Microbial ecology of chlorinated solvent biodegradation.

This study focused on the microbial ecology of tetrachloroethene (PCE) degradation to trichloroethene, cis-1,2-dichloroethene and vinyl chloride to evaluate the relationship between the microbial community and the potential accumulation or degradation of these toxic metabolites. Multiple soil microcosms supplied with different organic substrates were artificially contaminated with PCE. A thymidine analogue, bromodeoxyuridine (BrdU), was added to the microcosms and incorporated into the DNA of actively replicating cells. We compared the total and active bacterial communities during the 50-day incubations by using phylogenic microarrays and 454 pyrosequencing to identify microorganisms and functional genes associated with PCE degradation to ethene. By use of this integrative approach, both the key community members and the ecological functions concomitant with complete PCE degradation could be determined, including the presence and activity of microbial community members responsible for producing hydrogen and acetate, which are critical for Dehalococcoides-mediated PCE degradation. In addition, by correlation of chemical data and phylogenic microarray data, we identified several bacteria that could potentially oxidize hydrogen. These results demonstrate that PCE degradation is dependent on some microbial community members for production of appropriate metabolites, while other members of the community compete for hydrogen in soil at low redox potentials.

Selective Sensing in Microbial Fuel Cell Biosensors: Insights from Toxicity-Adapted and Non-Adapted Biofilms for Pb(II) and Neomycin Sulfate Detection.

This study introduces the utilization of self-powered microbial fuel cell (MFC)-based biosensors for the detection of biotoxicity in wastewater. Current MFC-based biosensors lack specificity in distinguishing between different pollutants. To address this limitation, a novel approach is introduced, capitalizing on the adaptive capabilities of anodic biofilms. By acclimating these biofilms to specific pollutants, an enhancement in the selectivity of MFC biosensors is achieved. Notably, electrochemically active bacteria (EAB) were cultivated on 3D porous carbon felt with and without a model toxicant (target analyte), resulting in the development of toxicant-resistant anodic biofilms. The model toxicants, Pb2+ ions and the antibiotic neomycin sulfate (NS), were deployed at a concentration of 1 mg L-1 during MFC operation. The influence of toxicity on biofilm growth and power production was investigated through polarization and power density curves. Concurrently, the electrochemical activity of both non-adapted and toxicity-adapted biofilms was investigated using cyclic voltammetry. Upon maturation and attainment of peak powers, the MFC reactors were evaluated individually as self-powered biosensors for pollutant detection in fresh wastewater, employing the external resistor (ER) mode. The selected ER, corresponding to the maximum power output, was positioned between the cathode and anode of each MFC, enabling output signal tracking through a data logging system. Subsequent exposure of mature biofilm-based MFC biosensors to various concentrations of the targeted toxicants revealed that non-adapted mature biofilms generated similar current-time profiles for both toxicity models, whereas toxicity-adapted biofilms produced distinctive current-time profiles. Accordingly, these results suggested that merely by adapting the anodic biofilm to the targeted toxicity, distinct and identifiable current-time profiles can be created. Furthermore, these toxicity-adapted and non-adapted biofilms can be employed to selectively detect the pollutant via the differential measurement of electrical signals. This differentiation offers a promising avenue for selective pollutant detection. To the best of our current knowledge, this approach, which harnesses the natural adaptability of biofilms for enhanced sensor selectivity, represents a pioneering effort in the realm of MFC-based biosensing.

Untreated vs. Treated Carbon Felt Anodes: Impacts on Power Generation in Microbial Fuel Cells.

This research sought to enhance the efficiency and biocompatibility of anodes in bioelectrochemical systems (BESs) such as microbial fuel cells (MFCs), with an aim toward large-scale, real-world applications. The study focused on the effects of acid-heat treatment and chemical modification of three-dimensional porous pristine carbon felt (CF) on power generation. Different treatments were applied to the pristine CF, including coating with carbon nanofibers (CNFs) dispersed using dodecylbenzene sulfonate (SDBS) surfactant and biopolymer chitosan (CS). These processes were expected to improve the hydrophilicity, reduce the internal resistance, and increase the electrochemically active surface area of CF anodes. A high-resolution scanning electron microscopy (HR-SEM) analysis confirmed successful CNF coating. An electrochemical analysis showed improved conductivity and charge transfer toward [Fe(CN)6]3-/4- redox probe with treated anodes. When used in an air cathode single-chamber MFC system, the untreated CF facilitated quicker electroactive biofilm growth and reached a maximum power output density of 3.4 W m-2, with an open-circuit potential of 550 mV. Despite a reduction in charge transfer resistance (Rct) with the treated CF anodes, the power densities remained unchanged. These results suggest that untreated CF anodes could be most promising for enhancing power output in BESs, offering a cost-effective solution for large-scale MFC applications.

Accessing the soil metagenome for studies of microbial diversity.

