MicrobeGR: supporting environmental microbiology and ...

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Feb 12, 2013 (4 years and 8 months ago)

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MicrobeGR: supporting
environmental microbiology and
biotechnology in Western Greece
Kostas Bourtzis,University of Ioannina, Greece
EU-Funded Project
￿
SEVENTH FRAMEWORK PROGRAMME
￿
Capacities
￿
Research Potential
￿
Coordination and Support Actions
Presentation outline
￿
Concept and objectives
￿
Implementation
￿
Impact
￿
Ethical issues
Presentation outline
￿
Concept and objectives
￿
￿
Implementation
Implementation
￿
￿
Impact
Impact
￿
￿
Ethical issues
Ethical issues
MicrobeGR: Concept
￿
Microbial pathogens
￿
Insect pest & disease vectors
￿
Environmental Management & Protection
￿
Unexplored Microbial Diversity
￿
MikroBioKosmos

Pathogens

Beneficial
MicrobeGR: General Objective
￿
to reinforce environmental microbiology and
biotechnology research potential in Western
Greece
MicrobeGR: Specific Objectives
￿
acquire new research equipment
￿
transfer knowledge & experienced researchers
￿
networking / twinning with experienced EU teams
￿
develop a multiplex pathogen/symbiont detection system
￿
assess the hidden microbial diversity
￿
biotechnological applications
Current Activities I
￿
“Management of insect pests and disease vectors by
using novel, symbiont-based and environment-
friendly approaches”

Symbionts

(a) Wolbachia

(b) Other primary and/or secondary symbionts

Insect Pests & Disease Vectors

(a) Tephritids (medfly, olivefly, cherry fruit fly)

(b) Aphids

(c) Tsetse flies
Current Activities II (January 2008)
￿
“Detection, identification and characterization of
microbial populations in diverse and extreme
environments”
￿
Solar salterns (Halophiles) (A)
￿
Lakes (Trichonida, Kastoria etc)(A)
￿
Etoliko lagoon (Metagenomic analysis in progress)(A)
￿
Olive Mill Waste(A)
￿
Wastewater biological treatment stations(A)
￿
Acidic waste from Gold Mines (Acidophiles, Alkalophiles)(A)
￿
Hot water springs (Thermophiles, hyperthermophiles)
￿
Cold water springs (Psychrophiles)
Current Activities II (January 2010)
￿
“Detection, identification and characterization of microbial
populations in diverse and extreme environments”
￿
Solar salterns (Halophiles) (A)
￿
Lakes (Trichonida, Kastoria etc)(A)
￿
Etoliko lagoon (Metagenomic analysis in progress)(A)
￿
Olive Mill Waste(A)
￿
Wastewater biological treatment stations(A)
￿
Acidic waste from Gold Mines (Acidophiles, Alkalophiles)(A)
￿
Chromium industrial waste(A)
￿
Svallbard (Arctic)(A)
￿
Sahara desert(N)
￿
Sahara dust(N)
￿
Hot water springs (Thermophiles, hyperthermophiles)(F)
￿
Cold water springs (Psychrophiles)(F)
MicrobeGR: Supporting Actions I
￿
acquire new research equipment

DNA microarray system

Genetic analyzer

DGGE & imaging system

Anaerobic chamber
MicrobeGR: Supporting Actions II
￿
transfer knowledge & experienced researchers

Two postdocs
￿
experienced on DNA microarrays
￿
experienced on microbial molecular ecology techniques
and/or proteomics
MicrobeGR: Supporting Actions III
(Jan.2008)
￿
networking / twinning with experienced EU teams

Prof. Tim Vogel (Environmental Microbial Genomics,
Univ. of Lyon, France)

Prof. Daniele Daffonchio (Microbiology, Univ. of Milan,
Italy)

