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FEMS Microbiology Ecology

Cover image for Vol. 90 Issue 3

December 2014

Volume 90, Issue 3

Pages i–ii, 543–969

  1. Issue Information

    1. Top of page
    2. Issue Information
    3. MiniReview
    4. Research Articles
    5. Chief Editor's Choice
    6. Research Articles
    1. You have free access to this content
      Issue Information (pages i–ii)

      Version of Record online: 8 DEC 2014 | DOI: 10.1111/1574-6941.12211

  2. MiniReview

    1. Top of page
    2. Issue Information
    3. MiniReview
    4. Research Articles
    5. Chief Editor's Choice
    6. Research Articles
    1. You have full text access to this OnlineOpen article
      A guide to statistical analysis in microbial ecology: a community-focused, living review of multivariate data analyses (pages 543–550)

      Pier Luigi Buttigieg and Alban Ramette

      Version of Record online: 5 NOV 2014 | DOI: 10.1111/1574-6941.12437

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      We describe GUSTA ME: an online, community-oriented resource which aims to promote understanding and currency in multivariate statistics for microbial ecology.

  3. Research Articles

    1. Top of page
    2. Issue Information
    3. MiniReview
    4. Research Articles
    5. Chief Editor's Choice
    6. Research Articles
    1. You have free access to this content
      Contrasting diversity of epibiotic bacteria and surrounding bacterioplankton of a common submerged macrophyte, Potamogeton crispus, in freshwater lakes (pages 551–562)

      Dan He, Lijuan Ren and Qinglong L. Wu

      Version of Record online: 19 SEP 2014 | DOI: 10.1111/1574-6941.12414

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      Our study suggested that epibiotic bacteria exhibited higher diversity and distinct community composition from the surrounding source bacterioplankton and called more attention to this productive and diverse microbial habitats on submerged macrophytes.

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      A high-throughput sequencing ecotoxicology study of freshwater bacterial communities and their responses to tebuconazole (pages 563–574)

      Noémie Pascault, Simon Roux, Joan Artigas, Stéphane Pesce, Julie Leloup, Rémy D. Tadonleke, Didier Debroas, Agnès Bouchez and Jean-François Humbert

      Version of Record online: 15 SEP 2014 | DOI: 10.1111/1574-6941.12416

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      The combination of classical methods and NGS approach is necessary when tackling the ecotoxicological responses of microbial communities to pollutants.

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      Windrow composting mitigated CH4 emissions: characterization of methanogenic and methanotrophic communities in manure management (pages 575–586)

      Ruirui Chen, Yiming Wang, Shiping Wei, Wei Wang and Xiangui Lin

      Version of Record online: 26 SEP 2014 | DOI: 10.1111/1574-6941.12417

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      Manure management influenced CH4 emissions via changing the abundance and structure of methanogenic and methanotrophic communities.

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      Acetoclastic methane formation from Eucalyptus detritus in pristine hydrocarbon-rich river sediments by Methanosarcinales (pages 587–598)

      Sabrina Beckmann and Mike Manefield

      Version of Record online: 15 SEP 2014 | DOI: 10.1111/1574-6941.12418

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      Acetoclastic methanogens release substantial amounts of methane in pristine Eucalyptus-rich river sediments, fuelled by previously undiscovered hydrocarbon-degrading bacteria.

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      Temporal changes and the effect of subtherapeutic concentrations of antibiotics in the gut microbiota of swine (pages 599–608)

      Devin B. Holman and Martin R. Chénier

      Version of Record online: 2 OCT 2014 | DOI: 10.1111/1574-6941.12419

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      Pigs were fed one of two different antibiotics starting at weaning and the effect that each antibiotic had on the swine gut microbial community was determined using Illumina-based sequencing.

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      Anthropogenic land use shapes the composition and phylogenetic structure of soil arbuscular mycorrhizal fungal communities (pages 609–621)

      Mari Moora, John Davison, Maarja Öpik, Madis Metsis, Ülle Saks, Teele Jairus, Martti Vasar and Martin Zobel

      Version of Record online: 22 SEP 2014 | DOI: 10.1111/1574-6941.12420

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      By analysing AM fungal DNA in soil from different habitats, its shown that forested and open habitats harbour different fungal communities, while disturbance changes the phylogenetic structure of fungal communities.

