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https://www.readbyqxmd.com/read/28812698/urbanization-erodes-ectomycorrhizal-fungal-diversity-and-may-cause-microbial-communities-to-converge
#1
Dietrich J Epp Schmidt, Richard Pouyat, Katalin Szlavecz, Heikki Setälä, D Johan Kotze, Ian Yesilonis, Sarel Cilliers, Erzsébet Hornung, Miklós Dombos, Stephanie A Yarwood
Urbanization alters the physicochemical environment, introduces non-native species and causes ecosystem characteristics to converge. It has been speculated that these alterations contribute to loss of regional and global biodiversity, but so far most urban studies have assessed macro-organisms and reported mixed evidence for biodiversity loss. We studied five cities on three continents to assess the global convergence of urban soil microbial communities. We determined the extent to which communities of bacteria, archaea and fungi are geographically distributed, and to what extent urbanization acts as a filter on species diversity...
April 10, 2017: Nature ecology & evolution
https://www.readbyqxmd.com/read/28812261/backbone-and-side-chain-1-h-15-n-and-13-c-resonance-assignments-of-two-sac10b-family-members-mvo10b-and-mth10btqqa-from-archaea
#2
Jinsong Xuan, Hongwei Yao, Yingang Feng, Jinfeng Wang
The Sac10b family proteins, also named as Alba, are small, basic, nucleic acid-binding proteins widely distributed in archaea. They possess divergent physiological functions such as binding to both DNA and RNA with a high affinity and involving in genomic DNA compaction, RNA transactions and transcriptional regulations. The structures of many Sac10b family proteins from hyperthermophilic archaea have been reported, while those from thermophilic and mesophilic archaea are largely unknown. As was pointed out, the homologous members from thermophilic and mesophilic archaea may have functions different from the hyperthermophilic members...
August 16, 2017: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/28809486/assembling-glycan-charged-dolichol-phosphates-chemoenzymatic-synthesis-of-a-haloferax-volcanii-n-glycosylation-pathway-intermediate
#3
Yifat Elharar, Ananda R Podilapu, Ziqiang Guan, Suvarn S Kulkarni, Jerry Eichler
N-glycosylation, the covalent attachment of glycans to select protein target Asn residues, is a post-translational modification performed by all three domains of life. In the halophilic archaea Haloferax volcanii, where understanding of this universal protein-processing event is relatively well-advanced, genes encoding the components of the Agl (archaeal glycosylation) pathway responsible for the assembly and attachment of an N-linked pentasaccharide have been identified. As elsewhere, the N-linked glycan is assembled on phosphodolichol carriers before transfer to target Asn residues...
August 15, 2017: Bioconjugate Chemistry
https://www.readbyqxmd.com/read/28808742/a-more-comprehensive-community-of%C3%A2-ammonia-oxidizing-archaea-aoa-revealed-by-genomic-dna-and-rna-analyses-of-amoa-gene-in-subtropical-acidic-forest-soils
#4
Ruo-Nan Wu, Han Meng, Yong-Feng Wang, Wensheng Lan, Ji-Dong Gu
Ammonia-oxidizing bacteria (AOB) and archaea (AOA) are the main nitrifiers which are well studied in natural environments, and AOA frequently outnumber AOB by orders especially in acidic conditions, making AOA the most promising ammonia oxidizers. The phylogeny of AOA revealed in related studies, however, often varied and hardly reach a consensus on functional phylotypes. The objective of this study was to compare ammonia-oxidizing communities by amoA gene and transcript based on both genomic DNA and RNA in extremely acidic forest soils (pH <4...
August 14, 2017: Microbial Ecology
https://www.readbyqxmd.com/read/28808230/environmental-drivers-of-a-microbial-genomic-transition-zone-in-the-ocean-s-interior
#5
Daniel R Mende, Jessica A Bryant, Frank O Aylward, John M Eppley, Torben Nielsen, David M Karl, Edward F DeLong
The core properties of microbial genomes, including GC content and genome size, are known to vary widely among different bacteria and archaea (1,2) . Several hypotheses have been proposed to explain this genomic variability, but the fundamental drivers that shape bacterial and archaeal genomic properties remain uncertain (3-7) . Here, we report the existence of a sharp genomic transition zone below the photic zone, where bacterial and archaeal genomes and proteomes undergo a community-wide punctuated shift...
