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

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

 

PhD:

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)

Video

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

Kuramae EE, Hillekens RHE, de Hollander M, van der Heijden MGA, van den Berg M, van Straalen NM, Kowalchuk GA. Structural and functional variation in soil fungal communities associated with litter bags containing maize leaf.  FEMS Microbiol Ecol. DOI: 10.1111/1574-6941.12080, 2013
 
Navarrete AA, Kuramae EE, de Hollander M, Pijl A, van Veen J, Tsai SM. Acidobacterial community responses to agricultural management of soybean in Amazon forest soils. FEMS Microbiol Ecol. 83: 607-621, 2013
 
Verbruggen E, Kuramae EE, Hillekens R, de Hollander M, Kiers ET, Rolling WF, Kowalchuk GA, van der Heijden MG. Testing potential effects of Bt maize on mycorrhizal fungal communities via DNA- and RNA- based pyrosequencing and molecular fingerprinting. Appl Environ Microbiol. 78: 7384-7392, 2012
 
Kuramae EE, Yergeau E, Wong L, Pijl A, van Veen JA, Kowalchuk GA. Soil characteristics more strongly influence soil microbial communities than land management. FEMS Microbiol Ecol. 79: 1–271, 2012
 
Mondego JM, Vidal RO, Carazzolle MF, Tokuda EK, Parizzi LP, Costa GG, Pereira LF, Andrade AC, Colombo CA, Vieira LG, Pereira GA et al., incl. Kuramae EE. An EST-based analysis identities new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora. BMC Plant Biol. 8:11-30. 2011
 
Kuramae EE, Gamper H, van Veen J, Kowalchuk G. Soil and plant factors driving the community of soil-borne microorganisms across chronosequences of secondary succession of chalk grasslands with a neutral pH. FEMS Microbiol Ecol. 77:229–459, 2011
 
Doornbos RF, Geraats BPJ, Kuramae EE, Van Loon CL, Bakker P. Effects of jasmonic acid, ethylene, and salicylic acid signaling on the rhizosphere bacterial community of Arabidopsis thaliana. Molecular Plant-Microbe Interactions 395–407, 2011
 
Kuramae EE, Gamper HA, Regeau E, Piceno YM, Brodie EL, DeSantis TZ, Andersen GL, van Veen JA, Kowalchuk GA. Microbial secondary succession in a chronosequence of chalk grasslands. ISME J. 4: 711-715, 2010
 
Kielak A, Rodrigues JL, Kuramae EE, Chain PS, van Veen JA, Kowalchuk GA. Phylogenetic and metagenomic analysis of Verrucomicrobia in former agricultural grassland soil. FEMS Microbiol Ecol. 71:23-33, 2010
 
Bovers M, Hagen F, Kuramae EE, Boekhout T. Prosmiscuous mitochondria in Cryptococcus gattii. FEMS Yeast Res. 9:489-503, 2009.
 
Nunes WMC, Corazza MJ, Souza SACD, Tsai SM, Kuramae EE. Characterization of Xanthomonas axonopodis pv. phaseoli isolates. Summa Phytopathologica 34: 228-231, 2008
 
Bovers M, Hagen F, Kuramae EE, Hoogveld H, Dromer F, Germain G, Boekhout T. AIDS patient death caused by novel Cryptococcus neoformans x C. gattii hybrid. Emerging Infectious Diseases 14:1105-1108, 2008
 
Bovers M, Hagen F, Kuramae EE, Boekhout T. Six monophyletic lineages identified within Cryptococcus neoformans and Cryptococcus gattii by multi-locus sequence typing. Fungal Genetics & Biology 45:400-421, 2008
 
Xu J, Saunders CW, Hu P, Grant RA, Boekhout T, Kuramae EE, Kronstad JW, DeAngelis YM, Reeder NL, Johnstone KR, Leland M, Fieno AM, Begley WM, Sun Y, Lacey MP, Chaudhary T, Keough T, Chu L, Sears R, Yuan B, Dawson TL. Dandruff-associated Malassezia genomes reveal convergent and divergent virulence traits shared with plant and human fungal pathogens. PNAS 104,  2007
 
Kuramae EE, Robert V, Echavarri-Erasun C, Boekhout T. Cophenetic correlation analysis as a strategy to select phylogenetically informative proteins: an example from the fungal kingdom. BMC Evolutionary Biology7:134, 2007
 
Kuramae EE, Buzeto AL, Nakatani AK, Souza NL. rDNA-based characterization of a new binucleateRhizoctonia spp. causing root rot on kale in Brazil. Eur J Plant Pathol. 119, 2007
 
van Passel MWJ, Kuramae EE, Luyf ACM, Bart A, Boekhout T. Thereach of the genome signature in prokaryotes. BMC Evolutionary Biology 84, 2006
 
