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https://www.readbyqxmd.com/read/28338684/seven-enzymes-create-extraordinary-molecular-complexity-in-an-uncultivated-bacterium
#1
Michael F Freeman, Maximilian J Helf, Agneya Bhushan, Brandon I Morinaka, Jörn Piel
Uncultivated bacteria represent a massive resource of new enzymes and bioactive metabolites, but such bacteria remain functionally enigmatic. Polytheonamides are potent peptide cytotoxins produced by uncultivated bacteria that exist as symbionts in a marine sponge. Outside glycobiology, polytheonamides represent the most heavily post-translationally modified biomolecules that are derived from amino acids. The biosynthesis of polytheonamides involves up to 50 site-specific modifications to create a membrane-spanning β-helical structure...
April 2017: Nature Chemistry
https://www.readbyqxmd.com/read/28314620/selenium-speciation-in-seleniferous-agricultural-soils-under-different-cropping-systems-using-sequential-extraction-and-x-ray-absorption-spectroscopy
#2
Hai-Bo Qin, Jian-Ming Zhu, Zhi-Qing Lin, Wen-Po Xu, De-Can Tan, Li-Rong Zheng, Yoshio Takahashi
Selenium (Se) speciation in soil is critically important for understanding the solubility, mobility, bioavailability, and toxicity of Se in the environment. In this study, Se fractionation and chemical speciation in agricultural soils from seleniferous areas were investigated using the elaborate sequential extraction and X-ray absorption near-edge structure (XANES) spectroscopy. The speciation results quantified by XANES technique generally agreed with those obtained by sequential extraction, and the combination of both approaches can reliably characterize Se speciation in soils...
March 14, 2017: Environmental Pollution
https://www.readbyqxmd.com/read/28283818/genome-sequences-of-a-capulavirus-infecting-plantago-lanceolata-in-the-%C3%A3-land-archipelago-of-finland
#3
Hanna Susi, Anna-Liisa Laine, Denis Filloux, Simona Kraberger, Kata Farkas, Pauline Bernardo, Mikko J Frilander, Darren P Martin, Arvind Varsani, Philippe Roumagnac
The discovery and full-genome sequences of two isolates of a fourth capulavirus species are reported. The viruses were discovered during a viral metagenomics survey of uncultivated Plantago lanceolata plants in the Åland archipelago of south western Finland. The newly discovered viruses apparently produce no symptoms in P. lanceolata. They have a genome organization that is very similar to that of the three known capulavirus species and additionally share between 62.9 and 67.1% genome-wide sequence identity with the isolates of these species...
March 10, 2017: Archives of Virology
https://www.readbyqxmd.com/read/28278219/development-and-performance-assessment-of-a-luminex-xmap%C3%A2-direct-hybridization-assay-for-the-detection-and-identification-of-indoor-air-fungal-contamination
#4
Xavier Libert, Ann Packeu, Fabrice Bureau, Nancy H Roosens, Sigrid C J De Keersmaecker
Considered as a public health problem, indoor fungal contamination is generally monitored using classical protocols based on culturing. However, this culture dependency could influence the representativeness of the fungal population detected in an analyzed sample as this includes the dead and uncultivable fraction. Moreover, culture-based protocols are often time-consuming. In this context, molecular tools are a powerful alternative, especially those allowing multiplexing. In this study a Luminex xMAP® assay was developed for the simultaneous detection of 10 fungal species which are most frequently in indoor air and that may cause health problems...
2017: PloS One
https://www.readbyqxmd.com/read/28273103/functional-metagenomics-reveals-novel-%C3%AE-galactosidases-not-predictable-from-gene-sequences
#5
Jiujun Cheng, Tatyana Romantsov, Katja Engel, Andrew C Doxey, David R Rose, Josh D Neufeld, Trevor C Charles
The techniques of metagenomics have allowed researchers to access the genomic potential of uncultivated microbes, but there remain significant barriers to determination of gene function based on DNA sequence alone. Functional metagenomics, in which DNA is cloned and expressed in surrogate hosts, can overcome these barriers, and make important contributions to the discovery of novel enzymes. In this study, a soil metagenomic library carried in an IncP cosmid was used for functional complementation for β-galactosidase activity in both Sinorhizobium meliloti (α-Proteobacteria) and Escherichia coli (γ-Proteobacteria) backgrounds...
