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Environmental Microbiology

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https://www.readbyqxmd.com/read/29230925/novel-pressure-sensors-and-bioreporters-in-the-synthetic-biology-era
#1
Miguel A Matilla
No abstract text is available yet for this article.
December 12, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29215213/identifying-protist-consumers-of-photosynthetic-picoeukaryotes-in-the-surface-ocean-using-stable-isotope-probing
#2
William D Orsi, Susanne Wilken, Javier Del Campo, Thierry Heger, Erick James, Thomas A Richards, Patrick J Keeling, Alexandra Z Worden, Alyson E Santoro
Photosynthetic picoeukaryotes contribute a significant fraction of primary production in the upper ocean. Micromonas pusilla is an ecologically relevant photosynthetic picoeukaryote, abundantly and widely distributed in marine waters. Grazing by protists may control the abundance of picoeukaryotes such as M. pusilla, but the diversity of the responsible grazers is poorly understood. To identify protists consuming photosynthetic picoeukaryotes in a productive North Pacific Ocean region, we amended seawater with living 15 N, 13 C-labeled M...
December 7, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29215193/metabolomics-of-tomato-xylem-sap-during-bacterial-wilt-reveals-ralstonia-solanacearum-produces-abundant-putrescine-a-metabolite-that-accelerates-wilt-disease
#3
Tiffany M Lowe-Power, Connor G Hendrich, Edda von Roepenack-Lahaye, Bin Li, Dousheng Wu, Raka Mitra, Beth L Dalsing, Patrizia Ricca, Jacinth Naidoo, David Cook, Amy Jancewicz, Patrick Masson, Bart Thomma, Thomas Lahaye, Anthony J Michael, Caitilyn Allen
Ralstonia solanacearum thrives in plant xylem vessels and causes bacterial wilt disease despite the low nutrient content of xylem sap. We found that R. solanacearum manipulates its host to increase nutrients in tomato xylem sap, enabling it to grow better in sap from infected plants than in sap from healthy plants. Untargeted GC/MS metabolomics identified 22 metabolites enriched in R. solanacearum-infected sap. Eight of these could serve as sole carbon or nitrogen sources for R. solanacearum. Putrescine, a polyamine that is not a sole carbon or nitrogen source for R...
December 7, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29215192/forest-conversion-induces-seasonal-variation-in-microbial-%C3%AE-diversity
#4
Shengen Liu, Hang Wang, Ye Deng, Peng Tian, Qingkui Wang
World-wide conversion of natural forests to other land uses has profound effects on soil microbial communities. However, how soil microbial β-diversity responds to land-use change and its driving mechanisms remains poorly understood. In this study, therefore, we examined the effect of forest conversion from native broad-leaved forest to coniferous plantation on soil microbial β-diversity and its underlying mechanisms in both summer and winter in subtropical China. Microbial communities increasingly differed in structure as geographical distance between them increased, and the slope of the relationship among distances and community similarity differed among forest covers...
December 7, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29215190/organohalide-respiration-in-pristine-environments-implications-for-the-natural-halogen-cycle
#5
Siavash Atashgahi, Max M Häggblom, Hauke Smidt
Halogenated organic compounds, also termed organohalogens, were initially considered to be of almost exclusively anthropogenic origin. However, over 5000 naturally-synthesized organohalogens are known today. This has also fuelled the hypothesis that the natural and ancient origin of organohalogens could have primed development of metabolic machineries for their degradation, especially in microorganisms. Among these, a special group of anaerobic microorganisms was discovered that could conserve energy by reducing organohalogens as terminal electron acceptor in a process termed organohalide respiration...
December 7, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29205750/spatially-distinct-temporally-stable-microbial-populations-mediate-biogeochemical-cycling-at-and-below-the-seafloor-in-hydrothermal-vent-fluids
#6
Caroline S Fortunato, Benjamin Larson, David A Butterfield, Julie A Huber
At deep-sea hydrothermal vents, microbial communities thrive across geochemical gradients above, at, and below the seafloor. In this study, we determined the gene content and transcription patterns of microbial communities and specific populations to understand the taxonomy and metabolism both spatially and temporally across geochemically different diffuse fluid hydrothermal vents. Vent fluids were examined via metagenomic, metatranscriptomic, genomic binning, and geochemical analyses from Axial Seamount, an active submarine volcano on the Juan de Fuca Ridge in the NE Pacific Ocean, from 2013-2015 at three different vents: Anemone, Marker 33, and Marker 113...
