Skip to main content
  • Nederlands
  • English

Internet search

Menu
  • What's new
    • News
    • Press releases
    • Calendar
  • About us
    • Who we are
    • Our building
    • Our history
  • Research
    • Publications
    • Research themes
    • Datasets
    • Facilities
  • Departments
    • Animal Ecology
    • Aquatic Ecology
    • Microbial Ecology
    • Terrestrial Ecology
    • Other
  • Themes
    • Chemical ecology
    • Disease ecology
    • Eco-evolutionary dynamics
    • Ecological epigenetics
    • Global environmental change
    • Microbiomes
    • Restoration ecology
  • Society
    • Relevance to society
    • Citizen science projects
    • Educational information
  • Vacancies
  • Contact
    • Address & route
    • Staff

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.

  • About
  • News
  • Staff
  • Groups
  • Projects
  • Publications
  • Student Subjects

Recent publications (2015 - )

  • Hannula, E., Di Lonardo, P., Christensen, B. T., Crotty, F. V., Elsen, A., Erp, P. J. V., Hansen, E. M., Rubæk, G. H., Tits, M., Tóth, Z., & Termorshuizen, A. J. (Accepted/In press). Inconsistent effects of agricultural practices on soil fungal communities across twelve European long-term experiments. European Journal of Soil Science, in press.
  • 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
  • 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
  • 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. https://doi.org/10.1007/s11104-020-04580-7
  • Moretti, L. G., 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, in press. https://doi.org/10.1007/s42729-020-00263-5
  • Su, L., Zhang, L., Qiu, P., Nie, D., Kuramae, E., Shen, B., & Shen, Q. (2020). Bacterial Tomato Pathogen Ralstonia solanacearum Invasion Modulates Rhizosphere Compounds and Facilitates the Cascade Effect of Fungal Pathogen Fusarium solani. Microorganisms, in press. https://doi.org/10.3390/microorganisms8060806
  • Song, C., Zhu, F., Carrión, V. J., & Cordovez, V. (2020). Beyond Plant Microbiome Composition: Exploiting Microbial Functions and Plant Traits via Integrated Approaches. Frontiers in bioengineering and biotechnology, 8, [896]. https://doi.org/10.3389/fbioe.2020.00896
  • Orama, N. J., van Groeningen, J. W., Bodelier, P., Brenzinger, K., Cornelissen, J. H. C., De Deyn, G., & Abalos, D. (2020). Can flooding-induced greenhouse gas emissions be mitigated by trait-based plant species choice? Science of the Total Environment, 727(20 July), [138476]. https://doi.org/10.1016/j.scitotenv.2020.138476
  • Costa, N., Andreotti, M., Costa Crusciol, C. A., Magelhaes Pariz, C., Bossolani, J. W., de Castilhos, A. M., Costa do Nascimento, C. A., da Rocha Lima, C. G., dos Santos Batista Bonini, C., & Kuramae, E. (2020). Can Palisade and Guinea Grass Sowing Time in Intercropping Systems Affect Soybean Yield and Soil Chemical Properties? Frontiers In Sustainable Food Systems, 4, [81]. https://doi.org/10.3389/fsufs.2020.00081
  • Contreras-Dávila, C. A., Carrión, V. J., Vonk, V. R., Buisman, C. N. J., & Strik, D. P. B. T. B. (2020). Consecutive lactate formation and chain elongation to reduce exogenous chemicals input in repeated-batch food waste fermentation. Water Research, 169, [115215]. https://doi.org/10.1016/j.watres.2019.115215
  • Zheng, Y., Hu, X., Jia, Z., Bodelier, P., Guo, Z., Zhang, Y., Li, F., Li, X., & He, P. (2020). Co-occurrence patterns among prokaryotes across an age gradient in pit mud of Chinese strong-flavor liquor. Canadian Journal of Microbiology, Online. https://doi.org/10.1139/cjm-2020-0012
  • Costa, O. Y. A., De Hollander, M., Pijl, A., Liu, B., & Kuramae, E. (2020). Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. Microbiome, in press, [76]. https://doi.org/10.1186/s40168-020-00836-7
  • Drost, S. M., Rutgers, M., Wouterse, M., De Boer, W., & Bodelier, P. (2020). Decomposition of mixtures of cover crop residues increases microbial functional diversity. Geoderma, 361, [114060]. https://doi.org/10.1016/j.geoderma.2019.114060
  • Masteling, R., Voorhoeve, L., Ijsselmuiden, J., Dini-Andreote, F., De Boer, W., & Raaijmakers, J. M. (2020). DiSCount: computer vision for automated quantification of Striga seed germination. Plant Methods, 16(60). https://doi.org/10.1186/s13007-020-00602-8
  • 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. (2020). Discovery of Thanafactin A, a Linear Proline-containing Octa-Lipopeptide from Pseudomonas sp. SH-C52, Motivated by Genome Mining. Journal of Natural Products, in press. https://doi.org/10.1021/acs.jnatprod.0c01174
  • Zhang, L., Dumont, M. G., Bodelier, P. L. E., Adams, J. M., He, D., & Chu, H. (2020). DNA stable-isotope probing highlights the effects of temperature on functionally active methanotrophs in natural wetlands. Soil Biology & Biochemistry, 149, [107954]. https://doi.org/10.1016/j.soilbio.2020.107954
  • Kirchner, N., Cano-Prieto, C., van der Voort, M., Raaijmakers, J. M., & Gross, H. (2020). Draft Genome Sequence of Lipopeptide-Producing Strain Pseudomonas fluorescens DSM 11579 and Comparative Genomics with Pseudomonas sp. Strain SH-C52, a Closely Related Lipopeptide-Producing Strain. MICROBIOLOGY RESOURCE ANNOUNCEMENTS, 9(21), [00304-20]. https://doi.org/10.1128/MRA.00304-20
  • Lourenço, K. S., Suleiman, A. K. A., Pijl, A., Cantarella, H., & Kuramae, E. (2020). Dynamics and resilience of soil mycobiome under multiple organic and inorganic pulse disturbances. Science of the Total Environment, 733(1 september), [139173]. https://doi.org/10.1016/j.scitotenv.2020.139173
  • Costa, O. Y. A., Pijl, A., & Kuramae, E. (2020). Dynamics of active potential bacterial and fungal interactions in the assimilation of acidobacterial EPS in soil. Soil Biology & Biochemistry, 148. https://doi.org/10.1016/j.soilbio.2020.107916
  • Costa, O. Y. A. (2020). Ecological functions and environmental fate of exopolymers of Acidobacteria (PhD Thesis). http://hdl.handle.net/1887/123274
  • van Bergeijk, D. A., Terlouw, B. R., Medema, M. H., & van Wezel, G. P. (2020). Ecology and genomics of Actinobacteria: new concepts for natural product discovery. Nature Reviews Microbiology. https://doi.org/10.1038/s41579-020-0379-y
  • Alderliesten, J. B., Duxbury, S. J. N., Zwart, M. P., de Visser, J. A. G. M., Stegeman, A., & Fischer, E. A. J. (2020). Effect of donor-recipient relatedness on the plasmid conjugation frequency: a meta-analysis. BMC Microbiology, 20(1). https://doi.org/10.1186/s12866-020-01825-4
  • Di Lonardo, D. P., van der Wal, A., Harkes, P., & de Boer, W. (2020). Effect of nitrogen on fungal growth efficiency. Plant Biosystems. https://doi.org/10.1101/2020.01.19.911727, https://doi.org/10.1080/11263504.2020.1779849
  • Moretti, L. G., Crusciol, C. A. C., Kuramae, E., Bossolani, J. W., Moreira, A., Costa, N. R., Alves, C. J., Pascoaloto, I. M., Rondina, A. B. L., & Hungria, M. (2020). Effects of growth-promoting bacteria on soybean root activity, plant development and yield. Agronomy Journal, 112(1), 418-428. https://doi.org/10.1002/agj2.20010
  • Qi, Y., Ossowicki, A., Yang, X., Huerta Lwanga, E., Dini-Andreote, F., Geissen, V., & Garbeva, P. (2020). Effects of plastic mulch film residues on wheat rhizosphere and soil properties. Journal of Hazardous Materials, 387, [121711]. https://doi.org/10.1016/j.jhazmat.2019.121711
  • van Oers, K., Sepers, B., Sies, W., Gawehns - Bruning, F. K. K., Verhoeven, K., & Laine, V. (2020). Epigenetics of animal personality: DNA methylation cannot explain the heritability of exploratory behavior in a songbird. Integrative and Comparative Biology, in press, [icaa138]. https://doi.org/10.1093/icb/icaa138
  • van Erven, G., Kleijn, A. F., Patyshakuliyeva, A., Di Falco, M., Tsang, A., de Vries, R. P., van Berkel, W. J. H., & Kabel, M. A. (2020). Evidence for ligninolytic activity of the ascomycete fungus Podospora anserina. Biotechnology for Biofuels, 13. https://doi.org/10.1186/s13068-020-01713-z
  • Suleiman, A. K. A., Lourenço, K. S., Clark, C., Luz, R. L., Silva, G. H. R., Vet, L. E. M., Cantarella, H., Fernandes, T. V., & Kuramae, E. (2020). From toilet to agriculture: Fertilization with microalgal biomass from wastewater impacts the soil and rhizosphere active microbiomes, greenhouse gas emissions and plant growth. Resources, Conservation and Recycling, 161, [104924]. https://doi.org/10.1016/j.resconrec.2020.104924
  • Moisan, K., Aragón, M., Gort, G., Dicke, M., Cordovez, V., Raaijmakers, J. M., & Lucas-Barbosa, D. (2020). Fungal volatiles influence plant defence against aboveground and belowground herbivory. Functional Ecology, 34(11), 2259-2269. https://doi.org/10.1111/1365-2435.13633
  • Sedighian, N., Krijger, M., Taparia, T., Taghavi, S. M., Wicker, E., Van Der Wolf, J. M., & Osdaghi, E. (2020). Genome resource of two potato strains of ralstonia solanacearum biovar 2 (phylotype IIB/sequevar 1) and biovar 2T (phylotype IIB/sequevar 25) isolated from lowlands in Iran. Molecular Plant-Microbe Interactions, 33(5). https://doi.org/10.1094/MPMI-02-20-0026-A
  • Bodelier, P., & Hallin, S. (2020). Grand challenges in Terrestrial Microbiology: moving on from a decade of progress in microbial biogeochemistry: SPECIALTY GRAND CHALLENGE ARTICLE. Frontiers in Microbiology, 11, [981]. https://doi.org/10.3389/fmicb.2020.00981
  • Costa, O. Y. A., Oguejiofor, C., Zuehlke, D., Barreto, C. C., Wünsche, C., Riedel, K., & Kuramae, E. (2020). Impact of different trace elements on the growth and proteome of two strains of Granulicella, class “Acidobacteriia”. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.01227
  • Trebuch, L. M., Oyserman, B. O., Janssen, M., Wijffels, R. H., Vet, L. E. M., & Fernandes, T. V. (2020). Impact of hydraulic retention time on community assembly and function of photogranules for wastewater treatment. Water Research, 173, [115506]. https://doi.org/10.1016/j.watres.2020.115506
  • Qi, Y., Beriot, N., Gort, G., Huerta Lwanga, E., Gooren, H., Yang, X., & Geissen, V. (2020). Impact of plastic mulch film debris on soil physicochemical and hydrological properties. Environmental Pollution, 266, Part 3, [115097]. https://doi.org/10.1016/j.envpol.2020.115097
  • Martín-Sánchez, L., Ariotti, C., Garbeva, P., & Vigani, G. (2020). Investigating the effect of belowground microbial volatiles on plant nutrient status: perspective and limitations. Journal of Plant Interactions, 15(1), 188-195. https://doi.org/10.1080/17429145.2020.1776408
  • Ponizovskaya, V. B., Grum-Grzimaylo, A. A., Georgieva, M. L., Kokaeva, L. Y., & Bilanenko, E. N. (2020). Lecanicillium gracile (Cordycipitaceae), a new species isolated from mineral building materials. Phytotaxa. https://doi.org/10.11646/phytotaxa.443.3.3
  • Bossolani, J. W., Crusciol, C. A. C., Merloti, L. F., Moretti, L. G., Costa, N., Tsai, S. M., & Kuramae, E. (2020). Long-term lime and gypsum amendment increase nitrogen fixation and decrease nitrification and denitrification gene abundances in the rhizosphere and soil in a tropical no-till intercropping system. Geoderma, 375. https://doi.org/10.1016/j.geoderma.2020.114476
  • Navarrete, A. A., Bonassi, R. C., Americo-Pinheiro, J. H. P., Vazquez, G. H., Mendes, L. W., Loureiro, E. S., Kuramae, E., & Tsai, S. M. (2020). Methods to Identify Soil Microbial Bioindicators of Sustainable Management of Bioenergy Crops. In L. C. Carvalhais, & P. G. Dennis [Eds.], The Plant Microbiome: Methods and Protocols (pp. 251-263). (Methods in Molecular Biology; Vol. 2232). Springer Nature. https://doi.org/10.1007/978-1-0716-1040-4_19
  • Ossowicki, A., Tracanna, V., Petrus, M. L. C., van Wezel, G., Raaijmakers, J. M., Medema, M. H., & Garbeva, P. (2020). Microbial and volatile profiling of soils suppressive to Fusarium culmorum of wheat. Proceedings of the Royal Society B-Biological Sciences, 287(1921), [ 20192527.]. https://doi.org/10.1098/rspb.2019.2527
  • Mocali, S., Kuramae, E., Kowalchuk, G., Fornasier, F., & Priori, S. (2020). Microbial functional diversity in vineyard soils: sulfur metabolism and links with grapevine plants and wine quality. Frontiers in Environmental Science, 8. https://doi.org/10.3389/fenvs.2020.00075
  • Rocha, K. F., Kuramae, E., Borges, B. M. F., Leite, M. F. A., & Rosolem, C. A. (2020). Microbial N‑cycling genes abundance are affected by cover crop specie and development stage in an integrated cropping system. Archives of Microbiology. https://doi.org/10.1007/s00203-020-01910-2
  • Qi, Y. (2020). Microplastics in the agroecosystem: effects of plastic mulch film residues on the soil-plant system (PhD Thesis). https://doi.org/10.18174/532052
