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Environmental Microbiology Reports

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https://www.readbyqxmd.com/read/28429584/dna-metabarcoding-of-unfractionated-water-samples-relates-phyto-zoo-and-bacterioplankton-dynamics-and-reveals-a-single-taxon-bacterial-bloom
#1
Christian Wurzbacher, Katrin Attermeyer, Marie Therese Kettner, Clara Flintrop, Norman Warthmann, Sabine Hilt, Hans-Peter Grossart, Michael T Monaghan
Most studies of aquatic plankton focus on either macroscopic or microbial communities, and on either eukaryotes or prokaryotes. This separation is primarily for methodological reasons, but can overlook potential interactions among groups. We tested whether DNA metabarcoding of unfractionated water samples with universal primers could be used to qualitatively and quantitatively study the temporal dynamics of the total plankton community in a shallow temperate lake. We found significant changes in the relative proportions of normalized sequence reads of eukaryotic and prokaryotic plankton communities over a three-month period in spring...
April 21, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28418094/the-skin-microbiome-of-the-common-thresher-shark-alopias-vulpinus-has-low-taxonomic-and-potential-metabolic-%C3%AE-diversity
#2
Michael P Doane, John Matthew Haggerty, Dovi Kacev, Bhavya Papudeshi, Elizabeth A Dinsdale
The health of sharks is linked with emergent properties of its microbiome. Most marine organisms have mucus overlying the skin, but shark have dermal denticles that protrude above the mucus. We characterized the microbiome from the skin of the common thresher shark (Alopias vulpinus) to investigate the structure and composition of the skin microbiome. An average of 618,812 reads per metagenomic library contained open reading frames (80.9% ± S.D. 0.44%), and 7.6 to 12.8% matched known protein sequences...
April 18, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28419783/high-occurrence-of-bathyarchaeota-mcg-in-the-deep-sea-sediments-of-south-china-sea-quantified-using-newly-designed-pcr-primers
#3
Tiantian Yu, Qianyong Liang, Mingyang Niu, Fengping Wang
The archaeal phylum Bathyarchaeota, which is composed of a large number of diverse lineages, is widespread and abundant in marine sediments. Environmental factors that control the distribution, abundance, and evolution of this largely diversified archaeal phylum are currently unclear. In this study, a new pair of specific primers that target the major marine subgroups of bathyarchaeotal 16S rRNA genes was designed and evaluated to investigate the distribution and abundance of Bathyarchaeota in marine sediments...
April 17, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28419734/the-life-sulfuric-microbial-ecology-of-sulfur-cycling-in-marine-sediments
#4
REVIEW
Kenneth Wasmund, Marc Mußmann, Alexander Loy
Almost the entire seafloor is covered with sediments that can be more than 10,000 m thick and represent a vast microbial ecosystem that is a major component of Earth's element and energy cycles. Notably, a significant proportion of microbial life in marine sediments can exploit energy conserved during transformations of sulfur compounds among different redox states. Sulfur cycling, which is primarily driven by sulfate reduction, is tightly interwoven with other important element cycles (carbon, nitrogen, iron, manganese) and therefore has profound implications for both cellular- and ecosystem-level processes...
April 17, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28401694/effects-of-grazing-phosphorus-and-light-on-the-growth-rates-of-major-bacterioplankton-taxa-in-the-coastal-nw-mediterranean
#5
Olga Sánchez, Michal Koblížek, Josep M Gasol, Isabel Ferrera
Estimation of growth rates is crucial to understand the ecological role of prokaryotes and their contribution to marine biogeochemical cycling. However, there are only a few estimates for individual taxa. Two top-down (grazing) and bottom-up (phosphorus (P) availability) manipulation experiments were conducted under different light regimes in the NW Mediterranean Sea. Growth rate of different phylogenetic groups, including the Bacteroidetes, Rhodobacteraceae, SAR11, Gammaproteobacteria and its subgroups Alteromonadaceae and the NOR5/OM60 clade, were estimated from changes in cell numbers...
April 12, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28401690/oxygen-and-the-activity-and-distribution-of-marine-thaumarchaeota
#6
James T Hollibaugh
No abstract text is available yet for this article.
