MicrobiologyOpen

Cover image for Vol. 5 Issue 4

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

Edited by Pierre Cornelis, Microbial Interactions, VIB Department of Structural Biology, Vrije Universiteit Brussel, Brussels, Belgium

Impact Factor: 2.148

ISI Journal Citation Reports © Ranking: 2015: 78/123 (Microbiology)

Online ISSN: 2045-8827

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  1. 1 - 32
  1. Original Research

    1. You have full text access to this OnlineOpen article
      The [4Fe-4S] clusters of Rpo3 are key determinants in the post Rpo3/Rpo11 heterodimer formation of RNA polymerase in Methanosarcina acetivorans

      Matthew E. Jennings, Faith H. Lessner, Elizabeth A. Karr and Daniel J Lessner

      Version of Record online: 25 AUG 2016 | DOI: 10.1002/mbo3.399

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      The Rpo3 subunit of RNA polymerase (RNAP) from numerous species of archaea contains a ferredoxin-like domain harboring [4Fe-4S] cluster(s), the function of which is unknown. The two [4Fe-4S] cluster Rpo3 from Methanosarcina acetivorans was mutated and characterized, which revealed that the clusters are not essential, but are important factors in the formation of RNAP after the assembly of the Rpo3/Rpo11 heterodimer.

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      Mutations in genes encoding antibiotic substances increase the synthesis of poly-γ-glutamic acid in Bacillus amyloliquefaciens LL3

      Weixia Gao, Fenghong Liu, Wei Zhang, Yufen Quan, Yulei Dang, Jun Feng, Yanyan Gu, Shufang Wang, Cunjiang Song and Chao Yang

      Version of Record online: 18 AUG 2016 | DOI: 10.1002/mbo3.398

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      Poly-γ-glutamic acid (γ-PGA) is an important natural biopolymer that is used widely in fields of foods, medicine, cosmetics, and agriculture. Several B. amyloliquefaciens LL3 mutants were constructed to improve γ-PGA synthesis via single or multiple marker-less in-frame deletions of four gene clusters (itu, bae, srf, and fen) encoding antibiotic substances. The four gene clusters’ roles in swarming motility and biofilm formation were also studied.

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      Lysis-lysogeny coexistence: prophage integration during lytic development

      Qiuyan Shao, Jimmy T. Trinh, Colby S. McIntosh, Brita Christenson, Gábor Balázsi and Lanying Zeng

      Version of Record online: 17 AUG 2016 | DOI: 10.1002/mbo3.395

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      Propagation via lytic or lysogenic pathways is an essential decision that temperate viruses make for their survival. Historically, it is understood that infection by phage lambda culminates either in cell lysis and progeny release or prophage integration and cell growth. Here we find that phage DNA often integrates into the host chromosome during lytic development, suggesting that a phage can utilizes concurrent developmental pathways, potentially as a fitness-enhancing means to adapt to the ever-changing environment.

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      The effect of environmental contamination on the community structure and fructification of ectomycorrhizal fungi

      Qibiao Sun, Yaping Liu, Huatao Yuan and Bin Lian

      Version of Record online: 11 AUG 2016 | DOI: 10.1002/mbo3.396

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      This study investigated the ectomycorrhizal fungal fruiting bodies and community composition between unpolluted and polluted sites by living garbage. This study makes us have a better understanding to the fruiting body's formation condition required and the relationships between ectomycorrhizal fungal community structure and environmental conditions, moreover, provide a new thought to excavate and utilize the resource of antistress ectomycorrhizal fungi.

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      Marine and giant viruses as indicators of a marine microbial community in a riverine system

      Lisa M. Dann, Stephanie Rosales, Jody McKerral, James S. Paterson, Renee J. Smith, Thomas C. Jeffries, Rod L. Oliver and James G. Mitchell

      Version of Record online: 9 AUG 2016 | DOI: 10.1002/mbo3.392

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      This study investigates riverine viral communities around a small rural town that influences local water inputs. Overall, the majority of abundant viral species were or were most similar to those of marine origin. At over 60 km to the river mouth, the presence of marine communities suggests the microbial marine to freshwater transition region extends well beyond the salinity front, the river contains relict microbial communities, or that marine communities are intruding with the rising salinity in this regulated river. We conclude marine microbial species may occur more frequently in freshwater systems than previously assumed, and hence may play important roles in some freshwater ecosystems within tens to a hundred kilometers from the sea.