  • Zwart, M., & Elena, S. F. (2020). Modeling multipartite virus evolution: the genome formula facilitates rapid adaptation to heterogeneous environments. Virus Evolution, 6(1). https://doi.org/10.1093/ve/veaa022
  • Jeon, J. S. (2020). Modulation of plant chemistry by rhizosphere bacteria (PhD Thesis). http://hdl.handle.net/1887/123229
  • Taparia, T., Krijger, M., Haynes, E., Elphinstone, J. G., Noble, R., & Van Der Wolf, J. (2020). Molecular characterization of Pseudomonas from Agaricus bisporus caps reveal novel blotch pathogens in Western Europe. BMC Genomics, 21(1), [505]. https://doi.org/10.1186/s12864-020-06905-3
  • Rossmann, M., Pérez-Jaramillo, J. E., Kavamura, V. N., Chiaramonte, J. B., Dumack, K., Fiore-Donno, A. M., Mendes, L. W., Ferreira, M. M. C., Bonkowski, M., Raaijmakers, J. M., Mauchline, T. H., & Mendes, R. (2020). Multitrophic interactions in the rhizosphere microbiome of wheat: from bacteria and fungi to protists. FEMS Microbiology Ecology, 96(4), [fiaa032]. https://doi.org/10.1093/femsec/fiaa032
  • Samad, M. S., Lee, H. J., Cerbin, S., Meima-Franke, M., & Bodelier, P. (2020). Niche Differentiation of Host-associated Pelagic Microbes and Their Potential Contribution to Biogeochemical Cycling in Artificially Warmed Lakes. Frontiers in Microbiology, 11. https://doi.org/10.3389/fmicb.2020.00582
  • Moisan, K., Lucas-Barbosa, D., Villela, A., Greenberg, L. O., Cordovez, V., Raaijmakers, J. M., & Dicke, M. (2020). No evidence of modulation of indirect plant resistance of Brassica rapa plants by volatiles from soil-borne fungi. Ecological Entomology, in press. https://doi.org/10.1111/een.12906
  • Moisan, K. (2020). Odours from friends and foes: ecological consequences of volatiles from soil-borne fungi on plant growth and defence against herbivores (PhD Thesis). https://doi.org/10.18174/528099
  • Crusciol, C. A. C., Portugal, J. R., Momesso, L., Bossolani, J. W., Pariz, C. M., Castilhos, A. M., Costa, N. R., Costa, C. H. M., Costa, C., Franzluebbers, A. J., & Cantarella, H. (2020). Overcoming Competition From Intercropped Forages on Upland Rice With Optimized Nitrogen Input to Food Production in Tropical Region. Frontiers In Sustainable Food Systems, 4, [129]. https://doi.org/10.3389/fsufs.2020.00129
  • 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. (2020). Plant functional group drives the community structure of saprophytic fungi in a grassland biodiversity experiment. Plant and Soil, Online. https://doi.org/10.1007/s11104-020-04454-y
  • Avalos, M., Garbeva, P., Raaijmakers, J. M., & van Wezel, G. P. (2020). Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces. ISME Journal, 14, 568-583. https://doi.org/10.1101/450833, https://doi.org/10.1038/s41396-019-0537-2
  • Schneijderberg, M., Cheng, X., Franken, C., de Hollander, M., van Velzen, R., Schmitz, L., Heinen, R., Geurts, R., van der Putten, W. H., Bezemer, T. M., & Bisseling, T. (2020). Quantitative comparison between the rhizosphere effect of Arabidopsis thaliana and co-occurring plant species with a longer life history. ISME Journal, 14(10), 2433-2448. https://doi.org/10.1038/s41396-020-0695-2
  • Ho, A., Mendes, L. W., Lee, H. J., Kaupper, T., Mo, Y., Poehlein, A., Bodelier, P., Jia, Z., & Horn, M. A. (2020). Response of a methane-driven interaction network to stressor intensification. FEMS Microbiology Ecology, 96(10), [fiaa180]. https://doi.org/10.1093/femsec/fiaa180
  • Costa, O. Y. A., Zerillo, M., Zühlke, D., Kielak, A. M., Pijl, A., Riedel, K., & Kuramae, E. (2020). Responses of Acidobacteria Granulicella sp. WH15 to high carbon revealed by integrated omics analyses. Microorganisms, 8(2), [244]. https://doi.org/10.3390/microorganisms8020244
  • Gutierrez Landazuri, C. F., Sanabria Gómez, J., Raaijmakers, J. M., & Oyserman, B. O. (2020). Restoring degraded microbiome function with self-assembled communities. FEMS Microbiology Ecology, 96(12), [fiaa225]. https://doi.org/10.1093/femsec/fiaa225
  • Hannula, E., Morrien, E., van der Putten, W. H., & de Boer, W. (2020). Rhizosphere fungi actively assimilating plant-derived carbon in a grassland soil. Fungal Ecology, 48, [100988]. https://doi.org/10.1016/j.funeco.2020.100988
  • Taparia, T., Krijger, M., Hodgetts, J., Hendriks, M., Elphinstone, J. G., & van der Wolf, J. (2020). Six Multiplex TaqManTM-qPCR Assays for Quantitative Diagnostics of Pseudomonas Species Causative of Bacterial Blotch Diseases of Mushrooms. Frontiers in Microbiology, 11, 989. https://doi.org/10.3389/fmicb.2020.00989
  • Kuramae, E., Derksen, S., Schlemper, T., Dimitrov, M., Costa, O. Y. A., & da Silveira, A. P. D. (2020). Sorghum Growth Promotion by Paraburkholderia tropica and Herbaspirillum frisingense: Putative Mechanisms Revealed by Genomics and Metagenomics. Microorganisms, 8(5), [E725]. https://doi.org/10.3390/microorganisms8050725
  • Bossolani, J. W., dos Santos, F. L., Meneghette, H. H. A., Sanches, I. R., Moretti, L. G., Parra, L. F., & Lazarini, E. (Accepted/In press). 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, in press. https://doi.org/10.1007/s42729-020-00347-2
  • Hannula, E., Ma, H., Perez Jaramillo, J. E., Pineda, A. M., & Bezemer, T. M. (2020). Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen. Environmental Microbiology, 22(2), 660-676. https://doi.org/10.1111/1462-2920.14882
  • Zhang, Q., & Laanbroek, H. J. (2020). Tannins from senescent Rhizophora mangle mangrove leaves have a different effect on prokaryotic and eukaryotic communities in a Distichlis spicata salt marsh soil. FEMS Microbiology Ecology, 96(9). https://doi.org/10.1093/femsec/fiaa148
  • de Vries, R. P., Patyshakuliyeva, A., Garrigues, S., & Agarwal-Jans, S. (2020). The Current Biotechnological Status and Potential of Plant and Algal Biomass Degrading/Modifying Enzymes from Ascomycete Fungi. In H. Nevalainen [Ed.], Grand challenges in Fungal Biotechnology (pp. 81-120). Springer. https://doi.org/10.1007/978-3-030-29541-7_4
  • Tyc, O., Putra, R., Gols, R., Harvey, J. A., & Garbeva, P. (2020). The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom. MicrobiologyOpen, 9(1), [e00954]. https://doi.org/10.1002/mbo3.954
  • Clocchiatti, A., Hannula, E., Van den Berg, M., Korthals, G., & De Boer, W. (2020). The hidden potential of saprotrophic fungi in arable soil: patterns of short-term stimulation by organic amendments. Applied Soil Ecology, 147, [103434]. https://doi.org/10.1016/j.apsoil.2019.103434
  • Godoy Labanca, E. R., Andrade, S. A. L., Kuramae, E., & da Silveira, A. P. D. (2020). The modulation of sugarcane growth and nutritional profile under aluminum stress is dependent on beneficial endophytic bacteria and plantlet origin. Applied Soil Ecology, 156, [103715]. https://doi.org/10.1016/j.apsoil.2020.103715
  • Dini-Andreote, F., Kowalchuk, G. A., Prosser, J. I., & Raaijmakers, J. M. (Accepted/In press). Towards meaningful scales in ecosystem microbiome research. Environmental Microbiology, in press. https://doi.org/10.1111/1462-2920.15276
  • Rodrigues, G. R., Pinto, O. H. B., Schroeder, L. F., Fernandes, G. D. R., Costa, O. Y. A., Quirino, B. F., Kuramae, E., & Barreto, C. C. (2020). Unraveling the xylanolytic potential of Acidobacteria bacterium AB60 from Cerrado soils. FEMS Microbiology Letters, 367(18), [fnaa149]. https://doi.org/10.1093/femsle/fnaa149
  • Momesso, L., Crusciol, C. A. C., Soratto, R. P., Tanaka, K. S., Costa, C. H. M., Cantarella, H., & Kuramae, E. (2020). Upland rice yield enhanced by early nitrogen fertilization on previous palisade grass. Nutrient Cycling in Agroecosystems, in press. https://doi.org/10.1007/s10705-020-10088-4
  • Li, X. G., Garbeva, P., Liu, X., Klein Gunnewiek, P. J. A., Clocchiatti, A., Hundscheid, M. P. J., Wang, X., & De Boer, W. (2020). Volatile-mediated antagonism of soil bacterial communities against fungi. Environmental Microbiology, 22(3), 1025-1035. https://doi.org/10.1111/1462-2920.14808
  • Moisan, K., Raaijmakers, J. M., Dicke, M., Lucas-Barbosa, D., & Cordovez, V. (2020). Volatiles from soil-borne fungi affect directional growth of roots. Plant, Cell and Environment, 44(1), 339–345. https://doi.org/10.1111/pce.13890
  • Moisan, K., Dicke, M., Raaijmakers, J. M., Rachmawati, E., & Cordovez, V. (2020). Volatiles from the fungus Fusarium oxysporum affect interactions of Brassica rapa plants with root herbivores. Ecological Entomology, in press. https://doi.org/10.1111/een.12956
  • Leite, M. F. A., & Kuramae, E. (2020). You must choose, but choose wisely: model-based approaches for microbial community analysis. Soil Biology & Biochemistry, 151, [108042]. https://doi.org/10.1016/j.soilbio.2020.108042
  • Kuramae, E. E., & de Assis Costa, O. Y. (2019). Acidobacteria. In T. M. Schmidt [Ed.], Encyclopedia of Microbiology (Fourth Edition) (pp. 1-8). Academic Press. https://doi.org/10.1016/B978-0-12-809633-8.20780-2
  • Sedlacek, C. J., McGowan, B., Suwa, Y., Sayavedra-Soto, L., Laanbroek, H. J., Stein, L. Y., Norton, J. M., Klotz, M. G., & Bollmann, A. (2019). A Physiological and Genomic Comparison of Nitrosomonas Cluster 6a and 7 Ammonia-Oxidizing Bacteria. Microbial Ecology, 78(4), 985-994. https://doi.org/10.1007/s00248-019-01378-8
  • Silva Costa, F., Figueiredo Sena Macedo, M. W., Araujo, A., Rodrigues, C., Kuramae, E. E., Alcanfor, S., Pessoa-Filho, M., & Barreto, C. C. (2019). Assessing nickel tolerance of bacteria isolated from serpentine soils. Brazilian Journal of Microbiology, 50(3), 705-713. https://doi.org/10.1007/s42770-019-00111-4
  • Yao, Z., Du, S., Liang, C., Zhao, Y., Dini-Andreote, F., Wang, K., & Zhang, D. (2019). Bacterial Community Assembly in a Typical Estuarine Marsh with Multiple Environmental Gradients. Applied and Environmental Microbiology, 85(6), [e02602]. https://doi.org/10.1128/AEM.02602-18
  • Cipriano, M., Suleiman, A. K. A., da Silveira, A. P. D., Carmo, J. B., & Kuramae, E. E. (2019). Bacterial community composition and diversity of two different forms of an organic residue of bioenergy crop. PeerJ, 7, [e6768]. https://doi.org/10.7717/peerj.6768
  • Janssens, T. K. S., Tyc, O., Besselink, H., De Boer, W., & Garbeva, P. V. (2019). Biological activities associated with the volatile compound 2,5-bis(1-methylethyl)-pyrazine. FEMS Microbiology Letters, [fnz023]. https://doi.org/10.1093/femsle/fnz023
  • Harkes, P., Suleiman, A. K. A., van den Elsen, S., De Haan, J., Holterman, M., Kuramae, E., & Helder, J. (2019). Conventional & organic soil management as divergent drivers of resident and active fractions of major soil food web constituents. Scientific Reports, 9, [13521 (2019)]. https://doi.org/10.1038/s41598-019-49854-y
  • Perez Jaramillo, J. E., De Hollander, M., Ramirez, C. A., Mendes, R., Raaijmakers, J. M., & Carrión, V. J. (2019). Deciphering rhizosphere microbiome assembly of wild and modern common bean (Phaseolus vulgaris) in native and agricultural soils from Colombia. Microbiome, 7, [114]. https://doi.org/10.1186/s40168-019-0727-1
  • Cordovez, V., Dini-Andreote, F., Carrión, V. J., & Raaijmakers, J. M. (2019). Ecology and Evolution of Plant Microbiomes. Annual Review of Microbiology, Online. https://doi.org/10.1146/annurev-micro-090817-062524
  • Pennanen, T., Fritze, H., de Boer, W., & Baldrian, P. (2019). Editorial: special issue on the ecology of soil microorganisms. FEMS Microbiology Ecology, 95(12), [fiz154]. https://doi.org/10.1093/femsec/fiz154
  • Di Lonardo, P., De Boer, W., Zweers, A. J., & Van der Wal, A. (2019). Effect of the amount of organic trigger compounds, nitrogen and soil microbial biomass on the magnitude of priming of soil organic matter. PLoS One, 15(5), [0216730]. https://doi.org/10.1371/journal.pone.0216730
  • Yan, Y., Klinkhamer, P. G. L., van Veen, J. A., & Kuramae, E. E. (2019). Environmental filtering: A case of bacterial community assembly in soil. Soil Biology & Biochemistry, 136, [107531]. https://doi.org/10.1016/j.soilbio.2019.107531
  • van der Waals, M., Plugge, C. M., Meima-Franke, M., de Waard, P., Bodelier, P. L. E., Smidt, H., & Gerritse, J. (2019). Ethyl tert-butyl ether (EtBE) degradation by an algal-bacterial culture obtained from contaminated groundwater. Water Research, 148(January), 314-323. https://doi.org/10.1016/j.watres.2018.10.050
  • da Silveira, A. P. D., Iório, R. D. P. F. I., Marcos, F. C. C., Fernandes, A. O., De Souza, S. A. C. D., Kuramae, E. E., & Cipriano, M. (2019). Exploitation of new endophytic bacteria and their ability to promote sugarcane growth and nitrogen nutrition. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 112(2), 283-295. https://doi.org/10.1007/s10482-018-1157-y