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      Off-site impacts of agricultural composting: role of terrestrially derived organic matter in structuring aquatic microbial communities and their metabolic potential (pages 622–632)

      Thomas Pommier, Asmaa Merroune, Yvan Bettarel, Patrice Got, Jean-Louis Janeau, Pascal Jouquet, Thuy D. Thu, Tran D. Toan and Emma Rochelle-Newall

      Version of Record online: 30 SEP 2014 | DOI: 10.1111/1574-6941.12421

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      Organic fertilizers from terrestrial leaching do impact metabolic abilities, composition and diversity of aquatic microbial communities.

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      Microbial community composition and in silico predicted metabolic potential reflect biogeochemical gradients between distinct peatland types (pages 633–646)

      Zuzana Urbanová and Jiří Bárta

      Version of Record online: 22 SEP 2014 | DOI: 10.1111/1574-6941.12422

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      The study reveals the transitional status of spruce swamp forests between bogs and fens and showed the strong effect of environmental conditions on microbial community composition and functioning.

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      Halophyte plant colonization as a driver of the composition of bacterial communities in salt marshes chronically exposed to oil hydrocarbons (pages 647–662)

      Vanessa Oliveira, Newton C.M. Gomes, Daniel F.R. Cleary, Adelaide Almeida, Artur M.S. Silva, Mário M.Q. Simões, Helena Silva and Ângela Cunha

      Version of Record online: 2 OCT 2014 | DOI: 10.1111/1574-6941.12425

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      In-depth molecular characterization (DGGE and barcoded pyrosequencing) of bacterial communities in salt marsh sediments was used to provide a comprehensive overview of the rhizosphere bacterial communities associated with two important halophyte plants of a temperate estuary chronically exposed to oil hydrocarbon.

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      Study of methanogen communities associated with different rumen protozoal populations (pages 663–677)

      Alejandro Belanche, Gabriel de la Fuente and Charles J. Newbold

      Version of Record online: 29 SEP 2014 | DOI: 10.1111/1574-6941.12423

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      Enteric methane emissions from ruminants represent a concern of global magnitude. Understanding the microbial interactions in this process is therefore vital to develop adequate methane mitigation strategies.

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      The bacterial microbiota of Stolotermes ruficeps (Stolotermitidae), a phylogenetically basal termite endemic to New Zealand (pages 678–688)

      Nicola M. Reid, Sarah L. Addison, Mark A. West and Gareth Lloyd-Jones

      Version of Record online: 29 SEP 2014 | DOI: 10.1111/1574-6941.12424

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      Pyrotag analysis of 16S rRNA gene and 16S rRNA applied to the gut contents derived from Stolotermes ruficeps termite, colonies inhabiting different tree host species.

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      Phylogenetic and clonality analysis of Bacillus pumilus isolates uncovered a highly heterogeneous population of different closely related species and clones (pages 689–698)

      Raquel Branquinho, Luís Meirinhos-Soares, João A. Carriço, Manuela Pintado and Luísa V. Peixe

      Version of Record online: 6 OCT 2014 | DOI: 10.1111/1574-6941.12426

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      Genomic characterization of Bacillus pumilus isolates, a species with attributed biotechnological and pharmaceutical relevance, revealed a highly heterogeneous population comprising different species (B. pumilus, B. safensis, B. invictae) and clones.

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      Symbiotic archaea in marine sponges show stability and host specificity in community structure and ammonia oxidation functionality (pages 699–707)

      Fan Zhang, Lucía Pita, Patrick M. Erwin, Summara Abaid, Susanna López-Legentil and Russell T. Hill

      Version of Record online: 20 OCT 2014 | DOI: 10.1111/1574-6941.12427

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      By comparing archaea communities associated with two sponge genera, our results show that sponge host-specific processes, such as host ecological strategy and evolutionary history, control the sponge-archaeal communities.

