Department of Microbial Ecology

Micro-organisms form a huge, largely undiscovered potential. A treasure-trove for researchers from the department of Microbial Ecology.

Recent publications (2015 - )

Alderliesten, J. B., Zwart, M. P., de Visser, J. A. G. M., Stegeman, A., & Fischer, E. A. J. (2022). Second compartment widens plasmid invasion conditions: Two-compartment pair-formation model of conjugation in the gut. Journal of Theoretical Biology, 533, [110937]. https://doi.org/10.1016/j.jtbi.2021.110937
Schorn, M. A., Verhoeven, S., Ridder, L., Huber, F., Acharya, D. D., Aksenov, A. A., Aleti, G., Moghaddam, J. A., Aron, A. T., Aziz, S., Bauermeister, A., Bauman, K. D., Baunach, M., Beemelmanns, C., Beman, J. M., Berlanga-Clavero, M. V., Blacutt, A. A., Bode, H. B., Boullie, A.,... van der Hooft, J. J. J. (2021). A community resource for paired genomic and metabolomic data mining. Nature Chemical Biology, 17(4), 363-368. https://doi.org/10.1038/s41589-020-00724-z
Bento, M. D. S., Barros, D. J., Araújo, M. G. D. S., Da Róz, R., Carvalho, G. A., Braga do Carmo, J., Toppa, R. H., Neu, V., Forsberg, B. R., Bodelier, P., Tsai, S. M., & Navarrete, A. A. (2021). Active methane processing microbes and the disproportionate role of NC10 phylum in methane mitigation in Amazonian floodplains. Biogeochemistry, 156, 293-317. https://doi.org/10.1007/s10533-021-00846-z
Hunt, K. A., Forbes, J., Taub, F., Elliott, N., Hardwicke, J., Petersen, R., Stopnisek, N., Beck, D. A. C., & Stahl, D. A. (2021). An automated multiplexed turbidometric and data collection system for measuring growth kinetics of anaerobes dependent on gaseous substrates. Journal of Microbiological Methods, 188, [106294]. https://doi.org/10.1016/j.mimet.2021.106294
Lammers, A., Zweers, H., Sandfeld, T., Bilde, T., Garbeva, P., Schramm, A., & Lalk, M. (2021). Antimicrobial Compounds in the Volatilome of Social Spider Communities. Frontiers in Microbiology, 12, [700693]. https://doi.org/10.3389/fmicb.2021.700693
Blin, K., Shaw, S., Kloosterman, A. M., Charlop-Powers, Z., Van Wezel, G. P., Medema, M. H., & Weber, T. (2021). AntiSMASH 6.0: Improving cluster detection and comparison capabilities. Nucleic Acids Research, 49(W1), W29-W35. https://doi.org/10.1093/nar/gkab335
Moretti de Souza, L., Crusciol, C. A. C., Bossolani, J. W., Calonego, J. C., Moreira, A., Garcia, A., Momesso, L., Kuramae, E., & Hungria, M. (2021). Beneficial microbial species and metabolites alleviate soybean oxidative damage and increase grain yield during short dry spells. European Journal of Agronomy, 127, [126293]. https://doi.org/10.1016/j.eja.2021.126293
Avalos Garcia, M., Garbeva, P., Vader, L., van Wezel, G., Dickschat, J. S., & Ulanova, D. (2021). Biosynthesis, Evolution and Ecology of Microbial Terpenoids. Natural Product Reports, In press. https://doi.org/10.1039/D1NP00047K
Clocchiatti, A. (2021). Bringing soil fungi into action: Options for forward-looking agriculture (PhD Thesis). Wageningen University. https://doi.org/10.18174/537032
Taparia, T., Hendrix, E., Hendriks, M., Nijhuis, E., de Boer, W., & van der Wolf, J. (2021). Casing soil microbiome mediates suppression of bacterial blotch of mushrooms during consecutive cultivation cycles. Soil Biology and Biochemistry, 155, [108161]. https://doi.org/10.1016/j.soilbio.2021.108161
Duxbury, S. J. N., Alderliesten, J. B., Zwart, M. P., Stegeman, A., Fischer, E. A. J., & de Visser, J. A. G. M. (2021). Chicken gut microbiome members limit the spread of an antimicrobial resistance plasmid in Escherichia coli. Proceedings of the Royal Society B: Biological Sciences, 288(1962), [20212027]. https://doi.org/10.1098/rspb.2021.2027
Andreo-Jimenez, B., Schilder, M. T., Nijhuis, E. H., Te Beest, D. E., Bloem, J., Visser, J. H. M., van Os, G., Brolsma, K., de Boer, W., & Postma, J. (2021). Chitin- and Keratin-Rich Soil Amendments Suppress Rhizoctonia solani Disease via Changes to the Soil Microbial Community. Applied and Environmental Microbiology, 87(11). https://doi.org/10.1128/AEM.00318-21
Nurfikari, A., & de Boer, W. (2021). Chitin Determination in Residual Streams Derived from Insect Production by LC-ECD and LC-MS/MS methods. Frontiers In Sustainable Food Systems, In press, [795694]. https://doi.org/10.3389/fsufs.2021.795694
Taparia, T., Hendrix, E., Hendriks, M., Krijger, M., De Boer, W., & Van der Wolf, J. (2021). Comparative studies on the disease prevalence and population dynamics of ginger blotch and brown blotch pathogens of button mushrooms. Plant Disease, 105(3), 542-547. https://doi.org/10.1094/PDIS-06-20-1260-RE
