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Microbial genomics

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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
#1
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/28808688/adaptive-mistranslation-accelerates-the-evolution-of-fluconazole-resistance-and-induces-major-genomic-and-gene-expression-alterations-in-candida-albicans
#2
Tobias Weil, Rodrigo Santamaría, Wanseon Lee, Johan Rung, Noemi Tocci, Darren Abbey, Ana R Bezerra, Laura Carreto, Gabriela R Moura, Mónica Bayés, Ivo G Gut, Attila Csikasz-Nagy, Duccio Cavalieri, Judith Berman, Manuel A S Santos
Regulated erroneous protein translation (adaptive mistranslation) increases proteome diversity and produces advantageous phenotypic variability in the human pathogen Candida albicans. It also increases fitness in the presence of fluconazole, but the underlying molecular mechanism is not understood. To address this question, we evolved hypermistranslating and wild-type strains in the absence and presence of fluconazole and compared their fluconazole tolerance and resistance trajectories during evolution. The data show that mistranslation increases tolerance and accelerates the acquisition of resistance to fluconazole...
July 2017: MSphere
https://www.readbyqxmd.com/read/28808230/environmental-drivers-of-a-microbial-genomic-transition-zone-in-the-ocean-s-interior
#3
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/28805729/systems-biology-approach-to-bioremediation-of-nitroaromatics-constraint-based-analysis-of-2-4-6-trinitrotoluene-biotransformation-by-escherichia-coli
#4
Maryam Iman, Tabassom Sobati, Yunes Panahi, Meysam Mobasheri
Microbial remediation of nitroaromatic compounds (NACs) is a promising environmentally friendly and cost-effective approach to the removal of these life-threating agents. Escherichia coli (E. coli) has shown remarkable capability for the biotransformation of 2,4,6-trinitro-toluene (TNT). Efforts to develop E. coli as an efficient TNT degrading biocatalyst will benefit from holistic flux-level description of interactions between multiple TNT transforming pathways operating in the strain. To gain such an insight, we extended the genome-scale constraint-based model of E...
August 14, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28804480/microbial-community-structure-and-the-persistence-of-cyanobacterial-populations-in-salt-crusts-of-the-hyperarid-atacama-desert-from-genome-resolved-metagenomics
#5
Kari M Finstad, Alexander J Probst, Brian C Thomas, Gary L Andersen, Cecilia Demergasso, Alex Echeverría, Ronald G Amundson, Jillian F Banfield
Although once thought to be devoid of biology, recent studies have identified salt deposits as oases for life in the hyperarid Atacama Desert. To examine spatial patterns of microbial species and key nutrient sources, we genomically characterized 26 salt crusts from three sites along a fog gradient. The communities are dominated by a large variety of Halobacteriales and Bacteroidetes, plus a few algal and Cyanobacterial species. CRISPR locus analysis suggests the distribution of a single Cyanobacterial population among all sites...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28802076/single-cell-sequencing-unveils-the-lifestyle-and-crispr-based-population-history-of-hydrotalea-sp-in-acid-mine-drainage
#6
J D Medeiros, L R Leite, V S Pylro, F S Oliveira, V M Almeida, G R Fernandes, A C M Salim, F M G Araújo, A C Volpini, G Oliveira, S Cuadros-Orellana
Acid mine drainage (AMD) is characterized by an acid and metal-rich runoff that originates from mining systems. Despite having been studied for many decades, much remains unknown about the microbial community dynamics in AMD sites, especially during their early development, when the acidity is moderate. Here, we describe draft genome assemblies from single cells retrieved from an early-stage AMD sample. These cells belong to the genus Hydrotalea, and is closely related to H. flava. The phylogeny and average nucleotide identity analysis suggest that all single-amplified genomes (SAGs) form two clades that may represent different strains...
