References of "Wilmotte, Annick"
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See detailGenome-wide transcriptional analysis suggests hydrogenase- and nitrogenase-mediated hydrogen production in Clostridium butyricum CWBI 1009
Calusinska, Magda; Hamilton, Christopher; Monsieurs, Pieter et al

in Biotechnology for Biofuels (2015), 8(27), 1-16

Background: Molecular hydrogen, given its pollution-free combustion, has great potential to replace fossil fuels in future transportation and energy production. However, current industrial hydrogen ... [more ▼]

Background: Molecular hydrogen, given its pollution-free combustion, has great potential to replace fossil fuels in future transportation and energy production. However, current industrial hydrogen production processes, such as steam reforming of methane, contribute significantly to the greenhouse effect. Therefore alternative methods, in particular the use of fermentative microorganisms, have attracted scientific interest in recent years. However the low overall yield obtained is a major challenge in biological H2 production. Thus, a thorough and detailed understanding of the relationships between genome content, gene expression patterns, pathway utilisation and metabolite synthesis is required to optimise the yield of biohydrogen production pathways. Results: In this study transcriptomic and proteomic analyses of the hydrogen-producing bacterium Clostridium butyricum CWBI 1009 were carried out to provide a biomolecular overview of the changes that occur when the metabolism shifts to H2 production. The growth, H2-production, and glucose-fermentation profiles were monitored in 20 L batch bioreactors under unregulated-pH and fixed-pH conditions (pH 7.3 and 5.2). Conspicuous differences were observed in the bioreactor performances and cellular metabolisms for all the tested metabolites, and they were pH dependent. During unregulated-pH glucose fermentation increased H2 production was associated with concurrent strong up-regulation of the nitrogenase coding genes. However, no such concurrent up-regulation of the [FeFe] hydrogenase genes was observed. During the fixed pH 5.2 fermentation, by contrast, the expression levels for the [FeFe] hydrogenase coding genes were higher than during the unregulated-pH fermentation, while the nitrogenase transcripts were less abundant. The overall results suggest, for the first time, that environmental factors may determine whether H2 production in C. butyricum CWBI 1009 is mediated by the hydrogenases and/or the nitrogenase. Conclusions: This work, contributing to the field of dark fermentative hydrogen production, provides a multidisciplinary approach for the investigation of the processes involved in the molecular H2 metabolism of clostridia. In addition, it lays the groundwork for further optimisation of biohydrogen production pathways based on genetic engineering techniques. [less ▲]

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See detailPRESPHOTO – a project to improve the preservation of cyanobacteria and diatom cultures
Deprez, Karolien; Vanormelingen, Pieter; Crahay, Charlotte ULg et al

Poster (2014, November 18)

The availability of biological material of guaranteed identity and quality in Biological Resource Centers is considered fundamental for scientific research and R&D, but depends heavily on adequate ... [more ▼]

The availability of biological material of guaranteed identity and quality in Biological Resource Centers is considered fundamental for scientific research and R&D, but depends heavily on adequate preservation methods. We present a new BRAIN-BE project on improving the preservation of two groups of photosynthetic microorganisms, cyanobacteria and diatoms, in two collections of the Belgian Co-ordinated Collections of Micro-organisms (BCCM). First, we will improve the cultivation success of diatoms from different habitats by testing different culture media. For organisms that keep resisting cultivation, we will develop DNA extraction and amplification, as well as morphological investigation based on single cells. Secondly, we will design and validate improved cryopreservation protocols for both diatoms and cyanobacteria, since cryopreservation is now the preferred method for the long-term storage of microalgal cultures. For that, the two-step cryopreservation method will be tested using several cryoprotectants and strains in different growth stages. Moreover, this will be compared with the encapsulation/dehydration method. For cyanobacteria, viability tests will be performed with vital dyes whereas diatoms’ survival will be assessed by PAM fluorometry. In addition, genome resequencing will be applied to determine the impact of the cryopreservation protocol(s) on genomic stability. Finally, a genomic DNA bank will be constructed and validated. This is highly complementary to preservation as living strains, given that some users require only genomic DNA and it may not be feasible to preserve the global microalgal species diversity as living cultures. [less ▲]

