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Environmental Microbiology

Pasquale Filannino, Maria De Angelis, Raffaella Di Cagno, Giorgia Gozzi, Ylenia Riciputi, Marco Gobbetti
Triplets of Lactobacullus plantarum strains were isolated from nine contrasting habitats. Without any passage through other culture media, isolation and cultivation were on model media that strictly reproduced the chemical and physical conditions and stressors of the habitats of origin. Here, we demonstrated how L. plantarum regulates and shapes its transcriptome in response to contrasting habitats. Firstly, multivariate clustering analysis of transcriptional data (RNA-Seq), complemented with metabolomics and phenomics, grouped the strains according to the habitats of origin...
August 9, 2018: Environmental Microbiology
Dave Stahl
No abstract text is available yet for this article.
August 7, 2018: Environmental Microbiology
Trine Markussen, Elisabeth M Happel, Jonna E Teikari, Vimala Huchaiah, Johannes Alneberg, Anders F Andersson, Kaarina Sivonen, Lasse Riemann, Mathias Middelboe, Veljo Kisand
Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination of genetic responses of the entire microbial community to environmental change. However, it is challenging to link metagenomes directly to biogeochemical process rates. Here, we investigate metagenomic responses in natural bacterioplankton communities to simulated environmental stressors in the Baltic Sea, including increased river water input, increased nutrient concentration, and reduced oxygen level...
August 6, 2018: Environmental Microbiology
Antonia Herrero, Enrique Flores
Heterocyst-forming cyanobacteria are filamentous organisms that perform oxygenic photosynthesis and CO2 fixation in vegetative cells and nitrogen fixation in heterocysts, which are formed under deprivation of combined nitrogen. These organisms can acclimate to use different sources of nitrogen and respond to different levels of CO2 . Following work mainly done with the best studied heterocyst-forming cyanobacterium, Anabaena, here we summarize the mechanisms of assimilation of ammonium, nitrate, urea and N2 , the latter involving heterocyst differentiation, and describe aspects of CO2 assimilation that involves a carbon concentration mechanism...
August 1, 2018: Environmental Microbiology
Kojadinovic-Sirinelli Mila, Villain Adrien, Puppo Carine, Fon Sing Sophie, Prioretti Laura, Hubert Pierre, Grégori Gérald, Zhang Yizhi, Sassi Jean-François, Claverie Jean-Michel, Blanc Guillaume, Gontero Brigitte
Most of our knowledge on the mechanisms underlying diatom-bacterial interactions has been acquired through studies involving isolation of culturable partners. Here, we established a laboratory model of intermediate complexity between complex natural communities and laboratory pure culture models. We investigated the whole community formed by the freshwater diatom Asterionella formosa and its associated bacteria in a laboratory context, including both culturable and unculturable bacteria. Combining cellular and molecular approaches, we showed that in laboratory cultures, A...
July 31, 2018: Environmental Microbiology
Letícia B Matter, Miguel A Ares, Judith Abundes-Gallegos, María L Cedillo, Jorge A Yáñez, Martínez Laguna Ygnacio, Miguel A De la Cruz, Jorge A Girón
Avian pathogenic Escherichia coli (APEC) causes localized and systemic avian infections and is responsible for considerable economic losses in the poultry industry. This organism adheres and invades human and avian cells however the regulatory networks that dictate its virulence are largely unknown. The CpxRA two-component system is responsible for sensing and controlling outer-membrane stress and detecting misfolded proteins in the bacterial periplasmic space. CpxA is a membrane sensor kinase and CpxR is a cytoplasmic transcriptional regulator...
July 30, 2018: Environmental Microbiology
Sophia Wirth, Maritta Kunert, Lisa-Marija Ahrens, Katrin Krause, Selina Broska, Christian Paetz, Olaf Kniemeyer, Elke-Martina Jung, Wilhelm Boland, Erika Kothe
The regulator of G-protein signaling, Thn1, is involved in sexual development through pheromone signaling in the mushroom forming basidiomycete Schizophyllum commune affecting hyphal morphology and mating interactions. Thn1 plays a key role in coordinating sesquiterpene production, pheromone response and sexual development. The gene thn1 is transcriptionally regulated in response to mating with a role in clamp cell development and hydrophobin gene transcription. Further, it negatively regulates cAMP signaling and secondary metabolism...
