Publications
2019
Kuramae, E. E., & de Assis Costa, O. Y. (2019). Acidobacteria. In T. M. Schmidt [Ed.], Encyclopedia of Microbiology (Fourth Edition) (pp. 1-8). Oxford: Academic Press. https://doi.org/10.1016/B978-0-12-809633-8.20780-2Silva Costa, F., Figueiredo Sena Macedo, M. W., Araujo, A., Rodrigues, C., Kuramae, E. E., Alcanfor, S.,... 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/s42770-019-00111-4Cipriano, 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.6768Kurm, V., van der Putten, W. H., Weidner, S., Geisen, S., Snoek, B. L., Bakx, T., & Hol, W. H. G. (2019). Competition and predation as possible causes of bacterial rarity. Environmental Microbiology, 21(4), 1356-1368. https://doi.org/10.1111/1462-2920.14569Contreras-Dávila, C. A., Carrión, V. J., Vonk, V. R., Buisman, C. N. J., & Strik, D. P. B. T. B. (2019). Consecutive lactate formation and chain elongation to reduce exogenous chemicals input in repeated-batch food waste fermentation. Water Research. https://doi.org/10.1016/j.watres.2019.115215Harkes, 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-yPerez 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/s40168-019-0727-1Drost, S. M., Rutgers, M., Wouterse, M., De Boer, W., & Bodelier, P. (2019). Decomposition of mixtures of cover crop residues increases microbial functional diversity. Geoderma. https://doi.org/10.1016/j.geoderma.2019.114060Cordovez, 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-090817-062524Qi, Y., Ossowicki, A., Yang, X., Huerta Lwanga, E., Dini-Andreote, F., Geissen, V., & Garbeva, P. (2019). Effects of plastic mulch film residues on wheat rhizosphere and soil properties. Journal of Hazardous Materials, Online. https://doi.org/10.1016/j.jhazmat.2019.121711Yan, 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.2019.107531da 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-ySilva, G. H. R., Sueitt, A. P. E., Haimes, S., Tripidaki, A., van Zwieten, R., & Fernandes, T. V. (2019). Feasibility of closing nutrient cycles from black water by microalgae-based technology. Algal Research, 44. https://doi.org/10.1016/j.algal.2019.101715Hannula, S. E., Zhu, F., Heinen, R., & Bezemer, T. M. (2019). Foliar-feeding insects acquire microbiomes from the soil rather than the host plant. Nature Communications, 10, [1254(2019)]. https://doi.org/10.1038/s41467-019-09284-wWagg, 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. https://doi.org/10.1038/s41467-019-12798-yMasteling, 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.2019.09.006in '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, Online, [AEM.01369-19]. https://doi.org/10.1128/AEM.01369-19Dignam, 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.2019.05.020Wilschut, R. A., Geisen, S., Martens, H. J., Kostenko, O., De Hollander, M., Ten Hooven, F. C.,... 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.14657Li, 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/s41396-018-0300-0Rosado, P. M., Leite, D. C. A., Duarte, G. A. S., Chaloub, R. M., Jospin, G., Nunes da Rocha, U.,... 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/s41396-018-0323-6Thakur, M. P., van der Putten, W. H., Cobben, M. M. P., Van Kleunen, M., & Geisen, S. (2019). Microbial invasions in terrestrial ecosystems. Nature Reviews Microbiology, Online, 621-631. https://doi.org/10.1038/s41579-019-0236-zCassman, 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/10.1111/1462-2920.14557Suleiman, 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.2019.133885Carrión, V. J., Perez Jaramillo, J. E., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz Buck, D.,... 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.aaw9285de Tender, C., Mesuere, B., van der Jeugt, F., Haegeman, A., Ruttink, T., Vandecasteele, B.,... 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-xHeinen, R., Biere, A., & Bezemer, T. M. (2019). Plant traits shape soil legacy effects on individual plant-insect interactions. Oikos, Online. https://doi.org/10.1111/oik.06812Zhao, Z-B., He, J-Z., Geisen, S., Han, L-L., Wang, J-T., Shen, J-P.,... Zhang, L-M. (2019). Protist communities are more sensitive to nitrogen fertilization than other microorganisms in diverse agricultural soils. Microbiome, 7(1). https://doi.org/10.1186/s40168-019-0647-0Gao, Z., Karlsson, I., Geisen, S., Kowalchuk, G., & Jousset, A. (2019). Protists: Puppet Masters of the Rhizosphere Microbiome. Trends in Plant Science, 24(2), 165-176. https://doi.org/10.1016/j.tplants.2018.10.011Ramirez, K. S., Snoek, L. B., Koorem, K., Geisen, S., Bloem, L. J., ten