Dr. Eiko Kuramae
ResearcherMicrobial Ecology |
Research expertiseBioinformatics Environmental genomics Genomics Microbial network Soil microbial ecology
Page last updated: 22-11-2019
PROFESSIONAL APPOINTMENTS
2012 - to date: Senior Scientist and Project Leader, Netherlands Institute of Ecology (NIOO-KNAW)
2010 - 2011: Scientist, Netherlands Institute of Ecology (NIOO-KNAW)
2009 - 2011: Research Scientist, Free University Amsterdam (VU)
2007 - 2008: Post-doctoral researcher, Netherlands Institute of Ecology (NIOO-KNAW)
2003 - 2007: Post-doctoral researcher, CBS-Fungal Biodiversity Centr
2001 - 2002: Assistant professor, University of Sao Paulo State (UNESP), Brazil
1996 - 2000: Young scientist, University of Sao Paulo State (UNESP), Brazil
1992 - 1995: PhD Biological Sciences, Genetics, University of Sao Paulo State (UNESP), Brazil
1991 - 1992: Research Scientist, Agroflora - Plant Seed Company, Brazil
1987 - 1991: Agronomist, Brazilian Agriculture Cooperative of Cotia, Brazil
EDUCATION
1992 – November 1995
PhD in Biological Sciences, area: Genetics University of Sao Paulo State (UNESP) Botucatu, Sao Paulo, Brazil
September 1989 - July 1991
MSc Molecular BiologyVrije Universiteit Brussel (VUB), Belgium
March 1984 - December 1987
Agronomic EngineeringUniversity of Sao Paulo State (UNESP) Botucatu, Brazil
AWARDS
Prize CAPES (Coordination for the Improvement of Higher Education Personnel) Honor Award 2015 to Lucas W. Mendes for his PhD thesis "Metagenome of Amazon forest conversion: impacts on soil-borne microbial diversity and functions" of . The studies were carried out at ME-NIOO/KNAW and CENA/USP. The promoter Sui M. Tsai (Brazil) and co-promoter Eiko E. Kuramae (The Netherlands) were also honored.
Prize CAPES of the Brazilian Ministry of Education to the Best PhD thesis in agro sciences defended in 2013. PhD Acacio Navarrete and promoter/co-promoters (Tsai SM, van Veen JA, Kuramae EE )
Special Visiting Researcher - Sciences Without Borders (CAPES), Catholic University of Brasilia, Post Graduate program in Genomics and Biotechnology, Brazil (2014-2018)
Special Visiting Researcher - Sciences Without Borders, University of Maranhão, Post Graduate program in Agroecology, Brazil (2013-2016)
Award “Summa Phytopathologica” (2005)
Scientific and Technological Honour Award from the Brazilian President of Republic Fernando Henrique Cardoso - Xylella fastidiosa Genome (2000)
Honour Award from the University of Sao Paulo State (UNESP, Brazil) as coordinator of sequencing laboratory BF and annotation of Xylella fastidiosa Genome Project (2000)
Young Geneticist Award by Brazilian Genetics Society (1996)
Award Young Scientist for Emergent Centres FAPESP (1996)
REVIEWING ACTIVITIES
The ISME journal, FEMS Microbiology Ecology, Applied and Environmental Microbiology, Environmental Microbiology, European Journal of Soil Biology, Ecosystems, Global Change Biology, Molecular Diversity Preservation International, Journal of Ecology, FEMS Microbiology Letters, BMC Genomics, In Silico Biology, BMC Evolutionary Biology, Summa Phytopathologica, Revista Brasileira de Fruticultura, GigaScience, Pedosphere.