July 30, 2018: Environmental Microbiology
Jin-Li Ding, Yue-Jin Peng, Xin-Ling Chu, Ming-Guang Feng, Sheng-Hua Ying
Autophagy is a conserved degradation system in eukaryotic cells that includes non-selective and selective processes. Selective autophagy functions as a selective degradation mechanism for specific substrates in which autophagy-related protein 11 (ATG11) acts as an essential scaffold protein. In B. bassiana, there is a unique ATG11 family protein, which is designated as BbATG11. Disruption of BbATG11 resulted in significantly reduced conidial germination under starvation stress. The mutant ΔBbATG11 displayed enhanced sensitivity to oxidative stress and impaired asexual reproduction...
July 30, 2018: Environmental Microbiology
C Bryce, N Blackwell, C Schmidt, J Otte, Y Huang, S Kleindienst, E Tomaszewski, M Schad, V Warter, C Peng, J M Byrne, A Kappler
Iron is the most abundant redox-active metal in the Earth's crust. The one electron transfer between the two most common redox states, Fe(II) and Fe(III), plays a role in a huge range of environmental processes from mineral formation and dissolution to contaminant remediation and global biogeochemical cycling. It has been appreciated for more than a century that microorganisms can harness the energy of this Fe redox transformation for their metabolic benefit. However, this is most widely understood for anaerobic Fe(III)-reducing or aerobic and microaerophilic Fe(II)-oxidizing bacteria...
July 30, 2018: Environmental Microbiology
Saray Santamaría-Hernando, José Juan Rodríguez-Herva, Pedro M Martínez-García, Isabel Río-Álvarez, Pablo Gonzalez-Melendi, Jaime Zamorano, Carlos Tapia, Pablo Rodríguez-Palenzuela, Emilia López-Solanilla
Light is pervasive in the leaf environment, creating opportunities for both plants and pathogens to cue into light as a signal to regulate plant-microbe interactions. Light enhances plant defenses and regulates opening of stomata, an entry point for foliar bacterial pathogens such as Pseudomonas syringae pv. tomato DC3000 (PsPto). The effect of light perception on gene expression and virulence was investigated in PsPto. Light induced genetic reprogramming in PsPto that entailed significant changes in stress tolerance and virulence...
July 30, 2018: Environmental Microbiology
Qiuyuan Liu, Yidong Liu, Zhaoqi Kang, Dan Xiao, Chao Gao, Ping Xu, Cuiqing Ma
2,3-Butanediol (2,3-BD) is a primary microbial metabolite that enhances the virulence of Pseudomonas aeruginosa and alters the lung microbiome. 2,3-BD exists in three stereoisomeric forms: (2R,3R)-2,3-BD, meso-2,3-BD, and (2S,3S)-2,3-BD. In this study, we investigated whether and how P. aeruginosa PAO1 utilizes these 2,3-BD stereoisomers and showed that all three stereoisomers were transformed into acetoin by (2R,3R)-2,3-butanediol dehydrogenase (BDH) or (2S,3S)-2,3-BDH. Acetoin was cleaved to form acetyl-CoA and acetaldehyde by acetoin dehydrogenase enzyme system (AoDH ES)...
July 30, 2018: Environmental Microbiology
Albert L Müller, Claus Pelikan, Julia R de Rezende, Kenneth Wasmund, Martina Putz, Clemens Glombitza, Kasper U Kjeldsen, Bo Barker Jørgensen, Alexander Loy
Seafloor microorganisms impact global carbon cycling by mineralizing vast quantities of organic matter (OM) from pelagic primary production, which is predicted to increase in the Arctic because of diminishing sea ice cover. We studied microbial interspecies-carbon-flow during anaerobic OM degradation in arctic marine sediment using stable isotope probing. We supplemented sediment incubations with 13 C-labeled cyanobacterial necromass (spirulina), mimicking fresh OM input, or acetate, an important OM degradation intermediate, and monitored sulfate reduction rates and concentrations of volatile fatty acids (VFAs) during substrate degradation...
July 26, 2018: Environmental Microbiology
Francisca C García, María Ll Calleja, Najwa Al-Otaibi, Anders Røstad, Xosé Anxelu G Morán
The ecological status of an ecosystem can be approached by the taxa present but also by the size of individual organisms. In aquatic ecosystems, flow cytometry (FC) allows to study the individual size spectra and broad community composition through the evaluation of cytometric categories. The Red Sea represents a warm oligotrophic environment with a strong diel signal of vertically migrating mesopelagic fish, which feed at night at the surface and release dissolved organic carbon (DOC) at depth during day-time...
July 26, 2018: Environmental Microbiology
Kathryn M Docherty, Douglas S Pearce, Kristina M Lemmer, Rebecca L Hale
Airborne bacteria are abundant and can vary with land use. Urban expansion is increasing rapidly at a global scale, altering natural sources of airborne bacterial biodiversity, as soils and native plants are replaced by pavement and managed yards. Urbanization homogenizes the biodiversity of larger organisms, but its effects are understudied with respect to microbes. This study uses categorical and gradient approaches to examine airborne bacterial communities in southwest Michigan (USA). Airborne communities carried a gut-microbial signature and were equally homogenous above urban and rural sites, despite greater homogeneity of soil communities at urban sites...
