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See detailMarked Succession of Cyanobacterial Communities Following Glacier Retreat in the High Arctic
Pessi, Igor S; Puschkareva, Ekaterina; Lara, Yannick ULiege et al

in Microbial Ecology (2019), 77

Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we ... [more ▼]

Cyanobacteria are important colonizers of recently deglaciated proglacial soil but an in-depth investigation of cyanobacterial succession following glacier retreat has not yet been carried out. Here, we report on the successional trajectories of cyanobacterial communities in biological soil crusts (BSCs) along a 100-year deglaciation gradient in three glacier forefields in central Svalbard, High Arctic. Distance from the glacier terminus was used as a proxy for soil age (years since deglaciation), and cyanobacterial abundance and community composition were evaluated by epifluorescence microscopy and pyrosequencing of partial 16S rRNA gene sequences, respectively. Succession was characterized by a decrease in phylotype richness and a marked shift in community structure, resulting in a clear separation between early (10–20 years since deglaciation), mid (30–50 years), and late (80–100 years) communities. Changes in cyanobacterial community structure were mainly connected with soil age and associated shifts in soil chemical composition (mainly moisture, SOC, SMN, K, and Na concentrations). Phylotypes associated with early communities were related either to potentially novel lineages (< 97.5% similar to sequences currently available in GenBank) or lineages predominantly restricted to polar and alpine biotopes, suggesting that the initial colonization of proglacial soil is accomplished by cyanobacteria transported from nearby glacial environments. Late communities, on the other hand, included more widely distributed genotypes, which appear to establish only after the microenvironment has been modified by the pioneering taxa. [less ▲]

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See detailAdaptations to extreme conditions: the strategy of the Antarctic cyanobacterium ULC007
Lara, Yannick ULiege; Durieu, Benoit ULiege; Javaux, Emmanuelle ULiege et al

Conference (2018, December 18)

In Polar regions, freshwater ecosystems range from cryoecosystems and ice shelf meltwater ponds to perennially ice-covered lakes where conspicuous benthic microbial mat communities constitute most of the ... [more ▼]

In Polar regions, freshwater ecosystems range from cryoecosystems and ice shelf meltwater ponds to perennially ice-covered lakes where conspicuous benthic microbial mat communities constitute most of the biomass. In these mats, cyanobacteria form the matrix in which other microorganisms can live, and where they are the key primary producers and main drivers of the carbon and food webs. To provide a better understanding of the survival strategies of Polar mat-forming cyanobacteria, we investigated the genome of a strain of the widely distributed Antarctic cyanobacterium, Phormidium priestleyi ULC007. We used high-throughput sequencing technologies to investigate its geographic distribution and genome evolution. More precisely, we investigated the abundance of genes involved in cold adaptation and circadian oscillation. In cold habitats, low temperatures lead to the success of particular organisms featuring adaptations to molecular and cellular disturbances such as higher rigidity of membranes, reduction of enzyme-catalyzed reactions, and reduction of solute transport. Our main results underline the importance of functional categories of genes involved in the production of key molecules for the survival of P. priestleyi in cold conditions (e.g. synthesis of exopolysaccharides, chaperone proteins, fatty acids and phospholipids). [less ▲]

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See detailBCCM/ULC: a collection of cyanobacteria linking Poles to Space
Wilmotte, Annick ULiege; Beets, Kim ULiege; Santoro, Mariano ULiege et al

Conference (2018, December 18)

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the cyanobacterial diversity with a focus on Polar biotopes (e.g. limnetic ... [more ▼]

