Microbial Biotechnology

Cover image for Vol. 7 Issue 5

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

Edited By: Kenneth N. Timmis, Juan Luis Ramos, Willem de Vos, Willy Verstraete, and Martin Rosenberg

Impact Factor: 3.023

ISI Journal Citation Reports © Ranking: 2013: 40/119 (Microbiology); 47/165 (Biotechnology & Applied Microbiology)

Online ISSN: 1751-7915

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  1. 1 - 38
  1. Research Articles

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      Molecular annotation of ketol-acid reductoisomerases from Streptomyces reveals a novel amino acid biosynthesis interlock mediated by enzyme promiscuity

      Karina Verdel-Aranda, Susana T. López-Cortina, David A. Hodgson and Francisco Barona-Gómez

      Article first published online: 9 OCT 2014 | DOI: 10.1111/1751-7915.12175

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      Here, we obtain steady-state enzyme kinetic parameters for ten IlvC homologs from the genera Streptomyces and Corynebacterium, upon eight selected chemically diverse substrates. This biochemical data suggested a Streptomyces biosynthetic interlock between proline and the branched-chain amino acids, mediated by enzyme substrate promiscuity, which was confirmed via mutagenesis and complementation analyses of the proC, ilvC1 and ilvC2 genes in Streptomyces coelicolor. These results also allowed us to assess substrate promiscuity indices as a tool to annotate new molecular functions with metabolic implications.

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      Functional and structural diversity in GH62 α-L-arabinofuranosidases from the thermophilic fungus Scytalidium thermophilum

      Amrit Pal Kaur, Boguslaw P. Nocek, Xiaohui Xu, Michael J. Lowden, Juan Francisco Leyva, Peter J. Stogios, Hong Cui, Rosa Di Leo, Justin Powlowski, Adrian Tsang and Alexei Savchenko

      Article first published online: 29 SEP 2014 | DOI: 10.1111/1751-7915.12168

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      This article describes the expression, structural and functional characterization of three GH62 alpha-L-arabinofuranosidases from a thermophilic fungus Scytalidium thermophilum. Phylogenetic, structural and sequence comparison between two subfamilies of GH62 enzymes revealed their distinct phylogenetic origin and adaptable mode of substrate binding.

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      Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism

      Kyohei Baito, Satomi Imai, Makoto Matsushita, Miku Otani, Yu Sato and Hiroyuki Kimura

      Article first published online: 29 SEP 2014 | DOI: 10.1111/1751-7915.12179

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      A novel biogas production system that combines the bioreactors for producing CH4 and H2 and a natural subterranean methane reactor in a deep aquifer associated with an accretionary prism.

  2. Minireview

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  3. Research Articles

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      Generalist hydrocarbon-degrading bacterial communities in the oil-polluted water column of the North Sea

      Panagiota-Myrsini Chronopoulou, Gbemisola O. Sanni, Daniel I. Silas-Olu, Jan Roelof van der Meer, Kenneth N. Timmis, Corina P. D. Brussaard and Terry J. McGenity

      Article first published online: 24 SEP 2014 | DOI: 10.1111/1751-7915.12176

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      A permitted release of light crude oil into the North Sea resulted in no change in bacterial community composition 3 m beneath the spill. In contrast, there was a decrease in the dominant SAR11 phylotype and an increase in Pseudoalteromonas spp. in oiled mesocosms on board the ship (simulating a heavy spill in a harbour), as a consequence of the longer incubation, closer proximity of the samples to oil, and the lack of replenishment with seawater. Pseudoalteromonas spp. were enriched in media with hydrocarbons, whereas obligate hydrocarbonclastic bacteria were not; suggesting that generalist oil-degrading bacteria may be important in the water column beneath an oil slick.

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      N-acyl-homoserine lactones-producing bacteria protect plants against plant and human pathogens

      Casandra Hernández-Reyes, Sebastian T. Schenk, Christina Neumann, Karl-Heinz Kogel and Adam Schikora

      Article first published online: 19 SEP 2014 | DOI: 10.1111/1751-7915.12177

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      In this report, we present a translational approach in which we demonstrate that the resistance-inducing effect of Sinorhizobium meliloti on crop plants depends on the production of the quorum sensing molecule, oxo-C14-HSL. In addition, using the Arabidopsis-Salmonella model, we also demonstrate that the application of AHL-producing bacteria could be a successful strategy to prevent plant-originated infections with human pathogens.

