Prsentation PowerPoint

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Results from FP5 Biodiversity project MIDI- CHIP
Annick Wilmotte, CIP, University of Liège,
Belgium Coordinator
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MIDI-CHIP Design and testing of DNA microarrays
to monitor microbial diversity with adequate
biodiversity indexes, using cyanobacteria in
freshwater as a model system
MIDI-CHIP-TOX Linking cyanobacterial diversity
and cyanotoxins 
1 April 2000 31 october 2003
EC Scientific officer Dr Martin Sharman
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dedicated to the memory of Dr. Malgorzata
Tarczynska
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• State of the art
• Knowledge about the diversity, role, threats,
  dynamics of microbial organisms is very poor.
• Morphology-based taxonomy of cyanobacteria is
  very problematic and confused. Still, it is
  widely used.
• Molecular tools have revolutionised the field of
  microbial diversity studies and offer new
  opportunities, for in situ and ex situ
  studies. Different markers are available rDNA,
  toxin genes, RNA polymerase, RuBisCo operon,
• The DNA microarray technology has enabled
  breakthroughs in qualitative and quantitative
  genetic analysis. Its use in environmental
  diagnostics should open new possibilities for
  fast, automated, cheap monitoring of a very large
  number of microorganisms.

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The organisms
The cyanobacteria
to the ancestors of plastids
From architects of the earth atmosphere
to the basis of food chain
to the planktic bloom- and toxin-producers
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What would you see under the microscope?
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Participation of taxonomic experts, so that the
new knowledge can be translated into taxonomic
floras and determination keys
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Interdisciplinarity ecologists, classical
taxonomists, molecular biologists
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Deliverables

• Standardised sampling procedures
• Standardised molecular analysis protocols
• A report on the measurement of diversity for
  cyanobacterial studies as part of the MIDI-CHIP
  project
•  Collection of water samples (ca 500)

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• Collection of strains (ca 500)
• Inventory of morphotypes (ca 150)
• Improvement of the taxonomic system
• Thousands of 16S rRNA gene sequences, hundreds of
  alternative taxonomic markers (rpoC, cpcBA,
  rbcLX) and cyanotoxin gene sequences

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Poland Czech Republic Luxembourg Italy Finland Bel
gium (Fl)
Anabaena/Aphanizomenon
Nodularia
Anabaena
Nostoc
Planktothrix
Woronichinia
Synechococcus
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It could not be isolated in culture, but its
sequence was determined after micromanipulation
and PCR
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• Identification and quantification of cyanotoxins
  in MIDI-CHIP strains and samples
• Demonstration version of a DNA microarray for
  cyanobacterial diversity
• Finnish patents N 20030770 and 20030771
  introduced in May 2003 for 2 DNA microarrays

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Probes on a DNA Chip
Hybridization with DNA from environmental sample
Determination, analysis and interpretation of the
hybridization events
Detection of particular sequences identification
of organisms assessment of diversity
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A repository of our data, so that it is not lost
after the end of the project, and will be at
disposal of the scientific community. The
database allows also more sophisticated data
analyses.
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WEBSITE www.ulg.ac.be/cingprot/midi-chip/index.ht
m
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Contribution to BAP 6) Promoting research
activities using molecular methods in
biodiversity measurement and validation of these
technologies 13) Apply modern taxonomy to build
scientific tools for policy on conservation and
sustainable use, to fill gaps in taxonomy
knowledge 14) Promote the development of a system
of indicators (here linked to eutrophication,
see Water Framework Directive)
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Valorisations of the project
Cooperation in discussion with EC project PEPCY
Collaboration to WHO survey
NORFA courses on cyanobacterial taxonomy
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Biodiversity of microorganisms some comments and
suggestions for the future
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Microalgae we do not know, which algae should
be present in a water body, which are extinct or
which invaded the biotope recently. We know
neither the full range of the original algal
biodiversity nor the changes to be expected in
the future (Mollenhauer et al., 1999).
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 Complete enumeration of biotas in terms of
phylogeny is desirable to avoid uncertainties in
the use of indicator groups, and this is
achievable now for bacteria  Crozier, 1997,
Ann. Rev. Ecol. Syst. 28 243-268.
American Society for Microbiology (2000)
Microbial diversity measurement can be a
sensitive and suitable index of environmental
status and trends
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What happens in USA?
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THE MICROBE PROJECT
Only about 1.75m of the 30M species of living
organisms on earth have been scientifically
described. The vast majority of undescribed
species are prokaryotic and eukaryotic
microorganisms. Exploration of this reservoir
of diversity is needed for a coherent
understanding of food webs, ecological change and
stability, disease, biogeochemical cycles and
evolution .
M. Kane, NSF
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NSF/USDA INTERAGENCY MICROBIAL GENOME SEQUENCING
PROGRAM

• VIRUSES, BACTERIA, ARCHAEA, FUNGI, PROTISTS
• Novel microbial biochemistry, physiology,
  development
• Microbial diversity and environmental roles
• Impact of microorganisms on agriculture, natural
  resources, forestry and food safety
• Organization and evolution of microbial genomes

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MICROBIAL OBSERVATORIES From Genes and Genomes
to Ecosystems and the Biosphere.
Photo Credit Dr. Sarah Boomer Red Layer
Microbial Observatory, Western Oregon University
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MICROBIAL OBSERVATORIES 1999-2003
DEVELOP A NETWORK OF SITES TO 1) discover as
yet undescribed microorganisms and microbial
consortia from diverse habitats (2)
characterize the properties and activities of
newly described or poorly understood microbes and
microbial communities.
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Out of sight, out of mind!
- Include the microbial component in biodiversity
studies e.g. effect of stresses on plants,
whole food chain characterisation in lakes

TAKE SAMPLES FOR LATER
- Support studies of the genetic diversity of
microorganisms in selected biotopes e.g.
exploration and discovery of small world,
relation diversity/functioning, resilience to
perturbations, endemism, biotechnological
exploitation,
- Improve molecular methods to allow High
Throughput
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