August 14, 2017: Nature Microbiology
https://www.readbyqxmd.com/read/28808132/defining-electron-bifurcation-in-the-electron-transferring-flavoprotein-family
#6
Amaya M Garcia Costas, Saroj Poudel, Anne-Frances Miller, Gerrit J Schut, Rhesa N Ledbetter, Kathryn R Fixen, Lance C Seefeldt, Michael W W Adams, Caroline S Harwood, Eric S Boyd, John W Peters
Electron bifurcation is the coupling of exergonic and endergonic redox reactions to simultaneously generate (or utilize) low and high potential electrons. It is the third recognized form of energy conservation in biology and has recently been described in select electron transferring flavoproteins (Etfs). Etfs are flavin-containing heterodimers best known for donating electrons derived from fatty acid and amino acid oxidation to an electron transfer respiratory chain via ETF quinone oxidoreductase. Canonical examples contain a flavin adenine dinucleotide (FAD) that is involved in electron transfer as well as a non-redox active adenosine monophosphate (AMP)...
August 14, 2017: Journal of Bacteriology
https://www.readbyqxmd.com/read/28803698/genomics-and-ecology-of-novel-n2o-reducing-microorganisms
#7
REVIEW
Sara Hallin, Laurent Philippot, Frank E Löffler, Robert A Sanford, Christopher M Jones
Microorganisms with the capacity to reduce the greenhouse gas nitrous oxide (N2O) to harmless dinitrogen gas are receiving increased attention due to increasing N2O emissions (and our need to mitigate climate change) and to recent discoveries of novel N2O-reducing bacteria and archaea. The diversity of denitrifying and nondenitrifying microorganisms with capacity for N2O reduction was recently shown to be greater than previously expected. A formerly overlooked group (clade II) in the environment include a large fraction of nondenitrifying N2O reducers, which could be N2O sinks without major contribution to N2O formation...
August 10, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28799297/exploring-the-microbial-diversity-in-jordanian-hot-springs-by-comparative-metagenomic-analysis
#8
Emad I Hussein, Jacob H Jacob, Muhamad Ali K Shakhatreh, Mutaz A Abd Al-Razaq, Abdul-Salam F Juhmani, Christopher T Cornelison
A culture-independent approach was utilized in this study to reveal the microbial diversity in Jordanian hot springs represented by Ma'in and Afra hot springs. Water samples from Ma'in and Afra hot springs were collected in June 2015. The in situ temperature of water samples range was 38-59°C and the pH range was 7.4-8.4. The metagenome was extracted and analyzed using the next generation technology (bTEFAP(®) ). A total of 314,310 sequences were parsed and 288,452 were then clustered. The sequences were predominated by bacteria (>84%) and the relative abundance of archaea in each sample was <1%...
August 10, 2017: MicrobiologyOpen
https://www.readbyqxmd.com/read/28798731/mechanisms-and-regulation-of-extracellular-dna-release-and-its-biological-roles-in-microbial-communities
#9
REVIEW
Alejandra L Ibáñez de Aldecoa, Olga Zafra, José E González-Pastor
The capacity to release genetic material into the extracellular medium has been reported in cultures of numerous species of bacteria, archaea, and fungi, and also in the context of multicellular microbial communities such as biofilms. Moreover, extracellular DNA (eDNA) of microbial origin is widespread in natural aquatic and terrestrial environments. Different specific mechanisms are involved in eDNA release, such as autolysis and active secretion, as well as through its association with membrane vesicles. It is noteworthy that in microorganisms, in which DNA release has been studied in detail, the production of eDNA is coordinated by the population when it reaches a certain cell density, and is induced in a subpopulation in response to the accumulation of quorum sensing signals...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798309/quantitative-response-relationships-between-net-nitrogen-transformation-rates-and-nitrogen-functional-genes-during-artificial-vegetation-restoration-following-agricultural-abandonment
#10
Honglei Wang, Na Deng, Duoyang Wu, Shu Hu
A comprehensive understanding of how microbial associated with nitrogen (N) cycling respond to artificial vegetation restoration is still lacking, particularly in arid to semi-arid degraded ecosystems. We compared soil net N mineralization rates and the abundance of bacteria, archaea, and eleven N microbial genes on the northern Loess Plateau of China during the process of artificial vegetation restoration. The quantitative relationships between net N mineralization rates and N microbial genes were determined...