August 12, 2017: Molecular Ecology
https://www.readbyqxmd.com/read/28800138/phylogenetically-conserved-resource-partitioning-in-the-coastal-microbial-loop
#7
Samuel Bryson, Zhou Li, Francisco Chavez, Peter K Weber, Jennifer Pett-Ridge, Robert L Hettich, Chongle Pan, Xavier Mayali, Ryan S Mueller
Resource availability influences marine microbial community structure, suggesting that population-specific resource partitioning defines discrete niches. Identifying how resources are partitioned among populations, thereby characterizing functional guilds within the communities, remains a challenge for microbial ecologists. We used proteomic stable isotope probing (SIP) and NanoSIMS analysis of phylogenetic microarrays (Chip-SIP) along with 16S rRNA gene amplicon and metagenomic sequencing to characterize the assimilation of six (13)C-labeled common metabolic substrates and changes in the microbial community structure within surface water collected from Monterey Bay, CA...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28800137/chemical-dispersants-enhance-the-activity-of-oil-and-gas-condensate-degrading-marine-bacteria
#8
Julien Tremblay, Etienne Yergeau, Nathalie Fortin, Susan Cobanli, Miria Elias, Thomas L King, Kenneth Lee, Charles W Greer
Application of chemical dispersants to oil spills in the marine environment is a common practice to disperse oil into the water column and stimulate oil biodegradation by increasing its bioavailability to indigenous bacteria capable of naturally metabolizing hydrocarbons. In the context of a spill event, the biodegradation of crude oil and gas condensate off eastern Canada is an essential component of a response strategy. In laboratory experiments, we simulated conditions similar to an oil spill with and without the addition of chemical dispersant under both winter and summer conditions and evaluated the natural attenuation potential for hydrocarbons in near-surface sea water from the vicinity of crude oil and natural gas production facilities off eastern Canada...
August 11, 2017: ISME Journal
https://www.readbyqxmd.com/read/28798742/preservation-and-significance-of-extracellular-dna-in-ferruginous-sediments-from-lake-towuti-indonesia
#9
Aurèle Vuillemin, Fabian Horn, Mashal Alawi, Cynthia Henny, Dirk Wagner, Sean A Crowe, Jens Kallmeyer
Extracellular DNA is ubiquitous in soil and sediment and constitutes a dominant fraction of environmental DNA in aquatic systems. In theory, extracellular DNA is composed of genomic elements persisting at different degrees of preservation produced by processes occurring on land, in the water column and sediment. Extracellular DNA can be taken up as a nutrient source, excreted or degraded by microorganisms, or adsorbed onto mineral matrices, thus potentially preserving information from past environments. To test whether extracellular DNA records lacustrine conditions, we sequentially extracted extracellular and intracellular DNA from anoxic sediments of ferruginous Lake Towuti, Indonesia...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28798101/genomic-exploration-of-the-diversity-ecology-and-evolution-of-the-archaeal-domain-of-life
#10
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/28797098/comparative-genomics-of-two-super-shedder-isolates-of-escherichia-coli-o157-h7
#11
Robab Katani, Rebecca Cote, Indira T Kudva, Chitrita DebRoy, Terrance M Arthur, Vivek Kapur
Shiga toxin-producing Escherichia coli O157:H7 (O157) are zoonotic foodborne pathogens and of major public health concern that cause considerable intestinal and extra-intestinal illnesses in humans. O157 colonize the recto-anal junction (RAJ) of asymptomatic cattle who shed the bacterium into the environment through fecal matter. A small subset of cattle, termed super-shedders (SS), excrete O157 at a rate (≥ 104 CFU/g of feces) that is several orders of magnitude greater than other colonized cattle and play a major role in the prevalence and transmission of O157...