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      Culturable fungal assemblages growing within Cenococcum sclerotia in forest soils (pages 708–717)

      Keisuke Obase, Greg W. Douhan, Yosuke Matsuda and Matthew E. Smith

      Version of Record online: 30 SEP 2014 | DOI: 10.1111/1574-6941.12428

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      Cenococcum sclerotia act as a substrate for diverse fungi and several of common fungi in sclerotia may be active parasites or may preferencially use sclerotia as a nutrient source.

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      Soil type-dependent effects of a potential biocontrol inoculant on indigenous bacterial communities in the rhizosphere of field-grown lettuce (pages 718–730)

      Susanne Schreiter, Guo-Chun Ding, Rita Grosch, Siegfried Kropf, Kai Antweiler and Kornelia Smalla

      Version of Record online: 31 OCT 2014 | DOI: 10.1111/1574-6941.12430

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      The introduction of the potential biocontrol inoculant Pseudomonas jesseniiRU47 into three soil types at the same field site had a negligible effect on the bacterial community in the rhizosphere of field-grown lettuce.

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      Identification and activity of acetate-assimilating bacteria in diffuse fluids venting from two deep-sea hydrothermal systems (pages 731–746)

      Matthias Winkel, Petra Pjevac, Manuel Kleiner, Sten Littmann, Anke Meyerdierks, Rudolf Amann and Marc Mußmann

      Version of Record online: 13 OCT 2014 | DOI: 10.1111/1574-6941.12429

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      This is the first cultivation-independent study using stable isotopic and molecular tools addressing the heterotrophic potential of free-living microbes in diffuse hydrothermal fluids.

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      Chemolithotrophic growth of the aerobic hyperthermophilic bacterium Thermocrinis ruber OC 14/7/2 on monothioarsenate and arsenite (pages 747–760)

      Cornelia Härtig, Regina Lohmayer, Steffen Kolb, Marcus A. Horn, William P. Inskeep and Britta Planer-Friedrich

      Version of Record online: 10 OCT 2014 | DOI: 10.1111/1574-6941.12431

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      Growth of Thermocrinis ruber OC14/7/2 is supported by microbial oxidation of the products of abiotic monothioarsenate transformation (i.e. elemental sulfur, thiosulfate, arsenite) and by direct microbial oxidation of monothioarsenate.

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      The catecholamine stress hormones norepinephrine and dopamine increase the virulence of pathogenic Vibrio anguillarum and Vibrio campbellii (pages 761–769)

      Gde Sasmita J. Pande, Nguyen Thao Suong, Peter Bossier and Tom Defoirdt

      Version of Record online: 13 OCT 2014 | DOI: 10.1111/1574-6941.12432

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      Sensing of catecholamine stress hormones affects the host-pathogen interaction by increasing motility and growth under iron limited conditions of pathogenic vibrios.

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      Artificial soil studies reveal domain-specific preferences of microorganisms for the colonisation of different soil minerals and particle size fractions (pages 770–782)

      Michael Hemkemeyer, Geertje J. Pronk, Katja Heister, Ingrid Kögel-Knabner, Rainer Martens and Christoph C. Tebbe

      Version of Record online: 10 NOV 2014 | DOI: 10.1111/1574-6941.12436

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      Artificial soils composed of different minerals reveal soil particle-specific colonisation by Bacteria, Archaea and Fungi. These domain-specific responses to minerals may contribute to the high microbial diversity in natural soils.

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      Conversion of phenyl methyl ethers by Desulfitobacterium spp. and screening for the genes involved (pages 783–790)

      Felix S. Mingo, Sandra Studenik and Gabriele Diekert

      Version of Record online: 20 OCT 2014 | DOI: 10.1111/1574-6941.12433

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      O-demethylation coupled to fumarate, nitrate, thiosulfate or Fe(III) reduction was found to be a common metabolic feature of the genus Desulfitobacterium.