April 12, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28345298/effects-of-t-loop-modification-on-the-pii-signaling-protein-structure-of-uridylylated-escherichia-coli-glnb-bound-to-atp
#7
Carles Palanca, Vicente Rubio
To adapt to environments with variable nitrogen sources and richness, the widely distributed homotrimeric PII signaling proteins bind their allosteric effectors ADP/ATP/2-oxoglutarate, and experience nitrogen-sensitive uridylylation of their flexible T-loops at Tyr51, regulating their interactions with effector proteins. To clarify whether uridylylation triggers a given T-loop conformation, we determined the crystal structure of the classical paradigm of PII protein, Escherichia coli GlnB (EcGlnB), in fully uridylylated form (EcGlnB-UMP3 )...
March 26, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28296273/cyclic-di-gmp-signalling-meets-extracellular-polysaccharide-synthesis-in-bacillus-subtilis
#8
Jan Kampf, Jörg Stülke
In order to resist harmful environmental conditions, many bacteria form multicellular aggregates called biofilms. In these biofilms, they protect themselves in a self-produced matrix consisting of extracellular polysaccharides, proteins and DNA. In many bacteria, biofilm formation is stimulated in the presence of the second messenger cyclic di-GMP. In this issue of Environmental Microbiology Reports, Bedrunka and Graumann have studied matrix production by the proteins encoded in the Bacillus subtilis ydaJKLMN operon...
March 13, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28296199/antibiotics-in-the-environment-an-annotated-selection-of-world-wide-web-sites-relevant-to-the-topics-in-environmental-microbiology
#9
Lawrence P Wackett
No abstract text is available yet for this article.
March 13, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28294562/hierarchical-mutational-events-compensate-for-glutamate-auxotrophy-of-a-bacillus-subtilis-gltc-mutant
#10
Miriam Dormeyer, Anastasia L Lübke, Peter Müller, Sabine Lentes, Daniel R Reuß, Andrea Thürmer, Jörg Stülke, Rolf Daniel, Sabine Brantl, Fabian M Commichau
Glutamate is the major donor of nitrogen for anabolic reactions. The Gram-positive soil bacterium Bacillus subtilis either utilizes exogenously provided glutamate or synthesizes it using the gltAB-encoded glutamate synthase (GOGAT). In the absence of glutamate, the transcription factor GltC activates expression of the GOGAT genes for glutamate production. Consequently, a gltC mutant strain is auxotrophic for glutamate. Using a genetic selection and screening system, we could isolate and differentiate between gltC suppressor mutants in one step...
March 13, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28276199/new-insights-into-a-hot-environment-for-early-life
#11
REVIEW
Jianghong Dai
Investigating the physical-chemical setting of early life is a challenging task. In this contribution, the author attempted to introduce a provocative concept from cosmology - cosmic microwave background (CMB), which is the residual thermal radiation from a hot early Universe - to the field. For this purpose, the author revisited a recently deduced biomarker, the 1,6-anhydro bond of sugars in bacteria. In vitro, the 1,6-anhydro bond of sugars reflects and captures residual thermal radiation in thermochemical processes and therefore is somewhat analogous to CMB...
March 9, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28276162/novel-insights-into-ecological-distribution-and-plant-growth-promotion-by-nitrogen-fixing-endophytes-how-specialised-are-they
#12
Ray Dixon, Anton Hartmann
No abstract text is available yet for this article.
March 9, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28251810/the-water-channel-protein-aquaporin-1-regulates-cellular-metabolism-and-competitive-fitness-in-a-global-fungal-pathogen-cryptococcus-neoformans
#13
Gena Lee Meyers, Kwang-Woo Jung, Soohyun Bang, Jungyeon Kim, Sooah Kim, Joohyeon Hong, Eunji Cheong, Kyoung Heon Kim, Yong-Sun Bahn
In this study, an aquaporin protein, Aqp1, in Cryptococcus neoformans, which can lead either saprobic or parasitic lifestyles and causes life-threatening fungal meningitis was identified and characterized. AQP1 expression was rapidly induced (via the HOG pathway) by osmotic or oxidative stress. In spite of such transcriptional regulation, Aqp1 was found to be largely unnecessary for adaptation to diverse environmental stressors, regardless of the presence of the polysaccharide capsule. The latter is shown here to be a key environmental-stress protectant for C...
