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https://www.readbyqxmd.com/read/28077874/asgard-archaea-illuminate-the-origin-of-eukaryotic-cellular-complexity
#1
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
#2
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
#3
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
#4
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
#5
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
#6
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
#7
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
#8
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 sequences, termed spacers, that guide Cas proteins to cleave foreign DNA(1,2). Class 2 CRISPR-Cas systems are streamlined versions in which a single Cas protein bound to RNA recognizes and cleaves targeted sequences(3,4). The programmable nature of these minimal systems has enabled their repurposing as a versatile technology that is broadly revolutionizing biological and clinical research(5). However, current CRISPR-Cas technologies are based solely on systems from isolated bacteria, leaving untapped the vast majority of enzymes from organisms that have not been cultured...
December 22, 2016: Nature
https://www.readbyqxmd.com/read/27996008/unusual-marine-unicellular-symbiosis-with-the-nitrogen-fixing-cyanobacterium-ucyn-a
#9
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
#10
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
#11
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
#12
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
#13
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
#14
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 the current study was to explore the 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 thousand kilometre long transect of South Africa, including agricultural soil, a gold mine tailings 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
#15
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
https://www.readbyqxmd.com/read/27924592/microbial-community-profiling-using-terminal-restriction-fragment-length-polymorphism-t-rflp-and-denaturing-gradient-gel-electrophoresis-dgge
#16
José F Siqueira, Mitsuo Sakamoto, Alexandre S Rosado
In their natural environments, microorganisms usually live in organized communities. Profiling analysis of microbial communities has recently assumed special relevance as it allows a thorough understanding of the diversity of the microbiota, its behavior over time, and the establishment of patterns associated with health and disease. The application of molecular biology approaches holds the advantage of including culture-difficult and as-yet-uncultivated phylotypes in the profiles, providing a more comprehensive picture of the microbial community...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27923729/ph-gradient-ion-exchange-microbial-cell-chromatography-as-a-simple-method-for-microbial-separation
#17
Yoshiteru Aoi, Yuji Kaneko, Satoshi Tsuneda
Selective separation of specific microbial types from a heterogeneous microbial population, such as an environmental microbial community, is an important process for microbial research and biotechnological industries. In the present study, pH-gradient ion-exchange microbial cell chromatography (PIE-MCC) was developed as a new method for microbial separation. The proposed method enables target microorganisms to be separated from a microbial community based on differences in microbial surface characteristics, because these characteristics, such as the ζ (zeta)-potential, vary among microbial cells...
December 3, 2016: Journal of Bioscience and Bioengineering
https://www.readbyqxmd.com/read/27906039/peering-below-the-diffraction-limit-robust-and-specific-sorting-of-viruses-with-flow-cytometry
#18
Shea T Lance, David J Sukovich, Kenneth M Stedman, Adam R Abate
BACKGROUND: Viruses are incredibly diverse organisms and impact all forms of life on Earth; however, individual virions are challenging to study due to their small size and mass, precluding almost all direct imaging or molecular analysis. Moreover, like microbes, the overwhelming majority of viruses cannot be cultured, impeding isolation, replication, and study of interesting new species. Here, we introduce PCR-activated virus sorting, a method to isolate specific viruses from a heterogeneous population...
December 1, 2016: Virology Journal
https://www.readbyqxmd.com/read/27878346/salinity-affects-the-composition-of-the-aerobic-methanotroph-community-in-alkaline-lake-sediments-from-the-tibetan-plateau
#19
Yongcui Deng, Yongqin Liu, Marc Dumont, Ralf Conrad
Lakes are widely distributed on the Tibetan Plateau, which plays an important role in natural methane emission. Aerobic methanotrophs in lake sediments reduce the amount of methane released into the atmosphere. However, no study to date has analyzed the methanotroph community composition and their driving factors in sediments of these high-altitude lakes (>4000 m). To provide new insights on this aspect, the abundance and composition in the sediments of six high-altitude alkaline lakes (including both freshwater and saline lakes) on the Tibetan Plateau were studied...
November 22, 2016: Microbial Ecology
https://www.readbyqxmd.com/read/27869614/cutaneous-granulomas-in-dolphins-caused-by-novel-uncultivated-paracoccidioides-brasiliensis
#20
Raquel Vilela, Gregory D Bossart, Judy A St Leger, Leslie M Dalton, John S Reif, Adam M Schaefer, Peter J McCarthy, Patricia A Fair, Leonel Mendoza
Cutaneous granulomas in dolphins were believed to be caused by Lacazia loboi, which also causes a similar disease in humans. This hypothesis was recently challenged by reports that fungal DNA sequences from dolphins grouped this pathogen with Paracoccidioides brasiliensis. We conducted phylogenetic analysis of fungi from 6 bottlenose dolphins (Tursiops truncatus) with cutaneous granulomas and chains of yeast cells in infected tissues. Kex gene sequences of P. brasiliensis from dolphins showed 100% homology with sequences from cultivated P...
December 2016: Emerging Infectious Diseases
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