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      Impact of lifestyle on the gut microbiota of healthy infants and their mothers – the ALADDIN birth cohort (pages 791–801)

      Helena M. Hesla, Fredrik Stenius, Lotta Jäderlund, Ronald Nelson, Lars Engstrand, Johan Alm and Johan Dicksved

      Version of Record online: 3 NOV 2014 | DOI: 10.1111/1574-6941.12434

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      This study provides new information on the impact of early life exposures on the infant microbiota, which in turn has been associated with later health outcomes such as allergy.

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      Integrated ‘omics analysis for studying the microbial community response to a pH perturbation of a cellulose-degrading bioreactor culture (pages 802–815)

      Amy A. Boaro, Young-Mo Kim, Allan E. Konopka, Stephen J. Callister and Birgitte K. Ahring

      Version of Record online: 31 OCT 2014 | DOI: 10.1111/1574-6941.12435

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      We evaluated the functional response of a microbial community cultured in a bioreactor to a pulse of acid using ‘omics techniques.

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      The marine bacterium Marinobacter hydrocarbonoclasticus SP17 degrades a wide range of lipids and hydrocarbons through the formation of oleolytic biofilms with distinct gene expression profiles (pages 816–831)

      Julie Mounier, Arantxa Camus, Isabelle Mitteau, Pierre-Joseph Vaysse, Philippe Goulas, Régis Grimaud and Pierre Sivadon

      Version of Record online: 3 NOV 2014 | DOI: 10.1111/1574-6941.12439

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      This paper describes the genetic study of a microbial biofilm dedicated to the degradation of a large panel of marine hydrophobic organic compounds in order to identify the biological processes involved in the recycling of the insoluble oily carbon in oceans.

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      GeoChip-based insights into the microbial functional gene repertoire of marine sponges (high microbial abundance, low microbial abundance) and seawater (pages 832–843)

      Kristina Bayer, Lucas Moitinho-Silva, Franz Brümmer, Carlo V. Cannistraci, Timothy Ravasi and Ute Hentschel

      Version of Record online: 10 NOV 2014 | DOI: 10.1111/1574-6941.12441

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      GeoChip analyses of sponge and seawater microbiomes revealed differences in nitrogen-, carbon metabolism, and stress response. The HMA/LMA dichotomy was confirmed on the level of functional genes.

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      Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species (pages 844–857)

      Damaris Desgarennes, Etzel Garrido, Miryam J. Torres-Gomez, Juan J. Peña-Cabriales and Laila P. Partida-Martinez

      Version of Record online: 4 NOV 2014 | DOI: 10.1111/1574-6941.12438

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      The structure of bacterial communities associated with Agave species is distinct among soil, episphere and endosphere, where diazotrophic bacteria may facilitate adaption of these crassulacean acid metabolism-plants to low-nutrient environments.

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      Transformation of monothioarsenate by haloalkaliphilic, anoxygenic photosynthetic purple sulfur bacteria (pages 858–868)

      Christian F. Edwardson, Britta Planer-Friedrich and James T. Hollibaugh

      Version of Record online: 5 NOV 2014 | DOI: 10.1111/1574-6941.12440

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      Purple sulfur bacteria from Mono Lake, CA were found to be able to grow on and transform the arsenic-sulfur compound monothioarsenate.

  4. Chief Editor's Choice

    1. Top of page
    2. Issue Information
    3. MiniReview
    4. Research Articles
    5. Chief Editor's Choice
    6. Research Articles
    1. You have free access to this content
      Epifluorescence, SEM, TEM and nanoSIMS image analysis of the cold phenotype of Clostridium psychrophilum at subzero temperatures (pages 869–882)

      Amedea Perfumo, Andreas Elsaesser, Sten Littmann, Rachel A. Foster, Marcel M.M. Kuypers, Charles S. Cockell and Gerhard Kminek

      Version of Record online: 4 NOV 2014 | DOI: 10.1111/1574-6941.12443

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      Epifluorescence, SEM, TEM and nanoSIMS image analysis of the cold-phenotype of Clostridium psychrophilum at subzero temperatures.