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the cyanobacterial diversity with a focus on Polar biotopes (e.g. limnetic microbial mats, soil crusts, cryoconites, endolithes). It represents an exclusive Biological Resource Centre (BRC) where characterized polar cyanobacterial strains are available for researchers to study the taxonomy, biogeography, evolution, synthesis of secondary metabolites, adaptation to harsh environmental conditions, and genomic make-up. It currently holds 190 strains, including over 120 of Polar origin (online catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). Living cultures are regularly transferred, and the majority are also cryopreserved (as back-up), in order to assure their preservation and the rapid delivery of strains to clients for fundamental and applied research in both academia and industry. Genomic DNA is also available on request. The collection has obtained the ISO 9001:2015 certification for deposit and distribution of strains, as part of the multi-site certification for the Belgian Coordinated Collections of Microorganisms (BCCM) consortium. A polyphasic approach based on morphological and molecular identifications (based on SSU rRNA sequences) show that the strains belong to the Synechococcales, Oscillatoriales, Chroococcidiopsidales, Pleurocapsales, and Nostocales orders. This large diversity renders the BCCM/ULC collection particularly interesting for taxonomic, biogeographic and phylogenomic studies. Furthermore, the sequencing of the genomes of several strains has started. The BRC also aims to become a source for researchers to study further applications of cyanobacteria in astrobiology as shown by investigations of the resistance to desiccation and radiation of strains of Chroococcidiopsis sp. dominating rock-dwelling communities in extreme dry environments [1]. In paleontology, cyanobacteria represent model organisms thanks to their fundamental role in the oxygenation of the atmosphere and oceans during the Great Oxidation Event. Lastly, the mat-forming cyanobacterial strains may represent “critical organisms” in the investigation of the factors that determine the boundaries of microbial survival and growth on Earth and in the space environment, by virtue of the fact that they are components of microbial mat model systems which are more and more used to elucidate Earth’s past and the detection of life’s biosignatures. [less ▲]

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See detailThe BCCM/ULC collection of cyanobacteria in the spotlight at ULiège
Santoro, Mariano ULiege; Beets, Kim ULiege; Simons, Véronique et al

Poster (2018, October 11)

The ULC public collection of cyanobacteria belongs since 2011 to the consortium of Belgian Co-Ordinated Collections of Microorganisms (BCCM). It aims to conserve ‘ex situ’ a representative portion of the ... [more ▼]

The ULC public collection of cyanobacteria belongs since 2011 to the consortium of Belgian Co-Ordinated Collections of Microorganisms (BCCM). It aims to conserve ‘ex situ’ a representative portion of the biodiversity of cyanobacterial diversity of different origins, with a focus on Antarctic and Artic cyanobacteria isolated from terrestrial and aquatic ecosystems. BCCM/ULC currently holds 174 cyanobacterial strains that are available for researchers who study taxonomy, evolution, biogeography and the adaptation to harsh environmental conditions. The strains are identified by morphology and molecular characterization (based on rRNA sequences) and belong to the Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales orders. This large taxonomic distribution renders it a suitable reference point for phylogenomic and genomic make-up studies. Regular transfer of living cultures ensures the conservation of strains, whose majority are also cryopreserved in order to limit the genetic drift. BCCM/ULC obtained an ISO 9001:2015 certification for public and safe deposits, and for distribution of living strains and genomic DNA. The BCCM policy continuously aims to guarantee a safe fit-for-use microbiological material and data compliant with the rules on access and utilization of the Nagoya Protocol. In addition, BCCM/ULC provides, to clients from academia & industry, a service of morphological identification and molecular characterization, along with other scientific services as tailor-made trainings and collaborations. The public collection is progressively enriched by public deposits from other geographical areas and by incorporating the most interesting strains from the research collection of the host laboratory. The latter is also involved in the valorisation of the collection and collaborations, aiming to study the molecular mechanisms of adaptation to cold stress in polar strains, their production of potential bioactive compounds, to decipher and analyze their genomes and to determine the usefulness of their pigments as ‘traces of life’ in astrobiology. [less ▲]

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See detailEx-situ conservation and exploration of polar cyanobacteria in the BCCM/ULC Collection
Wilmotte, Annick ULiege; Santoro, Mariano; Beets, Kim ULiege et al

Poster (2018, October)

The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins ... [more ▼]

The BCCM/ULC public collection funded by the Belgian Science Policy Office since 2011 aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.). It makes it available for researchers to study the taxonomy, evolution, adaptations to harsh environmental conditions, and genomic make-up. It presently includes 174 cyanobacterial strains, with more than half being of polar origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). [less ▲]

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See detailThe MIDICHIP database
Lara, Yannick ULiege; Wilmotte, Annick ULiege

Report (2018)

In order to be protected, biodiversity must be evaluated. For cyanobacteria, the traditional morphological measures of biodiversity are unsatisfactory. We utilize molecular markers (like SSU rRNA) to ... [more ▼]

