MicrobiologyOpen

Cover image for Vol. 5 Issue 6

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 - 33
  1. ORIGINAL RESEARCH

    1. You have full text access to this OnlineOpen article
      The gastrointestinal tract of farmed mink (Neovison vison) maintains a diverse mucosa-associated microbiota following a 3-day fasting period

      Martin I. Bahl, Anne S. Hammer, Tove Clausen, Anabelle Jakobsen, Søren Skov and Lars Andresen

      Version of Record online: 16 JAN 2017 | DOI: 10.1002/mbo3.434

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      The first report of mink gut microbiota characterization by high-throughput sequencing. The microbiota within the mink colon mucosa was diverse, dissimilar from feed microbiota and not severely impacted by fasting.

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      Intracellular fate of Ureaplasma parvum entrapped by host cellular autophagy

      Fumiko Nishiumi, Michinaga Ogawa, Yukiko Nakura, Yusuke Hamada, Masahiro Nakayama, Jiro Mitobe, Atsushi Hiraide, Norio Sakai, Makoto Takeuchi, Tamotsu Yoshimori and Itaru Yanagihara

      Version of Record online: 15 JAN 2017 | DOI: 10.1002/mbo3.441

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      U. parvum was internalized into HeLa cells by endocytosis and entrapped by the autophagic machinery. However, autophagy was inadequate for the complete elimination. U. parvum also reached recycling endosome and exported from HeLa cells through exocytosis.

  2. Original Research

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      Population genetic analysis of Giardia duodenalis: genetic diversity and haplotype sharing between clinical and environmental sources

      Mauricio Durigan, Maisa Ciampi-Guillardi, Ricardo C. A. Rodrigues, Juliane A. Greinert-Goulart, Isabel C. V. Siqueira-Castro, Diego A. G. Leal, Sandra Yamashiro, Taís R. Bonatti, Maria I. Zucchi, Regina M. B. Franco and Anete P. de Souza

      Version of Record online: 11 JAN 2017 | DOI: 10.1002/mbo3.424

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      The aim of this study was to compare groups of Giardia duodenalis from clinical and environmental sources through population genetic analyses. The results showed that there is high diversity of haplotypes and substantial genetic similarity between clinical and environmental groups of G. duodenalis. The genetic similarity of Giardia isolates among human, veterinary, and environmental groups reinforced the correlation between clinical and environmental isolates in this region, which is of great importance for public health.

  3. ORIGINAL RESEARCH

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      Functional and structural studies on the Neisseria gonorrhoeae GmhA, the first enzyme in the glycero-manno-heptose biosynthesis pathways, demonstrate a critical role in lipooligosaccharide synthesis and gonococcal viability

      Igor H. Wierzbicki, Ryszard A. Zielke, Konstantin V. Korotkov and Aleksandra E. Sikora

      Version of Record online: 7 JAN 2017 | DOI: 10.1002/mbo3.432

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      The first enzymes in the nucleotide-activated-glycero-manno-heptose pathways, such as GmhA, are attractive targets for development of broad-spectrum antibacterial drugs. Functional and structural studies revealed that GmhA of Neisseria gonorrhoeae and N. meningitidis are interchangeable, cytoplasmic, tetrameric metalloenzymes critical for lipooligosaccharide synthesis and bacterial growth.

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      Hysteresis in myo-inositol utilization by Salmonella Typhimurium

      Jessica Hellinckx and Thilo M. Fuchs

      Version of Record online: 27 DEC 2016 | DOI: 10.1002/mbo3.431

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      A heterogeneous phenotype of Salmonella enterica serovar Typhimurium is observed during growth with myo-inositol (MI) as the sole carbon and energy source. This study demonstrates that a Salmonella population has a memory for MI degradation, and that this memory is gradually lost after several hours of growth in rich medium. This hysteresis is confirmed on a single-cell level by flow cytometry and also shown to be independent of the repressor IolR.