Tian, L., Chang, J., Shi, S., Ji, L., Zhang, J., Sun, Y., Li, X., Li, X., Xie, H., Cai, Y., Chen, D., Wang, J., van Veen, J. A., Kuramae, E., Phan Tran, L-S., & Tian, C. (2022). Comparison of methane metabolism in the rhizomicrobiomes of wild and related cultivated rice accessions reveals a strong impact of crop domestication. Science of the Total Environment, 803, [150131]. https://doi.org/10.1016/j.scitotenv.2021.150131
Costa, O. Y. A., Meima-Franke, M., & Bodelier, P. (2021). Complete and Draft Genome Sequences of Aerobic Methanotrophs Isolated from a Riparian Wetland. Microbiology Resource Announcements, 10(9), [e01438-20]. https://doi.org/10.1128/MRA.01438-20
Liu, X., Hannula, S. E., Li, X., Hundscheid, M. P. J., Gunnewiek, P. J. A. K., Clocchiatti, A., Ding, W., & Boer, W. D. (2021). Decomposing cover crops modify root-associated microbiome composition and disease tolerance of cash crop seedlings. Soil Biology and Biochemistry, 160, [108343]. https://doi.org/10.1016/j.soilbio.2021.108343
Song, C., Jin, K., & Raaijmakers, J. M. (2021). Designing a home for beneficial plant microbiomes. Current Opinion in Plant Biology, 62, [102025]. https://doi.org/10.1016/j.pbi.2021.102025
Kirchner, N., Cano-Prieto, C., Schulz-Finke, A., Gütschow, M., Ortlieb, N., Moschny, J., Niedermeyer, T., Horak, J., Lämmerhofer, M., van der Voort, M., Raaijmakers, J. M., & Gross, H. (2021). Discovery of Thanafactin A, a Linear Proline-containing Octa-Lipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining. Journal of Natural Products, 84(1), 101–109. https://doi.org/10.1021/acs.jnatprod.0c01174
van Dijk, H., Kaupper, T., Bothe, C., Lee, H. J., Bodelier, P., Horn, M. A., & Ho, A. (2021). Discrepancy in exchangeable and soluble ammonium-induced effects on aerobic methane oxidation: a microcosm study of a paddy soil. Biology and Fertility of Soils, 57, 873–880. https://doi.org/10.1007/s00374-021-01579-9
Ossowicki, A., Raaijmakers, J. M., & Garbeva, P. (2021). Disentangling soil microbiome functions by perturbation. Environmental Microbiology Reports, 13(5), 582-590. https://doi.org/10.1111/1758-2229.12989
Tracanna, V., Ossowicki, A., Petrus, M. L. C., Overduin, S., Terlouw, B. R., Lund, G., Robinson, S. L., Warris, S., Schijlen, E. G. W. M., van Wezel, G. P., Raaijmakers, J. M., Garbeva, P., & Medema, M. H. (2021). Dissecting disease-suppressive rhizosphere microbiomes by functional amplicon sequencing and 10X metagenomics. mSystems, 6(3), [e01116-20]. https://doi.org/10.1128/mSystems.01116-20
Sun, R. L., Jing, Y. L., de Boer, W., Guo, R-J., & Li, S. D. (2021). Dominant hyphae-associated bacteria of Fusarium oxysporum f. sp. cucumerinum in different cropping systems and insight into their functions. Applied Soil Ecology, 165, [103977]. https://doi.org/10.1016/j.apsoil.2021.103977
Momesso, L., Crusciol, C. A. C., Soratto, R. P., Nascimento, C. A. C., Rosolem, C. A., Moretti de Souza, L., Kuramae, E., & Cantarella, H. (2021). Early nitrogen supply as an alternative management for a cover crop-maize sequence under a no-till system. Nutrient Cycling in Agroecosystems. https://doi.org/10.1007/s10705-021-10158-1
Zhan, Q., Stratmann, C. N., van der Geest, H. G., Veraart, A. J., Brenzinger, K., Lürling, M., & de Senerpont Domis, L. N. (2021). Effectiveness of phosphorus control under extreme heatwaves: implications for sediment nutrient releases and greenhouse gas emissions. Biogeochemistry, 156, 421-436. https://doi.org/10.1007/s10533-021-00854-z
Jeon, J-S., Etalo, D. W., Carreno-Quintero, N., de Vos, R. C. H., & Raaijmakers, J. M. (2021). Effects of Sulfur Assimilation in Pseudomonas fluorescens SS101 on Growth, Defense, and Metabolome of Different Brassicaceae. Biomolecules, 11(11). https://doi.org/10.3390/biom11111704
Clocchiatti, A., Hannula, E., Van den Berg, M., Hundscheid, M. P. J., & de Boer, W. (2021). Evaluation of phenolic root exudates as stimulants of saprotrophic fungi in the rhizosphere. Frontiers in Microbiology, 12, [644046]. https://doi.org/10.3389/fmicb.2021.644046
Hawkes, C. V., Kjøller, R., Raaijmakers, J. M., Riber, L., Christensen, S., Bjorholm Dahl, A., Cairo Westergaard, J., Nielsen, M., Brown-Guedira, G., & Hestbjerg Hansen, L. (2021). Extension of Plant Phenotypes by the Foliar Microbiome. Annual Review of Plant Biology, 72, 823-846. https://doi.org/10.1146/annurev-arplant-080620-114342
Oyserman, B. O., Cordovez, V., Sarango Flores, S. W., Nijveen, H., Medema, M. H., & Raaijmakers, J. M. (2021). Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes. Frontiers in Microbiology, 11, [574053]. https://doi.org/10.1101/863399, https://doi.org/10.3389/fmicb.2020.574053
