A drift-barrier model drives the genomic landscape of a structured bacterial population.

Bacterial populations differentiate over time and space to form distinct genetic units. The mechanisms governing this diversification are presumed to result from the ecological context of living units to adapt to specific niches. Recently, a model assuming the acquisition of advantageous genes among populations rather than whole genome sweeps has emerged to explain population differentiation. However, the characteristics of these exchanged, or flexible, genes and whether their evolution is driven by adaptive or neutral processes remain controversial. By analysing the flexible genome of single-amplified genomes of co-occurring populations of the marine Prochlorococcus HLII ecotype, we highlight that genomic compartments - rather than population units - are characterized by different evolutionary trajectories. The dynamics of gene fluxes vary across genomic compartments and therefore the effectiveness of selection depends on the fluctuation of the effective population size along the genome. Taken together, these results support the drift-barrier model of bacterial evolution.

A pan-genomic approach reveals novel Sulfurimonas clade in the ferruginous meromictic Lake Pavin.

The permanently anoxic waters in meromictic lakes create suitable niches for the growth of bacteria using sulphur metabolisms like sulphur oxidation. In Lake Pavin, the anoxic water mass hosts an active cryptic sulphur cycle that interacts narrowly with iron cycling, however the metabolisms of the microorganisms involved are poorly known. Here we combined metagenomics, single-cell genomics, and pan-genomics to further expand our understanding of the bacteria and the corresponding metabolisms involved in sulphur oxidation in this ferruginous sulphide- and sulphate-poor meromictic lake. We highlighted two new species within the genus Sulfurimonas that belong to a novel clade of chemotrophic sulphur oxidisers exclusive to freshwaters. We moreover conclude that this genus holds a key-role not only in limiting sulphide accumulation in the upper part of the anoxic layer but also constraining carbon, phosphate and iron cycling.

Comparison of methane yield of a novel strain of Methanothermobacter marburgensis in pure and mixed adapted culture derived from a methanation bubble column bioreactor.

The ongoing discussion regarding the use of mixed or pure cultures of hydrogenotrophic methanogenic archaea in Power-to-Methane (P2M) bioprocess applications persists, with each option presenting its own advantages and disadvantages. To address this issue, a comparison of methane (CH4) yield between a novel methanogenic archaeon belonging to the species Methanothermobacter marburgensis (strain Clermont) isolated from a biological methanation column, and the community from which it originated, was conducted. This comparison included the type strain M. marburgensis str. Marburg. The evaluation also examined how exposure to oxygen (O2) for up to 240 min impacted the CH4 yield across these cultures. While both Methanothermobacter strains exhibit comparable CH4 yield, slightly higher than that of the mixed adapted culture under non-O2-exposed conditions, strain Clermont does not display the lag time observed for strain Marburg.

Self-construction of supramolecular polyrotaxane films by an electrotriggered morphogen-driven process.

The design of films using a one-pot process has recently attracted increasing interest in the field of polymer thin film formation. Herein we describe the preparation of one-pot supramolecular polyrotaxane (PRX) films using the morphogen-driven self-construction process. This one-pot buildup strategy where the film growth is triggered by the electrochemical formation and diffusion of a catalyst in close vicinity of the substrate has recently been introduced by our group. A one-pot mixture was used that contained (i) poly(acrylic acid) (PAA) functionalized by azide groups grafted on the polymer chain through oligo(ethylene glycol) (EG) arms, leading to PAA-EG13-N3, (ii) cyclodextrins (α and ß CD), as macrocycles that can be threaded along EG arms, (iii) alkyne-functionalized stoppers (ferrocene or adamantane), to cap the PRX assembly by click chemistry, and (iv) copper sulfate. The one-pot mixture solution was brought into contact with a gold electrode. Cu(I), the morphogen, was generated electrochemically from Cu(II) at the electrode/one-pot solution interface. This electrotriggered click reaction leads to the capping of polypseudorotaxane yielding to PRXs. The PRXs can self-assemble through lateral supramolecular interactions to form aggregates and ensure the cohesion of the film. The film buildup was investigated using different types of CD and alkyne functionalized stoppers. Supramolecular PRX aggregates were characterized by X-ray diffraction measurements. The film topographies were imaged by atomic force microscopy. The influence of the concentration in CD and the presence of a competitor were studied as well. The stability of the resulting film was tested in contact with 8 M urea and during the electrochemical oxidation of ferrocene.

Wood ash amendment to biogas reactors as an alternative to landfilling? A preliminary study on changes in process chemistry and biology.

