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The Marnes Bleues Formation from the Vocontian Basin (Southeastern France) shows many dark-colored levels, some concomitant to oceanic anoxic events OAE1a (the so-called Goguel Level) and OAE1b (the Jacob, Kilian, and, above all, Paquier levels). These levels are usually referred to as being organic-rich; they are scattered through a thick, rather homogeneous, succession of marls, that is poor in organic matter (OM). Through a multi-parameter approach, the dark levels from the Aptian-Albian were characterized. Our results show that all dark levels are not OM-rich and that the dark levels exhibit variable characteristics, such as OM nature (marine vs. continental), sedimentation and accumulation rates, redox conditions, surface-water productivity and relative sea level, but they all show low to modest enrichments in OM. Furthermore, all the levels share in common the fact that they formed under conditions of normal to low productivity and oxic to suboxic conditions. Thus, our results strongly suggest that, in the absence of high productivity and anoxic bottom conditions, the other factors reputed to favor OM accumulation only led to sporadic and low enrichments in organic contents. It is as if such factors could only enhance OM accumulation but could not induce it alone. What was true for the Vocontian Basin may be extended to other settings, regardless of their time of deposition or location.

The Tithonian-Berriasian interval in the southern part of the Neuquén Basin is represented by the Vaca Muerta and the Picún Leufú Formations. Facies analysis and correlation of the Vaca Muerta Formation and the lower part of the Picún Leufú Formation in the Picún Leufú Anticline allow us to characterize the evolution of successive facies belts representing siliciclastic shelf and mixed ramp environments. Shoreface and offshore facies are developed on the siliciclastic shelf in the western and southern parts of the Picún Leufú Anticline. The offshore transition domain is characterized by storm beds and slump features, whereas the offshore domain corresponds to black to grey shales and turbidites. The mixed siliciclastic-carbonate ramp is characterized by the development of a lagoon and high-energy shoal in the proximal part of the inner ramp, whereas the distal part comprises a tidal complex. The mid-ramp zone is characterized by storm influence and the outer ramp by fine-grained deposits. Two major transgressive-regressive sequences and five high-frequency transgressive-regressive sequences are recognized. The high-frequency transgressive-regressive sequences make up three progradational sequences, an aggradational-progradational sequence and an aggradational sequence. The geochemical characteristics and clay mineralogy of the Tithonian-Berriasian interval in the southern Neuquén Basin indicate that (1) climate played a key role in the evolution of the sedimentary environment, (2) a “normal marine” depositional environment with oxic sea water and sediment pore waters, rapidly changing to suboxic conditions at shallow depth below the seabed and (3) the occurrence of episodically restricted water-mass circulation at the onset of deposition of the Vaca Muerta Formation.

Single-cell CRISPR-based transcriptome screens are potent genetic tools for concomitantly assessing the expression profiles of cells targeted by a set of guides RNA (gRNA), and inferring target gene functions from the observed perturbations. However, due to various limitations, this approach lacks sensitivity in detecting weak perturbations and is essentially reliable when studying master regulators such as transcription factors. To overcome the challenge of detecting subtle gRNA induced transcriptomic perturbations and classifying the most responsive cells, we developed a new supervised autoencoder neural network method. Our Sparse supervised autoencoder (SSAE) neural network provides selection of both relevant features (genes) and actual perturbed cells. We applied this method on an in-house single-cell CRISPR-interference-based (CRISPRi) transcriptome screening (CROP-Seq) focusing on a subset of long non-coding RNAs (lncRNAs) regulated by hypoxia, a condition that promote tumor aggressiveness and drug resistance, in the context of lung adenocarcinoma (LUAD). The CROP-seq library of validated gRNA against a subset of lncRNAs and, as positive controls, HIF1A and HIF2A, the 2 main transcription factors of the hypoxic response, was transduced in A549 LUAD cells cultured in normoxia or exposed to hypoxic conditions during 3, 6 or 24 h. We first validated the SSAE approach on HIF1A and HIF2 by confirming the specific effect of their knock-down during the temporal switch of the hypoxic response. Next, the SSAE method was able to detect stable short hypoxia-dependent transcriptomic signatures induced by the knock-down of some lncRNAs candidates, outperforming previously published machine learning approaches. This proof of concept demonstrates the relevance of the SSAE approach for deciphering weak perturbations in single-cell transcriptomic data readout as part of CRISPR-based screening.

