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See detailPolyphasic study of Antarctic cyanobacterial strains
Taton, A.; Grubisic, Stana ULg; Ertz, D. et al

in Journal of Phycology (2006), 42(6), 1257-1270

We isolated 59 strains of cyanobacteria from the benthic microbial mats of 23 Antarctic lakes, from five locations in two regions, in order to characterize their morphological and genotypic diversity. On ... [more ▼]

We isolated 59 strains of cyanobacteria from the benthic microbial mats of 23 Antarctic lakes, from five locations in two regions, in order to characterize their morphological and genotypic diversity. On the basis of their morphology, the cyanobacteria were assigned to 12 species that included four Antarctic endemic taxa. Sequences of the ribosomal RNA gene were determined for 56 strains. In general, the strains closely related at the 16S rRNA gene level belonged to the same morphospecies. Nevertheless, divergences were observed concerning the diversity in terms of species richness, novelty, and geographical distribution. For the 56 strains, 21 operational taxonomic units (OTUs, defined as groups of partial 16S rRNA gene sequences with more than 97.5% similarity) were found, including nine novel and three exclusively Antarctic OTUs. Sequences of Petalonema cf. involvens and Chondrocystis sp. were determined for the first time. The internally transcribed spacer (ITS) between the 16S and the 23S rRNA genes was sequenced for 33 strains, and similar groupings were observed with the 16S rRNA gene and the ITS, even when the strains were derived from different lakes and regions. In addition, 48 strains were screened for antimicrobial and cytotoxic activities, and 17 strains were bioactive against the gram-positive Staphylococcus aureus, or the fungi Aspergillus fumigatus and Cryptococcus neoformans. The bioactivities were not in coincidence with the phylogenetic relationships, but rather were specific to certain strains. [less ▲]

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See detailThe cyanophyte Arthrospira fusiformis from Mozambique, Africa: Morphological and molecular characterization
Mussagy, Aidate; Wilmotte, Annick ULg; Cronberg, Gertrud

in Algological Studies (2006), 121

The morphology and the Internally Transcribed Spacer sequences of two Arthrospira (Cyanobacteria) strains with tightly coiled and loosely coiled trichome, isolated from waste water treatment ponds in ... [more ▼]

The morphology and the Internally Transcribed Spacer sequences of two Arthrospira (Cyanobacteria) strains with tightly coiled and loosely coiled trichome, isolated from waste water treatment ponds in Maputo, Mozambique, were investigated. According to the accepted traditional classification the tightly coiled strains were assigned as Arthrospira fusiformis and the loosely coiled as Arthrospira maxima. In both clonal cultures, initiated from a tightly coiled (strain 1) or a loosely coiled trichome (strain 2), different variants arose, in which the tightly coiled forms were more lax than the inoculated cloned trichomes, and loosely coiled forms became tightly coiled. In both cultures, different transient forms appeared, and even straight trichomes were observed. The straight form (variant 1) was isolated and cultivated under different light intensities. After two months, this straight form had not changed into coiled trichomes. However, the trichomes obtained after growth of the hormogonia of the straight trichomes contained a mixture of loosely coiled and straight trichomes.On the basis of the morphological analysis of Arthrospira, it is evident that the degree of coiling is highly variable, which creates uncertainty when used to define the different species. The DNA from the two clonal strains 1 and 2 was isolated and a part of the rRNA operon (including the 3' end of the 16S rRNA gene and the Internally Transcribed Spacer) was determined after amplification by PCR using specific primers. The two ITS sequences were identical and belonged to the subcluster I.A., as defined by Baurain et al. (2002). Variant 1 gave also an identical ITS sequence. A PCR to test the presence of mcyE, a gene involved in the synthesis of the microcystin synthetase, was negative for the two strains and the variant 1. This study showed that for a reliable identification of Arthrospira species, information from specimens collected in the field, cultured strains, developmental stages, and molecular analysis, should be combined. [less ▲]

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See detailBiogeographical distribution and ecological ranges of benthic cyanobacteria in East Antarctic lakes
Taton, A.; Grubisic, Stana ULg; Balthasart, Pierre ULg et al

in FEMS Microbiology Ecology (2006), 57(2), 272-289

For the first time, the cyanobacterial diversity from microbial mats in lakes of Eastern Antarctica was investigated using microscopic and molecular approaches. The present study assessed the ... [more ▼]

