Publications of Emmanuelle Javaux
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See detail1.1 billion years old porphyrins and their isotopic composition establish a marine ecosystem dominated by bacterial primary producers
Gueneli, Nur; McKenna, AC; Ohkouchi et al

in Proceedings of the National Academy of Sciences of the United States of America (2018)

The average cell size of marine phytoplankton is critical for the flow of energy and nutrients from the base of the food web to higher trophic levels. Thus, the evolutionary succession of primary ... [more ▼]

The average cell size of marine phytoplankton is critical for the flow of energy and nutrients from the base of the food web to higher trophic levels. Thus, the evolutionary succession of primary producers through Earth’s history is important for our understanding of the radiation of modern protists ∼800 million years ago and the emergence of eumetazoan animals ∼200 million years later. Currently, it is difficult to establish connections between primary production and the proliferation of large and complex organisms because the mid-Proterozoic (∼1,800–800 million years ago) rock record is nearly devoid of recognizable phytoplankton fossils. We report the discovery of intact porphyrins, the molecular fossils of chlorophylls, from 1,100-million-year-old marine black shales of the Taoudeni Basin (Mauritania), 600 million years older than previous findings. The porphyrin nitrogen isotopes (δ15Npor = 5.6–10.2‰) are heavier than in younger sedimentary sequences, and the isotopic offset between sedimentary bulk nitrogen and porphyrins (εpor = −5.1 to −0.5‰) points to cyanobacteria as dominant primary producers. Based on fossil carotenoids, anoxygenic green (Chlorobiacea) and purple sulfur bacteria (Chromatiaceae) also contributed to photosynthate. The low εpor values, in combination with a lack of diagnostic eukaryotic steranes in the time interval of 1,600–1,000 million years ago, demonstrate that algae played an insignificant role in mid-Proterozoic oceans. The paucity of algae and the small cell size of bacterial phytoplankton may have curtailed the flow of energy to higher trophic levels, potentially contributing to a diminished evolutionary pace toward complex eukaryotic ecosystems and large and active organisms. [less ▲]

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See detailPaleoproterozoic HP-LT eclogites from the DRCongo: Implications for the onset of plate tectonics on Earth
François, Camille ULiege; Debaille, Vinciane; Paquette, Jean-Louis et al

Poster (2018, June)

Knowing the plate tectonic regime of the early Earth is a fundamental but ongoing question and its resolution implies to know when and how plate tectonics and subduction began on Earth. Today, the ... [more ▼]

Knowing the plate tectonic regime of the early Earth is a fundamental but ongoing question and its resolution implies to know when and how plate tectonics and subduction began on Earth. Today, the tectonic regime is ruled by mobile-lid tectonics including subduction. However, in the early Earth stagnant-lid tectonics (or sagduction) could also occur. The possible range for the onset of mobile-lid plate tectonic spans from the early Archean to mid-Proterozoic, even though the Neoarchean-Paleoproterozoic boundary seems to be a crucial period and a time of major change in tectonic style regime on Earth. The study of High Pressure-Low Temperature (HP-LT) metamorphic rocks is powerful because today, these rocks are only produced in subduction settings. Here, we characterize the oldest HP-LT eclogite worldwide (2089 ± 13 Ma; 20-25 kbar / 550-600°C) discovered in the Kasai Block (DRCongo) attesting subduction process. We also identify the gabbroic protolith of this rock formed at 2216 ± 26 Ma in a rift-type basin, then was buried at high depth (> 65 km) in a subduction zone and exhumed during a Wilson cycle of ca. 130 Ma, testifying a modern-style plate tectonics at 2.2-2.1 Ga. [less ▲]

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See detailRaman microspectroscopy, bitumen reflectance and illite crystallinity scale: comparison of different geothermometry methods on fossiliferous Proterozoic sedimentary basins (DR Congo, Mauritania and Australia)
Kabamba Baludikay, Blaise ULiege; François, Camille ULiege; Sforna, Marie-Catherine ULiege et al

in International Journal of Coal Geology (2018)

Sedimentary rocks containing microfossils are crucial archives to reconstitute early life evolution on Earth. However, the preservation of microfossils within rocks depends on several physico-chemical ... [more ▼]