Wood ash addition to biogas plants represents an alternative to commonly used landfilling by improving the reactor performance, raising the pH and alleviating potential limits of trace elements. This study is the first on the effects of wood ash on reactor conditions and microbial communities in cattle slurry-based biogas reactors. General process parameters [temperature, pH, electrical conductivity, ammonia, volatile fatty acids, carbon/nitrogen (C/N), total solids (TS), volatile solids, and gas quantity and quality] were monitored along with molecular analyses of methanogens by polymerase chain reaction- denaturing gradient gel electrophoresis and modern microarrays (archaea and bacteria). A prompt pH rise was observed, as was an increase in C/N ratio and volatile fatty acids. Biogas production was inhibited, but recovered to even higher production rates and methane concentration after single amendment. High sulphur levels in the wood ash generated hydrogen sulphide and potentially hampered methanogenesis. Methanosarcina was the most dominant methanogen in all reactors; however, diversity was higher in ash-amended reactors. Bacterial groups like Firmicutes, Proteobacteria and Acidobacteria were favoured, which could improve the hydrolytic efficiency of the reactors. We recommend constant monitoring of the chemical composition of the used wood ash and suggest that ash amendment is adequate if added to the substrate at a rate low enough to allow adaptation of the microbiota (e.g. 0.25 g g(-1) TS). It could further help to enrich digestate with important nutrients, for example phosphorus, calcium and magnesium, but further experiments are required for the evaluation of wood ash concentrations that are tolerable for anaerobic digestion.

Not Just Another Methanation Catalyst: Depleted Uranium Meets Nickel for a High-Performing Process Under Autothermal Regime.

Ni-based catalysts prepared through impregnation of depleted uranium oxides (DU) have successfully been employed as highly efficient, selective, and durable systems for CO2 hydrogenation to substituted natural gas (SNG; CH4 ) under an autothermal regime. The thermo-physical properties of DU and the unique electronic structure of f-block metal-oxides combined with a nickel active phase, generated an ideal catalytic assembly for turning waste energy back into useful energy for catalysis. In particular, Ni/UOx stood out for the capacity of DU matrix to control the extra heat (hot-spots) generated at its surface by the highly exothermic methanation process. At odds with the benchmark Ni/γ-Al2 O3 catalyst, the double action played by DU as a "thermal mass" and "dopant" for the nickel active phase unveiled the unique performance of Ni/UOx composites as CO2 methanation catalysts. The ability of the weakly radioactive ceramic (UOx ) to harvest waste heat for more useful purposes was demonstrated in practice within a rare example of a highly effective and long-term methanation operated under autothermal regime (i. e., without any external heating source). This finding is an unprecedented example that allows a real step-forward in the intensification of "low-temperature" methanation with an effective reduction of energy wastes. At the same time, the proposed catalytic technology can be regarded as an original approach to recycle and bring to a second life a less-severe nuclear by-product (DU), providing a valuable alternative to its more costly long-term storage or controlled disposal.

Not Just Another Methanation Catalyst: Depleted Uranium Meets Nickel for a High-Performing Process Under Autothermal Regime.

Invited for this month's cover are collaborating teams from academia-the French ICPEES and IS2M of Centre national de la recherche scientifique (CNRS) and the Italian ICCOM of Consiglio Nazionale delle Ricerche (CNR)-and industry with the participation of the ORANO group. The cover picture shows a CO2 -to-CH4 process promoted by nickel nanoparticles supported on depleted uranium oxide under exceptionally low temperature values or autothermal conditions. The Research Article itself is available at 10.1002/cssc.202201859.

FreshOmics: A manually curated and standardized -omics database for investigating freshwater microbiomes.

Freshwater is a critical resource for human survival but severely threatened by anthropogenic activities and climate change. These changes strongly impact the abundance and diversity of the microbial communities which are key players in the functioning of these aquatic ecosystems. Although widely documented since the emergence of high-throughput sequencing approaches, the information on these natural microbial communities is scattered among thousands of publications and it is therefore difficult to investigate the temporal dynamics and the spatial distribution of microbial taxa within or across ecosystems. To fill this gap and in the FAIR principles context we built a manually curated and standardized microbial freshwater -omics database (FreshOmics). Based on recognized ontologies (ENVO, MIMICS, GO, ISO), FreshOmics describes 29 different types of freshwater ecosystems and uses standardized attributes to depict biological samples, sequencing protocols and article attributes for more than 2487 geographical locations across 71 countries around the world. The database contains 24,808 sequence identifiers (i.e., Run_Id / Exp_ID, mainly from SRA/DDBJ SRA/ENA, GSA and MG-RAST repositories) covering all sequence-based -omics approaches used to investigate bacteria, archaea, microbial eukaryotes, and viruses. Therefore, FreshOmics allows accurate and comprehensive analyses of microbial communities to answer questions related to their roles in freshwater ecosystems functioning and resilience, especially through meta-analysis studies. This collection also highlights different sort of errors in published works (e.g., wrong coordinates, sample type, material, spelling).

