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Environmental Microbiology

Hye Yeon Koh, Hyun Park, Jun Hyuck Lee, Se Jong Han, Young Chang Sohn, Sung Gu Lee
Psychrobacter sp. PAMC 21119, isolated from Antarctic permafrost soil, grows and proliferates at subzero temperatures. However, its major mechanism of cold adaptation regulation remains poorly understood. We investigated the transcriptomic and proteomic responses of this species to cold temperatures by comparing profiles at -5°C and 20°C to understand how extreme microorganisms survive under subzero conditions. We found a total of 2,906 transcripts and 584 differentially expressed genes (≥ 2 fold, p <0...
October 17, 2016: Environmental Microbiology
S A Sarker, B Berger, Y Deng, S Kieser, F Foata, D Moine, P Descombes, S Sultana, S Huq, P K Bardhan, V Vuillet, F Praplan, H Brüssow
A T4-like coliphage cocktail was given with different oral doses to healthy Bangladeshi children in a placebo-controlled randomized phase I safety trial. Fecal phage detection was oral dose dependent suggesting passive gut transit of coliphages through the gut. No adverse effects of phage application were seen clinically and by clinical chemistry. Similar results were obtained for a commercial phage preparation (Coliproteus from Microgen/Russia). By 16S rRNA gene sequencing only a low degree of fecal microbiota conservation was seen in healthy children from Bangladesh who were sampled over a time interval of 7 days suggesting a substantial temporal fluctuation of the fecal microbiota composition...
October 17, 2016: Environmental Microbiology
Eva-Maria Niehaus, Lena Studt, Katharina W von Bargen, Wiebke Kummer, Hans-Ulrich Humpf, Gunter Reuter, Bettina Tudzynski
In this study, we compared the secondary metabolite profile of Fusarium fujikuroi and the histone deacetylase mutant ΔHDA1. We identified a novel peak in ΔHDA1, which was identified as beauvericin (BEA). Going in line with a 1000-fold increased BEA production, the respective non-ribosomal peptide synthetase (NRPS)-encoding gene (BEA1), as well as two adjacent genes (BEA2-BEA3), were significantly up-regulated in ΔHDA1 compared to the wild type. A special role was revealed for the ABC transporter Bea3: deletion of the encoding gene resulted in significant up-regulation of BEA1 and BEA2 and drastically elevated product yields...
October 17, 2016: Environmental Microbiology
Habiba Ennouri, Paul d'Abzac, Florence Hakil, Priscilla Branchu, Murielle Naïtali, Anne-Marie Lomenech, Rhida Oueslati, Jacques Desbrières, Pierre Sivadon, Régis Grimaud
The assimilation of the nearly water insoluble substrates hydrocarbons and lipids by bacteria entails specific adaptations such as the formation of oleolytic biofilms. The present article reports that the extracellular matrix of an oleolytic biofilm formed by Marinobacter hydrocarbonoclasticus at n-hexadecane-water interfaces is largely composed of proteins typically cytoplasmic such as translation factors and chaperones, and a lesser amount of proteins of unknown function that are predicted extra-cytoplasmic...
October 11, 2016: Environmental Microbiology
Peter Kupferschmied, Tiancong Chai, Pascale Flury, Jochen Blom, Theo H M Smits, Monika Maurhofer, Christoph Keel
Some plant-beneficial pseudomonads can invade and kill pest insects in addition to their ability to protect plants from phytopathogens. We explored the genetic basis of O-polysaccharide (O-PS, O-antigen) biosynthesis in the representative insecticidal strains Pseudomonas protegens CHA0 and Pseudomonas chlororaphis PCL1391 and investigated its role in insect pathogenicity. Both strains produce two distinct forms of O-PS, but differ in the organization of their O-PS biosynthesis clusters. Biosynthesis of the dominant O-PS in both strains depends on a gene cluster similar to the O-specific antigen (OSA) cluster of Pseudomonas aeruginosa...
October 11, 2016: Environmental Microbiology
Abhijit Sarkar, Marta Marszalkowska, Martin Schäfer, Tobias Pees, Hannah Klingenberg, Franziska Macht, Barbara Reinhold-Hurek
The endophyte Azoarcus sp. BH72, fixing nitrogen microaerobically, encounters low O2 -tensions in flooded roots. Therefore, its transcriptome upon shift to microaerobiosis was analyzed using oligonucleotide microarrays. 8.7% of the protein-coding genes were significantly modulated. Aerobic conditions induced expression of genes involved in oxidative stress protection, while under microaerobiosis 233 genes were up-regulated, encoding hypothetical proteins, transcriptional regulators, and proteins involved in energy metabolism, among them a cbb3 -type terminal oxidase contributing to but not essential for N2 -fixation...