For the first time, the cyanobacterial diversity from microbial mats in lakes of Eastern Antarctica was investigated using microscopic and molecular approaches. The present study assessed the biogeographical distribution of cyanobacteria in Antarctica. Five samples were taken from four lakes spanning a range of different ecological environments in Larsemann Hills, Vestfold Hills and Rauer Islands to evaluate the influence of lake characteristics on the cyanobacterial diversity. Seventeen morphospecies and 28 16S rRNA gene-based operational taxonomic units belonging to the Oscillatoriales, Nostocales and Chroococcales were identified. The internal transcribed spacer was evaluated to complement the 16S rRNA gene data and showed similar but more clear-cut tendencies. The molecular approach suggested that potential Antarctic endemic species, including a previously undiscovered diversity, are more abundant than has been estimated by morphological methods. Moreover, operational taxonomic units, also found outside Antarctica, were more widespread over the continent than potential endemics. The cyanobacterial diversity of the most saline lakes was found to differ from the others, and correlations between the sampling depth and the cyanobacterial communities can also be drawn. Comparison with database sequences illustrated the ubiquity of several cyanobacterial operational taxonomic units and their remarkable range of tolerance to harsh environmental conditions. [less ▲]

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See detailTesting of primers for the study of cyanobacterial molecular diversity by DGGE
Boutte, C.; Grubisic, Stana ULg; Balthasart, Pierre ULg et al

in Journal of Microbiological Methods (2006), 65(3), 542-550

Denaturing Gradient Gel electrophoresis (DGGE) is a PCR-based technique which is widely used in the study of microbial communities. Here, the use of the three specific 16S rRNA cyanobacterial specific ... [more ▼]

Denaturing Gradient Gel electrophoresis (DGGE) is a PCR-based technique which is widely used in the study of microbial communities. Here, the use of the three specific 16S rRNA cyanobacterial specific primers CYA359F, CYA781R(a) and CYA781R(b) on the assessment of the molecular diversity of cyanobacterial communities is examined. Assignments of the reverse primers CYA781R(a) and CYA781R(b) with cyanobacterial strain sequences showed that the former preferentially targets filamentous cyanobacteria whereas the latter targets unicellular cyanobacteria. The influence of the GC clamp position on the forward Or on reverse primer and the use of the two reverse primers separately or in equimolar mixture were investigated. Three environmental samples were subjected to amplification with 6 combinations of primers. The 6 banding patterns as well as the sequences of the bands extracted were analysed and compared. In addition, to assess the effect of the position of the GC clamp, the melting profiles of the sequences of Aphanizomenon flos-aquae PMC9707 and Synechococcus sp. MH305 were determined, with the GC clamp in the 3' or 5' position. Results showed that the use of two separate amplifications allowed a more complete study of the molecular diversity of the cyanobacterial community investigated. Furthermore, similar richness and identical phylogenctic assignments of extracted bands were obtained irrespective of the positioning of the GC clamp. (c) 2005 Elsevier B.V. All rights reserved. [less ▲]

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See detailUltrastructure and taxonomic position of two species of the cyanobacterial genus Schizothrix
Komarek, J.; Taton, A.; Sulek, J. et al

in Cryptogamie Algologie (2006), 27(1), 53-62

The cyanobacterial genus Schizothrix is traditionally classified in the special family Schizotrichaceae (order Oscillatoriales) according to the structure of the filaments and thallus: one, two, or more ... [more ▼]

The cyanobacterial genus Schizothrix is traditionally classified in the special family Schizotrichaceae (order Oscillatoriales) according to the structure of the filaments and thallus: one, two, or more ensheathed and fasciculated trichomes are enveloped by common sheaths. The fine Structure of cells and filaments of two natural populations of typical Schizothrix-species (S. facilis, S lacustris) were investigated in our Study. The ultrastructure of trichomes was found to be similar to the pseudartabaenacean types (thylakoid arrangement, inclusions, cell wall), and indicates the close relationship to this group of simple filamentous cyanobacteria. The special life form, which was considered as the most important phenotypic intergeneric (and interfamilial) differentiating character was proven: Fasciculated trichomes are enveloped by their own sheaths, and form (usually heteropolar) filaments enveloped by mother common sheath. However, in spite of the fact that the ultrastructure and morphology of trichomes were found to be similar to other pseudanabacnacean types, the relationship to Pseudanabaenaceae must await detailed molecular studies to be more completely evaluated. The first molecular results concerning a few Schizothrix-like strains from Antarctica show that most belong to a cluster, which is separated from the other oscillatorian clusters. This could support the genetic basis of the Schizothrix genus. [less ▲]