2017: PloS One
https://www.readbyqxmd.com/read/28254264/influence-of-nitrogen-rich-substrates-on-biogas-production-and-on-the-methanogenic-community-under-mesophilic-and-thermophilic-conditions
#6
Bernhard Munk, Georg M Guebitz, Michael Lebuhn
Grass silage was evaluated as a possible substrate in anaerobic digestion for generation of biogas in mesophilic and thermophilic long-term operation. Furthermore, the molecular biological parameter Metabolic Quotient (MQ) was evaluated as early warning system to predict process disturbance. Since this substrate is rich in nitrogen, high ammonia concentration of up to 2.2 g * kgFM(-1) emerged. The high buffer capacity of the ammonium/ammonia system can disguise upcoming process acidification. At organic loading rates (OLR) below 1...
February 22, 2017: Anaerobe
https://www.readbyqxmd.com/read/28220773/new-crispr-cas-systems-discovered
#7
Hui Yang, Dinshaw J Patel
In bacteria and archaea, CRISPR-Cas adaptive immune systems utilize RNA-guided endonucleases to defend against invasion by foreign nucleic acids of bacteriophage, virus and plasmid origin. In a recent paper published in Nature, Burstein et al. identified the first Cas9 protein in uncultivated archaea and two novel CRISPR-CasX and CRISPR-CasY systems in uncultivated bacteria by capitalizing on analysis of terabase-scale metagenomic datasets from natural uncultivated organisms.
March 2017: Cell Research
https://www.readbyqxmd.com/read/28211847/syntrophic-linkage-between-predatory-carpediemonas-and-specific-prokaryotic-populations
#8
Emmo Hamann, Halina E Tegetmeyer, Dietmar Riedel, Sten Littmann, Soeren Ahmerkamp, Jianwei Chen, Philipp F Hach, Marc Strous
Most anoxic environments are populated by small (<10 μm) heterotrophic eukaryotes that prey on different microbial community members. How predatory eukaryotes engage in beneficial interactions with other microbes has rarely been investigated so far. Here, we studied an example of such an interaction by cultivating the anerobic marine flagellate, Carpediemonas frisia sp. nov. (supergroup Excavata), with parts of its naturally associated microbiome. This microbiome consisted of so far uncultivated members of the Deltaproteobacteria, Bacteroidetes, Firmicutes, Verrucomicrobia and Nanoarchaeota...
February 17, 2017: ISME Journal
https://www.readbyqxmd.com/read/28197130/mineralizing-filamentous-bacteria-from-the-prony-bay-hydrothermal-field-give-new-insights-into-the-functioning-of-serpentinization-based-subseafloor-ecosystems
#9
Céline Pisapia, Emmanuelle Gérard, Martine Gérard, Léna Lecourt, Susan Q Lang, Bernard Pelletier, Claude E Payri, Christophe Monnin, Linda Guentas, Anne Postec, Marianne Quéméneur, Gaël Erauso, Bénédicte Ménez
Despite their potential importance as analogs of primitive microbial metabolisms, the knowledge of the structure and functioning of the deep ecosystems associated with serpentinizing environments is hampered by the lack of accessibility to relevant systems. These hyperalkaline environments are depleted in dissolved inorganic carbon (DIC), making the carbon sources and assimilation pathways in the associated ecosystems highly enigmatic. The Prony Bay Hydrothermal Field (PHF) is an active serpentinization site where, similar to Lost City (Mid-Atlantic Ridge), high-pH fluids rich in H2 and CH4 are discharged from carbonate chimneys at the seafloor, but in a shallower lagoonal environment...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28161356/a-retrospective-cross-sectional-quantitative-molecular-approach-in-biological-samples-from-patients-with-syphilis
#10
Miguel Pinto, Minia Antelo, Rita Ferreira, Jacinta Azevedo, Irene Santo, Maria José Borrego, João Paulo Gomes
Syphilis is the sexually transmitted disease caused by Treponema pallidum, a pathogen highly adapted to the human host. As a multistage disease, syphilis presents distinct clinical manifestations that pose different implications for diagnosis. Nevertheless, the inherent factors leading to diverse disease progressions are still unknown. We aimed to assess the association between treponemal loads and dissimilar disease outcomes, to better understand syphilis. We retrospectively analyzed 309 DNA samples distinct anatomic sites associated with particular syphilis manifestations...