CURRENT RESEARCH TOPICS AND INTERESTS
Research theme: Ecosystem functioning and biodiversity in soil
Soil-borne microbes perform a wide range of essential services to the sustainable function of all ecosystems, by acting as the primary driving agents of nutrient cycling; regulating the dynamics of soil organic matter, soil carbon sequestration and greenhouse gas emission; affecting soil physical structure and water regimes; enhancing the amount and efficiency of nutrient acquisition by the vegetation through symbiotic and associative microorganisms; influencing plant health through the interaction of pathogens and pests with their natural predators, parasites and associate endophytes. Therefore, understanding human impacts on the soil-borne microbial communities and functions is of utmost practical and scientifical importance. My group focuses on studies on C, N, P and S biogeochemistry, greenhouse gases (GHG) emission and soil fertility to better understand the contribution of the microbes (bacteria, archaea and fungi) on the ecology and quality of the soil under the sustainable practices. Our major research topics are:
(I) Land Use Changes and (II) Global Climate Change
The impacts of agriculture practices and the conversion of forest to agriculture on soil-borne microbial community composition and function, and the consequences in ecosystem functioning are not known. The agriculture practices (liming, nutrients, etc) have large impact on soil biochemistry that certainly has huge impact on belowground inhabitants, and consequences in GHG emissions, which are the contributors for global warming. Therefore our studies focus on determine (1) microbial taxonomical and functional bio-indicators to predict the consequences of changes in land use due to abandoning of agricultural land (biodiversity restoration practice), deforestation (forest converted to agriculture), sustainable agriculture (Amazon Black Earth as model), sustainable biomass production for the bio-based economy, and changes in arable cropping regimes; (2) genes in key functions (nitrification, nitrogen fixation, denitrification, methane oxidation), recalcitrant organic matter decomposition most indicative of specific soil status, in particular in soils with crops for biofuelbiomass production; (3) determine functional bio-indicators involved in the emission/sequestration of greenhouse gasses (CO2, CH4 and N2O); (4) develop high throughput platform to assess and monitor bio-indicators.
(III) Microbial diversity loss
Loss of soil-borne microbial diversity versus plant production (plant biomass quality and secondary metabolites). Plant defense may change when they are exposure to varying soil microbial community range of microbial diversities. Using metagenomics and metatranscriptomics approaches we study the effect of microbial community diversity loss by decreasing richness through inoculating in the sterile soil with a serial dilution of microbial suspensions from the same unsterilized soil.
(IV) Bioinformatics
With the advent of the post-genomic era and the access to the bioinformatics, the information that is made available can be transferred immediately to the bench, allowing the understanding of the functionality of the biological systems for the conservation of the microbial biodiversity and its use for monitoring the soil quality. We focus on implementation of computacional/bioinformatics/statistical tools to analyze genomics/environmental genomics (next generation sequencing, microarrays, metagenomics) and post-genomics (metatranscriptomics) data and environmental/soil physicochemical data into soil microbial ecology.
CURRENT SUPERVISION
Post Doctorate
Nidia Costa
Aleksandrina Patyshakuliyeva
PhD:
Han Wang. (2019-2022). Utrecht University, The Netherlands
Cristina Rotoni. (2019-2023). Utrecht University, The Netherlands
Laura Migliorini. (2019-2022). University of Campinas (UNICAMP, Brazil)
Joao Bossolani. (2017-2020). University of Sao Paulo State (UNESP, Brazil
Luiz Moretti . (2017-2020). University of Sao Paulo State (UNESP. Brazil)