2017: PloS One
https://www.readbyqxmd.com/read/28796488/direct-interaction-of-chivosazole-f-with-actin-elicits-cell-responses-similar-to-latrunculin-a-but-distinct-from-chondramide
#12
Ireos Filipuzzi, Jason Ray Thomas, Verena Pries, David Estoppey, Michael Salcius, Christian Studer, Markus Schirle, Dominic Hoepfner
The microbial metabolite Chivosazole F has been described to affect the cytoskeleton and to inhibit actin polymerization in vitro. Applying orthogonal genomic and proteomics approaches we now show for the first time that Chivosazole F exerts its effect by directly interacting with actin and demonstrate the cellular impact of Chivosazole F in an unbiased, genome-wide context in yeast and in mammalian cells. Furthermore, mutation-based resistance mapping identifies two SNPs located in the putative Chivosazole F binding site of actin...
August 10, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28794612/investigation-of-associations-of-arms2-cd14-and-tlr4-gene-polymorphisms-with-wet-age-related-macular-degeneration-in-a-greek-population
#13
Antonia Sarli, Iosif Skalidakis, Aliki Velissari, Chryssanthi Koutsandrea, Maria Stefaniotou, Michael B Petersen, Christos Kroupis, George Kitsos, Marilita M Moschos
BACKGROUND: Age-related macular degeneration (AMD) is a multifactorial degenerative ocular disease that leads to loss of central vision. Functional gene polymorphisms have already been associated with the disease (for example, ARMS2 A69S, rs10490924). AIM: The goal of our study was to verify the correlation of the aforementioned ARMS2 variation with the disease, to examine, for the first time, the role of the CD14 C260T variation (rs2569190), and to investigate the association of two TLR4 polymorphisms (Asp299Gly or rs4986790 and Thr399Ile or rs4986791) in a Greek population with the wet form of AMD...
2017: Clinical Ophthalmology
https://www.readbyqxmd.com/read/28790992/the-cyanobacteria-dominated-sponge-dactylospongia-elegans-in-the-south-china-sea-prokaryotic-community-and-metagenomic-insights
#14
Zhao-Ming Gao, Guo-Wei Zhou, Hui Huang, Yong Wang
The South China Sea is a special reservoir of sponges of which prokaryotic communities are less studied. Here, a new record of the sponge Dactylospongia elegans is reported near the coast of Jinqing Island in the South China Sea, and its prokaryotic community is comprehensively investigated. Sponge specimens displayed lower microbial diversity compared with surrounding seawater. At the phylum level, prokaryotic communities were consistently dominated by Proteobacteria, followed by Cyanobacteria, Chloroflexi, Acidobacteria, Actinobacteria, Gemmatimonadetes, Thaumarchaeota, and Poribacteria...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28789673/gene-and-transcript-abundances-of-bacterial-type-iii-secretion-systems-from-the-rumen-microbiome-are-correlated-with-methane-yield-in-sheep
#15
Janine Kamke, Priya Soni, Yang Li, Siva Ganesh, William J Kelly, Sinead C Leahy, Weibing Shi, Jeff Froula, Edward M Rubin, Graeme T Attwood
BACKGROUND: Ruminants are important contributors to global methane emissions via microbial fermentation in their reticulo-rumens. This study is part of a larger program, characterising the rumen microbiomes of sheep which vary naturally in methane yield (g CH4/kg DM/day) and aims to define differences in microbial communities, and in gene and transcript abundances that can explain the animal methane phenotype. METHODS: Rumen microbiome metagenomic and metatranscriptomic data were analysed by Gene Set Enrichment, sparse partial least squares regression and the Wilcoxon Rank Sum test to estimate correlations between specific KEGG bacterial pathways/genes and high methane yield in sheep...
