Dr. Eiko Kuramae
ResearcherMicrobial Ecology |
Research expertiseBioinformatics Environmental genomics Genomics Microbial network Soil microbial ecology
Page last updated: 20-03-2018
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PROFESSIONAL APPOINTMENTS
EDUCATION
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
CURRENT RESEARCH TOPICS AND INTERESTS
CURRENT SUPERVISION
Afnan Suleiman. Unravelling the mechanisms underlying health and productivity promoting agricultural practices by fine-mapping rhizosphere communities (2015-2018), NWO-Green
Mauricio Dimitrov. Harnessing the rhizosphere microbiome to enhance plant productivity (2014-2017), NWO/CNPq
Adriano Lucheta. Microbiome Core for soil ecosystem functioning (2014-2015), CAPES/NUFFIC 057-14
Marcelo Zerillo. (2015-2016), CAPES/NUFFIC 037-12
Matheus Cipriano. (2014-2015), CAPES/NUFFIC 037-12
Anna Kielak. Metagenomic tools for intelligent gene mining (2012-2015), NIOO/KNAW
Ohana Costa. (2016-2020). Leiden University, The Netherlands
Késia Lourenço. (2014-2018). Agronomic Institute of Campinas (IAC), Brazil
Elaine Labanca. (2014-2018. Agronomic Institute of Campinas (IAC), Brazil
Noriko Cassman. (2014-2018). Leiden University, The Netherlands
Marcio Leite. (2014-2018). Leiden University, The Netherlands
Thiago Schlemper. (2013-2017). Leiden University, The Netherlands
Yan Yan. (2012-2016), Leiden University, The Netherlands
Leonardo Pitombo. (2012-2016), University of Sao Carlos (UFSCAR, Brazil)
Afnan Suleiman. (2013-2016). Federal University of Santa Maria, Brazil
Johnny Soares. (2013-2016). Agronomic Institute of Campinas (IAC), Brazil
Manoeli Lupattini. (2012-2015). Leiden University, The Netherlands
FORMER SUPERVISION (1998-2006)
Post Doctorate in functional genomics/metagenomics (5)
PhD in Metagenomics (5)
PhD in Plant Pathology and Genetics (5)
MSC in Metagenomics (2)
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)
CURRENT PROJECTS
NWO-Green (2015-2018): Unravelling the mechanisms underlying health and productivity promoting agricultural practices by fine-mapping rhizosphere communities
FAPESP-BE-BASIC:(Dutch)/BIOEN (Brazilian) (2015-2017). F08.002.06 BIOEN Unravelling the sinks and sources of nitrous oxide in sustainable bio based agriculture
Program Nuffic/CAPES (Netherlands/Brazil) (2014-2018). Microbiome core for soil ecosystem functioning.
NWO/CNPq (2014-2018). Harnessing the rhizosphere microbiome to enhance plant productivity.
NWO/FAPESP (2014-2018). Microbial Networks in control of greenhouse gases emissions in Bio-based agriculture MiniBag.
CNPq/CAPES - Sciences Without Borders (2014-2018), Genomic, transcriptomic and proteomic of Acidobacteria from Cerrado Biome
CNPq/CAPES - Sciences Without Borders Program (2014-2018). Impacts of land use and of the Babassu palm on microbial community composition and function and on sol quality in Maranhão State, earsten periphery of Amazonia
CNPq (2013-2017). Production of bio-fertilizer organo-mineral bioactive phophate.
VN-Basic (2013-2017). Soil Health & Quality monitoring for sustainable biomass production in Vietnam
CAPES/BRAZIL (International collaboration Netherlands/Brazil) (2012-2016). Soil-borne microbes in soil restoration: why they live there, how they respond to environmental factors, and what are the consequences in ecosystem services?