Letusa Momesso. (2017-2020). Utrecht University, The Netherlands
Ohana Costa. (2016-2020). Leiden University, The Netherlands
Marcio Leite. (2014-2019). Utrecht University, The Netherlands
FORMER SUPERVISION (1998-2006)
Post Doctorate in functional genomics/metagenomics (11)
PhD in Metagenomics (14)
PhD in Plant Pathology and Genetics (5)
MSC in Metagenomics (4)
MSc in Plant Pathology and Genetics (14)
Bioinformatics and meta-genomics/transcriptomics (2)
Hooghschool (10)
Scientific Initiation - Brazil (5)
Genomics training for undergraduate students, Brazil (16)
Genomics training for technician - Brazil (3)
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- 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
- Costa, O. Y. A., Raaijmakers, J. M., & Kuramae, E. E. (2018). Microbial extracellular polymeric substances – ecological functions and impact on soil aggregation. Frontiers in Microbiology, 9, [1636]. https://doi.org/10.3389/FMICB.2018.01636
- Armada, E., Leite, M. F. A., Medina Penafiel, M. A., Azcón, R., & Kuramae, E. E. (2018). Native bacteria promote plant growth under drought stress condition without impacting the rhizomicrobiome. FEMS Microbiology Ecology, 94(7), [fiy092]. https://doi.org/10.1093/femsec/fiy092
- Lourenço, K. S., Cassman, N., Pijl, A. S., van Veen, J. A., Cantarella, H., & Kuramae, E. E. (2018). Nitrosospira sp. govern nitrous oxide emissions in a tropical soil amended with residues of bioenergy crop. Frontiers in Microbiology, 9, [674]. https://doi.org/10.3389/fmicb.2018.00674
- 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
- Lourenço, K. S., Suleiman, A. K. A., Pijl, A. S., van Veen, J. A., Cantarella, H., & Kuramae, E. E. (2018). Resilience of the resident soil microbiome to organic and inorganic amendment disturbances and to temporary bacterial invasion. Microbiome, 6, [142]. https://doi.org/10.1186/s40168-018-0525-1
- 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
- Kielak, A. M., Castellane, T. C. L., Campanharo, J. C., Colnago, L. A., Costa, O. Y. A., Corradi da Silva, M. L.,... Kuramae, E. E. (2017). Characterization of novel Acidobacteria exopolysaccharides with potential industrial and ecological applications. Scientific Reports, 7, [41193]. https://doi.org/10.1038/srep41193
- 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
- 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
- Leite, M. F. A., Pan, Y., Bloem, J., ten Berge, H., & Kuramae, E. E. (2017). Organic nitrogen rearranges both structure and activity of the soil-borne microbial seedbank. Scientific Reports, 7, [42634]. https://doi.org/10.1038/srep42634
- Schlemper, T. R., Leite, M. F. A., Reis Lucheta, A., Shimels, M., Bouwmeester, H. J., van Veen, J. A., & Kuramae, E. E. (2017). Rhizobacterial community structure differences among sorghum cultivars in different growth stages and soils. FEMS Microbiology Ecology, 93(8), [fix096]. https://doi.org/10.1093/femsec/fix096
- 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
- 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
- Kielak, A. M., Cipriano, M. A. P., & Kuramae, E. E. (2016). Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Archives of Microbiology, 198(December), 987-993. https://doi.org/10.1007/s00203-016-1260-2
- Kielak, A., Scheublin, T., Mendes, L. W., Van Veen, J. A., & Kuramae, E. E. (2016). Bacterial community succession in pine-wood decomposition. Frontiers in Microbiology, 7, [00231]. https://doi.org/10.3389/fmicb.2016.00231
- Pitombo, L., do Carmo, J. B., De Hollander, M., Rosetto, R., Lopez, M. V., Cantarella, H., & Kuramae, E. E. (2016). Exploring soil microbial 16S rRNA sequence data to increase carbon yield and nitrogen efficiency of a bioenergy crop. Global Change Biology Bioenergy, 8(5), 867-879. https://doi.org/10.1111/gcbb.12284
- Reis Lucheta, A., Souza Cannavan, F. S., Roesch, L., Tsai, S. M., & Kuramae, E. E. (2016). Fungal community assembly in the Amazonian Dark Earth. Microbial Ecology, 71(May), 962-973. https://doi.org/10.1007/s00248-015-0703-7