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See detailMicrobial ecology of the closed artificial ecosystem MELiSSA (Micro-Ecological Life Support System Alternative): Reinventing and compartmentalizing the Earth's food and oxygen regeneration system for long-haul space exploration missions
Hendrickx, Larissa; De Wever, Heleen; Hermans, Veronik et al

in Research in Microbiology (2006), 157

MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system ... [more ▼]

MELiSSA is a bioregenerative life support system designed by the European Space Agency (ESA) for the complete recycling of gas, liquid and solid wastes during long distance space exploration. The system uses the combined activity of different living organisms: microbial cultures in bioreactors, a plant compartment and a human crew. In this minireview, the development of a short-cut ecological system for the biotransformation of organic waste is discussed from a microorganism's perspective. The artificial ecological model—still in full development—that is inspired by Earth's own geomicrobiological ecosystem serves as an ideal study object on microbial ecology and will become an indispensable travel companion in manned space exploration. [less ▲]

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See detailBiogeographic trends in Antarctic lake communities
Gibson, John; Wilmotte, Annick ULg; Taton, Arnaud et al

in Bergstrom, Dana; Convey, Peter; Huiskes, Ad HL (Eds.) Trends in Antarctic terrestrial and limnetic ecosystems (2006)

The basic biogeographic zones proposed many years ago – the Subantarctic islands, Maritime Antarctica and Continental Antarctica – continue to hold up, though they cannot be seen as absolute dividers of ... [more ▼]

The basic biogeographic zones proposed many years ago – the Subantarctic islands, Maritime Antarctica and Continental Antarctica – continue to hold up, though they cannot be seen as absolute dividers of biodiversity. For example, subantarctic Macquarie Island appears to be biogeographically separate from the islands of the Kerguelen Province, and on the continent there are species that are present in lakes of more than one zone. Furthermore, there are numerous lake environments that have yet to be investigated, and it is probable that some of these lakes could turn up surprises that will bring into question these basic divisions. An important question to be answered is whether these biogeographic zones reflect climate attributes, or whether they were moulded long ago by barriers to dispersal. Again, our imperfect knowledge of Antarctic lacustrine biogeography means that this question cannot at present be answered. However, as discussed elsewhere in this volume (Chown and Convey), there are indications of a strong biogeographical boundary for terrestrial species between the Maritime and Continental Antarctic zones. A palaeolimnological approach will assist in answering this question: understanding how Antarctic biogeography has developed through time will provide necessary insights into current distributions. A prime example is the occurrence of the copepod Boeckella poppei in Beaver Lake. Pugh et al. (2002) initially concluded that this species was an anthropogenic introduction, then Bayly et al. (2003) provided morphological evidence for long habitation in the area of Beaver Lake. Recent palaeolimnological work has shown that the species has been present in nearby Lake Terrasovoje for at least 9000 yrs (L. Cromer, A. Bissett, J. Gibson and K. Swadling, unpublished data). Even though this lake has only existed in the Holocene, cosmogenic exposure dates in the same area of exposed rock can exceed 106 years (D. Gore and D. White, personal communication). From these observations it can be concluded that Boeckella poppei has been associated with the Beaver Lake area for at least the entire Holocene and probably well back into the Pleistocene, and that its occurrence outside its ‘preferred’ biogeographical zone (Maritime Antarctica) is not a reflection of current climate, rather of history. The majority of our knowledge regarding Antarctic lacustrine biodiversity and biogeography has come from classic taxonomic studies, where the morphology (or biochemistry for bacteria) has been of greatest importance. In many cases this has led to questionable identification, correct identification of species is paramount if the true biodiversity and biogeography of Antarctica is to be deduced. It is only in the last few years that the more objective approach of molecular genetics has been applied to Antarctic lacustrine organisms, and then only for more cryptic groups, such as bacteria and cyanobacteria. As more samples and organisms are studied by these methods it is likely that new relationships between species distributions will be found. Due to the limited number of species in Antarctica (compared to more temperate zones), it may be possible in the future to record the make-up of selected genes of most, if not all, of the biota, which will allow more precise analysis. There is increasing evidence for endemism amongst the inhabitants of lakes both on the Antarctic continent and the subantarctic islands, from bacteria to crustacea. Use of molecular genetic techniques to identify more cryptic species will most likely add to the list of putative endemics. It is clear, however, that recent colonisation and current climate also play important roles in the distribution of the biota, as most of the lakes in Antarctica are of relatively recent (Holocene) origin. Colonising species have to be adapted to transport from source areas, which can either involve inter- or intra-continental movement, as well as survival on arrival at potential habitat. Flexibility in nutritional and habitat requirements is an important factor in determining whether a species will be a successful coloniser. The buffering to environmental extremes provided by the liquid water habitat means that conditions further south will not be as harsh as those experienced by their terrestrial counterparts. As the climate changes in the future, it will be interesting to note the effects of these changes on the lacustrine biota. Will new species colonise the Antarctic Peninsula where temperatures are warming? In the longer term, the biogeography of Antarctic lakes will continue to be dynamic. New species will arrive, others will become extinct. The biogeographic zones long-proposed may continue to hold, though more precise knowledge of current distributions and responses to climate change may refine our view. [less ▲]