Echavarri-Erasun C, Kuramae EE. Yeast Genome 10th Anniversary. FEMS Yeast Research 2006
 
Kuramae EE, Robert V, Snel B, Boekhout T. Conflicting phylogenetic position of Schizosaccharomyces pombe. Genomics 88: 387-393, 2006
 
Kuramae EE, Robert V, Snel B, Weiß M, Boekhout T. Phylogenomics reveal a robust Fungal Tree of Life. FEMS Yeast Research 6:1213–1220, 2006
 
Vieira LG, incl. Kuramae EE et al. Brazilian coffee genome project: an EST-based genomic resource. Braz. J. Plant Physiol. 18:95-108, 2006
 
Bovers M, Hagen F, Kuramae  EE, Diaz MR, Spanjaard L, Dromer F, Hoogveld HL, Boekhout T. Unique hybrids between fungal pathogens Cryptococcus neoformans and Cryptococcus gattii. FEMS Yeast Research 599-607, 2006
 
Ciampi MB, Kuramae EE, Fenille RC, Meyer MC, Souza NL, Ceresini PC. 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 J. Plant Pathol. 113: 183–196, 2005
 
Fenille RC, Ciampi MB, Souza NL, Nakatani AK, Kuramae EE. Binucleate Rhizoctonia sp. AG G causing root rot in yacon (Smallanthus sonchifolius) in Brazil. Plant Pathology 54: 325–330, 2005
 
Rosa DD, Fenille RC, Souza N, Kuramae EE. Caracterização citomorforlógica,  molecular e patogênica de isolados de Rhizoctonia solani na cultura da batata (Solanum tuberosum). Summa Phytopathologica 31, 2005
 
Kurokawa SC, Lopes CR, Sugizaki MF, Kuramae EE, Franco MF, Peraçoli MTS. Virulence profile of ten Paracoccidioides brasiliensis isolates. Association with morphologic and genetic patterns Rev. Inst. Med. Trop.  47:257-262, 2005
 
Fenille RC, Ciampi MB, Souza NL, Nakatani AK, Kuramae EE. Binucleate Rhizoctonia sp. AG G causing root rot in yacon (Smallanthus sonchifolius) in Brazil. Plant Pathology 54: 325–330, 2005
 
Monteiro-Vitorello CB et al. incl. Kuramae EE. The Genome Sequence of the Gram-Positive Sugarcane Pathogen Leifsonia xyli subsp. Xyli. Molecular Plant-Microbe Interactions 17:827-836, 2004
 
Vincentz M et al, incl. Kuramae EE. Evaluation of Monocot and Eudicot Divergence Using the Sugarcane Transcriptome. Plant Physiology, 134: 951–959, 2004
 
Nascimento AL et al., incl. Kuramae EE. Comparative Genomics of Two Leptospira interrogans Serovars Reveals Novel Insights into Physiology and Pathogenesis. J.  Bacteriol. 186:2164–2172, 2004
 
Kuramae EE, Buzeto AL, Ciampi MB, Souza NL. 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 Pathology109:391-395, 2003
 
Rosa DD, de Marque JM, Fenille RC, Souza NL, Kuramae EE. Análise filogenética de Phytophthora capsici Leonian do Estado de São Paulo baseada na seqüência de nucleotídeos da região ITS-5.8S rDNA. Acta Scientiarum 25: 429-434, 2003
 
Fenille RC, Ciampi MB, Kuramae EE, Souza NL. Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences. Fitopatologia Brasileira 28:413-419, 2003
 
Marino RH, Eira AF, Kuramae EE, Queiroz EC. Morphomolecular characterization of Pleurotus ostreatus (Jacq. Fr.) kummer strains in relation to luminosity and temperature of frutification. Scientia Agricola 60, 531-535, 2003
 
Barbosa FH, Morais FV, Montenegro MR, Kuramae EE, Montes B, McEwen JG, Bagagli E, Puccia R. 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, 2003
 
Vettore AL et al, incl. Kuramae EE. Analysis and Functional Annotation of an Expressed Sequence Tag Collection for the Tropical Crop Sugarcane. Genome Research 13: 2725-2735, 2003
 
Kuramae EE, Buzeto AL, Ciampi MB and Souza NL. 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, 2003
 
Van Sluys MA et al., incl. Kuramae EE. 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, 2003
 
Fenille RC, Ciampi MB, Kuramae EE, Souza NL.  Identification of Rhizoctonia solani associated with soybean in Brazil by rDNA-ITS sequences. Fitopatologia Brasileira 28:413-419, 2003
 
Kuramae EE, Fenille RC, Rosa Jr, VE, Rosa DD, Ulian EC. Mining the enzymes involved in detoxification of reactive oxygen species (ROS) in sugarcane EST genome project. Molecular Plant Pathology, 3: 251-259, 2002
 
