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See detailStudy and conservation of Antarctic cyanobacterial diversity in the BCCM/ULC collection
Wilmotte, Annick ULg; Renard, Marine; Ould Amer, Yasmine et al

Poster (2013, July)

The BCCM/ULC public collection presently includes 72 Antarctic cyanobacterial strains and its catalogue is available on http://bccm.belspo.be/db/ulc_search_form.php. An ISO9001 certificate was obtained ... [more ▼]

The BCCM/ULC public collection presently includes 72 Antarctic cyanobacterial strains and its catalogue is available on http://bccm.belspo.be/db/ulc_search_form.php. An ISO9001 certificate was obtained for the public deposition and distribution of strains. The purpose of this collection is to gather a representative sample of Antarctic cyanobacterial diversity from different biotopes (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.) and make it available for researchers to study the diversity, evolution, physiology, and genomic make-up. This is particularly important in view of the emerging use of metagenomic approaches on environmental samples, where the comparison with well-defined strain genome sequences can be very useful. [less ▲]

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See detailA cultivation-independent approach for the genetic and cyanotoxin characterization of colonial cyanobacteria
Lara, Yannick ULg; Lambion, Alexandre ULg; Menzel, Diana et al

in Aquatic Microbial Ecology (2013), 69

To bypass the constraint of cyanobacterial strain isolation and cultivation, a combination of whole genome amplification (WGA) and enzyme-linked immunoassay (ELISA) for microcystin toxins (MCs) was tested ... [more ▼]

To bypass the constraint of cyanobacterial strain isolation and cultivation, a combination of whole genome amplification (WGA) and enzyme-linked immunoassay (ELISA) for microcystin toxins (MCs) was tested on individual colonies of Microcystis and Woronichinia, taken directly from aquatic environments. Genomic DNA of boiled cells was amplified by multiple strand displacement amplification (MDA), followed by several specific PCR reactions to characterize the genotype of each colony. Sequences of 3 different housekeeping genes (ftsZ, gltX, and recA), of 3 MC biosynthesis genes (mcyA, mcyB, and mcyE), and the Internal Transcribed Spacer (ITS) were analyzed for 11 colonies of Microcystis. MCs were detected and quantified by ELISA in 7 of the 11 Microcystis colonies tested, in agreement with the detection of mcy genes. Sequence types (ST) based on the concatenated sequences of housekeeping genes from cyanobacterial colonies from Belgian water bodies appeared to be endemic when compared to those of strains described in the literature. One colony appeared to belong to a yet undiscovered lineage. A similar protocol was used for 6 colonies of the genus Woronichinia, a taxon that is very difficult to cultivate in the laboratory. The 16S rRNA sequences of 2 colonies were obtained and were quasi identical to that of W. naegeliana 0LE35S01. For one Woronichinia colony, the mcyE PCR gave a non-specific PCR product. The corresponding amino acid sequence was 50% identical to a Microcystis ketoacyl carrier protein transferase. This approach for the simultaneous detection and quantification of MCs with mcy genotyping, at single colony level, offers potential for the ecotoxicological characterization of environmental populations of cyanobacteria without the need for strain isolation and culture. [less ▲]

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See detailPotentiel secondary metabolite biosynthesis operons in environmental colonies of Woronischinia
Lara, Yannick ULg; Lambion, Alexandre ULg; Codd, Goeffrey A. et al

Poster (2010, September 01)

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See detailBacillus amyloliquefaciens GA1 as a source of potent antibiotics and other secondary metabolites for biocontrol of plant pathogens.
Arguelles-Arias, A.; Ongena, MARC ULg; Halimi, B. et al

in Microbial Cell Factories (2009), 8(1), 63

ABSTRACT: BACKGROUND: Phytopathogenic fungi affecting crop and post-harvested vegetables are a major threat to food production and food storage. To face these drawbacks, producers have become increasingly ... [more ▼]

