environmental impacts of biorenewables and biofuelsecogenomics-based approaches to assess, and...
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BIOEN, SP november 25,2010 1
Environmental impacts of Biorenewables
and Biofuels
Bram BrouwerCEO of BioDetection Systems BV
Leadership team member of BE-Basic
Ecogenomics-based approaches to assess, and options to
resolve environmental impacts of Biorenewables and
Biofuels
BIOEN, SP november 25,20102
Merger industrial/environmental consortia
Environmental
footprintEcogenomics
Opportunities /solutions
Ecosystem services
challenges
White biotechnology
improvements
FS 240910 3
BE-BASIC Mission
Mission:
“Be-Basic develops new bio-based concepts for the chemicals, energy and materials industry as well as for monitoring
, controlling and reducing the impact on the environment and society”
BIOEN, SP november 25,2010 4
BE-BASIC overview
BE-Basic programme organized in Flagships
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BE-BASIC Flagship 7 and 8
ECOGENOMICS APPROACHES : SOME EXAMPLES
Ecogenomics-based biodiversity analysis
Ecogenomics-based chemical & environmental safety assessment
Ecogenomics-based nature mining and HTP experimentation
Environmental solutions in Factory-of-the-Future concept
Ecosystem services analysis and sustainable use of soil
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Ecogenomics approaches and options for
environmental impact assessment in the field
Ecogenomics-based biodiversity analysis: DNA Barcoding
BIOEN, SP november 25,2010
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How genomics changes biodiversity analysis
species No of sitesNo of
species
Last
observedAt-2 At-1 At
%
decreaseRL
Chrysolina
quadrigemin
a
1 1 1919 1 1 0 50% 0
Chrysolina
analis 4 4 1926 1 1 0 50% 0
Chrysolina
cerealis 23 34 1979 9 3 1 67% 1
Chrysolina
geminata 19 22 1957 7 4 1 59% 1
Gonioctena
linnaeana 7 11 1972 5 2 1 55% 1
Timarcha
metallica 2 5 1971 2 1 1 25% 1
Classical ecological impact assessment
BIOEN, SP november 25,2010
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How genomics changes biodiversity analysis
Future biodiversity assessment:
species identification and counting
by DNA barcoding
BIOEN, SP november 25,2010
PhyloChip
16S-rDNA
amplification
DNA Barcoding of microbial communities in soil
BIOEN, SP november 25,2010
22,2
15,2
6,83,619
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involved in nitrogen cycling
carbon metabolism
sulfur reduction
methane reduction and oxidation
involved in metal reduction and resistance
involved in degradation of organic compounds
Gene category Unique probes Group probes Total
Nitrogen fixation 1225 0 1225
Nitrification/N metabolism 865 902 1767
Denitrification 1805 501 2306
Sulfur reduction 1286 329 1615
Methane reduction and oxidation 437 333 770
Carbon fixation 584 215 799
Carbon polymer degradation 2532 276 2808
Metal reduction and resistance 4039 507 4546
Organic contaminant degradation 6920 1087 8007
Total 19693 4150 23843
He et al. 2005. Appl. Environ. Microbiol. 71:3753-3760.