  • Oyserman, B. O., Cordovez, V., Sarango Flores, S. W., Nijveen, H., Medema, M. H., & Raaijmakers, J. M. (2019). Extracting the GEMs: Genotype, Environment and Microbiome interactions shaping host phenotypes. bioRxiv, Preprint. https://doi.org/10.1101/863399
  • Wagg, C., Schlaeppi, K., Banerjee, S., Kuramae, E., & Van der Heijden, M. G. A. (2019). Fungal-bacterial diversity and microbiome complexity predict ecosystem functioning. Nature Communications, 10, [4841]. https://doi.org/10.1038/s41467-019-12798-y
  • Masteling, R., Lombard, L., De Boer, W., Raaijmakers, J. M., & Dini-Andreote, F. (2019). Harnessing the microbiome to control plant parasitic weeds. Current Opinion in Microbiology, 49(June), 26-33. https://doi.org/10.1016/j.mib.2019.09.006
  • in 't Zandt, M. H., Kip, N., Frank, J., Jansen, S., van Veen, J. A., Jetten, M. S. M., & Welte, C. U. (2019). High-level abundance of Methanobacteriales and Syntrophobacterales may help to prevent corrosion of metal sheet piles. Applied and Environmental Microbiology, 85(20), [AEM.01369-19]. https://doi.org/10.1128/AEM.01369-19
  • Zwart, M., Ali, G., van Strien, E. A., Schijlen, E. G. W. M., van der Werf, W., Vlak, J. M., & Wang, M. (2019). Identification of loci associated with enhanced virulence in Spodoptera litura nucleopolyhedrovirus isolates using a deep sequencing approach. Viruses, 11(9), [872]. https://doi.org/10.3390/v11090872
  • Cassman, N. (2019). Impact of nitrogen fertilization on the soil microbiome and nitrous oxide emissions (PhD Thesis). https://openaccess.leidenuniv.nl/handle/1887/71732
  • Perez Jaramillo, J. E. (2019). Impact of plant domestication on spermosphere and rhizosphere microbiome composition (PhD Thesis). https://openaccess.leidenuniv.nl/handle/1887/70478
  • Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A., & Wakelin, S. A. (2019). Impacts of long-term plant residue management on soil organic matter quality, Pseudomonas community structure and disease suppressiveness. Soil Biology & Biochemistry, online, 396-406. https://doi.org/10.1016/j.soilbio.2019.05.020
  • Momesso, L., Crusciol, C. A. C., Soratto, R. P., Vyn, T. J., Tanaka, K. S., Costa, C. H. M., Neto, J. F., & Cantarella, H. (2019). Impacts of Nitrogen Management on No-Till Maize Production Following Forage Cover Crops. Agronomy Journal, 111(2), 639-649. https://doi.org/10.2134/agronj2018.03.0201
  • Wilschut, R. A., Geisen, S., Martens, H. J., Kostenko, O., De Hollander, M., Ten Hooven, F. C., Weser, C., Snoek, B., Bloem, J., Caković, D., Čelik, T., Koorem, K., Krigas, N., Manrubia, M., Ramirez, K. S. R., Tsiafouli, M. A., Vreš, B., & van der Putten, W. H. (2019). Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants. Global Change Biology, 25(8), 2714-2726. https://doi.org/10.1111/gcb.14657
  • Li, X. G., Jousset, A., De Boer, W., Carriön, V. J., Zhang, T., Wang, X., & Kuramae, E. E. (2019). Legacy of land use history determines reprogramming of plant physiology by soil microbiome. ISME Journal, 13, 738-751. https://doi.org/10.1038/s41396-018-0300-0
  • Ampt, E. A., van Ruijven, J., Raaijmakers, J. M., Termorshuizen, A. J., & Mommer, L. (2019). Linking ecology and plant pathology to unravel the importance of soil-borne fungal pathogens in species-rich grasslands. European Journal of Plant Pathology, 154(1), 141-156. https://doi.org/10.1007/s10658-018-1573-x
  • Lupatini, M., Korthals, G. W., Roesch, L. F. W., & Kuramae, E. E. (2019). Long-term farming systems modulate multi-trophic responses. Science of the Total Environment, 646, 480-490. https://doi.org/10.1016/j.scitotenv.2018.07.323
  • Rosado, P. M., Leite, D. C. A., Duarte, G. A. S., Chaloub, R. M., Jospin, G., Nunes da Rocha, U., P. Saraiva, J., Dini-Andreote, F., Eisen, J. A., Bourne, D. G., & Peixoto, R. S. (2019). Marine probiotics: increasing coral resistance to bleaching through microbiome manipulation. ISME Journal, 13(4), 921-936. https://doi.org/10.1038/s41396-018-0323-6
  • Bodelier, P. L. E., Pérez, G., Veraart, A. J., & Krause, S. (2019). Methanotroph Ecology, Environmental distribution and functioning. In E. Y. Lee [Ed.], Methanotrophs: Microbiology Fundamentals and Biotechnological Applications (Microbiology Monographs MICROMONO; Vol. 32). Springer. https://doi.org/10.1007/978-3-030-23261-0_1
  • Ghashghavi, M., Belova, S., Bodelier, P. L. E., Dedysh, S., Kox, M. A. R., Speth, D., Frenzel, P., Jetten, M., Lücker, S., & Lüke, C. (2019). Methylotetracoccus oryzae Strain C50C1 Is a Novel Type Ib Gammaproteobacterial Methanotroph Adapted to Freshwater Environments. mSphere, 4, [e00631-18]. https://doi.org/10.1128/mSphere.00631-18
  • Schmidt, R. L., Ulanova, D., Wick, L. Y., Bode, H. B., & Garbeva, P. V. (2019). Microbe-driven chemical ecology – past, present and future. ISME Journal, 13, 2656-2663. https://doi.org/10.1038/s41396-019-0469-x
  • Lupatini, M., Suleiman, A. K. A., Jacques, R. J. S., Pylro, V. S., van Veen, J. A., Kuramae, E. E., & Roesch, L. F. W. (2019). Moisture is more important than Temperature for Assembly of Both Potentially Active and Whole Prokaryotic Communities in Subtropical Grassland. Microbial Ecology, 77(2), 460-470. https://doi.org/10.1007/s00248-018-1310-1
  • Cassman, N., Soares, J. R., Pijl, A. S., Lourenço, K. S., van Veen, J. A., Cantarella, H., & Kuramae, E. E. (2019). Nitrification inhibitors effectively target N2O-producing Nitrosospira spp. in tropical soil. Environmental Microbiology, 21(4), 1241-1254. https://doi.org/10.1111/1462-2920.14557
  • Willemsen, A., & Zwart, M. P. (2019). On the stability of sequences inserted into viral genomes. Virus Evolution, 5(2), [vez045]. https://doi.org/10.1093/ve/vez045
  • Suleiman, A. K. A., Harkes, P., van den Elsen, S., Holterman, M., Korthals, G. W., Helder, J., & Kuramae, E. E. (2019). Organic amendment strengthens interkingdom associations in the soil and rhizosphere of barley (Hordeum vulgare). Science of the Total Environment, [133885]. https://doi.org/10.1016/j.scitotenv.2019.133885
  • Carrión, V. J., Perez Jaramillo, J. E., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz Buck, D., Mendes, L. W., van IJcken, W. F. J., Gómez Expósito, R., Elsayed, S. S., Mohanraju, P., Arifah, A., van der Oost, J., Paulson, J. N., Mendes, R., van Wezel, G., Medema, M. H., & Raaijmakers, J. M. (2019). Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science, 366(6465), 606-612. https://doi.org/10.1126/science.aaw9285
  • De Boer, W., Li, X. G., Meisner, A., & Garbeva, P. V. (2019). Pathogen suppression by microbial volatile organic compounds in soils. FEMS Microbiology Ecology, 95(8), [fiz105]. https://doi.org/10.1093/femsec/fiz105
  • de Tender, C., Mesuere, B., van der Jeugt, F., Haegeman, A., Ruttink, T., Vandecasteele, B., Dawyndt, P., Debode, J., & Kuramae, E. E. (2019). Peat substrate amended with chitin modulates the N-cycle, siderophore and chitinase responses in the lettuce rhizobiome. Scientific Reports, 9. https://doi.org/10.1038/s41598-019-46106-x
  • Crusciol, C. A. C., Momesso, L., & Nascimento, C. A. C. (2019). Phosphate fertilization on nutritional status and growth of upland rice cultivars. Journal of Plant Nutrition, 42(13), 1516-1528. https://doi.org/10.1080/01904167.2019.1628971
  • Martín-Sánchez, L., Saurabh Singh, K., Avalos Garcia, M., van Wezel, G. P., Dickschat, J. S., & Garbeva, P. V. (2019). Phylogenomic analyses and distribution of terpene synthases among Streptomyces. Beilstein Journal of Organic Chemistry, 15, 1181–1193. https://doi.org/10.3762/bjoc.15.115
  • Barel, J. M., Kuyper, T. W., de Boer, W., & De Deyn, G. B. (2019). Plant presence reduces root and shoot litter decomposition rates of crops and wild relatives. Plant and Soil, 438(1), 313-327. https://doi.org/10.1007/s11104-019-03981-7
  • van der Aart, L. T., Nouioui, I., Kloosterman, A., Igual, J-M., Willemse, J., Goodfellow, M., & van Wezel, G. P. (2019). Polyphasic classification of the gifted natural product producer Streptomyces roseifaciens sp. nov. International Journal of Systematic and Evolutionary Microbiology, 69(4), 899-908. http://10.1099/ijsem.0.003215
  • Mendes, L. W., Gonçalves De Chaves, M., da Fonseca, M. D. C., Mendes, R., Raaijmakers, J. M., & Tsai, S. M. (2019). Resistance breeding of common bean shapes the physiology of the rhizosphere microbiome. Frontiers in Microbiology, 10, [2019.02252]. https://doi.org/10.3389/fmicb.2019.02252
  • Kaminsky, R. A., Wakelin, S. A., Highton, M. P., Samad, M. S., & Morales, S. E. (2019). Resolving broad patterns of prokaryotic community structure in New Zealand pasture soils. New Zealand Journal of Agricultural Research, Online, 1-19. https://doi.org/10.1080/00288233.2019.1678491
  • Maarastawi, S. A., Frindte, K., Bodelier, P. L. E., & Knief, C. (2019). Rice straw serves as additional carbon source for rhizosphere microorganisms and reduces root exudate consumption. Soil Biology & Biochemistry, 135(August), 235-238. https://doi.org/10.1016/j.soilbio.2019.05.007
  • Chen, S., Waghmode, T. R., Sun, R., Kuramae, E., Hu, C., & Liu, B. (2019). Root-associated microbiomes of wheat under the combined effect of plant development and nitrogen fertilization. Microbiome, 7, [136(2019)]. https://doi.org/10.1186/s40168-019-0750-2
  • Wilschut, R. A., van der Putten, W. H., Garbeva, P. V., Harkes, P., Konings, W., Kulkarni, P., Martens, H. J., & Geisen, S. (2019). Root traits and belowground herbivores relate to plant-soil feedback variation among congeners. Nature Communications, 10, [1564(2019)]. https://doi.org/10.1038/s41467-019-09615-x
  • Gu, X., Wang, Y., Laanbroek, H. J., Xu, X., Song, B., Huo, Y., Chen, S., Li, L., & Zhang, L. (2019). Saturated N2O emission rates occur above the nitrogen deposition level predicted for the semi-arid grasslands of Inner Mongolia, China. Geoderma, 341, 18-25. https://doi.org/10.1016/j.geoderma.2019.01.002
  • Lourenço, K. S., Rossetto, R., Vitti, A. C., Montezano, Z. F., Soares, J. R., Sousa, R. M., Carmo, J. B., Kuramae, E. E., & Cantarella, H. (2019). Strategies to mitigate the nitrous oxide emissions from nitrogen fertilizer applied with organic fertilizers in sugarcane. Science of the Total Environment, 650, Part I, 1476-1486. https://doi.org/10.1016/j.scitotenv.2018.09.037
  • Di Lonardo, P. (2019). The microbial side of soil priming effects (PhD Thesis). https://edepot.wur.nl/470122
  • Schlemper, T. R. (2019). The rhizomicrobiome of Sorghum : impact on plant growth and stress tolerance (PhD Thesis). http://hdl.handle.net/1887/68467
  • Teurlincx, S., Kuiper, J. J., Hoevenaar, E. C. M., Lurling, M., Brederveld, R. J., Veraart, A. J., Janssen, A. B. G., Mooij, W. M., & Domis, L. N. D. S. (2019). Towards restoring urban waters: understanding the main pressures. Current Opinion in Environmental Sustainability, 36, 49-58. https://doi.org/10.1016/j.cosust.2018.10.011
  • Ho, A., Lee, H. J., Reumer, M. R., Meima-Franke, M., Raaijmakers, C. E., Zweers, A. J., De Boer, W., van der Putten, W. H., & Bodelier, P. L. E. (2019). Unexpected role of canonical aerobic methanotrophs in upland agricultural soils. Soil Biology & Biochemistry, 131(April), [1-8]. https://doi.org/10.1016/j.soilbio.2018.12.020
  • Moisan, K., Cordovez, V., van de Zande, E. M., Raaijmakers, J. M., Dicke, M., & Lucas-Barbosa, D. (2019). Volatiles of pathogenic and non-pathogenic soil-borne fungi affect plant development and resistance to insects. Oecologia, 190(3), 589-604. https://doi.org/10.1007/s00442-019-04433-w
  • Barel, J. M., Kuyper, T. W., Paul, J., de Boer, W., Cornelissen, J. H. C., & De Deyn, G. B. (2019). Winter cover crop legacy effects on litter decomposition act through litter quality and microbial community changes. Journal of Applied Ecology, 56(1), 132-143. https://doi.org/10.1111/1365-2664.13261
  • Kuramae, E. E., Leite, M. F. A., Suleiman, A. K. A., Gough, C. M., Castillo, B., Faller, L., Franklin, R., & Syring, J. (2019). Wood Decay Characteristics and Interspecific Interactions Control Bacterial Community Succession in Populus grandidentata (Bigtooth Aspen). Frontiers in Microbiology, 10, [2019.00979]. https://doi.org/10.3389/fmicb.2019.00979
  • Stötter, T., Bastviken, D., Bodelier, P. L. E., Hardenbroek, M. V., Rinta, P., Schilder, J., Schubert, C. J., & Heiri, O. (2018). Abundance and δ13C values of fatty acids in lacustrine surface sediments: Relationships with in-lake methane concentrations. Quaternary Science Reviews, 191, 337 - 347. https://doi.org/10.1016/j.quascirev.2018.04.029