  2. Reviews

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      The rich somatic life of Wolbachia

      Jose E. Pietri, Heather DeBruhl and William Sullivan

      Version of Record online: 26 JUL 2016 | DOI: 10.1002/mbo3.390

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      Over the last decade many studies have emerged highlighting the prominence of Wolbachia in somatic tissues, implicating somatic tissue tropism as an important aspect of the life history of this endosymbiont. Here, we review our current understanding of Wolbachia–host interactions at both the cellular and organismal level, with a focus on Wolbachia in somatic tissues.

  3. Original Research

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      Isolation of a novel alginate lyase-producing Bacillus litoralis strain and its potential to ferment Sargassum horneri for biofertilizer

      Mingpeng Wang, Lei Chen, Zhengyi Liu, Zhaojie Zhang, Song Qin and Peisheng Yan

      Version of Record online: 20 JUL 2016 | DOI: 10.1002/mbo3.387

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      A novel alginate-degrading strain named as Bacillus litoralis was isolated and used for seaweed fermentation. Fermentation process of seaweed by Bacillus litoralis were well studied and production of alginate oligosaccharides were stable with different fermentation scale. Alginate oligosaccharide was an unique and effective component in our seaweed fermentation extract for promoting growth of tomato.

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      Influence of temperature, mixing, and addition of microcystin-LR on microcystin gene expression in Microcystis aeruginosa

      Pia I. Scherer, Uta Raeder, Juergen Geist and Katrin Zwirglmaier

      Version of Record online: 14 JUL 2016 | DOI: 10.1002/mbo3.393

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      Cyanobacteria, such as the toxin producer Microcystis aeruginosa, are predicted to be favored by global warming. In this study, a new RT-qPCR assay was used to investigate the changes in mcyB and mcyD expression, genes responsible for the biosynthesis of the cyanotoxin microcystin, in response to selected environmental factors associated with global warming.

  4. Reviews

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      Recent developments in detection and enumeration of waterborne bacteria: a retrospective minireview

      Rehan A. Deshmukh, Kopal Joshi, Sunil Bhand and Utpal Roy

      Version of Record online: 10 JUL 2016 | DOI: 10.1002/mbo3.383

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      Waterborne diseases pose constant threats to public health. Therefore, public healthcare needs rapid, sensitive, and accurate detection of pathogens for the diagnosis and treatment.

  5. Original Research

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      Analysis of propionate-degrading consortia from agricultural biogas plants

      Stephan Ahlert, Rita Zimmermann, Johannes Ebling and Helmut König

      Version of Record online: 1 JUL 2016 | DOI: 10.1002/mbo3.386

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      Syntrophic communities form complex networks of microbial interactions. Here, we shed light on the microbial composition of propionate-degrading consortia and postulate an involvement of syntrophic acetate oxidation and autotrophic homoacetogenesis in stable propionate degradation.

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      Performance of MALDI biotyper compared with Vitek 2 compact system for fast identification and discrimination of Staphylococcus species isolated from bovine mastitis

      Ayman Elbehiry, Musaad Al-Dubaib, Eman Marzouk, Salama Osman and Husam Edrees

      Version of Record online: 1 JUL 2016 | DOI: 10.1002/mbo3.389

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      Bovine mastitis is considered as one of the most significant problem in the dairy industry all over the world. Therefore, a comparison of MALDI-TOF-MS with an automated colorimetric technique using Vitek 2 Compact System for identification and typing of S. aureus and CNS strains as well as discrimination of MRSA from MSSA can be highly important in Saudi Arabia.

