Combined effects of micropollutants and their degradation on prokaryotic communities at the sediment-water interface.

Pesticides and pharmaceuticals enter aquatic ecosystems as complex mixtures. Various processes govern their dissipation and effect on the sediment and surface waters. These micropollutants often show persistence and can adversely affect microorganisms even at low concentrations.

Unlocking secrets of microbial ecotoxicology: recent achievements and future challenges.

Environmental pollution is one of the main challenges faced by humanity. By their ubiquity and vast range of metabolic capabilities, microorganisms are affected by pollution with consequences on their host organisms and on the functioning of their environment. They also play key roles in the fate of pollutants through the degradation, transformation, and transfer of organic or inorganic compounds.

Proteogenomics of the novel Dehalobacterium formicoaceticum strain EZ94 highlights a key role of methyltransferases during anaerobic dichloromethane degradation.

Dichloromethane (DCM, methylene chloride) is a toxic, high-volume industrial pollutant of long-standing. Anaerobic biodegradation is crucial for its removal from contaminated environments, yet prevailing mechanisms remain unresolved, especially concerning dehalogenation. In this study, we obtained an assembled genome of a novel DCM-degrading strain, Dehalobacterium formicoaceticum strain EZ94, from a stable DCM-degrading consortium, and we analyzed its proteome during degradation of DCM.

FluorMango, an RNA-Based Fluorogenic Biosensor for the Direct and Specific Detection of Fluoride.

Nucleic acids are not only essential actors of cell life but also extremely appealing molecular objects in the development of synthetic molecules for biotechnological application, such as biosensors to report on the presence and concentration of a target ligand by emission of a measurable signal. In this work, FluorMango, a fluorogenic ribonucleic acid (RNA)-based biosensor specific for fluoride is introduced. The molecule consists of two RNA aptamer modules, a fluoride-specific sensor derived from the crcB riboswitch which changes its structure upon interaction with the target ion, and the light-up RNA Mango-III that emits fluorescence when complexed with a fluorogen.

A Methylotrophic Bacterium Growing with the Antidiabetic Drug Metformin as Its Sole Carbon, Nitrogen and Energy Source.

Metformin is one of the most prescribed antidiabetic agents worldwide and is also considered for other therapeutic applications including cancer and endocrine disorders. It is largely unmetabolized by human enzymes and its presence in the environment has raised concern, with reported toxic effects on aquatic life and potentially also on humans. We report on the isolation and characterisation of strain MD1, an aerobic methylotrophic bacterium growing with metformin as its sole carbon, nitrogen and energy source.

High-quality genome of the basidiomycete yeast Dioszegia hungarica PDD-24b-2 isolated from cloud water.

The genome of the basidiomycete yeast Dioszegia hungarica strain PDD-24b-2 isolated from cloud water at the summit of puy de Dôme (France) was sequenced using a hybrid PacBio and Illumina sequencing strategy. The obtained assembled genome of 20.98 Mb and a GC content of 57% is structured in 16 large-scale contigs ranging from 90 kb to 5.

Complete Genome of Sphingomonas aerolata PDD-32b-11, Isolated from Cloud Water at the Summit of Puy de Dôme, France.

The complete genome of Sphingomonas aerolata PDD-32b-11, a bacterium isolated from cloud water, was sequenced. It features four circular replicons, a chromosome of 3.99 Mbp, and three plasmids.

Genome-Wide Transcription Start Sites Mapping in Grown with Dichloromethane and Methanol.

Dichloromethane (DCM, methylene chloride) is a toxic halogenated volatile organic compound massively used for industrial applications, and consequently often detected in the environment as a major pollutant. DCM biotransformation suggests a sustainable decontamination strategy of polluted sites. Among methylotrophic bacteria able to use DCM as a sole source of carbon and energy for growth, DM4 is a longstanding reference strain.

Growth-Associated Droplet Shrinkage for Bacterial Quantification, Growth Monitoring, and Separation by Ultrahigh-Throughput Microfluidics.

Microbiology still relies on en masse cultivation for selection, isolation, and characterization of microorganisms of interest. This constrains the diversity of microbial types and metabolisms that can be investigated in the laboratory also because of intercellular competition during cultivation. Cell individualization by droplet-based microfluidics prior to experimental analysis provides an attractive alternative to access a larger fraction of the microbial biosphere, miniaturizing the required equipment and minimizing reagent use for increased and more efficient analytical throughput.

Water table fluctuations affect dichloromethane biodegradation in lab-scale aquifers contaminated with organohalides.

Dichloromethane (DCM) is a toxic industrial solvent frequently detected in multi-contaminated aquifers. It can be degraded biotically or abiotically, and under oxic or anoxic conditions. The extent and pathways of DCM degradation in aquifers may thus depend on water table fluctuations and microbial responses to hydrochemical variations.

C-chloromethane incubations provide evidence for novel bacterial chloromethane degraders in a living tree fern.

Chloromethane (CH Cl) is the most abundant halogenated volatile organic compound in the atmosphere and contributes to stratospheric ozone depletion. CH Cl has mainly natural sources such as emissions from vegetation. In particular, ferns have been recognized as strong emitters.

Dichloromethane Degradation Pathway from Unsequenced sp. MC8b Rapidly Explored by Pan-Proteomics.

Several bacteria are able to degrade the major industrial solvent dichloromethane (DCM) by using the conserved dehalogenase DcmA, the only system for DCM degradation characterised at the sequence level so far. Using differential proteomics, we rapidly identified key determinants of DCM degradation for sp. MC8b, an unsequenced facultative methylotrophic DCM-degrading strain.

Unexpected high production of biohydrogen from the endogenous fermentation of grape must deposits.

