Microbial Biotechnology

Cover image for Vol. 10 Issue 6

Early View (Online Version of Record published before inclusion in an issue)

Edited By: Kenneth N. Timmis, Juan Luis Ramos, Willem de Vos, Siegfried E. Vlaeminck, and Auxiliadora Prieto. Genomics Update Editor: Antoine Danchin

Impact Factor: 3.513

ISI Journal Citation Reports © Ranking: 2016: 39/125 (Microbiology); 42/160 (Biotechnology & Applied Microbiology)

Online ISSN: 1751-7915

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  1. 1 - 39
  1. Research Articles

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      Enhancement of methane production from 1-hexadecene by additional electron donors

      A. M. S. Paulo, A. F. Salvador, J. I. Alves, R. Castro, A. A. M. Langenhoff, A. J. M. Stams and A. J. Cavaleiro

      Version of Record online: 7 DEC 2017 | DOI: 10.1111/1751-7915.12886

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      In this work, different stimulation strategies were tested for accelerating 1-hexadecene conversion to methane, namely addition of hydrogenotrophic methanogens or extra electron donors. Our results show that methane production was 7 and 3 times faster in yeast extract- and lactate-stimulated cultures, respectively, compared to non-stimulated cultures. The involvement of Syntrophus/Smithella-related species in 1-hexadecene methanogenic degradation is shown for the first time.

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      Citrate, low pH and amino acid limitation induce citrate utilization in Lactococcus lactis biovar diacetylactis

      Oscar van Mastrigt, Emma E. Mager, Casper Jamin, Tjakko Abee and Eddy J. Smid

      Version of Record online: 7 DEC 2017 | DOI: 10.1111/1751-7915.13031

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      Regulation of citrate utilization by pH, nutrient limitation and the presence of citrate has been studied in Lactococcus lactis biovar diacetylactis. More specifically, we investigated the impact of these parameters on citP transcription, on the copy number of the citP containing plasmid, on processing of citP mRNA and on citrate utilization capactity.

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      A bifunctional cellulase–xylanase of a new Chryseobacterium strain isolated from the dung of a straw-fed cattle

      Hao Tan, Renyun Miao, Tianhai Liu, Lufang Yang, Yumin Yang, Chunxiu Chen, Jianrong Lei, Yuhui Li, Jiabei He, Qun Sun, Weihong Peng, Bingcheng Gan and Zhongqian Huang

      Version of Record online: 4 DEC 2017 | DOI: 10.1111/1751-7915.13034

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      (i) high activity level and catalytic efficiency which are in the front rank of the known cellulases and xylanases; (ii) high thermophilicity (90 °C) that only a few cellulase or xylanase can be comparable with; (iii) using similar amount of enzymatic activity units, the enzyme could obtain much higher yield of glucose and xylose from both straw and spent mushroom substrate than a mixed commercial cellulase+xylanase of Novozymes.

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      The efficacy, biodistribution and safety of an inhibin DNA vaccine delivered by attenuated Salmonella choleraesuis

      Wei-zhen Chen, Ying-mei Li, Xue Yu, Yue Li, Wen-ke Li, Qing-ling Wang, Ai-xin Liang, Xiang Li, Li-guo Yang and Li Han

      Version of Record online: 4 DEC 2017 | DOI: 10.1111/1751-7915.13029

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      The efficacy of an inhibin DNA vaccine delivered by attenuated Salmonella choleraesuis in primate was confirmed. The biodistribution and safety of the novel vaccine in mouse was studied.

  2. Editorial

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  3. Editorial: The microbiome as a source of new enterprises and job creation

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      Designing synbiotics for improved human health

      Sean M. Kearney and Sean M. Gibbons

      Version of Record online: 4 DEC 2017 | DOI: 10.1111/1751-7915.12885

  4. Research Articles

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      Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

      Yvonne Stolze, Andreas Bremges, Irena Maus, Alfred Pühler, Alexander Sczyrba and Andreas Schlüter

      Version of Record online: 4 DEC 2017 | DOI: 10.1111/1751-7915.12982

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      In this study, the applied genome bin-based metatranscriptomics approach enabled insights into the in situ transcriptional activity of four mostly non-cultivated and novel species represented by the genome bins in their respective habitats and therefore complements analogous analyses for isolates from biogas communities.

