we live in a microbial world, · • nuffic neso brazil: capes • full doctorate abroad: capes •...
TRANSCRIPT
26-11-2012
1
Bio-indicators for soil quality monitoring for
sustainable management of biomass production
Eiko E. Kuramae [email protected]
BE-Basic
We live in a microbial world,
one gram of soil
…contains as many bacteria…
…as humans on earth!!
Intestine ± 10 X human cells
Decomposition
Structure
(Soil)
Ferlilizers
Export
Biogeochemical cycles
ProductionDiversity
Plant
Soil Biota
Biodiversity
Community structure
Functional
Bacteria Fungi
SOIL-BORNE MICROORGANISMS
High-throughput experimentation & (meta)genomic
mining
Environmental impact of chemicals, bio-based
molecules and processes
BE-Basic
Biobased Ecologically Balanced Sustainable Industrial Chemistry
HTE and (meta) genomic mining
• Develop and apply high-throughput
approaches
• Explore the metagenome (DNA
directly from environmental
samples)
• Engineer and screen enzymes and
other products for improved
properties.
Increased pressure on soil services
• Intensive agriculture
• Pollution
• Changing land usage
• Genetically modified crops
• Climate change
• Bio-based economy
� Demand for sustainable agricultural
development
� Agriculture and global change
� Demand for sustainable agricultural
development
� Agriculture and global change
26-11-2012
2
� Bio-indicators
� Develop the most predictive markers for
high-throughput analyses of soil status
Goal BE-Basic
Bio-indicators are microbial species,
functional genes or processes that are
indicative of ecosystem changes in early stage
Decomposition
Fertilizer +
subproducts, residues
+ straw
Export
Biogeochemical cycles
Plant
CO2
N2OCH4
Community structure
Functional
Soil Biota
Bacteria Fungi
Biomass production
Bio-Indicators Soil Quality/Health
• Micro-arrays (PhyloChips, GeoChips, etc.)
• New Generation Sequencing methods
• Developments in Bioinformatics
High Throughput tools for observations of
soil-borne communities
Rhizosphere
Sustainable agriculture (Black Earth-slash and burn)
Agriculture soils (nutrient input)
Bio-economy (Soybean)
DeforestationTropical Forest Temperate Forest
Soil parameters
Bioinformatics
Selection (genes/taxa)
correlated with
environmental factors
Testing
Quantitative
experiments to examine
predictive power of
potential indicator
genes / taxa
Environmental factors
Molecular methods (genomics and post-
genomics)
Kuramae et al. ISME, 2010; Kuramae et al. FEMSME, 2011, 2012; Verbruggen et al. New Phytologist, 2011; Verbruggen et al. AEM, 2012Navarrete et al. FEMSME, 2012
Crops Pasture
Deforestation simplifies bacterial networks in
Amazon soil
Navarrete et al. 2012
117
connections
93
connections
Abundance of soil bacterial groups based on pyrosequencing analysis and quantitative real-time PCR measurements in the southeastern Brazilian Amazon forest (FS) and deforested (DS) sites
26-11-2012
3
Forest to Agriculture
CONVERSIONCONVERSION
13 NETHERLANDS INSTITUTE OF ECOLOGY
Sustainable soybean cropping agriculture
systems
Minimum tillageCrop rotationIntegration Crop-Livestock
Borges et al. in prep
Interactions between
microorganisms and ecosystem
functon
Bulk Soil
Rhizosphere
Bulk soil Rhizosphere
“Functional bio-indicators for soil quality monitoring
for sustainable management of sugarcane biomass
production (BIOSQ)”
Joint BE-Basic/FAPESP project
• Changing agricultural practices
• Drive towards lower CO2 ,CH4, N2O
emissions and greater sustainability
Partners
Nederlands Institute of Ecology (NIOO-KNAW)G. A. KowalchukE. E. KuramaeH. van Veen
Biodetection Systems b.v. (BDS)
Wageningen University
Bioclear b.v.
H. SmidtPhD student (vacancy)
T. JanssensB. van der BurgM. SchmidtR. Winter
I. J. T. DinklaG. FaberN. Hofman
B. GeurkinkS. Doddema J. Krooneman
University of São Paulo – USP
S. M. TsaiP. C.O. TrivelinD. G.G. Caldas
Agronomic Institute – IAC
H. Cantarella
Sao Paulo State University – UNESP
N. La Scala Jr.J. A. M. de Souza
Federal University of São Carlos –UFSCar
J. Carmo
P. BodelierM. De Hollander • CAPES/Wageningen: CAPES
• Nuffic Neso Brazil: CAPES
• Full Doctorate Abroad: CAPES
• Global Climate Change: FAPESP
• Biota Biodiversity Microorganism: FAPESP
• BIOEN/BE-Basic: FAPESP
Programs