In order to be protected, biodiversity must be evaluated. For cyanobacteria, the traditional morphological measures of biodiversity are unsatisfactory. We utilize molecular markers (like SSU rRNA) to define taxa on the basis of phylogeny. In freshwater ecosystems huge populations of cyanobacteria can occur. These blooms may release toxins that make the water poisonous. A second part of the study is to compare the temporal dynamics of biodiversity in both natural and disturbed lakes. This comparative analysis requires the use of ecological indexes to summarise the diversity of the samples and allow inferences about the ecosystem to be made. [less ▲]

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See detailBCCM/ULC: a unique Biological Resource Center of (sub)polar cyanobacteria
Santoro, Mariano ULiege; Beets, Kim ULiege; Lara, Yannick ULiege et al

Poster (2018, September 13)

The BCCM/ULC public collection of cyanobacteria funded by the Belgian Science Policy Office (BELSPO) focusses on the ‘ex situ’ conservation of a representative portion of the (sub)polar cyanobacterial ... [more ▼]

The BCCM/ULC public collection of cyanobacteria funded by the Belgian Science Policy Office (BELSPO) focusses on the ‘ex situ’ conservation of a representative portion of the (sub)polar cyanobacterial diversity with different origins, isolated from terrestrial (e.g. soil crusts, cryoconites, endoliths) and aquatic ecosystems (e.g. limnetic microbial mats, freshwater lakes and marine environments). BCCM/ULC currently holds 175 cyanobacterial strains, including over 100 of polar origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The strains are available for researchers who study the taxonomy, evolution, biogeography, adaptation to harsh environmental conditions, etc. Morphological and molecular identifications (based on SSU rRNA sequences) indicate that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, Chroococcidiopsidales and Nostocales. This large taxonomic distribution makes the collection interesting for phylogenomic and genomic make-up studies, hence the genome sequencing of several strains is ongoing. Continuous maintenance of living cultures ensures the preservation of strains, whose majority are cryopreserved (as back-up at -70°C) in order to limit the genetic drift. BCCM/ULC obtained an ISO 9001:2015 certification for public and safe deposits, and distributions of strains, as part of the multi-site certification for the Belgian Coordinated Collections of Microorganisms (BCCM) consortium. The policies of acquisition and distribution of the collection are translated respectively into contracts called Material Accession Agreements (MAA) and Material Transfer Agreements (MTA). This guarantees safe fit-for-use microbiological material and data compliant with the rules on access and utilization of the Nagoya Protocol under the Convention on Biological Diversity (12 October 2014). BCCM/ULC progressively incorporates the most interesting strains from the research collection of the host laboratory into the public collection, whose variety is also enriched by public deposits from other geographical areas (more temperate). The collection is also interested to test new cultivation methods to better reproduce the complex ecological interactions experienced in nature. In addition, Antarctic cyanobacterial strains are known to produce a range of secondary metabolites with different potential bioactivities, as well as the exploration of some unknown gene clusters identified in the first Antarctic cyanobacterial genome ever determined may potentially lead to discover novel peptides which could have biotechnological or biomedical applications. [less ▲]

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See detailCold Adaptation Strategy of the Antarctic Cyanobacterium P. priestleyi ULC007
Durieu, Benoit ULiege; Baurain, Denis ULiege; Wilmotte, Annick ULiege et al

Poster (2018, June 19)

In Antarctica, Cyanobacteria are key primary producers and play a major role in the colonization of deglaciated habitats. Cyanobacterial mats are widespread in aquatic biotopes and often dominate the ... [more ▼]

In Antarctica, Cyanobacteria are key primary producers and play a major role in the colonization of deglaciated habitats. Cyanobacterial mats are widespread in aquatic biotopes and often dominate the total phototrophic biomass. In order to gain further insights on the mechanisms underlying the ecological success of Antarctic cyanobacteria, we studied the gene repertoire of Phormidesmis priestleyiULC007, a filamentous cyanobacterium isolated from shallow freshwater lake microbial mats in the Larsemann Hills. Here, we investigate the occurrence of genes involved in the cold stress response as a proxy to the adaptation to environmental conditions in Antarctica. We compare a selection of 42 PEGs (protein encoding genes) linked to cold adaptation in 72 cyanobacterial genomes. Polar strains have the highest number of copies of genes coding for fructose aldolase, chaperone Hsp, and universal stress protein and a high number of fatty acid desaturase and genes involved in exopolysaccharide (EPS) biosynthesis. To provide a better overview of the genetic mechanisms of adaptation to cold, we investigated the gene functional categories based on the RAST subsystems technology. Polar strains have the most occurrences for subsystems “Choline and Betain Biosynthesis”, “DNA repair”, “EPS biosynthesis” and “Heat shock DnaK gene cluster”. Our results underline the importance of these functions in the adaptation mechanisms of cyanobacteria to the polar environment. [less ▲]