  5. Minireviews

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      Maintenance and assessment of cell viability in formulation of non-sporulating bacterial inoculants

      Teresa Berninger, Óscar González López, Ana Bejarano, Claudia Preininger and Angela Sessitsch

      Version of Record online: 4 DEC 2017 | DOI: 10.1111/1751-7915.12880

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      Biostimulants and biopesticides based on non-sporulating bacteria are of great interest in agriculture, but their low shelf life and efficacy under field conditions is often a limiting factor to practical application. Protective formulations are thus necessary. A range of methods to maintain and monitor cell viability is presented to decide on suitable approaches for formulation development.

  6. Opinion

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      The race for antimicrobials in the multidrug resistance era

      Carlos Molina-Santiago, Antonio de Vicente and Diego Romero

      Version of Record online: 4 DEC 2017 | DOI: 10.1111/1751-7915.12884

  7. Highlights

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  8. Brief reports

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  9. Research Articles

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      Development of a specific fluorescent phage endolysin for in situ detection of Clostridium species associated with cheese spoilage

      Natalia Gómez-Torres, Matthew Dunne, Sonia Garde, Rob Meijers, Arjan Narbad, Marta Ávila and Melinda J. Mayer

      Version of Record online: 21 NOV 2017 | DOI: 10.1111/1751-7915.12883

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      A fluorescently labelled bacteriophage endolysin was shown to be specific for Clostridium species and was able to detect cheese spoilage strains in the cheese matrix, and to bind to spores. The lysin represents a tool for detection, for understanding clostridial development during cheesemaking and for investigating links between lysin structure and function.

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      Fine-tuning the P. pastoris iMT1026 genome-scale metabolic model for improved prediction of growth on methanol or glycerol as sole carbon sources

      Màrius Tomàs-Gamisans, Pau Ferrer and Joan Albiol

      Version of Record online: 21 NOV 2017 | DOI: 10.1111/1751-7915.12871

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      In this study P. pastoris is characterised using chemostat cultures, with glycerol or methanol as sole carbon sources, and over a wide range of growth rates. As a result, new experimental physiological data, including the representation of biomass composition for these growth conditions is provided. In addition the derived biomass composition equations have been incorporated into iMT1026 (the consensus genome-scale metabolic model for P. pastoris). As a striking outcome, a new version of the GEM model iMT1026 (v3.0) is provided with enhanced and improved prediction capabilities.

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      Enrichment of syngas-converting communities from a multi-orifice baffled bioreactor

      Ana L. Arantes, Joana I. Alves, Alfons J. M. Stams, M. Madalena Alves and Diana Z. Sousa

      Version of Record online: 21 NOV 2017 | DOI: 10.1111/1751-7915.12864

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      Anaerobic cultures able to convert CO were enriched from reactor sludge acclimatized to syngas. Acetobacterium and Sporomusa species were predominant, and operated together with methanogens. The role of Sporomusa species in the enrichment was further elucidated.

  10. Brief Reports

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      The enzymatic detoxification of the mycotoxin deoxynivalenol: identification of DepA from the DON epimerization pathway

      Jason Carere, Yousef I. Hassan, Dion Lepp and Ting Zhou

      Version of Record online: 17 NOV 2017 | DOI: 10.1111/1751-7915.12874

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      This report describes the discovery of a dehydrogenase responsible for the selective oxidation of mycotoxin deoxynivalenol (DON) at the C3 position. The enzyme was shown to readily convert DON to 3-keto-DON, a less toxic intermediate in the DON epimerization pathway. This enzyme may be part of a feasible strategy for DON mitigation within the near future.