  4. Brief Reports

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      Improved cytotoxic effects of Salmonella-producing cytosine deaminase in tumour cells

      Beatriz Mesa-Pereira, Carlos Medina, Eva María Camacho, Amando Flores and Eduardo Santero

      Article first published online: 16 SEP 2014 | DOI: 10.1111/1751-7915.12153

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      We have increased the cytotoxic activity of a Salmonella strain carrying a salicylate-inducible expression system that controls cytosine deaminase production. To that end, we have increased the cytosine deaminase translation rates and the time span in which it is produced by generating a 5-FU resistant Salmonella. The inclusion of a purD mutation in the producer strain has also allowed us to control its intracellular proliferation and analyse the effects of cytosine deaminase production by different strains in tumour cell cultures.

  5. Research Articles

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      Characterization of the rumen lipidome and microbiome of steers fed a diet supplemented with flax and echium oil

      Sharon Ann Huws, Eun Jun Kim, Simon J. S. Cameron, Susan E. Girdwood, Lynfa Davies, John Tweed, Hannah Vallin and Nigel David Scollan

      Article first published online: 16 SEP 2014 | DOI: 10.1111/1751-7915.12164

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      we evaluated the effects of supplementing steer diet with flax and echium oil on the rumen lipide and micro biome. In this study we demonstrate that both oil supplementations changed the rumen lipide and micro biome. The linkages between the rumen micro biome and their lipid metabolic capacity now requires further study.

  6. Minireview

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      Extraction and purification of high-value metabolites from microalgae: essential lipids, astaxanthin and phycobiliproteins

      Sara P. Cuellar-Bermudez, Iris Aguilar-Hernandez, Diana L. Cardenas-Chavez, Nancy Ornelas-Soto, Miguel A. Romero-Ogawa and Roberto Parra-Saldivar

      Article first published online: 15 SEP 2014 | DOI: 10.1111/1751-7915.12167

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      This article based on literature framework describes lipids and pigments as two representative classes of high value compounds synthesized by algae.In the case of lipids, metabolic production, extraction and quantification methods are discussed. For pigments, the extraction and purification methods for astaxanthin, phycocyanin and phycoerytrin are described.

  7. Research Articles

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      Biocontrol and plant growth-promoting activity of rhizobacteria from Chinese fields with contaminated soils

      Xuefei Wang, Dmitri V. Mavrodi, Linfeng Ke, Olga V. Mavrodi, Mingming Yang, Linda S. Thomashow, Na Zheng, David M. Weller and Jibin Zhang

      Article first published online: 15 SEP 2014 | DOI: 10.1111/1751-7915.12158

      Growth-promoting rhizobacteria in polluted soils

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      Construction of a chimeric lysin Ply187N-V12C with extended lytic activity against staphylococci and streptococci

      Qiuhua Dong, Jing Wang, Hang Yang, Cuihua Wei, Junping Yu, Yun Zhang, Yanling Huang, Xian-En Zhang and Hongping Wei

      Article first published online: 15 SEP 2014 | DOI: 10.1111/1751-7915.12166

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      a novel chimeric lysin (Ply187N-V12C) was constructed by fusing the catalytic domain (Ply187N) of the bacteriophage lysin Ply187 with the cell binding domain (146-314aa, V12C) of the lysin PlyV12. Our work demonstrated that the generating novel chimeric lysin with an extended lytic spectrum was feasible through fusing catalytic domain with cell binding domains from lysins with lytic spectra across multiple genera.

  8. Brief Reports

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      Endogenous biotin-binding proteins: an overlooked factor causing false positives in streptavidin-based protein detection

      Hanne L. P. Tytgat, Geert Schoofs, Michèle Driesen, Paul Proost, Els J. M. Van Damme, Jos Vanderleyden and Sarah Lebeer

      Article first published online: 11 SEP 2014 | DOI: 10.1111/1751-7915.12150

  9. Genomics update

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  10. Research Article

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      Meta-barcoded evaluation of the ISO standard 11063 DNA extraction procedure to characterize soil bacterial and fungal community diversity and composition