Zhou, X., Leite, M. F. A., Zhang, Z., Tian, L., Chang, J., Ma, L., Li, X., van Veen, H., Tian, C., & Kuramae, E. (2021). Facilitation in the soil microbiome does not necessarily lead to niche expansion. Environmental Microbiome, 16, [4]. https://doi.org/10.1186/s40793-021-00373-2
Momesso, L., Crusciol, C. A. C., Leite, M. F. A., Bossolani, J. W., & Kuramae, E. (2022). Forage grasses steer soil nitrogen processes, microbial populations, and microbiome composition in a long-term tropical agriculture system. Agriculture, Ecosystems and Environment, 323, [107688]. https://doi.org/10.1016/j.agee.2021.107688
McDaniel, E. A., Wever, R., Oyserman, B. O., Noguera, D. R., & McMahon, K. D. (2021). Genome-resolved metagenomics of a photosynthetic bioreactor performing biological nutrient removal. Microbiology Resource Announcements, 10(18), [e00244-21]. https://doi.org/10.1128/MRA.00244-21
Clocchiatti, A., Hannula, S. E., Rizaludin, M. S., Hundscheid, M. P. J., klein Gunnewiek, P. J. A., Schilder, M. T., Postma, J., & de Boer, W. (2021). Impact of Cellulose-Rich Organic Soil Amendments on Growth Dynamics and Pathogenicity of Rhizoctonia solani. Microorganisms, 9(6), [1285]. https://doi.org/10.3390/microorganisms9061285
Jeon, J-S., Carreno-Quintero, N., van Eekelen, H. D. L. M., De Vos, R. C. H., Raaijmakers, J. M., & Etalo, D. W. (2021). Impact of root-associated strains of three Paraburkholderia species on primary and secondary metabolism of Brassica oleracea. Scientific Reports, 11, [2781]. https://doi.org/10.1038/s41598-021-82238-9
Brandenburg, K. M., Krock, B., Klip, H. C. L., Sluijs, A., Garbeva, P., & Van de Waal, D. B. (2021). Intraspecific variation in multiple trait responses of Alexandrium ostenfeldii towards elevated pCO₂. Harmful Algae, 101, [101970]. https://doi.org/10.1016/j.hal.2020.101970
McDaniel, E. A., Moya-Flores, F., Beach, N. K., Camejo, P. Y., Oyserman, B. O., Kizaric, M., Khor, E. H., Noguera, D. R., & McMahon, K. D. (2021). Metabolic differentiation of co-occurring accumulibacter clades revealed through genome-resolved metatranscriptomics. mSystems, 6(4), [e00474-21]. https://doi.org/10.1128/mSystems.00474-21
Wang, Z., Xu, Z., Chen, Z., Kowalchuk, G. A., Fu, X., & Kuramae, E. (2021). Microbial inoculants modulate growth traits, nutrients acquisition and bioactive compounds accumulation of Cyclocarya paliurus. Forest Ecology and Management, 482. https://doi.org/10.1016/j.foreco.2020.118897
Weisskopf, L., Schulz, S., & Garbeva, P. (2021). Microbial volatile organic compounds in intra-kingdom and inter-kingdom interactions. Nature Reviews Microbiology, 19, 391–404. https://doi.org/10.1038/s41579-020-00508-1
Bossolani, J. W., Crusciol, C. A. C., Leite, M. F. A., Merloti, L. F., Moretti de Souza, L., Pascoaloto, I. M., & Kuramae, E. (2021). Modulation of the soil microbiome by long-term Ca-based soil amendments boosts soil organic carbon and physicochemical quality in a tropical no-till crop rotation system. Soil Biology & Biochemistry, 156, [108188]. https://doi.org/10.1016/j.soilbio.2021.108188
Kuramae, E., Dimitrov, M., Silva, G. H. R., Lucheta, A., Mendes, L. W., Luz, R. L., Vet, L. E. M., & Fernandes, T. V. (2021). On-site blackwater treatment fosters microbial groups and functions to efficiently and robustly recover carbon and nutrients. Microorganisms, 9, [75]. https://doi.org/10.3390/microorganisms9010075
Vargas, P., Bosmans, L., Van Kerckhove, S., Van Calenberge, B., Raaijmakers, J. M., Lievens, B., & Rediers, H. (2021). Optimizing biocontrol activity of Paenibacillus xylanexedens for management of hairy root disease in tomato grown in hydroponic greenhouses. Agronomy Journal, 11(5), [817]. https://doi.org/10.3390/agronomy11050817
Momesso, L., Crusciol, C. A. C., Cantarella, H., Tanaka, K. S., Kowalchuk, G., & Kuramae, E. (2021). Optimizing cover crop and fertilizer timing for high maize yield and nitrogen cycle control. Geoderma, 405, [115423]. https://doi.org/10.1016/j.geoderma.2021.115423
Francioli, D., van Rijssel, S. Q., van Ruijven, J., Termorshuizen, A. J., Cotton, T. E. A., Dumbrell, A. J., Raaijmakers, J. M., Weigelt, A., & Mommer, L. (2021). Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment. Plant and Soil, 461, 91-105. https://doi.org/10.1007/s11104-020-04454-y
Cipriano, M., Freitas-Iório, R. D. P., Dimitrov, M., Andrade, S. A. L., Kuramae, E., & da Silveira, A. P. D. (2021). Plant-Growth Endophytic Bacteria Improve Nutrient Use Efficiency and Modulate Foliar N-Metabolites in Sugarcane Seedling. Microorganisms, 9(3), [479]. https://doi.org/10.3390/microorganisms9030479
Angulo, V., Beriot, N., Garcia-Hernandez, E., Li, E., Masteling, R., & Lau, J. (2021). Plant-Microbe Eco-Evolutionary Dynamics in a Changing World. New Phytologist, in press.