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See detailBiogeography of Cyanobacteria in Antarctic Mats and Implication for Conservation
Durieu, Benoit ULiege; Lara, Yannick ULiege; Stelmach Pessi, Igor et al

Conference (2018, June 19)

On the Antarctic continent, cyanobacterial mats are widespread in the lacustrine biotopes and they often dominate the phototrophic biomass. Their diversity and biogeography are poorly understood because ... [more ▼]

On the Antarctic continent, cyanobacterial mats are widespread in the lacustrine biotopes and they often dominate the phototrophic biomass. Their diversity and biogeography are poorly understood because most studies cover a limited geographic area or are based only on morphotypes. Therefore, cyanobacteria are not fully taken into account in the biological datasets used to delineate conservation biogeographic regions (ACBRs). Recently, we have shown by 454 pyrosequencing of cyanobacteria-specific 16S rRNA amplicons that their distribution across the lacustrine ecosystems could be explained by ecological parameters (e.g. salinity and dissolved organic carbon). In order to further test this hypothesis, we significantly increased the spatial coverage of our samples. Here, we describe the results of 16S rRNA amplicons Illumina sequencing of 98 cyanobacterial mat samples from 10 ACBRs. From the 16012393 raw reads, 713 OTUs were obtained by bioinformatics analysis. Preliminary results show that both ecological parameters and latitude could explain the patterns of cyanobacterial communities. Indeed, nonmetric multidimensional scaling shows that sub-Antarctic samples (Macquarie and Marion Islands) group with North-East Antarctic Peninsula samples, whereas more continental samples (e.g. East Antarctica, South Victoria Land) group together. These findings can form the basis for a better understanding and a more adequate conservation of lacustrine ecosystems in Antarctica. [less ▲]

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See detailEx-situ Conservation of Polar Cyanobacteria in the BCCM/ULC Collection
Wilmotte, Annick ULiege; Beets, Kim; Simons, Véronique et al

Poster (2018, June)

The BCCM/ULC public collection is funded by the Belgian Science Policy Office (BELSPO) and aims to gather a representative portion of Polar cyanobacterial diversity from different ecological origins ... [more ▼]

The BCCM/ULC public collection is funded by the Belgian Science Policy Office (BELSPO) and aims to gather a representative portion of Polar cyanobacterial diversity from different ecological origins (limnetic microbial mats, soil crusts, cryoconites, endoliths, etc.) and ensure their ex-situ conservation in a context of global change. These strains are available for researchers to study the biodiversity, taxonomy, evolution, adaptations to harsh environmental conditions, and genomic make-up of Polar cyanobacteria. Currently, there are 120 cyanobacterial strains of Polar origin in the collection (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). The strains are kept living and their cryopreservation is currently tested. The collection is ISO 9001 certified for depositing and distributing strains, as part of the multi-site certification of the Belgian Coordinated Collections of Microorganisms (BCCM) consortium. Morphological and molecular identification (based on 16S rRNA sequences) indicate that the strains belong to the orders Chroococcales, Chroococcidiopsidales, Nostocales, Oscillatoriales, Pleurocapsales, and Synechococcales. This broad genotypic distribution makes the BCCM/ULC collection particularly interesting for phylogenomic studies. The genomes of several strains are currently being sequenced and the first genome of an Antarctic cyanobacterial strain, Phormidesmis priestleyi ULC007 was recently published. [less ▲]

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See detailKeeping microalgae safe and available
Santoro, Mariano ULiege; Chaerle, Peter; Lara, Yannick ULiege et al

Poster (2018, May)

ULC and DCG public collections of cyanobacteria and diatoms, respectively, are funded by the Belgian Science Policy Office and belong to the consortium of Belgian Co-Ordinated Collections of ... [more ▼]