FAPESP/BIOEN (Bioenergy) - Program Nuffic/CAPES (Netherlands/Brazil) (2012-2016). Greenhouse gas emissions (N2O, CO2 and CH4) from soil with sugarcane production and impact on microbial community structure and function
CNPq (National Council for Scientific and Technological Development) (2011-2015). Analyses of the soil microbial communities in soils under different land uses at the agricultural expansion border located at the Southwest of Amazonia
BE-Basic (2012-2017) – Next Generation Array Systems for sensing soil Health Status
BE-Basic (2012-2017)- Project: 7.3.2-WP3: Metagenomic tools for intelligent gene mining
FORMER PROJECTS
FAPESP BIOTA-Biodiversity: 2011/50914-3 (2012-2014) – in collaboration. The microbiome of Amazonian dark earth: structure and function of the microbial communities from rhizosphere and biochar associated to biogeochemical cycles
FAPESP-BE-BASIC:(Dutch)/BIOEN (Brazilian): 2011/51749-6 (2012-2014) and F08.002.005. Functional bio-indicators for soil quality monitoring for sustainable management of sugarcane biomass production (BIOSQ)
FAPESP (2010-2014) – in collaboration. Biodiversity and functional activity of microorganisms in mangroves from State of Sao Paulo
BIOEN/FAPESP: 2008/58187-0 (2012-2014) – in collaboration. The impact of tillage and harvest practices on soil CO2 emission of sugarcane production areas, Southern Brazil
FAPESP Global Climate Change: 2008/58114-3 (2009-2013). Monitoring the microbial diversity and functional activities in response to land-use changes and deforestation under soybean and sugarcane cultivation
EcoLinc – NWO (2011-2013) – Quantitative Array System for Soil Health
ERGO – NWO (2010-2012)- in collaboration. Examining bacterial and fungal plant organic matter decomposition via integrated pyrosequencing-based approaches ERGO
WP.2.1. Genomic analysis of microbial community structure: Provide phylogenetic microarray analyses of several series of agricultural fields varying in land management in order to gain insight into the normal operating range of microbial community structure with respect to "natural" variation
WP. 2.2. Functional analysis of nutrient cycling: To apply functional gene arrays, focussed on crucial steps of key nutrient cycles, to determine the natural variation, resilience, using a rapid and sensitive system for the analysis of microbial communities based upon high-density micro-array technology
Phylogenetic microarray analysis of soil-borne bacterial communities across chronosequences of chalk grassland secondary succession
NWO Ecogenomics (2007-2011) – in collaboration
Genomic analysis of microbial community structure and Functional analysis of nutrient cycling
FAPESP/Brazil -2003), Molecular Plant Pathology.
FAPESP/Brazil (2000-2002), Agronomical & Environmental Genomes Sequencing Consortium Projects (Xylella fastidiosa, Leifsonia xyli subsp. xyli, EST Coffea arabica and Coffea canephora, Leptospira interrogans).
FAPESP/Brazil (2001), Molecular Plant Pathology.
FAPESP Functional genomics of sugarcane (2001), University of Sao Paulo State, UNESP, Brazil.
FAPESP/Brazil (1999 –2001), Sugarcane EST Genome Project – Data Mining. ESTs involved in the mechanisms of defence against plant pathogen and environmental stress.
FAPESP/Brazil 99/04266-6 (1999 - 2001) – Functional genomics of Xylella fastidiosa (collaboration).
FAPESP/Brazil 99/02856-0 (1999 – 2000). Sugarcane EST Genome Project – Sequencing.
Xylella fastidiosa genome project (1997 – 2000).
FAPESP/Brazil (1995-2000), Project Young Scientist– Molecular Plant Pathology.
Wageningen University (WUR): Dr. Hans Helder; Dr. Gerlinde de Deyn; Dr. Jaap Bloem; Prof. Hauke Smidt
Plant Research International, Wageningen (PRI): Dr. Hein ten Berge
CMBI, Bacterial Genomics, Nijmegen: Dr. Sacha van Hijum
Utrecht University (UU): Dr. Bas Dutilh; Dr. Heike Schmitt; Prof. George Kowalchuk
Leiden University: Prof. Peter Klinkhamer
Laurence Berkeley National Laboratory, USA; Dr. Eoin Bordie; Dr. Gary Andersen
Federal Univerisyt of Maranhão, Brazil: Prof. Christoph Gehring
Catholic University of Brasília, Brazil: Dr. Cristine Barreto; Dr. Beatriz Guimaraes
Research Station ART, Switzerland: Prof. Marcel van der Heijden
CEUMA University, MA, Brazil: Dr. Flavio H. R. Moraes
University of São Paulo-CENA/USP, Brazil: Prof. Siu M. Tsai
FCAV, Unesp, Brazil: Prof. Eliana G. Lemos; Prof. Newton La Scala Jr.