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See detailInternational Committee on Systematics of Prokaryotes. Subcommittee on the taxonomy of phototrophic bacteria: Minutes of the meetings, 11 August 2009, Montreal, Canada
Imhoff, Johannes; Wilmotte, Annick ULg

in International Journal of Systematic and Evolutionary Microbiology (2014), 64

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See detailThe phycologist Pierre Compère: his contribution to cyanobacterial studies
Golubic, Stjepko; Wilmotte, Annick ULg

in Plant Ecology and Evolution (2014), 147(3), 307-310

At the occasion of the 80th birthday of Pierre Compère, his rich career as a phycologist and cyanobacteriologist is placed in the context of the advances of the scientific theories, the evolution of the ... [more ▼]

At the occasion of the 80th birthday of Pierre Compère, his rich career as a phycologist and cyanobacteriologist is placed in the context of the advances of the scientific theories, the evolution of the cyanobacterial taxonomy and the nomenclatural discussions linked to the utilization of two different Codes of nomenclature. [less ▲]

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See detailBiogeographical patterns of Antarctic cyanobacteria
Stelmach Pessi, Igor ULg; de Carvalho Maalouf, Pedro; Laughinghouse IV, Haywood Dail et al

Poster (2014, September)

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See detailTHE BCCM/ULC CULTURE COLLECTION TO CONSERVE AND STUDY THE DIVERSITY OF (SUB)POLAR CYANOBACTERIA
Wilmotte, Annick ULg; Renard, Marine ULg; Kleinteich, Julia et al

Poster (2014, September)

The BCCM/ULC public collection of (sub)polar cyanobacteria is funded since 2011 by the Belgian Science Policy Office. A Quality Management System was implemented and is continuously improved since then ... [more ▼]

The BCCM/ULC public collection of (sub)polar cyanobacteria is funded since 2011 by the Belgian Science Policy Office. A Quality Management System was implemented and is continuously improved since then. An ISO9001 certificate was obtained for the public deposition and distribution of strains, as part of the multi-site certification for the BCCM consortium. BCCM/ULC is currently holding 134 cyanobacterial strains and the catalogue is available on http://bccm.belspo.be/catalogues/ulc-catalogue-search. Continuous maintenance of living cultures, some of which are also cryopreserved, ensure the preservation and the possibility to rapidly deliver strains to clients for fundamental and applied research. The collection includes 113 (sub)polar strains. In such extreme environments, cyanobacteria are important phototrophs and primary producers in terrestrial and freshwater ecosystems. The purpose of this collection is to gather a representative portion of the cyanobacterial diversity with different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.) and make it available for researchers to study the taxonomy, evolution, adaptations to environmental conditions, and genomic make-up. Thus, 102 cyanobacterial strains were isolated from the three main biogeographic zones of the Antarctic continent. In addition, 7 strains were isolated in Arctic biotopes and 4 from Siberian lakes. The molecular characterization is underway, on the basis of 16S rRNA and ITS sequences. Moreover, a Multilocus Sequence Analysis is tested on diverse strains to improve their systematics. The diversity encompasses the three main cyanobacterial orders: Chroococcales, Oscillatoriales and Nostocales. In addition, cyanobacteria are known to produce a range of secondary metabolites (e.g. alkaloides, cyclic and linear peptides, polyketides) with different bioactive properties (e.g. antibiotic, antiviral, antifungal, anticancer). The potential of the polar strains to produce cyanotoxins is currently studied by ELISA and the detection by PCR of genes involved in their production. Due to the geographic isolation and the strong environmental stressors of the habitat, the exploration of these metabolites in Antarctic cyanobacterial strains seems promising for biotechnology or biomedical applications. [less ▲]

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See detailUnveiling biogeographic patterns of Antarctic cyanobacteria by 454 pyrosequencing
Wilmotte, Annick ULg; Stelmach Pessi, Igor ULg; De Carvalho, Pedro et al

Poster (2014, August)

Cyanobacteria are often considered as the dominant phototrophs in Antarctic lacustrine environments, primarily occurring in benthic or floating microbial mat communities. Previous studies have indicated ... [more ▼]

Cyanobacteria are often considered as the dominant phototrophs in Antarctic lacustrine environments, primarily occurring in benthic or floating microbial mat communities. Previous studies have indicated the presence of endemic cyanobacteria in the Antarctic Realm, but the extent and patterns of cyanobacterial bioregionalisation, if any, is still largely unknown. Therefore, our objective is to assess the cyanobacterial diversity in Antarctic lacustrine microbial mats using 454 pyrosequencing, in order to determine if cyanobacterial biogeographic patterns are similar to those observed for multicellular organisms. This will be useful also as baseline data, for later comparisons and assessments of the impact of global change. [less ▲]