Ampt, E., van Ruijven, J., Zwart, M., Raaijmakers, J. M., Termorshuizen, A. J., & Mommer, L. (2021). Plant neighbours can make or break the disease transmission chain of a fungal root pathogen. New Phytologist, In press.
Su, L., Qiu, P., Fang, Z., Sun, J., Mo, X., Liu, Y., Kuramae, E., Zhang, R., Shen, B., & Shen, Q. (2021). Potassium phosphite enhances the antagonistic capability of Bacillus amyloliquefaciens to manage tomato bacterial wilt. Plant Disease, in press. https://doi.org/10.1094/PDIS-08-21-1601-RE
Leite, M. F. A., Dimitrov, M., Iório, R. D. P. F. I., De Hollander, M., Cipriano, M., Andrade, S. A. L., da Silveira, A. P. D., & Kuramae, E. (2021). Rearranging the sugarcane holobiont via plant growth-promoting bacteria and nitrogen input. Science of the Total Environment, 800, [149493]. https://doi.org/10.1016/j.scitotenv.2021.149493
Kaminsky, R. A., Wakelin, S. A., Highton, M. P., Samad, M. S., & Morales, S. E. (2021). Resolving broad patterns of prokaryotic community structure in New Zealand pasture soils. New Zealand Journal of Agricultural Research, 64(2), 143-161. https://doi.org/10.1080/00288233.2019.1678491
Sun, Y., Tian, L., Chang, J., Shi, S., Zhang, J., Xie, H., Cai, Y., Chen, D., Kuramae, E., van Veen, J. A., Li, W., Tran, L-S. P., & Tian, C. (2021). Rice domestication influences the composition and function of the rhizosphere bacterial chemotaxis systems. Plant and Soil, 466. https://doi.org/10.1007/s11104-021-05036-2
Chang, J., Shi, S., Tian, L., Leite, M. F. A., Chang, C., Ji, L., Ma, L., Tian, C., & Kuramae, E. (2021). Self-crossing leads to weak co-variation of the bacterial and fungal communities in the rice rhizosphere. Microorganisms, 9(1). https://doi.org/10.3390/microorganisms9010175
Meisner, A., Snoek, B., Nesme, J., Dent, E., Jacquiod, S., Classen, A. T., & Priemé, A. (2021). Soil microbial legacies differ following drying-rewetting and freezing-thawing cycles. ISME Journal, 15, 1207-1221. https://doi.org/10.1038/s41396-020-00844-3
Grum-Grzhimaylo, A. A., Bastiaans, E., van den Heuvel, J., Berenguer Millanes, C., Debets, A. J. M., & Aanen, D. K. (2021). Somatic deficiency causes reproductive parasitism in a fungus. Nature Communications, 12, [783]. https://doi.org/10.1038/s41467-021-21050-5
Bossolani, J. W., dos Santos, F. L., Meneghette, H. H. A., Sanches, I. R., Moretti, L. G., Parra, L. F., & Lazarini, E. (2021). Soybean in Crop Rotation with Maize and Palisade Grass Intercropping Enhances the Long-term Effects of Surface Liming in No-till System. Journal of Soil Science and Plant Nutrition, 21(1), 119–130. https://doi.org/10.1007/s42729-020-00347-2
Brenzinger, K., Costa, O. Y. A., Ho, A., Koorneef, G., Robroek, B. J. M., Molenaar, D., Korthals, G., & Bodelier, P. (2021). Steering microbiomes by organic amendments towards climate-smart agricultural soils. Biology and Fertility of Soils, In press. https://doi.org/10.1007/s00374-021-01599-5
Clocchiatti, A., Hannula, S. E., Hundscheid, M. P. J., Klein Gunnewiek, P. J. A., & de Boer, W. (2021). Stimulated saprotrophic fungi in arable soil extend their activities to the rhizosphere and root microbiomes of crop seedlings. Environmental Microbiology, In press. https://doi.org/10.1111/1462-2920.15563
Wang, Z., Chen, Z., Kowalchuk, G., Xu, Z., Fu, X., & Kuramae, E. (2021). Succession of the Resident Soil Microbial Community in Response to Periodic Inoculations. Applied and Environmental Microbiology, 87(9), [e00046-21]. https://doi.org/10.1128/AEM.00046-21
Cordovez, V., Rotoni, C., Dini-Andreote, F., Oyserman, B. O., Carrión, V. J., & Raaijmakers, J. M. (2021). Successive plant growth amplifies genotype-specific assembly of the tomato rhizosphere microbiome. Science of the Total Environment, 772, [144825]. https://doi.org/10.1016/j.scitotenv.2020.144825
Rossetto, L., Pierangeli, G. M. F., Kuramae, E., Xavier, M., Cipriano, M., & da Silveira, A. P. D. (2021). Sugarcane pre-sprouted seedlings produced with beneficial bacteria and arbuscular mycorrhizal fungi. Bragantia, 80. https://doi.org/10.1590/1678-4499.20200276
Rizaludin, M. S., Stopnisek, N., Raaijmakers, J. M., & Garbeva, P. (2021). The Chemistry of Stress: Understanding the ‘Cry for Help’ of Plant Roots. Metabolites, 11(6). https://doi.org/10.3390/metabo11060357
Costa, O. Y. A., & Kuramae, E. (2021). The influence of agar brands and micronutrients in the growth optimization of Granulicella sp. (Acidobacteriota). Journal of Microbiological Methods, 181, [106148]. https://doi.org/10.1016/j.mimet.2021.106148