Federal University of São Carlos, UFSCAR, Brazil: Dr. Janaina B. do Carmo
Institute Agronomic of Campinas, IAC, Brazil: Dr. Heitor Cantarella; Dr. Adriana Siveira
Universidade Federal do Pampa, RS, Brazil: Dr. Luiz F.W. Roesch
Past collaboration:
Free University Amsterdam (VU): Prof. Nico van Straalen
Universidad Complutense de Madrid, Spain: Dr. Luis Balaguer
University of Oklahoma, USA: Dr. Zhili He; Prof. Jizhong Zhou
INRA-Nancy, France: Prof. Francis Martin
Université catholique de Louvain-MUCL, Belgium: Dr. Stephane Declerck
University of São Paulo - ESALQ/USP, Brazil: Dr. Fernando Andreote
University of Texas, Arlington, USA: Dr. Jorge Rodrigues
Agricultural Research Concil-CRA, Italy: Dr. Stefano Mocali
Kielak AM, Cipriano MAP, Kuramae EE.Acidobacteria strains from subdivision 1 act as plant growth-promoting bacteria. Archives of Microbiology, doi:10.1007/s00203-016-1260-2, 2016
Kielak AM, Barreto, Kowalchuk GA, van Veen JA, Kuramae EE. The ecology of Acidobacteria: moving beyond genes and genomes. Review. Frontiers in Microbiology, doi: 10.3389/fmicb.2016.00744, 2016
Cassman NA, Leite MFA, Pan Y, de Hollander M, van Veen JA, Kuramae EE. Plant and soil fungal but not soil bacterial communities are linked in long-term fertilized grassland. Scientific Reports, 6:23680, doi: 10.1038/srep23680, 2016
Suleiman AKA, Gonzatto R, Aita C, Lupatini M, Jacques RJS, Kuramae EE, Antoniolli ZI, Roesch LFW. Temporal variability of soil microbial communities after application of dicyandiamide-treated swine slurry and mineral fertilizers. Soil Biology & Biochemistry, 97:71-82, doi:10.1016/j.soilbio.2016.03.002, 2016
Kielak AM, Scheublin T, Mendes LW, Van Veen JA, Kuramae EE. Bacterial community succession in pine-wood decomposition. Frontiers in Microbiology, 7, doi: 10.3389/fmicb.2016.00231, 2016
Lucheta AR, Cannavan FS, RoeschLFW, Tsai SM, Kuramae EE. Fungal community assembly in the Amazonian Dark Earth. Microbial Ecology, 71:962–973, doi: 10.1007/s00248-015-0703-7, 2016
Mendes LM, Brossi MJL, Kuramae EE, Tsai SM. Land-use system shapes soil bacterial communities in Southeastern Amazon region. Applied Soil Ecology 95:151-160., doi:10.1016/j.apsoil.2015.06.005, 2015
Navarrete AA, Soares T, Rossetto R, van Veen JA, Tsai SM, Kuramae EE. Verrucomicrobial community structure and size as indicators for changes in chemical factors linked to soil fertility. Antonie Van Leeuwenhoek. 2015; 108(3): 741–752, doi:10.1007/s10482-015-0530-3, 2015
Hol G, De Boer W, de Hollander M, Kuramae EE, Meisner A, van der Putten W. Context dependency and saturating effects of loss of rare soil microbes on plant productivity. Frontiers in Plant Science, http://dx.doi.org/10.3389/fpls.2015.00485, 2015
Pitombo LM, do Carmo JB, Cantarella H, Rossetto R, de Hollander M, López MV, Kuramae EE. Exploring soil microbial 16S rRNA sequence data to increase carbon yield and nitrogen efficiency of a bioenergy crop. Global Change Biology Bioenergy, DOI: 10.1111/gcbb.12284, 2015
Mendes LW, Navarrete AA, Borges SCD, Kuramae EE, Tsai SM. Impact of land-use changes in the Amazon on bacterial diversity, composition and distribution. In: Land-use Change Impacts on Soil Process: Tropical and Savannah Ecosystems, Edition: 1, Chapter: 5, Publisher: CABI Publisher, Editors: Francis Q. Brearley, Andrew D. Thomas, pp.41-54, 2015
Hol G, Garbeva P, Hordijk C, Hundscheid M, Gunnewiek PK, van Agtmaal M, Kuramae EE, de Boer W. Non-random species loss in bacterial communities reduces antifungal volatile production. Ecology, 96:2042–2048, http://dx.doi.org/10.1890/14-2359.1, 2015
Yan Y, Kuramae EE, Klinkhamer PGL, van Veen JA. Revisiting the dilution procedure used to manipulate microbial biodiversity in terrestrial systems. Applied and Environmental Microbiology, 81(13):4246-4252, doi: 10.1128/AEM.00958-15, 2015
Navarrete AA, Tsai SM, Mendes LW, Faust K, de Hollander M, Cassman NA, Raes J, van Veen JA, Kuramae EE. Soil microbiome responses to the short-term effects of Amazonian deforestation. Molecular Ecology. 24(10): 2433-2448. http://dx.doi.org/10.1111/mec.13172, 2015
Mendes LW, Tsai SM, Navarrete AA, de Hollander M, van Veen JA, Kuramae EE. Soil-Borne Microbiome: Linking Diversity to Function. Microbial Ecology, 70 (1):255-265, doi:10.1007/s00248-014-0559-2., 2015
Mendes LW, Kuramae EE, Navarrete AA, Van Veen JA, Tsai SM. Taxonomical and functional microbial community selection in soybean rhizosphere. The ISME Journal 1:1-11, 2014
Varon-Lopez M, Dias ACF, Fasanella CC, Durrer A, Melo IS, Kuramae EE, Andreote FD. Sulphur-oxidizing and sulphate-reducing communities in Brazilian mangrove sediments. Environ Microbiol 16:845-855, 2014
Lupatini M, Suleiman AKA, Jacques RJS, Antoniolli ZI, de Siqueira FAO, Kuramae EE, Roesch LFW. Network topology reveals high connectance levels and few key microbial genera within soils. Frontiers Environ Science, 2:10, 2014