Prof. John Mansfield (Biology, Imperial College, UK)
MicrobeGR: Supporting Actions III
(Jan. 2010)
￿
networking / twinning with experienced EU teams
￿
Prof. Tim Vogel (Environmental Microbial Genomics, Univ. of Lyon, France)
￿
Prof. Daniele Daffonchio (Microbiology, Univ. of Milan, Italy)
￿
Prof. John Mansfield (Biology, Imperial College, UK)
￿
Prof. Henk Braig (Biological Sciences, University of Bangor, UK)
￿
Dr. Aziz Heddi (INRA, Univ. of Lyon, France)
￿
Prof. Claudio Bandi (Veterinary, Univ. of Milan, Italy)
￿
Prof. Luciano Sacchi (Biology, Univ. of Pavia, Italy)
MicrobeGR: Contribution to the
coordination of high quality research I
￿
Symbionts / Pathogens

assess hidden microbial diversity

environment protection

food production (quality and quantity)

public health
MicrobeGR: Contribution to the
coordination of high quality research II
￿
Other environmental microbes

beneficial microbes in soil

beneficial microbes in plant

other environments (eg lakes, lagoons, olive mill wastes, mines)

environment health & protection -public health

food production (quality and quantity)

biotechnology
MicrobeGR: Workplan I
￿
Four Work Packages (WPs)

WP1: Management of the consortium

WP2: Recruitment of experienced researchers and
acquisition of equipment

WP3: Network / Twinning

WP4: Dissemination / Exploitation
MicrobeGR: Workplan II
Management of
the Consortium
(WP1)
Dissemination/
Exploitation
(WP4)
Recruitment of new
experienced researchers/
Acquisition of new
equipment (WP2)
Networking/Twinning
(WP3)
Presentation outline
￿
￿
Concept and objectives
Concept and objectives
￿
Implementation
￿
￿
Impact
Impact
￿
￿
Ethical issues
Ethical issues
MicrobeGR: Implementation I
￿
Management structure and procedures
￿
Individual participants
￿
Resources to be committed
MicrobeGR: Implementation II
￿
Management structure and procedures

Co-ordinator

Scientific committee (Management Steering Committee) –Annual
meetings
￿
Prof. Kostas Bourtzis
￿
Prof. Tim Vogel
￿
Prof. Daniele Daffonchio
￿
Prof. John Mansfield
￿
Dr. George Tsiamis
￿
Dr. Elpida Papargyriou

Secretary

Communication flow (email, summary progress, meetings)

Monitoring methods (major tasks, milestones, deliverables, flow
charts)

Reports to Commission (annual and final)
MicrobeGR: Implementation III
(Jan. 2008)
￿
Individual participants

Dr. Kostas Bourtzis, Co-ordinator

Dr. George Tsiamis

Dr. Aggeliki Saridaki

[Dr. Charalambos Paraskevopoulos]

[Dr. Zoe Veneti]

[Dr. Vassiliki Karapapa]

Panagiotis Ioannidis

Panagiotis Sapountzis

Stefanos Siozios

Athina Chamalaki

Ilias Kounatidis

[Aikaterini Katsaveli]

[Stelios Ntalaperas]

[Manolis Dokiannakis]
MicrobeGR: Implementation III
(Jan. 2010)
￿
Individual participants

Dr. Kostas Bourtzis, Co-ordinator

Dr. George Tsiamis

Dr. Aggeliki Saridaki

Dr. Antonios Avgoustinos

[Dr. Charalambos Paraskevopoulos]

[Dr. Zoe Veneti]

[Dr. Vassiliki Karapapa]

Panagiotis Ioannidis (ex PhD)

Panagiotis Sapountzis (ex PhD)

Stefanos Siozios (ex PhD)

Ilias Kounatidis (ex PhD)

Athina Chamalaki

Aikaterini Katsaveli

Evangelos Diakoumis

Evangelos Doudoumis

Maria Theodoraki

Athina Zygouri
MicrobeGR: Implementation IV
￿
Resources to be committed

Molecular Biology and Biochemistry Lab with its currently
available equipment

New equipment
Presentation outline
￿
￿
Concept and objectives
Concept and objectives
￿
￿
Implementation
Implementation
￿
Impact
￿
￿
Ethical issues
Ethical issues
MicrobeGR: Expected impacts I
￿
human resources, knowledge, experience and
equipment to address the significant environmental
and agricultural problems of Western Greece
￿
better integration in the European Research Area
￿
improved capacity for participation in FP7 projects
￿
improve our capacity and quality of research
MicrobeGR: Expected impacts II
￿
Reinforce the environmental microbiology and
biotechnology research potential in Western Greece

