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Environmental Microbiology Reports

Yanglei Yi, Elrike Frenzel, Jan Spoelder, J Theo M Elzenga, Jan Dirk van Elsas, Oscar P Kuipers
Tracking of fluorescent protein (FP)-labeled rhizobacteria is a key prerequisite to gain insights into plant-bacteria interaction mechanisms. However, the performance of FPs mostly has to be optimized for the bacterial host and for the environment of intended application. We report on the construction of mutational libraries of the superfolder green fluorescent protein sfGFP and the red fluorescent protein mKate2 in the bacterium B. mycoides, which next to its potential as plant-biocontrol agent occasionally enters an endophytic lifestyle...
December 1, 2017: Environmental Microbiology Reports
Georg Steinert, Johanna Gutleben, Akhirta Atikana, Rene H Wijffels, Hauke Smidt, Detmer Sipkema
Marine sponges are benthic 'filter-feeding' invertebrates that can host dense and diverse bacterial, archaeal, and eukaryotic communities. Due to the finding of several genes encoding symbiosis factors, such as adhesins, ankyrin repeats and tetratricopeptide repeats, the candidate phylum 'Poribacteria' is considered as a promising model microorganism for studying the origin of host-symbiont interactions in sponges. However, relatively little is known about its global diversity and phylogenetic distribution among different sponge hosts...
December 1, 2017: Environmental Microbiology Reports
Agota Aučynaitė, Rasa Rutkienė, Renata Gasparavičiūtė, Rolandas Meškys, Jaunius Urbonavičius
Modified nucleotides are present in many RNA species in all Domains of Life. While the biosynthetic pathways of such nucleotides are well studied, much less is known about the degradation of RNAs and the return to the metabolism of modified nucleotides, their respective nucleosides or heterocyclic bases. Using an E. coli uracil auxotroph, we screened the metagenomic libraries for genes, which would allow the conversion of 2-thiouracil to uracil and thereby lead to the growth on a defined synthetic medium. We show that a gene encoding a protein consisting of previously uncharacterized Domain of Unknown Function 523 (DUF523) is responsible for such phenotype...
December 1, 2017: Environmental Microbiology Reports
Kristie Tanner, José Manuel Martí, Josabel Belliure, Mar Fernández-Méndez, Esther Molina-Menor, Juli Peretó, Manuel Porcar
Solar panels located on high (Arctic and Antarctic) latitudes combine the harshness of the climate with that of the solar exposure. We report here that these polar solar panels are inhabited by similar microbial communities in taxonomic terms, dominated by Hymenobacter spp., Sphingomonas spp., and Ascomycota. Our results suggest that solar panels, even on high latitudes, can shape a microbial ecosystem adapted to irradiation and desiccation. This article is protected by copyright. All rights reserved.
December 1, 2017: Environmental Microbiology Reports
Mercedes Nieves-Morión, Enrique Flores
Cyanobacteria are generally capable of photoautotrophic growth and are widely distributed on Earth. The model filamentous, heterocyst-forming strain Anabaena sp. PCC 7120 has been long considered a strict photoautotroph but is now known to be able to assimilate fructose. We have previously described two components of ABC glucoside uptake transporters from Anabaena that are involved in uptake of the sucrose analog esculin: GlsC (a nucleotide-binding domain subunit [NBD]) and GlsP (a transmembrane component [TMD])...
November 21, 2017: Environmental Microbiology Reports
Theresa Hölscher, Tina Schiklang, Anna Dragoš, Anne-Kathrin Dietel, Christian Kost, Ákos T Kovács
The competent state is a developmentally distinct phase, in which bacteria are able to take up and integrate exogenous DNA into their genome. Bacillus subtilis is one of the naturally competent bacterial species and the domesticated laboratory strain 168 is easily transformable. In this study, we report a reduced transformation frequency of B. subtilis mutants lacking functional and structural flagellar components. This includes hag, the gene encoding the flagellin protein forming the filament of the flagellum...
November 10, 2017: Environmental Microbiology Reports
Caitlin A Lawson, Jean-Baptiste Raina, Tim Kahlke, Justin R Seymour, David J Suggett
Dinoflagellates of the genus Symbiodinium underpin the survival and ecological success of corals. The use of cultured strains has been particularly important to disentangle the complex life history of Symbiodinium and their contribution to coral host physiology. However, these cultures typically harbour abundant bacterial communities which likely play important, but currently unknown, roles in Symbiodinium biology. We characterised the bacterial communities living in association with a wide phylogenetic diversity of Symbiodinium cultures (18 types spanning 5 clades) to define the core Symbiodinium microbiome...