December 4, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194965/a-denitrifying-community-associated-with-a-major-marine-nitrogen-fixer
#7
Christopher J Coates, Michael Wyman
The diazotrophic cyanobacterium, Trichodesmium, is an integral component of the marine nitrogen cycle and contributes significant amounts of new nitrogen to oligotrophic, tropical/subtropical ocean surface waters. Trichodesmium forms macroscopic, fusiform (tufts), spherical (puffs) and raft-like colonies that provide a pseudobenthic habitat for a host of other organisms including marine invertebrates, microeukaryotes and numerous other microbes. The diversity and activity of denitrifying bacteria found in association with the colonies was interrogated using a series of molecular-based methodologies targeting the gene encoding the terminal step in the denitrification pathway, nitrous oxide reductase (nosZ)...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194950/multiplex-quantitative-silac-for-analysis-of-archaeal-proteomes-a-case-study-of-oxidative-stress-responses
#8
Lana J McMillan, Sungmin Hwang, Rawan E Farah, Jin Koh, Sixue Chen, Julie A Maupin-Furlow
Stable isotope labeling of amino acids in cell culture (SILAC) is a quantitative proteomic method that can illuminate new pathways used by cells to adapt to different lifestyles and niches. Archaea, while thriving in extreme environments and accounting for ∼20-40% of the Earth's biomass, have not been analyzed with the full potential of SILAC. Here we report SILAC for quantitative comparison of archaeal proteomes, using Haloferax volcanii as a model. A double auxotroph was generated that allowed for complete incorporation of 13 C/15 N-lysine and 13 C-arginine such that each peptide digested with trypsin was labeled...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194931/antibiotic-resistome-in-a-large-scale-healthy-human-gut-microbiota-deciphered-by-metagenomic-and-network-analyses
#9
Jie Feng, Bing Li, Xiaotao Jiang, Ying Yang, George F Wells, Tong Zhang, Xiaoyan Li
The human gut microbiota is an important reservoir of antibiotic resistance genes (ARGs). A metagenomic approach and network analysis were used to establish a comprehensive antibiotic resistome catalog and to obtain co-occurrence patterns between ARGs and microbial taxa in fecal samples from 180 healthy individuals from 11 different countries. In total, 507 ARG subtypes belonging to 20 ARG types were detected with abundances ranging from 7.12 × 10-7 to 2.72 × 10-1 copy of ARG/copy of 16S-rRNA gene. Tetracycline, multidrug, macrolide-lincosamide-streptogramin, bacitracin, vancomycin, beta-lactam and aminoglycoside resistance genes were the top seven most abundant ARG types...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194930/metabolic-versatility-of-a-novel-n2-fixing-alphaproteobacterium-isolated-from-a-marine-oxygen-minimum-zone
#10
Clara Martínez-Pérez, Wiebke Mohr, Anne Schwedt, Julia Dürschlag, Cameron M Callbeck, Harald Schunck, Julien Dekaezemacker, Caroline R T Buckner, Gaute Lavik, Bernhard M Fuchs, Marcel M M Kuypers
The N2 -fixing (diazotrophic) community in marine ecosystems is dominated by non-cyanobacterial microorganisms. Yet, very little is known about their identity, function and ecological relevance due to a lack of cultured representatives. Here we report a novel heterotrophic diazotroph isolated from the oxygen minimum zone (OMZ) off Peru. The new species belongs to the genus Sagittula (Rhodobacteraceae, Alphaproteobacteria) and its capability to fix N2 was confirmed in laboratory experiments. Genome sequencing revealed that it is a strict heterotroph with a high versatility in substrate utilization and energy acquisition mechanisms...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194923/tracking-active-groundwater-microbes-with-d2-o-labeling-to-understand-their-ecosystem-function
#11