In general, GeoChips covers > 10,000 genes in > 150 functional groups
DNA-barcode application:
Microbial community and ecosystem services
BIOEN, SP november 25,2010
= Nitrification
= Nitrogen reductase
= Dissimilatory sulfate reductase
= methane oxidation
= Carbon fixation
= Nitrogen fixation
= methane generation
= Metal reductase
= Carbon degradation
= Organic remediation
Gene category cluster analysis: Soil Thermometer
BIOEN, SP november 25,2010
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Ecogenomics approaches and options
BIOEN, SP november 25,2010
Ecogenomics-based chemical & environmental safety assessment
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very little/no
tested
100,106 chemicals on market in 1981 (“existing substances”);
1 % tested on hazardous properties
For most compounds in use the risks for harmful effects are
unknown, let alone their potential interactions in mixtures
Major effort ongoing to assess and evaluate potential harmful
effects for thousands of chemicals in next decade
This should not result in increased use of experimental animals
REACH chemicals registration & evaluation
BIOEN, SP november 25,2010
Nucleus
Ligandbinding
Cytosol
Transcription
Proteins
Enzymes
Luciferase
Add substrate (luciferine)
Light
ChemicalResponsiveElement(CRE)
Ligand
Transport protein
Hsp
Chemical receptor
Array-based target identification
of toxic responsesGeneration of toxicity-based
reporter cells (CALUX)
ISQ- chip; phylo-chip; ZF-array
Hu. cell array
Bio-based safety screening of chemicals
Toxicity target identification & reporter cell development
BIOEN, SP november 25,2010
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Compare gene expression profiles with standard profiles in database
ReferencesTest compound
Prediction
Gene expression profiles as indicator of toxicity
BIOEN, SP november 25,2010
LUCIFERASEReceptor binding elements
LUCIFERASE mRNA
LUCIFERASE protein
ReceptorLight signal
proportional to amount of biological
active chemical insample
CHEMICAL(mix)
ENDOGENOUS GENE
BIOLOGICAL EFFECT
CALUX® luminescent reporter cells
for chemical safety assessment
BIOEN, SP november 25,2010
•Identification of specific effects/compound groups; glucocorticoids
•Identification of hot spots of pollution
B D I H P
MS
1S
2W
1W
2W
3
ERa (E2)
PR (Org2058)
GR (Dex)
AR (DHT)
TRb (T3)
0
50
100
150
200
250
Eq
uiv
ale
nts
(n
g/l)
Water type
Bioassay
ERa (E2)
PR (Org2058)
GR (Dex)
AR (DHT)
TRb (T3)
Van der Linden et al. Env. Science & Technology 2008
Example of activity profiling in waste water,
using CALUX reporter cells
BIOEN, SP november 25,2010
ER AR PR TR GR RAR DR
KappaB cytox PPAR
• Endocrine
ER AR PR TR GR RAR DR
KappaB nrf2 p53 p21 cytox
PPAR
• Repro
ER AR TR GR RAR DR
KappaB cytox PPAR
• DevelopmentER AR PR TR GR RAR DR
KappaB nrf2 p53 p21 cytox
PPAR
• Muta/carcinogen
ER AR PR GR RAR DR
KappaB nrf2 cytox PPAR
• Immuno
KappaB nrf2 p53 p21 cytox • Acute
Animal free-safety profiling of chemicals with
CALUX® battery
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Ecogenomics approaches and options
Ecogenomics-based nature mining and HTP experimentation
BIOEN, SP november 25,2010
Flagship management:
Hans van Veen, [email protected]
Dick Janssen [email protected]
Aim: Develop and apply high-throughput approaches and tools to explore and mine untapped natural resources and to engineer and screen enzymes and other products for improved properties and application in the bio-based economy.
Rationale: Nature contains huge numbers of products, i.e. enzymes, antibiotics , vital to the biobased economy. In particular the microbial world around us, is a largely untapped source of valuable products. (Meta)genomics, high-throughput analysis, and laboratory evolution of organisms and enzymes are key technologies to exploit natural activities of microorganisms and enzymes in industrial biotechnology and for sustainable production
High throughput experimentation and
(Meta)genomic mining
BIOEN, SP november 25,2010
1. traditional screening &
microbiological enrichment:
purification, cloning, expression
2. protein engineering,
directed evolution: only with
known genes and proteins
4. genomics, expression
and analysis of putative
enzymes
3. exploring the
metagenome,
environmental gene
libraries
5. de novo protein
design
6. catalytic
antibodies S P
Sources of new & better biocatalysts
BIOEN, SP november 25,2010
Metagenomics:= the genomic analysis of microorganisms by direct
extraction and cloning of DNA from an assemblage of microorganisms
Metagenomics arose in reaction to the observation that as-yet-uncultured micro-organisms represent the vast majority of organisms in most environments on earth.