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See detailEx-situ’ conservation of Antarctic cyanobacteria : a culture collection to explore diversity and bioactivity
Wilmotte, Annick ULg; Renard, Marine ULg; Kleinteich, J et al

Poster (2014, August)

Cyanobacteria appear as the dominant phototrophs in Antarctic terrestrial and freshwater ecosystems. Since 2011, the Belgian Science Policy Office has funded the BCCM/ULC public collection of (sub)polar ... [more ▼]

Cyanobacteria appear as the dominant phototrophs in Antarctic terrestrial and freshwater ecosystems. Since 2011, the Belgian Science Policy Office has funded the BCCM/ULC public collection of (sub)polar cyanobacteria. It is currently holding 102 Antarctic cyanobacterial strains and the catalogue is available on http://bccm.belspo.be/db/ulc_search_form.php. A Quality Management System was implemented and an ISO9001 certificate was obtained for the public deposition and distribution of strains. The strains are kept as living cultures, and their cryopreservation is in progress. The Antarctic cyanobacterial strains were isolated from samples of the three main biogeographic provinces. The purpose of this public collection is to gather a representative portion of the cyanobacterial diversity with different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.) and make it available for researchers to study the diversity, evolution, adaptations to the environmental conditions, and genomic make-up. Three cyanobacterial orders are represented: Chroococcales, Oscillatoriales and Nostocales. This is particularly important in view of the emerging use of metagenomic approaches on environmental samples, where the comparisons with the genome sequences from well-defined strains is very useful. They could also serve as references for compounds such as fatty acids and pigments. In addition, cyanobacteria produce a range of secondary metabolites (e.g. alkaloides, cyclic and linear peptides, polyketides) with different bioactive potential (e.g. antibiotic, antiviral, anticancer, cytotoxic, genotoxic). Bioassays have shown antifungal activities of the cell extracts of strains Plectolyngbya hodgsonii ULC009 and Phormidium priestleyi ULC026. Due to the geographic isolation and the strong environmental stressors of the habitat, the exploration of these metabolites in Antarctic cyanobacterial strains seems especially promising for biotechnology or biomedical applications. In summary, the BCCM/ULC public collection could serve as a general reference for Antarctic cyanobacteria with multiple applications, as well as a resource for novel bioactive compounds. [less ▲]

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See detailOrganic and mineral imprints in fossil photosynthetic mats of an East Antarctic lake
Lepot, Kevin; Compère, Philippe ULg; Gerard, E et al

in Geobiology (2014), 12(5), 424-450

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See detailA Phylogenomic analysis of the origin of plastids
Cornet, Luc ULg; Javaux, Emmanuelle ULg; Wilmotte, Annick ULg et al

Conference (2014, June 24)

Cyanobacteria are a morphologically diverse phylum, with their first occurrence dating from the Precambrian. Oxygenic photosynthesis appeared in this group during the same geological period. Several ... [more ▼]

Cyanobacteria are a morphologically diverse phylum, with their first occurrence dating from the Precambrian. Oxygenic photosynthesis appeared in this group during the same geological period. Several publications have established, without any doubt, that plastids (both primary and complex) form a monophyletic ensemble emerging from Cyanobacteria. However, the exact position of plastids within Cyanobacteria is still uncertain, with several recent papers leading to very different hypotheses. Here we present a phylogenomic analysis of the origin of plastids. Our study takes advantage of all the available genomes and thus represents the best taxonomic sampling seen so far: 140 genomes of Cyanobacteria, 101 genomes of plastids and 27 outgroups taken in Melainabacteria and Chloroflexi. It results in an analysis using state-of-the-art methods (e.g., orthology assessment using USEARCH and OrthoMCL, phylogenetic inference using CAT and CAT-GTR models) based on more than 160 protein alignments totalizing over 20,000 unambiguously aligned amino acids. To confirm our results, we performed gene jackknife inferences and gene reconciliation analyses on the same dataset. We expect that out approach accounts for potential phylogenetic artefacts due to changes in the evolutionary process having occurred when the guest cyanobacterium became an endosymbiont and eventually a plastid. Meanwhile, we improve the phylogeny of Cyanobacteria per se, notably because of the presence of Melainabacteria in our dataset. [less ▲]

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See detailThe BCCM/ULC collection to safeguard and exploit polar cyanobacterial diversity
Wilmotte, Annick ULg

Conference (2014, June 21)