  4. Original Research

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      Investigation of the microbial communities colonizing prepainted steel used for roofing and walling

      Tran T. Huynh, Ili Jamil, Nicole A. Pianegonda, Stephen J. Blanksby, Philip J. Barker, Mike Manefield and Scott A. Rice

      Version of Record online: 20 DEC 2016 | DOI: 10.1002/mbo3.425

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      The microbial communities found on painted steel surfaces were geographically distinct and changed significantly over the 52-week experiment.

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      Metagenomic profiling of gut microbial communities in both wild and artificially reared Bar-headed goose (Anser indicus)

      Wen Wang, Sisi Zheng, Kirill Sharshov, Hao Sun, Fang Yang, Xuelian Wang, Laixing Li and Zhixiong Xiao

      Version of Record online: 20 DEC 2016 | DOI: 10.1002/mbo3.429

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      In this study, high-throughput and sequence-based comparative metagenomics were applied on the Illumina HiSeq 2500 platform (1) to investigate and to compare the gut microbiota associated with both wild and artificially reared Bar-headed geese, and (2) to try to relate the functional genes of the gut microbial communities to the biological characteristics of this species.

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      Agarolytic bacterium Persicobacter sp. CCB-QB2 exhibited a diauxic growth involving galactose utilization pathway

      Go Furusawa, Nyok-Sean Lau, Appalasamy Suganthi and Abdullah Al-Ashraf Amirul

      Version of Record online: 17 DEC 2016 | DOI: 10.1002/mbo3.405

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      The agarolytic bacterium Persicobacter sp. CCB-QB2, which possesses agarase and galactose utilization genes, exhibited a diauxic growth in the presence of two kinds of nutrients, such as tryptone and agar. These genes were highly expressed in the second growth phase of diauxic growth, indicating that QB2 cells use galactose hydrolyzed from agar by its agarases and exhibit nutrient prioritization.

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      Global transcriptome responses including small RNAs during mixed-species interactions with methicillin-resistant Staphylococcus aureus and Pseudomonas aeruginosa

      Christine L. Miller, Tricia A. Van Laar, Tsute Chen, S. L. Rajasekhar Karna, Ping Chen, Tao You and Kai P. Leung

      Version of Record online: 21 NOV 2016 | DOI: 10.1002/mbo3.427

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      Polymicrobial biofilm infections comprised of P. aeruginosa and S. aureus lead to more wound healing impairment and are more antibiotic resistant compared to biofilm infections by just one of these pathogens alone. Therefore, our work utilized custom RNA-sequencing methods to unbiasedly capture the global transcriptome response, including small RNAs, of each species during polymicrobial growth to reveal novel interspecies interactions and foster identification of targets for future therapeutics. Our work identified novel genes facilitating the success and persistence of each species in a polymicrobial biofilm, shed light on the physiological role of numerous small RNAs, and found that small RNAs of known function parallel with the genomic response to presumably coordinate these interspecies interactions.

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      Polymetallic nodules, sediments, and deep waters in the equatorial North Pacific exhibit highly diverse and distinct bacterial, archaeal, and microeukaryotic communities

      Christine N. Shulse, Brianne Maillot, Craig R. Smith and Matthew J. Church

      Version of Record online: 21 NOV 2016 | DOI: 10.1002/mbo3.428

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      In this study, we used 16S and 18S rRNA gene sequencing to investigate the microbial communities associated with the polymetallic nodules, sediments, and water column within a region of the Clarion-Clipperton Fracture Zone in the Pacific Ocean of interest for mining. We identify several specific operational taxonomic unit (OTUs) differentially represented on nodules relative to sediments that may play a role in metal cycling on nodules. Including all three domains of life, as well as all three available habitats (water column, sediment, nodules), our study represents the most comprehensive assessment to date of microbial diversity within this threatened deep-sea benthic ecosystem.

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      Diversification of the kinetic properties of yeast NADP-glutamate-dehydrogenase isozymes proceeds independently of their evolutionary origin

      Carlos Campero-Basaldua, Héctor Quezada, Lina Riego-Ruíz, Dariel Márquez, Erendira Rojas, James González, Mohammed El-Hafidi and Alicia González

      Version of Record online: 19 NOV 2016 | DOI: 10.1002/mbo3.419

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      S. cerevisiae retained a duplicated pair of NADP-GDH encoding genes, originated from the Whole Genome Duplication event, while K. lactis and L. kluyveri conserved a single NADP-Gdh1, generated from a GDH clade originated from a hybrid strain. Functional diversification of the orthologous genes and encoded isozymes, resulted in similarities of the kinetic properties and heterologous complementation patterns, indicating that retention and further diversification proceeds independently of the evolutionary origin of the diverging genes.