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See detailA polyphasic approach to assess the cyanobacterial diversity of summer samples from Czech reservoirs
Boutte, Christophe; Komarkova, Jarka; Grubisic, Stana ULg et al

in Algological Studies (2005), 117

We used a polyphasic approach combining data from microscopic assessment of fresh biomass and from clone libraries and DGGE fingerprints based on 16S rRNA gene sequences to investigate the cyanobacterial ... [more ▼]

We used a polyphasic approach combining data from microscopic assessment of fresh biomass and from clone libraries and DGGE fingerprints based on 16S rRNA gene sequences to investigate the cyanobacterial diversity of Czech reservoirs during the summer in 2001 and 2002. In total, 15 genera were identified using the microscopic analysis in 38 samples analysed. They were Aphanizomenon, Anabaena, Anabaenopsis, Aphanocapsa, Aphanothece, Pseudanabaena, Planktothrix, Planktolyngbya, Limnothrix, Woronichinia, Snowella, Romeria, Microcystis, Merismopedia, and Coelomoron. We recovered 113 DGGE band sequences from the same samples. In addition, 128 partial 16S rRNA sequences were obtained from two clone libraries of reservoirs Pilská and Orlík. The phylogenetic comparison with the currently available rRNA sequences in databases showed that our sequences belonged to 8 clusters: Woronichinia, Microcystis, Synechococcus, Snowella, Planktothrix, Anabaena/Aphanizomenon, Limnothrix and a plastid related to Chrysochromulina polylepis. The microscopic enumeration and the molecular results were generally congruent concerning the major populations determined in these samples (for 32 samples among 38). Anabaena/Aphanizomenon, Microcystis and Woronichinia were the major genera in the Czech reservoirs during summer, and were present in most of the samples. This study showed some discrepancies between the genera retrieved by the traditional method and the molecular analyses. Differences concerned the presence of minor populations belonging to Aphanothece, Romeria, Merismopedia, Synechococcus, Snowella and Pseudanabena. These differences could be explained by biases specific to each method (competitive amplification, difficulty to obtain sequences from DGGE bands, not precise microscopic observation of the small-sized genera). [less ▲]

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See detail(WO/2004/104211) METHOD FOR DETECTING TOXIC AND NON-TOXIC CYANOBACTERIA
SIVONEN, Kaarina; RANTALA, Anne; Rouhianen, Leo et al

Patent (2004)

This invention is related to a method for detecting toxic and non-toxic cyanobacteria. The method comprises that nucleic acid from a biological sample is brought into contact with an oligonucleotide ... [more ▼]

This invention is related to a method for detecting toxic and non-toxic cyanobacteria. The method comprises that nucleic acid from a biological sample is brought into contact with an oligonucleotide designed to be specific for particular regions of the mcyE gene, the mcyE in combination with mcyD, and with an oligonucleotide designed to be specific for 16SrDNA, and the presence or absence of toxic cyanobacteria is detected by a suitable molecular biology method. The invention is related also to oligonucleotides used in the method. [less ▲]