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See detailBCCM/ULC, a culture collection to explore diversity and bioactivity of (sub)polar cyanobacteria
Wilmotte, Annick ULg; Renard, Marine ULg; Kleinteich, Julia et al

Poster (2014, June)

The BCCM/ULC public collection of (sub)polar cyanobacteria is funded since 2011 by the Belgian Science Policy Office. A Quality Management System was implemented and is continuously improved since then ... [more ▼]

The BCCM/ULC public collection of (sub)polar cyanobacteria is funded since 2011 by the Belgian Science Policy Office. A Quality Management System was implemented and is continuously improved since then. An ISO9001 certificate was obtained for the public deposition and distribution of strains, as part of the multi-site certification for the BCCM consortium. BCCM/ULC is currently holding 134 cyanobacterial strains and the catalogue is available on http://bccm.belspo.be/catalogues/ulc-catalogue-search Continuous maintenance of living cultures, some of which are also cryopreserved, ensure the preservation and the possibility to rapidly deliver strains to clients for fundamental and applied research. The collection includes 113 (sub)polar strains. In such extreme environments, cyanobacteria are important phototrophs and primary producers in terrestrial and freshwater ecosystems. The purpose of this public collection is to gather a representative portion of the cyanobacterial diversity with different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.) and make it available for researchers to study the taxonomy, evolution, adaptations to environmental conditions, and genomic make-up. Thus, 102 cyanobacterial strains were isolated from the three main biogeographic zones of the Antarctic continent. In addition, 7 strains were isolated in Arctic biotopes and 4 from Siberian lakes. The molecular characterization is underway, on the basis of 16S rRNA and ITS sequences. The diversity encompasses the three main cyanobacterial orders: Chroococcales, Oscillatoriales and Nostocales. This is particularly important in view of the emerging use of metagenomic approaches on environmental samples, where the comparisons with the genome sequences from well-defined strains is very useful. In addition, cyanobacteria are known to produce a range of secondary metabolites (e.g. alkaloides, cyclic and linear peptides, polyketides) with different bioactive potential (e.g. antibiotic, antiviral, antifungal, anticancer, cytotoxic). The potential of the polar strains to produce cyanotoxins is currently studied by ELISA and the detection by PCR of genes involved in their production. Due to the geographic isolation and the strong environmental stressors of the habitat, the exploration of these metabolites in Antarctic cyanobacterial strains seems especially promising for biotechnology or biomedical applications. In summary, the BCCM/ULC public collection could serve as a general reference for (sub)polar cyanobacteria with multiple applications (pigments, UV screens, …), as well as a resource for novel bioactive compounds [less ▲]

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See detailAssessment of bioinformatic pipelines for the analysis of 454 pyrosequencing data using artificial cyanobacterial communities
Stelmach Pessi, Igor ULg; de Carvalho Maalouf, Pedro; Laughinghouse IV, Haywood Dail et al

Poster (2013, November)

Detailed reference viewed: 178 (15 ULg)
See detailBioregionalisation and biodiversity of Cyanobacterial communities in East- Antarctic lakes
de Carvalho Maalouf, Pedro; Stelmach Pessi, Igor ULg; Verleyen, Elie et al

Poster (2013, July)

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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 detailBiodiversity studies in Open-Top Chambers in continental Antarctica
Mano, Marie-José ULg; Namsaraev, Zorigto; Obbels, Dagmar et al

Poster (2013, July)

Open Top Chambers are passive warming systems used to experimentally assess the effect of climate change on terrestrial ecosystems, and they were used in several Antarctic regions to study the response of ... [more ▼]

Open Top Chambers are passive warming systems used to experimentally assess the effect of climate change on terrestrial ecosystems, and they were used in several Antarctic regions to study the response of biotic communities. In the BELSPO BELDIVA project, OTCs were used in continental Eastern Antarctica, where environmental conditions are very extreme. In January 2010, 8 Open-Top Chambers (OTC) were installed in four ice-free regions of the Sör Rondane Mountains, namely on the Utsteinen ridge, the Tanngarden granite outcrop, the Teltet nunatak and the fourth nunatak of the Pingvinane range. [less ▲]

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See detailHuman impacts on Antarctic ecosystems: do not forget the microorganisms!
Hughes, Kevin; Verleyen, Elie; Vyverman, Wim et al

Conference (2013, July)

The tiny and microscopic creatures that are the permanent inhabitants of the Antarctic continent are often overlooked in environmental impact assessments and when new management and protection strategies ... [more ▼]