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      FolC2-mediated folate metabolism contributes to suppression of inflammation by probiotic Lactobacillus reuteri

      Carissa M. Thomas, Delphine M. A. Saulnier, Jennifer K. Spinler, Peera Hemarajata, Chunxu Gao, Sara E. Jones, Ashley Grimm, Miriam A. Balderas, Matthew D. Burstein, Christina Morra, Daniel Roeth, Markus Kalkum and James Versalovic

      Version of Record online: 28 JUN 2016 | DOI: 10.1002/mbo3.371

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      The bifunctional dihydrofolate synthase/folylpolyglutamate synthase type 2 (folC2) gene is necessary for 5,10-methenyltetrahydrofolic acid production by Lactobacillus reuteri, while the folC gene encodes the enzyme responsible for polyglutamylation of 5,10-methenyltetrahydrofolate. The folC2 gene is important for suppression of the proinflammatory cytokine, tumor necrosis factor (TNF), in vitro, and for protection against trinitrobenzene sulfonic acid (TNBS)-induced colitis and mucosal inflammation in vivo. In addition, there is a link between 5,10-methenyltetrahydrofolic acid production and histamine, a known potent immunoregulatory molecule produced by probiotics. Specifically, the folC2 mutant yields diminished expression of the hdc gene cluster, which is responsible for the conversion of l-histidine to histamine as well as diminished histamine production.

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      Possible association of diazotrophs with marine zooplankton in the Pacific Ocean

      Kazi Md. Azimuddin, Junya Hirai, Shotaro Suzuki, Md. Nurul Haider, Aiko Tachibana, Keigo Watanabe, Minoru Kitamura, Fuminori Hashihama, Kazutaka Takahashi and Koji Hamasaki

      Version of Record online: 28 JUN 2016 | DOI: 10.1002/mbo3.385

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      To understand the diversity and abundance of putative diazotrophic communities associated with marine zooplankton, especially copepods, the molecular diversity of the nifH gene was studied by nested PCR amplification, followed by cloning and sequencing of zooplankton-associated microorganisms DNA collected from the Pacific Ocean.

  6. Reviews

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      Pseudomonas aeruginosa in premise plumbing of large buildings

      Emilie Bédard, Michèle Prévost and Eric Déziel

      Version of Record online: 28 JUN 2016 | DOI: 10.1002/mbo3.391

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      Pseudomonas aeruginosa is an opportunistic bacterial pathogen that is widely occurring in the environment and is recognized for its capacity to form or join biofilms. This review consolidates current knowledge on P. aeruginosa ecology and its implication in healthcare facilities premise plumbing.

  7. Original Research

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      Isolation of Bdellovibrio sp. from soil samples in Mexico and their potential applications in control of pathogens

      Omotayo Opemipo Oyedara, Erick de Jesus De Luna-Santillana, Omar Olguin-Rodriguez, Xianwu Guo, Marco Antonio Mendoza-Villa, Jorge Luis Menchaca-Arredondo, Temidayo Oluyomi Elufisan, Javier Alfonso Garza-Hernandez, Israel Garcia Leon and Mario Alberto Rodriguez-Perez

      Version of Record online: 13 JUN 2016 | DOI: 10.1002/mbo3.382

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      We characterized two strains of Bdellovibrio isolated from soil in Mexico. The two strains were observed to exhibit different phenotypic and molecular characteristics. Also, different gram-negative bacteria were preyed upon by these two Bdellovibrio strains thereby suggesting the possibility of using them as future biocontrol agent against bacteria of economic importance.

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      Exploring the mechanisms of action of human secretory RNase 3 and RNase 7 against Candida albicans

      Vivian A. Salazar, Javier Arranz-Trullén, Susanna Navarro, Jose A. Blanco, Daniel Sánchez, Mohammed Moussaoui and Ester Boix

      Version of Record online: 8 JUN 2016 | DOI: 10.1002/mbo3.373

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      Human RNases 3 and 7 are wide-spectrum host defense antimicrobial proteins. We have chosen here a eukaryotic pathogen to study their mechanism of action. Comparison of wild-type proteins versus active site and cell binding mutants on yeast cultures revealed a dual role. Contribution of enzymatic activity to the RNases antifungal properties envisages cellular RNA targeting as an effective strategy for antibiotic design.

