Implementation of a Nanopore metagenomic workflow for time-series of complex microbial communities: MAG catalog and functional annotation.

International audienc

Oxygen-reducing bidirectional microbial electrodes designed in real domestic wastewater

Microbial electrodes were designed in domestic wastewaters to catalyse the oxidation of organic matter (anode) and the reduction of oxygen (cathode) alternately. The successive aeration phases (cathode) enhanced the anodic efficiency, resulting in current densities of up to 6.4 Am-2 without the addition of any substrate. Using nitrogen during the anodic phases affected the microbial populations and the electrodes showed a lower ability to subsequently turn to O2 reduction than the microbial anodes formed in open-to-air conditions did. No strong difference was observed between internal and external biofilm, both of which showed a very large variety of taxa in terms of abundance as well as variance. They comprised a mix of aerobic and anaerobic species, many of which have already been identified separately in bioelectrochemical systems. Such a large diversity, which had not been observed in aerobic bidirectional bioelectrodes so far, can explain the efficiency and robustness observed here. Keywords: Electroactive biofilm; Bioanode; Microbial snorkel; Microbial Fuel Cell; Microbial population

Ecological consequences of abrupt temperature changes in anaerobic digesters

International audienceTemperature is a key parameter of anaerobic digestion. Its modification can have drastic consequences on microbial communities and performances. However it can be an interesting parameter to adjust the productivity, energy efficiency or stability of bioreactors. The objective of this work was to give insights into the consequences of abrupt temperature modifications on the microbiota of anaerobic digestion. Two complementary experiments were performed. A continuously stirred lab-scale bioreactor (5-L) simulated the functioning of a semi-continuous industrial digester. Five batch-fed incubations (1-L) served as replicated experiments. Each experiment was divided into three successive steps: reactors were first operated at 35 degrees C followed by an abrupt increase to 55 degrees C and finally a decrease to 35 degrees C. After the first temperature shock, gas production rate increased temporarily and then fell for 1 month before a new steady-state was reached. When temperature was reset to 35 degrees C in step 3 gas production decreased sharply again. The semi-continuous reactor recovered after 15 days while the batch-fed incubations never recovered. Ecological changes associated to these performance drops and recovery were sought using 16S sequencing of Bacteria and Archaea and multivariate analyses. In brief, Bacteroidales order was rapidly and strongly affected by temperature increase, while Clostridiales became dominant in thermophilic conditions. Several thermotolerant Bacteria were identified as responsible for reactors early recovery, but were outcompeted by a very diverse bacterial population a few weeks after temperature shock. Methanosarcina and Methanobacterium Archaea dominated at 35 degrees C but were slowly replaced by thermophilic Methanoculleus or Methanosarcina at 55 degrees C that were essential to methane production. In step 3, when returning to initial temperature conditions after the thermophilic period, Ruminococcaceae and Methanobacterium appeared to drive digester resilience

Upscaling of Microbial Electrolysis Cell Integrating Microbial Electrosynthesis: Insights, Challenges and Perspectives

Recent development of microbial electrochemical technologies has allowed microbial electrosynthesis (MES) of organic molecules with microbial electrolysis cell treating waste organic matter. An electrolytic cell with a MES cathode (ME-ME cell) can produce soluble organic molecules with higher market price than biomethane, and thus satisfy both economic and environmental interest. However, the sustainability of bioanode activity could become a major concern. In this work, a 15-liter ME-ME reactor was designed with specific electrode configurations. An electrochemical model was established to assess the feasibility and possible performance of the design, considering the “aging” effect of the bioanode. The reactor was then built and operated for performance evaluation as well as bioanode regeneration assay. Biowaste from an industrial deconditioning platform was used as substrate for bioanode. The COD removal rate in the anodic chamber reached 0.83 g day -1 L -1 of anolyte and the anodic coulombic efficiency reached 98.6%. Acetate was produced with a rate of 0.53 g day -1 L -1 of catholyte, reaching a maximum concentration of 8.3 g L -1 . A potential difference was applied between the bioanode and biocathode independent of reference electrodes. The active biocathode was dominated by members of the Genus Pseudomonas , rarely reported so far for MES activity

Denitrifying bio-cathodes developed from constructed wetland sediments exhibit electroactive nitrate reducing biofilms dominated by the genera Azoarcus and Pontibacter

International audienceTo limit the nitrate contamination of ground and surface water, stimulation of denitrification by electrochemical approach is an innovative way to be explored. Two nitrate reducing bio-cathodes were developed under constant polarization (-0.5 V vs SCE) using sediments and water from a constructed wetland (Rampillon, Seine-et-Marne, France). The bio-cathodes responded to nitrate addition on chronoamperometry through an increase of the reductive current. The denitrification efficiency of the pilots increased by 47% compared to the negative controls without electrodes after polarization. 16S rRNA gene sequencing of the biofilms and sediments evidenced the significant and discriminating presence of the Azoarcus and Pontibacter genera in the biofilms from biocathodes active for nitrate reduction. Our study shows the possibility to promote the development of efficient Azoarcus-dominated biocathodes from freshwater sediment to enhance nitrate removal from surface waters

Generic mitigating and promoting effect of zeolite on anaerobic digestion: Physicochemical and metataxonomic data