November 10, 2017: Environmental Microbiology Reports
Yuan Liu, Sara R Palmer, Hsiaochi Chang, Ashton N Combs, Robert A Burne, Hyun Koo
Streptococcus mutans strongly influences the development of pathogenic biofilms associated with dental caries. Our understanding of S. mutans behavior in biofilms is based on a few well-characterized laboratory strains; however, individual isolates vary widely in genome content and virulence-associated phenotypes, such as biofilm formation and environmental stress sensitivity. Using an ecological biofilm model, we assessed the impact of co-cultivation of several S. mutans isolates with Streptococcus oralis and Actinomyces naeslundii on biofilm composition following exposure to sucrose...
November 10, 2017: Environmental Microbiology Reports
Guntars O Martinson, Bianca Pommerenke, Franziska B Brandt, Jürgen Homeier, Juan Ignacio Burneo, Ralf Conrad
Several thousands of tank bromeliads per hectare of neotropical forest create a unique wetland ecosystem that emits substantial amounts of CH4 . Tank bromeliads growing in the forest canopy (functional type-II tank bromeliads) were found to emit more CH4 than tank bromeliads growing on the forest floor (functional type-I tank bromeliads) but the reasons for this difference and the underlying microbial CH4-cycling processes have not been studied. Therefore, we characterized archaeal communities in bromeliad tanks of the two different functional types in a neotropical montane forest of southern Ecuador using terminal-restriction fragment length polymorphism (T-RFLP) and performed tank-slurry incubations to measure CH4 production potential, stable carbon isotope fractionation and pathway of CH4 formation...
November 10, 2017: Environmental Microbiology Reports
Naofumi Kamimura, Kenji Takahashi, Kosuke Mori, Takuma Araki, Masaya Fujita, Yudai Higuchi, Eiji Masai
Lignin is the most abundant phenolic polymer; thus, its decomposition by microorganisms is fundamental to carbon cycling on earth. Lignin breakdown is initiated by depolymerization catalyzed by extracellular oxidoreductases secreted by white-rot basidiomycetous fungi. On the other hand, bacteria play a predominant role in the mineralization of lignin-derived heterogeneous low-molecular-weight aromatic compounds. The outline of bacterial catabolic pathways for lignin-derived bi- and monoaryls are typically composed of the following sequential steps: i) funneling of a wide variety of lignin-derived aromatics into vanillate and syringate, ii) O demethylation of vanillate and syringate to form catecholic derivatives, and iii) aromatic ring-cleavage of the catecholic derivatives to produce tricarboxylic acid cycle intermediates...
October 20, 2017: Environmental Microbiology Reports
Emma Sevilla, Luis Yuste, Renata Moreno, Fernando Rojo
Alcanivorax borkumensis, a marine bacterium highly specialized in degrading linear and branched alkanes, plays a key ecological role in the removal of marine oil spills. It contains several alternative enzyme systems for terminal hydroxylation of alkanes, including three P450 cytochromes (P450-1, P450-2 and P450-3). The present work shows cytochrome P450-1 to be expressed from the promoter of the upstream gene fdx. Promoter Pfdx was more active when C8 -C18 n-alkanes or pristane were assimilated than when pyruvate was available...
October 20, 2017: Environmental Microbiology Reports
Javier Torregrosa-Crespo, Pedro González-Torres, Vanesa Bautista, Julia M Esclapez, Carmen Pire, Mónica Camacho, María José Bonete, David J Richardson, Nicholas J Watmough, Rosa María Martínez-Espinosa
Microorganisms, including Bacteria and Archaea, play a key role in denitrification, which is the major mechanism by which fixed nitrogen returns to the atmosphere from soil and water. Whilst the enzymology of denitrification is well understood in Bacteria, the details of the last two reactions in this pathway, which catalyse the reduction of nitric oxide (NO) via nitrous oxide (N2 O) to nitrogen (N2 ), are little studied in Archaea, and hardly at all in haloarchaea. This work describes an extensive interspecies analysis of both complete and draft haloarchaeal genomes aimed at identifying the genes that encode respiratory nitric oxide reductases (Nors)...
September 19, 2017: Environmental Microbiology Reports
Venkata G Poosarla, Thammajun L Wood, Lei Zhu, Daniel S Miller, Bei Yin, Thomas K Wood
Biofilms of sulfate-reducing bacteria (SRB) are often the major cause of microbiologically influenced corrosion. The representative SRB Desulfovibrio vulgaris has previously been shown to have a biofilm that consists primarily of protein. In this study, by utilizing lectin staining, we identified that the biofilm of D. vulgaris also consists of the matrix components mannose, fucose, and N-acetylgalactosamine (GalNAc), with mannose predominating. Based on these results, we found that the addition of mannose and the non-metabolizable mannose analog 2-deoxy-D-glucose inhibits the biofilm formation of D...