Hooven, F.,... van der Putten, W. H. (2019). Range-expansion effects on the belowground plant microbiome. Nature Ecology and Evolution. https://doi.org/10.1038/s41559-019-0828-zVeen, G. F., Snoek, B., Bakx-Schotman, J. M. T., Wardle, D. A., & van der Putten, W. H. (2019). Relationships between fungal community composition in decomposing leaf litter and home-field advantage effects. Functional Ecology, 33(8), 1524-1535. https://doi.org/10.1111/1365-2435.13351Wang, M., Ruan, W., Kostenko, O., Carvalho, S., Hannula, S. E., Mulder, P. P. J.,... Bezemer, T. M. (2019). Removal of soil biota alters soil feedback effects on plant growth and defense chemistry. New Phytologist, 221(3), 1478-1491. https://doi.org/10.1111/nph.15485Mendes, 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, In press. https://doi.org/10.3389/fmicb.2019.02252Chen, 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/s40168-019-0750-2Wilschut, R. A., van der Putten, W. H., Garbeva, P. V., Harkes, P., Konings, W., Kulkarni, P.,... 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-xWubs, E. R. J., van der Putten, W. H., Mortimer, S. R., Korthals, G. W., Duyts, H., Wagenaar, R., & Bezemer, T. M. (2019). Single introductions of soil biota and plants generate long-term legacies in soil and plant community assembly. Ecology Letters, 22(7). https://doi.org/10.1111/ele.13271Tyc, O., Putra, R., Gols, R., Harvey, J. A., & Garbeva, P. (2019). The ecological role of bacterial seed endophytes associated with wild cabbage in the United Kingdom. MicrobiologyOpen, in press. https://doi.org/10.1002/mbo3.954Thakur, M. P., Phillips, H. R. P., Brose, U., De Vries, F. T., Lavelle, P., Loreau, M.,... Cameron, E. K. (2019). Towards an integrative understanding of soil biodiversity. Biological Reviews, Online. https://doi.org/10.1111/brv.12567Thakur, M. P., & Geisen, S. (2019). Trophic regulations of the soil microbiome. Trends in Microbiology, 27(9). https://doi.org/10.1016/j.tim.2019.04.008Kuramae, E. E., Leite, M. F. A., Suleiman, A. K. A., Gough, C. M., Castillo, B., Faller, L.,... 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.2019.009792018
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/s41396-018-0234-6Schulz-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/s41396-017-0035-3Ma, H., Pineda, A. M., van der Wurff, A. W. G., & Bezemer, T. M. (2018). Carry-over effects of soil inoculation on plant growth and health under sequential exposure to soil-borne diseases. Plant and Soil, 433(1-2), 257-270. https://doi.org/10.1007/s11104-018-3837-9Benevenuto, 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.2018.00660Siegel-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.2018.00568Schlemper, 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/s00248-017-1108-6Huerta 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.2017.12.144Schmidt, R. L., Durling, M., de Jager, V. C. L., Menezes, R. C., Nordkvist, E., Svatos, A.,... 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/fiy078Lourenço, K. S., Dimitrov, M., Pijl, A. S., Soares, J. R., do Carmo, J. B., van Veen, J. A.,... 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.12519Meisner, 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.2018.00294Schlemper, 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.5346Heinen, R., Biere, A., Harvey, J. A., & Bezemer, T. M. (2018). Effects of soil organisms on aboveground plant-insect interactions in the field: patterns, mechanisms and the role of methodology. Frontiers in Ecology and Evolution, [106]. https://doi.org/10.3389/fevo.2018.00106Dini-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.2018.03.013Krause, 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/s41598-018-27168-9de 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/fix161Semchenko, M., Leff, J. W., Lozano, Y. M., Saar, S., Davison, J., Wilkinson, A.,... Bardgett, R. D. (2018). Fungal diversity regulates plant-soil feedbacks in temperate grassland. Science advances, 4(11), [eaau4578]. https://doi.org/10.1126/sciadv.aau4578Cassman, 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/s13068-018-1254-1Geesink, 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/fiy164Avalos 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.2018.02.011Liao, H., Lu, X., Rensing, C., Friman, V. P., Geisen, S., Chen, Z.,... Zhu, Y. (2018). Hyperthermophilic Composting Accelerates the Removal of Antibiotic Resistance Genes and Mobile Genetic Elements in Sewage