Barbosa LA, Cannavan FS, Navarrete AA, Teixeira WGE, Kuramae EE, Tsai SM. Amazonian dark earth and plant species from the Amazon region contribute to shape rhizosphere bacterial communities. Microbial Ecology 8: 2014
Pan Y, Cassman N, de Hollander M, Mendes LW, Korevaar H, Geerts RHEM, van Veen JA, Kuramae EE. Impact of long term N, P, K and NPK fertilization on the composition and potential functions of the bacterial community in grassland soil. FEMS Microbiology, Ecology Oct;90(1):195-205. doi: 10.1111/1574-6941.12384, 2014
Kuramae EE, Zhou JZ, Kowalchuk GA, van Veen JA. Soil-Borne Microbial Functional Structure across Different Land Uses. The Scientific World Journal, 1-8, 2014
Lupatini M, Suleiman AKA, Jacques RJS, Antoniolli ZI, Kuramae EE, Camargo FAO, Roesch LFW. Soil-Borne Bacterial Structure and Diversity Does Not Reflect Community Activity in Pampa Biome. PLoS ONE 8(10): e76465. doi:10.1371/journal.pone.0076465, 2013
Kuramae EE, Verbruggen E, Hillekens R, de Hollander M, Röling WFM, van der Heijden MGA, Kowalchuk GA. Tracking Fungal Community Responses to Maize Plants by DNA- and RNA-Based Pyrosequencing. PLoS ONE 8(7): e69973. doi:10.1371/journal.pone.0069973, 2013
- 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, in press, [fiy092]. doi:10.1093/femsec/fiy092
- 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]. doi:10.3389/fmicb.2018.00660
- 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]. doi:10.1186/s13068-018-1036-9
- 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]. doi:10.3389/fmicb.2018.00674
- 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, in press. doi:10.1111/gcbb.12519
- 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. doi:10.1016/j.scitotenv.2018.03.116
- 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]. doi:10.7717/peerj.2915
- 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]. doi:10.1038/srep41193
- 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]. doi: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]. doi:10.1038/srep42634
- 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]. doi:10.3389/fmicb.2016.02064
- 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. 27(October), 832-845. doi:10.1016/S1002-0160(17)60415-6
- 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]. doi:10.1093/femsec/fix096
- Schlemper, T. R., van Veen, J. A., & Kuramae, E. E. (2017). Co-variation of bacterial and fungal communities in different sorghum cultivars and growth stages is soil dependent. Microbial Ecology, in press. doi:10.1007/s00248-017-1108-6
- 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. doi:10.1038/ismej.2016.108
- 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]. doi:10.1093/femsle/fnw245
- 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]. doi:10.1038/srep23680
- 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]. doi:10.1093/femsec/fiw197
- 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. doi:10.1016/j.funbio.2016.01.012
- 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]. doi:10.3389/fmicb.2016.00231
- 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]. doi:10.3389/fmicb.2016.00744
- 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. doi:10.1007/s00203-016-1260-2
- 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. doi: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. doi:10.1007/s00248-015-0703-7
- 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]. doi:10.1038/srep30349
- 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. doi:10.1016/j.soilbio.2016.03.002
- 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. doi:10.1007/s00248-014-0472-8
- 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. doi:10.1890/14-2359.1
- 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]. doi: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. 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. doi:10.1007/s00248-014-0559-2
- 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. doi:10.1016/j.apsoil.2015.06.005
- 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. doi: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. doi:10.1007/s10482-015-0530-3
- 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. doi:10.1128/AEM.00958-15
- 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. doi:10.1155/2014/216071
- 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]. doi:10.3389/fenvs.2014.00010
- 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. doi:10.1038/ismej.2014.17
- 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. doi:10.1111/1574-6941.12384
- 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. doi:10.1111/1462-2920.12237
- 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]. doi:10.1371/journal.pone.0069973
- 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. doi:10.1111/1574-6941.12080
- 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]. doi:10.1371/journal.pone.0076465
- 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. doi:10.1111/1574-6941.12018