- Cipriano, M. A. P., Lupatini, M., Santos, L., Silva, M. D., Roesch, L. F. W., Destefano, S.,... Kuramae, E. E. (2016). Lettuce and rhizosphere microbiome responses to growth promoting Pseudomonas species under field conditions. FEMS Microbiology Ecology, 92(12), [fiw197]. https://doi.org/10.1093/femsec/fiw197
- Soares, J. R., Cassman, N., Kielak, A. M., Pijl, A. S., do Carmo, J. B., Lourenço, K. S.,... Kuramae, E. E. (2016). Nitrous oxide emission related to ammonia-oxidizing bacteria and mitigation options from N fertilization in a tropical soil. Scientific Reports, 6, [30349]. https://doi.org/10.1038/srep30349
- Campanharo, J. C., Kielak, A. M., Castellane, T. C., Kuramae, E. E., & Lemos, E. G. (2016). Optimized medium culture for Acidobacteia subdivision 1 strains. FEMS Microbiology Letters, 363(21), [fnw245]. https://doi.org/10.1093/femsle/fnw245
- Gonzalez, D., Rodriguez-Carres, M., Boekhout, T., Stalpers, J., Kuramae, E. E., Nakatani, A. K.,... Cubeta, M. A. (2016). Phylogenetic relationships of Rhizoctonia fungi within the Cantharellales. Fungal Biology, 120(4), 603-619. https://doi.org/10.1016/j.funbio.2016.01.012
- Cassman, N., Leite, M. F. A., Pan, Y., De Hollander, M., van Veen, J. A., & Kuramae, E. E. (2016). Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland. Scientific Reports, 6, [23680]. https://doi.org/10.1038/srep23680
- Suleiman, A. K. A., Gonzatto, R., Aita, C., Lupatini, M., Jacques, R., Kuramae, E. E.,... Roesch, L. (2016). Temporal variability of soil microbial communities after application of dicyandiamide-treated swine slurry and mineral fertilizers. Soil Biology & Biochemistry, 97, 71-82. https://doi.org/10.1016/j.soilbio.2016.03.002
- Kielak, A. M., Barreto, C. C., Kowalchuk, G. A., van Veen, J. A., & Kuramae, E. E. (2016). The ecology of Acidobacteria: moving beyond genes and genomes. Frontiers in Microbiology, [744]. https://doi.org/10.3389/fmicb.2016.00744
- 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
- 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. 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.
- 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
- 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
- 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
- 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.,... 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
- Navarrete, A. A., Soares, T., Rosetto, R., Van Veen, J. A., Tsai, S. M., & Kuramae, E. E. (2015). Verrucomicrobial community structure and size as indicators for changes in chemical factors linked to soil fertility. Antonie Van Leeuwenhoek International Journal of General and Molecular Microbiology, 108(3), 741-752. https://doi.org/10.1007/s10482-015-0530-3
- Pan, Y., Cassman, N., De Hollander, M., Mendes, L. W., Korevaar, H., Geerts, R. H. E. M.,... 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
- Lupatini, M., Suleiman, A., Jacques, R., Antoniolli, Z., de Siqueira Ferreira, A., Kuramae, E. E., & Roesch, L. (2014). Network topology reveals high connectance levels and few key microbial genera within soils. Frontiers in Environmental Science, 2, [10]. https://doi.org/10.3389/fenvs.2014.00010
- Kuramae, E. E., Zhou, J., Kowalchuk, G. A., & Van Veen, J. A. (2014). Soil-borne microbial functional structure across different land uses. The Scientific World Journal, 2014, 216071. https://doi.org/10.1155/2014/216071
- Varon-Lopez, M., Dias, A. C. F., Fasanella, C. C., Durrer, A., Melo, I. S., Kuramae, E. E., & Andreote, F. D. (2014). Sulphur-oxidising and Sulphate-reducing Communities in Brazilian Mangrove Sediments. Environmental Microbiology, 16(3), 845-855. https://doi.org/10.1111/1462-2920.12237
- Mendes, L. W., Kuramae, E. E., Navarrete, A. A., Van Veen, J. A., & Tsai, S. M. (2014). Taxonomical and functional microbial community selection in soybean rhizosphere. ISME Journal, 8, 1577-1587. https://doi.org/10.1038/ismej.2014.17
- 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