ULC and DCG public collections of cyanobacteria and diatoms, respectively, are funded by the Belgian Science Policy Office and belong to the consortium of Belgian Co-Ordinated Collections of Microorganisms. They have an ISO9001 certification for the deposits and distributions of strains. BCCM/ULC is one of the largest BRC of documented (sub)polar cyanobacteria. It aims to represent the (sub)polar cyanobacterial diversity from a wide range of different habitats and to promote understanding of cyanobacterial adaptation mechanisms in high latitudes. It comprises 175 cyanobacterial strains (120 of polar origin) belonging to the more representative orders. Public, safe deposits and strains distribution (or genomic DNA) are provided to clients for fundamental and applied research. The first sequenced Antarctic cyanobacterial genome contains protein encoding genes involved in stress response and unknown gene clusters, potentially leading to discover novel secondary metabolites [1], in agreement with previous findings of antimicrobial activity of compounds from Antarctic strains [2]. BCCM/ULC will develop a culturomics approach to isolate target microorganisms. BCCM/DCG is the only BRC specialized in diatoms, the most species-rich group of aquatic photosynthetic organisms in freshwater and marine ecosystems. BCCM/DCG currently holds 514 publicly available strains originating from a wide geographic area and belonging to 48 species (representing all the principal phylogenetic lineages and ecological groups) most of which are cryopreserved. Next to the biological material, there is for the majority of the strains, extra data available: growth temperature, mating system, auxosporulation information, initial and minimal cell size, and sequence data. Additionally, many of the strains/taxa available at BCCM/DCG have been subject of published research focused on diatom genomics, cell and life cycle, determination and comparison of (eco)physiological properties, algae-bacteria interaction, and diatom population genetics, evolution and diversity. [1] Lara et al. (2017) Genome Announc, 5 (e01546-16) [2] Taton et al. (2006) J. Phycology, 42 (1257–1270) [less ▲]

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See detailBiosignatures of modern and fossil cyanobacteria
Demoulin, Catherine ULiege; Lara, Yannick ULiege; François, Camille ULiege et al

Poster (2018, March 21)

The Proterozoic is an important eon for the evolution of early life on Earth, and especially for the diversification of cyanobacteria, a major group of photosynthetic microorganisms. In paleontology, much ... [more ▼]

The Proterozoic is an important eon for the evolution of early life on Earth, and especially for the diversification of cyanobacteria, a major group of photosynthetic microorganisms. In paleontology, much effort and work are devoted to the study of cyanobacteria, due to their key-role in the oxygenation of the atmosphere and oceans during the GOE (Great Oxidation Event, around 2.4 Ga). Moreover, the development of oxygenated ecological niches is one of the factors linked to the diversification of eukaryotes. However, identifying extremely old microfossil structures as cyanobacteria remains often disputed. The oldest fossil cyanobacterium (~ 1.9 Ga) determined so far with certainty is Eoentophysalis belcherensis Hofmann, a microorganism forming mats and colonies in silicified stromatolites from the Belcher Islands, Hudson Bay, Canada [1]. Its identification as a cyanobacterium relies mainly on morphological comparison to a modern cyanobacterium, Entophysalis Ercegović [2]. In this context, our research project, financed by the ERC StG ELiTE, mainly aims at characterizing the biosignatures of Proterozoic cyanobacteria in order to get new insights into the origin and early evolution of cyanobacteria and oxygenic phtosynthesis. Methodologically, we are using optical microscopy, electron microscopy (SEM and TEM) and Raman and FTIR microspectroscopy techniques, applied on modern specimens and microfossils. This approach is expected to test the biological nature of Paleoproterozoic and younger microstructures, to resolve the affinities of possible prokaryotic microfossils and, thus, to assess their taxonomic placement among cyanobacteria. [less ▲]

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See detailPolar cyanobacteria in the BCCM/ULC collection : diversity and characterization
Lara, Yannick ULiege; Beets, Kim ULiege; Simons, Véronique et al

Poster (2018, March)

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (e.g ... [more ▼]