develop research collaborations with established groups

become more competitive in seeking funds at any level

facilitate “academia to meet industry”

spread excellence, exploit results and disseminate knowledge
MicrobeGR: Expected impacts III
￿
Assessment of impact:

collaborations / partnerships with EU groups

publications in peer reviewed journals

presentations (oral, posters) in [inter] national conferences
MicrobeGR: Spreading excellence,
exploiting results and disseminating
knowledge I
￿
technical audience

research community

regional authorities and administrators

SMEs
￿
non-technical audience

high schools

general public
MicrobeGR: Spreading excellence,
exploiting results and disseminating
knowledge II
￿
Activities:

MicrobeGR leaflet
￿
SMEs
￿
regional authorities and administrators
￿
high schools
￿
pdf on the website
MicrobeGR: Spreading excellence,
exploiting results and disseminating
knowledge III
￿
Activities
:

Internet communication
￿
website
￿
internet days –live discussion with pupils
￿
thematic podcasts
1.
Microarrays (Prof. T. Vogel, Univ. of Lyon, France)
2.
Metagenomics (Dr. N. Kyrpides, JGI, USA)
3.
Microbial community structure (Prof. D. Daffonchio, Univ. of Milan, Italy)
4.
Microscopy and microbes (Prof. J. Mansfield, Imperial College, UK)
5.
Plant-insect interactions (Prof. Atle Bones, Univ. of Oslo, Norway)
MicrobeGR: Spreading excellence,
exploiting results and disseminating
knowledge IV
￿
Activities:

open days for high schools

seminars
￿
molecular techniques for pathogen detection and identification
￿
microarrays
￿
real-time PCR
￿
assessment of microbial community structure
￿
insect symbiosis
￿
symbiont-based pest and disease control
MicrobeGR: Spreading excellence,
exploiting results and disseminating
knowledge V
￿
Activities:

Workshop I: “Advanced molecular approaches to
unravel the hidden microbial world in insects”

Workshop II: “Microarrays: from theory to practice”

Conference: “Use of advanced molecular
technologies for improving agricultural and
environmental management”
Presentation outline
￿
￿
Concept and objectives
Concept and objectives
￿
￿
Implementation
Implementation
￿
￿
Impact
Impact
￿
Ethical issues
MicrobeGR: Ethical issues
￿
None!
MicrobeGR: supporting
environmental microbiology and
biotechnology in Western Greece
FIRST & SECOND YEAR PROGRESS
Kostas Bourtzis,University of Ioannina, Greece
MicrobeGR: Workplan
￿
Four Work Packages (WPs)

WP1: Management of the consortium

WP2: Recruitment of experienced researchers and
acquisition of equipment

WP3: Networking / Twinning

WP4: Dissemination / Exploitation
MicrobeGR: Workplan
￿
WP1: Management of the consortium
￿
￿
WP2:
WP2:
Recruitment of experienced researchers
Recruitment of experienced researchers
and acquisition of equipment
and acquisition of equipment
￿
￿
WP3:
WP3:
Network / Twinning
Network / Twinning
￿
￿
WP4:
WP4:
Dissemination / Exploitation
Dissemination / Exploitation
MicrobeGR: Management of the
consortium I
￿
Project co-ordinator
￿
Secretarial assistance
(Maria Theodoraki, Athina Chamalaki)

reports

cost statements

leaflets

workshops and conferences

agendas and minutes

discussion papers

Online archive of project docs and info
￿
Website
(George Fragkogiannis)
MicrobeGR: Management of the
consortium II
￿
Deliverables

D1: Website (6 months) –
DONE
microbegr.env.uoi.gr

D3: Mid-term assessment (18 months) –
(to be submitted with
the 2
nd
year report by 31 March 2010)

D14: Scientific assessment (36 months)