March 2017: Microbial Pathogenesis
https://www.readbyqxmd.com/read/28137256/production-and-characterization-of-a-novel-antifungal-chitinase-identified-by-functional-screening-of-a-suppressive-soil-metagenome
#11
Francesca Berini, Ilaria Presti, Fabrizio Beltrametti, Marco Pedroli, Kjell M Vårum, Loredano Pollegioni, Sara Sjöling, Flavia Marinelli
BACKGROUND: Through functional screening of a fosmid library, generated from a phytopathogen-suppressive soil metagenome, the novel antifungal chitinase-named Chi18H8 and belonging to family 18 glycosyl hydrolases-was previously discovered. The initial extremely low yield of Chi18H8 recombinant production and purification from Escherichia coli cells (21 μg/g cell) limited its characterization, thus preventing further investigation on its biotechnological potential. RESULTS: We report on how we succeeded in producing hundreds of milligrams of pure and biologically active Chi18H8 by developing and scaling up to a high-yielding, 30 L bioreactor process, based on a novel method of mild solubilization of E...
January 31, 2017: Microbial Cell Factories
https://www.readbyqxmd.com/read/28111470/metagenomics-uncultivated-microbes-reveal-new-crispr-cas-systems
#12
Ross Cloney
No abstract text is available yet for this article.
January 23, 2017: Nature Reviews. Genetics
https://www.readbyqxmd.com/read/28077874/asgard-archaea-illuminate-the-origin-of-eukaryotic-cellular-complexity
#13
Katarzyna Zaremba-Niedzwiedzka, Eva F Caceres, Jimmy H Saw, Disa Bäckström, Lina Juzokaite, Emmelien Vancaester, Kiley W Seitz, Karthik Anantharaman, Piotr Starnawski, Kasper U Kjeldsen, Matthew B Stott, Takuro Nunoura, Jillian F Banfield, Andreas Schramm, Brett J Baker, Anja Spang, Thijs J G Ettema
The origin and cellular complexity of eukaryotes represent a major enigma in biology. Current data support scenarios in which an archaeal host cell and an alphaproteobacterial (mitochondrial) endosymbiont merged together, resulting in the first eukaryotic cell. The host cell is related to Lokiarchaeota, an archaeal phylum with many eukaryotic features. The emergence of the structural complexity that characterizes eukaryotic cells remains unclear. Here we describe the 'Asgard' superphylum, a group of uncultivated archaea that, as well as Lokiarchaeota, includes Thor-, Odin- and Heimdallarchaeota...
January 19, 2017: Nature
https://www.readbyqxmd.com/read/28058599/epiphytic-bacterial-communities-of-the-alga-fucus-vesiculosus-in-oil-contaminated-water-areas-of-the-barents-sea
#14
D V Pugovkin, A Liaimer, J B Jensen
Taxonomic compositions of epiphytic bacterial communities in water areas differing in levels of oil pollution were revealed. In total, 82 bacterial genera belonging to 16 classes and 11 phyla were detected. All detected representatives of epiphytic bacterial communities belonged to the phyla Actinobacteria, Bacteroidetes, Planctomycetes, Proteobacteria, Verrucomicrobia, Acidobacteria, Cyanobacteria, Firmicutes, and Fusobacteria and candidate division TM7. The ratio of the phyla in the communities varied depending on the levels of oil pollution...
November 2016: Doklady Biological Sciences: Proceedings of the Academy of Sciences of the USSR, Biological Sciences Sections
https://www.readbyqxmd.com/read/28043039/vertical-and-lateral-distribution-of-fallout-137-cs-and-soil-properties-along-representative-toposequences-of-central-rif-morocco
#15
Haytam Mesrar, Abdelhamid Sadiki, Ali Faleh, Laura Quijano, Leticia Gaspar, Ana Navas
The purpose of this study is to understand and quantify the relationships between current (137)Cs inventories and the soil properties and the physiographic characteristics. A total of 36 cores were taken in seven transects with different slopes, lithology and land use. The analysis focused on the (137)Cs mass activity as well as inventories and its relationship with soil properties as grain size and organic matter. The mass activity of (137)Cs and the inventories varied between 3.6 and 63.7 Bq kg(-1) and between 521...