August 10, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28798133/structure-of-histone-based-chromatin-in-archaea
#11
Francesca Mattiroli, Sudipta Bhattacharyya, Pamela N Dyer, Alison E White, Kathleen Sandman, Brett W Burkhart, Kyle R Byrne, Thomas Lee, Natalie G Ahn, Thomas J Santangelo, John N Reeve, Karolin Luger
Small basic proteins present in most Archaea share a common ancestor with the eukaryotic core histones. We report the crystal structure of an archaeal histone-DNA complex. DNA wraps around an extended polymer, formed by archaeal histone homodimers, in a quasi-continuous superhelix with the same geometry as DNA in the eukaryotic nucleosome. Substitutions of a conserved glycine at the interface of adjacent protein layers destabilize archaeal chromatin, reduce growth rate, and impair transcription regulation, confirming the biological importance of the polymeric structure...
August 11, 2017: Science
https://www.readbyqxmd.com/read/28798101/genomic-exploration-of-the-diversity-ecology-and-evolution-of-the-archaeal-domain-of-life
#12
REVIEW
Anja Spang, Eva F Caceres, Thijs J G Ettema
About 40 years ago, Archaea were recognized as a major prokaryotic domain of life besides Bacteria. Recently, cultivation-independent sequencing methods have produced a wealth of genomic data for previously unidentified archaeal lineages, several of which appear to represent newly revealed branches in the tree of life. Analyses of some recently obtained genomes have uncovered previously unknown metabolic traits and provided insights into the evolution of archaea and their relationship to eukaryotes. On the basis of our current understanding, much archaeal diversity still defies genomic exploration...
August 11, 2017: Science
https://www.readbyqxmd.com/read/28798063/alignment-of-the-protein-substrate-hairpin-along-the-seca-two-helix-finger-primes-protein-transport-in-escherichia-coli
#13
Qi Zhang, Sudipta Lahiri, Tithi Banerjee, Zhongmou Sun, Donald Oliver, Ishita Mukerji
A conserved hairpin-like structure comprised of a signal peptide and early mature region initiates protein transport across the SecY or Sec61α channel in Bacteria or Archaea and Eukarya, respectively. When and how this initiator substrate hairpin forms remains a mystery. Here, we have used the bacterial SecA ATPase motor protein and SecYEG channel complex to address this question. Engineering of a functional miniprotein substrate onto the end of SecA allowed us to efficiently form ternary complexes with SecYEG for spectroscopic studies...
August 10, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/28797902/effects-of-microcystins-contamination-on-soil-enzyme-activities-and-microbial-community-in-two-typical-lakeside-soils
#14
Qing Cao, Alan D Steinman, Xiaomei Su, Liqiang Xie
A 30-day indoor incubation experiment was conducted to investigate the effects of different concentrations of microcystin (1, 10, 100 and 1000 μg eq. MC-LR L(-1)) on soil enzyme activity, soil respiration, physiological profiles, potential nitrification, and microbial abundance (total bacteria, total fungi, ammonia-oxidizing bacteria and archaea) in two lakeside soils in China (Soil A from the lakeside of Lake Poyanghu at Jiujiang; Soil B from the lakeside of Lake Taihu at Suzhou). Of the enzymes tested, only phenol oxidase activity was negatively affected by microcystin application...
August 7, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28794466/a-family-of-archaea-like-carboxylesterases-preferentially-expressed-in-the-symbiotic-phase-of-the-mychorrizal-fungus-tuber-melanosporum
#15
Davide Cavazzini, Guido Grossi, Elisabetta Levati, Francesca Vallese, Barbara Montanini, Angelo Bolchi, Giuseppe Zanotti, Simone Ottonello
An increasing number of esterases is being revealed by (meta) genomic sequencing projects, but few of them are functionally/structurally characterized, especially enzymes of fungal origin. Starting from a three-member gene family of secreted putative "lipases/esterases" preferentially expressed in the symbiotic phase of the mycorrhizal fungus Tuber melanosporum ("black truffle"), we show here that these enzymes (TmelEST1-3) are dimeric, heat-resistant carboxylesterases capable of hydrolyzing various short/medium chain p-nitrophenyl esters...