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      Harnessing novel chromosomal integration loci to utilize an organosolv-derived hemicellulose fraction for isobutanol production with engineered Corynebacterium glutamicum

      Julian Lange, Felix Müller, Ralf Takors and Bastian Blombach

      Version of Record online: 8 NOV 2017 | DOI: 10.1111/1751-7915.12879

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      We identified 16 chromosomal integration loci termed C. glutamicum landing pads (CgLPs). C. glutamicum was engineered for d-xylose and l-arabinose utilization which showed high growth rates on a hemicellulose fraction derived of beech wood organosolv processing. Finally, we demonstrated a zero-growth isobutanol production process exploiting the hemicellulose fraction with engineered C. glutamicum.

  11. Research Articles

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      Disruption of N-acyl-homoserine lactone-specific signalling and virulence in clinical pathogens by marine sponge bacteria

      José A. Gutiérrez-Barranquero, F. Jerry Reen, María L. Parages, Ronan McCarthy, Alan D. W. Dobson and Fergal O'Gara

      Version of Record online: 3 NOV 2017 | DOI: 10.1111/1751-7915.12867

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      The marine environment is an emergent source of novel novel bioactive compounds with biotechnological and pharmaceutical potential. In this study we have harnessed the QS inhibition (QSI) potential of marine sponge microbiota and through culture based discovery have uncovered small molecule signal mimics that neutralise virulence phenotypes in clinical pathogens. Isolation of novel QSI activities has significant potential for future therapeutic development.

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      Tetraselmis suecica F&M-M33 growth is influenced by its associated bacteria

      Natascia Biondi, Giulia Cheloni, Liliana Rodolfi, Carlo Viti, Luciana Giovannetti and Mario R. Tredici

      Version of Record online: 3 NOV 2017 | DOI: 10.1111/1751-7915.12865

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      Bacterial communities (LAB, OUT) and single bacterial isolates (ABP3, AAD3, LB1, LB4, LG3, ABG2, AG2, LBG3, ARS1, CIgi, CIar) influence Tetraselmis suecica F&M-M33 growth under nutrient limitation. The effect on growth varies from neutral to positive to detrimental.

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      A standardized workflow for surveying recombinases expands bacterial genome-editing capabilities

      Deirdre E. Ricaurte, Esteban Martínez-García, Ákos Nyerges, Csaba Pál, Víctor de Lorenzo and Tomás Aparicio

      Version of Record online: 2 NOV 2017 | DOI: 10.1111/1751-7915.12846

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      Recombineering is limited by availability of recombinases that promote invasion of the replication fork by ssDNA. An experimental workflow has been designed that allows rapid prototyping of new recombinases active in G(–) bacteria. One new recombinase named Rec2 is shown to deliver unprecedented recombineering efficiency in Pseudomonas putida.

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      Promoter mutagenesis for fine-tuning expression of essential genes in Mycobacterium tuberculosis

      Francesca Boldrin, Giulia Degiacomi, Agnese Serafini, Gaëlle S. Kolly, Marcello Ventura, Claudia Sala, Roberta Provvedi, Giorgio Palù, Stewart T. Cole and Riccardo Manganelli

      Version of Record online: 27 OCT 2017 | DOI: 10.1111/1751-7915.12875

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      We report an enhanced TetR/Pip-OFF repressible promoter system that allows more effective control of genes expressed at low level. Subjecting the Pptr promoter to targeted mutagenesis, we produced several promoters with different strength, able to improve the performances of TetR/Pip-OFF repressible system both in vitro and in vivo increasing its stringency. Such promoters were used to construct bacterial biosensors with different sensitivity to DprE1 inhibitors and to develop a whole cell screening assay to identify inhibitors of this enzyme.