Detecting unknown sequences with DNA microarrays: explorative probe design strategies.

Designing environmental DNA microarrays that can be used to survey the extreme diversity of microorganisms existing in nature, represents a stimulating challenge in the field of molecular ecology. Indeed, recent efforts in metagenomics have produced a substantial amount of sequence information from various ecosystems, and will continue to accumulate large amounts of sequence data given the qualitative and quantitative improvements in the next-generation sequencing methods. It is now possible to take advantage of these data to develop comprehensive microarrays by using explorative probe design strategies. Such strategies anticipate genetic variations and thus are able to detect known and unknown sequences in environmental samples. In this review, we provide a detailed overview of the probe design strategies currently available to construct both phylogenetic and functional DNA microarrays, with emphasis on those permitting the selection of such explorative probes. Furthermore, exploration of complex environments requires particular attention on probe sensitivity and specificity criteria. Finally, these innovative probe design approaches require exploiting newly available high-density microarray formats.

In-depth molecular and phenotypic characterization in a rice insertion line library facilitates gene identification through reverse and forward genetics approaches.

We report here the molecular and phenotypic features of a library of 31,562 insertion lines generated in the model japonica cultivar Nipponbare of rice (Oryza sativa L.), called Oryza Tag Line (OTL). Sixteen thousand eight hundred and fourteen T-DNA and 12,410 Tos17 discrete insertion sites have been characterized in these lines. We estimate that 8686 predicted gene intervals--i.e. one-fourth to one-fifth of the estimated rice nontransposable element gene complement--are interrupted by sequence-indexed T-DNA (6563 genes) and/or Tos17 (2755 genes) inserts. Six hundred and forty-three genes are interrupted by both T-DNA and Tos17 inserts. High quality of the sequence indexation of the T2 seed samples was ascertained by several approaches. Field evaluation under agronomic conditions of 27,832 OTL has revealed that 18.2% exhibit at least one morphophysiological alteration in the T1 progeny plants. Screening 10,000 lines for altered response to inoculation by the fungal pathogen Magnaporthe oryzae allowed to observe 71 lines (0.7%) developing spontaneous lesions simulating disease mutants and 43 lines (0.4%) exhibiting an enhanced disease resistance or susceptibility. We show here that at least 3.5% (four of 114) of these alterations are tagged by the mutagens. The presence of allelic series of sequence-indexed mutations in a gene among OTL that exhibit a convergent phenotype clearly increases the chance of establishing a linkage between alterations and inserts. This convergence approach is illustrated by the identification of the rice ortholog of AtPHO2, the disruption of which causes a lesion-mimic phenotype owing to an over-accumulation of phosphate, in nine lines bearing allelic insertions.

HiSpOD: probe design for functional DNA microarrays.

MOTIVATION: The use of DNA microarrays allows the monitoring of the extreme microbial diversity encountered in complex samples like environmental ones as well as that of their functional capacities. However, no probe design software currently available is adapted to easily design efficient and explorative probes for functional gene arrays. RESULTS: We present a new efficient functional microarray probe design algorithm called HiSpOD (High Specific Oligo Design). This uses individual nucleic sequences or consensus sequences produced by multiple alignments to design highly specific probes. Indeed, to bypass crucial problem of cross-hybridizations, probe specificity is assessed by similarity search against a large formatted database dedicated to microbial communities containing about 10 million coding sequences (CDS). For experimental validation, a microarray targeting genes encoding enzymes involved in chlorinated solvent biodegradation was built. The results obtained from a contaminated environmental sample proved the specificity and the sensitivity of probes designed with the HiSpOD program. AVAILABILITY: http://fc.isima.fr/~g2im/hispod/.

3D multiscale analysis of the hierarchical porosity in Coscinodiscus sp. diatoms using a combination of tomographic techniques.

