Department of Microbial Ecology

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

Recent publications (2015 - )

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
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
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
Moretti, L. G., Crusciol, C. A. C., Kuramae, E., Bossolani, J. W., Moreira, A., Costa, N. R.,... 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
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
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
Rossmann, M., Pérez-Jaramillo, J. E., Kavamura, V. N., Chiaramonte, J. B., Dumack, K., Fiore-Donno, A. M.,... 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
Francioli, D., van Rijssel, S. Q., van Ruijven, J., Termorshuizen, A. J., Cotton, T. E. A., Dumbrell, A. J.,... 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
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
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
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
Li, X. G., Garbeva, P., Liu, X., Klein Gunnewiek, P. J. A., Clocchiatti, A., Hundscheid, M. P. J.,... 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
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/B978-0-12-809633-8.20780-2
Sedlacek, C. J., McGowan, B., Suwa, Y., Sayavedra-Soto, L., Laanbroek, H. J., Stein, L. Y.,... 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.,... 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).
Perez Jaramillo, J. E. (2019). Impact of plant domestication on spermosphere and rhizosphere microbiome composition (PhD Thesis).
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.,... 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.,... 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.,... 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). Heidelberg: 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.,... 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.,... 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.,... 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.
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.,... 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.,... 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.,... 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).
Schlemper, T. R. (2019). The rhizomicrobiome of Sorghum : impact on plant growth and stress tolerance (PhD Thesis).
Teurlincx, S., Kuiper, J. J., Hoevenaar, E. C. M., Lurling, M., Brederveld, R. J., Veraart, A. J.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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.,... 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
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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
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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
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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
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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
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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.,... 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
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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
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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
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Suleiman, 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.2018.03.116
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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
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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
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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).
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
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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
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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
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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
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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
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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.
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.,... 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.,... 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.,... 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
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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
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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
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Schulz, K., Hunger, S., Brown, G. G., Tsai, S. M., Cerri, C. C., Conrad, R., & Drake, H. (2015). Methanogenic Food Web in Gut Contents of the Methane-Emitting Earthworm Eudrilus eugeniae from Brazil. ISME Journal, 9, 1778-1792. https://doi.org/10.1038/ismej.2014.262
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Song, C., Mazzola, M., Cheng, X., Oetjen, J., Alexandrov, T., Dorrestein, P. C.,... 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.
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.,... 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.,... 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.,... 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
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Department of Microbial Ecology

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

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