Igneous basaltic intrusions into young organic-rich sedimentary basins have a major impact not only on the carbon cycle but also on major and trace element transfers between deep and superficial geological reservoirs. The actively rifting Guaymas Basin in the Gulf of California, which was drilled by the International Ocean Discovery Program during Expedition 385, represents the nascent stage of an ocean characterized by siliceous organic-rich sediments (diatom ooze) intruded by a very dense network of basaltic sills. This study focuses on Site U1546 where the relatively high geothermal gradient (over 200 ∘C km−1) induces early diagenetic transformations in both pore waters and sediments, involving sulfide, carbonate and silica. Geochemical and mineralogical characterizations of the sediment at sill contacts indicate that sulfides and silica polymorphs are the main phases impacted by contact metamorphism, being evident by a transition from opal-CT to quartz and pyrite to pyrrhotite, respectively. Mass balance calculations have been used to estimate mass transfers in metamorphic aureoles. In the top contact aureole, predominantly isochemical metamorphism is reflected by the presence of authigenic quartz and disseminated 20–50 µm sized pyrrhotite crystals, filling primary interstitial space, and partial dissolution of detrital feldspar grains. In the bottom contact aureole, quartz and euhedral pyrrhotite crystals occur, which are up to 4 times larger than those at the top contact. Significant metamorphism of sediments is observed in the lower contact aureole, where plagioclase recrystallizes around the detrital feldspars and locally euhedral pyroxenes are included in patches of carbonate cement; this suggests precipitation from carbon-rich fluids at temperatures (T) higher than 300 ∘C. The lower contact aureole also is more enriched in CaO, Na2O, Fe2O3 and trace elements (Cu, As, Zn, etc.) compared to the upper contact. Based on these petrological investigations, a conceptual model of magma–sediment–fluid interaction is proposed distinguishing top and bottom contact processes. Initial contact metamorphism due to sill emplacement is characterized by dehydration reactions in sediments and crystallization of new minerals. It was followed by carbonate precipitation from the released fluids. At a final stage, the temperature re-equilibrated with the geothermal gradient and the rocks were further altered by hydrothermal fluids.

The Mesozoic witnessed some episodes of marked accumulation and burial of organic matter (OM) in the Tethys Ocean and satellite basins, such as the Vocontian Basin (SE-France). These famous episodes, termed Oceanic Anoxic Events (OAEs), resulted from various factors, acting in complex synergies; the consensus about the key factors has not been reached yet. The Aptian–Albian Blue Marls Formation (Fm.) of the Vocontian Basin recorded the various substages of OAE1, plus additional organic-rich levels of regional extension. The semi-pelagic marlstones of the Blue Marls Fm. allow to carry out a detailed examination of the molecular fossils, to assess the respective weights of the factors involved in the OM storage process. In this work, we examined the lipid biomarkers of six organic-rich levels ranging from the Goguel Level to the Paquier Level in stratigraphic order. Biomarkers reputed to be characteristic of some OAEs are observed here: 2-methylhopanoids in the Goguel Level (OAE1a) and archaeal lipids in the Jacob, Kilian and Paquier Levels (OAE1b). This study shows that, in the Vocontian Basin, OM deposition resulted mostly from local factors and that each level has its own peculiarities; however, overarching connections with the Tethys Ocean were critical for the recording of global anoxic events.

