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 - )

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
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
Garbeva, P., & Weisskopf, L. (2019). Airborne medicine - Bacterial volatiles and their influence on plant health. New Phytologist, Online. https://doi.org/10.1111/nph.16282
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
Drost, 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.2019.114060
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
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
Moretti, L. G., Crusciol, C. A. C., Kuramae, E., Bossolani, J. W., Moreira, A., Costa, N. R.,... Hungria, M. (2019). Effects of growth-promoting bacteria on soybean root activity, plant development and yield. Agronomy Journal, Online. https://doi.org/10.1002/agj2.20010
Qi, 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.2019.121711
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. 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
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
Patyshakuliyeva, A., Falkoski, D. L., Wiebenga, A., Timmermans, K., & Vries, R. P. D. (2019). Macroalgae Derived Fungi Have High Abilities to Degrade Algal Polymers. Microorganisms, 8(1). https://doi.org/10.3390/microorganisms8010052
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.
Avalos, M., Garbeva, P., Raaijmakers, J. M., & van Wezel, G. P. (2019). Production of glycine-derived ammonia as a low-cost and long-distance antibiotic strategy by Streptomyces. ISME Journal, Online. https://doi.org/10.1101/450833, https://doi.org/10.1038/s41396-019-0537-2
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
Hannula, E., Ma, H., Perez Jaramillo, J. E., Pineda, A. M., & Bezemer, T. M. (2019). Structure and ecological function of the soil microbiome affecting plant-soil feedbacks in the presence of a soil-borne pathogen. Environmental Microbiology, Online. https://doi.org/10.1111/1462-2920.14882
Tyc, 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/mbo3.954
Clocchiatti, A., Hannula, E., Van den Berg, M., Korthals, G., & De Boer, W. (2019). The hidden potential of saprotrophic fungi in arable soil: patterns of short-term stimulation by organic amendments. Applied Soil Ecology. https://doi.org/10.1016/j.apsoil.2019.103434
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
Li, X. G., Garbeva, P., Liu, X., Klein Gunnewiek, P. J. A., Clocchiatti, A., Hundscheid, M. P. J.,... De Boer, W. (Accepted/In press). Volatile-mediated antagonism of soil bacterial communities against fungi. Environmental Microbiology, Online. https://doi.org/10.1111/1462-2920.14808
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
Lourenço, 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.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
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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
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.
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.,... 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.,... 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.,... 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). Wallingford, UK: CABI Publisher.
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.,... 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).
Medema, M. H., Kottmann, R., Yilmaz, P., Cummings, M., Biggins, J. B., Blin, K.,... 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.,... 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
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.,... 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.,... 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
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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
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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
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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
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Department of Microbial Ecology

The power of the small

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

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Department of Microbial Ecology

The power of the small

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

Recent publications (2015 - )

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