  • Diaz-Trujillo, C., Chong, P., Stergiopoulos, I., Cordovez, V., Guzman, M., de Wit, P. J. G. M., Meijer, H. J. G., Scalliet, G., Sierotzki, H., Peralta, E. L., Arango Isaza, R. E., & Kema, G. H. J. (2018). A new mechanism for reduced sensitivity to demethylation‐inhibitor fungicides in the fungal banana black Sigatoka pathogen Pseudocercospora fijiensis. Molecular Plant Pathology, 19(6), 1491-1503. https://doi.org/10.1111/mpp.12637
  • Ibrahim, B., Arkhipova, K., Andeweg, A. C., Posada-Céspedes, S., Enault, F., Gruber, A., Koonin, E. V., Kupczok, A., Lemey, P., McHardy, A. C., McMahon, D. P., Pickett, B. E., Robertson, D. L., Scheuermann, R. H., Zhernakova, A., Zwart, M. P., Schönhuth, A., Dutilh, B. E., & Marz, M. (2018). Bioinformatics Meets Virology: The European Virus Bioinformatics Center's Second Annual Meeting. Viruses, 10(5), [256]. https://doi.org/10.3390/v10050256
  • Mendes, L. W., Mendes, R., Raaijmakers, J. M., & Tsai, S. M. (2018). Breeding for soil-borne pathogen resistance impacts active rhizosphere microbiome of common bean. ISME Journal, 12, 3038-3042. https://doi.org/10.1038/s41396-018-0234-6
  • Schulz-Bohm, K., Gerards, S., Hundscheid, M. P. J., Melenhorst, J., De Boer, W., & Garbeva, P. V. (2018). Calling from distance: Attraction of soil bacteria by plant root volatiles. ISME Journal, 12. https://doi.org/10.1038/s41396-017-0035-3
  • Trusch, F., Loebach, L., Wawra, S., Durward, E., Wuensch, A., Iberahim, N. A., De Bruijn, I., MacKenzie, K., Willems, A., Toloczkoa, A., Diéguez-Uribeondo, J., Rasmussen, T., Schraderf, T., Bayer, P., Secombes, C. J., & van West, P. (2018). Cell entry of a host-targeting protein of oomycetes requires gp96. Nature Communications, 9, [2347]. https://doi.org/10.1038/s41467-018-04796-3
  • Benevenuto, J., Texeira-Silva, N. S., Kuramae, E. E., Croll, D., & Vitorello, C. B. M. (2018). Comparative Genomics of Smut Pathogens: Insights From Orphans and Positively Selected Genes Into Host Specialization. Frontiers in Microbiology, 9, [660]. https://doi.org/10.3389/fmicb.2018.00660
  • Siegel-Hertz, K., Edel-Hermann, V., Chapelle, E., Terrat, S., Raaijmakers, J. M., & Steinberg, C. (2018). Comparative microbiome analysis of a Fusarium wilt suppressive soil and a Fusarium wilt conducive soil from the Châteaurenard region. Frontiers in Microbiology, 9, 568. https://doi.org/10.3389/FMICB.2018.00568
  • Schlemper, T. R., van Veen, J. A., & Kuramae, E. E. (2018). Co-variation of bacterial and fungal communities in different sorghum cultivars and growth stages is soil dependent. Microbial Ecology, 76(1), 205-214. https://doi.org/10.1007/s00248-017-1108-6
  • De Bruijn, I., & Verhoeven, K. J. F. (2018). Cross-species interference of gene expression: Comment. Nature Communications, 9, [5019]. https://doi.org/10.1038/s41467-018-07353-0
  • Huerta Lwanga, E., Thapa, B., Yang, X., Gertsen, H., Salánki, T., Geissen, V., & Garbeva, P. V. (2018). Decay of low-density polyethylene by bacteria extracted from earthworm’s guts: a potential for soil restoration. Science of the Total Environment, 624, 753-757. https://doi.org/10.1016/j.scitotenv.2017.12.144
  • Schmidt, R. L., Durling, M., de Jager, V. C. L., Menezes, R. C., Nordkvist, E., Svatos, A., Dubey, M., Lauterbach, L., Dikschat, J. S., Karlsson, M., & Garbeva, P. V. (2018). Deciphering the genome and secondary metabolome of the plant pathogen Fusarium culmorum. FEMS Microbiology Ecology, 94(6), [fiy078]. https://doi.org/10.1093/femsec/fiy078
  • Ramirez, K. S., Knight, C. G., de Hollander, M., Brearley, F. Q., Constantinides, B., Cotton, A., Creer, S., Crowther, T. W., Davison, J., Delgado-Baquerizo, M., Dorrepaal, E., Elliott, D. R., Fox, G., Griffiths, R. I., Hale, C., Hartman, K., Houlden, A., Jones, D. L., Krab, E. J.,... De Vries, F. T. (2018). Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology, 3, 189-196. https://doi.org/10.1038/s41564-017-0062-x
  • Lourenço, K. S., Dimitrov, M., Pijl, A. S., Soares, J. R., do Carmo, J. B., van Veen, J. A., Cantarella, H., & Kuramae, E. E. (2018). Dominance of bacterial ammonium oxidizers and fungal denitrifiers in the complex nitrogen cycle pathways related to nitrous oxide emission. GCB Bioenergy, 10(9), 645-660. https://doi.org/10.1111/gcbb.12519
  • Meisner, A., Samuel, J., Snoek, B., Ten Hooven, F. C., & van der Putten, W. H. (2018). Drought legacy effects on the composition of soil fungal and prokaryote communities. Frontiers in Microbiology, 9, [294]. https://doi.org/10.3389/fmicb.2018.00294
  • Schlemper, T. R., Dimitrov, M., Silva Gutierrez, F., van Veen, J. A., Silveira, A. P. D., & Kuramae, E. E. (2018). Effect of Burkholderia tropica and Herbaspirillum frisingense strains on sorghum growth is plant genotype dependent. PeerJ, 6, [e5346]. https://doi.org/10.7717/peerj.5346
  • Laanbroek, H. J., Zhang, Q., Leite, M. F. A., Verhoeven, J. T. A., & Whigham, D. F. (2018). Effects of Rhizophora mangle leaf litter and seedlings on carbon and nitrogen cycling in salt marshes - potential consequences of climate-induced mangrove migration. Plant and Soil, 426(May 2018), 383-400. https://doi.org/10.1007/s11104-018-3611-z
  • Dini-Andreote, F., & Raaijmakers, J. M. (2018). Embracing community ecology in plant microbiome research. Trends in Plant Science, 23(6), 467-469. https://doi.org/10.1016/j.tplants.2018.03.013
  • Krause, S., Meima-Franke, M., Veraart, A. J., Ren, G., Ho, A., & Bodelier, P. L. E. (2018). Environmental legacy contributes to the resilience of methane consumption in a laboratory microcosm system. Scientific Reports, 9, [8862]. https://doi.org/10.1038/s41598-018-27168-9
  • de Bruijn, I., Liu, Y., Wiegertjes, G. F., & Raaijmakers, J. M. (2018). Exploring fish microbial communities to mitigate emerging diseases in aquaculture. FEMS Microbiology Ecology, 94(1), [fix161]. https://doi.org/10.1093/femsec/fix161
  • Bäumel, S., Tytgat, H. L. P., Nemec, B., Schmidt, R. L., Chia, L. W., & Smidt, H. (2018). Fifty Percent Human - how art brings us in touch with our microbial cohabitants. Microbial Biotechnology, 11(4). https://doi.org/10.1111/1751-7915.13285
  • Cassman, N., Lourenço, K. S., Braga do Carmo, J., Cantarella, H., & Kuramae, E. E. (2018). Genome-resolved metagenomics of sugarcane vinasse bacteria. Biotechnology for Biofuels, 11, [48]. https://doi.org/10.1186/s13068-018-1036-9, https://doi.org/10.1186/s13068-018-1254-1
  • Willemsen, A., Carrasco, J. L., Elena, S. F., & Zwart, M. (2018). Going, going, gone: predicting the fate of genomic insertions in plant RNA viruses. Heredity, 121, 499-509. https://doi.org/10.1038/s41437-018-0086-x
  • Geesink, P., Tyc, O., Küsel, K., Taubert, M., van de Velde, C., Kumar, S., & Garbeva, P. V. (2018). Growth Promotion and Inhibition Induced by Interactions of Groundwater Bacteria. FEMS Microbiology Ecology, 94(11), [fiy164]. https://doi.org/10.1093/femsec/fiy164
  • Avalos Garcia, M., van Wezel, G. P., Raaijmakers, J. M., & Garbeva, P. V. (2018). Healthy scents: microbial volatiles as new frontier in antibiotic research? Current Opinion in Microbiology, 45(October), 84-91. https://doi.org/10.1016/j.mib.2018.02.011
  • van der Aart, L. T., Spijksma, G. K., Harms, A., Vollmer, W., Hankemeier, T., & van Wezel, G. P. (2018). High-Resolution Analysis of the Peptidoglycan Composition in Streptomyces coelicolor. Journal of Bacteriology, 200(20), [e00290-18]. https://doi.org/10.1128/JB.00290-18
  • Reumer, M., Harnisz, M., Lee, H. J., Reim, A., Grunert, O., Putkinen, A., Fritze, H., Bodelier, P. L. E., & Ho, A. (2018). Impact of peat mining, and restoration on methane turnover potentials and methane-cycling microorganisms in a northern bog. Applied and Environmental Microbiology, 84(3), [e02218-17]. https://doi.org/10.1128/AEM.02218-17
  • Al-Jubury, A., lu, C., Walter Kania, P., von Gersdorff Jørgensen, L., Liu, Y., De Bruijn, I., Raaijmakers, J. M., & Buchman, K. (2018). Impact of Pseudomonas H6 surfactant on all external life cycle stages of the fish parasitic ciliate Ichthyophthirius multifiliis. Journal of Fish Diseases, 41(7), 1147-1152. https://doi.org/10.1111/jfd.12810
  • Mendes, L. W., Raaijmakers, J. M., De Hollander, M., Mendes, R., & Tsai, S. M. (2018). Influence of resistance breeding in common bean on rhizosphere microbiome composition and function. ISME Journal, 2017(12), 212-224. https://doi.org/10.1038/ismej.2017.158
  • Van der Meij, A., Willemse, J., Schneijderberg, M. A., Geurts, R., Raaijmakers, J., & van Wezel, G. (2018). Inter- and intracellular colonization of Arabidopsis roots by endophytic actinobacteria and the impact of plant hormones on their antimicrobial activity. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 111(5), 679-690. https://doi.org/10.1101/222844, https://doi.org/10.1007/s10482-018-1014-z
  • Carrion, V. J., Cordovez, V., Tyc, O., Etalo, D. W., De Bruijn, I., de Jager, V. C. L., Medema, M. H., Eberl, L., & Raaijmakers, J. M. (2018). Involvement of Burkholderiaceae and sulfurous volatiles in disease suppressive soils. ISME Journal, 12, 2307-2321. https://doi.org/10.1038/s41396-018-0186-x
  • Le, C. N., Hoang, T. K., Thai, T. H., Tran, T. L., Phan, T. P. N., & Raaijmakers, J. M. (2018). Isolation, characterization and comparative analysis of plant-associated bacteria for suppression of soil-borne diseases of field-grown groundnut in Vietnam. Biological Control, in press, 256-262. https://doi.org/10.1016/j.biocontrol.2018.03.014
  • Kulkarni, P., A. Wilschut, R., J.F. Verhoeven, K., H. van der Putten, W., & Garbeva, P. (2018). LAESI mass spectrometry imaging as a tool to differentiate the root metabolome of native and range-expanding plant species. Planta, 248(December), 1515-1523. https://doi.org/10.1101/322867, https://doi.org/10.1007/s00425-018-2989-4
  • Etalo, D. W., Díez-Simón, C., De Vos, R. C. H., & Hall, R. D. (2018). Laser Ablation Electrospray Ionization-Mass Spectrometry Imaging (LAESI-MS) for Spatially Resolved Plant Metabolomics. In Plant Metabolomics (pp. 253-267). (Methods in Molecular Biology; Vol. 1778). Humana Press. https://doi.org/10.1007/978-1-4939-7819-9_18
  • Barel, J. M., Kuyper, T. W., de Boer, W., Douma, J. C., & De Deyn, G. B. (2018). Legacy effects of diversity in space and time driven by winter cover crop biomass and nitrogen concentration. Journal of Applied Ecology, 55(1), 299-310. https://doi.org/10.1111/1365-2664.12929
  • Lourenço, K. S. (2018). Linking soil microbial community dynamics to N2O emission after bioenergy residue amendments (PhD Thesis). http://hdl.handle.net/1887/61514
  • Veraart, A. J., Garbeva, P. V., van Beersum, F., Ho, A., Hordijk, C. A., Meima-Franke, M., Zweers, A. J., & Bodelier, P. L. E. (2018). Living apart together – Bacterial volatiles influence methanotrophic growth and activity. ISME Journal, 12, 1163-1166. https://doi.org/10.1038/s41396-018-0055-7
  • Mommer, L., Cotton, T., Raaijmakers, J. M., Termorshuizen, A. J., van Ruijven, J., Hendriks, M., van Rijssel, S. Q., van de Mortel, J. E., van der Paauw, J. W., Schijlen, E. G. W. M., Smit-Tiekstra, A. E., Berendse, F., de Kroon, H., & Dumbrell, A. J. (2018). Lost in diversity: the interactions between soil-borne fungi, biodiversity and plant productivity. New Phytologist, 218(2), 542-553. https://doi.org/10.1111/nph.15036
  • Qi, Y., Yang, X., Pelaez, A. M., Huerta Lwanga, E., Beriot, N., Gertsen, H., Garbeva, P. V., & Geissen, V. (2018). Macro- and micro- plastics in soil-plant system: effects of plastic mulch film residues on wheat (Triticum aestivum) growth. Science of the Total Environment, 645(15 december 2018), 1048-1056. https://doi.org/10.1016/j.scitotenv.2018.07.229
  • Durán, P., Tortella, G., Viscardi, S., Barra, P. J., Carrión, V. J., Mora, M. D. L. L., & Pozo, M. J. (2018). Microbial Community Composition in Take-All Suppressive Soils. Frontiers in Microbiology, 9. https://doi.org/10.3389/fmicb.2018.02198
  • Costa, O. Y. A., Raaijmakers, J. M., & Kuramae, E. E. (2018). Microbial extracellular polymeric substances – ecological functions and impact on soil aggregation. Frontiers in Microbiology, 9, [1636]. https://doi.org/10.3389/FMICB.2018.01636
  • Heijboer, A., de Ruiter, P. C., Bodelier, P. L. E., & Kowalchuk, G. A. (2018). Modulation of litter decomposition by the soil microbial food web under influence of land use change. Frontiers in Microbiology, 9, [02860]. https://doi.org/10.3389/fmicb.2018.02860