September 19, 2017: Environmental Microbiology Reports
Jessica A Lisa, Amal Jayakumar, Bess B Ward, Bongkeun Song
Molecular analysis of dissimilatory nitrite reductase genes (nirS) was conducted using a customized microarray containing 165 nirS probes (archetypes) to identify members of sedimentary denitrifying communities. The goal of this study was to examine denitrifying community responses to changing environmental variables over spatial and temporal scales in the New River Estuary (NRE), NC, USA. Multivariate statistical analyses revealed three denitrifier assemblages and uncovered "generalist" and "specialist" archetypes based on the distribution of archetypes within these assemblages...
September 15, 2017: Environmental Microbiology Reports
Sofia Duarte, Juanita Mora-Gómez, Anna M Romaní, Fernanda Cássio, Cláudia Pascoal
A consequence of drought in streams is the emersion of decomposing leaf litter, which may alter organic matter recycling. We assessed the effects of emersion on decomposition of black poplar leaves and associated microbes (microbial biomass, extracellular enzyme activities and microbial diversity) in two streams with distinct characteristics, in particular nutrients, temperature and oxygen levels. Leaf decomposition rates, fungal biomass and extracellular enzyme activities were lower in the most impacted stream (high nutrients and temperature, low oxygen)...
September 15, 2017: Environmental Microbiology Reports
Lawrence P Wackett
No abstract text is available yet for this article.
December 2017: Environmental Microbiology Reports
Ram Maharjan, Thomas Ferenci
The relationship between bacterial drug resistance and growth fitness is a contentious topic, but some antibiotic resistance mutations clearly have a fitness cost in the laboratory. Whether these costs translate into deleterious effects in natural habitats is less certain however. Previously, fitness effects of resistance mutations were mostly characterized in nutrient-rich, fast-growth conditions, which bacteria rarely encounter in natural habitats. Carbon, phosphate, iron or oxygen limitations are conditions met by bacterial pathogens in various compartments of the human body...
October 2017: Environmental Microbiology Reports
Mamoru Oshiki, Keisuke Mizuto, Zen-Ichiro Kimura, Tomonori Kindaichi, Hisashi Satoh, Satoshi Okabe
Anaerobic ammonium-oxidizing (anammox) bacteria affiliated with the genus 'Candidatus Scalindua' are responsible for significant nitrogen loss in oceans, and thus their ecophysiology is of great interest. Here, we enriched a marine anammox bacterium, 'Ca. S. japonica' from a Hiroshima bay sediment in Japan, and comparative genomic and proteomic analyses of 'Ca. S. japonica' were conducted. Sequence of the 4.81-Mb genome containing 4019 coding regions of genes (CDSs) composed of 47 contigs was determined. In the proteome, 1762 out of 4019 CDSs in the 'Ca...
September 11, 2017: Environmental Microbiology Reports
Daisuke Takamatsu, Aya Osawa, Keiko Nakamura, Mikio Yoshiyama, Masatoshi Okura
Melissococcus plutonius is the causative agent of European foulbrood of honey bee larvae. Among its three genetically distinct groups (CC3, CC12 and CC13), CC3 strains have been suggested to be more virulent at the colony level. Honey bee larvae are fed royal or worker jellies by adult bees, and these jellies exhibit antimicrobial activity. Since M. plutonius orally infects larvae via brood food, we herein investigated the resistance of M. plutonius to the antimicrobial activity of royal jelly (RJ). The results obtained revealed that M...
September 11, 2017: Environmental Microbiology Reports
Jessica Tout, Carmen Astudillo-García, Michael W Taylor, Gene W Tyson, Roman Stocker, Peter J Ralph, Justin R Seymour, Nicole S Webster
Marine sponges host stable and species-specific microbial symbionts that are thought to be acquired and maintained by the host through a combination of vertical transmission and filtration from the surrounding seawater. To assess whether the microbial symbionts also actively contribute to the establishment of these symbioses, we performed in situ experiments on Orpheus Island, Great Barrier Reef, to quantify the chemotactic responses of natural populations of seawater microorganisms towards cellular extracts of the reef sponge Rhopaloeides odorabile...
September 11, 2017: Environmental Microbiology Reports
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