de Jonge, C., Kuramae, E., Radujković, D., Weedon, J. T., Janssens, I. A., & Peterse, F. (2021). The influence of soil chemistry on branched tetraether lipids in mid- and high latitude soils: implications for brGDGT- based paleothermometry. Geochimica et Cosmochimica Acta, 310, 95-112. https://doi.org/10.1016/j.gca.2021.06.037
Chang, J., Sun, Y., Tian, L., Ji, L., Luo, S., Nasir, F., Kuramae, E., & Tian, C. (2021). The structure of rhizosphere fungal communities of wild and domesticated rice: changes in diversity and co-occurrence patterns. Frontiers in Microbiology, 12. https://doi.org/10.3389/fmicb.2021.610823
Dini-Andreote, F., Kowalchuk, G. A., Prosser, J. I., & Raaijmakers, J. M. (2021). Towards meaningful scales in ecosystem microbiome research. Environmental Microbiology, 23(1). https://doi.org/10.1111/1462-2920.15276
Colina, M., Meerhoff, M., Pérez, G., Veraart, A., Bodelier, P., van der Horst, A., & Kosten, S. (2021). Trophic and non-trophic effects of fish and macroinvertebrates on carbon emissions. Freshwater Biology, 66(9), 1831-1845. https://doi.org/10.1111/fwb.13795
Ossowicki, A. (2021). Understanding disease suppressive soils: molecular and chemical identification of microorganisms and mechanisms involved in soil suppressiveness to Fusarium culmorum of wheat (PhD Thesis). https://hdl.handle.net/1887/3180746
Zwart, M. P., Blanc, S., Johnson, M., Manrubia, S., Michalakis, Y., & Sofonea, M. T. (2021). Unresolved advantages of multipartitism in spatially structured environments. Virus Evolution, 7(1), [veab004]. https://doi.org/10.1093/ve/veab004
Crusciol, C. A. C., Momesso, L., Portugal, J. R., Costa, C. H. M., Bossolani, J. W., Costa, N. R., Pariz, C. M., Castilhos, A. M., Rodrigues, V. A., Costa, C., Franzluebbers, A. J., & Cantarella, H. (2021). Upland rice intercropped with forage grasses in an integrated crop-livestock system: Optimizing nitrogen management and food production. Field Crops Research, 261, [108008]. https://doi.org/10.1016/j.fcr.2020.108008
Cheng, X-Y., Liu, X-Y., Wang, H-M., Su, C-T., Zhao, R., Bodelier, P., Wang, W-Q., Ma, L-Y., & Lu, X-L. (2021). USCγ Dominated Community Composition and Cooccurrence Network of Methanotrophs and Bacteria in Subterranean Karst Caves. Microbiology spectrum, 9(1), [e00820-21]. https://doi.org/10.1128/Spectrum.00820-21
Moisan, K., Dicke, M., Raaijmakers, J. M., Rachmawati, E., & Cordovez, V. (2021). Volatiles from the fungus Fusarium oxysporum affect interactions of Brassica rapa plants with root herbivores. Ecological Entomology, 46(2), 240-248. https://doi.org/10.1111/een.12956
Garbeva, P., & Weisskopf, L. (2020). Airborne medicine - Bacterial volatiles and their influence on plant health: Transley review. New Phytologist, 226(1), 32-43. https://doi.org/10.1111/nph.16282
Floková, K., Shimels, M., Andreo Jimenez, B., Bardaro, N., Strnad, M., Novák, O., & Bouwmeester, H. J. (2020). An improved strategy to analyse strigolactones in complex sample matrices using UHPLC-MS/MS. Plant Methods, 16(1), [125]. https://doi.org/10.1186/s13007-020-00669-3
Gulati, S., Ballhausen, M-B., Kulkarni, P., Grosch, R., & Garbeva, P. (2020). A non-invasive soil based setup to study tomato root volatiles released by healthy and infected roots. Scientific Reports, 10, [12704]. https://doi.org/10.1038/s41598-020-69468-z
Elsayed, S. S., Genta-Jouve, G., Carrión, V. J., Nibbering, P. H., Siegler, M. A., de Boer, W., Hankemeier, T., & van Wezel, G. P. (2020). Atypical Spirotetronate Polyketides Identified in the Underexplored Genus Streptacidiphilus. Journal of organic chemistry, 85(16), 10648-10657. https://doi.org/10.1021/acs.joc.0c01210
Gehring, C., Zelarayán, M. C., Luz, R. L., Almeida, R. B., Boddey, R. M., & Leite, M. F. A. (2020). Babassu palm (Attalea speciosa Mart.) super-dominance shapes its surroundings via multiple biotic, soil chemical, and physical interactions and accumulates soil carbon: a case study in eastern Amazonia. Plant and Soil, 454(1-2), 447–460. https://doi.org/10.1007/s11104-020-04580-7
Moretti de Souza, L., Cruciol, C. A. C., Bossolani, J. W., Momesso, L., Garcia, A., Kuramae, E., & Hungria, M. (2020). Bacterial consortium and microbial metabolites increase grain quality and soybean yield. Journal of Soil Science and Plant Nutrition, 20(4), 1923–1934. https://doi.org/10.1007/s42729-020-00263-5
