gene phylogeny. Protist 168: 362-373. doi: 10.1016/j.protis.2017.04.004.
  • Dumack K, Mausbach P, Hegmann M, Bonkowski M (2017) Polyphyly in the thecate amoeba genus Lecythium (Chlamydophryidae, Tectofilosida, Cercozoa), Redescription of its type species L. hyalinum, description of L. jennyae sp. nov. and the establishment of Fisculla gen. nov. and Fiscullidae fam. nov. Protist 168:294-310.
  • Dumack K, Öztoprak H, Rüger L, Bonkowski M (2017) Shedding light on the polyphyletic thecate amoeba genus Plagiophrys: Transition of some of its species to Rhizaspis (Tectofilosida, Thecofilosea, Cercozoa) and the establishment of Sacciforma gen. nov. and Rhogostomidae fam. nov. (Cryomonadida, Thecofilosea, Cercozoa). Protist 168: 92-108.
  • Seppey CVW, Singer D, Dumack K, Fournier B, Belbahri L, Mitchell EAD, Lara E (2017) Distribution patterns of soil microbial eukaryotes suggests widespread algivory by phagotrophic protists as an alternative pathway for nutrient cycling. Soil Biology and Biochemistry 112: 68-76.

2016

  • Trap J, Bonkowski M, Plassard C, Villenave C, Blanchart E (2016) Marschner Review: Ecological importance of soil bacterivores on ecosystem functions. Plant and Soil 398, 1-24.
  • Andriuzzi, W.S., Ngo, P.-T., Geisen, S., Keith, A.M., Dumack, K., Bolger, T., Bonkowski, M., Brussaard, L., Faber, J.H., Chabbi, A., Rumpel, C., Schmidt, O. (2016) Organic matter composition and the protist and nematode communities around anecic earthworm burrows. Biology and Fertility of Soils 52: 91-100.
  • Bohan, D.A., Landuyt, D., Ma, A., Macfadyen, S., Martinet, V., Massol, F., McInerny, G., Montoya, J.M., Mulder, C., Pascual, U., Pocock, M.J., White, P., Blanchemanche, S., Bonkowski, M., Bretagnolle, V., Bronmark, C., Dicks, L., Dumbrell, A., Eisenhauer, N., Friberg, N., Gessner, M.O., Gill, R.J., Gray, C., Haughton, A., Ibanez, S., Jensen, J., Jeppesen, E., Jokela, J., Lacroix, G., Lannou, C., Lavorel, S., Le Galliard, J.F., Lescourret, F., Liu, S., Loeuille, N., McLaughlin, O., Muggleton, S., Penuelas, J., Petanidou, T., Petit, S., Pomati, F., Raffaelli, D., Rasmussen, J., Raybould, A., Reboud, X., Richard, G., Scherber, C., Scheu, S., Sutherland, W.J., Tamaddoni-Nezhad, A., ter Braak, C., Termansen, M., Thompson, M.S., Tscharntke, T., Vacher, C., van der Geest, H., Voigt, W., Vonk, J.A., Zhou, X., Woodward, G. (2016) Networking Our Way to Better Ecosystem Service Provision. Trends in Ecology & Evolution. 31: 112-121.
  • Kramer S, Dibbern D, Moll J, Huenninghaus M, Koller R, Krueger D, Marhan S, Urich T, Wubet T, Bonkowski M, Buscot F, Lueders T, Kandeler E (2016) Resource partitioning between bacteria, fungi, and protists in the detritusphere of an agricultural soil. Frontiers in Microbiology 7: 1524.
  • Ploch S, Rose L, Bass D, Bonkowski M (2016) High diversity revealed in leaf associated Protists (Rhizaria: Cercozoa) of Brassicaceae. Journal of Eukaryotic Microbiology 63: 635-641.
  • Fiore-Donno AM, Weinert J, Wubet T, Bonkowski M (2016) Metacommunity analysis of amoeboid protists in grassland soils. Scientific Reports 6: 19068.
  • Geisen S, Koller R, Hünninghaus M, Dumack K, Urich T, Bonkowski M (2016) The soil food web revisited: Diverse and widespread mycophagous soil protists. Soil Biology and Biochemistry 94:10-18..
  • Dumack K, Koller R, Weber B, Bonkowski M (2016) Estimated heterotrophic protist abundances and their diversity in South African biological soil crusts. South African Journal of Science 112: 1-5.
  • Dumack K, Müller M, Bonkowski M (2016) Description of Lecythium terrestris sp. nov. (Chlamydophryidae, Cercozoa), a soil dwelling protist feeding on fungi and algae. Protist 167: 93-105.
  • Dumack K, Schuster J, Bass D, Bonkowski M (2016) A novel lineage of ‘naked filose amoebae’; Kraken carinae gen. nov. sp. nov. (Cercozoa) with a remarkable locomotion by disassembly of its cell body. Protist 167: 268-278
  • Dumack K, Baumann C, Bonkowski M (2016) A bowl with marbles: Revision of the thecate amoeba genus Lecythium (Chlamydophryidae, Tectofilosida, Cercozoa, Rhizaria) including a description of four new species and an identification key. Protist 167: 440-459.
  • Kretzschmar M, Kuhnt A, Bonkowski M, Fiore-Donno AM (2016) Phylogeny of the Highly Divergent Echinosteliales (Amoebozoa) Journal of Eukaryotic Microbiology 63: 453-459.
