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Environmental Microbiology

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https://www.readbyqxmd.com/read/29659156/mosaic-patterns-of-b-vitamin-synthesis-and-utilization-in-a-natural-marine-microbial-community
#1
Laura Gómez-Consarnau, Rohan Sachdeva, Scott M Gifford, Lynda S Cutter, Jed A Fuhrman, Sergio A Sañudo-Wilhelmy, Mary Ann Moran
Aquatic environments contain large communities of microorganisms whose synergistic interactions mediate the cycling of major and trace nutrients, including vitamins. B-vitamins are essential coenzymes that many organisms cannot synthesize. Thus their exchange among de-novo synthesizers and auxotrophs is expected to play an important role in the microbial consortia and explain some of the temporal and spatial changes observed in diversity. In this study, we analyzed metatranscriptomes of a natural marine coastal microbial community, diel sampled quarterly over one year to try to identify the potential major B-vitamin synthesizers and consumers...
April 16, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29659127/launching-environmental-microbiology-the-most-effective-way-to-do-it-is-to-do-it
#2
Amanda McLean-Inglis, Simon Rallison
No abstract text is available yet for this article.
April 16, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29633519/genome-based-evolutionary-history-of-pseudomonas-spp
#3
Cedar Hesse, Frederik Schulz, Carolee T Bull, Brenda T Shaffer, Qing Yan, Nicole Shapiro, Karl A Hassan, Neha Varghese, Liam D H Elbourne, Ian T Paulsen, Nikos Kyrpides, Tanja Woyke, Joyce E Loper
Pseudomonas is a large and diverse genus of Gammaproteobacteria. To provide a framework for discovery of evolutionary and taxonomic relationships of these bacteria, we compared the genomes of type strains of 163 species and 3 additional subspecies of Pseudomonas, including 118 genomes sequenced herein. A maximum likelihood phylogeny of the 166 type strains based on protein sequences of 100 single-copy orthologous genes revealed thirteen groups of Pseudomonas, composed of two to sixty six species each. Pairwise average nucleotide identities (ANI) and alignment fractions (AF) were calculated for the dataset of the 166 type strains and 1223 genomes of Pseudomonas available in public databases...
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29633455/colonization-of-medical-devices-by-staphylococci
#4
Yue Zheng, Lei He, Titus K Asiamah, Michael Otto
The use of medical devices in modern medicine is constantly increasing. Despite the multiple precautionary strategies that are being employed in hospitals, which include increased hygiene and sterilization measures, bacterial infections on these devices still happen frequently. Staphylococci are among the major causes of medical device infection. This is mostly due to the strong capacity of those bacteria to form device-associated biofilms, which provide resistance to chemical and physical treatments as well as attacks by the host's immune system...
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29626385/microbial-conservation-in-the-anthropocene
#5
EDITORIAL
Nicole S Webster, Michael Wagner, Andrew P Negri
No abstract text is available yet for this article.
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29626380/the-arbuscular-mycorrhizal-fungus-rhizophagus-irregularis-uses-a-reductive-iron-assimilation-pathway-for-high-affinity-iron-uptake
#6
Elisabeth Tamayo, Simon A B Knight, Ascensión Valderas, Andrew Dancis, Nuria Ferrol
Arbuscular mycorrhizal (AM) fungi can improve iron (Fe) acquisition of their host plants. Here, we report a characterization of two components of the high-affinity reductive Fe uptake system of Rhizophagus irregularis, the ferric reductase (RiFRE1) and the high affinity Fe permeases (RiFTR1-2). In the extraradical mycelia (ERM), Fe deficiency induced activation of a plasma membrane-localized ferric reductase, an enzyme that reduces Fe(III) sources to the more soluble Fe(II). Yeast mutant complementation assays showed that RiFRE1 encodes a functional ferric reductase and RiFTR1 an iron permease...
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29626379/patterns-of-thaumarchaeal-gene-expression-in-culture-and-diverse-marine-environments
#7
Paul Carini, Christopher L Dupont, Alyson E Santoro
Thaumarchaea are ubiquitous in marine habitats where they participate in carbon and nitrogen cycling. Although metatranscriptomes suggest thaumarchaea are active microbes in marine waters, we understand little about how thaumarchaeal gene expression patterns relate to substrate utilization and activity. Here, we report the global transcriptional response of the marine ammonia-oxidizing thaumarchaeon 'Candidatus Nitrosopelagicus brevis' str. CN25 to ammonia limitation using RNA-Seq. We further describe the genome and transcriptome of Ca...