A full 3D analysis of the hierarchical porosity in Coscinodiscus sp. diatom structures was carried out by using a multiscale approach that combines three advanced volumetric imaging techniques with resolutions and fields of view covering all the porous characteristics of such complex architectures: electron tomography, "slice and view" approach that uses a dual-beam microscope (FIB-SEM), and array tomography consisting of serial imaging of ultrathin specimen sections. This multiscale approach allowed the whole porosity network to be quantified and provided an unprecedented structural insight into these natural nanostructured materials with internal organization ranging from micrometer to nanometer. The analysed species is made of several nested layers with different pore sizes, shapes and connectivities and characterized by the presence of interconnected pores structured in various ways. The first evidence of the presence of a nanometric porosity made of ellipsoidal pores in the siliceous diatom frustules is also provided.

Bacterial community composition of biological degreasing systems and health risk assessment for workers.

Biological degreasing system is a new technology based on the degradation capabilities of microorganisms to remove oil, grease, or lubricants from metal parts. No data is available about the potential biological health hazards in such system. Thus, a health risk assessment linked to the bacterial populations present in this new degreasing technology is, therefore, necessary for workers. We performed both cultural and molecular approaches in several biological degreasing systems for various industrial contexts to investigate the composition and dynamics of bacterial populations. These biological degreasing systems did not work with the original bacterial populations. Indeed, they were colonized by a defined and restricted group of bacteria. This group replaced the indigenous bacterial populations known for degrading complex substrates. Klebsiella pneumoniae, Klebsiella oxytoca, Pseudomonas aeruginosa, and Pantoea agglomerans were important members of the microflora found in most of the biological degreasing systems. These bacteria might represent a potential health hazard for workers.

Identification of sulfur-cycle prokaryotes in a low-sulfate lake (Lake Pavin) using aprA and 16S rRNA gene markers.

Geochemical researches at Lake Pavin, a low-sulfate-containing freshwater lake, suggest that the dominant biogeochemical processes are iron and sulfate reduction, and methanogenesis. Although the sulfur cycle is one of the main active element cycles in this lake, little is known about the sulfate-reducer and sulfur-oxidizing bacteria. The aim of this study was to assess the vertical distribution of these microbes and their diversities and to test the hypothesis suggesting that only few SRP populations are involved in dissimilatory sulfate reduction and that Epsilonproteobacteria are the likely key players in the oxidative phase of sulfur cycle by using a PCR aprA gene-based approach in comparison with a 16S rRNA gene-based analysis. The results support this hypothesis. Finally, this preliminary work points strongly the likelihood of novel metabolic processes upon the availability of sulfate and other electron acceptors.

Detecting variants with Metabolic Design, a new software tool to design probes for explorative functional DNA microarray development.

BACKGROUND: Microorganisms display vast diversity, and each one has its own set of genes, cell components and metabolic reactions. To assess their huge unexploited metabolic potential in different ecosystems, we need high throughput tools, such as functional microarrays, that allow the simultaneous analysis of thousands of genes. However, most classical functional microarrays use specific probes that monitor only known sequences, and so fail to cover the full microbial gene diversity present in complex environments. We have thus developed an algorithm, implemented in the user-friendly program Metabolic Design, to design efficient explorative probes. RESULTS: First we have validated our approach by studying eight enzymes involved in the degradation of polycyclic aromatic hydrocarbons from the model strain Sphingomonas paucimobilis sp. EPA505 using a designed microarray of 8,048 probes. As expected, microarray assays identified the targeted set of genes induced during biodegradation kinetics experiments with various pollutants. We have then confirmed the identity of these new genes by sequencing, and corroborated the quantitative discrimination of our microarray by quantitative real-time PCR. Finally, we have assessed metabolic capacities of microbial communities in soil contaminated with aromatic hydrocarbons. Results show that our probe design (sensitivity and explorative quality) can be used to study a complex environment efficiently. CONCLUSIONS: We successfully use our microarray to detect gene expression encoding enzymes involved in polycyclic aromatic hydrocarbon degradation for the model strain. In addition, DNA microarray experiments performed on soil polluted by organic pollutants without prior sequence assumptions demonstrate high specificity and sensitivity for gene detection. Metabolic Design is thus a powerful, efficient tool that can be used to design explorative probes and monitor metabolic pathways in complex environments, and it may also be used to study any group of genes. The Metabolic Design software is freely available from the authors and can be downloaded and modified under general public license.

Oryza Tag Line, a phenotypic mutant database for the Genoplante rice insertion line library.