  • Nguyen T A D, Abolafia J, Bonkowski M, Peña-Santiago R, Álvarez-Ortega S (2016) Two atypical new species of the genus Sectonema Thorne, 1930 (Nematoda, Dorylaimida, Aporcelaimidae) from Vietnam. European Journal of Taxonomy 171:1-20.
  • Nguyen T A D, Bonkowski M, Peña-Santiago R, , Abolafia J (2016) Re-description of Cephalobus topali Andrássy, 1970 (Rhabditida, Cephalobidae) from Vietnam, and transfer to Acrobeloides (Cobb, 1924) Thorne, 1937. Zootaxa 4092: 593-600.
  • Álvarez-Ortega S, Nguyen TAD, Abolafia J, Vu TTT, Bonkowski M, Peña-Santiago R (2016) Three new species of the genus Sectonema Thorne, 1930 (Nematoda, Dorylaimida, Aporcelaimidae) from Vietnam. Nematology 18: 517-536.
  • Alvarez-Ortega S, Nguyen TAD, Abolafia J, Bonkowski M, Pena-Santiago R (2016) Sectonema caobangense sp. n. from Vietnam (Nematoda, Dorylaimida, Aporcelaimidae). Journal of Nematology 48 (2):95.
  • Nguyen TAD, Abolafia J, Bonkowski M, Peña-Santiago R (2016) A third new species of Aporcelinus Andrássy, 2009 (Dorylaimida, Aporcelaimidae) from Vietnam, with the first SEM study of a representative of the genus. Journal of Nematology 48: 104-108.
  • Nguyen TAD, Abolafia J, Bonkowski M, Peña-Santiago R (2016) Two new species of the genus Aporcelinus Andrássy, 2009 (Nematoda, Dorylaimida) from Vietnam. Zootaxa 4103: 550-560.
  • Pham CT, Nguyen TQ, Bonkowski M, Ziegler T (2016) A new species of Odorrana (Amphibia: Anura: Ranidae) from Vietnam. Zootaxa 4084: 421–435.
  • Stone R., Blomkvist P., Hendriksen N.B., Bonkowski M., Jørgensen H.B., Carvalho F., Dunbar M.B., Gardi C., Geisen S., Griffiths R., Hug A.S., Jensen J., Laudon H., Mendes S., Morais P.V., Orgiazzi A., Plassart P., Römbke J., Rutgers M., Schmelz R.M., Sousa J.P., Steenbergen E., Suhadolc M., Winding A., Zupan M., Lemanceau P., Creamer R.E. 2016. A method of establishing a transect for biodiversity and ecosystem function monitoring across Europe. Applied Soil Ecology 97:3-11.
  • Griffiths BS, Römbke J, Schmelz R, Scheffczyk A, Faber J, Bloem J, Pérès G, Cluzeau D, Chabbi A, Suhadolc M, Sousa P, Martins da SIlva P, Carvalho F, Mendes S, Morais P, Francisco R, Pereira C, Bonkowski M, Geisen S, Bardgett R, de Vries F, Bolger T, Dirilgen T, Schmidt O, Winding A, Hendriksen N, Johansen A, Philippot L, Plassart P, Bru D, Thompson B, Griffiths R, Keith A, Rutgers M, Mulder C, Hannula E, Creamer R, Stone D (2015) Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function. Ecological Indicators 69: 213-223.
  • ten Hagen L, Rodríguez A, Menke N, Göcking C, Bisping M, Frommolt K-H, Ziegler T, Bonkowski M, Vences M (2016) Vocalizations in juvenile anurans: common spadefoot toads (Pelobates fuscus) regularly emit calls before sexual maturity. Naturwissenschaften 103: 75.
  • Luu QV, Calame T, Nguyen QT, Le MD, Bonkowski M, Ziegler T (2016) Cyrtodactylus rufford, a new cave-dwelling bent-toed gecko (Squamata: Gekkonidae) from Khammouane Province, central Laos. Zootaxa 4067: 185-199.
  • Luu QV, Nguyen QT, Le MD, Bonkowski M, Ziegler T (2016) A new species of karst-dwelling bent-toed gecko (Squamata: Gekkonidae) from Khammouane Province, central Laos. Zootaxa 4079: 87–102.
  • Luu VQ, Bonkowski M,Nguyen TQ, Le MD, Schneider N, Ziegler T (2016) Evolution in karst massifs: Cryptic diversity among bent-toed geckos along the Truong Son Range with descriptions of three new species and one new country record from Laos. Zootaxa 4107 (2): 101–140.
  • van Schingen M, Ha QQ, Pham CT, Le TQ, Nguyen TQ, Bonkowski M, Ziegler T (2016) Discovery of a new crocodile lizard population in Vietnam: Population trends, future prognoses and identification of key habitats for conservation. Revue Suisse de Zoologie 123: 241-251.
  • Zaller JG, König N, Tiefenbacher A, Muraoka Y, Querner P, Ratzenböck A, Bonkowski M, Koller R (2016) Pesticide seed dressings can affect the activity of various soil organisms and reduce decomposition of plant material. BMC Ecology 16:37.
  • Imparato, V., Santos, S.S., Johansen, A., Geisen, S., Winding, A. (2016) Stimulation of bacteria and protists in rhizosphere of glyphosate-treated barley. Applied Soil Ecology 98: 47-55.