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      Characterization of the interactions between Escherichia coli receptors, LPS and OmpC, and bacteriophage T4 long tail fibers

      Ayaka Washizaki, Tetsuro Yonesaki and Yuichi Otsuka

      Version of Record online: 6 JUN 2016 | DOI: 10.1002/mbo3.384

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      Bacteriophage T4 adsorbs to E. coli via two different modes, OmpC-dependent and OmpC-independent. Analysis of T4 phage mutants strongly suggests that the top surface of the distal tip head domain of T4 long tail fibers interacts with lipopolysaccharide (LPS) and its lateral surface interacts with OmpC.

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      Protein engineering of Saccharomyces cerevisiae transporter Pdr5p identifies key residues that impact Fusarium mycotoxin export and resistance to inhibition

      Amanda B. Gunter, Anne Hermans, Whynn Bosnich, Douglas A. Johnson, Linda J. Harris and Steve Gleddie

      Version of Record online: 4 JUN 2016 | DOI: 10.1002/mbo3.381

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      Fusarium mycotoxins are efficiently exported from yeast cells by the multidrug resistance exporter Pdr5p. This ATP-binding cassette transporter can be modified to resist inhibition by both FK506 and enniatin B which suggests it may be possible to use this to engineer Fusarium resistance in plants.

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      The bactericidal activity of glutaraldehyde-impregnated polyurethane

      Sandeep K. Sehmi, Elaine Allan, Alexander J. MacRobert and Ivan Parkin

      Version of Record online: 3 JUN 2016 | DOI: 10.1002/mbo3.378

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      Novel antibacterial surfaces were obtained using a simple, up-scalable “swell-encapsulation-shrink” technique to prepare polymer samples incorporating low concentrations of glutaraldehyde. Glutaraldehyde-impregnated samples demonstrated greater bactericidal effects against Escherichia coli and Staphylococcus aureus than glutaraldehyde-coated polyurethane over short exposure times (h). However, the glutaraldehyde-impregnated polymer did not retain antibacterial activity over longer time frames (days), thus, further work is needed to determine if chemical modification can be used to improve the stability of the antibacterial agent within the polymer in order to render these novel materials useful in reducing the cycle of transmission between patients, staff and the environment in healthcare facilities.

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      Abundance of sulfur-degrading bacteria in a benthic bacterial community of shallow sea sediment in the off-Terengganu coast of the South China Sea

      Zahar Marziah, Akbariah Mahdzir, Md. Nor Musa, Abu Bakar Jaafar, Azran Azhim and Hirofumi Hara

      Version of Record online: 3 JUN 2016 | DOI: 10.1002/mbo3.380

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      An Illustration of bacteria diversity and phylogenetic distribution based on NCBI BLASTx database. The Ribosomal Database Project (RDP) bar was generated based on operational taxonomic unit (OTU) with the range of 21–27 phylum levels, 35–51 class levels, 46–62 order levels, 76–108 family levels, and 134–217 of genus levels were identified in two sampling location, respectively.

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      Ectomycorrhizal and saprotrophic fungi respond differently to long-term experimentally increased snow depth in the High Arctic

      Sunil Mundra, Rune Halvorsen, Håvard Kauserud, Mohammad Bahram, Leho Tedersoo, Bo Elberling, Elisabeth J. Cooper and Pernille Bronken Eidesen

      Version of Record online: 2 JUN 2016 | DOI: 10.1002/mbo3.375

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      Long-term increase in snow depth imposes negative effect on the richness of ectomycorrhizal fungi, while positive effect on saprotrophic fungi, which suggests that some fungal species are favored, while some fungi may go locally extinct due to changes in the amount of snow.

