References of "FEMS Microbiology Ecology"
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See detailBacterial and eukaryotic biodiversity patterns in terrestrial and aquatic habitats in the 1 Sør Rondane Mountains, Dronning Maud Land, East Antarctica
Obbels, Dagmar; Verleyen, Elie; Mano, Marie-José et al

in FEMS Microbiology Ecology (2016), 92

The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane ... [more ▼]

The bacterial and microeukaryotic biodiversity were studied using pyrosequencing analysis on a 454 GS FLX+ platform of partial SSU rRNA genes in terrestrial and aquatic habitats of the Sør Rondane Mountains, including soils, on mosses, endolithic communities, cryoconite holes and supraglacial and subglacial meltwater lenses. This inventory was complemented with Denaturing Gradient Gel Electrophoresis targeting Chlorophyta and Cyanobacteria. OTUs belonging to the Rotifera, Chlorophyta, Tardigrada, Ciliophora, Cercozoa, Fungi, Bryophyta, Bacillariophyta, Collembola and Nematodawere present with a relative abundance of at least 0.1% in the eukaryotic communities. Cyanobacteria, Proteobacteria, Bacteroidetes, Acidobacteria, FBP and Actinobacteria were the most abundant bacterial phyla. Multivariate analyses of the pyrosequencing data revealed a general lack of differentiation of both eukaryotes and prokaryotes according to habitat type. However, the bacterial community structure in the aquatic habitats was dominated by the filamentous cyanobacteria Leptolyngbya and appeared to be significantly different compared with those in dry soils, on mosses, and in endolithic habitats. A striking feature in all datasets was the detection of a relatively large amount of sequences new to science, which underscores the need for additional biodiversity assessments in Antarctic inland locations. [less ▲]

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See detailBacterial community composition in relation to bedrock type and macrobiota in soils 1 from the Sør Rondane Mountains, East Antarctica
Tytgat, Bjorn; Verleyen, Elie; Sweetlove, Maxime et al

in FEMS Microbiology Ecology (2016), 92

Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high altitude regions. We hypothesized that the bedrock ... [more ▼]

Antarctic soils are known to be oligotrophic and of having low buffering capacities. It is expected that this is particularly the case for inland high altitude regions. We hypothesized that the bedrock type and the presence of macrobiota in these soils enforce a high selective pressure on their bacterial communities. To test this, we analysed the bacterial community structure in 52 soil samples from the western Sør Rondane Mountains (Dronning Maud Land, East Antarctica) using the Illumina MiSeq platform in combination with ARISA fingerprinting. The samples were taken along broad environmental gradients in an area covering nearly 1000 km². Ordination and variation partitioning analyses revealed that the total organic carbon content was the most significant variable in structuring the bacterial communities, followed by pH, electric conductivity, bedrock type and the moisture content, while spatial distance was of relatively minor importance. Acidobacteria (Chloracidobacteria) and Actinobacteria (Actinomycetales) dominated gneiss derived mineral soil samples, while Proteobacteria (Sphingomonadaceae), Cyanobacteria, Armatimonadetes and candidate division FBP dominated soil samples with a high total organic carbon content that were mainly situated on granite derived bedrock. [less ▲]

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See detailAdding mucins to an in vitro batch fermentation model of the large intestine induces changes in microbial population isolated from porcine feces depending on the substrate
Tran, Thi Hanh Tham ULg; Boudry, Christelle ULg; Everaert, Nadia ULg et al

in FEMS Microbiology Ecology (2016), 92(2), 13

Adding mucus to in vitro fermentation models of the large intestine showed that some genera, namely lactobacilli, are dependent on host-microbiota interactions and that they rely on mucosa layers to ... [more ▼]

Adding mucus to in vitro fermentation models of the large intestine showed that some genera, namely lactobacilli, are dependent on host-microbiota interactions and that they rely on mucosa layers to increase their activity. This study investigates whether this dependence on mucus is substrate-dependent and to which extend other genera are impacted by the presence of mucus. Inulin and cellulose were fermented in vitro by a fecal inoculum from pig in the presence or not of mucin-beads in order to compare fermentation patterns and bacterial communities. Mucins increased final gas production with inulin and shifted short-chain fatty acids molar ratios (P<0.001). QPCR analyses revealed that Lactobacillus spp. and Bifidobacterium spp. decreased with mucins, but Bacteroides spp. increased when inulin was fermented. A more in-depth community analysis indicated that the mucins increased Proteobacteria (0.55 vs. 0.25 %, P=0.013), Verrucomicrobia (5.25 vs. 0.03 %, P=0.032), Ruminococcaceae, Bacteroidaceae, and Akkermansia spp.. Proteobacteria (5.67 vs. 0.55 %, P<0.001) and Lachnospiraceae (33 vs. 10.4 %) were promoted in the mucuscompared to the broth, while Ruminococcaceae decreased. The introduction of mucins affected many microbial genera and fermentation patterns, but from PCA results, the impact of mucus was independent from the fermentation substrate. [less ▲]