To organize data resulting from the phenotypic characterization of a library of 30,000 T-DNA enhancer trap (ET) insertion lines of rice (Oryza sativa L cv. Nipponbare), we developed the Oryza Tag Line (OTL) database (http://urgi.versailles.inra.fr/OryzaTagLine/). OTL structure facilitates forward genetic search for specific phenotypes, putatively resulting from gene disruption, and/or for GUSA or GFP reporter gene expression patterns, reflecting ET-mediated endogenous gene detection. In the latest version, OTL gathers the detailed morpho-physiological alterations observed during field evaluation and specific screens in a first set of 13,928 lines. Detection of GUS or GFP activity in specific organ/tissues in a subset of the library is also provided. Search in OTL can be achieved through trait ontology category, organ and/or developmental stage, keywords, expression of reporter gene in specific organ/tissue as well as line identification number. OTL now contains the description of 9721 mutant phenotypic traits observed in 2636 lines and 1234 GUS or GFP expression patterns. Each insertion line is documented through a generic passport data including production records, seed stocks and FST information. 8004 and 6101 of the 13,928 lines are characterized by at least one T-DNA and one Tos17 FST, respectively that OTL links to the rice genome browser OryGenesDB.

New insights into the pelagic microorganisms involved in the methane cycle in the meromictic Lake Pavin through metagenomics.

Advances in metagenomics have given rise to the possibility of obtaining genome sequences from uncultured microorganisms, even for those poorly represented in the microbial community, thereby providing an important means to study their ecology and evolution. In this study, metagenomic sequencing was carried out at four sampling depths having different oxygen concentrations or environmental conditions in the water column of Lake Pavin. By analyzing the sequenced reads and matching the contigs to the proxy genomes of the closest cultivated relatives, we evaluated the metabolic potential of the dominant planktonic species involved in the methane cycle. We demonstrated that methane-producing communities were dominated by the genus Methanoregula while methane-consuming communities were dominated by the genus Methylobacter, thus confirming prior observations. Our work allowed the reconstruction of a draft of their core metabolic pathways. Hydrogenotrophs, the genes required for acetate activation in the methanogen genome, were also detected. Regarding methanotrophy, Methylobacter was present in the same areas as the non-methanotrophic, methylotrophic Methylotenera, which could suggest a relationship between these two groups. Furthermore, the presence of a large gene inventory for nitrogen metabolism (nitrate transport, denitrification, nitrite assimilation and nitrogen fixation, for instance) was detected in the Methylobacter genome.

Synthesis and characterization of nickel-doped ceria nanoparticles with improved surface reducibility.

Nickel-doped ceria nanoparticles (Ni0.1Ce0.9O2-x NPs) were fabricated from Schiff-base complexes and characterized by various microscopic and spectroscopic methods. Clear evidence is provided for incorporation of nickel ions in the ceria lattice in the form of Ni3+ species which is considered as the hole trapped state of Ni2+. The Ni0.1Ce0.9O2-x NPs exhibit enhanced reducibility in H2 as compared to conventional ceria-supported Ni particles, while in O2 the dopant nickel cations are oxidized at higher valence than the supported ones.

Anchoring and promotion effects of metal oxides on silica supported catalytic gold nanoparticles.

The understanding of the interactions between the different components of supported metal doped gold catalysts is of crucial importance for selecting and designing efficient gold catalysts for reactions such as CO oxidation. To progress in this direction, a unique supported nano gold catalyst Au/SS was prepared, and three doped samples (Au/SS@M) were elaborated. The samples before and after test were characterized by Transmission Electron Microscopy (TEM) and X-ray Photoelectron Spectroscopy (XPS). It is found that the doping metal species prefer to be located on the surface of gold nanoparticles and that a small amount of additional reductive metal leads to more efficient reaction. During the catalytic test, the nano-structure of the metal species transforms depending on its chemical nature. This study allows one to identify and address the contribution of each metal on the CO reaction in regard to oxidative species of gold, silica and dopants. Metal doping leads to different exposure of interface sites between Au and metal oxide, which is one of the key factors for the change of the catalytic activity. The metal oxides help the activation of oxygen by two actions: mobility inside the metal bulk and transfer of water species onto of gold nanoparticles.

Durable PROX catalyst based on gold nanoparticles and hydrophobic silica.

3 nm gold nanoparticles obtained by direct chemical reduction of AuPPh3Cl in the presence of hydrophobic silica are highly active and selective over a prolonged period of time in the low temperature oxidation of CO in the presence of hydrogen.