      Sebastien Terrat, Pierre Plassart, Emilie Bourgeois, Stéphanie Ferreira, Samuel Dequiedt, Nathalie Adele-Dit-De-Renseville, Philippe Lemanceau, Antonio Bispo, Abad Chabbi, Pierre-Alain Maron and Lionel Ranjard

      Article first published online: 4 SEP 2014 | DOI: 10.1111/1751-7915.12162

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      This study was designed to assess the influence of three soil DNA extraction procedures, namely the ISO-11063, GnS-GII, and ISOm, on the taxonomic diversity and composition of soil bacterial and fungal communities. The efficacy of each soil DNA extraction method was assessed on five soils, differing in their physico-chemical characteristics and land use. In conclusion, we recommend using the ISOm method for studies focusing on both the bacterial and fungal communities.

  11. Research Articles

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      Cytometric patterns reveal growth states of Shewanella putrefaciens

      Susanne Melzer, Gudrun Winter, Kathrin Jäger, Thomas Hübschmann, Gerd Hause, Frank Syrowatka, Hauke Harms, Attila Tárnok and Susann Müller

      Article first published online: 3 SEP 2014 | DOI: 10.1111/1751-7915.12154

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      Growth states of Shewanella putrefaciens can be followed and interpreted using flow cytometry and new bioinformatics tools. The results allow a fingerprint like description of the strains behavior under various mirco-environments like aerobic and anaerobic as well as feast or famine conditions or the strains planktonic or biofilm growth. The developed workflow is universal and can be applied to other organisms and environments.

  12. Opinion

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      Vegetable microbiomes: is there a connection among opportunistic infections, human health and our ‘gut feeling'?

      Gabriele Berg, Armin Erlacher, Kornelia Smalla and Robert Krause

      Article first published online: 3 SEP 2014 | DOI: 10.1111/1751-7915.12159

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      We discuss the occurrence of potential pathogens in vegetable microbiomes, the impact of farming and processing practices, and plant and human health issues.

  13. Research Articles

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      Improved bioethanol production in an engineered Kluyveromyces lactis strain shifted from respiratory to fermentative metabolism by deletion of NDI1

      María Isabel González-Siso, Alba Touriño, Ángel Vizoso, Ángel Pereira-Rodríguez, Esther Rodríguez-Belmonte, Manuel Becerra and María Esperanza Cerdán

      Article first published online: 3 SEP 2014 | DOI: 10.1111/1751-7915.12160

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      We have constructed and characterized an engineered Kluyveromyces lactis strain by deletion of the KlNDI1 gene that encodes the single internal NADH:ubiquinone oxidoreductase in the mitochondria of K. lactis. The Δklndi1 mutation shifts glucose metabolism to fermentative, thus increasing the performance of the Δklndi1 strain for bioethanol production from lactose present in waste cheese whey. This is a biotechnological advantage versus the fermentative yeast Saccharomyces cerevisiae, which is unable to metabolize lactose, and versus K. lactis expressing NDI1, which is highly respiratory.

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      Whole genome and transcriptome analyses of environmental antibiotic sensitive and multi-resistant Pseudomonas aeruginosa isolates exposed to waste water and tap water

      Thomas Schwartz, Olivier Armant, Nancy Bretschneider, Alexander Hahn, Silke Kirchen, Martin Seifert and Andreas Dötsch

      Article first published online: 3 SEP 2014 | DOI: 10.1111/1751-7915.12156

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      An antibiotic sensitive and a multi-resistant Pseudomonas aeruginosa isolate originating from wastewaters were compared via whole genome and transcriptome Illumina sequencing after exposure to municipal wastewater and tap water. The exposure of both isolates to polluted wastewater and oligotrophic tap water resulted in similar expression profiles of genes mediating genetic mobility and resistance towards antibiotics and heavy metals.

  14. Brief Reports

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      Compositional profile of α / β-hydrolase fold proteins in mangrove soil metagenomes: prevalence of epoxide hydrolases and haloalkane dehalogenases in oil-contaminated sites

      Diego Javier Jiménez, Francisco Dini-Andreote, Júlia Ronzella Ottoni, Valéria Maia de Oliveira, Jan Dirk van Elsas and Fernando Dini Andreote

      Article first published online: 29 AUG 2014 | DOI: 10.1111/1751-7915.12157

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      We present an bioprospection report regarding the diversity of α/β-hydrolases-fold proteins in mangrove soil metagenomes. We highlight for the prevalence of epoxide hydrolases and haloalkane dehalogenases.