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      Elucidating the impact of microbial community biodiversity on pharmaceutical biotransformation during wastewater treatment

      Lauren B. Stadler, Jeseth Delgado Vela, Sunit Jain, Gregory J. Dick and Nancy G. Love

      Version of Record online: 27 OCT 2017 | DOI: 10.1111/1751-7915.12870

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      A wastewater microbial community was experimentally manipulated using a dilution-to-extinction approach to investigate the impact of biodiversity on community function, here defined as the biotransformation of a suite of pharmaceutical compounds commonly detected in wastewater. Taxonomic and functional biodiversity were measured using both 16S rRNA gene and transcript sequencing, and shotgun metagenomics and metatranscriptomics. Taxa and genes were identified whose activity and transcript abundances associated with individual pharmaceutical biotransformation rates and were lost across the biodiversity gradient.

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      Studies on the aerobic utilization of synthesis gas (syngas) by wild type and recombinant strains of Ralstonia eutropha H16

      Daniel Heinrich, Matthias Raberg and Alexander Steinbüchel

      Version of Record online: 13 OCT 2017 | DOI: 10.1111/1751-7915.12873

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      Genes coding for the carbon monoxide dehydrogenase (CODH) of Oligotropha carboxidovorans were overexpressed in Ralstonia eutropha H16. The resulting recombinant R. eutropha strains were able to utilize CO as a source of carbon under aerobic conditions but were dependent on external hydrogen supply to gain energy.

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      Expression of fluorescent proteins in Lactobacillus rhamnosus to study host–microbe and microbe–microbe interactions

      Irina Spacova, Elke Lievens, Tine Verhoeven, Hans Steenackers, Jos Vanderleyden, Sarah Lebeer and Mariya I. Petrova

      Version of Record online: 13 OCT 2017 | DOI: 10.1111/1751-7915.12872

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      Fluorescent tagging of Lactobacillus probiotic strains is an important tool to unravel their modes of action. In this study, the implementation of heterologously expressed mTagBFP2 and mCherry for the labeling of Lactobacillus rhamnosus GG and Lactobacillus rhamnosus GR-1 was explored. The novel fluorescent strains were used to study in vitro aspects of probiotoc microbe-microbe and microbe-host interactions. The fluorescent L. rhamnosus strains developed in this study can serve as novel tools for the study of probiotic interactions with their environment.

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      The parasporal crystals of Bacillus pumilus strain 15.1: a potential virulence factor?

      Diana C. Garcia-Ramon, Colin Berry, Carmen Tse, Alberto Fernández-Fernández, Antonio Osuna and Susana Vílchez

      Version of Record online: 12 OCT 2017 | DOI: 10.1111/1751-7915.12771

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      In this work we characterize the crystal inclusions produced by the newly described entomopathogenic strain Bacillus pumilus 15.1. It was demonstrated that the composition of the crystal was mainly the enzyme oxalate decarboxylase. To our knowledge this is the first time that an enzyme is described to be part of a bacterial parasporal inclusion.

  12. Research articles

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      Opportunities for groundwater microbial electro-remediation

      Narcís Pous, Maria Dolors Balaguer, Jesús Colprim and Sebastià Puig

      Version of Record online: 6 OCT 2017 | DOI: 10.1111/1751-7915.12866

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      Groundwater pollution is a serious worldwide concern. Microbial electro-remediation, by the means of microbial electrochemical technologies (MET) can become a promising alternative in the near future. This document reviews the current knowledge achieved on microbial electro-remediation of groundwater and its applications.

  13. Research Articles

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      1,4-Dioxane-degrading consortia can be enriched from uncontaminated soils: prevalence of Mycobacterium and soluble di-iron monooxygenase genes

      Ya He, Jacques Mathieu, Marcio L.B. da Silva, Mengyan Li and Pedro J.J. Alvarez

      Version of Record online: 6 OCT 2017 | DOI: 10.1111/1751-7915.12850

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      Two bacterial consortia were enriched from uncontaminated soil by virtue of their ability to grow on 1,4-dioxane (dioxane) as a sole carbon and energy source. Based on 16S rRNA sequencing, Mycobacterium was the dominant genus. DNA sequence analyses showed 3- to 7-fold enrichment of group-5 and group-6 soluble diiron monooxygenase genes relative to the original soil samples.