- 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. doi: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. doi:10.1128/AEM.01372-12
- 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. doi: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. doi:10.1111/j.1574-6941.2011.01110.x
- 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. doi:10.1186/1471-2229-11-30
- 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. doi:10.1111/j.1574-6941.2009.00785.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. doi:10.1038/ismej.2010.11
- 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. doi:10.3201/eid1407.080122
- 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. doi:10.1016/j.fgb.2007.12.004
- 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. doi:10.1590/S0100-54052008000300004
- 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. doi:10.1007/s10658-007-9175-z
- 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. doi:10.1186/1471-2148-7-134
- 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. doi:10.1590/S0100-54052007000200005
- 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. doi:10.1073/pnas.0706756104
- 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. doi:10.1111/j.1567-1364.2006.00082.x
- 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). doi: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). doi:10.1111/j.1567-1364.2006.00119.x
- 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.
- van Passel MWJ, Kuramae EE, Luyf ACM, Bart A, Boekhout T (2006). Thereach of the genome signature in prokaryotes. BMC Evolutionary Biology, 84.
- Kuramae, E. E., & Echavarri-Erasun, C. (2006). Yeast Genome 10th Anniversary. FEMS Yeast Research. doi:10.1111/j.1567-1364.2006.00169.x
- 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. 47, 257-262. doi:10.1590/S0036-46652005000500004
- 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. doi:10.1007/s10658-005-2231-7
- 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. doi:10.1111/j.1365-3059.2005.01161.x
- 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. doi: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. doi: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. doi:10.1094/MPMI.2004.17.8.827
- Fenille RC, Ciampi MB, Kuramae EE, Souza NL (2003). Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences. 28, 413-419.
- 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. doi:10.1128/JB.185.3.1018-1026.2003
- 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. doi:10.1023/A:1023591520981
- 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. doi:10.1128/JCM.41.12.5735-5737.2003
- 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. 60, 531-535.
- 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.
- 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. doi:10.4025/actascibiolsci.v25i2.2033
- Ferrari, R. S. F., & Kuramae, E. E. (2002). Análise do DNA plasmidial de Rhizoctonia solani spp. Associadas com feijoeiro e amendoinzeiro. Acta Scientiarum - Agronomy, 24, 1317-1320. doi:10.4025/actasciagron.v24i0.2287
- Kuramae, E. E. (2002). Plasmídeos Mitocondriais em Fungos. 85-95.
- 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. doi:10.1046/j.1439-0434.2002.00732.x
- Cardoso LR, Martins D, Kuramae EE, Tanaka RH, Mori ES (2002). Variabilidade genética de acessos de aguapé coletados no Estado de São Paulo. 20, 1-5. doi:10.1590/S0100-83582002000400001
- 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.
- 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. doi:10.1046/j.1364-3703.2002.00119.x
- 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. doi:10.4025/actasciagron.v24i0.2409
- 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.
- 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. doi:10.1023/A:1020811019189
- Machado MA, Souza AA, Coletta Filho HD, Kuramae EE, Takita MA. (2001). Genome and pathogenicity of Xylella fastidiosa. 2, 33-43.
- Machado MA, Coletta Filho HD, de Souza A, Takita MA, Kuramae EE (2001). Projeto Genoma da Xylella fastidiosa. 9, 63-77.
- 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.
- Kuramae, E. E., & Fenille RC, Rosa Jr. VE (2001). Idenfication of 14-3-3-like protein in sugarcane (Saccharum officinarum). 24. doi:10.1590/S1415-47572001000100007
- 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, A. J., 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. doi:10.1038/35018003
- Kuramae, E. E., & Souza, N. (1999). Métodos tradicionais e modernos na diagnose de doenças. 24, 235-236.
- 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. doi: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. 189-200.
- Kuramae, E. E. (1997). A rapid, easy and high yield protocol for total genomic DNA isolation from Colletotrichum gloeosporioides and Fusarium oxysporum for RAPD. 19, 683-689.
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