October 11, 2016: Environmental Microbiology
Maryam Zamani, George C diCenzo, Branislava Milunovic, Turlough M Finan
We report that the smb20752 gene of the alfalfa symbiont Sinorhizobium meliloti is a novel symbiotic gene required for full N2 -fixation. Deletion of smb20752 resulted in lower nitrogenase activity and smaller nodules without impacting overall nodule morphology. Orthologs of smb20752 were present in all alpha and beta rhizobia, including the ngr_b20860 gene of Sinorhizobium fredii NGR234. A ngr_b20860 mutant formed Fix(-) determinate nodules that developed normally to a late stage of the symbiosis on the host plants Macroptillium atropurpureum and Vigna unguiculata...
October 11, 2016: Environmental Microbiology
Lizi Bensoussan, Sarah Moraïs, Bareket Dassa, Nir Friedman, Bernard Henrissat, Vincent Lombard, Edward A Bayer, Itzhak Mizrahi
The cellulosome is an extracellular multi-enzyme complex that is considered one of the most efficient plant cell wall-degrading strategies devised by nature. Its unique modular architecture, achieved by high affinity and specific interaction between protein modules (cohesins and dockerins) enables formation of various enzyme combinations. Extensive research has been dedicated to the mechanistic nature of the cellulosome complex. Nevertheless, little is known regarding its distribution and abundance among microbes in natural plant fiber-rich environments...
October 6, 2016: Environmental Microbiology
Arianna Smerilli, Ida Orefice, Federico Corato, Antonio Gavalás Olea, Alexander V Ruban, Christophe Brunet
Photosynthesis is known to produce reactive oxygen species together with the transformation of light into biochemical energy. To fill the gap of the knowledge on the protective antioxidant network of microalgae, we performed a series of experiments to explore the role of spectral composition and intensity of light in the modulation of the photodefence mechanisms developed by the coastal diatom Skeletonema marinoi. We analysed the modulation of the total phenolic content, ascorbic acid, and the enzymes glutathione reductase, catalase, ascorbate peroxidase and superoxide dismutase together with xanthophyll cycle and non-photochemical quenching in response to variations in the light environment...
October 6, 2016: Environmental Microbiology
M Romina Schiaffino, Enrique Lara, Leonardo D Fernández, Vanessa Balagué, David Singer, Christophe C W Seppey, Ramon Massana, Irina Izaguirre
Microbial eukaryotes play important roles in aquatic ecosystem functioning. Unravelling their distribution patterns and biogeography provides important baseline information to infer the underlying mechanisms that regulate the biodiversity and complexity of ecosystems. We studied the distribution patterns and factors driving diversity gradients in microeukaryote communities (total, abundant, uncommon and rare community composition) along a latitudinal gradient of lakes distributed from Argentinean Patagonia to Maritime Antarctica using both denaturing gradient gel electrophoresis (DGGE) and high-throughput sequencing (IlluminaHiSeq)...
October 6, 2016: Environmental Microbiology
Siavash Atashgahi, Yue Lu, Ying Zheng, Edoardo Saccenti, Maria Suarez-Diez, Javier Ramiro-Garcia, Heinrich Eisenmann, Martin Elsner, Alfons J M Stams, Dirk Springael, Winnie Dejonghe, Hauke Smidt
Biostimulation is widely used to enhance reductive dechlorination of chlorinated ethenes in contaminated aquifers. However, the knowledge on corresponding biogeochemical responses is limited. In this study, glycerol was injected in an aquifer contaminated with cis-dichloroethene (cDCE), and geochemical and microbial shifts were followed for 265 days. Consistent with anoxic conditions and sulfate reduction after biostimulation, MiSeq 16S rRNA gene sequencing revealed temporarily increased relative abundance of Firmicutes, Bacteriodetes and sulfate reducing Deltaproteobacteria...
October 6, 2016: Environmental Microbiology
Jaime Hernandez-Maldonado, Benjamin Sanchez-Sedillo, Brendon Stoneburner, Alison Boren, Laurence Miller, Shelley McCann, Michael Rosen, Ronald S Oremland, Chad W Saltikov
'Photoarsenotrophy', the use of arsenite as an electron donor for anoxygenic photosynthesis, is thought to be an ancient form of phototrophy along with the photosynthetic oxidation of Fe(II), H2 S, H2 and NO2-. Photoarsenotrophy was recently identified from Paoha Island's (Mono Lake, CA) arsenic-rich hot springs. The genomes of several photoarsenotrophs revealed a gene cluster, arxB2AB1CD, where arxA is predicted to encode for the sole arsenite oxidase. The role of arxA in photosynthetic arsenite oxidation was confirmed by disrupting the gene in a representative photoarsenotrophic bacterium, resulting in the loss of light-dependent arsenite oxidation...
October 6, 2016: Environmental Microbiology
James P Tauber, Volker Schroeckh, Ekaterina Shelest, Axel A Brakhage, Dirk Hoffmeister
Basidiomycete fungi are characterized ecologically for their vital functional role in ecosystem carbon recycling and chemically for their capacity to produce a diverse array of small molecules. Chromophoric natural products derived from the quinone precursor atromentin, such as variegatic acid and involutin, have been shown to function in redox cycling. Yet, in the context of an inter-kingdom natural system these pigments are still elusive. Here, we co-cultured the model saprotrophic basidiomycete Serpula lacrymans with an ubiquitous terrestrial bacterium, either Bacillus subtilis, Pseudomonas putida, or Streptomyces iranensis...