August 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28792539/active-microorganisms-thrive-among-extremely-diverse-communities-in-cloud-water
#16
Pierre Amato, Muriel Joly, Ludovic Besaury, Anne Oudart, Najwa Taib, Anne I Moné, Laurent Deguillaume, Anne-Marie Delort, Didier Debroas
Clouds are key components in Earth's functioning. In addition of acting as obstacles to light radiations and chemical reactors, they are possible atmospheric oases for airborne microorganisms, providing water, nutrients and paths to the ground. Microbial activity was previously detected in clouds, but the microbial community that is active in situ remains unknown. Here, microbial communities in cloud water collected at puy de Dôme Mountain's meteorological station (1465 m altitude, France) were fixed upon sampling and examined by high-throughput sequencing from DNA and RNA extracts, so as to identify active species among community members...
2017: PloS One
https://www.readbyqxmd.com/read/28791907/a-one-step-procedure-for-immobilising-the-thermostable-carbonic-anhydrase-sspca-on-the-surface-membrane-of-escherichia-coli
#17
Sonia Del Prete, Rosa Perfetto, Mosè Rossi, Fatmah A S Alasmary, Sameh M Osman, Zeid AlOthman, Claudiu T Supuran, Clemente Capasso
The carbonic anhydrase superfamily (CA, EC 4.2.1.1) of metalloenzymes is present in all three domains of life (Eubacteria, Archaea, and Eukarya), being an interesting example of convergent/divergent evolution, with its seven families (α-, β-, γ-, δ-, ζ-, η-, and θ-CAs) described so far. CAs catalyse the simple, but physiologically crucial reaction of carbon dioxide hydration to bicarbonate and protons. Recently, our groups characterised the α-CA from the thermophilic bacterium, Sulfurihydrogenibium yellowstonense finding a very high catalytic activity for the CO2 hydration reaction (kcat = 9...
December 2017: Journal of Enzyme Inhibition and Medicinal Chemistry
https://www.readbyqxmd.com/read/28790990/ammonia-oxidizing-archaea-are-more-resistant-than-denitrifiers-to-seasonal-precipitation-changes-in-an-acidic-subtropical-forest-soil
#18
Jie Chen, Yanxia Nie, Wei Liu, Zhengfeng Wang, Weijun Shen
Seasonal precipitation changes are increasingly severe in subtropical areas. However, the responses of soil nitrogen (N) cycle and its associated functional microorganisms to such precipitation changes remain unclear. In this study, two projected precipitation patterns were manipulated: intensifying the dry-season drought (DD) and extending the dry-season duration (ED) but increasing the wet-season storms following the DD and ED treatment period. The effects of these two contrasting precipitation patterns on soil net N transformation rates and functional gene abundances were quantitatively assessed through a resistance index...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28783564/improved-methane-production-from-sugarcane-vinasse-with-filter-cake-in-thermophilic-uasb-reactors-with-predominance-of-methanothermobacter-and-methanosarcina-archaea-and-thermotogae-bacteria
#19
Valciney Gomes de Barros, Rose Maria Duda, Juliana da Silva Vantini, Wellington Pine Omori, Maria Inês Tiraboschi Ferro, Roberto Alves de Oliveira
Biogas production from sugarcane vinasse has enormous economic, energy, and environmental management potential. However, methane production stability and biodigested vinasse quality remain key issues, requiring better nutrient and alkalinity availability, operational strategies, and knowledge of reactor microbiota. This study demonstrates increased methane production from vinasse through the use of sugarcane filter cake and improved effluent recirculation, with elevated organic loading rates (OLR) and good reactor stability...
July 24, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28781080/structural-analysis-of-a-family-81-glycoside-hydrolase-implicates-its-recognition-of-%C3%AE-1-3-glucan-quaternary-structure
#20
Benjamin Pluvinage, Alexander Fillo, Patricia Massel, Alisdair B Boraston
Family 81 glycoside hydrolases (GHs), which are known to cleave β-1,3-glucans, are found in archaea, bacteria, eukaryotes, and viruses. Here we examine the structural and functional features of the GH81 catalytic module, BhGH81, from the Bacillus halodurans protein BH0236 to probe the molecular basis of β-1,3-glucan recognition and cleavage. BhGH81 displayed activity on laminarin, curdlan, and pachyman, but not scleroglucan; the enzyme also cleaved β-1,3-glucooligosaccharides as small as β-1,3-glucotriose...
July 17, 2017: Structure
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