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https://www.readbyqxmd.com/read/28211847/syntrophic-linkage-between-predatory-carpediemonas-and-specific-prokaryotic-populations
#1
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
#2
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
#3
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...
February 2, 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
#4
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
#5
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
#6
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
#7
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
#8
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
#9
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
#10
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
#11
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
#12
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
#13
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
https://www.readbyqxmd.com/read/27996008/unusual-marine-unicellular-symbiosis-with-the-nitrogen-fixing-cyanobacterium-ucyn-a
#14
REVIEW
Jonathan P Zehr, Irina N Shilova, Hanna M Farnelid, Maria Del Carmen Muñoz-MarínCarmen, Kendra A Turk-Kubo
Nitrogen fixation - the reduction of dinitrogen (N2) gas to biologically available nitrogen (N) - is an important source of N for terrestrial and aquatic ecosystems. In terrestrial environments, N2-fixing symbioses involve multicellular plants, but in the marine environment these symbioses occur with unicellular planktonic algae. An unusual symbiosis between an uncultivated unicellular cyanobacterium (UCYN-A) and a haptophyte picoplankton alga was recently discovered in oligotrophic oceans. UCYN-A has a highly reduced genome, and exchanges fixed N for fixed carbon with its host...
December 20, 2016: Nature Microbiology
https://www.readbyqxmd.com/read/27976721/a-large-scale-genome-wide-association-and-meta-analysis-identified-four-novel-susceptibility-loci-for-leprosy
#15
Zhenzhen Wang, Yonghu Sun, Xi'an Fu, Gongqi Yu, Chuan Wang, Fangfang Bao, Zhenhua Yue, Jianke Li, Lele Sun, Astrid Irwanto, Yongxiang Yu, Mingfei Chen, Zihao Mi, Honglei Wang, Pengcheng Huai, Yi Li, Tiantian Du, Wenjun Yu, Yang Xia, Hailu Xiao, Jiabao You, Jinghui Li, Qing Yang, Na Wang, Panpan Shang, Guiye Niu, Xiaojun Chi, Xiuhuan Wang, Jing Cao, Xiujun Cheng, Hong Liu, Jianjun Liu, Furen Zhang
Leprosy, a chronic infectious disease, results from the uncultivable pathogen Mycobacterium leprae (M. leprae), and usually progresses to peripheral neuropathy and permanent progressive deformity if not treated. Previously published genetic studies have identified 18 gene/loci significantly associated with leprosy at the genome-wide significant level. However as a complex disease, only a small proportion of leprosy risk could be explained by those gene/loci. To further identify more susceptibility gene/loci, we hereby performed a three-stage GWAS comprising 8,156 leprosy patients and 15,610 controls of Chinese ancestry...
December 15, 2016: Nature Communications
https://www.readbyqxmd.com/read/27976264/an-endophytic-fungus-phyllosticta-capitalensis-harboring-uncultivable-endosymbiotic-bacterium-herbaspirillum-sp-produces-lactam-fused-4-pyrones
#16
W X Wang, S Kusari, P Kusari, O Kayser, M Spiteller
No abstract text is available yet for this article.
December 2016: Planta Medica
https://www.readbyqxmd.com/read/27966282/enzyme-from-an-uncultivated-sponge-bacterium-catalyzes-s-methylation-in-a-ribosomal-peptide
#17
Maximilian Helf, Aurelia Jud, Jörn Piel
Amino acid modifications are essential for the structural diversity and bioactivity of ribosomally synthesized and posttranslationally modified peptide natural products (RiPPs). A particularly large and virtually untapped pool of unusual RiPPs and associated modifying enzymes is provided by uncultivated bacteria. An example is the chemically rich sponge symbiont 'Candidatus Entotheonella factor' that produces the hypermodified polytheonamides of the poorly studied proteusin RiPP family. In addition to the polytheonamide genes, 'E...
December 14, 2016: Chembiochem: a European Journal of Chemical Biology
https://www.readbyqxmd.com/read/27959345/new-roles-in-hemicellulosic-sugar-fermentation-for-the-uncultivated-bacteroidetes-family-bs11
#18
Lindsey M Solden, David W Hoyt, William B Collins, Johanna E Plank, Rebecca A Daly, Erik Hildebrand, Timothy J Beavers, Richard Wolfe, Carrie D Nicora, Sam O Purvine, Michelle Carstensen, Mary S Lipton, Donald E Spalinger, Jeffrey L Firkins, Barbara A Wolfe, Kelly C Wrighton
Ruminants have co-evolved with their gastrointestinal microbial communities that digest plant materials to provide energy for the host. Some arctic and boreal ruminants have already shown to be vulnerable to dietary shifts caused by changing climate, yet we know little about the metabolic capacity of the ruminant microbiome in these animals. Here, we use meta-omics approaches to sample rumen fluid microbial communities from Alaskan moose foraging along a seasonal lignocellulose gradient. Winter diets with increased hemicellulose and lignin strongly enriched for BS11, a Bacteroidetes family lacking cultivated or genomically sampled representatives...
December 13, 2016: ISME Journal
https://www.readbyqxmd.com/read/27930842/hydrolysis-of-nitriles-by-soil-bacteria-variation-with-soil-origin
#19
O K L Rapheeha, M P Roux-van der Merwe, J Badenhorst, V Chhiba, M L Bode, K Mathiba, D Brady
AIMS: The aim of this study was to explore bacterial soil diversity for nitrile biocatalysts, in particular, those for hydrolysis of β-substituted nitriles, to the corresponding carboxamides and acids that may be incorporated into peptidomimetics. To achieve this, we needed to compare the efficiency of isolation methods and determine the influence of land use and geographical origin of the soil sample. METHODS AND RESULTS: Nitrile-utilizing bacteria were isolated from various soil environments across a 1000 km long transect of South Africa, including agricultural soil, a gold mine tailing dam and uncultivated soil...
December 8, 2016: Journal of Applied Microbiology
https://www.readbyqxmd.com/read/27926817/description-of-immundisolibacter-cernigliae-gen-nov-sp-nov-a-high-molecular-weight-polycyclic-aromatic-hydrocarbon-degrading-bacterium-within-the-class-gammaproteobacteria-and-proposal-of-immundisolibacterales-ord-nov-and-immundisolibacteraceae-fam-nov
#20
Elizabeth M Corteselli, Michael D Aitken, David R Singleton
The bacterial strain TR3.2T was isolated from aerobic bioreactor-treated soil from a polycyclic aromatic hydrocarbon (PAH)-contaminated site in Salisbury, North Carolina, USA. Strain TR3.2T was identified as a member of "Pyrene Group 2" or "PG2", a previously uncultivated cluster of organisms associated with the degradation of high-molecular-weight PAHs by stable-isotope probing. Based on its 16S rRNA gene sequence the strain was classified as a member of the class Gammaproteobacteria but possessed only 90...
December 7, 2016: International Journal of Systematic and Evolutionary Microbiology
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