  5. Research Articles

    1. Top of page
    2. Issue Information
    3. MiniReview
    4. Research Articles
    5. Chief Editor's Choice
    6. Research Articles
    1. You have free access to this content
      Unique and shared responses of the gut microbiota to prolonged fasting: a comparative study across five classes of vertebrate hosts (pages 883–894)

      Kevin D. Kohl, James Amaya, Celeste A. Passement, M. Denise Dearing and Marshall D. McCue

      Version of Record online: 3 NOV 2014 | DOI: 10.1111/1574-6941.12442

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      Prolonged fasting significantly changes gut microbial communities; some responses are shared while others differ across various hosts (fish, amphibians, reptiles, birds, and mammals).

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      Exploring new roles for the rpoS gene in the survival and virulence of the fire blight pathogen Erwinia amylovora (pages 895–907)

      Ricardo D. Santander, Mercedes Monte-Serrano, José J. Rodríguez-Herva, Emilia López-Solanilla, Pablo Rodríguez-Palenzuela and Elena G. Biosca

      Version of Record online: 4 NOV 2014 | DOI: 10.1111/1574-6941.12444

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      We describe new roles for the rpoS gene in Erwinia amylovora, including its contribution to starvation responses, cross protection, motility, exopolysaccharide synthesis, virulence and survival during incompatible plant–pathogen interactions.

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      In-depth analyses of deep subsurface sediments using 454-pyrosequencing reveals a reservoir of buried fungal communities at record-breaking depths (pages 908–921)

      Vanessa Rédou, Maria Cristina Ciobanu, Maria G. Pachiadaki, Virginia Edgcomb, Karine Alain, Georges Barbier and Gaëtan Burgaud

      Version of Record online: 17 NOV 2014 | DOI: 10.1111/1574-6941.12447

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      Unexpected fungal diversity in the deep subseafloor of the Canterbury basin.

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      Diversity and geochemical structuring of bacterial communities along a salinity gradient in a carbonate aquifer subject to seawater intrusion (pages 922–934)

      Marina Héry, Aurélie Volant, Charlotte Garing, Linda Luquot, Françoise Elbaz Poulichet and Philippe Gouze

      Version of Record online: 19 NOV 2014 | DOI: 10.1111/1574-6941.12445

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      Distinct bacterial communities are shaped by physico-chemical gradients in the freshwater-saltwater mixing zone of an aquifer. The wide range of their potential metabolic capacities can impact the groundwater geochemical properties.

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      Pezizomycotina dominates the fungal communities of South China Sea Sponges Theonella swinhoei and Xestospongia testudinaria (pages 935–945)

      Liling Jin, Fang Liu, Wei Sun, Fengli Zhang, Valliappan Karuppiah and Zhiyong Li

      Version of Record online: 12 NOV 2014 | DOI: 10.1111/1574-6941.12446

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      The fungi community structures of sponges Theonella swinhoei and Xestospongia testudinaria are different from that of ambient seawater. 18S rRNA vs. 18S rRNA gene analysis indicates that the major part of sponge-associated fungi are viable in vivo, especially the predominant Pezizomycotina in sponge-fungi symbioses.

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      Symbiotic Chlorella variabilis incubated under constant dark conditions for 24 hours loses the ability to avoid digestion by host lysosomal enzymes in digestive vacuoles of host ciliate Paramecium bursaria (pages 946–955)

      Yuuki Kodama and Masahiro Fujishima

      Version of Record online: 10 NOV 2014 | DOI: 10.1111/1574-6941.12448

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      Some factors induced by light are prerequisite for symbiotic algal resistance to the host Paramecium lysosomal enzymes.

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      Sulfate reduction and sulfide oxidation in extremely steep salinity gradients formed by freshwater springs emerging into the Dead Sea (pages 956–969)

      Stefan Häusler, Miriam Weber, Christian Siebert, Moritz Holtappels, Beatriz E. Noriega-Ortega, Dirk De Beer and Danny Ionescu

      Version of Record online: 17 NOV 2014 | DOI: 10.1111/1574-6941.12449

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      Sulfur oxidizers and reducers are active around underwater freshwater springs in the Dead Sea. They benefit from compounds provided by the springs but are inhibited by fluctuations in water flow.

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