Sludge. Environmental Science and Technology, 52(1), 266-276. https://doi.org/10.1021/acs.est.7b04483Le, 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.2018.03.014Lupatini, M., Korthals, G. W., Roesch, L. F. W., & Kuramae, E. E. (2018). Long-term farming systems modulate multi-trophic responses. Science of the Total Environment, 646, 480-490. https://doi.org/10.1016/j.scitotenv.2018.07.323Geisen, S., & Bonkowski, M. (2018). Methodological advances to study the diversity of soil protists and their functioning in soil food webs. Applied Soil Ecology, 123(February), -. https://doi.org/10.1016/j.apsoil.2017.05.021Costa, 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.2018.01636Heijboer, 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.2018.02860Armada, 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/fiy092Lourenço, 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.2018.00674Heinen, R., van der Sluijs, M., Biere, A., Harvey, J. A., & Bezemer, T. M. (2018). Plant community composition but not plant traits determine the outcome of soil legacy effects on plants and insects. Journal of Ecology, 106(3), 1217-1229. https://doi.org/10.1111/1365-2745.12907Wubs, J., & Bezemer, T. M. (2018). Plant community evenness responds to spatial plant-soil feedback heterogeneity primarily through the diversity of soil conditioning. Functional Ecology, 32(2), 509-521. https://doi.org/10.1111/1365-2435.13017Bezemer, T. M., Jing, J., Bakx-Schotman, J. M. T., & Bijleveld, E-J. (2018). Plant competition alters the temporal dynamics of plant-soil feedbacks. Journal of Ecology, 106(6), 2287-2300. https://doi.org/10.1111/1365-2745.12999Schnyder, 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.2138Cordovez, V., Schop, S., Hordijk, C. A., Dupré de Boulois, H., Coppens, F., Hanssen, I.,... 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.01865-18Suleiman, A. K. A., Lourenço, K. S., Pitombo, L., Mendes, L. W., Roesch, L. F. W., Pijl, A. S.,... 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.2018.03.116Lourenço, 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/s40168-018-0525-1van 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.2018.01714Oyserman, 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.2017.11.023Berg, G., & Raaijmakers, J. M. (2018). Saving Seed Microbiomes. ISME Journal, 12, 1167-1170. https://doi.org/10.1038/s41396-017-0028-2Kurm, V., van der Putten, W. H., Pineda, A. M., & Hol, W. H. G. (2018). Soil microbial species loss affects plant biomass and survival of an introduced bacterial strain, but not inducible plant defences. Annals of Botany, 121(12), 311-319. [mcx162]. https://doi.org/10.1093/aob/mcx162Zhu, F., Heinen, R., van der Sluijs, M., Raaijmakers, C. E., Biere, A., & Bezemer, T. M. (2018). Species-specific plant soil feedbacks affect herbivore-induced gene expression and defense chemistry in Plantago lanceolata. Oecologia, 188(3), 801-811. https://doi.org/10.1007/s00442-018-4245-9Ma, H., Pineda, A. M., van der Wurff, A. W. G., & Bezemer, T. M. (2018). Synergistic and antagonistic effects of mixing monospecific soils on plant-soil feedbacks. Plant and Soil, 429(1-2), 271-279. https://doi.org/10.1007/s11104-018-3694-6Wubs, J., & Bezemer, T. M. (2018). Temporal carry-over effects in sequential plant-soil feedbacks. Oikos, 127(2), 220-229. https://doi.org/10.1111/oik.04526Griffiths, B. S., de Groot, G. A., Laros, I., Stone, D., & Geisen, S. (2018). The need for standardisation: Exemplified by a description of the diversity, community structure and ecological indices of soil nematodes. Ecological Indicators, 87, 43 - 46. https://doi.org/10.1016/j.ecolind.2017.12.002Perez 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-z2017
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-yReis 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)60415-6Koorem, K., Tulva, I., Davison, J., Jairus, T., Öpik, M., Vasar, M.,... Moora, M. (2017). Arbuscular mycorrhizal fungal communities in forest plant roots are simultaneously shaped by host characteristics and canopy-mediated light availability. Plant and Soil, 410(1-2), 259-271. https://doi.org/10.1007/s11104-016-3004-0Kielak, A. M., Castellane, T. C. L., Campanharo, J. C., Colnago, L. A., Costa, O. Y. A., Corradi da Silva, M. L.,... Kuramae, E. E. (2017). Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications. Scientific Reports, 7, [41193]. https://doi.org/10.1038/srep41193Dassen, 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.14175Yan, 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.2016.108Van 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.2017.08.018Schulz-Bohm, K., Tyc, O., De Boer, W., Peereboom, N., Debets, F., Zaagman, N.,... 