Sedimentary rocks containing microfossils are crucial archives to reconstitute early life evolution on Earth. However, the preservation of microfossils within rocks depends on several physico-chemical factors. Among these factors, the thermal evolution of the host rocks can be decisive. Here, we investigated carbonaceous shale samples containing exquisitely preserved organic-walled microfossils assemblages from three Proterozoic shallow marine sedimentary sequences: the Mbuji-Mayi Supergroup (Democratic Republic of Congo, Congo Basin), the Atar/El Mreïti Group (Mauritania, Taoudeni Basin) and the Kanpa Formation (Australia, Officer Basin). Thermal maturity of these rock samples is evaluated with Raman geothermometry, Raman reflectance, solid bitumen reflectance, illite crystallinity and Thermal Alteration Index. The comparison of results coming from these different techniques validates the use of Raman reflectance on Proterozoic carbonaceous material and especially for poorly-ordered carbonaceous material. We show that extracted kerogen (microfossils and amorphous organic material) is more accurate to estimate the thermal maturity of low-grade temperature Proterozoic sequences than kerogen in thin section. All techniques provide consistent range of temperatures except for Raman geothermometry, giving slightly higher estimates. Raman reflectance appears to be a fast, robust and non-destructive tool to evaluate the thermal maturity of poorly-organized carbonaceous material from Proterozoic rocks. [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 detailFTIR micro-spectroscopy: a tool to identify microfossils
Cornet, Yohan ULiege; Javaux, Emmanuelle ULiege

Conference (2018, March 20)

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See detailMicrofossil assemblages from the Paleoproterozoic (Changcheng Group) and Mesoproterozoic (Huailai Group) of North China
Shi, Min; Feng, G; Zhao, C et al

Conference (2018, March)

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See detailEvidence of Paleoproterozoic plate tectonics: eclogitic subduction
François, Camille ULiege; Debaille, Vinciane; Paquette, Jean-Louis et al

Conference (2018, March)

The question of how and when plate tectonics and subduction processes initiated on Earth is still a subject of debate. Subduction requires the oceanic lithosphere to sustain differential stress without ... [more ▼]

The question of how and when plate tectonics and subduction processes initiated on Earth is still a subject of debate. Subduction requires the oceanic lithosphere to sustain differential stress without creep. Today, mid- to high-pressure mineral assemblages are commonly interpreted in terms of plate tectonic processes including subduction. While in the Early Earth, mid- to high pressure assemblages could have been also produced by sagduction (or stagnant-lid tectonics) of dense mafic lithology into their light silicic crustal basement, the first evidence of high pressure rocks (i.e. eclogites) seems to appear only at the Neoarchean-Paleoproterozoic boundary. In fact, this limit seems to be a crucial period and a time of major change in tectonic style regime. Here, we characterize and date the oldest compelling eclogites discovered so far, dated at 2089 ± 13 Ma from the Northern margin of the Kasai block (Democratic Republic of the Congo). We also identify the protolith of these eclogites as being originally a gabbro formed at 2216 ± 26 Ma in an intra-cratonic rift-type basin, which was buried at high pressure and low temperature (20-25 kbar and 550-600°C) in a subduction zone and then exhumed during a Wilson cycle of ca. 130 Ma, testifying a modern style plate tectonics at 2.2-2.1 Ga. [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 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 detailUse of different geothermometry methods on fossiliferous Proterozoic sediments to constrain thermal maturity of microfossils and sedimentary basins (DRCongo, Mauritania & Australia)
Kabamba Baludikay, Blaise ULiege; François, Camille ULiege; Sforna, Marie-Catherine ULiege et al

Poster (2018, March)

Evaluate the thermal maturity of old sedimentary basins containing microfossils is crucial to reconstruct early life evolution on Earth. Here, we investigate carbonaceous shale samples containing ... [more ▼]

Evaluate the thermal maturity of old sedimentary basins containing microfossils is crucial to reconstruct early life evolution on Earth. Here, we investigate carbonaceous shale samples containing exquisitely preserved organic-walled microfossil assemblages from three Proterozoic shallow marine sedimentary sequences: the Mbuji-Mayi Supergroup (Democratic Republic of Congo, Congo Basin), the Atar/El Mreïti Group (Mauritania, Taoudeni Basin) and the Kanpa Formation (Australia, Officer Basin). By comparison with Raman geothermometry, solid bitumen reflectance, illite crystallinity and Thermal Alteration Index, we evaluate and validate the use of Raman reflectance on Proterozoic carbonaceous material and especially for poorly-ordered carbonaceous material. We show that extracted kerogen (microfossils and amorphous organic material) is more accurate to estimate the thermal maturity of low-grade temperature Proterozoic sequences than kerogen in thin section. All the techniques provide consistent range of temperatures except for Raman geothermometry, giving slightly higher estimates. Raman reflectance appears to be a fast and robust tool to evaluate the thermal maturity of poorly-organized carbonaceous material from Proterozoic rocks and by extension could be used to assess the thermal evolution of a sedimentary successions. This work was supported by the ERC StG ELITE FP7/308074; BELSPO IAP PLANET TOPERS, and the Marie-Curie Cofund program. [less ▲]

