Objective
Micromat: Biodiversity of microbial mats in Antarctica
The microbial mats from Antarctica will be used as a community model for the determination of biodiversity by different approaches, as well as a new source of valuable biotechnological compounds. We will assess and improve the different steps of the study of the microbial cultivated and 'yet-to-be cultivated' biodiversity of bacteria, protists, and fungi. In addition, we will use this Antarctic gene pool as a biotechnological resource, by screening the strains and environmental samples for novel cold-adapted enzymes, pharmaceutical compounds and cyanotoxins.
Microbial mats grow on the bottom of Antarctic lakes with salinities varying from freshwater to hypersaline. The mats have accumulated for thousands of years and are virtually undisturbed due to the particular climatic conditions and the absence of larger metazoans. Other types of mats grow in temporary flowing waters in summer and become dried out and frozen in winter. The mats are inhabited by all major groups of microorganisms (bacteria, protists, fungi) which have developed adaptations to the harsh environmental conditions, including UV-screening pigments, anti-freeze proteins, resistances to desiccation and hypersalinity, low temperature enzymes... New species of microorganisms have been described from Antarctic biotopes and it is expected that this continent harbours novel and unique gene pools, yet to be discovered and cultivated. It has recently been demonstrated that classical cultivation techniques on standard media resulted in the isolation of only a small percentage of the true biodiversity and that molecular methods like those based on the SSU rDNA detected many as yet unknown organisms. In addition, the molecular information (sequences, probes,....) can be used to monitor the corresponding organisms in the samples and during the isolation steps. Moreover, molecular biodiversity studies have shown that similar phenotypes could comprise different genotypes, and that morphological observation alone underestimated the true biodiversity of a biotope. A combination of different approaches is thus necessary to appreciate the total biodiversity.
In this project, laboratories with expertise in the study of eubacteria, archaebacteria, cyanobacteria, photosynthetic protists, heterotrophic protists, and fungi are joining forces to isolate and characterise the culturable biodiversity and to identify sequences from clone libraries or DGGE patterns indicative of 'yet-to-be cultivated' strains. Three companies and one subcontractor will screen the strains and the environmental DNA for biotechnologically valuable compounds and genes. One of the companies will set up a completely new line of screening for the cyanobacteria and protists.
I The work packaqe 1 is based on the sampling campaigns funded by the British and Australian Antarctic programs. The physicochemical environment of the samples will be determined, as well as the analysis of biomarkers and light- and UV-protective compounds.
II. In the work Packaqe 2, the cultivated diversity of all types of microorganisms will be isolated in the different EC laboratories and in a research station in Antarctica. The Benthic Gradient Chamber (BGC), a recently invented device mimicking the natural environment of the mats will be improved and used for enrichment and cultivation of all microorganisms, as well as for the long-term maintenance of living mats. The representative strains will be characterized in detail by phenotypic and genotypic methods based on SSU rDNA. The isolated strains will be screened by three companies looking for biotechnologically valuable compounds (low-III) temperature enzymes, pharmaceutical compounds) and by one subcontractor testing for cyanotoxins.
III In the work packaqe 3, the biodiversity will be studied by molecular techniques based on the SSU rDNA to detect the 'yet-to-be cultivated' microorganisms. Because DNA extraction from environmental samples is often problematic, a joint workshop will be organized at the start of the project, and companies commercializing DNA extraction kits will be involved in this first and essential step. Clone libraries will be constructed from the environmental DNA after amplification of the SSU rDNA genes by PCR. Representative SSU rDNA sequences will be determined and used to make probes and PCR primers. These will be used to estimate the total biodiversity by hybridizations to the clone libraries and the DGGE gels. These results, together with the ecological characterization of the samples carried out during the sampling, will give a first clue to the environmental conditions favouring the presence of 'yet-to-be cultivated' organisms and enable new strategies to be devised. The relation between biomarkers and pigments with the sequence diversity found in fossil mat layers will be studied. The DNA isolated from environmental samples will also be screened for the Presence of interesting protease and cellulase genes by one company and for peptide synthase genes by one subcontractor.
Fields of science (EuroSciVoc)
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
CORDIS classifies projects with EuroSciVoc, a multilingual taxonomy of fields of science, through a semi-automatic process based on NLP techniques. See: The European Science Vocabulary.
- natural sciences biological sciences microbiology bacteriology
- natural sciences biological sciences genetics DNA
- natural sciences biological sciences microbiology mycology
- natural sciences biological sciences ecology ecosystems
- natural sciences biological sciences biochemistry biomolecules proteins enzymes
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Coordinator
4000 Liège
Belgium
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