D15: Audit certificate (36 months) –
DONE
MicrobeGR: Workplan
￿
￿
WP1:
WP1:
Management of the consortium
Management of the consortium
￿
WP2: Recruitment of experienced researchers
and acquisition of equipment
￿
￿
WP3:
WP3:
Network / Twinning
Network / Twinning
￿
￿
WP4:
WP4:
Dissemination / Exploitation
Dissemination / Exploitation
MicrobeGR:
Recruitment of experienced
researchers and acquisition of equipment
I
￿
Recruit two post-doctoral fellows

experienced in microarrays
(Dr. George Tsiamis)

experienced in DDGE, other microbial molecular ecology c
and/or proteomics
(Dr. Aggeliki Saridaki)

experienced in insect molecular genetics
(Dr. Antonios
Avgoustinos)
￿
Acquire four novel equipments

DNA microarray system –
DONE

Genetic analyzer –
DONE

DDGE and DNA imaging system –
DONE

Anaerobic chamber –
DONE
Equipment
MicrobeGR:
Recruitment of experienced
researchers & acquisition of equipment
II
￿
Deliverables

D2: Installation certificates from the acquired instruments (12
months) -
DONE

D13: Final report on activities performed by the experienced
researchers (36 months)
MicrobeGR: Workplan
￿
￿
WP1:
WP1:
Management of the consortium
Management of the consortium
￿
￿
WP2:
WP2:
Recruitment of experienced researchers
Recruitment of experienced researchers
and acquisition of equipment
and acquisition of equipment
￿
WP3: Network / Twinning
￿
￿
WP4:
WP4:
Dissemination / Exploitation
Dissemination / Exploitation
MicrobeGR: Networking / Twinning I
￿
Exchange scientific knowledge and
experience through secondment of research
staff

training at Vogel’s lab –
DONE (GT)

training at Daffonchio’s lab –
DONE (AH & GT)

training at Braig’s lab –
DONE (AS)

training at Heddi’s lab –
DONE (AS)

training at Mansfield’s lab –
TO BE DONE (GT)

training at Bandi / Sacchi lab -
TO BE DONE (?)
MicrobeGR: Networking / Twinning II
￿
Deliverables

D9: Report after training(s) at Vogel’s lab (36 months)

D10: Report after training(s) at Daffonchio’s lab (36 months)

D11: Report after training(s) at Mansfield’s lab (36 months)
MicrobeGR: Workplan
￿
￿
WP1:
WP1:
Management of the consortium
Management of the consortium
￿
￿
WP2:
WP2:
Recruitment of experienced researchers
Recruitment of experienced researchers
and acquisition of equipment
and acquisition of equipment
￿
￿
WP3:
WP3:
Network / Twinning
Network / Twinning
￿
WP4: Dissemination / Exploitation
MicrobeGR: Dissemination/Exploitation I
￿
Facilitate knowledge transfer at regional, national and international level

Leaflet for public: “MicrobeGR”–
TO BE DONE (MARCH 2010)

Leaflet: “Principles of microarrays”–
TO BE DONE (JULY 2010)

Internet communication: podcasts, scientific forums –
TO START WITHIN 2010

Open days –
TO START WITHIN 2010

Workshop: “Advanced molecular approaches to unravel the hidden microbial world
in insects”–
DONE (OCTOBER 2009)

Workshop: “Microarrays: from theory to practice”–
TO BE DONE (MARCH 2010)

Conference: “Use of advanced molecular technologies for improving agricultural
and environmental management”
TO BE DONE (SEPTEMBER 2010)
MicrobeGR: Dissemination/Exploitation
II
￿
Deliverables

D4: Report for the Workshop “Advanced molecular approaches to unravel the
hidden microbial world in insects”(24 months)

D5: Leaflet for public “MicrobeGR”(26 months)

D6: Leaflet “Principles of Microarrays”(30 months)

D7: Report for the Workshop “Microarrays: from theory to practice”(30 months)

D8: Organization of the conference “Use of advanced molecular technologies for
improving agricultural and environmental management”(34 months)

D12: Report on dissemination activities (36 months)
MicrobeGR
￿
Milestones:

M1: Program start –WP1 (1 month) -
DONE

M2: Recruitment of experience researchers –WP2 (6 months) -
DONE

M3: Equipment upgrade –WP2 (12 months) -
DONE

M4: Mid-term assessment(18 months) –
TO BE DONE (by 31 March 2010)