  15. Minireview

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      Fungal biosynthesis of gold nanoparticles: mechanism and scale up

      Michael Kitching, Meghana Ramani and Enrico Marsili

      Article first published online: 26 AUG 2014 | DOI: 10.1111/1751-7915.12151

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      Recent studies on AuNPs biosynthesis in fungi are comprehensively reviewed.The mechanisms of AuNPs biosynthesis in fungal biomass and cell-free extracts are critically discussedBioreactors configurations and method for scale-up of AuNP biosynthesis are proposed

  16. Research Articles

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      A refined technique for extraction of extracellular matrices from bacterial biofilms and its applicability

      Akio Chiba, Shinya Sugimoto, Fumiya Sato, Seiji Hori and Yoshimitsu Mizunoe

      Article first published online: 23 AUG 2014 | DOI: 10.1111/1751-7915.12155

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      Graphical image of bacterial cells embedded in ECMs. ECM components including proteins, polysaccharides, and eDNAs can bind to bacterial cells or each other via electrostatic attractive forces, ionic attractive forces, hydrophobic interactions and van der Waals interactions. Increasing concentrations of salts and detergents (e.g., NaCl and SDS) potentially disrupt these interactions by coating cell surfaces and ECM constituents and therefore lead to detachment of ECMs from the cells.

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      Growth-promoting Sphingomonas paucimobilis ZJSH1 associated with Dendrobium officinale through phytohormone production and nitrogen fixation

      Suijuan Yang, Xinghai Zhang, Zhaoyun Cao, Kaipeng Zhao, Sai Wang, Mingxue Chen and Xiufang Hu

      Article first published online: 20 AUG 2014 | DOI: 10.1111/1751-7915.12148

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      Growth-promoting Sphingomonas paucimobilis ZJSH1, associated with Dendrobium officinale, a traditional Chinese medicinal plant, was characterized. The mechanism of growth promotion was attributed to a combination of phytohormones and nitrogen fixation.

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      Degradation of toluene by ortho cleavage enzymes in Burkholderia fungorum FLU100

      Daniel Dobslaw and Karl-Heinrich Engesser

      Article first published online: 18 AUG 2014 | DOI: 10.1111/1751-7915.12147

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      Burkholderia fungorum FLU100 simultaneously oxidised any mixture of toluene, benzene and mono-halogen benzenes to (3-substituted) catechols with a selectivity of nearly 100 % and mineralises these catechols by enzymes of the ortho cleavage pathway. During the transformation of 3-methylcatechol, 4-carboxymethyl-2-methylbut-2-en-4-olide (2-methyl-2-enelactone, 2-ML) accumulated transiently, being further mineralised only after a lag-phase of 2 h in case of cells pre-grown on benzene or mono-halogen benzenes. No lag-phase, however, occurred after growth on toluene.

  17. Minireview

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      Synthetic biology approaches to improve biocatalyst identification in metagenomic library screening

      María-Eugenia Guazzaroni, Rafael Silva-Rocha and Richard John Ward

      Article first published online: 13 AUG 2014 | DOI: 10.1111/1751-7915.12146

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      This review focuses on the interplay between Synthetic Biology and Functional Metagenomics that defines new strategies to obtain ideal candidate enzymes with specific characteristics from metagenomes.

  18. Research Articles

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      Kinetic and stoichiometric characterization of organoautotrophic growth of Ralstonia eutropha on formic acid in fed-batch and continuous cultures

      Stephan Grunwald, Alexis Mottet, Estelle Grousseau, Jens K. Plassmeier, Milan K. Popović, Jean-Louis Uribelarrea, Nathalie Gorret, Stéphane E. Guillouet and Anthony Sinskey

      Article first published online: 13 AUG 2014 | DOI: 10.1111/1751-7915.12149

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      In this work, organoautotrophic growth of Ralstonia eutropha on formic acid was studied using an approach combining stoichiometric modeling and controlled cultures in bioreactors. The maximal growth yield was determined at 0.16 Cmole.Cmole-1 and corresponded to 76 to 85% of the theoretical yield.