ABSTRACT: BACKGROUND: Phytopathogenic fungi affecting crop and post-harvested vegetables are a major threat to food production and food storage. To face these drawbacks, producers have become increasingly dependent on agrochemicals. However, intensive use of these compounds has led to the emergence of pathogen resistance and severe negative environmental impacts. There are also a number of plant diseases for which chemical solutions are ineffective or non-existent as well as an increasing demand by consumers for pesticide-free food. Thus, biological control through the use of natural antagonistic microorganisms has emerged as a promising alternative to chemical pesticides for more rational and safe crop management. RESULTS: The genome of the plant-associated B. amyloliquefaciens GA1 was sample sequenced. Several gene clusters involved in the synthesis of biocontrol agents were detected. Four gene clusters were shown to direct the synthesis of the cyclic lipopeptides surfactin, iturin A and fengycin as well as the iron-siderophore bacillibactin. Beside these non-ribosomaly synthetised peptides, three additional gene clusters directing the synthesis of the antibacterial polyketides macrolactin, bacillaene and difficidin were identified. Mass spectrometry analysis of culture supernatants led to the identification of these secondary metabolites, hence demonstrating that the corresponding biosynthetic gene clusters are functional in strain GA1. In addition, genes encoding enzymes involved in synthesis and export of the dipeptide antibiotic bacilysin were highlighted. However, only its chlorinated derivative, chlorotetaine, could be detected in culture supernatants. On the contrary, genes involved in ribosome-dependent synthesis of bacteriocin and other antibiotic peptides were not detected as compared to the reference strain B. amyloliquefaciens FZB42. CONCLUSION: The production of all of these antibiotic compounds highlights B. amyloliquefaciens GA1 as a good candidate for the development of biocontrol agents. [less ▲]

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See detailA new approach to analyze genotypes of colony-forming cyanobacteria from environmental samples.
Lara, Yannick ULg; BOUTTE, Christophe; PERETYATKO, Anatoly et al

Poster (2008, August 31)

Several studies have shown the efficiency of sequences as rRNA-ITS, cpcBA, rbcLX and other housekeeping genes to study taxonomy [1, 2, 3], population, community structure of cyanobacteria, or for Multi ... [more ▼]

Several studies have shown the efficiency of sequences as rRNA-ITS, cpcBA, rbcLX and other housekeeping genes to study taxonomy [1, 2, 3], population, community structure of cyanobacteria, or for Multi Locus Sequence Analysis [4]. Recently, the genotypic analysis of single colonies and single filaments directly isolated from the environment has been carried out by other authors. It appears that different genotypes of Microcystis are present in one population in one lake. Besides, succession of toxic and non-toxic genotypes may have a critical influence on toxin concentrations during the blooms [5]. Genotypic analysis of colony-forming cyanobacteria requires enough DNA. So far, the genotypes of environmental single colonies of Microcystis were characterized on the basis of one or two PCR [6]. As the DNA content of one single colony only allows for a few PCR reactions, we have developed a new approach using Whole Genome Amplification with Phi29 polymerase to allow for the Multi Locus Sequences Typing analysis of a single colony or filament. For the first time, we were able to amplify and sequence more than one locus of the genome of a single colony of Microcystis. In addition, we have obtained the first sequences of rpoC1, rbcLX and rRNA-ITS from a single colony of the genus Woronichinia ( identified by microscopy). This approach allows to work with a small amount of DNA, and represents a concrete answer to the lack of data on non-cultivable cyanobacteria. This research is supported by the Belgian Science policy under the science for a sustainable development (SSD) and Fonds de la Recherche Scientifique-FNRS with a FRIA fellowship. References: [1] Otsuka S, et al (1999) FEMS Microbiology Letters 172 15-21 [2] Gugger M, et al (2002) Int J Syst Evol Microbiol 52 1867-1880 [3] Haverkamp T, et al (2008) Environmental Microbiology 10(1) 174-188 [4] Lodders N, et al (2005) Environmental Microbiology 7 (3) 434-442 [5] Kardinaal E, and Visser P (2005) In Harmfuf cyanobacteria, Springer Dordrecht pp 41-64 [6] Janse I, et al (2004) Appl Environm Microbiol 70 (7) 3979–3987 [less ▲]

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See detailDiversité moléculaire des cyanobactéries planctonniques dans les eaux de surface belges
Lara, Yannick ULg; Lambion, Alexandre ULg; Simon, Patricia ULg et al

Poster (2008, April 02)