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      Biostimulation and microbial community profiling reveal insights on RDX transformation in groundwater

      Dongping Wang, Hakim Boukhalfa, Oana Marina, Doug S. Ware, Tim J. Goering, Fengjie Sun, Hajnalka E. Daligault, Chien-Chi Lo, Momchilo Vuyisich and Shawn R. Starkenburg

      Version of Record online: 17 NOV 2016 | DOI: 10.1002/mbo3.423

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      In this study, we aim to understand environmental and microbial signatures indicative of RDX degradation in groundwater. Our data highlight the importance of oxygen in shaping the microbial community composition during biostimulation and show that only strict anaerobic conditions are favorable to RDX degradation.

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      Convergent evolution of the arginine deiminase pathway: the ArcD and ArcE arginine/ornithine exchangers

      Elke E. E. Noens and Juke S. Lolkema

      Version of Record online: 1 NOV 2016 | DOI: 10.1002/mbo3.412

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      Bacterial gene clusters encoding the ADI pathway contain either the arcD or the arcE gene that encodes transporter proteins from two different transporter families. By all accounts, ArcD and ArcE function as the L-arginine/L-ornithine exchangers in the pathway.

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      A family of genus-specific RNAs in tandem with DNA-binding proteins control expression of the badA major virulence factor gene in Bartonella henselae

      Nhan Tu, Ronan K. Carroll, Andy Weiss, Lindsey N. Shaw, Gael Nicolas, Sarah Thomas, Amorce Lima, Udoka Okaro and Burt Anderson

      Version of Record online: 28 OCT 2016 | DOI: 10.1002/mbo3.420

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      We describe a novel regulatory system that controls badA expression in Bartonella henselae. It includes a sRNA (Brt1) and a second RNA element controlling transcription of the downstream DNA-binding protein (Trp1) that positively regulates badA. We hypothesize that this system coordinates badA expression and the associated biofilm formation.

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      One step forwards for the routine use of high-throughput DNA sequencing in environmental monitoring. An efficient and standardizable method to maximize the detection of environmental bacteria

      Antonia Bruno, Anna Sandionigi, Andrea Galimberti, Eleonora Siani, Massimo Labra, Clementina Cocuzza, Emanuele Ferri and Maurizio Casiraghi

      Version of Record online: 27 OCT 2016 | DOI: 10.1002/mbo3.421

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      Traditional microbiology techniques still rely on culture methods and/or on the detection of a few target microorganisms occurring in environmental matrices.

  5. Reviews

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      Understanding pine wilt disease: roles of the pine endophytic bacteria and of the bacteria carried by the disease-causing pinewood nematode

      Diogo N. Proença, Gregor Grass and Paula V. Morais

      Version of Record online: 26 OCT 2016 | DOI: 10.1002/mbo3.415

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      Here, we reviewed the possible roles of nematode-carried bacteria in pine wilt disease, what could be the definition of this group of microorganisms and questioned their origin as possible endophytes, discussing their relation within the endophytic community of pine trees. The diversity of the nematode-carried bacteria and the diversity of pine tree endophytes, reported until now, is revisited in detail in this review. What could signify a synergetic effect with pinewood nematode harming the plant, or what could equip bacteria with functions to control the presence of nematodes inside the tree, is outlined as two possible roles of the microbial community in the etiology of this disease.