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See detailPolyphasic characterization of 10 selected ecologically relevant filamentous cyanobacterial strains from the South Shetland Islands, Maritime Antarctica
Jancusova, Miroslava; Kovacik, Lubomir; Pereira, Antonio Batista et al

in FEMS Microbiology Ecology (2016), 92(7), 100

The evolutionary relationships of 10 Antarctic cyanobacterial strains of the order Oscillatoriales isolated from King George and Deception Islands, South Shetland Islands were studied by a polyphasic ... [more ▼]

The evolutionary relationships of 10 Antarctic cyanobacterial strains of the order Oscillatoriales isolated from King George and Deception Islands, South Shetland Islands were studied by a polyphasic approach (morphology, 16S rRNA and internal transcribed spacer sequences). The studied taxa are characteristic of coastal Antarctic biotopes, where they form distinct populations and ecologically delimited communities. They were isolated from terrestrial habitats: microbial mats in seepages; crusts on soil, rocks, bones and mosses; mud, sometimes close to bird colonies; and from guano. Based on major phenotypic features, the strains were divided into four distinct morphotypes: Leptolyngbya borchgrevinkii (A), Leptolyngbya frigida (B), Microcoleus sp. (C) and Wilmottia murrayi (D). This morphological identification was in agreement with the phylogenetic relationships. For the first time, the 16S rRNA gene sequence of a strain corresponding to the L. borchgrevinkii morphotype was determined. Morphotype B is most related to sequences assigned to L. frigida isolated from microbial mats of coastal lakes in East Antarctica. Morphotype C belongs to a cluster including strains with morphotypes corresponding to Microcoleus attenuatus, Microcoleus favosus and Microcoleus sp., which are from Antarctica and other continents. Morphotype D is grouped with sequences assigned to W. murrayi mostly isolated from Antarctica. [less ▲]

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See detailCyanobacterial community composition in Arctic soil crusts at different stages of development
Pushkareva, Ekaterina; Stelmach Pessi, Igor ULg; Wilmotte, Annick ULg et al

in FEMS Microbiology Ecology (2015), 91(12), 143

Cyanobacterial diversity in soil crusts has been extensively studied in arid lands of temperate regions, particularly semi-arid steppes and warm deserts. Nevertheless, Arctic soil crusts have received far ... [more ▼]

Cyanobacterial diversity in soil crusts has been extensively studied in arid lands of temperate regions, particularly semi-arid steppes and warm deserts. Nevertheless, Arctic soil crusts have received far less attention than their temperate counterparts. Here we describe the cyanobacterial communities from various types of soil crusts from Svalbard, High Arctic. Four soil crusts at different development stages (ranging from poorly-developed to well-developed soil crusts) were analysed using 454 pyrosequencing of the V3-V4 variable region of the cyanobacterial 16S rRNA gene. Analyses of 95660 cyanobacterial sequences revealed a dominance of OTUs belonging to the orders Synechococcales, Oscillatoriales, and Nostocales. The most dominant OTUs in the four studied sites were related to the filamentous cyanobacteria Leptolyngbya sp. Phylotype richness estimates increased from poorly- to mid-developed soil crusts and decreased in the well-developed lichenized soil crust. Moreover, pH, ammonium and organic carbon concentrations appeared significantly correlated with the cyanobacterial community structure. [less ▲]

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See detailGrowth of desferrioxamine deficient Streptomyces mutants through xenosiderophore piracy of airborne fungal contaminations
Arguelles Arias, Anthony ULg; Lambert, Stephany; Martinet, Loïc et al

in FEMS Microbiology Ecology (2015)

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See detailAcinetobacter is more prevalent than Asaia in natural populations of the mosquito vector Aedes albopictus with isolates showing diverse genomic architecture and substrate utilization.
Minard, Guillaume; Tran, Florence Hélène; Raharimalala, Fara Nantenaina ULg et al

in FEMS Microbiology Ecology (2013), 83

The presence of cultivable bacteria Acinetobacter and Asaia was recently demonstrated in the mosquito vector Aedes albopictus. However, it is not known how prevalent these bacteria are in field ... [more ▼]