- Lupatini, M., Suleiman, A., Jacques, R., Antoniolli, Z., Kuramae, E. E., Camargo, F., & Roesch, L. (2013). Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome. PLoS One, 8(10), [e76465]. https://doi.org/10.1371/journal.pone.0076465
- 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
- Kuramae, E. E., Yergeau, E., Wong, L., Pijl, A. S., Van Veen, J. A., & Kowalchuk, G. A. (2012). Soil characteristics more strongly influence soil bacterial communities than land-use type. FEMS Microbiology Ecology, 79(1), 12-24. https://doi.org/10.1111/j.1574-6941.2011.01192.x
- Verbruggen, E., Kuramae, E. E., Hillekens, R. H. E., De Hollander, M., Kiers, E. T., Roling, W. F. M.,... 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
- Mondego, J. M. C., Vidal, R. O., Carazzolle, M. F., Tokuda, E. K., Parizzi, L. P., Costa, G. G. L.,... Kuramae, E. E. (2011). An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC Plant Biology, 11, 30. https://doi.org/10.1186/1471-2229-11-30
- Doornbos, R. F., Geraats, B. P. J., Kuramae, E. E., van Loon, L. C., & Bakker, P. (2011). Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana. Molecular Plant-Microbe Interactions, 24(4), 395-407. https://doi.org/10.1094/MPMI-05-10-0115
- Kuramae, E. E., Gamper, H. A., Van Veen, J. A., & Kowalchuk, G. A. (2011). Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with neutral pH. FEMS Microbiology Ecology, 77(2), 285-294. https://doi.org/10.1111/j.1574-6941.2011.01110.x
- Kuramae, E. E., Gamper, H. A., Yergeau, E., Piceno, Y. M., Brodie, E. L., DeSantis, T. Z.,... Kowalchuk, G. A. (2010). Microbial secondary succession in a chronosequence of chalk grasslands. ISME Journal, 4(5), 711-715. https://doi.org/10.1038/ismej.2010.11
- Kielak, A. M., Rodrigues, J. L. M., Kuramae, E. E., Chain, P. S. G., Van Veen, J. A., & Kowalchuk, G. A. (2010). Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiology Ecology, 71(1), 23-33. https://doi.org/10.1111/j.1574-6941.2009.00785.x
- Bovers, M., Hagen, F., Kuramae, E. E., & Boekhout, T. (2009). Promiscuous mitochondria in Cryptococcus gattii. FEMS Yeast Research, 9(3), 489-503. https://doi.org/10.1111/j.1567-1364.2009.00494.x
- Bovers, M., Hagen, F., Kuramae, E. E., Hoogveld, H. L., Dromer, F., St-Germain, G., & Boekhout, T. (2008). AIDS patient death caused by novel Cryptococcus neoformans × C. gattii Hybrid. Emerging Infectious Diseases, 14(7), 1105-1108. https://doi.org/10.3201/eid1407.080122
- Nunes, W. M. C., Corazza, M. J., De Souza, S. A. C. D., Tsai, S. M., & Kuramae, E. E. (2008). Characterization of Xanthomonas axonopodis pv. phaseoli isolates. Summa Phytopathologica, 34(3), 228-231. https://doi.org/10.1590/S0100-54052008000300004
- Bovers, M., Hagen, F., Kuramae, E. E., & Boekhout, T. (2008). Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genetics and Biology, 45(4), 400-421. https://doi.org/10.1016/j.fgb.2007.12.004
- Souza, E. C., Kuramae, E. E., Nakatani, A. K., Basseto, M. A., Prabhu, A. S., & Ceresini, P. C. (2007). Citomorphological, cultural, molecular and pathogenical characterization of Rhizoctonia solani Kühn associated with rice in Tocantins, Brazil. Summa Phytopathologica, 33(2), 129-136. https://doi.org/10.1590/S0100-54052007000200005
- Kuramae, E. E., Robert, V., Echavarri-Erasun, C., & Boekhout, T. (2007). Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom. BMC Evolutionary Biology, 7, 134. https://doi.org/10.1186/1471-2148-7-134
- Xu, J., Saunders, C., Hu, P., Grant, R. A., Boekhout, T., Kuramae, E. E.,... Dawson Jr., T. L. (2007). Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. Proceedings of the National Academy of Sciences of the United States of America, 104(47), 18730-18735. https://doi.org/10.1073/pnas.0706756104
- Kuramae, E. E., Buzeto, A. L., Nakatani, A. K., & Souza, N. L. (2007). rDNA-based characterization of a new binucleate Rhizoctonia spp. causing root rot on kale in Brazil. European Journal of Plant Pathology, 119(4), 469-475. https://doi.org/10.1007/s10658-007-9175-z
- Vieira LG, incl. Kuramae EE et al (2006). Brazilian coffee genome project: an EST-based genomic resource. Brazilian Journal of Plant Physiology, 18, 95-108.
