PROFESSIONAL APPOINTMENTS
2012 - to date: Senior Scientist and Project Leader, Netherlands Institute of Ecology (NIOO-KNAW)
2020 -.... : Professor of Microbial Community Ecology & Environmental Genomics, Utrecht University
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
Ohana Costa
PhD:
Han Wang. (2019-2023). Utrecht University, The Netherlands
Zhiknag Wang. (2019-2022). Utrecht University, The Netherlands
Cristina Rotoni. (2019-2023). Utrecht University, The Netherlands
Rafaela Bulgarelli. (2019-2022). University of Campinas (UNICAMP, Brazil)
Joao Bossolani. (2018-2023). University of Sao Paulo State (UNESP, Brazil
Letusa Momesso. (2017-2021). Utrecht University, The Netherlands
Marcio Leite. (2014-2019). Utrecht University, The Netherlands
FORMER SUPERVISION (1998-2020)
Post Doctorate in functional genomics/metagenomics, microbiome (13)
PhD in Metagenomics, Microbiome (16)
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)