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De Bruijn, I., Cheng, X., de Jager, V. C. L., Gómez Expósito, R., Watrous, J., Patel, N., Postma, J., Dorrestein, P. C., Kobayashi, D., & Raaijmakers, J. M. (2015). Comparative genomics and metabolic profiling of the genus Lysobacter. BMC Genomics, 16, [991]. https://doi.org/10.1186/s12864-015-2191-z
Krause, S., Niklaus, P. A., Morcillo, S. B., Meima-Franke, M., Lüke, C., Reim, A., & Bodelier, P. L. E. (2015). Compositional and functional stability of aerobic methane consuming communities in drained and rewetted peat meadows. FEMS Microbiology Ecology, 91(11), [fiv119]. https://doi.org/10.1093/femsec/fiv119
Hol, G., De Boer, W., de Hollander, M., Kuramae, E. E., Meisner, A., & van der Putten, W. (2015). Context dependency and saturating effects of loss of rare soil microbes on plant productivity. Frontiers in Plant Science, 6, [485]. https://doi.org/10.3389/fpls.2015.00485
Mendes, R., & Raaijmakers, J. M. (2015). Cross-kingdom similarities in microbiome functions. ISME Journal, 9, 1905-1907. https://doi.org/10.1038/ismej.2015.7
Ho, A., & Bodelier, P. (2015). Diazotrophic methanotrophs in peatlands: the missing link? Plant and Soil, 389(1-2), 419-423. https://doi.org/10.1007/s11104-015-2393-9
Gómez Expósito, R., Postma, J., Raaijmakers, J. M., & de Bruijn, I. (2015). Diversity and activity of Lysobacter species from disease suppressive soils. Frontiers in Microbiology, 6(1243), [2015.01243]. https://doi.org/10.3389/fmicb.2015.01243
Cordovez, V., Carrion, V., Etalo, D. W., Mumm, R., Zhu, H., Van Wezel, G. P., & Raaijmakers, J. M. (2015). Diversity and functions of volatile organic compounds produced by Streptomyces from a disease-suppressive soil. Frontiers in Microbiology, 6. https://doi.org/10.3389/fmicb.2015.01081
Liu, Y., Rzeszutek, E., van der Voort, M., Wu, C. H., Thoen, E., Skaar, I., Bulone, V., Dorrestein, P. C., Raaijmakers, J. M., & De Bruijn, I. (2015). Diversity of aquatic Pseudomonas species and their activity against the fish pathogenic oomycete Saprolegnia. PLoS One, 10(8), [e0136241]. https://doi.org/10.1371/journal.pone.0136241
Wolf, A. B., Rudnick, M. B., De Boer, W., & Kowalchuk, G. A. (2015). Early colonizers of unoccupied habitats represent a minority of the soil bacterial community. FEMS Microbiology Ecology, 91(5), [fiv024]. https://doi.org/10.1093/femsec/fiv024
Bai, Y. (2015). Ecological functioning of bacterial chitinases in soil (PhD Thesis). Leiden University Press. https://openaccess.leidenuniv.nl/handle/1887/35971
Waghmode, T. R., Haque, M. M., Kim, S. Y., & Kim, P. J. (2015). Effective Suppression of Methane Emission by 2-Bromoethanesulfonate during Rice Cultivation. PLoS One, 10(11), [ e0142569]. https://doi.org/10.1371/journal.pone.0142569
Zhang, L., Hou, L., Laanbroek, H. J., Guo, D., & Wang, Q. (2015). Effects of Mowing Heights on N2O Emission from Temperate Grasslands in Inner Mongolia, Northern China. American Journal of Climate Change, 04(05), 397-407. https://doi.org/10.4236/ajcc.2015.45032
Benner, J., De Smet, D., Ho, A., Kerckhof, F-M., Vanhaecke, L., Heylen, K., & Boon, N. (2015). Exploring methane-oxidizing communities for the co-metabolic degradation of organic micropollutants. Applied Microbiology and Biotechnology, 99(8), 3609-3618. https://doi.org/10.1007/s00253-014-6226-1
Song, C., Schmidt, R. L., de Jager, V. C. L., Krzyzanowska, D., Jongedijk, E., Cankar, K., Beekwilder, J., van Veen, A., De Boer, W., van Veen, J. A., & Garbeva, P. V. (2015). Exploring the genomic traits of fungus-feeding bacterial genus Collimonas. BMC Genomics, 16, [1103]. https://doi.org/10.1186/s12864-015-2289-3
Henneberger, R., Chiri, E., Bodelier, P. L. E., Frenzel, P., Luke, C., & Schroth, M. H. (2015). Field-scale tracking of active methane-oxidizing communities in a landfill-cover soil reveals spatial and seasonal variability. Environmental Microbiology, 17(5), 1721-1737. https://doi.org/10.1111/1462-2920.12617
Wu, J-J., de Jager, V., Deng, W., & Leveau, J. (2015). Finished Genome Sequence of Collimonas arenae Cal35. Genome Announcements, 3(1), [e01408-14]. https://doi.org/10.1128/genomeA.01408-14
Cheng, X., van der Voort, M., & Raaijmakers, J. M. (2015). Gac-mediated changes in pyrroloquinoline quinone biosynthesis enhance the antimicrobial activity of Pseudomonas fluorescens SBW25. Environmental Microbiology Reports, 7(1), 139-147. https://doi.org/10.1111/1758-2229.12231