M5: Exchange of know-how and training –WP3 (36 months) –
TO BE DONE (by 31/3/2011)

M6: Dissemination activities –WP4 (36 months) –
TO BE DONE (by 31/3/2011)

M7: Audit certificate –WP1 (36 months) -
DONE

M8: Final scientific assessment by the Management Steering Committee (36 months) –
TO BE
DONE (by 31/3/2011)
MicrobeGR: supporting
environmental microbiology and
biotechnology in Western Greece
THIRD YEAR PLANS
Kostas Bourtzis,University of Ioannina, Greece
MicrobeGR: Workplan
￿
Four Work Packages (WPs)

WP1: Management of the consortium

WP2: Recruitment of experienced researchers and
acquisition of equipment

WP3: Networking / Twinning

WP4: Dissemination / Exploitation
WP3: Networking / Twinning
￿
GT to visit John Mansfiled’s lab for EM studies
on plant / pathogen specimens
￿
GT to visit Aziz Heddi’s lab for FISH studies on
insect / symbiont specimens
￿
GT to visit Tim Vogel’s lab for microarray design
WP4: Dissemination / Exploitation I
￿
Workshop: “Microarrays: from theory to practice”
￿
Participants: 25-30
(from Western Greece Perfecture)
￿
3 day course with practical session
￿
To be organized March 2010
WP4: Dissemination / Exploitation II
￿
Conference: “Use of advanced molecular
technologies for improving agricultural and
environmental management”(with an emphasis
on Applied Arthopod Symbiosis)
￿
Participants: Scientists & SMEs
￿
To be organized September 2010
MicrobeGR
￿
Publications I:
￿
Tsiamis G., K. Katsaveli, S. Ntougias, N. Kyrpides, Y. Piceno, G. Andersen and K. Bourtzis (2008).
Prokaryotic community profiles at different operational stages of a Greek solar saltern.Research in
Microbiology
, 159:609-627.
￿
Bordenstein S.R., C. Paraskevopoulos, J.C. Dunning-Hotopp, P. Sapountzis, N. Lo, C. Bandi, H. Tettelin,
J.H. Werren and K. Bourtzis (2009). Parasitism and mutualism in Wolbachia: what the phylogenomic trees
can and can not say.Molecular Biology and Evolution
, 26: 231-241.
￿
C. Caceres, D. F. Segura, T. Vera, V. Wornoayporn, A. Islam, JL Cladera, P. Teal, P. Sapountzis, K.
Bourtzis, A. Zacharopoulou and A. S. Robinson (2009). Incipient speciation revealed by studies on mating
compatibility, sex pheromones, hybridization and cytology, between laboratory strains of anastrepha
fraterculus from Peru and Argentina. Biological Journal of the Linnean Society
, 97: 152-165.
￿
L. Klasson, J. Westberg, P. Sapountzis, K. Näslund, Y. Lutnaes, A. C. Darby, Z. Veneti, L. Chen, H. R.
Braig, R. Garrett, K. Bourtzis and S. G. E. Andersson (2009). The mosaic genome structure of the
Wolbachia wRi strain infecting Drosophila simulans. Proceedings of the National Academy of Sciences of
the United States of America
,106: 5725-5730.
MicrobeGR
￿
Publications II:
￿
I. Kounatidis, E. Crotti, P. Sapountzis, L. Sacchi, A. Rizzi, B.Chouaia, C. Bandi, A. Alma, D. Daffonchio,
P. Mavragani-Tsipidou and K. Bourtzis (2009). Acetobacter tropicalisis a major symbiont in the olive fruit
fly Bactrocera oleae. Applied and Environmental Microbiology
, 75: 3281-3288.
￿
N. Ishmael, J.C. Dunning-Hotopp, P. Ioannidis, S. Biber, J. Sakamoto, S. Siozios, V. Nene, J. Werren, K.