  • Etalo, D., Jeon, J-S., & Raaijmakers, J. M. (2018). Modulation of plant chemistry by beneficial root microbiota. Natural Product Reports, 35(5), 398-409. https://doi.org/10.1039/C7NP00057J
  • Armada, E., Leite, M. F. A., Medina Penafiel, M. A., Azcón, R., & Kuramae, E. E. (2018). Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome. FEMS Microbiology Ecology, 94(7), [fiy092]. https://doi.org/10.1093/femsec/fiy092
  • Lourenço, K. S., Cassman, N., Pijl, A. S., van Veen, J. A., Cantarella, H., & Kuramae, E. E. (2018). Nitrosospira sp. govern nitrous oxide emissions in a tropical soil amended with residues of bioenergy crop. Frontiers in Microbiology, 9, [674]. https://doi.org/10.3389/fmicb.2018.00674
  • Laanbroek, H. J., Veenhuizen, P. T. M., Keijzer, R. M., & Hefting, M. M. (2018). Numerical relationships between archaeal and bacterial amoA genes vary by Icelandic Andosol classes. Microbial Ecology, 75(1), 204-215. https://doi.org/10.1007/s00248-017-1032-9
  • Martínez-García, L. B., Korthals, G. W., Brussaard, L., Jørgensen, H. B., & De Deyn, G. B. (2018). Organic management and cover crop species steer soil microbial community structure and functionality along with soil organic matter properties. Agriculture, Ecosystems and Environment, 263. https://doi.org/10.1016/j.agee.2018.04.018
  • Brenzinger, K., Drost, S. M., Korthals, G. W., & Bodelier, P. L. E. (2018). Organic residue amendments to modulate greenhouse gas emissions from agricultural soils. Frontiers in Microbiology, 9, [3035]. https://doi.org/10.3389/fmicb.2018.03035
  • Gutiérrez, S., & Zwart, M. (2018). Population bottlenecks in multicomponent viruses: First forays into the uncharted territory of genome-formula drift. Current Opinion in Virology, 33(December), 184-190. https://doi.org/10.1016/j.coviro.2018.09.001
  • Schnyder, E., Bodelier, P. L. E., Hartmann, M., Henneberger, R., & Niklaus, P. A. (2018). Positive diversity-functioning relationships in model communities of methanotrophic bacteria. Ecology, 99(3), 714-723. https://doi.org/10.1002/ecy.2138
  • Wen, X., Unger, V., Jurasinski, G., Koebsch, F., Horn, F., Rehder, G., Sachs, T., Zak, D., Lischeid, G., Knorr, K-H., Böttcher, M. E., Winkel, M., Bodelier, P. L. E., & Liebner, S. (2018). Predominance of methanogens over methanotrophs in rewetted fens characterized by high methane emissions. Biogeosciences, 15, 6519-6536. https://doi.org/10.5194/bg-15-6519-2018
  • Cordovez, V., Schop, S., Hordijk, C. A., Dupré de Boulois, H., Coppens, F., Hanssen, I., Raaijmakers, J. M., & Carrion, V. J. (2018). Priming of plant growth promotion by volatile compounds of root-associated Microbacterium. Applied and Environmental Microbiology, 84(22), [e01865-18. ]. https://doi.org/10.1128/AEM.01865-18
  • Ngo, T. T. N., Senior, A. M., Culina, A., Santos, E. S. A., Vlak, J. M., & Zwart, M. (2018). Quantitative analysis of the dose–response of white spot syndrome virus in shrimp. Journal of Fish Diseases, 41(11), 1733-1744. https://doi.org/10.1111/jfd.12877
  • Suleiman, A. K. A., Lourenço, K. S., Pitombo, L., Mendes, L. W., Roesch, L. F. W., Pijl, A. S., do Carmo, J. B., Cantarella, H., & Kuramae, E. E. (2018). Recycling organic residues in agriculture impacts soil-borne microbial community structure, function and N2O emissions. Science of the Total Environment, 631-632, 1089-1099. https://doi.org/10.1016/j.scitotenv.2018.03.116
  • Di Lonardo, P., Manrubia, M., De Boer, W., Zweers, A. J., Veen, G. F., & Van der Wal, A. (2018). Relationship between home-field advantage of litter decomposition and priming of soil organic matter. Soil Biology & Biochemistry, 126, 49-56. https://doi.org/10.1016/j.soilbio.2018.07.025
  • Lourenço, K. S., Suleiman, A. K. A., Pijl, A. S., van Veen, J. A., Cantarella, H., & Kuramae, E. E. (2018). Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion. Microbiome, 6, [142]. https://doi.org/10.1186/s40168-018-0525-1
  • van Kruistum, H., Bodelier, P. L. E., Ho, A., Meima-Franke, M., & Veraart, A. J. (2018). Resistance and Recovery of Methane Oxidizing Communities depends on Stress Regime and History. Frontiers in Microbiology, 9, [01714]. https://doi.org/10.3389/fmicb.2018.01714
  • Oyserman, B. O., Medema, M. H., & Raaijmakers, J. M. (2018). Road MAPs to engineer host microbiomes. Current Opinion in Microbiology, 43(June ), 46-54. https://doi.org/10.1016/j.mib.2017.11.023
  • Berg, G., & Raaijmakers, J. M. (2018). Saving Seed Microbiomes. ISME Journal, 12, 1167-1170. https://doi.org/10.1038/s41396-017-0028-2
  • Yan, Q., Lopes, L. D., Schaffer, B. T., Kidarsa, T., Vining, O., Philmus, B., Song, C., Stockwell, V. O., Raaijmakers, J. M., McPhail, K. L., Andreote, F. D., Chang, J. H., & Loper, J. E. (2018). Secondary metabolism and interspecific competition affect accumulation of spontaneous mutants in the gacS/gacA regulatory system in Pseudomonas protegens. mBio, 9(1), [e01845-17]. https://doi.org/10.1128/mBio.01845-17
  • Meisner, A., & De Boer, W. (2018). Strategies to maintain natural biocontrol of soil-borne crop diseases during severe drought and rainfall events. Frontiers in Microbiology, 9, [02279]. https://doi.org/10.3389/fmicb.2018.02279
  • Bartelme, R. P., Oyserman, B. O., Blom, J. E., Sepulveda-Villet, O. J., & Newton, R. J. (2018). Stripping Away the Soil: Plant Growth Promoting Microbiology Opportunities in Aquaponics. Frontiers in Microbiology, 9, [8]. https://doi.org/10.3389/fmicb.2018.00008
  • Li, X., De Boer, W., Zhang, Y., Ding, C., Zhang, T., & Wang, X. (2018). Suppression of soil-borne Fusarium pathogens of peanut by intercropping with the medicinal herb Atractylodes lancea. Soil Biology & Biochemistry, 116, 120 - 130. https://doi.org/10.1016/j.soilbio.2017.09.029
  • Sanders, T., & Laanbroek, H. J. (2018). The distribution of sediment and water column nitrification potential in the hyper-turbid Ems estuary. Aquatic Sciences, 80(4), 33. https://doi.org/10.1007/s00027-018-0584-1
  • Bohm, K. (2018). The ecological role of volatile mediated interactions belowground (PhD Thesis). http://library.wur.nl/WebQuery/wurpubs/fulltext/435386
  • Molinaro, F., Tyc, O., Beekwilder, J., Cankar, K., Bertea, C. M., Negre, M., & Garbeva, P. V. (2018). The effect of isabelin, a sesquiterpene lactone from Ambrosia artemisiifolia on soil microorganisms and human pathogens. FEMS Microbiology Letters, 365(4), [fny001]. https://doi.org/10.1093/femsle/fny001
  • Zhang, Q., & Laanbroek, H. J. (2018). The effects of condensed tannins derived from senescing Rhizophora mangle leaves on carbon, nitrogen and phosphorus mineralization in a Distichlis spicata salt marsh soil. Plant and Soil, 433(1-2), 37-53. https://doi.org/10.1007/s11104-018-3807-2
  • Mendes, L. W., Raaijmakers, J. M., & Mendes, R. (2018). The rhizosphere microbiome as an auxiliary breeding component in common bean against Fusarium oxysporum. Annual Report of the Bean Improvement Cooperative, LXI(61), 117-118. http://www.bic.uprm.edu/wp-content/uploads/2019/01/BIC-2018-VOL-61-2018.pdf
  • Perez Jaramillo, J. E., Carrion, V. J., De Hollander, M., & Raaijmakers, J. M. (2018). The wild side of plant microbiomes. Microbiome, 6(143). https://doi.org/10.1186/s40168-018-0519-z
  • Marcos, M. S., Barboza, A. D. H., Keijzer, R. M., & Laanbroek, H. J. (2018). Tide as steering factor in structuring archaeal and bacterial ammonia-oxidizing communities in mangrove forest soils dominated by Avicennia germinans and Rhizophora mangle. Microbial Ecology, 75(4), 997-1008. https://doi.org/10.1007/s00248-017-1091-y
  • Zwart, M., Schenk, M. F., Hwang, S., Koopmanschap, A. B., de Lange, N., van de Pol, L., Nga, T. T. T., Szendro, I. G., Krug, J., & de Visser, A. (2018). Unraveling the causes of adaptive benefits of synonymous mutations in TEM-1 β-lactamase. Heredity, 121, 406-421. https://doi.org/10.1038/s41437-018-0104-z
  • Van Agtmaal, M., Straathof, A. L., Termorshuizen, A. J., Lievens, B., Hoffland, E., & De Boer, W. (2018). Volatile-mediated suppression of plant pathogens is related to soil properties and microbial community composition. Soil Biology & Biochemistry, 164-174. https://doi.org/10.1016/j.soilbio.2017.11.015
  • Veraart, A. J., Dimitrov, M., Schrier-Uijl, A. P., Smidt, H., & de Klein, J. J. M. (2017). Abundance, activity and community structure of denitrifiers in drainage ditches, in relation to sediment characteristics, vegetation and land-use. Ecosystems, 20(5), 928-943. https://doi.org/10.1007/s10021-016-0083-y
  • Reis Lucheta, A., Souza Cannavan, F. S., Tsai, S. M., & Kuramae, E. E. (2017). Amazonian Dark Earth and its Black Carbon Particles Harbor Different Fungal Abundance and Diversity. Pedosphere, 27(October), 832-845. https://doi.org/10.1016/S1002-0160(17)60415-6
  • Pangesti, N., Vandenbrande, S., Pineda, A., Dicke, M., Raaijmakers, J. M., & Van Loon, J. J. A. (2017). Antagonism between two root-associated beneficial Pseudomonas strains does not affect plant growth promotion and induced resistance against a leaf-chewing herbivore. FEMS Microbiology Ecology, 93(4), [fix038]. https://doi.org/10.1093/femsec/fix038
  • Pinzari, F., Maggi, O., Lunghini, D., Di Lonardo, P., & Persiani, A. M. (2017). A simple method for measuring fungal metabolic quotient and comparing carbon use efficiency of different isolates: Application to Mediterranean leaf litter fungi. Plant Biosystems, 151(2), 371-376. https://doi.org/10.1080/11263504.2017.1284166
  • Wilschut, R. A., Silva, J. C. P., Garbeva, P. V., & van der Putten, W. H. (2017). Belowground plant-herbivore interactions vary among climate-driven range-expanding plant species with different degrees of novel chemistry. Frontiers in Plant Science, 8, [fpls.2017.01861]. https://doi.org/10.3389/fpls.2017.01861
  • Brinkman, E. P., Raaijmakers, C. E., De Boer, W., & van der Putten, W. H. (2017). Changing soil legacies to direct restoration of plant communities. AoB PLANTS, in press, [plx038]. https://doi.org/10.1093/aobpla/plx038
  • Kielak, A. M., Castellane, T. C. L., Campanharo, J. C., Colnago, L. A., Costa, O. Y. A., Corradi da Silva, M. L., van Veen, J. A., Lemos, E. G., & Kuramae, E. E. (2017). Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications. Scientific Reports, 7, [41193]. https://doi.org/10.1038/srep41193
  • Van der Meij, A., Worsley, S. F., Hutchings, M. I., & van Wezel, G. P. (2017). Chemical ecology of antibiotic production by actinomycetes. FEMS Microbiology Reviews, 41(3), 392-416. https://doi.org/10.1093/femsre/fux005
  • Gómez Expósito, R., De Bruijn, I., Postma, J., & Raaijmakers, J. M. (2017). Current insights into the role of rhizosphere bacteria in disease suppressive soils. Frontiers in Microbiology, [2529]. https://doi.org/10.3389/fmicb.2017.02529
  • Dassen, S., Cortois, R., Martens, H., De Hollander, M., Kowalchuk, G. A., van der Putten, W. H., & De Deyn, G. B. (2017). Differential responses of soil bacteria, fungi, archaea and protists to plant species richness and plant functional group identity. Molecular Ecology, 26(15), 4085-4098. https://doi.org/10.1111/mec.14175
  • van der Wal, A., & De Boer, W. (2017). Dinner in the dark: Illuminating drivers of soil organic matter decomposition. Soil Biology & Biochemistry, 105, 45-48. https://doi.org/10.1016/j.soilbio.2016.11.006
  • de Klein, J. J. M., Overbeek, C. C., Juncher Jørgensen, C., & Veraart, A. J. (2017). Effect of Temperature on Oxygen Profiles and Denitrification Rates in Freshwater Sediments. Wetlands, 37(5), 975-983. https://doi.org/10.1007/s13157-017-0933-1
  • Ho, A., Ijaz, U. Z., Janssens, T., Ruijs, R., Kim, S. Y., De Boer, W., Termorshuizen, A. J., van der Putten, W. H., & Bodelier, P. L. E. (2017). Effects of bio-based residue amendments on greenhouse gas emission from agricultural soil are stronger than effects of soil type with different microbial community composition. Global Change Biology Bioenergy, 9(12), 1707-1720. https://doi.org/10.1111/gcbb.12457
  • Tyc, O., de Jager, V. C. L., Van den Berg, M., Gerards, S., Janssens, T., Zaagman, N., Kai, M., Svatos, A., Zweers, A. J., Hordijk, C. A., Besselink, H., De Boer, W., & Garbeva, P. V. (2017). Exploring bacterial interspecific interactions for discovery of novel antimicrobial compounds. Microbial Biotechnology, 10(4), 910-925. https://doi.org/10.1111/1751-7915.12735
  • Van Agtmaal, M., Straathof, A. L., Termorshuizen, A. J., Teurlincx, S., Hundscheid, M. P. J., Ruyters, S., Busschaert, P., Lievens, B., & De Boer, W. (2017). Exploring the reservoir of potential fungal plant pathogens in agricultural soil. Applied Soil Ecology, 121, 152-160. https://doi.org/10.1016/j.apsoil.2017.09.032