December 30, 2016: Journal of Environmental Radioactivity
https://www.readbyqxmd.com/read/28042018/pcr-activated-cell-sorting-as-a-general-cultivation-free-method-for-high-throughput-identification-and-enrichment-of-virus-hosts
#16
Shaun W Lim, Shea T Lance, Kenneth M Stedman, Adam R Abate
Characterizing virus-host relationships is critical for understanding the impact of a virus on an ecosystem, but is challenging with existing techniques, particularly for uncultivable species. We present a general, cultivation-free approach for identifying phage-associated bacterial cells. Using PCR-activated cell sorting, we interrogate millions of individual bacteria for the presence of specific phage nucleic acids. If the nucleic acids are present, the bacteria are recovered via sorting and their genomes analyzed...
December 29, 2016: Journal of Virological Methods
https://www.readbyqxmd.com/read/28031351/evaluation-of-gulf-coast-ticks-acari-ixodidae-for-ehrlichia-and-anaplasma-species
#17
Michelle E J Allerdice, Joy A Hecht, Sandor E Karpathy, Christopher D Paddock
Amblyomma maculatum Koch (the Gulf Coast tick) is an aggressive, human-biting ixodid tick distributed throughout much of the southeastern United States and is the primary vector for Rickettsia parkeri, an emerging human pathogen. Amblyomma maculatum has diverse host preferences that include white-tailed deer, a known reservoir for Ehrlichia and Anaplasma species, including the human pathogens E. ewingii and E. chaffeensis To examine more closely the potential role of A. maculatum in the maintenance of various pathogenic Ehrlichia and Anaplasma species, we screened DNA samples from 493 questing adult A...
December 28, 2016: Journal of Medical Entomology
https://www.readbyqxmd.com/read/28028487/exploring-the-cockatiel-nymphicus-hollandicus-fecal-microbiome-bacterial-inhabitants-of-a-worldwide-pet
#18
Luis David Alcaraz, Apolinar M Hernández, Mariana Peimbert
BACKGROUND: Cockatiels (Nymphicus hollandicus) were originally endemic to Australia; now they are popular pets with a global distribution. It is now possible to conduct detailed molecular studies on cultivable and uncultivable bacteria that are part of the intestinal microbiome of healthy animals. These studies show that bacteria are an essential part of the metabolic capacity of animals. There are few studies on bird microbiomes and, to the best of our knowledge, this is the first report on the cockatiel microbiome...
2016: PeerJ
https://www.readbyqxmd.com/read/28008549/globisporangium-oryzicola-sp-nov-causing-poor-seedling-establishment-of-directly-seeded-rice
#19
Shihomi Uzuhashi, Kazuhide Hata, Shohei Matsuura, Motoaki Tojo
A new species, Globisporangium oryzicola, was isolated from directly seeded rice seedlings, and from soils of paddy fields and an uncultivated field. Despite their different origins, five of the seven isolates studied caused poor seedling establishment of rice in a laboratory inoculation experiment. The species is characterized by oogonia with smooth-walled or sometimes one projection, with one to two antheridia, and aplerotic oospores. Hyphal swellings were rarely observed. Phylogenetic analyses based on the internal transcribed spacer region of the ribosomal RNA gene and mitochondrial cytochrome c oxidase subunit 1 and 2 genes confirmed that the species differed from other Globisporangium species...
December 23, 2016: Antonie Van Leeuwenhoek
https://www.readbyqxmd.com/read/28005056/new-crispr-cas-systems-from-uncultivated-microbes
#20
David Burstein, Lucas B Harrington, Steven C Strutt, Alexander J Probst, Karthik Anantharaman, Brian C Thomas, Jennifer A Doudna, Jillian F Banfield
CRISPR-Cas systems provide microbes with adaptive immunity by employing short DNA sequences, termed spacers, that guide Cas proteins to cleave foreign DNA. Class 2 CRISPR-Cas systems are streamlined versions, in which a single RNA-bound Cas protein recognizes and cleaves target sequences. The programmable nature of these minimal systems has enabled researchers to repurpose them into a versatile technology that is broadly revolutionizing biological and clinical research. However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving the vast majority of enzymes from organisms that have not been cultured untapped...
February 9, 2017: Nature
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