protocolvector
host
insert size
screening
Metagenomics an approach for nature mining
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Options for industrial biotechnology
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From mono-cultures → microbial consortia
- For fermentation purposes - For bioremediation processes
Applications of newly discovered microbes and microbial enzymes
Options for industrial biotechnology
BIOEN, SP november 25,2010
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Environmental solutions implemented in
Factory of the Future concept
Environmental solutions in Factory-of-the-Future concept
BIOEN, SP november 25,2010
Environmental impact integrated
in Factory of the Future
BIOEN, SP november 25,2010
HTS monitoring
tools
Hazard identification
Hazard reduction: bio-degradation Emission
reduction
Demonstration WP9 Industrial- Factory of future
waste
Product safety
Demonstration WP4 Public/environmental - water
raw material
product
Factory of the Future
BIOEN, SP november 25,2010
waste
productsynthesisRaw materials
8.2 Bio-remediation
8.1Toxicity profile
9 LCA
8.2 Env. impact
8.1/8.2 Sensors
8.1 Risk assessment
Chemical factory
Factory of the Future
BIOEN, SP november 25,2010
wasteBacterial
degradation
Toxicity array
Bacterial Sensors
Non-toxic waste
Degradation potential and strategy
Toxic Safe
Factory of the Future
BIOEN, SP november 25,2010
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Ecogenomics approaches and options
Ecosystem services analysis & sustainable use of soil
Project 8.2.4: Assessing impacts of land use for bio-based economy
on soil and sediment biodiversity, ecosystem processes and services
Prof Wim van der Putten, NIOO-KNAW
BIOEN, SP november 25,2010
How can we use ecosystem services for promoting a
sustainable use of soils in agriculture?
FP7 research project (2008-2012)
http://www.kem.ekol.lu.se/soilservice/index.html
SOIL SERVICE research project
BIOEN, SP november 25,2010
Link soil biodiversity and ecosystem services in
agricultural production
Value soil ecosystem services as a part of
farmers economy
Predict future land use changes, based on
farmers economy and sustainable use of soils
SOIL SERVICE project aims
BIOEN, SP november 25,2010
Soil
biodiversity
Ecosystem
services
Quantify ES:
nutrient retention
carbon retention
resistance to pests
stability of services
Agricultural
land use:
crop rotation
biofuel crops
pastures
Link diversity to
functions:
biodiversity
food webs
Biodiversity tool box
BIOEN, SP november 25,2010
Run-off (C,N,P, S
pollutants)
Diversity Cycles
Remote sensing
Plant chemistryHPLC, LC-MS, NMR
Rates
NGS, micro arraysPhysico-chemistry Functional Micro arrays,
Biogeochemical Rates, Physico-chemistry
Waterquality
Biorefinery
Waste (C,N,P,
pollutants)
In situ Biomonitor using Nitrosomonas
genome array .
Task8.2.4.1
Task 8.2.4.1Task 8.2.4.2Task 8.2.4.3
GHG emission (CH4/N2O)
CyclesDiversity
Project Proposal 8.2.4 : proposed approach to assess impactsof land use for bio-based economy on soil and sediment
BIOEN, SP november 25,2010
Project Proposal 8.2.4: research questions
Can hyperspectral reflectance be used to monitor plant performance in relation
to differences in soil biodiversity ?
What will be the effects of runoff from bio-based production lands on adjacent
freshwater ecosystems ?
What is the role of nitrification, as key microbial process in crop production ?
and how is it affected by changing land use and environmental conditions ?
Project Proposal 8.2.4: research aims
To test how plant/crop species and growth conditions, measured by hyperspectal
reflectance, influence soil biodiversity,,and their feedback responses
To test applications of combined soil-plant interactions and remote sensing
approach to plant-soil systems
Make an inventory of microbial activity, diversity and gene expression in
wetland systems with varying degree of pollution and trophic status
Couple gene expression and abundance to selected ecosysem functions,
and calibrate these
select and test a subset of indicator genes to be used as an assessment tool
for effects of bio-based production, ecosystem services, and GHG emmission
Draw genetic stress response maps of the nitrifying bacterium N. europaea
and link it to inhibition of nitrification
Apply the stress response maps to screen for the presence of stress factors
in bio-based crop fields and their catchment water bodies
BIOEN, SP november 25,2010 37
Thank you for your attention.