The BCCM/ULC public collection funded by the Belgian Science Policy Office (BELSPO) aims to gather a representative portion of the polar cyanobacterial diversity with different ecological origins (e.g. limnetic microbial mats, soil crusts, cryoconites, endoliths). It makes it available for researchers to study the taxonomy, evolution, adaptation to harsh environmental conditions, and genomic make-up. It presently includes 177 cyanobacterial strains, including 120 of polar origin (catalogue: http://bccm.belspo.be/catalogues/ulc-catalogue-search). Continuous maintenance of living cultures, most of which are also cryopreserved (as back-up), ensure the preservation and the rapid delivery of strains to clients for fundamental and applied research. Genomic DNA is also available on request. The collection has obtained the ISO 9001 certification for deposition and distribution of strains, as part of the multi-site certification for the Belgian Coordinated Collections of Microorganisms (BCCM) consortium. Morphological and molecular identifications (based on SSU rRNA 16S sequences) show that the strains belong to the orders Synechococcales, Oscillatoriales, Pleurocapsales, and Nostocales. This broad ordinal distribution makes the BCCM/ULC collection particularly interesting for phylogenomic studies. Hence, the sequencing of the genomes of several strains is underway. In addition, cyanobacteria produce a range of secondary metabolites (e.g. alkaloides, peptides, polyketides) with different potential bioactivities. Due to their geographic isolation and strong environmental stressors in their habitat, the exploration of Antarctic cyanobacteria metabolites is likely promising for both biotechnology or biomedical applications. [less ▲]

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See detailThe survival toolkit of the Antarctic cyanobacterium Phormidesmis priestleyi ULC007
Lara, Yannick ULiege; Durieu, Benoit ULiege; Pessi, Igor et al

Conference (2018, March)

Extreme seasonality led by rapid changes in day length and harsh environmental conditions make Antarctica a unique habitat. Freshwater ecosystems range from cryoecosystems and ice shelf meltwater ponds to ... [more ▼]

Extreme seasonality led by rapid changes in day length and harsh environmental conditions make Antarctica a unique habitat. Freshwater ecosystems range from cryoecosystems and ice shelf meltwater ponds to perennially ice-covered lakes where conspicuous benthic microbial mat communities constitute most of the biomass. In these mats, cyanobacteria form the matrix in which other microorganisms can live, and where they are the key primary producers and main drivers of the carbon and food webs[1].
Narrow filamentous cyanobacteria belonging to the order Pseudanabaenales are especially abundant in polar microbial mats [2]. Despite the dominance of cyanobacteria on the Antarctic continent, there is currently no study available on the genomic evolution of Antarctic cyanobacteria. Here we investigate the genome of a widely distributed Antarctic cyanobacterium, Phormidium priestleyi ULC007. To provide a better understanding of the survival strategies of this taxon, we used high-throughput sequencing technologies to investigate its geographic distribution and genome evolution. More precisely, we investigated the abundance of genes in targeted functional categories based on the RAST subsystems technology, so as to provide a better overview of the genetic mechanisms involved in cold adaptation and circadian oscillation [3]. In Polar regions, low temperatures lead to the success of particular organisms featuring adaptations to molecular and cellular disturbances such as rigidity of membranes, reduction of enzyme-catalyzed reactions, and solute transport. Our main results underline the importance of functional categories of genes involved in the production of key molecules for the survival of polar P. priestleyi (e.g. exopolysaccharides, chaperone proteins, fatty acids and phospholipids). [less ▲]

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See detailBiosignatures of modern and fossil cyanobacteria
Demoulin, Catherine ULiege; Lara, Yannick ULiege; François, Camille ULiege et al

Conference (2018)

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See detailConsensus assessment of the contamination level of publicly available cyanobacterial genomes.
Cornet, Luc ULiege; Meunier, Loïc ULiege; Van Vlierberghe, Mick ULiege et al

in PLoS ONE (2018), 13(7), 0200323

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for ... [more ▼]

Publicly available genomes are crucial for phylogenetic and metagenomic studies, in which contaminating sequences can be the cause of major problems. This issue is expected to be especially important for Cyanobacteria because axenic strains are notoriously difficult to obtain and keep in culture. Yet, despite their great scientific interest, no data are currently available concerning the quality of publicly available cyanobacterial genomes. As reliably detecting contaminants is a complex task, we designed a pipeline combining six methods in a consensus strategy to assess the contamination level of 440 genome assemblies of Cyanobacteria. Two methods are based on published reference databases of ribosomal genes (SSU rRNA 16S and ribosomal proteins), one is indirectly based on a reference database of marker genes (CheckM), and three are based on complete genome analysis. Among those genome-wide methods, Kraken and DIAMOND blastx share the same reference database that we derived from Ensembl Bacteria, whereas CONCOCT does not require any reference database, instead relying on differences in DNA tetramer frequencies. Given that all the six methods appear to have their own strengths and limitations, we used the consensus of their rankings to infer that >5% of cyanobacterial genome assemblies are highly contaminated by foreign DNA (i.e., contaminants were detected by 5 or 6 methods). Our results will help researchers to check the quality of publicly available genomic data before use in their own analyses. Moreover, we argue that journals should make mandatory the submission of raw read data along with genome assemblies in order to facilitate the detection of contaminants in sequence databases. [less ▲]