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See detailDevelopment of a universal microarray based on the ligation detection reaction and 16S rRNA gene polymorphism to target diversity of cyanobacteria
Castiglioni, Bianca; Rizzi, Ermann; Frosini, Andrea et al

in Applied and Environmental Microbiology (2004), 70(12), 7161-7172

The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds ... [more ▼]

The cyanobacteria are photosynthetic prokaryotes of significant ecological and biotechnological interest, since they strongly contribute to primary production and are a rich source of bioactive compounds. In eutrophic fresh and brackish waters, their mass occurrences (water blooms) are often toxic and constitute a high potential risk for human health. Therefore, rapid and reliable identification of cyanobacterial species in complex environmental samples is important. Here we describe the development and validation of a microarray for the identification of cyanobacteria in aquatic environments. Our approach is based on the use of a ligation detection reaction coupled to a universal array. Probes were designed for detecting 19 cyanobacterial groups including Anabaena/Aphanizomenon, Calothrix, Cylindrospermopsis, Cylindrospermum, Gloeothece, halotolerants, Leptolyngbya, Palau Lyngbya, Microcystis, Nodularia, Nostoc, Planktothrix, Antarctic Phormidium, Prochlorococcus, Spirulina, Synechococcus, Synechocystis, Trichodesmium, and Woronichinia. These groups were identified based on an alignment of over 300 cyanobacterial 16S rRNA sequences. For validation of the microarrays, 95 samples (24 axenic strains from culture collections, 27 isolated strains, and 44 cloned fragments recovered from environmental samples) were tested. The results demonstrated a high discriminative power and sensitivity to 1 fmol of the PCR-amplified 16S rRNA gene. Accurate identification of target strains was also achieved with unbalanced mixes of PCR amplicons from different cyanobacteria and an environmental sample. Our universal array method shows great potential for rapid and reliable identification of cyanobacteria. It can be easily adapted to future development and could thus be applied both in research and environmental monitoring. [less ▲]

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See detailSalinity, depth and the structure and composition of microbial mats in continental Antarctic lakes
Sabbe, Koen; Hodgson, Dominic A.; Verleyen, Elie et al

in Freshwater Biology (2004), 49(3), 296-319

1. Lakes and ponds in the Larsemann Hills and Bolingen Islands (East-Antarctica) were characterised by cyanobacteria-dominated, benthic microbial mats. A 56-lake dataset representing the limnological ... [more ▼]

1. Lakes and ponds in the Larsemann Hills and Bolingen Islands (East-Antarctica) were characterised by cyanobacteria-dominated, benthic microbial mats. A 56-lake dataset representing the limnological diversity among the more than 150 lakes and ponds in the region was developed to identify and quantify the abiotic conditions associated with cyanobacterial and diatom communities. 2. Limnological diversity in the lakes of the Larsemann Hills and Bolingen Islands was associated primarily with conductivity and conductivity-related variables (concentrations of major ions and alkalinity), and variation in lake morphometry (depth, catchment and lake area). Low concentrations of pigments, phosphate, nitrogen, DOC and TOC in the water column of most lakes suggest extremely low water column productivity and hence high water clarity, and may thus contribute to the ecological success of benthic microbial mats in this region. 3. Benthic communities consisted of prostrate and sometimes finely laminated mats, flake mats, epilithic and interstitial microbial mats. Mat physiognomy and carotenoid/chlorophyll ratios were strongly related to lake depth, but not to conductivity. 4. Morphological-taxonomic analyses revealed the presence of 26 diatom morphospecies and 33 cyanobacterial morphotypes. Mats of shallow lakes (interstitial and flake mats) and those of deeper lakes (prostrate mats) were characterised by different dominant cyanobacterial morphotypes. No relationship was found between the distribution of these morphotypes and conductivity. In contrast, variation in diatom species composition was strongly related to both lake depth and conductivity. Shallow ponds were mainly characterised by aerial diatoms (e.g. Diadesmis cf. perpusilla and Hantzschia spp.). In deep lakes, communities were dominated by Psammothidium abundans and Stauroforma inermis. Lakes with conductivities higher than +/-1.5 mS cm(-1) became susceptible to freezing out of salts and hence pronounced conductivity fluctuations. In these lakes P. abundans and S. inermis were replaced by Amphora veneta. Stomatocysts were important only in shallow freshwater lakes. 5. Ice cover influenced microbial mat structure and composition both directly by physical disturbance in shallow lakes and by influencing light availability in deeper lakes, as well as indirectly by generating conductivity increases and promoting the development of seasonal anoxia. 6. The relationships between diatom species composition and conductivity, and diatom species composition and depth, were statistically significant. Transfer functions based on these data can therefore be used in paleolimnological reconstruction to infer changes in the precipitation-evaporation balance in continental Antarctic lakes. [less ▲]