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29626371/phosphodiesterase-pded-dynacortin-and-a-kelch-repeat-containing-protein-are-direct-gsk3-substrates-in-dictyostelium-that-contribute-to-chemotaxis-towards-camp
#8
Kimberly Baumgardner, Connie Lin, Richard A Firtel, Jesus Lacal
The migration of cells according to a diffusible chemical signal in their environment is called chemotaxis, and the slime mold Dictyostelium discoideum is widely used for the study of eukaryotic chemotaxis. Dictyostelium must sense chemicals, such as cAMP, secreted during starvation to move toward the sources of the signal. Previous work demonstrated that the gskA gene encodes the Dictyostelium homologue of glycogen synthase kinase 3 (GSK3), a highly conserved serine/threonine kinase, which plays a major role in the regulation of Dictyostelium chemotaxis...
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29626370/environmental-microbiology-too-much-food-for-thought-an-argument-for-reductionism
#9
Harald Brüssow
With the explosion of DNA sequencing and information technology, environmental microbiology goes through a big data driven period. In view of the central role of bacteriophages in the development of microbiology and molecular biology and their emerging role in ecosystem functioning, an argument is formulated to complement this trend of complexity inventorisation by a renewed reductionist approach. It is proposed to investigate the interaction of three biological model systems that are naturally linked, namely phage T4 infecting Escherichia coli colonizing the gut of mice, using molecular cell biology techniques at an organismal level...
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29624877/electron-acceptors-for-anaerobic-oxidation-of-methane-drive-microbial-community-structure-and-diversity-in-mud-volcanoes
#10
Ge Ren, Anzhou Ma, Yanfen Zhang, Ye Deng, Guodong Zheng, Xuliang Zhuang, Guoqiang Zhuang, Danielle Fortin
Mud volcanoes (MVs) emit globally significant quantities of methane into the atmosphere, however, methane cycling in such environments is not yet fully understood, as the roles of microbes and their associated biogeochemical processes have been largely overlooked. Here, we used data from high-throughput sequencing of microbial 16S rRNA gene amplicons from six MVs in the Junggar Basin in northwest China to quantify patterns of diversity and characterize the community structure of archaea and bacteria. We found anaerobic methanotrophs and diverse sulfate- and iron-reducing microbes in all of the samples, and the diversity of both archaeal and bacterial communities was strongly linked to the concentrations of sulfate, iron, and nitrate, which could act as electron acceptors in anaerobic oxidation of methane (AOM)...
April 6, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29614214/a-planktonic-diatom-displays-genetic-structure-over-small-spatial-scales
#11
Josefin Sefbom, Anke Kremp, Karin Rengefors, Per R Jonsson, Conny Sjöqvist, Anna Godhe
Marine planktonic microalgae have potentially global dispersal, yet reduced gene flow has been confirmed repeatedly for several species. Over larger distances (>200 km) geographic isolation and restricted oceanographic connectivity have been recognized as instrumental in driving population divergence. Here we investigated whether similar patterns, i.e. structured populations governed by geographic isolation and/or oceanographic connectivity, can be observed at smaller (6-152 km) geographic scales. To test this we established 425 clonal cultures of the planktonic diatom Skeletonema marinoi collected from 11 locations in the Archipelago Sea (northern Baltic Sea)...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29614213/what-will-it-take-to-understand-the-ecology-of-symbiotic-microorganisms
#12
Angela E Douglas
Many microbial taxa associated with healthy animals have both within-host and free-living populations, but little is known about the magnitude, persistence and dispersal of their populations in the external environment. Advances, particularly in our understanding of the population dynamics of free-living populations and microbial cycling between the external environment and hosts, can be achieved by the creative use of current technologies. In particular, there are opportunities to adapt methods, such as capture-mark-release techniques widely used in animal ecology, to the study of symbiotic microorganisms...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29614212/the-key-gluconeogenic-gene-pck1-is-crucial-for-virulence-of-botrytis-cinerea-via-initiating-its-conidial-germination-and-host-penetration
#13
Jian-Kang Liu, Hao-Wu Chang, Yue Liu, Yu Haity Qin, Ming-Zhe Zhang, Sheng-Nan Cao, Le-Tao Li, Wei Liu, Gui-Hua Li, Qing-Ming Qin