The aim of this work was to assess the performances of wine byproduct biomass for hydrogen production by dark fermentation. Grape must deposits from two grape varieties (Pinot Gris and Chardonnay) were considered, either with external microbial inoculum or without. We show that grape must residues contain endogenous microflora, well adapted to their environment, which can degrade sugars (initially contained in the biomass) to hydrogen without any nutrient addition.

Chlorinated ethene biodegradation and associated bacterial taxa in multi-polluted groundwater: Insights from biomolecular markers and stable isotope analysis.

Chlorinated ethenes (CEs) are most problematic pollutants in groundwater. Dehalogenating bacteria, and in particular organohalide-respiring bacteria (OHRB), can transform PCE to ethene under anaerobic conditions, and thus contribute to bioremediation of contaminated sites. Current approaches to characterize in situ biodegradation of CEs include hydrochemical analyses, quantification of the abundance of key species (e.

Biohydrogen production in a continuous liquid/gas hollow fiber membrane bioreactor: Efficient retention of hydrogen producing bacteria via granule and biofilm formation.

The aim of this work was to develop a continuous liquid/gas membrane bioreactor (L/G MBR), i.e. a fermenting module including hollow fibers membrane for L/G separation, for biohydrogen production by dark fermentation.

Dissipation of S-metolachlor and butachlor in agricultural soils and responses of bacterial communities: Insights from compound-specific isotope and biomolecular analyses.

The soil dissipation of the widely used herbicides S-metolachlor (SM) and butachlor (BUT) was evaluated in laboratory microcosms at two environmentally relevant doses (15 and 150 μg/g) and for two agricultural soils (crop and paddy). Over 80% of SM and BUT were dissipated within 60 and 30 days, respectively, except in experiments with crop soil at 150 μg/g. Based on compound-specific isotope analysis (CSIA) and observed dissipation, biodegradation was the main process responsible for the observed decrease of SM and BUT in the paddy soil.

Transcriptional regulation of organohalide pollutant utilisation in bacteria.

Organohalides are organic molecules formed biotically and abiotically, both naturally and through industrial production. They are usually toxic and represent a health risk for living organisms, including humans. Bacteria capable of degrading organohalides for growth express dehalogenase genes encoding enzymes that cleave carbon-halogen bonds.

Chlorine Isotope Fractionation of the Major Chloromethane Degradation Processes in the Environment.

Chloromethane (CHCl) is an important source of chlorine in the stratosphere, but detailed knowledge of the magnitude of its sources and sinks is missing. Here, we measured the stable chlorine isotope fractionation (ε) associated with the major abiotic and biotic CHCl sinks in the environment, namely, CHCl degradation by hydroxyl (OH) and chlorine (Cl) radicals in the troposphere and by reference bacteria CM4 and MB2 from terrestrial and marine environments, respectively. No chlorine isotope fractionation was detected for reaction of CHCl with OH and Cl radicals, whereas a large chlorine isotope fractionation (ε) of -10.

A Promiscuous CYP706A3 Reduces Terpene Volatile Emission from Arabidopsis Flowers, Affecting Florivores and the Floral Microbiome.

Flowers are essential but vulnerable plant organs, exposed to pollinators and florivores; however, flower chemical defenses are rarely investigated. We show here that two clustered terpene synthase and cytochrome P450 encoding genes ( and ) on chromosome 5 of Arabidopsis () are tightly coexpressed in floral tissues, upon anthesis and during floral bud development. TPS11 was previously reported to generate a blend of sesquiterpenes.

Methylotrophs and Methylotroph Populations for Chloromethane Degradation.

Chloromethane is a halogenated volatile organic compound, produced in large quantities by terrestrial vegetation. After its release to the troposphere and transport to the stratosphere, its photolysis contributes to the degradation of stratospheric ozone. A better knowledge of chloromethane sources (production) and sinks (degradation) is a prerequisite to estimate its atmospheric budget in the context of global warming.

Functional Genes and Bacterial Communities During Organohalide Respiration of Chloroethenes in Microcosms of Multi-Contaminated Groundwater.

Microcosm experiments with CE-contaminated groundwater from a former industrial site were set-up to evaluate the relationships between biological CE dissipation, dehalogenase genes abundance and bacterial genera diversity. Impact of high concentrations of PCE on organohalide respiration was also evaluated. Complete or partial dechlorination of PCE, TCE, -DCE and VC was observed independently of the addition of a reducing agent (NaS) or an electron donor (acetate).

Individual stages of bacterial dichloromethane degradation mapped by carbon and chlorine stable isotope analysis.

The fractionation of carbon and chlorine stable isotopes of dichloromethane (CHCl, DCM) upon dechlorination by cells of the aerobic methylotroph Methylobacterium extorquens DM4 and by purified DCM dehalogenases of the glutathione S-transferase family was analyzed. Isotope effects for individual steps of the multi-stage DCM degradation process, including transfer across the cell wall from the aqueous medium to the cell cytoplasm, dehalogenase binding, and catalytic reaction, were considered. The observed carbon and chlorine isotope fractionation accompanying DCM consumption by cell supensions and enzymes was mainly determined by the breaking of CCl bonds, and not by inflow of DCM into cells.

Toward Integrative Bacterial Monitoring of Metolachlor Toxicity in Groundwater.

Common herbicides such as metolachlor (MET), and their transformation products, are frequently detected in groundwater worldwide. Little is known about the response of groundwater bacterial communities to herbicide exposure, and its potential use for ecotoxicological assessment. The response of bacterial communities exposed to different levels of MET from the Ariège alluvial aquifer (Southwest of France) was investigated and in laboratory experiments.