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      Cryopreservation of artificial gut microbiota produced with in vitro fermentation technology

      Lea Bircher, Clarissa Schwab, Annelies Geirnaert and Christophe Lacroix

      Version of Record online: 4 OCT 2017 | DOI: 10.1111/1751-7915.12844

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      In this study, we evaluated the impact of the two cryoprotectives, glycerol (15% v/v) and inulin (5% w/v) alone and in combination, in preserving short chain fatty acid formation and recovery of major butyrate-producing bacteria in three artificial microbiota during cryopreservation for 3 months at −80°C. Our data indicate that butyrate producers, which are key organisms for gut health, can be well preserved with glycerol and inulin during frozen storage.

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      Transfer and analysis of Salmonella pdu genes in a range of Gram-negative bacteria demonstrate exogenous microcompartment expression across a variety of species

      Laura Graf, Kent Wu and James W. Wilson

      Version of Record online: 2 OCT 2017 | DOI: 10.1111/1751-7915.12863

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      Bacterial microcompartments (MCPs) are protein organelles that typically house toxic or volatile reaction intermediates involved in metabolic pathways. We cloned a 38 kb region from the Salmonella enterica serovar Typhimurium genome containing the pdu 1,2 propanediol (1,2 PD) utilization and cob/cbi genes using the FRT-Capture strategy to clone and transfer large genomic segments. We successfully isolated MCPs expressed from the clone from several, but not all, of recipient bacteria, and we observed this utilizing a range of different media and in the absence of protease inhibitor. We also present a mini-prep protocol that allows rapid, small-scale screening of strains for MCP production.

  14. Brief Reports

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      Quorum sensing improves current output with Acidithiobacillus ferrooxidans

      Nicolas Chabert, Violaine Bonnefoy and Wafa Achouak

      Version of Record online: 19 SEP 2017 | DOI: 10.1111/1751-7915.12797

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      Iron-based metabolism allows a higher current output than sulfur. C14 nAHLs improve biofilm formation on carbon felt electrode. Coupling C14 nAHLs and iron-based metabolism ameliorates biocathode efficiency.

  15. Research Articles

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      Nutrient and acetate amendment leads to acetoclastic methane production and microbial community change in a non-producing Australian coal well

      Michiel H. in 't Zandt, Sabrina Beckmann, Ruud Rijkers, Mike S.M. Jetten, Mike Manefield and Cornelia U. Welte

      Version of Record online: 19 SEP 2017 | DOI: 10.1111/1751-7915.12853

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      Coal mining is responsible for 11% of total anthropogenic methane emission thereby contributing considerably to climate change. Attempts to harvest coalbed methane for energy production are challenged by relatively low methane concentrations. In this study, we investigated whether nutrient and acetate amendment of a non-producing sub-bituminous coal well could transform the system to a methane source.

  16. Minireviews

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      Microbial ecology-based engineering of Microbial Electrochemical Technologies

      Christin Koch, Benjamin Korth and Falk Harnisch

      Version of Record online: 14 AUG 2017 | DOI: 10.1111/1751-7915.12802

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      Microbial ecology is vital for understanding and managing microbial electrochemical technologies. Based on a case study, best practice is provided for the application of microbial ecology techniques and key questions for experimental design, data acquisition and analysis are suggested.

  17. Research Articles

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      The bioelectric well: a novel approach for in situ treatment of hydrocarbon-contaminated groundwater

      Enza Palma, Matteo Daghio, Andrea Franzetti, Marco Petrangeli Papini and Federico Aulenta

      Version of Record online: 11 JUL 2017 | DOI: 10.1111/1751-7915.12760

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      Here we describe the “Bioelectric Well” a bioelectrochemical reactor configuration, which can be installed directly within groundwater wells and can be applied for in situ treatment of organic contaminants, such as petroleum hydrocarbons. The performance of a lab-scale prototype of the bioelectric well was assessed using phenol as model groundwater contaminant. Geobacter species enriched over the surface of the graphite anode, clearly pointing to a direct involvement of this electro-active bacterium in the current-generating and phenol-oxidizing process.