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      Identification of pigmented Serratia marcescens symbiotically associated with Rhynchophorus ferrugineus Olivier (Coleoptera: Curculionidae)

      Maria Scrascia, Carlo Pazzani, Franco Valentini, Marta Oliva, Valentina Russo, Pietro D'Addabbo and Francesco Porcelli

      Version of Record online: 1 JUN 2016 | DOI: 10.1002/mbo3.377

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      This study has contributed to the knowledge on the mutualistic relationship between bacteria and red palm weevil.

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      Effects of human serum and apo-Transferrin on Staphylococcus epidermidis RP62A biofilm formation

      Pengfei She, Lihua Chen, Yong Qi, Huan Xu, Yuan Liu, Yangxia Wang, Zhen Luo and Yong Wu

      Version of Record online: 16 MAY 2016 | DOI: 10.1002/mbo3.379

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      Human serum inhibits Staphylococcus epidermidis biofilm formation, and this is mainly due to the complement and serum proteins at the size more than 100 kDa; apo-Transferrin could partially reduce the biofilm formation at the concentration that do not inhibit planktonic cell growth.

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      Increased biofilm formation ability in Klebsiella pneumoniae after short-term exposure to a simulated microgravity environment

      Haili Wang, Yanfeng Yan, Dan Rong, Jing Wang, Hongduo Wang, Zizhong Liu, Jiaping Wang, Ruifu Yang and Yanping Han

      Version of Record online: 16 MAY 2016 | DOI: 10.1002/mbo3.370

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      The ability of biofilm formation in Klebsiella pneumoniae was enhanced after short-term exposure to the simulated microgravity environment. The cellulose is the major component of the biofilm produced by SMG-treated K. pneumoniae. Those genes responsible for type 3 fimbriae (MrkABCDF) and its regulator (MrkH) are upregulated in SMG-treated bacterial cells.

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      Comparative analysis of the fecal bacterial community of five harbor seals (Phoca vitulina)

      Daniela Numberger, Daniel P. R. Herlemann, Klaus Jürgens, Guido Dehnhardt and Heide Schulz-Vogt

      Version of Record online: 14 MAY 2016 | DOI: 10.1002/mbo3.369

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      We investigated the fecal bacterial community in five harbor seals by 454 amplicon sequencing and fluorescence in situ hybridization. The results showed that the fecal community mainly consisted of the bacterial phyla Firmicutes (19–43%), Bacteroidetes (22–36%), Fusobacteria (18–32%), and Proteobacteria (5–17%).

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      A new mercury-accumulating Mucor hiemalis strain EH8 from cold sulfidic spring water biofilms

      Enamul Hoque and Johannes Fritscher

      Version of Record online: 13 MAY 2016 | DOI: 10.1002/mbo3.368

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      Here, we report about a unique aquatic fungus Mucor hiemalis EH8 that can remove toxic ionic mercury from water by intracellular accumulation and reduction into elemental mercury. It removed 99% of mercury from water within 10–48 h after exposure to Hg(II). Scanning electron microscopy demonstrated occurrence of intracellular mercury in germinating sporangiospores exposed to mercury.

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      The endochitinase ChiA Btt of Bacillus thuringiensis subsp. tenebrionis DSM-2803 and its potential use to control the phytopathogen Colletotrichum gloeosporioides

      Norma M. de la Fuente-Salcido, Luz E. Casados-Vázquez, Ada P. García-Pérez, Uriel E. Barboza-Pérez, Dennis K. Bideshi, Rubén Salcedo-Hernández, Blanca E. García- Almendarez and José E. Barboza-Corona

      Version of Record online: 12 MAY 2016 | DOI: 10.1002/mbo3.372

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      It is reported for the first time the cloning and characterization of a chitinase synthesized by the commercial strain of Bacillus thuringiensis subsp. tenebrionis DSM-2803.We show that purified recombinant enzyme from B. thuringiensis is active against the fungus Colletotrichium gloeosporioides.