Soil microbial communities contain the highest level of prokaryotic diversity of any environment, and metagenomic approaches involving the extraction of DNA from soil can improve our access to these communities. Most analyses of soil biodiversity and function assume that the DNA extracted represents the microbial community in the soil, but subsequent interpretations are limited by the DNA recovered from the soil. Unfortunately, extraction methods do not provide a uniform and unbiased subsample of metagenomic DNA, and as a consequence, accurate species distributions cannot be determined. Moreover, any bias will propagate errors in estimations of overall microbial diversity and may exclude some microbial classes from study and exploitation. To improve metagenomic approaches, investigate DNA extraction biases, and provide tools for assessing the relative abundances of different groups, we explored the biodiversity of the accessible community DNA by fractioning the metagenomic DNA as a function of (i) vertical soil sampling, (ii) density gradients (cell separation), (iii) cell lysis stringency, and (iv) DNA fragment size distribution. Each fraction had a unique genetic diversity, with different predominant and rare species (based on ribosomal intergenic spacer analysis [RISA] fingerprinting and phylochips). All fractions contributed to the number of bacterial groups uncovered in the metagenome, thus increasing the DNA pool for further applications. Indeed, we were able to access a more genetically diverse proportion of the metagenome (a gain of more than 80% compared to the best single extraction method), limit the predominance of a few genomes, and increase the species richness per sequencing effort. This work stresses the difference between extracted DNA pools and the currently inaccessible complete soil metagenome.

Evolution of Sphingomonad Gene Clusters Related to Pesticide Catabolism Revealed by Genome Sequence and Mobilomics of Sphingobium herbicidovorans MH.

Bacterial degraders of chlorophenoxy herbicides have been isolated from various ecosystems, including pristine environments. Among these degraders, the sphingomonads constitute a prominent group that displays versatile xenobiotic-degradation capabilities. Four separate sequencing strategies were required to provide the complete sequence of the complex and plastic genome of the canonical chlorophenoxy herbicide-degrading Sphingobium herbicidovorans MH. The genome has an intricate organization of the chlorophenoxy-herbicide catabolic genes sdpA, rdpA, and cadABCD that encode the (R)- and (S)-enantiomer-specific 2,4-dichlorophenoxypropionate dioxygenases and four subunits of a Rieske non-heme iron oxygenase involved in 2-methyl-chlorophenoxyacetic acid degradation, respectively. Several major genomic rearrangements are proposed to help understand the evolution and mobility of these important genes and their genetic context. Single-strain mobilomic sequence analysis uncovered plasmids and insertion sequence-associated circular intermediates in this environmentally important bacterium and enabled the description of evolutionary models for pesticide degradation in strain MH and related organisms. The mobilome presented a complex mosaic of mobile genetic elements including four plasmids and several circular intermediate DNA molecules of insertion-sequence elements and transposons that are central to the evolution of xenobiotics degradation. Furthermore, two individual chromosomally integrated prophages were shown to excise and form free circular DNA molecules. This approach holds great potential for improving the understanding of genome plasticity, evolution, and microbial ecology.

Diversity of active microbial communities subjected to long-term exposure to chemical contaminants along a 40-year-old sediment core.

In estuarine ecosystems, metallic and organic contaminants are mainly associated with fine grain sediments which settle on mudflats. Over time, the layers of sediment accumulate and are then transformed by diagenetic processes mainly controlled by microbial activity, recording the history of the estuary's chemical contamination. In an environment of this specific type, we investigated the evolution of the chemical contamination and the structure of both total and active microbial communities, based on PhyloChip analysis of a 4.6-m core corresponding to a 40-year sedimentary record. While the archaeal abundance remained constant along the core, a decrease by one order of magnitude in the bacterial abundance was observed with depth. Both total and active microbial communities were dominated by Proteobacteria, Actinobacteria, and Firmicutes in all sediment samples. Among Proteobacteria, alpha-Proteobacteria dominated both total (from 37 to 60 %) and metabolically active (from 19.7 to 34.6 %) communities, including the Rhizobiales, Rhodobacter, Caulobacterales, and Sphingomonadales orders. Co-inertia analysis revealed a relationship between polycyclic aromatic hydrocarbons, zinc and some polychlorobiphenyls concentrations, and the structure of total and active microbial communities in the oldest and most contaminated sediments (from 1970 to 1975), suggesting that long-term exposure to chemicals shaped the structure of the microbial community.

Head-to-tail self-assembly of a calix[4]arene inclusion polymer controlled by a pendant arm.

A calix[4]arene functionalized at one phenolic group with a pendant ethoxy acetate group, forms an inclusion complex that is stable even in the presence of other potential guest molecules.

Large-scale metagenomic-based study of antibiotic resistance in the environment.