March 2, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28217926/reduction-oxidation-cycles-of-organic-matter-increase-bacterial-activity-in-the-pelagic-oxycline
#14
Maximilian P Lau, Michael Hupfer, Hans-Peter Grossart
Dissolved organic matter (DOM) in aquatic ecosystems contains redox-active moieties, which are prone to oxidation and reduction reactions. Oxidized moieties feature reduction potentials Eh , so that the moieties may be used as terminal electron acceptors (TEAs) in microbial respiration with a thermodynamic energy yield between nitrate and sulfate reduction. Here, we study the response of pelagic freshwater bacteria to exposure to native DOM with varying availabilities of oxidized moieties and hence redox state...
February 20, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28211189/influence-of-oxygen-availability-on-the-activities-of-ammonia-oxidizing-archaea
#15
Wei Qin, Kelley A Meinhardt, James W Moffett, Allan H Devol, E Virginia Armbrust, Anitra E Ingalls, David A Stahl
Recent studies point to the importance of oxygen (O2 ) in controlling the distribution and activity of marine ammonia-oxidizing archaea (AOA), one of the most abundant prokaryotes in the ocean. The AOA are associated with regions of low O2 tension in oceanic oxygen minimum zones (OMZs), and O2 availability is suggested to influence their production of the ozone-depleting greenhouse gas nitrous oxide (N2 O). We show that marine AOA available in pure culture sustain high ammonia oxidation activity at low μM O2 concentrations, characteristic of suboxic regions of OMZs (<10 µM O2 ), and that atmospheric concentrations of O2 may inhibit the growth of some environmental populations...
February 17, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28205388/hydrogen-or-formate-alternative-key-players-in-methanogenic-degradation
#16
REVIEW
Bernhard Schink, Dominik Montag, Anja Keller, Nicolai Müller
Hydrogen and formate are important electron carriers in methanogenic degradation in anoxic environments such as sediments, sewage sludge digestors, and biogas reactors. Especially in the terminal steps of methanogenesis, they determine the energy budgets of secondary (syntrophically) fermenting bacteria and their methanogenic partners. The literature provides considerable data on hydrogen pool sizes in such habitats, but little data exist for formate concentrations due to technical difficulties in formate determination at low concentration...
February 15, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28185400/microdiversity-shapes-the-traits-niche-space-and-biogeography-of-microbial-taxa
#17
REVIEW
Alyse A Larkin, Adam C Martiny
With rapidly improving sequencing technologies, scientists have recently gained the ability to examine diverse microbial communities at high genomic resolution, revealing that both free-living and host-associated microbes partition their environment at fine phylogenetic scales. This 'microdiversity,' or closely related (> 97% similar 16S rRNA gene) but ecologically and physiologically distinct sub-taxonomic groups, appears to be an intrinsic property of microorganisms. However, the functional implications of microdiversity as well as its effects on microbial biogeography are poorly understood...
February 10, 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/27894159/phylogenetic-and-ecological-diversity-of-apusomonads-a-lineage-of-deep-branching-eukaryotes
#18
Guifré Torruella, David Moreira, Purificación López-García
Apusomonads are a mysterious group of heterotrophic gliding biflagellates branching deeply in the eukaryotic tree of life as sister group to opisthokonts (including animals, fungi, and a variety of unicellular protists). Despite their evolutionary interest, their diversity and ecology remain largely unknown, with very few described species and environmental sequences in databases. Most environmental 18S rRNA gene-based studies generally fail to identify apusomonad sequences, which might be due to primer bias, low abundance, and/or to the fact that their biotopes remain poorly explored...
April 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28225574/the-future-of-environmental-microbiology-an-annotated-selection-of-world-wide-web-sites-relevant-to-the-topics-in-environmental-microbiology
#19
Lawrence P Wackett
No abstract text is available yet for this article.
February 2017: Environmental Microbiology Reports
https://www.readbyqxmd.com/read/28225573/corrigendum
#20
(no author information available yet)
No abstract text is available yet for this article.
February 2017: Environmental Microbiology Reports
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