August 8, 2017: BMC Research Notes
https://www.readbyqxmd.com/read/28782803/genomic-analyses-suggest-parallel-ecological-divergence-in-heliosperma-pusillum-caryophyllaceae
#16
Emiliano Trucchi, Božo Frajman, Thomas H A Haverkamp, Peter Schönswetter, Ovidiu Paun
The mosaic distribution of interbreeding taxa with contrasting ecology and morphology offers an opportunity to study microevolutionary dynamics during ecological divergence. We investigate here the evolutionary history of an alpine and a montane ecotype of Heliosperma pusillum (Caryophyllaceae) in the south-eastern Alps. From six pairs of geographically close populations of the two ecotypes (120 individuals) we obtained a high-coverage restriction site associated DNA sequencing (RADseq) dataset that was used for demographic inference to test the hypothesis of parallel evolution of the two ecotypes...
August 7, 2017: New Phytologist
https://www.readbyqxmd.com/read/28782454/use-of-gifu-anaerobic-medium-for-culturing-32-dominant-species-of-human-gut-microbes-and-its-evaluation-based-on-short-chain-fatty-acids-fermentation-profiles
#17
Aina Gotoh, Misaki Nara, Yuta Sugiyama, Mikiyasu Sakanaka, Hiroyuki Yachi, Aya Kitakata, Akira Nakagawa, Hiromichi Minami, Shujiro Okuda, Toshihiko Katoh, Takane Katayama, Shin Kurihara
Recently, a "human gut microbial gene catalogue," which ranks the dominance of microbe genus/species in human fecal samples, was published. Most of the bacteria ranked in the catalog are currently publicly available; however, the growth media recommended by the distributors vary among species, hampering physiological comparisons among the bacteria. To address this problem, we evaluated Gifu anaerobic medium (GAM) as a standard medium. Forty-four publicly available species of the top 56 species listed in the "human gut microbial gene catalogue" were cultured in GAM, and out of these, 32 (72%) were successfully cultured...
August 7, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28780492/known-unknowns-how-might-the-persistent-herpesvirome-shape-immunity-and-aging
#18
REVIEW
Janko Nikolich-Zugich, Felicia Goodrum, Kenneth Knox, Megan J Smithey
The microbial community that colonizes all living organisms is gaining appreciation for its contributions to both physiologic and pathogenic processes. The virome, a subset of the overall microbiome, large and diverse, including viruses that persistently inhabit host cells, endogenous viral elements genomically or epigenomically integrated into cells, and viruses that infect the other (bacterial, protozoan, fungal, and archaeal) microbiome phylla. These viruses live in the organism for its life, and therefore are to be considered part of the aging process experienced by the organism...
August 3, 2017: Current Opinion in Immunology
https://www.readbyqxmd.com/read/28777382/the-growing-tree-of-archaea-new-perspectives-on-their-diversity-evolution-and-ecology
#19
Panagiotis S Adam, Guillaume Borrel, Céline Brochier-Armanet, Simonetta Gribaldo
The Archaea occupy a key position in the Tree of Life, and are a major fraction of microbial diversity. Abundant in soils, ocean sediments and the water column, they have crucial roles in processes mediating global carbon and nutrient fluxes. Moreover, they represent an important component of the human microbiome, where their role in health and disease is still unclear. The development of culture-independent sequencing techniques has provided unprecedented access to genomic data from a large number of so far inaccessible archaeal lineages...
August 4, 2017: ISME Journal
https://www.readbyqxmd.com/read/28777379/metabolic-and-spatio-taxonomic-response-of-uncultivated-seafloor-bacteria-following-the-deepwater-horizon-oil-spill
#20
K M Handley, Y M Piceno, P Hu, L M Tom, O U Mason, G L Andersen, J K Jansson, J A Gilbert
The release of 700 million liters of oil into the Gulf of Mexico over a few months in 2010 produced dramatic changes in the microbial ecology of the water and sediment. Here, we reconstructed the genomes of 57 widespread uncultivated bacteria from post-spill deep-sea sediments, and recovered their gene expression pattern across the seafloor. These genomes comprised a common collection of bacteria that were enriched in heavily affected sediments around the wellhead. Although rare in distal sediments, some members were still detectable at sites up to 60 km away...
August 4, 2017: ISME Journal
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