van der Voort, M., Meijer, H., Schmidt, Y., Watrous, J., Dekkers, E., Mendes, R., Dorrestein, P. C., Gross, H., & Raaijmakers, J. M. (2015). Genome mining and metabolic profiling of the rhizosphere bacterium Pseudomonas sp. SH-C52 for antimicrobial compounds. Frontiers in Microbiology, 6, [693]. https://doi.org/10.3389/fmicb.2015.00693
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Hwang, H. Y., Kim, G. W., Lee, Y. B., Kim, P. J., & Kim, S. Y. (2015). Improvement of the Value of Green Manure via Mixed Hairy Vetch and Barley Cultivation in Temperate Paddy Soil. Field Crops Research, 183(November), 138-146. https://doi.org/10.1016/j.fcr.2015.08.001
Philmus, B., Shaffer, B., Kidarsa, T., Yan, Q., Raaijmakers, J., Begley, T., & Loper, J. (2015). Investigations into the biosynthesis, regulation and self-resistance of toxoflavin in Pseudomonas protegens Pf-5. ChemBioChem, 16(12), 1782-1790. https://doi.org/10.1002/cbic.201500247
Mendes, L. W., Brossi, M. J. L., Kuramae, E. E., & Tsai, S. M. (2015). Land-use system shapes soil bacterial communities in Southeastern Amazon region. Applied Soil Ecology, 95, 151-160. https://doi.org/10.1016/j.apsoil.2015.06.005
van Agtmaal, M., van Os, G., Hol, G., Hundscheid, M. P. J., Runia, W., Hordijk, C., & De Boer, W. (2015). Legacy effects of anaerobic soil disinfestation on soil bacterial community composition and production of pathogen-suppressing volatiles. Frontiers in Microbiology, 6, [701]. https://doi.org/10.3389/fmicb.2015.00701
Song, C., Sundqvist, G., Malm, E., de Bruijn, I., Kumar, A., van de Mortel, J., Bulone, V., & Raaijmakers, J. (2015). Lipopeptide biosynthesis in Pseudomonas fluorescens is regulated by the protease complex ClpAP. BMC Microbiology, 15, [29]. https://doi.org/10.1186/s12866-015-0367-y
Ho, A., El-Hawwary, A. H. M., Kim, S. Y., Meima-Franke, M., & Bodelier, P. (2015). Manure-associated stimulation of soil-borne methanogenic activity in agricultural soils. Biology and Fertility of Soils, 51(4), 511-516. https://doi.org/10.1007/s00374-015-0995-2
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Schulz, K., Hunger, S., Brown, G. G., Tsai, S. M., Cerri, C. C., Conrad, R., & Drake, H. (2015). Methanogenic Food Web in Gut Contents of the Methane-Emitting Earthworm Eudrilus eugeniae from Brazil. ISME Journal, 9, 1778-1792. https://doi.org/10.1038/ismej.2014.262
Ballhausen, M-B., van Veen, J. A., Hundscheid, M. P. J., & De Boer, W. (2015). Methods for baiting and enriching fungus-feeding (mycophagous) rhizosphere bacteria. Frontiers in Microbiology, 6, [01416]. https://doi.org/10.3389/fmicb.2015.01416
Lupatini, M. (2015). Microbial communities in Pampa soils; impact of land-use chenges; soil type and climate conditions (PhD Thesis). http://hdl.handle.net/1887/37037
Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K., de Bruijn, I., Chooi, Y. H., Claesen, J., Coates, R. C., Cruz-Morales, P., Duddela, S., Dusterhus, S., Edwards, D. J., Fewer, D. P., Garg, N., Geiger, C., Gomez-Escribano, J. P., Greule, A.,... Glockner, F. O. (2015). Minimum Information about a Biosynthetic Gene cluster: commentary. Nature Chemical Biology, 11(9), 625-631. https://doi.org/10.1038/nchembio.1890
Song, C., Mazzola, M., Cheng, X., Oetjen, J., Alexandrov, T., Dorrestein, P. C., Watrous, J., van der Voort, M., & Raaijmakers, J. (2015). Molecular and chemical dialogues in bacteria-protozoa interactions. Scientific Reports, 5, [12837]. https://doi.org/10.1038/srep12837
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Van der Wal, A., Ottosson, E. G. B., & De Boer, W. (2015). Neglected role of fungal community composition in explaining variation in wood decay rates. Ecology, 96(1), 124-133. https://doi.org/10.1890/14-0242.1
Balk, M., Laverman, A. M., Keuskamp, J. A., & Laanbroek, H. J. (2015). Nitrate ammonification in mangrove soils: A hidden source of nitrite? Frontiers in Microbiology, 6, [166]. https://doi.org/10.3389/fmicb.2015.00166
Hol, G., Garbeva, P., Hordijk, C., Hundscheid, M. P. J., Klein Gunnewiek, P. J. A., Van Agtmaal, M., Kuramae, E. E., & De Boer, W. (2015). Non-random species loss in bacterial communities reduces antifungal volatile production. Ecology, 96(8), 2042-2048. https://doi.org/10.1890/14-2359.1
Haque, M. M., Kim, S. Y., Kim, G. W., & Kim, P. J. (2015). Optimization of removal and recycling ratio of cover crop biomass using carbon balance to sustain soil organic carbon stocks in a mono-rice paddy system. Agriculture, Ecosystems and Environment, 207, 119-125. https://doi.org/10.1016/j.agee.2015.03.022