Evidence for macroscopic life in the Paleoproterozoic Era comes from 1.8 billion-year-old (Ga) compression fossils [Han TM, Runnegar B (1992) Science 257:232-235; Knoll et al. (2006) Philos Trans R Soc Lond B 361:1023-1038], Stirling biota [Bengtson S et al. (2007) Paleobiology 33:351-381], and large colonial organisms exhibiting signs of coordinated growth from the 2.1-Ga Francevillian series, Gabon. Here we report on pyritized string-shaped structures from the Francevillian Basin. Combined microscopic, microtomographic, geochemical, and sedimentologic analyses provide evidence for biogenicity, and syngenicity and suggest that the structures underwent fossilization during early diagenesis close to the sediment-water interface. The string-shaped structures are up to 6 mm across and extend up to 170 mm through the strata. Morphological and 3D tomographic reconstructions suggest that the producer may have been a multicellular or syncytial organism able to migrate laterally and vertically to reach food resources. A possible modern analog is the aggregation of amoeboid cells into a migratory slug phase in cellular slime molds at times of starvation. This unique ecologic window established in an oxygenated, shallow-marine environment represents an exceptional record of the biosphere following the crucial changes that occurred in the atmosphere and ocean in the aftermath of the great oxidation event (GOE).

Illitisation requires potassium incorporation into a smectite precursor, a process akin to reverse weathering. However, it remains unclear whether microbes facilitate K+ uptake to the sediments and whether illitisation was important in the geological past. The 2.1 billion-year-old Francevillian Series of Gabon has been shown to host mat-related structures (MRS) and, in this regard, these rocks offer a unique opportunity to test whether ancient microbes induced illitisation. Here, we show high K content confined to illite particles that are abundant in the facies bearing MRS, but not in the host sandstone and black shale. This observation suggests that microbial biofilms trapped K+ from the seawater and released it into the pore-waters during respiration, resulting in illitisation. The K-rich illite developed exclusively in the fossilized MRS thus provides a new biosignature for metasediments derived from K-feldspar-depleted rocks that were abundant crustal components on ancient Earth.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth's surface environments following the first appreciable rise of free atmospheric oxygen concentrations ∼2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. While most sedimentary successions deposited during this time interval have experienced thermal overprinting from burial diagenesis and metamorphism, the ca. 2.1 Ga black shales of the Francevillian B Formation (FB2) cropping out in southeastern Gabon have not. The Francevillian Formation contains centimeter-sized structures interpreted as organized and spatially discrete populations of colonial organisms living in an oxygenated marine ecosystem. Here, new material from the FB2 black shales is presented and analyzed to further explore its biogenicity and taphonomy. Our extended record comprises variably sized, shaped, and structured pyritized macrofossils of lobate, elongated, and rod-shaped morphologies as well as abundant non-pyritized disk-shaped macrofossils and organic-walled acritarchs. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowed the evolution and ecological expansion of complex megascopic life.

The Paleoproterozoic Era witnessed crucial steps in the evolution of Earth's surface environments following the first appreciable rise of free atmospheric oxygen concentrations ∼2.3 to 2.1 Ga ago, and concomitant shallow ocean oxygenation. While most sedimentary successions deposited during this time interval have experienced thermal overprinting from burial diagenesis and metamorphism, the ca. 2.1 Ga black shales of the Francevillian B Formation (FB2) cropping out in southeastern Gabon have not. The Francevillian Formation contains centimeter-sized structures interpreted as organized and spatially discrete populations of colonial organisms living in an oxygenated marine ecosystem. Here, new material from the FB2 black shales is presented and analyzed to further explore its biogenicity and taphonomy. Our extended record comprises variably sized, shaped, and structured pyritized macrofossils of lobate, elongated, and rod-shaped morphologies as well as abundant non-pyritized disk-shaped macrofossils and organic-walled acritarchs. Combined microtomography, geochemistry, and sedimentary analysis suggest a biota fossilized during early diagenesis. The emergence of this biota follows a rise in atmospheric oxygen, which is consistent with the idea that surface oxygenation allowed the evolution and ecological expansion of complex megascopic life.