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See detailA constrained SSU-rRNA phylogeny reveals the unsequenced diversity of photosynthetic Cyanobacteria (Oxyphotobacteria).
Cornet, Luc ULiege; Wilmotte, Annick ULiege; Javaux, Emmanuelle ULiege et al

in BMC Research Notes (2018), 11(1), 435

OBJECTIVE: Cyanobacteria are an ancient phylum of prokaryotes that contain the class Oxyphotobacteria. This group has been extensively studied by phylogenomics notably because it is widely accepted that ... [more ▼]

OBJECTIVE: Cyanobacteria are an ancient phylum of prokaryotes that contain the class Oxyphotobacteria. This group has been extensively studied by phylogenomics notably because it is widely accepted that Cyanobacteria were responsible for the spread of photosynthesis to the eukaryotic domain. The aim of this study was to evaluate the fraction of the oxyphotobacterial diversity for which sequenced genomes are available for genomic studies. For this, we built a phylogenomic-constrained SSU rRNA (16S) tree to pinpoint unexploited clusters of Oxyphotobacteria that should be targeted for future genome sequencing, so as to improve our understanding of Oxyphotobacteria evolution. RESULTS: We show that only a little fraction of the oxyphotobacterial diversity has been sequenced so far. Indeed 31 rRNA clusters of the 60 composing the photosynthetic Cyanobacteria have a fraction of sequenced genomes < 1%. This fraction remains low (min = 1%, median = 11.1%, IQR = 7.3%) within the remaining "sequenced" clusters that already contain some representative genomes. The "unsequenced" clusters are scattered across the whole Oxyphotobacteria tree, at the exception of very basal clades. Yet, these clades still feature some (sub)clusters without any representative genome. This last result is especially important, as these basal clades are prime candidate for plastid emergence. [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 detailMetagenomic assembly of new (sub)polar Cyanobacteria and their associated microbiome from non-axenic cultures.
Cornet, Luc ULiege; Bertrand, Amandine ULiege; Hanikenne, Marc ULiege et al

in Microbial Genomics (2018), 4

Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are ... [more ▼]

Cyanobacteria form one of the most diversified phyla of Bacteria. They are important ecologically as primary producers, for Earth evolution and biotechnological applications. Yet, Cyanobacteria are notably difficult to purify and grow axenically, and most strains in culture collections contain heterotrophic bacteria that were probably associated with Cyanobacteria in the environment. Obtaining cyanobacterial DNA without contaminant sequences is thus a challenging and time-consuming task. Here, we describe a metagenomic pipeline that enables the easy recovery of genomes from non-axenic cultures. We tested this pipeline on 17 cyanobacterial cultures from the BCCM/ULC public collection and generated novel genome sequences for 12 polar or subpolar strains and three temperate ones, including three early-branching organisms that will be useful for phylogenomics. In parallel, we assembled 31 co-cultivated bacteria (12 nearly complete) from the same cultures and showed that they mostly belong to Bacteroidetes and Proteobacteria, some of them being very closely related in spite of geographically distant sampling sites. [less ▲]

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See detailEvidence for ealry predation in Arctic Canada and implication for the evolution of Eukaryotes
Loron, Corentin ULiege; Rainbird, Robert; Turner, Elizabeth et al

Conference (2018)

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See detailImplications of selective predation on the macroevolution of eukaryotes: evidence from Arctic Canada
Loron, Corentin ULiege; Rainbird, Robert; Turner, Elizabeth et al

in Emerging Topics in Life Sciences (2018)

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See detailChasing Mesoproterozoic Eukaryotes: A sampling season in Arctic Canada
Loron, Corentin ULiege; Halverson, Galen; Rainbird, Robert et al

Conference (2018)

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See detailEvidence for earlier Proterozoic eukaryotic diversification in Arctic Canada
Loron, Corentin ULiege; Rainbird, Rob; Turner, Elizabeth 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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