Les développements massifs de cyanobactéries ou ‘blooms’ sont devenus un phénomène récurrent et de plus en plus important dans les eaux douces du monde entier durant la dernière décennie. Ces ... [more ▼]

Les développements massifs de cyanobactéries ou ‘blooms’ sont devenus un phénomène récurrent et de plus en plus important dans les eaux douces du monde entier durant la dernière décennie. Ces efflorescences présentent des risques potentiels majeurs pour la santé humaine et animale et interfèrent négativement avec l'utilisation des eaux de surface par exemple, pour le captage d'eau potable, les loisirs nautiques, l'irrigation, les exploitations piscicoles. Entre 25 et 70% des blooms sont toxiques. Comme beaucoup de pays la Belgique n'a pas échappé au problème des efflorescences de cyanobactéries toxiques, mais il y a encore relativement peu de données. Durant la dernière décennie, trois projets européens et nationaux (MIDICHIP 1999-2003, B-BLOOMS 2003-2005, B-BLOOMS 2 2007-2011) se sont intéressés à la diversité des cyanobactéries dans les eaux de surfaces belges. Nous présentons ici un arbre phylogénétique élaboré à partir d’ un pool de 249 séquences partielles du gène codant pour l’ARNr 16S obtenu à partir de 31 échantillons d’eaux belges issus de ces projets. Cet arbre représente la mise à jour d’une base de données qui constitue l’inventaire des cyanobactéries d’eaux douces belges. Cette base de données permet le suivi de l’évolution de la diversité observable de ces organismes en Belgique et la surveillance de l’apparition d’espèces tropicales comme conséquence aux changements climatiques globaux. [less ▲]

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See detailAnalyse bioinformatique de différents marqueurs génétiques pour la caractérisation taxonomique et génotypique des algues bleues.
Lara, Yannick ULg; Wilmotte, Annick ULg

Poster (2008, April)

Les cyanobactéries (ou algues bleues) sont des organismes procaryotes photosynthétiques considérés comme les ancêtres des plastes des végétaux eucaryotes. Présentes dans différents types d’habitats ... [more ▼]

Les cyanobactéries (ou algues bleues) sont des organismes procaryotes photosynthétiques considérés comme les ancêtres des plastes des végétaux eucaryotes. Présentes dans différents types d’habitats terrestres ou aquatiques, elles peuvent produire des composés bioactifs d’intérêt pour des industries pharmaceutiques, ou encore des toxines présentant un risque potentiel pour la santé humaine et animale. Il est donc important de pouvoir caractériser différentes espèces et différents génotypes de ces organismes de manière indubitable pour pouvoir détecter leur présence/absence, évaluer leur rôle au sein de leur écosystème, ainsi que l’influence des facteurs environnementaux sur leur cycle de vie. La caractérisation taxonomique des cyanobactéries a longtemps été réalisée par l’étude des critères morphologiques. Cependant cette approche s’avère délicate quand ces critères peuvent être altérés par la mise en culture. De plus, cette approche requiert une expérience importante et ne permet pas de différencier des génotypes toxiques. La séquence du gène codant pour l’ARN ribosomique 16S est utilisée pour différencier les cyanobactéries jusqu’au genre et parfois jusqu’à l’espèce. Mais, dans certains cas, elle ne coïncide ni avec la description morphologique spécifique, ni avec la production de certaines toxines. Dans le cadre de cette étude, nous proposons d’évaluer l’information taxonomique et génotypique de marqueurs génétiques singuliers présents dans les génomes de cyanobactéries séquencés d la base de données Genbank. Les distances génétiques entre les parties de 32 génomes suffisamment conservées pour être alignées ont été mesurées. Ces distances ont ensuite été comparées par régression linéaire aux distances génétiques de différents loci précis (ARNr 16S, kaiC, lexA, rpoC1, recA). Les résultats préliminaires montrent un R2 de 0,9141 pour la régression linéaire entre les distances génétiques du gène recA et des régions conservées des génomes séquencés appartenant au genre Prochlorococcus. Ce résultat suggère que recA serait potentiellement un bon marqueur pour génotyper des organismes du genre Prochlorococcus. [less ▲]

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