Martin Taubert, Stephan Stöckel, Patricia Geesink, Sophie Girnus, Nico Jehmlich, Martin von Bergen, Petra Rösch, Jürgen Popp, Kirsten Küsel
Microbial activity is key in understanding the contribution of microbial communities to ecosystem functions. Metabolic labeling with heavy water (D2 O) leads to the formation of carbon-deuterium bonds in active microorganisms. We illustrated how D2 O labeling allows monitoring of metabolic activity combined with a functional characterization of active populations in complex microbial communities. First, we demonstrated by single cell Raman microspectroscopy that all measured bacterial cells from groundwater isolates growing in complex medium with D2 O were labeled...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194919/a-novel-chromatiales-bacterium-is-a-potential-sulfide-oxidizer-in-multiple-orders-of-marine-sponges
#12
Adi Lavy, Ray Keren, Ke Yu, Brian C Thomas, Lisa Alvarez-Cohen, Jillian F Banfield, Micha Ilan
Sponges are benthic filter feeders that play pivotal roles in coupling benthic-pelagic processes in the oceans that involve transformation of dissolved and particulate organic carbon and nitrogen into biomass. While the contribution of sponge holobionts to the nitrogen cycle has been recognized in past years, their importance in the sulfur cycle, both oceanic and physiological, has only recently gained attention. Sponges in general, and Theonella swinhoei in particular, harbor a multitude of associated microorganisms that could affect sulfur cycling within the holobiont...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194914/cell-cell-recognition-and-social-networking-in-bacteria
#13
Vera Troselj, Pengbo Cao, Daniel Wall
The ability to recognize self and to recognize partnering cells allows microorganisms to build social networks that perform functions beyond the capabilities of the individual. In bacteria, recognition typically involves genetic determinants that provide cell surface receptors or diffusible signaling chemicals to identify proximal cells at the molecular level that can participate in cooperative processes. Social networks also rely on discriminating mechanisms to exclude competing cells from joining and exploiting their groups...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194913/regulation-of-nod-factor-biosynthesis-by-alternative-nodd-proteins-at-distinct-stages-of-symbiosis-provides-additional-compatibility-scrutiny
#14
Simon Kelly, John T Sullivan, Yasuyuki Kawaharada, Simona Radutoiu, Clive W Ronson, Jens Stougaard
The Lotus japonicus symbiont Mesorhizobium loti R7A encodes two copies of nodD and here we identify striking differences in Nod factor biosynthesis gene induction by NodD1 and NodD2 both in vitro and in planta. We demonstrate that induction of Nod factor biosynthesis genes is preferentially controlled by NodD1 and NodD2 at specific stages of symbiotic infection. NodD2 is primarily responsible for induction in the rhizosphere and within nodules, while NodD1 is primarily responsible for induction within root hair infection threads...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29194907/100-days-of-marine-synechococcus-ruegeria-pomeroyi-interaction-a-detailed-analysis-of-the-exoproteome
#15
Amandeep Kaur, Juan R Hernandez-Fernaud, Maria Del Mar Aguilo-Ferretjans, Elizabeth M Wellington, Joseph A Christie-Oleza
Marine phototroph and heterotroph interactions are vital in maintaining the nutrient balance in the oceans as essential nutrients need to be rapidly cycled before sinking to aphotic layers. The aim of this study was to highlight the molecular mechanisms that drive these interactions. For this we generated a detailed exoproteomic time-course analysis of a 100-day co-culture between the model marine picocyanobacterium Synechococcus sp. WH7803 and the Roseobacter strain Ruegeria pomeroyi DSS-3, both in nutrient-enriched and natural oligotrophic seawater...