The tiny and microscopic creatures that are the permanent inhabitants of the Antarctic continent are often overlooked in environmental impact assessments and when new management and protection strategies are designed. This lack of consideration is probably due to their small size and the need of sophisticated molecular methods to study their diversity, evolution and geographic distribution. However, considerable progress has been made in the field of molecular diversity in the last two decennia, and is still ongoing for Antarctic bacteria, cyanobacteria, protists, fungi, etc. Recent studies have shown the presence of highly diverse microbial communities and the existence of species endemic to Antarctic in some taxonomic groups. With the emergence of High Throughput Sequencing methodologies that are able to detect ‘rare’ taxa, it becomes crucial to find Antarctic locations that have not yet been impacted by human presence. These ‘pristine’ areas are essential to serve as reference sites and allow to distinguish the true Antarctic organisms from the imported ones. Indeed, recent studies have shown that humans unintentionally disperse their own microbial flora but may also spread organisms from other locations. In the extreme biotopes with a reduced diversity that are currently found in Antarctica, such contaminations might have a profound impact. It is important to raise the awareness of scientists, environmental managers and policy makers about the necessity to single out some areas that are kept untouched, or where stringent biosecurity measures are taken. The purpose is not to hinder scientific research, but to weigh carefully, when exploring a new area, the importance of the acquired piece of knowledge in relation to the possibility of hindering future microbiological research. Some parallels with other fields of research are interesting to consider. Archeologists are used to keeping some parts of the explored caves untouched because they foresee that technological progress will allow better analyses in future. The COSPAR Panel on Planetary Protection makes recommendations to avoid the contamination of other planets with microbes from Earth, which would obscure any discovery of extraterrestrial indigenous life forms. These examples illustrate the essential need to integrate the delineation of reference areas for future analyses in the design and execution of scientific research. In fact, the Madrid Protocol foresees the possibility to designate ‘inviolate areas’ (Annex V, Article 3), though this tool has rarely been used. It would be useful if scientists of all disciplines would reflect how to use this management option. [less ▲]

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See detailThe diversity and tolerance to osmotic stress of East Antarctic filamentous Cyanobacteria
Obbels, Dagmar; Verleyen, Elie; Tytgat, Bjorn et al

Poster (2013, July)

Filamentous cyanobacteria are keystone species in Antarctic lake ecosystems; they are the basis of the simple foodwebs, play a crucial role in biogeochemical cycling and form the structure of benthic ... [more ▼]

Filamentous cyanobacteria are keystone species in Antarctic lake ecosystems; they are the basis of the simple foodwebs, play a crucial role in biogeochemical cycling and form the structure of benthic microbial mats which act as habitats for other prokaryotic and (micro-eukaryotic biota. Despite this, little is known about their diversity, adaptation and survival strategies in the extreme Antarctic conditions. We studied the uncultivated prokaryotic diversity using a 454 metagenomic analysis at the 16S rRNA level (V1-V3 region) in Continental Antarctic lakes situated along a conductivity gradient (0.014-142.02 mS/cm). The quality and length of the amplicons was analyzed with a custom-made Mothur pipeline and the resulting sequences were mapped against the Greengenes database, which includes CyanoDB. Almost 27% of the sequences could be assigned to the phylum of the cyanobacteria. The most abundant cyanobacteria in the dataset belonged to the genera Microcoleus, Leptolyngbya, Pseudanabaena, Nodularia and Phormidum. Some 16S rRNA types (at the 97% similarity level), such as sequences related to Leptolynbya antarctica, were present in both freshwater and hypersaline lakes. In order to further investigate this distribution, we isolated filaments of Leptolyngbya from seven lakes with conductivities ranging between 26.8 mS/cm and 0.038 mS/cm. The complete 16S rRNA and ITS genes of the isolates were subsequently sequenced. We found several 16S types related to different lineages of filamentous cyanobacteria in the seven lakes that were supported by ITS data. Two 16S types, belonging to a Leptolyngbya antarctica and Leptolyngbya sp., were each present in two different freshwater lakes. Two different 16S types, both belonging to Leptolynbya antarctica were present in a freshwater and hypersaline lake, which indicates a high ‘intraspecific’ molecular diversity. In order to better understand the adaptation and/or wide tolerance to osmotic stress, we are currently performing ecophysiological experiments with these isolates aimed at assessing the potential local adaptation of these strains to conductivity and desiccation. [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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