  • Yan, Y., Kuramae, E. E., De Hollander, M., Klinkhamer, P. G. L., & van Veen, J. A. (2017). Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. ISME Journal, 11, 56-66. https://doi.org/10.1038/ismej.2016.108
  • Van der Wal, A., Klein Gunnewiek, P. J. A., De Hollander, M., & De Boer, W. (2017). Fungal diversity and potential tree pathogens in decaying logs and stumps. Forest Ecology and Management, 406, 266-273. https://doi.org/10.1016/j.foreco.2017.08.018
  • Schmidt, R. L., de Jager, V. C. L., Zühlke, D., Wolff, C., Bernhardt, J., Cankar, K., Beekwilder, J., van Ijcken, W., Sleutels, F., De Boer, W., Riedel, K., & Garbeva, P. V. (2017). Fungal volatile compounds induce production of the secondary metabolite Sodorifen in Serratia plymuthica PRI-2C. Scientific Reports, 7, [862 ]. https://doi.org/10.1038/s41598-017-00893-3
  • Schulz-Bohm, K., Tyc, O., De Boer, W., Peereboom, N., Debets, F., Zaagman, N., Janssens, T. K. S., & Garbeva, P. (2017). Fungus-associated bacteriome in charge of their host behaviour. Fungal Genetics and Biology, 102, 38-48. https://doi.org/10.1016/j.fgb.2016.07.011
  • Cheng, X., Etalo, D. W., van de Mortel, J. E., Dekkers, E., Nguyen, L., Medema, M. H., & Raaijmakers, J. M. (2017). Genome-wide analysis of bacterial determinants of plant growth promotion and induced systemic resistance by Pseudomonas fluorescens. Environmental Microbiology, 19(11), 4638-4656. https://doi.org/10.1111/1462-2920.13927
  • Zhang, S., Liu, X., Jiang, Q., Shen, G., & Ding, W. (2017). Legacy effects of continuous chloropicrin-fumigation for 3-years on soil microbial community composition and metabolic activity. AMB Express, 7(1), 178. https://doi.org/10.1186/s13568-017-0475-1
  • Perez Jaramillo, J. E., Carrion, V. J., Bosse, M., Ferrão, L. F. V., De Hollander, M., Garcia, A. A. F., Ramirez, C. A., Mendez, R., & Raaijmakers, J. M. (2017). Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME Journal, 11, 2244-2257. https://doi.org/10.1038/ismej.2017.85
  • Kurm, V., van der Putten, W. H., De Boer, W., Naus-Wiezer, S. M. H., & Hol, W. H. G. (2017). Low abundant soil bacteria can be metabolically versatile and fast growing. Ecology, 98(2), 555-564. https://doi.org/10.1002/ecy.1670
  • Geudens, N., Nasir, M. N., Crowet, J-M., Raaijmakers, J. M., Fehér, K., Coenye, T., Martins, J. C., Lins, L., Sinnaeve, D., & Deleu, M. (2017). Membrane Interactions of Natural Cyclic Lipodepsipeptides of the Viscosin Group. Biochimica et Biophysica Acta (BBA) - Biomembranes, 1859(3), 331-339. https://doi.org/10.1016/j.bbamem.2016.12.013
  • Kip, N., Jansen, S., Leite, M. F. A., De Hollander, M., Afanasyev, M., Kuramae, E. E., & van Veen, J. A. (2017). Methanogens predominate in natural corrosion protective layers on metal sheet piles. Scientific Reports, 7, [11899]. https://doi.org/10.1038/s41598-017-11244-7
  • Steenbergh, A. K., Veraart, A. J., Ho, A., & Bodelier, P. L. E. (2017). Microbial Ecosystem Functions in Wetlands Under Disturbance. In K. Tate [Ed.], Microbial Biomass: A Paradigm Shift in Terrestrial Biochemistry World Scientific. http://www.worldscientific.com/worldscibooks/10.1142/q0038
  • Schulz-Bohm, K., Martín-Sánchez, L., & Garbeva, P. V. (2017). Microbial volatiles: Small molecules with an important role in intra- and inter-kingdom interactions. Frontiers in Microbiology, 8, [02484]. https://doi.org/10.3389/fmicb.2017.02484
  • Gomez Exposito, R. (2017). Microbiome dynamics of disease suppresive soils (PhD Thesis). Wageningen University. http://edepot.wur.nl/412539
  • Leite, M. F. A., Pan, Y., Bloem, J., ten Berge, H., & Kuramae, E. E. (2017). Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank. Scientific Reports, 7, [42634]. https://doi.org/10.1038/srep42634
  • Cordovez, V., Mommer, L., Moisan, K., Lucas-Barbosa, D., Pierik, R., Mumm, R., Carrion, V. J., & Raaijmakers, J. M. (2017). Plant phenotypic and transcriptional changes induced by volatiles from the fungal root pathogen Rhizoctonia solani. Frontiers in Plant Science, 8, [01262]. https://doi.org/10.3389/fpls.2017.01262
  • Bosmans, L., de Bruijn, I., Gerards, S., Moerkens, R., Van Looveren, L., Wittemans, L., Van Calenberge, B., Paeleman, A., Van Kerckhove, S., Rozenski, J., de Mot, R., Rediers, H., Raaijmakers, J. M., & Lievens, B. (2017). Potential for biocontrol of hairy root disease by a Paenibacillus clade. Frontiers in Microbiology, 8, [447]. https://doi.org/10.3389/fmicb.2017.00447
  • Di Lonardo, P., De Boer, W., Klein Gunnewiek, P. J. A., Hannula, S. E., & Van der Wal, A. (2017). Priming of soil organic matter: Chemical structure of added compounds is more important than the energy content. Soil Biology & Biochemistry, 108, 41-54. https://doi.org/10.1016/j.soilbio.2017.01.017
  • Eisenhauer, N., Antunes, P. M., Bennett, A. E., Birkhofer, K., Bissett, A., Bowker, M. A., Caruso, T., Chen, B., Coleman, D. C., De Boer, W., De Ruiter, P. C., DeLuca, T. H., Frati, F., Griffiths, B. S., Hart, M. M., Hättenschwiler, S., Haimi, J., Heethoff, M., Kaneko, N.,... Powell, J. R. (2017). Priorities for research in soil ecology. Pedobiologia, 63(Supplement C), 1 - 7. https://doi.org/10.1016/j.pedobi.2017.05.003
  • Scheublin, T. R. (2017). Protocols for the Identification of Phyllosphere-Induced Pollutant Degradation Genes. In T. J. McGenity, K. N. Timmis, & B. Nogales [Eds.], Hydrocarbon and Lipid Microbiology Protocols: Field Studies (pp. 229-235). ( Springer Protocols Handbooks). Springer Verlag GmbH. https://doi.org/10.1007/8623_2015_176
  • Ho, A., Di Lonardo, P., & Bodelier, P. L. E. (2017). Revisiting life strategy concepts in environmental microbial ecology. FEMS Microbiology Ecology, 93(3), [fix006]. https://doi.org/10.1093/femsec/fix006
  • Schlemper, T. R., Leite, M. F. A., Reis Lucheta, A., Shimels, M., Bouwmeester, H. J., van Veen, J. A., & Kuramae, E. E. (2017). Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils. FEMS Microbiology Ecology, 93(8), [fix096]. https://doi.org/10.1093/femsec/fix096
  • Durán, P., Jorquera, M., Viscardi, S., Carrión, V. J., Mora, M. D. L. L., & Pozo, M. J. (2017). Screening and Characterization of Potentially Suppressive Soils against Gaeumannomyces graminis under Extensive Wheat Cropping by Chilean Indigenous Communities. Frontiers in Microbiology, 8, 1552. https://doi.org/10.3389/fmicb.2017.01552
  • Hannula, S. E., Morriën, E., De Hollander, M., van der Putten, W. H., van Veen, J. A., & De Boer, W. (2017). Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME Journal, 11, 2294-2304. https://doi.org/10.1038/ismej.2017.90
  • Paulo, A. M. S., Aydin, R., Dimitrov, M. R., Vreeling, H., Cavaleiro, A. J., García-Encina, P. A., Stams, A. J. M., & Plugge, C. M. (2017). Sodium lauryl ether sulfate (SLES) degradation by nitrate-reducing bacteria. Applied Microbiology and Biotechnology, 101(12), 5163-5173. https://doi.org/10.1007/s00253-017-8212-x
  • Lupatini, M., Korthals, G. W., De Hollander, M., Janssens, T. K. S., & Kuramae, E. E. (2017). Soil microbiome is more heterogeneous in organic than in conventional farming system. Frontiers in Microbiology, 7, [2064]. https://doi.org/10.3389/fmicb.2016.02064
  • Morriën, E., Hannula, S. E., Snoek, B., Helmsing, N. R., Zweers, H., De Hollander, M., Lujan Soto, R., Bouffaud, M. L., Buée, M., Dimmers, W., Duyts, H., Geisen, S., Girlanda, M., Griffiths, R. I., Jørgensen, H-B., Jensen, J., Plassart, P., Redecker, D., Schmelz, R. M.,... van der Putten, W. H. (2017). Soil networks become more connected and take up more carbon as nature restoration progresses. Nature Communications, 8, [14349]. https://doi.org/10.1038/ncomms14349
  • van Gils, S., Tamburini, G., Lorenzo, M., Biere, A., Van Agtmaal, M., Tyc, O., Kos, M., Kleijn, D., & van der Putten, W. H. (2017). Soil pathogen-aphid interactions under differences in soil organic matter and mineral fertilizer. PLoS One, 12(8), [0179695]. https://doi.org/10.1371/journal.pone.0179695
  • Daebeler, A., Bodelier, P. L. E., Hefting, M. M., Rütting, T., & Laanbroek, H. J. (2017). Soil warming and fertilization altered rates of nitrogen transformation processes and selected for adapted ammonia-oxidizing archaea in sub-arctic grassland soil. Soil Biology & Biochemistry, 107, 114-124. https://doi.org/10.1016/j.soilbio.2016.12.013
  • Van der Wal, A., Klein Gunnewiek, P. J. A., & De Boer, W. (2017). Soil-wood interactions: influence of decaying coniferous and broadleaf logs on composition of soil fungal communities. Fungal Ecology, 30(December), 132-134. https://doi.org/10.1016/j.funeco.2017.08.006
  • Dimitrov, M. R., Veraart, A. J., De Hollander, M., Smidt, H., van Veen, J. A., & Kuramae, E. E. (2017). Successive DNA extractions improve characterization of soil microbial communities. PeerJ, 5, [e2915]. https://doi.org/10.7717/peerj.2915
  • Ossowicki, A., Jafra, S., & Garbeva, P. V. (2017). The Antimicrobial Volatile Power of the Rhizospheric Isolate Pseudomonas donghuensis P482. PLoS One, 12(3), [174362]. https://doi.org/10.1371/journal.pone.0174362
  • Tyc, O., Song, C., Dickschat, J., Vos, M., & Garbeva, P. V. (2017). The Ecological Role of Volatile and Soluble Secondary Metabolites Produced by Soil Bacteria. Trends in Microbiology, 25(4), 280-292. https://doi.org/10.1016/j.tim.2016.12.002
  • Westhoff, S., van Leeuwe, T. M., Qachach, O., Zhang, Z., van Wezel, G. P., & Rozen, D. E. (2017). The evolution of no-cost resistance at sub-MIC concentrations of streptomycin in Streptomyces coelicolor. ISME Journal, 11, 1168-1178. https://doi.org/10.1038/ismej.2016.194
  • Schulz-Bohm, K., Geisen, S., Wubs, E. R. J., Song, C., De Boer, W., & Garbeva, P. V. (2017). The prey’s scent – volatile organic compound mediated interactions between soil bacteria and their protist predators. ISME Journal, 11, 817-820. https://doi.org/10.1038/ismej.2016.144
  • Hilt, S., Brothers, S., Jeppesen, E., Veraart, A. J., & Kosten, S. (2017). Translating Regime Shifts in Shallow Lakes into Changes in Ecosystem Functions and Services. BioScience, 67(10), 928-936. https://doi.org/10.1093/biosci/bix106
  • Schilder, J., Van Hardenbroek, M., Bodelier, P. L. E., Kirilova, E. P., Leuenberger, M., Lotter, A. F., & Heiri, O. (2017). Trophic state changes can affect the importance of methane-derived carbon in aquatic food webs. Proceedings of the Royal Society B-Biological Sciences, 284(1857), [278]. https://doi.org/10.1098/rspb.2017.0278
  • De Boer, W. (2017). Upscaling of fungal-bacterial interactions: from the lab to the field. Current Opinion in Microbiology, 37, 35-41. https://doi.org/10.1016/j.mib.2017.03.007
  • Schmidt, R. L. (2017). Volatile communication between fungi and bacteria (PhD Thesis). Wageningen University. http://edepot.wur.nl/422840
  • Kielak, A. M., Cipriano, M. A. P., & Kuramae, E. E. (2016). Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Archives of Microbiology, 198(December), 987-993. https://doi.org/10.1007/s00203-016-1260-2
  • Mesarich, C. H., Stergiopoulos, I., Beenen, H. G., Cordovez, V., Guo, Y., Karimi Jashni, M., Bradshaw, R. E., & de Wit, P. J. G. M. (2016). A conserved proline residue in Dothideomycete Avr4 effector proteins is required to trigger a Cf-4-dependent hypersensitive response. Molecular Plant Pathology, 17(1), 84-95. https://doi.org/10.1111/mpp.12265
  • Bosmans, L., De Bruijn, I., de Mot, R., Readers, H., & Lievens, B. (2016). Agar composition affects in vitro screening of biocontrol activity of antagonistic microorganisms. Journal of Microbiological Methods, 127, 7-9. https://doi.org/10.1016/j.mimet.2016.05.004
  • Yan, Y. (2016). Assemblage and functioning of bacterial communities in soil and rhizosphere (PhD Thesis). https://openaccess.leidenuniv.nl
  • Kielak, A., Scheublin, T., Mendes, L. W., Van Veen, J. A., & Kuramae, E. E. (2016). Bacterial community succession in pine-wood decomposition. Frontiers in Microbiology, 7, [00231]. https://doi.org/10.3389/fmicb.2016.00231
  • Ho, A., Angel, R., Veraart, A. J., Daebeler, A., Jia, Z., Kim, S. Y., Kerckhof, F. M., Boon, N., & Bodelier, P. L. E. (2016). Biotic interactions in microbial communities as modulators of biogeochemical processes: Methanotrophy as a model system. Frontiers in Microbiology, 7, [1285]. https://doi.org/10.3389/fmicb.2016.01285