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See detailCyanobacterial diversity in natural and artificial microbial mats of Lake Fryxell (McMurdo dry valleys, Antarctica): A morphological and molecular approach
Taton, A.; Grubisic, Stana ULg; Brambilla, E. et al

in Applied and Environmental Microbiology (2003), 69(9), 5157-5169

Currently, there is no consensus concerning the geographic distribution and extent of endemism in Antarctic cyanobacteria. In this paper we describe the phenotypic and genotypic diversity of cyanobacteria ... [more ▼]

Currently, there is no consensus concerning the geographic distribution and extent of endemism in Antarctic cyanobacteria. In this paper we describe the phenotypic and genotypic diversity of cyanobacteria in a field microbial mat sample from Lake Fryxell and in an artificial cold-adapted sample cultured in a benthic gradient chamber (BGC) by using an inoculum from the same mat. Light microscopy and molecular tools, including 16S rRNA gene clone libraries, denaturing gradient gel electrophoresis, and sequencing, were used. For the first time in the study of cyanobacterial diversity of environmental samples, internal transcribed spacer (ITS) sequences were retrieved and analyzed to complement the information obtained from the 16S rRNA gene. Microscopy allowed eight morphotypes to be identified, only one of which is likely to be an Antarctic endemic morphotype. Molecular analysis, however, revealed an entirely different pattern. A much higher number of phylotypes (15 phylotypes) was found, but no sequences from Nodularia and Hydrocoryne, as observed by microscopy, were retrieved. The 16S rRNA gene sequences determined in this study were distributed in 11 phylogenetic lineages, 3 of which were exclusively Antarctic and 2 of which were novel. Collectively, these Antarctic sequences together with all the other polar sequences were distributed in 22 lineages, 9 of which were exclusively Antarctic, including the 2 novel lineages observed in this study. The cultured BGC mat had lower diversity than the field mat. However, the two samples shared three morphotypes and three phylotypes. Moreover, the BGC mat allowed enrichment of one additional phylotype. ITS sequence analysis revealed a complex signal that was difficult to interpret. Finally, this study provided evidence of molecular diversity of cyanobacteria in Antarctica that is much greater than the diversity currently known based on traditional microscopic analysis. Furthermore, Antarctic endemic species were more abundant than was estimated on the basis of morphological features. Decisive arguments concerning the global geographic distribution of cyanobacteria should therefore incorporate data obtained with the molecular tools described here. [less ▲]

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See detailRemarkable conservation of internally transcribed spacer sequences of Arthrospira ("Spirulina") (Cyanophyceae, Cyanobacteria) strains from four continents and of recent and 30-year-old dried samples from Africa
Baurain, Denis ULg; Renquin, Laurent; Grubisic, Stana ULg et al

in Journal of Phycology (2002), 38(2), 384-393

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the ... [more ▼]

The internally transcribed spacer (ITS) sequences of 21 Arthrospira clonal strains from four continents and assigned to four different species (A. platensis, A. maxima, A. fusiformis, A. indica) in the culture collections were determined. Two main clusters, I and H, were differentiated by 49 positions out of 475 nt or 477 nt, respectively. Each cluster was further subdivided into two subclusters. Subclusters LA and I.B were separated by two substitutions, whereas subclusters II.A, and II.B were distinguished by four substitutions. After direct sequencing of the PCR products, three dried samples from Chad aged between 3 months and 35 years yielded a sequence belonging to subcluster I.A, as did a recent commercial product. The strains grown in production plants belonged to the same (sub)clusters as strains from culture collections, mainly LA and II. PCR primers specific for each cluster and subcluster were designed and tested with crude cell lysates of Arthrospira strains. One dried sample ("dihe' 1) and a herbarium sample from Lake Sonachi (Kenya) only contained I.A sequences, whereas the commercial product was a mixture of the four genotypes and the other two dried samples contained minor polymorphisms characteristic of different clusters. Five clonal Arthrospira strains, thought to be duplicates, showed the simultaneous presence of the two :Forms of the four diagnostic positions that distinguish subclusters genotype H.A and genotype II.B. This is likely to be caused by multiple copies of the rDNA operon, in a intermediate stage of homogenization between subcluster II.A and subcluster II.B. The high conservation of ITS sequences is in contrast with the assignment to four different species, the great morphological variability of the strains, and their wide geographic distribution. [less ▲]