- Kuramae, E. E., Robert, V., Snel, B., & Boekhout, T. (2006). Conflicting phylogenetic position of Schizosaccharomyces pombe. In Conflicting phylogenetic position of Schizosaccharomyces pombe (pp. 387-393). (Genomics; Vol. 88). https://doi.org/10.1016/j.ygeno.2006.07.001
- Kuramae, E. E., Robert, V., Snel, B., Weiß, M., & Boekhout, T. (2006). Phylogenomics reveal a robust fungal tree of life. In Phylogenomics reveal a robust fungal tree of life (pp. 1213-1220). (FEMS Yeast Research; Vol. 6). https://doi.org/10.1111/j.1567-1364.2006.00119.x
- van Passel MWJ, Kuramae EE, Luyf ACM, Bart A, Boekhout T (2006). The reach of the genome signature in prokaryotes. BMC Evolutionary Biology, 84.
- Bovers, M., Hagen, F., Kuramae, E. E., Diaz, M. R., Spanjaard, L., Dromer, F.,... Boekhout, T. (2006). Unique hybrids between the fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. FEMS Yeast Research, 6(4), 599-607. https://doi.org/10.1111/j.1567-1364.2006.00082.x
- Kuramae, E. E., & Echavarri-Erasun, C. (2006). Yeast Genome 10th Anniversary. FEMS Yeast Research. https://doi.org/10.1111/j.1567-1364.2006.00169.x
- Fenille RC, Ciampi MB, Souza NL, Nakatani AK, & Kuramae, E. E. (2005). Binucleate Rhizoctonia sp. AG G causing root rot in yacon (Smallanthus sonchifolius) in Brazil. Plant Pathology, 54, 325-330. https://doi.org/10.1111/j.1365-3059.2005.01161.x
- Ciampi MB, Kuramae EE, Fenille RC, Meyer MC, Souza NL, Ceresini PC (2005). Intraspecific evolution of Rhizoctonia solani AG-1 IA associated with soybean and rice in Brazil based on polymorphisms at the ITS-5.8S rDNA operon. European Journal of Plant Pathology, 113. https://doi.org/10.1007/s10658-005-2231-7
- Kurokawa SC, Lopes CR, Sugizaki MF, Kuramae EE, Franco MF, Peraçoli MTS (2005). Virulence profile of ten Paracoccidioides brasiliensis isolates. Association with morphologic and genetic patterns. Rev. Inst. Med. Trop., 47, 257-262. https://doi.org/10.1590/S0036-46652005000500004
- Nascimento AL et al., incl. Kuramae EE. (2004). Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis. Journal of Bacteriology, 186. https://doi.org/10.1128/JB.186.7.2164-2172.2004
- Vincentz M et al, incl. Kuramae EE (2004). Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome. Plant Physiology, 134, 951-959. https://doi.org/10.1104/pp.103.033878
- Monteiro-Vitorello CB et al. incl. Kuramae EE (2004). The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. Xyli. Molecular Plant-Microbe Interactions, 17, 827-836. https://doi.org/10.1094/MPMI.2004.17.8.827
- Rosa DD, de Marque JM, Fenille RC, Souza NL, & Kuramae, E. E. (2003). Análise filogenética de Phytophthora capsici Leonian do Estado de São Paulo baseada na seqüência de nucleotídeos da região ITS-5.8S rDNA. Acta Scientiarum - Biological Sciences, 25, 429-434. https://doi.org/10.4025/actascibiolsci.v25i2.2033
- Vettore, A. L., & Vetore, A. L. et al. inc E.E. Kuramae (2003). Analysis and Functional Annotation of an Expressed Sequence Tag Collection for the Tropical Crop Sugarcane. Genome Research, 13, 2725-2735.