  6. Original Research

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      Keeping it in the family: Coevolution of latrunculid sponges and their dominant bacterial symbionts

      Gwynneth F. Matcher, Samantha C. Waterworth, Tara A. Walmsley, Tendayi Matsatsa, Shirley Parker-Nance, Michael T. Davies-Coleman and Rosemary A. Dorrington

      Version of Record online: 26 OCT 2016 | DOI: 10.1002/mbo3.417

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      Latrunculiidae, a family of sponges characterized by their production of bioactive pyrroloiminoquinone secondary metabolites, exhibits unprecedented conservation of a dominant Betaproteobacterium species. We propose that these Betaproteobacteria represent specialized sponge endosymbionts that have coevolved with their hosts. We also identify a novel Spirochaetae species found only in Cyclacanthia and Tsitsikamma species that may be involved in secondary metabolites biosynthesis in these sponges.

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      Expanding the archaellum regulatory network – the eukaryotic protein kinases ArnC and ArnD influence motility of Sulfolobus acidocaldarius

      Lena Hoffmann, Andreas Schummer, Julia Reimann, Maria F. Haurat, Amanda J. Wilson, Morgan Beeby, Bettina Warscheid and Sonja-V. Albers

      Version of Record online: 22 OCT 2016 | DOI: 10.1002/mbo3.414

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      The protein kinases ArnC and ArnD specifically phosphorylate serine/threonine residues and play a role in the regulation of motility in the crenarchaeon Sulfolobus acidocaldarius.

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      Multiple roles for a novel RND-type efflux system in Acinetobacter baumannii AB5075

      Kyle A. Tipton, Marjan Farokhyfar and Philip N. Rather

      Version of Record online: 19 OCT 2016 | DOI: 10.1002/mbo3.418

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      A novel RND-type efflux system has been characterized in Acinetobacter baumannii. This efflux system has roles in phase variation, surface motility, and virulence. A divergently transcribed TetR repressor regulates this efflux system when overexpressed.

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      The Rhodococcus equi virulence protein VapA disrupts endolysosome function and stimulates lysosome biogenesis

      Adam P. Rofe, Luther J. Davis, Jean L. Whittingham, Elizabeth C. Latimer-Bowman, Anthony J. Wilkinson and Paul R. Pryor

      Version of Record online: 19 OCT 2016 | DOI: 10.1002/mbo3.416

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      VapA is essential for Rhodococcus equi survival inside cells. Here, we show that VapA disrupts endolysosomes as a mechanism to aid Rhodococcus equi survival.

    5. You have full text access to this OnlineOpen article
      Food to some, poison to others - honeybee royal jelly and its growth inhibiting effect on European Foulbrood bacteria

      Thomas V. Vezeteu, Otilia Bobiş, Robin F. A. Moritz and Anja Buttstedt

      Version of Record online: 14 OCT 2016 | DOI: 10.1002/mbo3.397

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      Honeybee larval food jelly inhibits the growth of the European Foulbrood (EFB) provoking bacterium M. plutonius and also decelerates the growth of other EFB-associated bacteria. This effect arises mainly from the main protein of royal jelly, major royal jelly protein 1, which inhibits all bacteria tested at a minimum concentration of 60 µg/ml.

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      AhpA is a peroxidase expressed during biofilm formation in Bacillus subtilis

      Joelie V. Zwick, Sarah Noble, Yasser K. Ellaicy, Gabrielle Dierker Coe, Dylan J. Hakey, Alyssa N. King, Alex J. Sadauskas and Melinda J. Faulkner

      Version of Record online: 28 SEP 2016 | DOI: 10.1002/mbo3.403

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      The results presented here show that the expression of ahpA is dependent on the transition-state regulator AbrB and the sporulation and biofilm formation transcription factor Spo0A. We show that ahpA is specifically produced during biofilm formation, and not during stationary phase or sporulation. These studies highlight the interplay between Spo0A and AbrB and suggest that derepression of ahpA by AbrB requires a signal specific to biofilm formation conditions.

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      No adverse effects of transgenic maize on population dynamics of endophytic Bacillus subtilis strain B916-gfp

      Chongsi Sun, Lili Geng, Meiling Wang, Gaoxiang Shao, Yongfeng Liu, Changlong Shu and Jie Zhang

      Version of Record online: 25 SEP 2016 | DOI: 10.1002/mbo3.404

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      Endophytic bacterial communities play a key role in promoting plant growth and combating plant diseases. This study investigated the colonization of cry1Ah Bt transgenic maize by Bacillus subtilis strain B916-gfp, which is present in the plant tissues and surrounding soil. The results indicate that transgenic modification of maize with the cry1Ah gene has no influence on colonization by the endophytic bacteria B916-gfp present in the plant and in bulk soil.