October 4, 2016: Environmental Microbiology
Maira P de Carvalho, Giuseppe Gulotta, Matheus W do Amaral, Heinrich Lünsdorf, Florenz Sasse, Wolf-Rainer Abraham
Pathogens embedded in biofilms are involved in many infections and are very difficult to treat with antibiotics because of higher resistance compared to planktonic cells. Therefore, new approaches for their control are urgently needed. One way to search for biofilm dispersing compounds is to look at defense strategies of organisms exposed to wet environments, which makes them prone to biofilm infections. It is reasonable to assume that mushrooms have developed mechanisms to control biofilms on their sporocarps (fruiting bodies)...
October 3, 2016: Environmental Microbiology
Fanny Larsonneur, Fernando A Martin, Adeline Mallet, Marta Martinez-Gil, Vincent Semetey, Jean-Marc Ghigo, Christophe Beloin
Initial adhesion of bacterial cells to surfaces or host tissues is a key step in colonisation and biofilm formation processes, and is mediated by cell surface appendages. We previously demonstrated that Escherichia coli K-12 possesses an arsenal of silenced chaperone-usher fimbriae that are functional when constitutively expressed. Among them, production of prevalent Yad fimbriae induces adhesion to abiotic surfaces. We undertook functional characterisation of Yad fimbriae, and identified YadN as the most abundant and potential major pilin, and YadC as the potential tip-protein of Yad fimbriae...
October 3, 2016: Environmental Microbiology
I Klawonn, N Nahar, J Walve, B Andersson, M Olofsson, B J Svedén, S Littmann, M J Whitehouse, Mmm Kuypers, H Ploug
We analysed N2 - and carbon (C) fixation in individual cells of Baltic Sea cyanobacteria by combining stable isotope incubations with secondary ion mass spectrometry (SIMS). Specific growth rates based on N2 - and C-fixation were higher for cells of Dolichospermum spp. than for Aphanizomenon sp. and Nodularia spumigena. The cyanobacterial biomass, however, was dominated by Aphanizomenon sp., which contributed most to total N2 -fixation in surface waters of the Northern Baltic Proper. N2 -fixation by Pseudanabaena sp...
October 1, 2016: Environmental Microbiology
Frances Medaney, Richard J Ellis, Ben Raymond
Bacterial plasmids are important carriers of virulence and antibiotic resistance genes. Nevertheless, we know little of the determinants of plasmid distribution in bacterial populations. Here we explored the factors affecting the diversity and distribution of the large plasmids of Escherichia coli in populations of cattle grazing on semi-natural grassland, a set of populations with low frequencies of antibiotic resistance genes. Critically, we also characterized the population genetic structure of bacterial hosts...
October 1, 2016: Environmental Microbiology
Nir Friedman, Eran Shriker, Ben Gold, Thomer Durman, Raphy Zarecki, Eytan Ruppin, Itzhak Mizrahi
Dietary changes are known to affect gut community structure, but questions remain about the mechanisms by which diet induces shifts in microbiome membership. Here we addressed these questions in the rumen microbiome ecosystem - a complex microbial community that resides in the upper digestive tract of ruminant animals and is responsible for the degradation of the ingested plant material. Our dietary intervention experiments revealed that diet affects the most abundant taxa within the microbiome and that a specific group of methanogenic archaea of the order Methanomicrobiales is highly sensitive to its changes...
October 1, 2016: Environmental Microbiology
Marcia F Marston, Jennifer B H Martiny
Understanding the structure and origin of natural bacteriophage genomic diversity is important in elucidating how bacteriophages influence the mortality rates and composition of their host communities. Here we examine the genetic structure and genomic diversification of naturally occurring bacteriophages by analyzing the full genomic sequences of over 100 isolates of Synechococcus-infecting cyanophages collected over 15 years from coastal waters of Southern New England, USA. Our analysis revealed well-supported cyanophage genomic clusters (genome-wide average nucleotide identity (ANI) >93%) and subclusters (genome-wide ANI >98%) that remained consistent for a decade or longer...
October 1, 2016: Environmental Microbiology
Alexandre Almeida, Cinthia Alves-Barroco, Elisabeth Sauvage, Ricardo Bexiga, Pedro Albuquerque, Fernando Tavares, Ilda Santos-Sanches, Philippe Glaser
Group B Streptococcus (GBS) is a host-generalist species, most notably causing disease in humans and cattle. However, the differential adaptation of GBS to its two main hosts, and the risk of animal to human infection remain poorly understood. Despite improvements in control measures across Europe, GBS is still one of the main causative agents of bovine mastitis in Portugal. Here, by whole-genome analysis of 150 bovine GBS isolates we discovered that a single CC61 clone is spreading throughout Portuguese herds since at least the early 1990s, having virtually replaced the previous GBS population...
October 1, 2016: Environmental Microbiology
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