- VAN SLUYS, M. A. DE OLIVEIRA, M. C. MONTEIRO-VITORELLO, C. B. MIYAKI, C. Y. FURLAN, L. R. CAMARGO, L. E. A. DA SILVA, A. C. R. MOON, D. H. TAKITA, M. A. LEMOS, E. G. M. MACHADO, M. A. FERRO, M. I. T. DA SILVA, F. R. GOLDMAN, M. H. S. GOLDMAN, G. H. LEMOS, M. V. F. EL-DORRY, H. TSAI, S. M. CARRER, H. CARRARO, D. M. DE OLIVEIRA, R. C. NUNES, L. R. SIQUEIRA, W. J. COUTINHO, L. L. KIMURA, E. T., FERRO, E. S. HARAKAVA, R. Kuramae, E. E. MARINO, C. L. GIGLIOTI, E. ABREU, I. L. ALVES, L. M. C. DO AMARAL, A. M. BAIA, G. S. BLANCO, S. R. BRITO, M. S. CANNAVAN, F. S. CELESTINO, A. V. DA CUNHA, A. F. FENILLE, R. C. FERRO, J. A. FORMIGHIERI, E. F. KISHI, L. T. LEONI, S. G. OLIVEIRA, A. R. ROSA, V. E. SASSAKI, F. T. SENA, J. A. D. DE SOUZA, A. A. TRUFFI, D. TSUKUMO, F. YANAI, G. M. ZAROS, L. G. CIVEROLO, E. L. SIMPSON, A. J. G. ALMEIDA, N. F. SETUBAL, J. C. KITAJIMA, J. P (2003). Comparative Analyses of the Complete Genome Sequences of Pierce’s Disease and Citrus Variegated Chlorosis Strains of Xylella fastidiosa. Journal of Bacteriology, 185, 1018-1026. https://doi.org/10.1128/JB.185.3.1018-1026.2003
- Barbosa FH, Morais FV, Montenegro MR, Kuramae EE, Montes B, McEwen JG, Bagagli E, Puccia R (2003). Comparison of the Sequences of the Internal Transcribed Spacer Regions and PbGP43 Genes of Paracoccidioides brasiliensis from Patients and Armadillos (Dasypus novemcinctus). Journal of Clinical Microbiology, 41, 5735-5737. https://doi.org/10.1128/JCM.41.12.5735-5737.2003
- Kuramae, E. E., & Buzeto AL, Ciampi MB and Souza NL (2003). Identification of Rhizoctonia solani AG 1-IB in Lettuce, AG 4 HG-I in Tomato and Melon, and AG 4 HG-III in Broccoli and Spinach, in Brazil. European Journal of Plant Pathology, 109, 391-395. https://doi.org/10.1023/A:1023591520981
- Fenille RC, Ciampi MB, Kuramae EE, Souza NL (2003). Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences. Fitopatologia Brasileira, 28, 413-419.
- Marino RH, Eira AF, Kuramae EE, Queiroz EC (2003). Morphomolecular characterization of Pleurotus ostreatus (Jacq. Fr.) kummer strains in relation to luminosity and temperature of frutification. Scientia Agricola, 60, 531-535.
- Ferrari, RSF., & Kuramae, E. E. (2002). Análise do DNA plasmidial de Rhizoctonia solani spp. Associadas com feijoeiro e amendoinzeiro. Acta Scientiarum - Agronomy, 24, 1317-1320. https://doi.org/10.4025/actasciagron.v24i0.2287
- Fenille RC, Souza NL, & Kuramae, E. E. (2002). Characterization of Rhizoctonia solani associated with soybean in Brazil. European Journal of Plant Pathology, 10, 783-792. https://doi.org/10.1023/A:1020811019189
- Kuramae, E. E., & Nozaki DN, Fenille RC, Souza NL (2002). Elemento extracromossomal dsRNA em Rhizoctonia solani AG4 HGI e AG2-2 IIIB e Rhizoctonia spp. binucleada associadas às culturas de feijão e amendoim. Summa Phytopathologica, 28, 52-57.