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.2016.07.011Cheng, 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/10.1111/1462-2920.13927Mendes, L. W., Raaijmakers, J. M., De Hollander, M., Mendes, R., & Tsai, S. M. (2017). 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.2017.158Perez Jaramillo, J. E., Carrion, V. J., Bosse, M., Ferrão, L. F. V., De Hollander, M., Garcia, A. A. F.,... 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.2017.85Kurm, 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.1670Kip, 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/s41598-017-11244-7Steenbergh, 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 Publishing. 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/srep42634Ho, 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/fix006Schlemper, 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/fix096Rasmann, S., Bennett, A. E., Biere, A., Karley, A., & Guerrieri, E. (2017). Root symbionts: Powerful drivers of plant above- and belowground indirect defenses. Insect Science, 24(6), 947-960. https://doi.org/10.1111/1744-7917.12464Geisen, S., Kostenko, O., Cnossen, M. C., ten Hooven, F. C., Vreš, B., & van Der Putten, W. H. (2017). Seed and root endophytic fungi in a range expanding and a related plant species. Frontiers in Microbiology, 8, [01645]. https://doi.org/10.3389/fmicb.2017.01645Hannula, 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.2017.90Gundale, M. J., Wardle, D. A., Kardol, P., Van der Putten, W. H., & Lucas, R. W. (2017). Soil handling methods should be selected based on research questions and goals: Letters. New Phytologist, 216(1), 18-23. https://doi.org/10.1111/nph.14659Lupatini, 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.2016.02064van Gils, S., Tamburini, G., Lorenzo, M., Biere, A., Van Agtmaal, M., Tyc, O.,... 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.0179695Geisen, S., Mitchell, E. A. D., Wilkinson, D. M., Adl, S., Bonkowski, M., Brown, M. W.,... Lara, E. (2017). Soil protistology rebooted: 30 fundamental questions to start with. Soil Biology & Biochemistry, 111, 94-103. https://doi.org/10.1016/j.soilbio.2017.04.001Van 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.2017.08.006Pineda, A., Kaplan, I., & Bezemer, T. M. (2017). Steering soil microbiomes to suppress aboveground insect pests. Trends in Plant Science, 22(9), 770-778. https://doi.org/10.1016/j.tplants.2017.07.002Dimitrov, 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.2915Tyc, 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.2016.12.002Simon, J-C., Biere, A., & Sugio, A. (2017). The promises and challenges of research on plant–insect–microbe interactions: Preface. Insect Science, 24(6), 904-909. https://doi.org/10.1111/1744-7917.12536Jousset, A., Bienhold, C., Chatzinotas, A., Gallien, L., Gobet, A., Kurm, V.,... Hol, W. H. G. (2017). Where less may be more: How the rare biosphere pulls ecosystems strings. ISME Journal, 11, 853-862. https://doi.org/10.1038/ismej.2016.1742016
Ho, A., Angel, R., Veraart, A. J., Daebeler, A., Jia, Z., Kim, S. Y.,... 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.2016.01285Rice, M. C., Norton, J. M., Valois, F., Bollmann, A., Bottomley, P. J., Klotz, M. G.,... 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/s40793-016-0168-4Adam, E., Groenenboom, A. E., Kurm, V. K., Rajewska, M., Schmidt, R. L., Tyc, O.,... 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.2016.01079Nguyen, D., Melnik, A. V., Koyama, N., Lu, X., Schorn, M., Fang, J.,... 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.2016.197Cipriano, M. A. P., Lupatini, M., Santos, L., Silva, M. D., Roesch, L. F. W., Destefano, 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/fiw197Soares, J. R., Cassman, N., Kielak, A. M., Pijl, A. S., do Carmo, J. B., Lourenço, K. S.,... 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/srep30349Campanharo, 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/fnw245Van 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/ecs2.1393Weisskopf, L., Garbeva, P. V., Ryu, C-M., & Raaijmakers, J. M. (2016). Smelly fumes: volatile-mediated communication between bacteria and other organisms. Frontiers in Microbiology, 7, [2031]. https://doi.org/10.3389/fmicb.2016.02031Tripathi, 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