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See detailMolecular and pigment studies of the picophytoplankton in a region of the Southern Ocean (42-54 degrees S, 141-144 degrees E) in March 1998
Wilmotte, Annick ULg; Demonceau, Caroline; Goffart, Anne ULg et al

in Deep-Sea Research Part II, Topical Studies in Oceanography (2002), 49(16), 3351-3363

Seven filtered seawater samples (depths between 30 and 55 m) collected during the SAZ project of the Austral summer of 1997-1998 were used for a simultaneous study of the picophytoplankton pigments based ... [more ▼]

Seven filtered seawater samples (depths between 30 and 55 m) collected during the SAZ project of the Austral summer of 1997-1998 were used for a simultaneous study of the picophytoplankton pigments based on high-performance liquid chromatography (HPLC) analyses and flow cytometry, and of the molecular diversity of the picophytoplankton based on their rDNA sequences. The sampling sites could be divided into three temperature zones, distinguished by their proximity to the Sub-Antarctic and Polar Fronts. HPLC analysis of total chlorophylls and carotenoids showed fairly low phytoplankton concentrations (77-262 ng chl al(-1)), with minimal values of the pigments in the two samples of the Polar Front Zone around 54degreesS (water temperature of 4degreesC at time of collection). In this zone, a similar decrease of particles, identified as cyanobacteria on the basis of their fluorescence, was observed by flow cytometry. Sequences very similar to the 16S rDNA sequence of Synechococcus WH8103 were present in all samples. This Synechococcus genotype is thus found in the Southern Ocean in addition to the Atlantic and Pacific locations where it has been previously observed. The yield of PCR products was lower in the two samples taken in the Polar Front Zone, showing a good agreement between molecular and pigment data. 16S rDNA sequences of plastids of eukaryotic algae also were retrieved, mostly related to those of an environmental clone called OM164, which has not been cultivated but has phylogenetic affinities to the Raphidophyceae. (C) 2002 Elsevier Science Ltd. All rights reserved. [less ▲]

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See detailAnalyse de séquences d'ITS de souches d'Arthrospira provenant de quatre continents
Baurain, Denis ULg; Wilmotte, Annick ULg

Scientific conference (2001, March 13)

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See detailPhylogenetic relationships among the cyanobacteria based on 16S rRNA sequences
Wilmotte, Annick ULg; Herdman, Michael

in Garrity, George M; Castenholz, Richard W (Eds.) Bergey's Manual of Systematic Bacteriology. Volume One : The Archaea and the Deeply Branching and Phototrophic Bacteria (2001)

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See detailMolecular diversity of Microcystis strains (Cyanophyceae, Chroococcales) based on 16S rDNA sequences
LEPERE, Claire ULg; Wilmotte, Annick ULg; Meyer, Barbara

in Systematics and Geography of Plants (2000), 70

Partial 16S rDNA sequences were determined for six Microcystis strains from lakes in the region of Plön (Northern Germany) assigned to four different species on the basis of their morphology. These ... [more ▼]

Partial 16S rDNA sequences were determined for six Microcystis strains from lakes in the region of Plön (Northern Germany) assigned to four different species on the basis of their morphology. These sequences appear very similar to each other and to those of 71 Microcystis strains from four continents available in the databases. This great genotypic homogeneity, as measured by 16S rDNA sequence similarity (334 characters), is contrasting with the conspicuous morphological differences observed for the studied strains. [less ▲]

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See detailArthrospira ('Spirulina') strains from four continents are resolved into only two clusters, based on amplified ribosomal DNA restriction analysis of the internally transcribed spacer
Scheldeman, Patsy; Baurain, Denis ULg; Bouhy, Rachel et al

in FEMS Microbiology Letters (1999), 172(2), 213-22

We present the results of a phylogenetic study, based on amplified ribosomal DNA restriction analysis of the rDNA operon, of 37 Arthrospira ('Spirulina') cultivated clonal strains from four continents. In ... [more ▼]