Kuramae EEFenille RC, Rosa Jr. VE, Dias DR, Monteiro JP, Gimenes MA, Palmieri DA, Lima MM, Fávaro RD. Sugarcane ESTs involved in the mechanisms against plant pathogen and environmental stress. Summa Phytopathologica 28: 315-324, 2002
 
Kuramae EE, Souza NL de. 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 24:1481-1485, 2002
 
Ferrari RSF, Kuramae EE. Análise do DNA plasmidial de Rhizoctonia solani spp. Associadas com feijoeiro e amendoinzeiro Acta Scientiarum 24:1317-1320, 2002
 
Kuramae EE, Fenille RC, Rosa Jr., VE, Rosa DD, Ulian EC. Mining the enzymes involved in detoxification of reactive oxygen species (ROS) in sugarcane EST genome project. Molecular Plant Pathology 3: 251-259, 2002
 
Fenille RC, Souza NL, Kuramae EE. Characterization of Rhizoctonia solani associated with soybean in Brazil.European Journal of Plant Pathology, 10:73-792, 2002
 
Kuramae EE, Nozaki DN, Fenille RC, Souza NL. 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, 2002
 
Cardoso LR, Martins D, Kuramae EE, Tanaka RH,  Mori ES Variabilidade genética de acessos de aguapé coletados no Estado de São Paulo. Planta Daninha 20:1-5, 2002
 
Peres NAR, Kuramae EE, Dias MSC, Souza NL. Identification and characterization of Colletotrichum spp. affecting fruit after harvest in Brazil. Journal of Phytopathology 150:128-134, 2002
 
Kuramae EE Book Chapter "Plasmídeos Mitocondriais em Fungos", in: "Melhoramento Genético de Plantas e Microrganismos". Embrapa Meio Ambiente 85-95, 2002
 
Kuramae EE, Fenille RC, Rosa Jr. VE. Idenfication of 14-3-3-like protein in sugarcane (Saccharum officinarum).Genetics and Molecular Biology 24:43-48, 2001
 
Sussel AAB, Fenille RC, Kuramae EE, Souza  NL. Caracterização de Rhizoctonia solani, agente etiológico do tombamento de mudas de café. Summa Phytopathologica 27:348-352, 2001
 
Machado MA, Coletta Filho HD, de Souza A, Takita MA, Kuramae EE. Projeto Genoma da Xylella fastidiosa. Eds. JM Fernandes, AM Prestes, EC Picinini. Revisão Anual de Patologia de Plantas RAPP, vol 9, pp. 63-77, 2001
 
Machado MA, Souza AA, Coletta Filho HD, Kuramae EE, Takita MA. Genome and pathogenicity of Xylella fastidiosa. Molecular Biology Today 2: 33-43, 2001
 
Simpson AJ et al., incl. Kuramae EE. The genome sequence of the plant pathogen Xylella fastidiosa. The Xylella fastidiosa Consortium of the Organization for Nucleotide Sequencing and Analysis. Nature, 406:151–157, 2000
 
Coneglian, RCC, Kuramae EE, Nali LR, Rodrigues JD, Ono EO. Avaliação de parâmetros físicos de frutos de manga (Mangifera indica L.) submetidos a aplicações de ethephon em pré-colheita. Agronomia 34: 31-37, 2000
 
Kuramae  EE, Souza N.L. Métodos tradicionais e modernos na diagnose de doenças. Fitopatologia Brasileira 24:235-236, 1999
 
Kuramae EE. 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, 1997
 
Kuramae EE, Souza NL, Machado MA, Lopes CR. Restriction endonuclease analysis of DNA of Colletotrichum gloeosporioides causing citrus postbloom fruit drop disease in Brazil. Fitopatologia brasileira 22:189-200, 1997
 
Kuramae EE, Souza N.L., Lopes CR, Machado MA. 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, 1997
 
Patent
Nascimento ALTO, Ko AI, Ho PL, Martins EAL, Leite LCC, Gamberini M, Setubal JC,Van Sluys MA, Camargo LEA, Monteiro-Vitorello CB, Kitajima JP, Ferro JA, Oliveira MC, Carrer H, Coutinho LL, Croda J, El-Dorry H, Ferro ES, Ferro MIT, Furlan LR, Giglioti EA, Goldman GH, Goldman MHS, Harakava R, Kimura ET, Kuramae EE, Lemos EGM, Lemos MVF, Marino CL, Nunes LR, de Oliveira RC, Pereira GG, dos Reis MG, Siqueira I, Siqueira WJ, Tsai SM. PATENT U.S. Application Serial No. 10/376,397 “Surface proteins of Leptospira” FAPESP 204.1 US (10303399). February 28, 2003

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