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      Restoration of a Mediterranean forest after a fire: bioremediation and rhizoremediation field-scale trial

      Paloma Pizarro-Tobías, Matilde Fernández, José Luis Niqui, Jennifer Solano, Estrella Duque, Juan-Luis Ramos and Amalia Roca

      Article first published online: 31 JUL 2014 | DOI: 10.1111/1751-7915.12138

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      Forest fires pose a serious threat to countries in the Mediterranean basin, often razing large areas of land each year. After fires, soils are more likely to erode and resilience is inhibited in part by the toxic aromatic hydrocarbons. In this study we explored the use of bioremediation and rhizoremediation techniques for soil restoration in a field-scale trial in a protected Mediterranean ecosystem after a controlled fire. Microbial population analysis revealed that fires induced changes in the indigenous microbiota, and that rhizoremediation favours the recovery of soil microbiota in time. Rhizoremediation is a viable and costly-effective alternative for the treatment of ecosystems affected by fires.

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      Colonization by endophytic Ochrobactrum anthropi Mn1 promotes growth of Jerusalem artichoke

      Xianfa Meng, Dekai Yan, Xiaohua Long, Changhai Wang, Zhaopu Liu and Zed Rengel

      Article first published online: 30 JUL 2014 | DOI: 10.1111/1751-7915.12145

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      O. anthropi Mn1 was isolated as endophytic diazotroph of Jerusalem artichoke which localized in roots and stems of host plant stably after infection. With sufficient nitrogen supplement, the strain could improve plant growth through symbiotic nitrogen fixation, root morphological optimization and enhanced nutrient uptake.

  19. Opinion

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      Apoptosis induced by Pseudomonas aeruginosa: a lonely killer?

      Alexis Broquet and Karim Asehnoune

      Article first published online: 14 JUL 2014 | DOI: 10.1111/1751-7915.12144

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  20. Research Articles

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      A reliable multiplex genotyping assay for HCV using a suspension bead array

      Yi-Chen Yang, Der-Yuan Wang, Hwei-Fang Cheng, Eric Y. Chuang and Mong-Hsun Tsai

      Article first published online: 10 JUL 2014 | DOI: 10.1111/1751-7915.12140

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      This genotyping platform enables the simultaneous detection and identification of more than one genotype in a same sample and is able to test 96 samples simultaneously. It could therefore provide a rapid, efficient, and reliable method of determining HCV genotypes in the future.

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      Multiple signals modulate the activity of the complex sensor kinase TodS

      Hortencia Silva-Jiménez, Álvaro Ortega, Cristina García-Fontana, Juan Luis Ramos and Tino Krell

      Article first published online: 1 JUL 2014 | DOI: 10.1111/1751-7915.12142

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      We have established previously that several aromatic hydrocarbons bind to the TodS sensor kinase, increasing thereby its activity which results ultimately in enhanced gene expression. We show here that the oxidative agent menadione reduces TodS activity in vitro and consequently gene expression in vivo. Data are presented indicating that the effect of menadione is linked to a chemical modification of the conserved cysteine residue 320 of TodS.

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      Membrane fatty acid composition and fluidity are involved in the resistance to freezing of Lactobacillus buchneri R1102 and Bifidobacterium longum R0175

      Séverine Louesdon, Séverine Charlot-Rougé, Raphaëlle Tourdot-Maréchal, Marielle Bouix and Catherine Béal

      Article first published online: 1 JUL 2014 | DOI: 10.1111/1751-7915.12132

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      Membrane properties were affected by the growth phase, stationary phase leading to low membrane fluidity and modified fatty acid composition.Improved survival of B. longum R0175 was associated to low membrane fluidity, as a result low unsaturated-to-saturated fatty acid ratio in bacterial membranes. Reduced maintenance of acidification activity in L. buchneri R1102 cells was linked to low membrane fluidity that was associated to low unsaturated-to-saturated fatty acid ratio and high cyclic-to-saturated fatty acid ratio in bacterial membranes.