Antibiotic resistance, including multiresistance acquisition and dissemination by pathogens, is a critical healthcare issue threatening our management of infectious diseases [1-3]. Rapid accumulation of resistance phenotypes implies a reservoir of transferable antibiotic resistance gene determinants (ARGDs) selected in response to inhibition of antibiotic concentrations, as found in hospitals [1, 3-5]. Antibiotic resistance genes were found in environmental isolates, soil DNA [4-6], secluded caves [6, 7], and permafrost DNA [7, 8]. Antibiotics target essential and ubiquitous cell functions, and resistance is a common characteristic of environmental bacteria [8-11]. Environmental ARGDs are an abundant reservoir of potentially transferable resistance for pathogens [9-12]. Using metagenomic sequences, we show that ARGDs can be detected in all (n=71) environments analyzed. Soil metagenomes had the most diverse pool of ARGDs. The most common types of resistances found in environmental metagenomes were efflux pumps and genes conferring resistance to vancomycin, tetracycline, or ß-lactam antibiotics used in veterinary and human healthcare. Our study describes the diverse and abundant antibiotic resistance genes in nonclinical environments and shows that these genes are not randomly distributed among different environments (e.g., soil, oceans or human feces).

Soil bacterial community shifts after chitin enrichment: an integrative metagenomic approach.

Chitin is the second most produced biopolymer on Earth after cellulose. Chitin degrading enzymes are promising but untapped sources for developing novel industrial biocatalysts. Hidden amongst uncultivated micro-organisms, new bacterial enzymes can be discovered and exploited by metagenomic approaches through extensive cloning and screening. Enrichment is also a well-known strategy, as it allows selection of organisms adapted to feed on a specific compound. In this study, we investigated how the soil bacterial community responded to chitin enrichment in a microcosm experiment. An integrative metagenomic approach coupling phylochips and high throughput shotgun pyrosequencing was established in order to assess the taxonomical and functional changes in the soil bacterial community. Results indicate that chitin enrichment leads to an increase of Actinobacteria, γ-proteobacteria and ß-proteobacteria suggesting specific selection of chitin degrading bacteria belonging to these classes. Part of enriched bacterial genera were not yet reported to be involved in chitin degradation, like the members from the Micrococcineae sub-order (Actinobacteria). An increase of the observed bacterial diversity was noticed, with detection of specific genera only in chitin treated conditions. The relative proportion of metagenomic sequences related to chitin degradation was significantly increased, even if it represents only a tiny fraction of the sequence diversity found in a soil metagenome.

From protected trialkoxysilyl-peptide building blocks to bioorganic-silica hybrid materials.

A straightforward method for the preparation of hybrid bioorganic-inorganic materials is reported. Common strategies to synthesize such promising materials require special surface modifications of silica followed by grafting of the organic moiety via chemoselective ligation. In this context, we set up a general and bottom-up strategy relying on modified peptides functionalized with a trialkoxysilane group. Used in mixtures with TEOS and a surfactant as the structure directing agent, these hybrid building blocks allow one step direct synthesis of bioorganic-inorganic hybrid materials. Two examples were chosen to demonstrate our general approach. (1) An antifouling surface was prepared by dip coating of a sol containing an antibacterial silylated peptide. (2) Organized mesoporous silica displaying a peptide catalyst in the pores was prepared in one step and tested.

Interactions between snow chemistry, mercury inputs and microbial population dynamics in an Arctic snowpack.

We investigated the interactions between snowpack chemistry, mercury (Hg) contamination and microbial community structure and function in Arctic snow. Snowpack chemistry (inorganic and organic ions) including mercury (Hg) speciation was studied in samples collected during a two-month field study in a high Arctic site, Svalbard, Norway (79 °N). Shifts in microbial community structure were determined by using a 16S rRNA gene phylogenetic microarray. We linked snowpack and meltwater chemistry to changes in microbial community structure by using co-inertia analyses (CIA) and explored changes in community function due to Hg contamination by q-PCR quantification of Hg-resistance genes in metagenomic samples. Based on the CIA, chemical and microbial data were linked (p = 0.006) with bioavailable Hg (BioHg) and methylmercury (MeHg) contributing significantly to the ordination of samples. Mercury was shown to influence community function with increases in merA gene copy numbers at low BioHg levels. Our results show that snowpacks can be considered as dynamic habitats with microbial and chemical components responding rapidly to environmental changes.

Designer amphiphiles based on para-acyl-calix[8]arenes.

The synthesis of a series of fully O-derivatised para-acyl-calix[8]arenes is described, where the acyl function is either octanoyl or hexadecanoyl. The groups attached at the phenolic face are, carboxymethoxy (anionic), carboxypropoxy (anionic), 4-sulfonatobutoxy (anionic), ethoxycarboxymethoxy (neutral), ethoxycarboxypropoxy (neutral), 2-methoxyethoxy (neutral) and 2-(2-methoxy)diethoxy (neutral). The use of specific synthetic routes has allowed complete substitution in high yields for all the compounds obtained. The interfacial properties of the compounds have been studied and stable monolayers have been obtained for certain compounds in the series having para-octanoyl substituents; all compounds studied in the series having para-hexadecanoyl substituents formed stable monolayers at the air-water interface. The interactions between O-4-sulfonatobutoxy-para-ocatanoylcalix[8]arene and a series of serum albumins have been studied by dynamic light scattering and specific adsorption of the calix-[8]-arene derivative onto the proteins observed. The anionic derivatives O-4-sulfonatobutoxy-para-ocatanoylcalix[8]arene and O-carboxymethoxy-para-ocatanoylcalix[8]arene have been shown to possess anticoagulant properties but to have no haemolytic toxicity.