Kim, S. Y., Park, C. K., Gwon, H. S., Khan, M. I., & Kim, P. J. (2015). Optimizing the harvesting stage of rye as a green manure to maximize nutrient production and to minimize methane production in mono-rice paddies. Science of the Total Environment, 537(December), 441-446. https://doi.org/10.1016/j.scitotenv.2015.07.061
Rudnick, M. B., van Veen, J. A., & De Boer, W. (2015). Oxalic acid: a signal molecule for fungus-feeding bacteria of the genus Collimonas? Environmental Microbiology Reports, 7(5), 709-714. https://doi.org/10.1111/1758-2229.12290
Deveau, A., Barret, M., Diedhiou, A. G., Leveau, J., de Boer, W., Martin, F., Sarniguet, A., & Frey-Klett, P. (2015). Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria. Microbial Ecology, 69(1), 146-159. https://doi.org/10.1007/s00248-014-0445-y
Robroek, B. J. M., Jassey, V. E. J., Kox, M. A. R., Berendsen, R. L., Mills, R. T. E., Cécillon, L., Puissant, J., Meima-Franke, M., Bakker, P. A. H. M., & Bodelier, P. (2015). Peatland vascular plant functional types affect methane dynamics by altering microbial community structure. Journal of Ecology, 103(4), 925-934. https://doi.org/10.1111/1365-2745.12413
Steenbergh, A., Bodelier, P., Hoogveld, H. L., Slomp, C. P., & Laanbroek, H. J. (2015). Phylogenetic characterization of phosphatase-expressing bacterial communities in Baltic Sea sediments. Microbes and Environments, 30(2), 192-195. [ME14074]. https://doi.org/10.1264/jsme2.ME14074
Balk, M., Keuskamp, J. A., & Laanbroek, H. J. (2015). Potential activity, size and structure of sulfate-reducing microbial communities in an exposed, grazed and a sheltered, non-grazed mangrove stands at the Red Sea coast. Frontiers in Microbiology, 6, [01478]. https://doi.org/10.3389/fmicb.2015.01478
Jeon, J-S., Kim, J. H., Park, C. L., & Kim, C. Y. (2015). Preparative Isolation of Polar Antioxidant Constituents from Abies koreana Using Centrifugal Partition Chromatography Guided by DPPH center dot-HPLC Experiment. JOURNAL OF LIQUID CHROMATOGRAPHY & RELATED TECHNOLOGIES, 38(18), 1681-1686. https://doi.org/10.1080/10826076.2015.1091010
Park, Y-S., Dutta, S., Ann, M., Raaijmakers, J. M., & Park, K. (2015). Promotion of plant growth by Pseudomonas fluorescens strain SS101 via novel volatile organic compounds. Biochemical and Biophysical Research Communications, 461(2), 361-365. https://doi.org/10.1016/j.bbrc.2015.04.039
Collet, S., Reim, A., Ho, A., & Frenzel, P. (2015). Recovery of paddy soil methanotrophs from long term drought. Soil Biology & Biochemistry, 88, 69-72. https://doi.org/10.1016/j.soilbio.2015.04.016
Yan, Y., Kuramae, E. E., Klinkhamer, P. G. L., & Van Veen, J. A. (2015). Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems revisited. Applied and Environmental Microbiology, 81(13), 4246-4252. https://doi.org/10.1128/AEM.00958-15
Zhang, Q., Tang, F-Y., Zhou, Y-J., Xu, J., Chen, H., Wang, M-J., & Laanbroek, H. J. (2015). Shifts in the pelagic ammonia-oxidizing microbial communities along the eutrophic estuary of Yong River in Ningbo City, China. Frontiers in Microbiology, 6, [1180]. https://doi.org/10.3389/fmicb.2015.01180
Keuskamp, J. A., Feller, I. C., Laanbroek, H. J., Verhoeven, J. T. A., & Hefting, M. M. (2015). Short- and long-term effects of nutrient enrichment on microbial exoenzyme activity in mangrove peat. Soil Biology & Biochemistry, 81(0), 38-47. https://doi.org/10.1016/j.soilbio.2014.11.003
Abrudan, M. I., Smakman, F., Grimbergen, A. J., Westhoff, S., Miller, E. L., van Wezel, G. P., & Rozen, D. E. (2015). Socially mediated induction and suppression of antibiosis during bacterial coexistence. Proceedings of the National Academy of Sciences of the United States of America, 112(5), 11054-11059. https://doi.org/10.1073/pnas.1504076112
Mendes, L. M., Tsai, S. M., Navarrete, A. A., De Hollander, M., Van Veen, J. A., & Kuramae, E. E. (2015). Soil-borne microbiome: linking diversity to function. Microbial Ecology, 70(1), 255-265. https://doi.org/10.1007/s00248-014-0559-2
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Department of Microbial Ecology

The power of the small

Micro-organisms form a huge, largely undiscovered potential. A treasure-trove for researchers from the department of Microbial Ecology.

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Department of Microbial Ecology

The power of the small

Micro-organisms form a huge, largely undiscovered potential. A treasure-trove for researchers from the department of Microbial Ecology.

Recent publications (2015 - )

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