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See detailCommunity structure and distribution of benthic cyanobacteria in Antarctic lacustrine microbial mats
Pessi, Igor S.; Lara, Yannick ULiege; Durieu, Benoit ULiege et al

in FEMS Microbiology Ecology (2018), 94(5), 042

The terrestrial Antarctic Realm has recently been divided into 16 Antarctic Conservation Biogeographic Regions (ACBRs) based on environmental properties and the distribution of biota. Despite their ... [more ▼]

The terrestrial Antarctic Realm has recently been divided into 16 Antarctic Conservation Biogeographic Regions (ACBRs) based on environmental properties and the distribution of biota. Despite their prominent role in the primary production and nutrient cycling in Antarctic lakes, cyanobacteria were only poorly represented in the biological dataset used to delineate these ACBRs. Here we provide a first high-throughput sequencing (HTS) insight into the spatial distribution of benthic cyanobacterial communities in Antarctic lakes located in four distinct, geographically distant ACBRs and covering a range of limnological conditions. Cyanobacterial community structure differed between saline and freshwater lakes. No clear bioregionalisation was observed, as clusters of community similarity encompassed lakes from distinct ACBRs. Most phylotypes (77.0%) were related to cyanobacterial lineages (defined at ≥ 99.0% 16S rRNA gene sequence similarity) restricted to the cold biosphere, including lineages potentially endemic to Antarctica (55.4%). The latter were generally rare and restricted to a small number of lakes, while more ubiquitous phylotypes were generally abundant and present in different ACBRs. These results point to a widespread distribution of some cosmopolitan cyanobacterial phylotypes across the different Antarctic ice-free regions, but also suggest the existence of dispersal barriers both within and between Antarctica and the other continents. [less ▲]

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See detailMolecular dataset from the European project MIDI-CHIP ( EVK2-CT-1999-00026)
Lara, Yannick ULiege; Wilmotte, Annick ULiege

Report (2017)

This entry is dedicated to answer the need of a link between molecular data, environmental parameters, and counting information in the field of microbial ecology. Indeed, it is necessary to implement a ... [more ▼]

This entry is dedicated to answer the need of a link between molecular data, environmental parameters, and counting information in the field of microbial ecology. Indeed, it is necessary to implement a new approach to link data that are deposited in GBIF with molecular data sets that are deposited in GenBank or that stay archived in lab computers. In the frame of the BRAIN-BE BELSPO project SAFRED, we attempted to achieve this goal by supplying a sequence template set as designed by the Microbial Antarctic Resource System (mARS). The MIDI CHIP molecular dataset contains cyanobacterial 16S rRNA sequences recovered from the study of strains, or communities using DGGE, TDGE, and clone libraries approaches, as well as rpoC1 and rbcLX sequences from cyanobacterial strains. The phytoplankton samples were mostly taken in Finnish, Italian, Luxembourg, Czech, and Polish lakes. The project is referenced in https://cordis.europa.eu/project/rcn/51244_en.html [less ▲]

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See detailDiversity and biogeography of microorganisms in microbial mats of Antarctic lakes
Wilmotte, Annick ULiege; Durieu, Benoit ULiege; Lara, Yannick ULiege et al

in Van de Putte, Anton (Ed.) Book of abstracts: XIIth SCAR Biology Symposium, Leuven, Belgium, 10-14 July 2017. (2017, July)

The BelSPO project CCAMBIO aims to study the biogeographical distribution of microorganisms (bacteria, cyanobacteria, microeukaryotes) in lacustrine microbial mats using a combination of techniques ... [more ▼]

The BelSPO project CCAMBIO aims to study the biogeographical distribution of microorganisms (bacteria, cyanobacteria, microeukaryotes) in lacustrine microbial mats using a combination of techniques including microscopic observations, strain isolation and genetic characterisation, and molecular diversity assessments using Next Generation Sequencing of environmental DNA. The samples were collected in different Antarctic and sub-Antarctic biogeographical regions. [less ▲]

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