  • van Dam, N. M., Weinhold, A., & Garbeva, P. V. (2016). Calling in the Dark: the Role of Volatiles for Communication in the Rhizosphere. In Deciphering Chemical language of Plant Communication (pp. 175-210). (Signaling and Communication in Plants). Springer. https://doi.org/10.1007/978-3-319-33498-1_8
  • Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A., & Wakelin, S. A. (2016). Challenges and opportunities in harnessing soil disease suppressiveness for sustainable pasture production. Soil Biology & Biochemistry, 95(April), 100-111. https://doi.org/10.1016/j.soilbio.2015.12.006
  • Rice, M. C., Norton, J. M., Valois, F., Bollmann, A., Bottomley, P. J., Klotz, M. G., Laanbroek, H. J., Suwa, Y., Stein, L. Y., Sayavedra-Soto, L., Woyke, T., Shapiro, N., Goodwin, L. A., Huntemann, M., Clum, A., Pillay, M., Kyrpides, N., Varghese, N., Mikhailova, N.,... Daum, C. (2016). Complete genome of Nitrosospira briensis C-128, an ammonia-oxidizing bacterium from agricultural soil. Standards in Genomic Sciences, 11(1), 46. https://doi.org/10.1186/s40793-016-0168-4
  • Adam, E., Groenenboom, A. E., Kurm, V. K., Rajewska, M., Schmidt, R. L., Tyc, O., Weidner, S., Berg, G., De Boer, W., & Salles, J. (2016). Controlling the microbiome: microhabitat adjustments for successful biocontrol strategies in soil and human gut: Opinion article. Frontiers in Microbiology, in press, [1079]. https://doi.org/10.3389/fmicb.2016.01079
  • Cai, Y., Yan, Z., Bodelier, P. L. E., Conrad, R., & Jia, Z. (2016). Conventional methanotrophs are responsible for atmospheric methane oxidation in paddy soils. Nature Communications, 7, [11728]. https://doi.org/10.1038/ncomms11728
  • Creamer, R. E., Hannula, S. E., Leeuwen, J. P. V., Stone, D., Rutgers, M., Schmelz, R. M., Ruiter, P. C. D., Hendriksen, N. B., Bolger, T., Bouffaud, M. L., Buee, M., Carvalho, F., Costa, D., Dirilgen, T., Francisco, R., Griffiths, B. S., Griffiths, R., Martin, F., Silva, P. M. D.,... Lemanceau, P. (2016). Ecological network analysis reveals the inter-connection between soil biodiversity and ecosystem function as affected by land use across Europe. Applied Soil Ecology, 97, 112-124. https://doi.org/10.1016/j.apsoil.2015.08.006
  • Weisskopf, L., Garbeva, P. V., Ryu, C-M., & Raaijmakers, J. M. (2016). Editorial: Smelly fumes: volatile-mediated communication between bacteria and other organisms. Frontiers in Microbiology, 7, [2031]. https://doi.org/10.3389/fmicb.2016.02031
  • Liu, Y., Zachow, C., Raaijmakers, J. M., & De Bruijn, I. (2016). Elucidating the diversity of aquatic Microdochium and Trichoderma species and their activity against the fish pathogen Saprolegnia diclina. International Journal of Molecular Sciences, 17, [140]. https://doi.org/10.3390/ijms17010140
  • Pitombo, L., do Carmo, J. B., De Hollander, M., Rosetto, R., Lopez, M. V., Cantarella, H., & Kuramae, E. E. (2016). Exploring soil microbial 16S rRNA sequence data to increase carbon yield and nitrogen efficiency of a bioenergy crop. Global Change Biology Bioenergy, 8(5), 867-879. https://doi.org/10.1111/gcbb.12284
  • Reis Lucheta, A., Souza Cannavan, F. S., Roesch, L., Tsai, S. M., & Kuramae, E. E. (2016). Fungal community assembly in the Amazonian Dark Earth. Microbial Ecology, 71(May), 962-973. https://doi.org/10.1007/s00248-015-0703-7
  • Chapelle, E., Mendes, R., Bakker, P. A. H. M., & Raaijmakers, J. (2016). Fungal invasion of the rhizosphere microbiome. ISME Journal, 10, 265-268. https://doi.org/10.1038/ismej.2015.82
  • Bai, Y., Eijsink, V. G. H., Kielak, A. M., Van Veen, J. A., & De Boer, W. (2016). Genomic comparison of chitinolytic enzyme systems from terrestrial and aquatic bacteria. Environmental Microbiology, 18(1), 38-49. https://doi.org/10.1111/1462-2920.12545
  • Kolter, R., & van Wezel, G. P. (2016). Goodbye to brute force in antibiotic discovery? Nature Microbiology, 1, 15020. https://doi.org/10.1038/nmicrobiol.2015.20
  • Perez Jaramillo, J. E., Mendes, R., & Raaijmakers, J. (2016). Impact of plant domestication on rhizosphere microbiome assembly and functions. Plant Molecular Biology, 90(6), 635-644. https://doi.org/10.1007/s11103-015-0337-7
  • van der Voort, M., Kempenaar, M., van Driel, M., Raaijmakers, J. M., & Mendes, R. (2016). Impact of soil heat on reassembly of bacterial communities in the rhizosphere microbiome and plant disease suppression. Ecology Letters, 19(4), 375-382. https://doi.org/10.1111/ele.12567
  • Nguyen, D., Melnik, A. V., Koyama, N., Lu, X., Schorn, M., Fang, J., Aguinaldo, K., Lincecum Jr., T., Ghequire, M., Carrion, V. J., Cheng, T., Malone, J., Mauchline, T., Sanchez, L., Marm Kilpatrick, A., Raaijmakers, J. M., De Mot, R., Moore, B., Medema, M. H., & Dorrestein, P. C. (2016). Indexing the Pseudomonas specialized metabolome enabled the discovery of poaeamide B and the bananamides. Nature Microbiology, 2, [16197]. https://doi.org/10.1038/nmicrobiol.2016.197
  • Flury, P., Aellen, N., Ruffner, B., Pechy-Tarr, M., Fataar, S., Metla, Z., Dominguez-Ferreras, A., Bloemberg, G., Frey, J., Goesmann, A., Raaijmakers, J. M., Duffy, B., Hofte, M., Blom, J., Smits, T. H. M., Keel, C., & Maurhofer, M. (2016). Insect pathogenicity in plant-beneficial pseudomonads: phylogenetic distribution and comparative genomics. ISME Journal, 10, 2527-2542. https://doi.org/10.1038/ismej.2016.5
  • Urem, M., Świątek-Połatyńska, M. A., Rigali, S., & van Wezel, G. P. (2016). Intertwining nutrient-sensory networks and the control of antibiotic production in Streptomyces. Molecular Microbiology, 102(2), 183-195. https://doi.org/10.1111/mmi.13464
  • Baltz, R. H., Ikeda, H., Katz, L., Kim, E-S., van Wezel, G. P., & Wright, G. (2016). Introduction to the Special Issue: "Natural Product Discovery and Development in the Genomic Era": Editorial. Journal of Industrial Microbiology and Biotechnology, 43(2-3), 109. https://doi.org/10.1007/s10295-015-1715-5
  • Rinkel, J., Rabe, P., Garbeva, P. V., & Dickschat, J. (2016). Lessons from 1,3-Hydride Shifts in Sesquiterpene Cyclizations. Angewandte Chemie, 55(43), 13593-13596. https://doi.org/10.1002/anie.201608042
  • Cipriano, M. A. P., Lupatini, M., Santos, L., Silva, M. D., Roesch, L. F. W., Destefano, S., Freitas, S., & Kuramae, E. E. (2016). Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions. FEMS Microbiology Ecology, 92(12), [fiw197]. https://doi.org/10.1093/femsec/fiw197
  • Song, C., Kidarsa, T., van de Mortel, J., Loper, J. E., & Raaijmakers, J. M. (2016). Living on the edge: emergence of spontaneous gac mutations in Pseudomonas protegens during swarming motility. Environmental Microbiology, 18(10), 3453-3465. https://doi.org/10.1111/1462-2920.13288
  • Wu, C., Choi, Y. H., & van Wezel, G. P. (2016). Metabolic profiling as a tool for prioritizing antimicrobial compounds. Journal of Industrial Microbiology and Biotechnology, 43(2-3), 299-312. https://doi.org/10.1007/s10295-015-1666-x
  • Schmidt, R., Etalo, D. N., de Jager, V. C. L., Gerards, S., Zweers, H., De Boer, W., & Garbeva, P. V. (2016). Microbial small talk: volatiles in fungal-bacterial interactions. Frontiers in Microbiology, 6, [01495]. https://doi.org/10.3389/fmicb.2015.01495
  • Tyc, O. (2016). Mining into interspecific bacterial interactions (PhD Thesis). Wageningen University. http://edepot.wur.nl/383745
  • Soares, J. R., Cassman, N., Kielak, A. M., Pijl, A. S., do Carmo, J. B., Lourenço, K. S., Laanbroek, H. J., Cantarella, H., & Kuramae, E. E. (2016). Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil. Scientific Reports, 6, [30349]. https://doi.org/10.1038/srep30349
  • Campanharo, J. C., Kielak, A. M., Castellane, T. C., Kuramae, E. E., & Lemos, E. G. (2016). Optimized medium culture for Acidobacteia subdivision 1 strains. FEMS Microbiology Letters, 363(21), [fnw245]. https://doi.org/10.1093/femsle/fnw245
  • Van der Wal, A., Klein Gunnewiek, P. J. A., Cornelissen, J. H. C., Crowther, T. W., & De Boer, W. (2016). Patterns of natural fungal community assembly during initial decay of coniferous and broadleaf tree logs. Ecosphere, 7(7), [1393]. https://doi.org/10.1002/ecs2.1393
  • Gonzalez, D., Rodriguez-Carres, M., Boekhout, T., Stalpers, J., Kuramae, E. E., Nakatani, A. K., Vilgalys, R., & Cubeta, M. A. (2016). Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biology, 120(4), 603-619. https://doi.org/10.1016/j.funbio.2016.01.012
  • Cassman, N., Leite, M. F. A., Pan, Y., De Hollander, M., van Veen, J. A., & Kuramae, E. E. (2016). Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland. Scientific Reports, 6, [23680]. https://doi.org/10.1038/srep23680
  • Balk, M., Keuskamp, J., & Laanbroek, H. J. (2016). Potential of sulfate reduction in mangrove forest soils: Comparison between two dominant species of the Americas. Frontiers in Microbiology, in press, [2016.01855]. https://doi.org/10.3389/fmicb.2016.01855
  • Hannula, S. E., & van Veen, J. A. (2016). Primer Sets Developed for Functional Genes Reveal Shifts in Functionality of Fungal Community in Soils. Frontiers in Microbiology, 7, [fmicb.2016.01897]. https://doi.org/10.3389/fmicb.2016.01897
  • Ferreira de Carvalho, J. L., de Jager, V. C. L., Van Gurp, T. P., Wagenmaker, N., & Verhoeven, K. J. F. (2016). Recent and dynamic transposable elements contribute to genomic divergence under asexuality. BMC Genomics, 17, [884]. https://doi.org/10.1186/s12864-016-3234-9
  • Ho, A., van den Brink, E., Reim, A., Krause, S., & Bodelier, P. L. E. (2016). Recurrence and frequency of disturbance have cumulative effect on methanotrophic activity, abundance, and community structure. Frontiers in Microbiology, 6, [01493]. https://doi.org/10.3389/fmicb.2015.01493
  • Ho, A., Lueke, C., Reim, A., & Frenzel, P. (2016). Resilience of (seed bank) aerobic methanotrophs and methanotrophic activity to desiccation and heat stress. Soil Biology & Biochemistry, 101(October), 130-138. https://doi.org/10.1016/j.soilbio.2016.07.015
  • Cheng, X., Cordovez, V., Etalo, D. W., van der Voort, M., & Raaijmakers, J. M. (2016). Role of the GacS Sensor Kinase in the Regulation of Volatile Production by Plant Growth-Promoting Pseudomonas fluorescens SBW25. Frontiers in Plant Science, 7, 1706. https://doi.org/10.3389/fpls.2016.01706
  • Griffiths, B. S., Römbke, J., Schmelz, R. M., Scheffczyk, A., Faber, J. H., Bloem, J., Pérès, G., Cluzeau, D., Chabbi, A., Suhadolc, M., Sousa, J. P., Martins Da Silva, P., Carvalho, F., Mendes, S., Morais, P., Francisco, R., Pereira, C., Bonkowski, M., Geisen, S.,... Stone, D. (2016). Selecting cost effective and policy-relevant biological indicators for European monitoring of soil biodiversity and ecosystem function. Ecological Indicators, 69, 213-223. https://doi.org/10.1016/j.ecolind.2016.04.023
  • Raaijmakers, J. M., & Mazzola, M. (2016). Soil immune responses. Science, 352(6292), 1392-1393. https://doi.org/10.1126/science.aaf3252
  • Uroz, S., Oger, P., Tisserand, E., Cebron, A., Turpault, M. -P., Buee, M., De Boer, W., Leveau, J. H. J., & Frey-Klett, P. (2016). Specific impacts of beech and Norway spruce on the structure and diversity of the rhizosphere and soil microbial communities. Scientific Reports, 6. https://doi.org/10.1038/srep27756
  • Kim, G. W., Ho, A., Kim, P. J., & Kim, S. Y. (2016). Stimulation of methane oxidation potential and effects on vegetation growth by bottom ash addition in a landfill final evapotranspiration cover. Waste Management, 55(September), 306-312. https://doi.org/10.1016/j.wasman.2016.03.058
  • Yagüe, P., Willemse, J., Koning, R. I., Rioseras, B., López-García, M. T., Gonzalez-Quiñonez, N., Lopez-Iglesias, C., Shliaha, P. V., Rogowska-Wrzesinska, A., Koster, A. J., Jensen, O. N., van Wezel, G. P., & Manteca, Á. (2016). Subcompartmentalization by cross-membranes during early growth of Streptomyces hyphae. Nature Communications, 7, 12467 EP -. https://doi.org/10.1038/ncomms12467
  • van der Aart, L. T., Lemmens, N., van Wamel, W. J., & van Wezel, G. P. (2016). Substrate Inhibition of VanA by D-Alanine Reduces Vancomycin Resistance in a VanX-Dependent Manner. Antimicrobial Agents and Chemotherapy, 60(8), 4930-4939. https://doi.org/10.1128/aac.00276-16
  • Haque, M. M., Biswas, J. C., Kim, S. Y., & Kim, P. J. (2016). Suppressing methane emission and global warming potential from rice fields through intermittent drainage and green biomass amendment. Soil Use and Management, 32(1), 72-79. https://doi.org/10.1111/sum.12229
  • Tecon, R., & Leveau, J. H. J. (2016). Symplasmata are a clonal, conditional, and reversible type of bacterial multicellularity. Scientific Reports, 6, [31914]. https://doi.org/10.1038/srep31914
