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Design and testing of dna microarrays to monitor microbial diversity with adequate biodiversity indexes, using cyanobacteria in freshwater as a model system

Objective

Problems to be solved
Microorganisms make up more than 2/3 of the total biodiversity on Earth and their activities are essential for the maintenance of higher life on this planet. However, we know far less about them than we do about the higher eukaryotic organisms. The study of microscopic diversity requires novel approaches to answer the question 'What is growing here?' Organisms visible to the human eye can generally be identified using their morphological characteristics. For microorganisms, information from morphology or biochemistry is often too limited or misleading, and must be supplemented with molecular data (like gene sequences). The use of molecular tools to study microbial diversity 'in site' is in its infancy and yet to be established as a standard method. Therefore, we still need to compare different methodologies and even to introduce novel genetic techniques in the fields of biodiversity, ecology and environmental monitoring.
Scientific objectives and approach
Our scientific goal is to boost knowledge of microbial biodiversity by improving and comparing the techniques used in the past, by testing the innovative technology of DNA micro arrays (DNA chips), and by writing new software to use data from various phenotypic and genotypic approaches to calculate and select appropriate biodiversity indices. These indices are used to 'summarise' the state of diversity in different environments, and detect variations and differences between them. Our technological goal is to apply, in biodiversity studies, the new technology of DNA microarrays that has revolutioned the genetic and cellular analyses. This tool comprises glass slides to which a very high number of defined gene segments are attached. These sequence segments are selected as characteristic of certain species ("signature") or certain functions (toxin production, fixation of nitrogen). When the DNA from an environmental sample is labelled and hybridised with one DNA chip, identical DNA segments will anneal to each other and this hybridisation is detected. The DNA-chips and software designed in this project should be utilisable by end-users (environmental agencies, water companies). Therefore our project includes two users who have to routinely monitor water bodies in their countries. To perform this methodological study, we have focussed on one type of microorganism: the cyanobacteria (or blue-green algae) in freshwater lakes or basins. These are ecologically very important because they are at the base of the food chain due to their capacity to photosynthesise, which results in the release of O2 and the production of organic matter from CO2 by the use of sunlight. In particular conditions, however, they can become a nuisance by forming blooms that can produce highly toxic compounds. From a genetic point of view, they form an homogeneous grouping which is clearly separated from other bacteria.
Expected impacts
The comparison of different techniques to study the variation between cyanobacterial populations in freshwater lakes or basins will allow us to define the weaknesses and strengths of each technique and to determine how and when to use them. By researching the novel technology of the DNA chips we want to solve the possible technical problems and so enable their utilisation in routine microbial analysis of water samples. Because of the high number of gene segments that can be used to analyse genetic diversity, DNA chips have the potential to allow automated sample analysis for a wide range of microorganisms.
B2B-ECOM consortium has developed & integrated a set of core specifications. Partners have integrated their tools within a pilot application for the electrical equipment domain. B2B-ECOM supports with innovative technology the integration of services along the supply chain through: content management at manufacturer and distributor: XML based offline and online information exchange between manufacturer and distributor; mapping of taxonomies (categories and parameters); integration of online services from manufacturer, distributor or third parties through API's. The innovation provided by B2B-ECOM offers added value to manufacturers, distributors, service providers and their professional end-users. It enables to anticipate on more demanding customer needs by addressing in a portal for the electrical Industry the whole value chain of the professional customer, beyond the currently supported buy and order processes.

Funding Scheme

CSC - Cost-sharing contracts

Coordinator

UNIVERSITE DE LIEGE
Address
17,Allee De La Chimie 3 - Bètiment B6
4000 Liege
Belgium

Participants (8)

FINNISH ENVIRONMENT INSTITUTE ***DO NOT USE THIS ACRONYM***
Finland
Address
Kesaekatu 6
00251 Helsinki
HOLDING ENERGIA RISORSE AMBIENTE - HERA SPA
Italy
Address
Viale Carlo Berti Pichat 2/4
40127 Bologna
NATIONAL RESEARCH COUNCIL OF ITALY
Italy
Address
Piazzale Delle Cascine 28
50144 Firenze
NATIONAL RESEARCH COUNCIL OF ITALY
Italy
Address
Via Fratelli Cervi 93
20090 Segrate
PISCES CONSERVATION LTD
United Kingdom
Address
Irc House, The Square? Pennington
SO41 8GN Lymington
UNIVERSITY OF HELSINKI
Finland
Address
9,Viikinkaari 9, Biocenter 1A
00014 Helsinki
UNIVERSITY OF LODZ
Poland
Address
Banacha 12/16
90-237 Lodz
UNIVERSITY OF SOUTH BOHEMIA
Czechia
Address
Branisovska 31
370 05 Ceske Budejovice