The process of initiation of host invasion and survival of some foliar phytopathogenic fungi in the absence of external nutrients on host leaf surfaces remains obscure. Here, we demonstrate that gluconeogenesis plays an important role in the process and nutrient-starvation adaptation before the pathogen host invasion. Deletion of phosphoenolpyruvate carboxykinase gene BcPCK1 in gluconeogenesis in Botrytis cinerea, the causative agent of gray mold, resulted in the failure of the ΔBcpck1 mutant conidia to germinate on hard and hydrophobic surface and penetrate host cells in the absence of glucose, reduction in conidiation, and slow conidium germination in a nutrient-rich medium...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29614211/histamine-catabolism-in-pseudomonas-putida-u-identification-of-the-genes-catabolic-enzymes-and-regulators
#14
Manuel de la Torre, José L Gómez-Botrán, Elías R Olivera, Francisco Bermejo, Joaquín Rodríguez-Morán, José M Luengo
In this study, the catabolic pathway required for the degradation of the biogenic amine histamine (Hin) was genetically and biochemically characterized in Pseudomonas putida U. The 11 proteins (HinABCDGHFLIJK) that participate in this pathway are encoded by genes belonging to three loci hin1, hin2 and hin3 and by the gene hinK. The enzymes HinABCD catalyze the transport and oxidative deamination of histamine to 4-imidazoleacetic acid (ImAA). This reaction is coupled to those of other well-known enzymatic systems (DadXAR and CoxBA-C) that ensure both the recovery of the pyruvate required for Hin deamination and the genesis of the energy needed for Hin uptake...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29614210/evidence-for-selective-bacterial-community-structuring-on-microplastics
#15
Martin Ogonowski, Asa Motiei, Karolina Ininbergs, Eva Hell, Zandra Gerdes, Klas I Udekwu, Zoltan Bacsik, Elena Gorokhova
In aquatic ecosystems, microplastics are a relatively new anthropogenic substrate that can readily be colonized by biofilm-forming organisms. To examine the effects of substrate type on microbial community assembly, we exposed ambient Baltic bacterioplankton to plastic substrates commonly found in marine environments (polyethylene, polypropylene, and polystyrene) as well as native (cellulose) and inert (glass beads) particles for two weeks under controlled conditions. The source microbial communities and those of the biofilms were analyzed by Illumina sequencing of the 16S rRNA gene libraries...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29614209/plant-potassium-nutrition-in-ectomycorrhizal-symbiosis-properties-and-roles-of-the-three-fungal-tok-potassium-channels-in-hebeloma-cylindrosporum
#16
Carmen Guerrero-Galán, Amandine Delteil, Kevin Garcia, Gabriella Houdinet, Genevieve Conéjéro, Isabelle Gaillard, Hervé Sentenac, Sabine D Zimmermann
Ectomycorrhizal fungi play an essential role in the ecology of boreal and temperate forests through the improvement of tree mineral nutrition. Potassium (K+ ) is an essential nutrient for plants and is needed in high amounts. We recently demonstrated that the ectomycorrhizal fungus Hebeloma cylindrosporum improves the K+ nutrition of Pinus pinaster under shortage conditions. Part of the transport systems involved in K+ uptake by the fungus has been deciphered, while the molecular players responsible for the transfer of this cation towards the plant remain totally unknown...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29614208/ecological-medicine
#17
Jack A Gilbert
No abstract text is available yet for this article.
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29611894/unravelling-a-new-catabolic-pathway-of-c-19-steroids-in-mycobacterium-smegmatis
#18
Lorena Fernández-Cabezón, Beatriz Galán, José L García
In this work, we have characterized the C-19+ gene cluster (MSMEG_2851 to MSMEG_2901) of Mycobacterium smegmatis. By in silico analysis we have identified the genes encoding enzymes involved in the modification of the A/B steroid rings during the catabolism of C-19 steroids in certain M. smegmatis mutants mapped in the PadR-like regulator (MSMEG_2868), that constitutively express the C-19+ gene cluster. By using gene complementation assays, resting-cell biotransformations and deletion mutants, we have characterized the most critical genes of the cluster, i...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29611893/comparative-proteome-analysis-of-propionate-degradation-by-syntrophobacter-fumaroxidans-in-pure-culture-and-in-coculture-with-methanogens
#19
Vicente T Sedano-Núñez, Sjef Boeren, Alfons J M Stams, Caroline M Plugge
Syntrophobacter fumaroxidans is a sulfate-reducing bacterium able to grow on propionate axenically or in syntrophic interaction with methanogens or other sulfate-reducing bacteria. We performed a proteome analysis of S. fumaroxidans growing with propionate axenically with sulfate or fumarate, and in syntrophy with Methanospirillum hungatei, Methanobacterium formicicum or Desulfovibrio desulfuricans. Special attention was put on the role of hydrogen and formate in interspecies electron transfer (IET) and energy conservation...
April 3, 2018: Environmental Microbiology
https://www.readbyqxmd.com/read/29578272/pleased-to-edit-you-discovering-the-world-of-science-as-a-journal-editor
#20
EDITORIAL
(no author information available yet)
No abstract text is available yet for this article.
March 26, 2018: Environmental Microbiology
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