The presence of cultivable bacteria Acinetobacter and Asaia was recently demonstrated in the mosquito vector Aedes albopictus. However, it is not known how prevalent these bacteria are in field populations. Here, the presence of these bacteria in Ae. albopictus populations from Madagascar was diagnosed by amplification of 16S rRNA gene fragments. Both genera were detected at relatively high frequencies, 46% for Asaia and 74% for Acinetobacter. The prevalence of Acinetobacter correlated significantly with mosquito gender, and the prevalence of Asaia with the interaction between mosquito gender and the sampling site. For each bacterial genus, more male than female mosquitoes were infected. Using pulse field gel electrophoresis, no significant difference in genome size was found between Acinetobacter isolates from mosquitoes compared with free-living Acinetobacter. However, a great diversity was observed in plasmid numbers (from 1 to 12) and sizes (from < 8 to 690 kb). Mosquito isolates utilized fewer substrates than free-living isolates, but some substrates known as blood or plant components were specifically utilized by mosquito isolates. Therefore it is likely that a specific subpopulation of Acinetobacter is selected by Ae. albopictus. Overall, this study emphasizes the need to gain a global view on the bacterial partners in mosquito vectors [less ▲]

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See detailLimited impact of abiotic stress on surfactin production in planta and on disease resistance induced by Bacillus amyloliquefaciens S499 in tomato and bean
Pertot, I.; Puopolo, G.; Hosni, T. et al

in FEMS Microbiology Ecology (2013), 86(3), 505-519

Understanding how temperature and water stress affect protocooperation between plants and beneficial rhizobacteria may enhance the efficacy of biocontrol agents in reducing plant diseases. However, little ... [more ▼]

Understanding how temperature and water stress affect protocooperation between plants and beneficial rhizobacteria may enhance the efficacy of biocontrol agents in reducing plant diseases. However, little is known about the impact of these factors on biocontrol mechanisms and effectiveness, especially when provided by beneficial Bacillus spp. This work aimed to evaluate the influence of low/high temperature combined with a normal and reduced water regime on the interaction between Bacillus amyloliquefaciens strain S499 and plants, resulting in the induction of systemic resistance (ISR). A reduction in ISR level was observed when plants were subjected to stress before bacterization; however, root treatment with S499 prior to stress exposure attenuated this negative effect. Colonization of S499 during exposure to temperature/water stress allowed the three crops to conserve their overall ability to mount defense lines to a similar degree at all the temperatures tested. Further investigation revealed that relative production of surfactin by S499 was clearly enhanced at low temperature, making it possible to counter-balance the negative effect on traits associated with rhizosphere fitness (colonization, motility, and biofilm formation) observed in vitro in cold conditions. This work thus represents a first step in deciphering the effect of high/low temperatures and/or drought on key plant-microorganism interactions culminating in ISR. © 2013 Federation of European Microbiological Societies. [less ▲]

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See detailImpact of rhizosphere factors on cyclic lipopeptide signature from the plant beneficial strain Bacillus amyloliquefaciens S499
Nihorimbere, Venant; Cawoy, Hélène ULg; Seyer, Alexandre et al

in FEMS Microbiology Ecology (2012), 79

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See detailNon-starch polysaccharide-degrading enzymes alter the microbial community and the fermentation patterns of barley cultivars and wheat products in an in vitro model of the porcine gastrointestinal tract
Bindelle, Jérôme ULg; Pieper, Robert; Montoya, Carlos A. et al

in FEMS Microbiology Ecology (2011), 76

An in vitro experiment was carried out to assess how non-starch polysaccharide (NSP)-degrading enzymes influence fermentation of dietary fibre in the pig large intestine. Seven wheat and barley products ... [more ▼]

An in vitro experiment was carried out to assess how non-starch polysaccharide (NSP)-degrading enzymes influence fermentation of dietary fibre in the pig large intestine. Seven wheat and barley products and cultivars with differing carbohydrate fractions (CHO) were hydrolyzed using pepsin and pancreatin in the presence or not of NSP-degrading enzymes (xylanase and b-glucanase) and the filter retentate fermented with sow fecal bacteria. Dry matter, starch, crude protein and β-glucan digestibilities during hydrolysis were measured. Fermentation kinetics of the hydrolyzed ingredients were modelled. Short-chain fatty acids (SCFA) production and molar ratio were compared after 12, 24 and 72 h. Microbial communities were analyzed after 72 h of fermentation using terminal restriction fragment length polymorphism (TRFLP). The results showed an increase of nutrient digestibility (P<0.001), whereas fermentability and SCFA production decreased (P<0.001) with addition of the enzyme. SCFA and bacterial community profiles indicated also a shift from propionate to acetate and an increase in cellulolytic Ruminoccocus- and xylanolytic Clostridium-like bacteria. This is explained by the increase in slowly fermentable insoluble CHO and the lower proportion of rapidly fermentable β-glucan and starch in the retentate when grains were incubated with NSP-degrading enzymes. Shifts were also different for the 4 barley varieties investigated, showing that the efficiency of the enzymes depends on the structure of the CHO fractions in cereal products and cultivars. [less ▲]