We present the results of a phylogenetic study, based on amplified ribosomal DNA restriction analysis of the rDNA operon, of 37 Arthrospira ('Spirulina') cultivated clonal strains from four continents. In addition, duplicates from different culture collections or markedly different morphotypes of particular strains established as clonal cultures were treated as separate entries, resulting in a total of 51 tested cultures. The strain Spirulina laxissima SAG 256.80 was included as outgroup. The 16S rRNA genes appeared too conserved for discrimination of the strains by amplified ribosomal DNA restriction analysis, and thus the internally transcribed spacer was selected as molecular taxonomic marker. The internally transcribed spacer sequences situated between the 16S and the 23S rRNA were amplified by polymerase chain reaction and yielded amplicons of about 540 bp. Direct use of cells for polymerase chain reaction seemed to inhibit the amplification reaction. This was overcome by the design of a crude lysis protocol and addition of bovine serum albumin in the polymerase chain reaction mix. The amplicons were digested with four restriction enzymes (EcoRV, Hhal, Hinfl, Msel) and the banding patterns obtained were analyzed. Cluster analysis showed the separation of all the strains into two main clusters. No clear relationships could be observed between this division into two clusters and the geographic origin of the strains, or their designation in the culture collections, or their morphology. [less ▲]

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See detailCharacterization of Arthrospira / Spirulina strains: Molecular Aspects
Baurain, Denis ULg; Scheldeman, Patsy; Renquin, Laurent et al

Report (1999)

We present the results of a phylogenetic study, based on ARDRA of the rDNA operon, of 38 Arthrospira (‘Spirulina’) cultivated clonal strains from four continents. In addition, duplicates from different ... [more ▼]

We present the results of a phylogenetic study, based on ARDRA of the rDNA operon, of 38 Arthrospira (‘Spirulina’) cultivated clonal strains from four continents. In addition, duplicates from different culture collections or markedly different morphotypes of particular strains established as clonal cultures were treated as separate entries, resulting in a total of 54 tested cultures. Three living samples from Earthrise Farms ponds (September 1997), four freeze-dried samples from EF ponds (August 1996, February and March 1997) and a powder of ‘Spirulina pacifica’ were also included in the study. The strain Spirulina laxissima SAG 256.80 was used as outgroup. The 16S rRNA genes appeared too conserved for discrimination of the strains by ARDRA, and thus the Internal Transcribed Spacer (ITS) was selected as a molecular taxonomic marker. The ITS sequences situated between the 16S and the 23S rRNA genes were amplified by PCR and yielded amplicons of about 540 bp. The amplicons were digested with four restriction enzymes (EcoR V, Hha I, Hinf I, Mse I) and the banding patterns obtained were analyzed. Cluster analysis showed the separation of all the strains into two main clusters (Clusters I and II), of which Cluster I was divided into Subclusters I.A and I.B. Four freeze-dried samples from EF cultivation ponds (Summer 1996 and Winter 1997), as well as a sample of powder sent as ‘Spirulina pacifica’ appeared to contain a mixture of genotypes from Clusters I and II. No clear relationships could be observed between this division into two clusters and the geographic origin of the strains, or their designation in the culture collections, or their morphology. Direct use of cells for PCR seemed to inhibit the amplification reaction. This was overcome by the design of a crude lysis protocol and addition of BSA (Bovine Serum Albumin) in the PCR mix. In order to study in more depth the genotypic relationships of Arthrospira, we have obtained the ITS sequence of 19 cultures and 7 samples (living or freeze-dried samples from EF ponds, dried natural samples and one commercial pill). The data confirmed the existence of Clusters I and II, but also subdivided each of them into two Subclusters (A and B). In three cultures, simultaneous presence of types II.A and II.B was detected. It is likely that sequences of both types are contained in different copies of the ITS and that the three cultures represent cryptic duplicates of one unique genotype. The strains cultivated in the EF ponds belong to types I.A, II.A and II.B, while the winter ponds samples were a mixture of types I and II. Though there was surprisingly little sequence variability in the ITS sequences, we designed PCR primers which are specific for the two clusters (44 different positions) and for the four subclusters (2 to 4 different positions). [less ▲]

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