Mattias de Hollander
Bio-informaticianAnimal EcologyAquatic EcologyMicrobial EcologyTerrestrial Ecology |
Research themes
Research expertiseBioinformatics Genomics High-throughput amplicon sequencing Linux Metagenomics Metatranscriptomics Python R Snakemake meta-analysis
Page last updated: 14-09-2020
PROFESSIONAL APPOINTMENTS
| 06.2011 - present | Bioinformatician, Netherlands Institute of Ecology (NIOO-KNAW) |
| 12.2010 - 06.2011 | Bioinformatician, Free University (VU) Amsterdam / Netherlands Institute of Ecology (NIOO-KNAW) |
EDUCATION
| 2008 - 2010 | MSc Bioinformatics, Wageningen University, the Netherlands |
| 2004 - 2008 | Bachelor of Applied Science (B AS), CUM LAUDE, BioInformatics, University of Applied Sciences (Hogeschool),Leiden |
| 2003 - 2004 | Scheikundige Technologie/Bioproces Technologie, TU Delft |
| 1997 - 2003 | Diploma Voorbereidend Wetenschappelijk Onderwijs (VWO), Natuur en Techniek, Rijnlands Lyceum, Oegstgeest |
RESEARCH INTERESTS
- Costa, O. Y. A., De Hollander, M., Pijl, A., Liu, B., & Kuramae, E. (2020). Cultivation-independent and cultivation-dependent metagenomes reveal genetic and enzymatic potential of microbial community involved in the degradation of a complex microbial polymer. Microbiome, in press, [76]. https://doi.org/10.1186/s40168-020-00836-7
- 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
- Wilschut, R. A., Geisen, S., Martens, H. J., Kostenko, O., De Hollander, M., Ten Hooven, F. C., Weser, C., Snoek, B., Bloem, J., Caković, D., Čelik, T., Koorem, K., Krigas, N., Manrubia, M., Ramirez, K. S. R., Tsiafouli, M. A., Vreš, B., & van der Putten, W. H. (2019). Latitudinal variation in soil nematode communities under climate warming-related range-expanding and native plants. Global Change Biology, 25(8), 2714-2726. https://doi.org/10.1111/gcb.14657
- Carrión, V. J., Perez Jaramillo, J. E., Cordovez, V., Tracanna, V., De Hollander, M., Ruiz Buck, D., Mendes, L. W., van IJcken, W. F. J., Gómez Expósito, R., Elsayed, S. S., Mohanraju, P., Arifah, A., van der Oost, J., Paulson, J. N., Mendes, R., van Wezel, G., Medema, M. H., & Raaijmakers, J. M. (2019). Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome. Science, 366(6465), 606-612. https://doi.org/10.1126/science.aaw9285
- Ramirez, K. S., Knight, C. G., de Hollander, M., Brearley, F. Q., Constantinides, B., Cotton, A., Creer, S., Crowther, T. W., Davison, J., Delgado-Baquerizo, M., Dorrepaal, E., Elliott, D. R., Fox, G., Griffiths, R. I., Hale, C., Hartman, K., Houlden, A., Jones, D. L., Krab, E. J.,... De Vries, F. T. (2018). Detecting macroecological patterns in bacterial communities across independent studies of global soils. Nature Microbiology, 3, 189-196. https://doi.org/10.1038/s41564-017-0062-x
- 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
- Perez Jaramillo, J. E., Carrion, V. J., De Hollander, M., & Raaijmakers, J. M. (2018). The wild side of plant microbiomes. Microbiome, 6(143). https://doi.org/10.1186/s40168-018-0519-z
- 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
- Yan, Y., Kuramae, E. E., De Hollander, M., Klinkhamer, P. G. L., & van Veen, J. A. (2017). Functional traits dominate the diversity-related selection of bacterial communities in the rhizosphere. ISME Journal, 11, 56-66. https://doi.org/10.1038/ismej.2016.108
- Van der Wal, A., Klein Gunnewiek, P. J. A., De Hollander, M., & De Boer, W. (2017). Fungal diversity and potential tree pathogens in decaying logs and stumps. Forest Ecology and Management, 406, 266-273. https://doi.org/10.1016/j.foreco.2017.08.018
- Perez Jaramillo, J. E., Carrion, V. J., Bosse, M., Ferrão, L. F. V., De Hollander, M., Garcia, A. A. F., Ramirez, C. A., Mendez, R., & Raaijmakers, J. M. (2017). Linking rhizosphere microbiome composition of wild and domesticated Phaseolus vulgaris to genotypic and root phenotypic traits. ISME Journal, 11, 2244-2257. https://doi.org/10.1038/ismej.2017.85
- Kip, N., Jansen, S., Leite, M. F. A., De Hollander, M., Afanasyev, M., Kuramae, E. E., & van Veen, J. A. (2017). Methanogens predominate in natural corrosion protective layers on metal sheet piles. Scientific Reports, 7, [11899]. https://doi.org/10.1038/s41598-017-11244-7
- Hannula, S. E., Morriën, E., De Hollander, M., van der Putten, W. H., van Veen, J. A., & De Boer, W. (2017). Shifts in rhizosphere fungal community during secondary succession following abandonment from agriculture. ISME Journal, 11, 2294-2304. https://doi.org/10.1038/ismej.2017.90
