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Bio-indicators for soil quality monitoring for

sustainable management of biomass production

Eiko E. Kuramae e.kuramae@nioo.knaw.nl

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

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� 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

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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