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See detailHigh-throughput method for comparative analysis of denaturing gradient gel electrophoresis profiles from human fecal samples reveals significant increases in two bifidobacterial species after inulin-type prebiotic intake.
Joossens, Marie; Huys, Geert; Van Steen, Kristel ULg et al

in FEMS Microbiology Ecology (2011), 75(2), 343-9

Denaturing gradient gel electrophoresis (DGGE) is one of the most commonly used molecular tools to study complex microbial communities. Despite its widespread use, meaningful interpretative analysis ... [more ▼]

Denaturing gradient gel electrophoresis (DGGE) is one of the most commonly used molecular tools to study complex microbial communities. Despite its widespread use, meaningful interpretative analysis remains a major drawback of this method. We evaluated the combination of computer-assisted band-matching with nonparametric statistics for comparative analysis of DGGE banding patterns. Fecal samples from 17 healthy volunteers who consumed 20 g of the prebiotic compound oligofructose-enriched inulin (OF-IN) for 4 weeks were analyzed before and after treatment. DGGE fingerprinting profiles were analyzed using bionumerics software version 4.6., which resulted in a data matrix that was used for statistical analysis. When comparing DGGE profiles before and after OF-IN intake with a Wilcoxon nonparametric test for paired data, two band-classes increased significantly after OF-IN intake (P<0.003 and <0.02). These two band-classes could be assigned to the species Bifidobacterium longum and Bifidobacterium adolescentis by band-sequencing analysis, and their significant increase was quantitatively confirmed with real-time PCR using species-specific primers (respectively P<0.012 and <0.010). Therefore, the nonparametric analysis of a data matrix obtained by computer-assisted band-matching of complex profiles facilitated the interpretative analysis of these profiles and provided an objective and high-throughput method for the detection of significant taxonomic differences in larger numbers of complex profiles. [less ▲]

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See detailBacterial diversity of field-caught mosquitoes, Aedes albopictus and Aedes aegypti, from different geographic regions of Madagascar.
Zouache, Karima; Raharimalala, Fara Nantenaina ULg; Raquin, Vincent et al

in FEMS Microbiology Ecology (2011)

Symbiotic bacteria are known to play important roles in the biology of insects, but the current knowledge of bacterial communities associated with mosquitoes is very limited and consequently their ... [more ▼]

Symbiotic bacteria are known to play important roles in the biology of insects, but the current knowledge of bacterial communities associated with mosquitoes is very limited and consequently their contribution to host behaviors is mostly unknown. In this study, we explored the composition and diversity of mosquito-associated bacteria in relation with mosquitoes’ habitats. Wild Aedes albopictus and Aedes aegypti were collected in three different geographic regions of Madagascar. Culturing methods and denaturing gradient gel electrophoresis (DGGE) and sequencing of the rrs amplicons revealed that Proteobacteria and Firmicutes were the major phyla. Isolated bacterial genera were dominated by Bacillus, followed by Acinetobacter, Agrobacterium and Enterobacter. Common DGGE bands belonged to Acinetobacter, Asaia, Delftia, Pseudomonas, Enterobacteriaceae and an uncultured Gammaproteobacterium. Double infection by maternally inherited Wolbachia pipientis prevailed in 98% of males (n = 272) and 99% of females (n = 413); few individuals were found to be monoinfected withWolbachia wAlbB strain. Bacterial diversity (Shannon–Weaver and Simpson indices) differed significantly per habitat whereas evenness (Pielou index) was similar. Overall, the bacterial composition and diversity were influenced both by the sex of individuals and by the environment inhabited by the mosquitoes; the latter might be related to both the vegetation and the animal host populations that Aedes used as food sources. [less ▲]

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See detailLow cyanobacterial diversity in biotopes of the Transantarctic Mountains and Shackleton Range (80-82°S), Antarctica.
Fernandez, Rafael; Hodgson, Dominic; Convey, Pete et al

in FEMS Microbiology Ecology (2011), 77

The evolutionary history and geographical isolation of the Antarctic continent have produced a unique environment rich in endemic organisms. In many regions of Antarctica, cyanobacteria are the dominant ... [more ▼]