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      Unravelling biocomplexity of electroactive biofilms for producing hydrogen from biomass

      Alex J. Lewis, Maria F. Campa, Terry C. Hazen and Abhijeet P. Borole

      Version of Record online: 11 JUL 2017 | DOI: 10.1111/1751-7915.12756

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      The challenge of understanding conversion of a complex mixture of compounds present in pyrolysis aqueous phase derived from whole biomass was investigated via biochemical and electrochemical analysis of the anode reactions. The results offer a deeper understanding of the bioelectrochemical breakdown process and renewable hydrogen production via microbial electrolysis.

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      Relative abundance of ‘Candidatus Tenderia electrophaga’ is linked to cathodic current in an aerobic biocathode community

      Anthony P. Malanoski, Baochuan Lin, Brian J. Eddie, Zheng Wang, W. Judson Hervey IV and Sarah M. Glaven

      Version of Record online: 11 JUL 2017 | DOI: 10.1111/1751-7915.12757

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      Results presented here show a positive correlation between the relative abundance of “Candidatus Tenderia electrophaga” and the amount of current at the cathode, substantiating its role as an electroautotroph. This finding is original and significant because to date there are no reports of previously uncharacterized marine bacteria directly linked to autotrophic extracellular electron transfer (EET) in a mixed microbial population enriched from the environment.”

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      Electro-fermentation triggering population selection in mixed-culture glycerol fermentation

      Roman Moscoviz, Eric Trably and Nicolas Bernet

      Version of Record online: 11 JUL 2017 | DOI: 10.1111/1751-7915.12747

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      In this study, a mixed-culture cathodic electro-fermentation of glycerol was investigated. Both microbial community structure and metabolic patterns were altered when compared to standard fermentation. 10% improvement of 1,3-propanediol was observed that did not require high energy input (< 1% of total electrons).

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      Bioelectroventing: an electrochemical-assisted bioremediation strategy for cleaning-up atrazine-polluted soils

      Ainara Domínguez-Garay, Jose Rodrigo Quejigo, Ulrike Dörfler, Reiner Schroll and Abraham Esteve-Núñez

      Version of Record online: 23 JUN 2017 | DOI: 10.1111/1751-7915.12687

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      Bioelectroventing is a bioelectrochemical strategy that aims to enhance the biodegradation of a pollutant in the environment by overcoming the electron acceptor limitation and maximizing metabolic oxidation.

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      Simultaneous fermentation of cellulose and current production with an enriched mixed culture of thermophilic bacteria in a microbial electrolysis cell

      Bradley G. Lusk, Alexandra Colin, Prathap Parameswaran, Bruce E. Rittmann and Cesar I. Torres

      Version of Record online: 29 MAY 2017 | DOI: 10.1111/1751-7915.12733

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      An enriched mixed culture of thermophilic (60°C) bacteria was assembled for the purpose of using cellulose to produce current in thermophilic microbial electrolysis cells (MECs). Cellulose was fermented into sugars and acids before being consumed by anode respiring bacteria (ARB) for current production. Current densities (j) were sustained at 6.5 ± 0.2 A m−2 in duplicate reactors with a Coulombic efficiency (CE) of 84 ± 0.3%, a Coulombic recovery (CR) of 54 ± 11%, and without production of CH4.

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      Silica immobilization of Geobacter sulfurreducens for constructing ready-to-use artificial bioelectrodes

      Marta Estevez-Canales, David Pinto, Thibaud Coradin, Christel Laberty-Robert and Abraham Esteve-Núñez

      Version of Record online: 11 APR 2017 | DOI: 10.1111/1751-7915.12561

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      We report a new approach to construct ready-to-use artificial bioelectrodes by immobilizing Geobacter sulfurreducens cells in composite materials associating silica gel and carbon felt fibers. The artificial bioelectrodes were evaluated in 3-electrodes reactors using acetate and lactate as electron donors. Therefore, ready-to-use artificial bioelectrodes, represent a versatile time and cost saving strategy for microbial electrochemical systems.

  18. Highlight

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