This article provides comprehensive data on degradation performance and microbial dynamics derived from a set of 24 lab-scale batch anaerobic digesters involving various types of inhibitors and the addition of zeolite as a support material. In the first series of 12 digesters, three inhibitors were investigated at the following concentrations: 20 g/L of sodium chloride, 400 mg/L of erythromycin, and 5 mg/L of S-metolachlor. Each inhibitor was tested in triplicate, along with a control condition without inhibition. A parallel series was set up identically, except that 15 g/L of zeolite was introduced into each digester to mitigate the inhibition and promote the degradation process. The provided data comprises information regarding the experimental setup, monitoring measurements that assess the degradation performance (production, composition, and apparent isotopic factor of biogas, pH, dissolved inorganic and organic carbon and volatile fatty acids concentrations), microbial samples information, and 16S rRNA gene sequencing data that decipher changes in microbial structure. This datapaper is associated with research article [1] and presents both the sequencing data and the associated physicochemical data in a structured table format. The sequencing data were generated using the Ion Torrent PGM sequencer and have been deposited in the European Nucleotide Archive (ENA) database at EMBL-EBI under accession number PRJEB65129 (https://www.ebi.ac.uk/ena/browser/view/PRJEB65129), with sample accession numbers ranging from ERS16257742 to ERS16257691 [2]. The data serves as a valuable resource for comparisons with data from other studies on lab-scale batch anaerobic digesters, particularly those utilizing zeolite as a support material or involving inhibition caused by similar types of inhibitors (salts, antibiotics, or pesticides)

Biorefinery for heterogeneous organic waste using microbial electrochemical technology

Environmental biorefineries aim to produce biofuels and platform biomolecules from organic waste. To this end, microbial electrochemical technologies theoretically allow controlled microbial electrosynthesis (MES) of organic molecules to be coupled to oxidation of waste. Here, we provide a first proof of concept and a robust operation strategy for MES in a microbial electrolysis cell (MEC) fed with biowaste hydrolysates. This strategy allowed stable operation at 5 A/m2 for more than three months in a labscale reactor. We report a two to four-fold reduction in power consumption compared to microbial electrosynthesis with water oxidation at the anode. The bioelectrochemical characterizations of the cells were used to compute energy and matter balances for biorefinery scenarios in which anaerobic digestion (AD) provides the electricity and CO2 required for the MEC. Calculations shows that up to 22% of electrons (or COD) from waste may be converted to organic products in the AD-MEC process

Integrative Analyses to Investigate the Link between Microbial Activity and Metabolite Degradation during Anaerobic Digestion

International audienceAnaerobic digestion (AD) is a promising biological process that converts waste into sustainable energy. To fully exploit AD's capability, we need to deepen our knowledge of the microbiota involved in this complex bioprocess. High-throughput methodologies open new perspectives to investigate the AD process at the molecular level, supported by recent data integration methodologies to extract relevant information. In this study, we investigated the link between microbial activity and substrate degradation in a lab-scale anaerobic codigestion experiment, where digesters were fed with nine different mixtures of three cosubstrates (fish waste, sewage sludge, and grass). Samples were profiled using 16S rRNA sequencing and untargeted metabolomics. In this article, we propose a suite of multivariate tools to statistically integrate these data and identify coordinated patterns between groups of microbial and metabolic profiles specific of each cosubstrate. Five main groups of features were successfully evidenced, including cadaverine degradation found to be associated with the activity of microorganisms from the order Clostridiales and the genus Methanosarcina. This study highlights the potential of data integration toward a comprehensive understanding of AD microbiota

Methane production and microbial community acclimation of five manure inocula during psychrophilic anaerobic digestion of swine manure

International audienceFor small-scale farms, the development of rustic and cheap psychrophilic anaerobic digestion systems appears as an opportunity to treat manure, mitigate gaseous emissions and promote decentralized renewable energy production. However, the development of such processes is limited by our understanding of their start-up. In this research, we tested the ability of one mesophilic digestate and four different manure to be used as inoculum for the start-up of psychrophilic anaerobic digestion of swine slurry at 13 • C. The most efficient inoculum appeared to be a swine manure that had been stored for 2 months in a pit. After 9 months of acclimation, the corresponding reactor produced a maximum methane yield of 42L of CH 4 /kg Volatile Solide substrate /day and a CH 4 volume of 125L of CH 4 /kg-Chemical Oxygen Demand added. The maximum methane production expressed at 13 • C was between 55% and 68% of that obtained at 37 • C. Monitoring of the microbial community dynamics by high throughput 16S rDNA sequencing showed the smooth adaptation of manure microbial species, underlining the transient dominance of the acetogen syntroph candidatus Cloacimonas during acclimation and the enrichment in the Methanosaeta and Methanosarcina methanogens for an efficient methane production

Study of a Pilot Scale Microbial Electrosynthesis Reactor for Organic Waste Biorefinery

Microbial electrochemical technologies now enable microbial electrosynthesis (MES) of organic compounds using microbial electrolysis cells handling waste organic materials. An electrolytic cell with an MES cathode may generate soluble organic molecules at a higher market price than biomethane, thereby satisfying both economic and environmental goals. However, the long-term viability of bioanode activity might become a major concern. In this work, a 15-L MES reactor was designed with specific electrode configurations. An electrochemical model was established to assess the feasibility and possible performance of the design, considering the aging of the bioanode. The reactor was then constructed and tested for performance as well as a bioanode regeneration assay. Biowaste from an industrial deconditioning platform was used as a substrate for bioanode. The chemical oxygen demand (COD) removal rate in the anodic chamber reached 0.83 g day−1 L−1 of anolyte. Acetate was produced with a rate of 0.53 g day−1 L−1 of catholyte, reaching a maximum concentration of 8.3 g L−1. A potential difference (from 0.6 to 1.2 V) was applied between the bioanode and biocathode independent of reference electrodes. The active biocathode was dominated by members of the genus Pseudomonas, rarely reported so far for MES activity