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      Occurrence and distribution of tomato seed-borne mycoflora in Saudi Arabia and its correlation with the climatic variables

      Abdulaziz A. Al-Askar, Khalid M. Ghoneem, Younes M. Rashad, Waleed M. Abdulkhair, Elsayed E. Hafez, Yasser M. Shabana and Zakaria A. Baka

      Article first published online: 25 JUN 2014 | DOI: 10.1111/1751-7915.12137

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      Occurrence and Distribution of Tomato Seed-Borne Mycoflora in Saudi Arabia and Its Correlation with the Climatic Variables

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      Production of lactic acid using a new homofermentative Enterococcus faecalis isolate

      Mohan Raj Subramanian, Suvarna Talluri and Lew P. Christopher

      Article first published online: 3 JUN 2014 | DOI: 10.1111/1751-7915.12133

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      In this study, we describe the production of lactic acid at high concentration, yield and volumetric productivity utilizing a novel homofermentative, facultative anaerobe Enterococcus faecalis CBRD01. The highest concentration of 182 g lactic acid l-1 was achieved after 38 h of fed-batch fermentation on glucose. The bacterial isolate utilized only 2-13% of carbon for its growth and energy metabolism, while 87-98% of carbon was converted to lactic acid at an overall volumetric productivity of 5 g l1 h1. At 13 h of fermentation, the volumetric productivity of lactate production reached 10.3 g l-1 h-1, which is the highest ever reported for microbial production of lactic acid.

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      Ethylene signalling affects susceptibility of tomatoes to Salmonella

      Massimiliano Marvasi, Jason T. Noel, Andrée S. George, Marcelo A. Farias, Keith T. Jenkins, George Hochmuth, Yimin Xu, Jim J. Giovanonni and Max Teplitski

      Article first published online: 29 MAY 2014 | DOI: 10.1111/1751-7915.12130

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      Salmonella proliferates less in the fruit of the tomato ethylene mutants (Nr, rin, nor) compared to the isogenic parent Ailsa Craig. Supplementation with exogenous ethylene modestly increased susceptibility of tomatoes to Salmonella

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      Microbial response to single-cell protein production and brewery wastewater treatment

      Jackson Z. Lee, Andrew Logan, Seth Terry and John R. Spear

      Article first published online: 16 MAY 2014 | DOI: 10.1111/1751-7915.12128

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      In this study, we investigate microbial response across a full-scale brewery wastewater treatment plant and a parallel pilot bioreactor modified to produce a SCP product.

  21. Brief Reports

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      Quantitative proteomic analysis of the Salmonella-lettuce interaction

      Yuping Zhang, Renu Nandakumar, Shannon L. Bartelt-Hunt, Daniel D. Snow, Laurie Hodges and Xu Li

      Article first published online: 11 FEB 2014 | DOI: 10.1111/1751-7915.12114

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      The goal of the study was to elucidate the global modulation of bacteria and plant protein expression after Salmonella internalizes lettuce. Quantitative proteomics results suggested that internalized Salmonella might utilize ascorbate as a carbon source and require multiple stress response proteins to cope with stresses encountered in plants. On the other hand, lettuce proteins involved in defense response to bacterial infection were up-regulated upon the internalization of Salmonella.

  22. Research Articles

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      Transcriptional profile of Salmonella enterica subsp. enterica serovar Weltevreden during alfalfa sprout colonization

      Kerstin Brankatschk, Tim Kamber, Joël F. Pothier, Brion Duffy and Theo H. M. Smits

      Article first published online: 6 DEC 2013 | DOI: 10.1111/1751-7915.12104

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      Whole transcriptome analysis of Salmonella Weltevreden grown with sprouts showed that mechanisms for attachment, motility and biofilm formation were significantly higher transcribed, but also genes involved in sulfate acquisition and structural and effector proteins of the SPI-2 type 3 secretion system. Insights on additional mechanisms for interactions with sprouts were obtained.

  23. Brief Reports

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      Spread and change in stress resistance of Shiga toxin-producing Escherichia coli O157 on fungal colonies

      Ken-ichi Lee, Naoki Kobayashi, Maiko Watanabe, Yoshiko Sugita-Konishi, Hirokazu Tsubone, Susumu Kumagai and Yukiko Hara-Kudo

      Article first published online: 6 AUG 2013 | DOI: 10.1111/1751-7915.12071

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      Shiga toxin-producing Escherichia coli form a biofilm structure on mould hyphae. Physical interaction of the bacterium and mould facilitate the bacterial spread along the hyphae and also confer the bacterial acid resistance.

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