- Peres NAR, Kuramae EE, Dias MSC, Souza N (2002). Identification and characterization of Colletotrichum spp. affecting fruit after harvest in Brazil. Journal of Phytopathology, 150. https://doi.org/10.1046/j.1439-0434.2002.00732.x
- Kuramae, E. E., & Fenille RC, Rosa Jr. VE, Dias DR, Monteiro JP, Gimenes MA, Palmieri DA, Lima MM, Fávaro RD (2002). Mining of Sugarcane ESTs involved in the mechanisms against plant pathogen and environmental stress. Summa Phytopathologica, 28, 315-324.
- Kuramae, E. E., & Fenille RC, Rosa Jr., VE, Rosa DD, Ulian EC (2002). Mining the enzymes involved in detoxification of reactive oxygen species (ROS) in sugarcane EST genome project. Molecular Plant Pathology, 3, 251-259. https://doi.org/10.1046/j.1364-3703.2002.00119.x
- Kuramae, E. E. (2002). Plasmídeos Mitocondriais em Fungos. Documentos, 85-95.
- Cardoso LR, Martins D, Kuramae EE, Tanaka RH, Mori ES (2002). Variabilidade genética de acessos de aguapé coletados no Estado de São Paulo. Planta Daninha , 20, 1-5. https://doi.org/10.1590/S0100-83582002000400001
- Kuramae, E. E., & Souza, N. (2002). Variabilidade genética entre formae speciales de Fusarium oxysporum e raças 1 e 2 de F. oxysporum f. sp. lycopersici através de RAPD e seqüências de regiões ITS e rDNA. Acta Scientiarum - Agronomy, 24, 1481-1485. https://doi.org/10.4025/actasciagron.v24i0.2409
- Sussel AAB, Fenille RC, Kuramae EE, Souza NL (2001). Caracterização de Rhizoctonia solani, agente etiológico do tombamento de mudas de café. Summa Phytopathologica, 27, 348-352.
- Machado MA, Souza AA, Coletta Filho HD, Kuramae EE, Takita MA. (2001). Genome and pathogenicity of Xylella fastidiosa. Molecular Biology Today, 2, 33-43.
- Kuramae, E. E., & Fenille RC, Rosa Jr. VE (2001). Idenfication of 14-3-3-like protein in sugarcane (Saccharum officinarum). Genetics and Molecular Biology , 24. https://doi.org/10.1590/S1415-47572001000100007
- Machado MA, Coletta Filho HD, de Souza A, Takita MA, Kuramae EE (2001). Projeto Genoma da Xylella fastidiosa. Revisão Anual de Patologia de Plantas (RAPP), 9, 63-77.
- Kuramae, E. E., Coneglian, R., Nali, L., Rodrigues, J., & Ono, E. (2000). Avaliação de parâmetros físicos de frutos de manga (Mangifera indica L.) submetidos a aplicações de ethephon em pré-colheita. Agronomia, 34(1/2), 31-37.
- Simpson, AJ., Kuramae, E. E., & et al. (2000). The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature, 406(13), 151-157. https://doi.org/10.1038/35018003
- Kuramae, E. E., & Souza, N. (1999). Métodos tradicionais e modernos na diagnose de doenças. Fitopatologia Brasileira, 24, 235-236.
- Kuramae, E. E. (1997). A rapid, easy and high yield protocol for total genomic DNA isolation from Colletotrichum gloeosporioides and Fusarium oxysporum for RAPD. Revista Unimar, 19, 683-689.
- Kuramae, E. E., Souza, N., Lopes, C., & Machado, M. (1997). Morphological and molecular characterization of Colletotrichum spp. from citrus orchards affected by postbloom fruit drop in Brazil. European Journal of Plant Pathology, 103, 323-329. https://doi.org/10.1023/A:1008627302706
- Kuramae, E. E., Souza, N., Machado, M., & Lopes, C. (1997). Restriction endonuclease analysis of DNA of Colletotrichum gloeosporioides causing citrus postbloom fruit drop disease in Brazil. Fitopatologia Brasileira, 189-200.