- Lupatini, M., Korthals, G. W., De Hollander, M., Janssens, T. K. S., & Kuramae, E. E. (2017). Soil microbiome is more heterogeneous in organic than in conventional farming system. Frontiers in Microbiology, 7, [2064]. https://doi.org/10.3389/fmicb.2016.02064
- Morriën, E., Hannula, S. E., Snoek, B., Helmsing, N. R., Zweers, H., De Hollander, M., Lujan Soto, R., Bouffaud, M. L., Buée, M., Dimmers, W., Duyts, H., Geisen, S., Girlanda, M., Griffiths, R. I., Jørgensen, H-B., Jensen, J., Plassart, P., Redecker, D., Schmelz, R. M.,... van der Putten, W. H. (2017). Soil networks become more connected and take up more carbon as nature restoration progresses. Nature Communications, 8, [14349]. https://doi.org/10.1038/ncomms14349
- Dimitrov, M. R., Veraart, A. J., De Hollander, M., Smidt, H., van Veen, J. A., & Kuramae, E. E. (2017). Successive DNA extractions improve characterization of soil microbial communities. PeerJ, 5, [e2915]. https://doi.org/10.7717/peerj.2915
- Pitombo, L., do Carmo, J. B., De Hollander, M., Rosetto, R., Lopez, M. V., Cantarella, H., & Kuramae, E. E. (2016). Exploring soil microbial 16S rRNA sequence data to increase carbon yield and nitrogen efficiency of a bioenergy crop. Global Change Biology Bioenergy, 8(5), 867-879. https://doi.org/10.1111/gcbb.12284
- Cassman, N., Leite, M. F. A., Pan, Y., De Hollander, M., van Veen, J. A., & Kuramae, E. E. (2016). Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland. Scientific Reports, 6, [23680]. https://doi.org/10.1038/srep23680
- 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, 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
- Navarrete, A. A., Tsai, S. M., Mendes, L. W., Faust, K., De Hollander, M., Cassman, N., Raes, J., Van Veen, J. A., & Kuramae, E. E. (2015). Soil microbiome responses to the short-term effects of Amazonian deforestation. Molecular Ecology, 24(10), 2433-2448. https://doi.org/10.1111/mec.13172
- Hiltemann, S., Mei, H., de Hollander, M., Palli, I., van der Spek, P., Jenster, G., & Stubbs, A. (2014). CGtag: complete genomics toolkit and annotation in a cloud-based Galaxy: Technical Note. GigaScience, 3, [1]. https://doi.org/10.1186/2047-217X-3-1
- Pan, Y., Cassman, N., De Hollander, M., Mendes, L. W., Korevaar, H., Geerts, R. H. E. M., Van Veen, J. A., & Kuramae, E. E. (2014). Impact of long term N, P, K and NPK fertilization on the composition and potential functions of bacterial community in grassland soil. FEMS Microbiology Ecology, 90(1), 195-205. https://doi.org/10.1111/1574-6941.12384
- Navarrete, A. A., Kuramae, E. E., De Hollander, M., Pijl, A. S., Van Veen, J. A., & Tsai, S. M. (2013). Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiology Ecology, 83(3), 607-621. https://doi.org/10.1111/1574-6941.12018
- Kuramae, E. E., Hillekens, R. H. E., De Hollander, M., Van der Heijden, M. G. A., Van den Berg, M., Van Straalen, N. M., & Kowalchuk, G. A. (2013). Structural and functional variation in soil fungal communities associated with litter bags containing maize. FEMS Microbiology Ecology, 84(3), 519-531. https://doi.org/10.1111/1574-6941.12080
- Kuramae, E. E., Verbruggen, E., Hillekens, R. H. E., De Hollander, M., Röling, W. F. M., Van der Heijden, M. G. A., & Kowalchuk, G. A. (2013). Tracking fungal community responses to maize plants by DNA- and RNA-based pyrosequencing. PLoS One, 8(7), [e69973]. https://doi.org/10.1371/journal.pone.0069973
- Vos, M., Quince, C., Pijl, A. S., De Hollander, M., & Kowalchuk, G. A. (2012). A comparison of rpoB and 16S rRNA as markers in pyrosequencing studies of bacterial diversity. PLoS One, 7(2), [e30600]. https://doi.org/10.1371/journal.pone.0030600
- Verbruggen, E., Kuramae, E. E., Hillekens, R. H. E., De Hollander, M., Kiers, E. T., Roling, W. F. M., Kowalchuk, G. A., & Van der Heijden, M. G. A. (2012). Testing Potential Effects of Maize Expressing the Bacillus thuringiensis Cry1Ab Endotoxin (Bt Maize) on Mycorrhizal Fungal Communities via DNA- and RNA-Based Pyrosequencing and Molecular Fingerprinting. Applied and Environmental Microbiology, 78(20), 7384-7392. https://doi.org/10.1128/AEM.01372-12
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- Costa, O. Y. A. (Author/Maker), De Hollander, M. (Author/Maker), Pijl, A. (Author/Maker), Liu, B. [Developer], & Kuramae, E. [Developer]. (2020). Video Byte: Forest floor microbes produce tough biofilm breaker: Exploring Solutions from Nature. Digital or Visual Products, Research Square. https://www.youtube.com/watch?v=FJ8qBKkbik8&feature=youtu.be
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