The evolutionary history and geographical isolation of the Antarctic continent have produced a unique environment rich in endemic organisms. In many regions of Antarctica, cyanobacteria are the dominant phototrophs in both aquatic and terrestrial ecosystems. We have used microscopic and molecular approaches to examine the cyanobacterial diversity of biotopes at two inland continental Antarctic sites (80-82°S). These are amongst the most southerly locations where freshwater-related ecosystems are present. Results showed a low cyanobacterial diversity, with only 3-7 Operational Taxonomic Units (OTUs) per sample obtained by a combination of strain isolations, clone libraries and DGGE based on 16S rRNA genes. One OTU was potentially endemic to Antarctica and is present in several regions of the continent. Four OTUs were shared by the samples from Forlidas Pond and the surrounding terrestrial mats. Only one OTU, but no Internal Transcribed Spacer (ITS) sequences, was common to Forlidas Pond and Lundström Lake. The ITS sequences were shown to further discriminate different genotypes within the OTUs. ITS sequences from Antarctic locations appear more closely related to each other than to non-Antarctic sequences. Future research in inland continental Antarctica will shed more light on the geographical distribution and evolutionary isolation of cyanobacteria in these extreme habitats. [less ▲]

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See detailCovariation between zooplankton community composition and cyanobacterial community dynamics in Lake Blaarmeersen (Belgium)
van Gremberghe, Ineke; Van Wichelen, Jeroen; Van der Gucht, Kathleen et al

in FEMS Microbiology Ecology (2008), 63

The cyanobacterial community composition in the mesotrophic Lake Blaarmeersen was determined by denaturing gradient gel electrophoresis (DGGE) of PCRamplified 16S rRNA gene fragments during two ... [more ▼]

The cyanobacterial community composition in the mesotrophic Lake Blaarmeersen was determined by denaturing gradient gel electrophoresis (DGGE) of PCRamplified 16S rRNA gene fragments during two consecutive years to assess the importance of different classes of explanatory variables (bottom-up and top-down factors, physical variables and phytoplankton) in cyanobacterial community dynamics. The most dominant cyanobacteria in Lake Blaarmeersen were Synechococcus (three genotypes), Limnothrix redekei and Anabaena/Aphanizomenon. Analyses of Similarity revealed that the cyanobacterial community in Lake Blaarmeersen differed significantly between the growing season and the winter season as well as between the epilimnion and hypolimnion during the stratified periods. Mantel tests revealed significant correlations between the DGGE data and bottom-up factors, physical variables, the phytoplankton community composition and, interestingly, the zooplankton community composition. In general, the zooplankton community composition (especially the cladoceran community) was more important in structuring the cyanobacterial community than the total zooplankton biomass. This study shows that grazing zooplankton communities can have a relatively strong impact on the cyanobacterial community dynamics and that this impact can be equally important as bottom-up processes regulated by nutrient concentrations and/or physical variables. [less ▲]

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See detailAllochthonous inputs of riverine picocyanobacteria to coastal waters in the Arctic Ocean
Waleron, M.; Waleron, Krzysztof ULg; Vincent, W. F. et al

in FEMS Microbiology Ecology (2007), 59(2), 356-365

The observed onset of climate change at high northern latitudes has highlighted the need to establish current baseline conditions in the Arctic Ocean, and has raised concern about the potential for the ... [more ▼]

The observed onset of climate change at high northern latitudes has highlighted the need to establish current baseline conditions in the Arctic Ocean, and has raised concern about the potential for the invasion and growth of biota that have warm temperature optima, such as cyanobacteria. In this study, we used 16S rRNA gene sequences as a molecular marker to evaluate the hypothesis that Arctic rivers provide a major inoculum of cyanobacteria into the coastal Arctic Ocean. Surface samples were collected along a transect extending from the Mackenzie River (Northwest Territories, Canada), across its estuary, to 200 km offshore at the edge of the perennial Arctic pack ice (Beaufort Sea). The highest picocyanobacteria concentrations occurred in the river, with concentrations an order of magnitude lower at offshore marine stations. The 16S rRNA gene clone libraries of five surface samples and five strains along this gradient showed that the cyanobacterial sequences were divided into eight operational taxonomic units (OTUs), six OTUs closely related to freshwater and brackish Synechococcus and two OTUs of filamentous cyanobacteria. No typically marine Synechococcus sequences and no Prochlorococcus sequences were recovered. These results are consistent with the hypothesis of an allochthonous origin of picocyanobacteria in the coastal Arctic Ocean, and imply survival but little net growth of picocyanobacteria under the present conditions in northern high-latitude seas. [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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