July 26, 2018: Environmental Microbiology
Ximao Lin, Yayi Wang, Xiao Ma, Yuan Yan, Min Wu, Philip L Bond, Jianhua Guo
Low temperature is recognized as one of the major barriers for the application of the anaerobic ammonium oxidation (anammox) process to treat mainstream wastewater. Studies are yet to reveal the underlying biological limitations and molecular mechanisms associated with the inhibition of low temperature on the anammox process. In this study, metaproteomics was used to examine proteome modulation patterns of the anammox community occurring at different temperatures. The anammox community remarkably altered their proteomes when the temperature decreased from 35 to 20°C...
July 26, 2018: Environmental Microbiology
Yanglei Yi, Zhibo Li, Chunxu Song, Oscar P Kuipers
Bacillus subtilis HS3 and Bacillus mycoides EC18 are two rhizosphere-associated bacteria with plant growth-promoting activity. The CRISPR-Cas9 system was implemented to study various aspects of plant-microbe interaction mechanisms of these two environmental isolates. The results show that fengycin and surfactin are involved in the antifungal activity of B. subtilis HS3. Moreover, this strain emits several other volatile organic compounds (VOCs) than 2,3-butanediol, contributing to plant growth promotion. CLSM (Confocal laser scanning microscopy) observations of the GFP-labelled strain showed that HS3 selectively colonizes root hairs of grass (Lolium perenne) in a hydroponic system...
July 26, 2018: Environmental Microbiology
Eric Kuhnert, Yan Li, Nan Lan, Qun Yue, Li Chen, Russell J Cox, Zhiqiang An, Kenichi Yokoyama, Gerald F Bills
Enfumafungin is a glycosylated fernene-type triterpenoid produced by the fungus Hormonema carpetanum. Its potent antifungal activity, mediated by its interaction with β-1,3-glucan synthase and the fungal cell wall, has led to its development into the semi-synthetic clinical candidate, SCY-078. We report on the preliminary identification of the enfumafungin biosynthetic gene cluster (BGC) based on genome sequencing, phylogenetic reconstruction, gene disruption, and cDNA sequencing studies. Enfumafungin synthase (efuA) consists of a terpene cyclase domain (TC) fused to a glycosyltransferase (GT) domain and thus represents a novel multifunctional enzyme...
July 26, 2018: Environmental Microbiology
Matilde Fernández, Andrés Corral-Lugo, Tino Krell
The interference of plant compounds with bacterial quorum sensing (QS) is a major mechanism through which plants and bacteria communicate. However, little is known about the modes of action and effects on signal integrity during this type of communication. We have recently shown that the plant compound rosmarinic acid (RA) specifically binds to the Pseudomonas aeruginosa RhlR QS receptor. To determine the effect of RA on expression patterns, we carried out global RNA-seq analysis. The results show that RA induces the expression of 128 genes, amongst which many virulence factor genes...
July 26, 2018: Environmental Microbiology
Shawna McCallin, Shafiqul A Sarker, Shamima Sultana, Frank Oechslin, Harald Brüssow
Bacteriophage therapy is a commonly used treatment for Staphylococcus aureus infections in countries of the former Soviet Union, using both single phages and phage cocktails. The scarce data available on Eastern phage cocktails prompted an investigation into commercially-available Pyophage cocktails from two different manufacturers used to treat skin and wound infections. Comparison of the metagenomic composition of two Pyophage products from Georgia and Russia revealed substantial differences in phage-types targeting Escherichia, Enterococcus, Salmonella, Pseudomonas aeruginosa, and Proteus, therefore indicating multiple strategies for composing phage cocktails against these bacterial pathogens...
July 26, 2018: Environmental Microbiology
Ye Deng, Daliang Ning, Yujia Qin, Kai Xue, Liyou Wu, Zhili He, Huaqun Yin, Yuting Liang, Vanessa Buzzard, Sean T Michaletz, Jizhong Zhou
Temperature is an important correlate of global patterns of biodiversity, yet the mechanisms driving these relationships are not well understood. Taxa-area relationships (TARs) have been intensively examined, but the effects of temperature on TARs, particularly for microbial communities, are largely undocumented. Here we present a continental-scale description of temperature-dependent nested TARs of microbial communities (bacteria and archaea) from soils of six forest sites spanning a temperature gradient from subalpine Colorado to tropical Panama...
July 26, 2018: Environmental Microbiology
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