December 1, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29160034/free-living-chemoautotrophic-and-particle-attached-heterotrophic-prokaryotes-dominate-microbial-assemblages-along-a-pelagic-redox-gradient
#16
Elizabeth A Suter, Maria Pachiadaki, Gordon T Taylor, Yrene Astor, Virginia P Edgcomb
Using the anoxic Cariaco Basin as a natural laboratory, particle association of bacterial and archaeal taxa was assessed by iTag sequencing and qPCR gene assays of samples spanning an oxic-anoxic-euxinic gradient. Ten to twelve percent of all bacterial and archaeal cells were found in the particle-associated (PA) fraction, operationally defined as prokaryotes captured on 2.7µm membranes. Both redox condition and size fraction segregated bacterial taxa. Archaeal taxa varied according to redox conditions, but were similar between size fractions...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29160027/identification-of-syntrophobacteraceae-as-major-acetate-degrading-sulfate-reducing-bacteria-in-italian-paddy-soil
#17
Pengfei Liu, Bianca Pommerenke, Ralf Conrad
Methane is an important greenhouse gas and acetate is the most important intermediate (average 70%) of the carbon flow to CH4 in paddy fields. Sulfate (e.g., gypsum) application can reduce CH4 emissions up to 70%. However, the effect of gypsum application on acetate degradation and the microbial communities involved are unclear. Therefore, we studied acetate-dependent sulfate reduction in anoxic microcosms of Italian rice paddy soil, combining profiling of 16S rRNA and dissimilatory sulfite reductase (dsrB) genes and transcripts and rRNA based stable isotope probing (SIP) analysis...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29160003/two-new-viruses-mcv1-and-mcv2-which-infect-marinitoga-bacteria-isolated-from-deep-sea-hydrothermal-vents-functional-and-genomic-analysis
#18
C Mercier, J Lossouarn, C L Nesbø, T H A Haverkamp, A C Baudoux, M Jebbar, N Bienvenu, S Thiroux, S Dupont, C Geslin
Viruses represent a driving force in the evolution of microorganisms including those thriving in extreme environments. However, our knowledge of the viral diversity associated to microorganisms inhabiting the deep-sea hydrothermal vents remains limited. The phylum of Thermotogae, including thermophilic bacteria, is well represented in this environment. Only one virus was described in this phylum, MPV1 carried by Marinitoga piezophila. In this study, we report on the functional and genomic characterization of two new bacterioviruses that infect bacteria from the Marinitoga genus...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29159997/sporulation-capability-and-amylosome-conservation-among-diverse-human-colonic-and-rumen-isolates-of-the-keystone-starch-degrader-ruminococcus-bromii
#19
Indrani Mukhopadhya, Sarah Morais, Jenny Laverde-Gomez, Paul O Sheridan, Alan W Walker, William Kelly, Athol V Klieve, Diane Ouwerkerk, Sylvia H Duncan, Petra Louis, Nicole Koropatkin, Darrell Cockburn, Ryan Kibler, Philip J Cooper, Carlos Sandoval, Emmanuelle Crost, Nathalie Juge, Edward A Bayer, Harry J Flint
Ruminococcus bromii is a dominant member of the human colonic microbiota that plays a 'keystone' role in degrading dietary resistant starch. Recent evidence from one strain has uncovered a unique cell surface 'amylosome' complex that organizes starch-degrading enzymes. New genome analysis presented here reveals further features of this complex and shows remarkable conservation of amylosome components between human colonic strains from three different continents and a R. bromii strain from the rumen of Australian cattle...
November 21, 2017: Environmental Microbiology
https://www.readbyqxmd.com/read/29159973/diverse-effect-of-phosphatidylcholine-biosynthetic-genes-on-phospholipid-homeostasis-cell-autophagy-and-fungal-developments-in-metarhizium-robertsii
#20
Yixiong Chen, Bing Li, Kai Cen, Yuzhen Lu, Siwei Zhang, Chengshu Wang
Phosphatidylcholine (PC) plays an important role in maintaining membrane integrity and functionality. In this study, two key genes (Mrpct and Mrpem) putatively involved in the cytidine diphosphate (CDP)-choline and phosphatidylethanolamine N-methyltransferase (PEMT) pathways for PC biosynthesis were characterized in the insect pathogenic fungus Metarhizium robertsii. The results indicated that disruption of Mrpct did not lead to any reduction of total PC content but impaired fungal virulence and increased cellular accumulation of triacylglycerol...
November 21, 2017: Environmental Microbiology
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