  • Suleiman, A. K. A., Gonzatto, R., Aita, C., Lupatini, M., Jacques, R., Kuramae, E. E., Antoniolli, Z., & Roesch, L. (2016). Temporal variability of soil microbial communities after application of dicyandiamide-treated swine slurry and mineral fertilizers. Soil Biology & Biochemistry, 97, 71-82. https://doi.org/10.1016/j.soilbio.2016.03.002
  • Kielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A., & Kuramae, E. E. (2016). The ecology of Acidobacteria: moving beyond genes and genomes. Frontiers in Microbiology, [744]. https://doi.org/10.3389/fmicb.2016.00744
  • Sedlacek, C. J., Nielsen, S., Greis, K. D., Haffey, W. D., Revsbech, N. P., Ticak, T., Laanbroek, H. J., & Bollmann, A. (2016). The effect of bacterial community members on the proteome of the ammonia-oxidizing bacterium Nitrosomonas sp. Is79. Applied and Environmental Microbiology, 82(15), 4776-4788. https://doi.org/10.1128/AEM.01171-16
  • Liu, Y. (2016). The fish egg microbiome: diversity and activity against the oomycete pathogen Saprolegnia (PhD Thesis). http://library.wur.nl/WebQuery/wda/2170985
  • Tripathi, B. M., Edwards, D. P., Mendes, L. W., Kim, M., Dong, K., Kim, H., & Adams, J. M. (2016). The impact of tropical forest logging and oil palm agriculture on the soil microbiome. Molecular Ecology, 25(10), 2244-2257. https://doi.org/10.1111/mec.13620
  • Ballhausen, M-B., & De Boer, W. (2016). The sapro-rhizosphere: Carbon flow from saprotrophic fungi into fungus-feeding bacteria. Soil Biology & Biochemistry, 102(November), 14-17. https://doi.org/10.1016/j.soilbio.2016.06.014
  • Ballhausen, M-B., Vandamme, P., & De Boer, W. (2016). Trait differentiation within the fungus-feeding (mycophagous) bacterial genus Collimonas. PLoS One, 11(6), [e0157552]. https://doi.org/10.1371/journal.pone.0157552
  • Kim, S. Y., Gutierrez, J., & Kim, P. J. (2016). Unexpected stimulation of CH4 emissions under continuous no-tillage system in mono-rice paddy soils during cultivation. Geoderma, 267, 34-40. https://doi.org/10.1016/j.geoderma.2015.12.021
  • Tyc, O., Tomás-Menor, L., Garbeva, P. V., Barrajón-Catalán, E., & Micol, V. (2016). Validation of the AlamarBlue® assay as a fast screening method to determine the antimicrobial activity of botanical extracts. PLoS One, 11(12), [e0169090]. https://doi.org/10.1371/journal.pone.0169090
  • Cordovez, V. (2016). Volatile-mediated interactions in the rhizosphere (PhD Thesis). Wageningen University. http://edepot.wur.nl/388360
  • Caizan Juanarena, L., ter Heijne, A., Buisman, C., & Van der Wal, A. (2016). Wood Degradation by Thermotolerant and Thermophilic Fungi for Sustainable Heat Production. ACS Sustainable Chemistry & Engineering, 4(12), 6355-6361. https://doi.org/10.1021/acssuschemeng.6b00914
  • Dignam, B. E. A., O'Callaghan, M., Condron, L. M., Raaijmakers, J. M., Kowalchuk, G. A., & Wakelin, S. A. (2015). A bioassay to compare the disease suppressive capacity of pasture soils. New Zealand Plant Protection, 68, 151-159. http://www.nzpps.org/nzpp_abstract.php?paper=681510
  • Schulz-Bohm, K., Zweers, H., De Boer, W., & Garbeva, P. (2015). A fragrant neighborhood: Volatile mediated bacterial interactions in soil. Frontiers in Microbiology, 6, [01212]. https://doi.org/10.3389/fmicb.2015.01212
  • Barbosa Lima, A., Souza Cannavan, F. S., Navarrete, A. A., Kuramae, E. E., Teixeira, W. G., & Tsai, S. M. (2015). Amazonian Dark Earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities. Microbial Ecology, 69(4), 855-866. https://doi.org/10.1007/s00248-014-0472-8
  • Daebeler, A., Bodelier, P. L. E., Hefting, M. M., & Laanbroek, H. J. (2015). Ammonia-limited conditions cause of Thaumarchaeal dominance in volcanic grassland soil. FEMS Microbiology Ecology, 91(3), [fiv014]. https://doi.org/10.1093/femsec/fiv014
  • Cretoiu, M., Berini, F., Kielak, A., Marinelli, F., & van Elsas, J. (2015). A novel salt-tolerant chitobiosidase discovered by genetic screening of a metagenomic library derived from chitin-amended agricultural soil: Applied Microbiology and Biotechnology. Applied Microbiology and Biotechnology, 99(19), 8199-8215. https://doi.org/10.1007/s00253-015-6639-5
  • De Boer, W., Hundscheid, M. P. J., Klein Gunnewiek, P. J. A., De Ridder-Duine, A. S., Thion, C., van Veen, J. A., & Van der Wal, A. (2015). Antifungal rhizosphere bacteria can increase as response to the presence of saprotrophic fungi. PLoS One, 10(9), [e0137988]. https://doi.org/10.1371/journal.pone.0137988
  • Cong, H., Zou, D., Wu, F., & Zhang, Q. (2015). A study on coupling and coordinating development mechanism of China's low-carbon development and environmental resources system. Nature Environment and Pollution Technology, 14(3), 611-619. http://www.neptjournal.com/upload-images/NL-53-24-(22)G-59.pdf
  • Rudnick, M. B., van Veen, J. A., & de Boer, W. (2015). Baiting of bacteria with hyphae of common soil fungi revealed a diverse group of potentially mycophagous secondary consumers in the rhizosphere. Soil Biology & Biochemistry, 88(September), 73-82. https://doi.org/10.1016/j.soilbio.2015.04.015
  • Veraart, A. J., Steenbergh, A. K., Ho, A., Kim, S. Y., & Bodelier, P. L. E. (2015). Beyond nitrogen: the importance of phosphorus for CH4 oxidation in soils and sediments. Geoderma, 259-260(December), 337-346. https://doi.org/10.1016/j.geoderma.2015.03.025
  • Ganendra, G., Mercado-Garcia, D., Hernandez-Sanabria, E., Peiren, N., De Campeneere, S., Ho, A., & Boon, N. (2015). Biofiltration of Methane from Ruminants Gas Effluent Using Autoclaved Aerated Concrete as the Carrier Material. Chemical Engineering Journal, 277, 318-323. https://doi.org/10.1016/j.cej.2015.04.128
  • Ganendra, G., Wang, J., Ramos, J. A., Derluyn, H., Rahier, H., Cnudde, V., Ho, A., & Boon, N. (2015). Biogenic concrete protection driven by the formate oxidation by Methylocystis parvus OBBP. Frontiers in Microbiology, 6, [786]. https://doi.org/10.3389/fmicb.2015.00786
  • Kim, S. Y., Veraart, A., Meima-Franke, M., & Bodelier, P. (2015). Combined effects of carbon, nitrogen and phosphorus on CH4 production and denitrification in wetland sediments. Geoderma, Online, 354-361. https://doi.org/10.1016/j.geoderma.2015.03.015
  • 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
  • Czajkowski, R., Ozymko, Z., de Jager, V., Siwinska, J., Smolarska, A., Ossowicki, A., Narajczyk, M., & Lojkowska, E. (2015). Genomic, proteomic and morphological characterization of two novel broad host lytic bacteriophages (phi)PD10.3 and (phi)PD23.1 infecting pectinolytic Pectobacterium spp. and Dickeya spp. PLoS One, 10(3), [e0119812]. https://doi.org/10.1371/journal.pone.0119812
  • Faassen, E. J., Veraart, A., Van Nes, E. H., Dakos, V., Lürling, M., & Scheffer, M. (2015). Hysteresis in an experimental phytoplankton population. Oikos, 124(12), 1617-1623. https://doi.org/10.1111/oik.02006
  • Mendes, L. W., Navarrete, A. A., Borges, C. D., Kuramae, E. E., & Tsai, S. M. (2015). Impact of land-use changes in the Amazon on bacterial diversity, composition and distribution. In F. Q. Brearley, & A. D. Thomas [Eds.], Land-use Change Impacts on Soil Process: Tropical and Savannah Ecosystems (Chapter 5 ed., pp. 41-54). CABI Publisher. http://www.cabi.org/bookshop/book/9781780642109
  • 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
  • Kim, P. J., Bodelier, P. L. E., & Lu, Y. (2015). Mechanisms controlling greenhouse gas emissions from soils. Geoderma, 259-260(December), 321-322. https://doi.org/10.1016/j.geoderma.2015.07.009
  • Ganendra, G., Mercado-Garcia, D., Hernandez-Sanabria, E., Boeckx, P., Ho, A., & Boon, N. (2015). Methane biofiltration using Autoclaved Aerated Concrete as the carrier material. Applied Microbiology and Biotechnology, 99(17), 7307-7320. https://doi.org/10.1007/s00253-015-6646-6
  • 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
  • Rudnick, M. B. (2015). Mycophagous soil bacteria (PhD Thesis). Wageningen University. http://library.wur.nl/WebQuery/wurpubs/484787
  • 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
  • Thomson, B. C., Tisserant, E., Plassart, P., Uroz, S., Griffiths, R. I., Hannula, S. E., Buée, M., Mougel, C., Ranjard, L., Van Veen, J. A., Martin, F., Bailey, M. J., & Lemanceau, P. (2015). Soil conditions and land use intensification effects on soil microbial communities across a range of European field sites. Soil Biology & Biochemistry, 88(September). https://doi.org/10.1016/j.soilbio.2015.06.012
  • Navarrete, A. A., Tsai, S. M., Mendes, L. W., Faust, K., De Hollander, M., Cassman, N., Raes, J., Van Veen, J. A., & Kuramae, E. E. (2015). Soil microbiome responses to the short-term effects of Amazonian deforestation. Molecular Ecology, 24(10), 2433-2448. https://doi.org/10.1111/mec.13172
  • Van Agtmaal, M. (2015). Suppression of soil-borne plant pathogens (PhD Thesis). Wageningen University. http://edepot.wur.nl/345218
  • Bodelier, P. L. E. (2015). Sustainability: Bypassing the methane cycle: News & Views. Nature, 523(7562), 534-535. https://doi.org/10.1038/nature14633
  • Czajkowski, R., Ozymko, Z., Siwinska, J., Ossowicki, A., de Jager, V., Narajczyk, M., & Łojkowska, E. (2015). The complete genome, structural proteome, comparative genomics and phylogenetic analysis of a broad host lytic bacteriophage ϕD3 infecting pectinolytic Dickeya spp. Standards in Genomic Sciences. Standards in Genomic Sciences, 10, [68]. https://doi.org/10.1186/s40793-015-0068-z
  • Kip, D. J., & Van Veen, J. A. (2015). The dual role of microbes in corrosion. ISME Journal, 9, 542-551. https://doi.org/10.1038/ismej.2014.169
  • Reis, M. D. P., Ávila, M., Keijzer, R. M., Barbosa, F. A. R., Chartone-Souza, E., Nascimento, A., & Laanbroek, R. H. J. (2015). The effect of human settlement on the abundance and community structure of ammonia oxidizers in tropical stream sediments. Frontiers in Microbiology, 6, [00898 ]. https://doi.org/10.3389/fmicb.2015.00898
  • Tyc, O., Wolf, A., & Garbeva, P. (2015). The effect of phylogenetically different bacteria on the fitness of Pseudomonas fluorescens in sand microcosms. PLoS One, 10(3), [e0119838]. https://doi.org/10.1371/journal.pone.0119838
  • Bonnichsen, L., Svenningsen, N. B., Rybtke, M., de Bruijn, I., Raaijmakers, J. M., Tolker-Nielsen, T., & Nybroe, O. (2015). The lipopeptide biosurfactant viscosin enhances dispersal of Pseudomonas fluorescens SBW25 biofilms. Microbiology, 161(12), 2289-2297. https://doi.org/10.1099/mic.0.000191
  • Raaijmakers, J. (2015). The minimal rhizosphere microbiome. In B. Lugtenberg [Ed.], Principles of Plant-Microbe Interactions (pp. 411-419). (Microbes for sustainable agriculture). Springer. https://doi.org/10.1007/978-3-319-08575-3_43
  • Zachow, C., Jahanshah, G., de Bruijn, I., Song, C., Ianni, F., Pataj, Z., Gerhardt, H., Pianet, I., Lämmerhofer, M., Berg, G., Gross, H., & Raaijmakers, J. M. (2015). The novel lipopeptide Poaeamide of the endophyte Pseudomonas poae RE*1-1-14 is involved in pathogen suppression and root colonization. Molecular Plant-Microbe Interactions, 28(7), 800-810. https://doi.org/10.1094/MPMI-12-14-0406-R
  • Song, C., van der Voort, M., van de Mortel, J., Hassan, K., Elbourne, L. D. H., Paulsen, I. T., Loper, J. E., & Raaijmakers, J. (2015). The Rsm regulon of plant growth-promoting Pseudomonas fluorescens SS101: role of small RNAs in regulation of lipopeptide biosynthesis. Microbial Biotechnology, 8(2), 296-310. https://doi.org/10.1111/1751-7915.12190
  • Ho, A., Reim, A., Kim, S. Y., Meima-Franke, M., Termorshuizen, A. J., De Boer, W., Van der Putten, W. H., & Bodelier, P. L. E. (2015). Unexpected stimulation of soil methane uptake as emergent property of agricultural soils following bio-based residue application. Global Change Biology, 21(10), 3864-3879. https://doi.org/10.1111/gcb.12974
  • Navarrete, A. A., Soares, T., Rosetto, R., Van Veen, J. A., Tsai, S. M., & Kuramae, E. E. (2015). Verrucomicrobial community structure and size as indicators for changes in chemical factors linked to soil fertility. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 108(3), 741-752. https://doi.org/10.1007/s10482-015-0530-3
  • Schmidt, R., Cordovez, V., De Boer, W., Raaijmakers, J., & Garbeva, P. (2015). Volatile affairs in microbial interactions. ISME Journal, 9, 2329-2335. https://doi.org/10.1038/ismej.2015.42
  • Tyc, O., Zweers, H., De Boer, W., & Garbeva, P. V. (2015). Volatiles in inter-specific bacterial interactions. Frontiers in Microbiology, 6, [2015.01412]. https://doi.org/10.3389/fmicb.2015.01412

Images

microbialgraphic.png

  • KNAW
  • intranet
  • privacy statement
  • login

NIOO KNAW