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      Zinc coordination is essential for the function and activity of the type II secretion ATPase EpsE

      Chelsea S. Rule, Marcella Patrick, Jodi L. Camberg, Natalie Maricic, Wim G. Hol and Maria Sandkvist

      Version of Record online: 10 MAY 2016 | DOI: 10.1002/mbo3.376

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      Type II secretion ATPases contain a unique zinc-binding domain which is absent from homologous type IV pilus retraction ATPases and type IV secretion ATPases. Removal of the entire zinc-binding domain or disruption of zinc coordination in the type II secretion ATPase EpsE abrogates secretion and prevents ATP hydrolysis, indicating that zinc coordination is essential for the function and activity of type II secretion ATPases.

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      Biochemical characterization of essential cell division proteins FtsX and FtsE that mediate peptidoglycan hydrolysis by PcsB in Streptococcus pneumoniae

      Ruchika Bajaj, Kevin E. Bruce, Amy L. Davidson, Britta E. Rued, Cynthia V. Stauffacher and Malcolm E. Winkler

      Version of Record online: 10 MAY 2016 | DOI: 10.1002/mbo3.366

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      The FtsEX:PcsB complex forms a molecular machine that carries out peptidoglycan (PG) hydrolysis during normal cell division of the major respiratory pathogenic bacterium, Streptococcus pneumoniae (pneumococcus). We report the purification and biochemical characterization of S. pneumoniae FtsE and full-length FtsX, including initial attempts to isolate and reconstitute the FtsEX:PcsB complex biochemically in detergent micelles and nanodiscs and to determine the ATP binding and ATPase activity of pneumococcal FtsE.

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      Revisiting the pink-red pigmented basidiomycete mirror yeast of the phyllosphere

      Alec Cobban, Virginia P. Edgcomb, Gaëtan Burgaud, Daniel Repeta and Edward R. Leadbetter

      Version of Record online: 10 MAY 2016 | DOI: 10.1002/mbo3.374

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      Ten isolates of the ballistoconidium-forming genus Sporobolomyces were recovered from leaf samples, seven from the eastern and three from the western coasts of the United States, to explore similarities in phylogeny and physiology within this polyphyletic genus. All isolates were similarly pigmented, capable of growth under aerobic and microaerophilic conditions, tolerant of freeze/thaw cycles, and moderately tolerant to desiccation and elevated temperatures. Phylogenies based on the D1/D2 region of the large subunit ribosomal RNA and on small subunit ribosomal RNA show these isolates to be closely related, suggesting the importance of future investigation of the taxonomy and shared characteristics of Sporobolomyces and its closest relatives.

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      Cecal microbiota of Tibetan Chickens from five geographic regions were determined by 16S rRNA sequencing

      Xueyan Zhou, Xiaosong Jiang, Chaowu Yang, Bingcun Ma, Changwei Lei, Changwen Xu, Anyun Zhang, Xin Yang, Qi Xiong, Peng Zhang, Shuai Men, Rong Xiang and Hongning Wang

      Version of Record online: 2 MAY 2016 | DOI: 10.1002/mbo3.367

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      The cecal bacterial populations of Tibetan Chickens were surveyed by high-throughput sequencing (HTS) of the bacterial 16S rRNA hypervariable region V3-V4 (16S rRNAV3-V4) combined with community-fingerprinting analysis of the 16S rRNA gene based on polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE). The cecal microbiota of Tibetan Chicken have slightly diverged due to exposure to different geographic environments. Differences in the intestinal bacterial communities of Tibetan Chicken and LM/DH were noted.

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      Exploring the directionality of Escherichia coli formate hydrogenlyase: a membrane-bound enzyme capable of fixing carbon dioxide to organic acid

      Constanze Pinske and Frank Sargent

      Version of Record online: 2 MAY 2016 | DOI: 10.1002/mbo3.365

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      The formate hydrogenlyase (FHL) complex of Escherichia coli has been characterized in vivo and in vitro. As well as performing hydrogen evolution linked to formate oxidation, FHL has now been shown to be capable of converting CO2 into formate using molecular hydrogen as reductant. The enzyme activity was analyzed in combination with a comprehensive mutagenic analysis of the subunits of the FHL membrane domain, HycC and HycD. FHL is probably not an energy-conserving enzyme.

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