Bourtzis, S.R. Bordenstein, H. Tettelin (2009). Extensive Genomic Diversity of Closely Related Wolbachia
Strains. Microbiology
, 155: 2211-2222.
￿
S. Zabalou, A. Apostolaki, I. Livadaras, G. Franz, A.S. Robinson, C. Savakis and K. Bourtzis (2009).
Incompatible Insect Technique: Incompatible Males from a Ceratitis capitata (Diptera: Tephritidae) Genetic
Sexing Strain. Entomologia Experimentalis et Applicata
, 132: 232-240.
￿
Roy Gross, Fabrice Vavre, Abdelaziz Heddi, Greg D. Hurst, Einat Zchori-Fein and K. Bourtzis (2009).
Immunity and Symbiosis. Molecular Microbiology
, 73: 751-759.
MicrobeGR
￿
Publications III:
￿
A. Saridaki and K. Bourtzis(2009). Wolbachia-induced reproductive parasitism and
applications. Entomologia Hellenica
, 18: 3-16.
￿
A. Saridaki and K. Bourtzis (2009). Wolbachia: more than just a bug in insects’genitals.
Current Opinion in Microbiology
13: 1-6.
MicrobeGR
￿
Conferences (Oral Presentations):
￿
Kounatidis et al. (2008) First Meeting of TEAM
￿
Sapountzis et al. (2008) First Meeting of TEAM
￿
Tsiamis & Bourtzis (2008) EMBO Workshop “Microbial diversity and metagenomics”
￿
Bourtzis & Tsiamis (2008) MikroBioKosmos meeting
￿
Bordenstein et al. (2008) 5
th
International Wolbachia Conference
￿
Bourtzis (2008) 5
th
International Wolbachia Conference
￿
Charlat et al. (2008) 5
th
International Wolbachia Conference
￿
Bourtzis (2008) COST FA0701 meeting
￿
Bourtzis (2008) Locust meeting
￿
Bourtzis (2008) 23
rd
International Congress of Entomology
￿
Tsiamis (2008) 1
st
MikroBioKosmos Conference
￿
Bourtzis (2008) 1
st
MikroBioKosmos Conference
￿
Kounatidis et al. (2009) 13
th
Greek Entomol. Congr.
￿
Tsiamis et al. (2009) 2
nd
MikroBioKosmos (MBK) Conference
MicrobeGR
￿
Conferences (Poster Presentations):
￿
Apostolaki et al. (2008) 5
th
International Wolbachia Conference
￿
Ioannidis et al. (2008) 5
th
International Wolbachia Conference
￿
Sapountzis et al. (2008a) 5
th
International Wolbachia Conference
￿
Sapountzis et al. (2008b) 5
th
International Wolbachia Conference
￿
Siozios et al. (2008) 5
th
International Wolbachia Conference
￿
Veneti et al. (2008) 5
th
International Wolbachia Conference
￿
Tsiamis et al. (2008) 33
rd
FEBS Congress
￿
Katsaveli et al. (2008) 33rd FEBS Congress
￿
Saridaki et al. (2008) 33rd FEBS Congress
￿
Saridaki et al. (2008) 1
st
MBK Conference
￿
Tsiamis et al. (2008a) 1
st
MBK Conference
￿
Tsiamis et al. (2008b) 1
st
MBK Conference
￿
Tsiamis et al. (2009) 10
th
BAGEGO
￿
Kounatidis et al. (2009a) 31
st
Greek Soc. Biol. Sci.
￿
Kounatidis et a. (2009b) 31
st
Greek Soc. Biol. Sci.
￿
Tsagkarakou et al. (2009) 13
th
Greek Entomol. Congr.
￿
Aimakopoulou et al. (2009) 13
th
Greek Entomol. Congr.
￿
Tsiamis et al. (2009) 60
th
Greek Soc. Bioch. Mol. Biol.
￿
Hamalaki et al. (2009) 2
nd
MBK Conference
￿
Katsaveli et al. (2009) 2
nd
MBK Conference
￿
Diakopanagiotis et al. (2009) 2
nd
MBK Conference
￿
Tekerlekopoulou et al. (2009) 2
nd
MBK Conference
￿
Sartsidis et al. (2009) 2
nd
MBK Conference
MicrobeGR
￿
Thanks for your attention!