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      Assessing the composition of microbial communities in textile wastewater treatment plants in comparison with municipal wastewater treatment plants

      Ken Meerbergen, Maarten Van Geel, Michael Waud, Kris A. Willems, Raf Dewil, Jan Van Impe, Lise Appels and Bart Lievens

      Version of Record online: 25 SEP 2016 | DOI: 10.1002/mbo3.413

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      Microbial community analysis of activated sludge from textile and municipal wastewater treatment plants (WWTPs) revealed differences in community composition and occurrence of important functional groups. Species richness was found to be lower in activated sludge from textile WWTPs. Nitrifying and denitrifying bacteria as well as phosphate-accumulating bacteria were more abundant in municipal WWTPs, whereas sulfate-reducing bacteria were almost only detected in textile WWTPs. High salinity, high organic loads and a higher water temperature were important variables driving the microbial community composition in textile WWTPs.

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      Expression of the phosphodiesterase BifA facilitating swimming motility is partly controlled by FliA in Pseudomonas putida KT2440

      Yujie Xiao, Huizhong Liu, Hailing Nie, Shan Xie, Xuesong Luo, Wenli Chen and Qiaoyun Huang

      Version of Record online: 23 SEP 2016 | DOI: 10.1002/mbo3.402

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      Our manuscript gave the evidence that the expression of phosphodiesterase BifA was controlled by the flagellar sigma factor FliA in Pseudomonas putidaKT2440. By enhancing expression of BifA, FliA acted as a negative regulator to modulate the c-di-GMP level to facilitate swimming motility. Our results imply a positive feedback function of FliA in swimming ability regulation.

    10. You have full text access to this OnlineOpen article
      Genetic diversity of Arcobacter isolated from bivalves of Adriatic and their interactions with Mytilus galloprovincialis hemocytes

      Donatella Ottaviani, Francesco Mosca, Serena Chierichetti, Pietro Giorgio Tiscar and Francesca Leoni

      Version of Record online: 20 SEP 2016 | DOI: 10.1002/mbo3.400

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      Our data demonstrate the high genetic diversity of Arcobacter spp. circulating in Adriatic Sea of Italy. Arcobacter–bivalve interaction suggests that these microorganisms do not have a potential to persist in the tissues of Mytilus galloprovincialis.

  7. Reviews

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      Lignin peroxidase functionalities and prospective applications

      Ayodeji O. Falade, Uchechukwu U. Nwodo, Benson C. Iweriebor, Ezekiel Green, Leonard V. Mabinya and Anthony I. Okoh

      Version of Record online: 7 SEP 2016 | DOI: 10.1002/mbo3.394

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      Ligninolytic extracellular enzymes are topical owing to their high redox potential and prospective industrial applicability. The applications of peroxidases spans through several sectors including cosmetology, dermatology and bioremediation industries. The litany of potentials attributed to lignin peroxidases is consequent to their versatility in the decolourization of melanin (synthetic or otherwise) and as well, the degradation of xenobiotic with phenolic and non-phenolic constituents.

  8. Original Research

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      Role of OmpA2 surface regions of Porphyromonas gingivalis in host–pathogen interactions with oral epithelial cells

      Kathryn L. Naylor, Magdalena Widziolek, Stuart Hunt, Mary Conolly, Matthew Hicks, Prachi Stafford, Jan Potempa, Craig Murdoch, C. W. Ian Douglas and Graham P. Stafford

      Version of Record online: 6 SEP 2016 | DOI: 10.1002/mbo3.401

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      This paper presents evidence that surface exposed loops of the OmpA2 outer membrane protein of the periodontitis causing pathogen Porphyromonas gingivalis directs interaction with oral epithelial cells and inert surfaces during biofilm formation. These data reveal new insight into two processes key to periodontal pathogen virulence and suggest new avenues for antimicrobial strategies for periodontitis.

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      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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      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.

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