Genomic Expansion of Domain Archaea Highlights Roles for Organisms from New Phyla in Anaerobic Carbon Cycling
Cindy J. Castelle,Kelly C. Wrighton,Brian C. Thomas,Laura A. Hug,Christopher T. Brown,Michael J. Wilkins,Kyle R. Frischkorn,Susannah G. Tringe,Andrea Singh,Lye Meng Markillie,Ronald C. Taylor,Kenneth H. Williams,Jillian F. Banfield +12 more
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TLDR
This study sequenced DNA from complex sediment and planktonic consortia from an aquifer adjacent to the Colorado River and reconstructed the first complete genomes for Archaea using cultivation-independent methods, which dramatically expand genomic sampling of the domain Archaea and clarify taxonomic designations within a major superphylum.About:
This article is published in Current Biology.The article was published on 2015-03-16 and is currently open access. It has received 463 citations till now. The article focuses on the topics: Nanohaloarchaea & Phylum.read more
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Marine archaea and archaeal viruses under global change
TL;DR: Research is urgently needed to better understand the impacts of global change on virus–archaea dynamics and how archaea and their viruses can interactively influence the ocean’s feedbacks on global change.
Journal ArticleDOI
Diversity and Abundance of Microbial Communities in UASB Reactors during Methane Production from Hydrolyzed Wheat Straw and Lucerne.
TL;DR: Overall microbial community development in UASB processes and changes related to acidification are provided, which showed decreased richness and diversity in the microbial community, and decreased relative abundance of bacteria in relation to archaea, after process acidification.
Journal ArticleDOI
Archaeal community variation in the Qinhuangdao coastal aquaculture zone revealed by high-throughput sequencing.
TL;DR: Investigation of archaeal community variation within the Qinhuangdao coastal aquaculture zone provides an important baseline understanding of the microbial ecology in this important ecosystem.
Journal ArticleDOI
Gulf of Mexico blue hole harbors high levels of novel microbial lineages.
Nastassia V. Patin,Z. A. Dietrich,A. Stancil,M. Quinan,Jordon S. Beckler,Eric Hall,Jim Culter,Christopher F. Smith,Martial Taillefert,Frank J. Stewart,Frank J. Stewart +10 more
TL;DR: In this paper, a metagenomic and geochemical characterization of Amberjack Hole on the Florida continental shelf (Gulf of Mexico) is presented, showing that dissolved oxygen became depleted at the hole's rim (32m water depth), remained low but detectable in an intermediate hypoxic zone (40-75m), and then increased to a secondary peak before falling below detection in the bottom layer (80-110m), concomitant with increases in nutrients, dissolved iron, and a series of sequentially more reduced sulfur species.
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Acetate Activates Deep Subsurface Fracture Fluid Microbial Communities in Olkiluoto, Finland
TL;DR: In this paper, the activating effect of different electron donors and acceptors was measured with redox sensing fluorescent dyes (5-Cyano-2,3-ditolyl tetrazolium chloride, CTC and RedoxSensor™ Green, RSG).
References
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Basic Local Alignment Search Tool
TL;DR: A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score.
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Fast gapped-read alignment with Bowtie 2
TL;DR: Bowtie 2 combines the strengths of the full-text minute index with the flexibility and speed of hardware-accelerated dynamic programming algorithms to achieve a combination of high speed, sensitivity and accuracy.
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MUSCLE: multiple sequence alignment with high accuracy and high throughput
TL;DR: MUSCLE is a new computer program for creating multiple alignments of protein sequences that includes fast distance estimation using kmer counting, progressive alignment using a new profile function the authors call the log-expectation score, and refinement using tree-dependent restricted partitioning.
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A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood.
Stéphane Guindon,Olivier Gascuel +1 more
TL;DR: This work has used extensive and realistic computer simulations to show that the topological accuracy of this new method is at least as high as that of the existing maximum-likelihood programs and much higher than the performance of distance-based and parsimony approaches.
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RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
TL;DR: UNLABELLED RAxML-VI-HPC (randomized axelerated maximum likelihood for high performance computing) is a sequential and parallel program for inference of large phylogenies with maximum likelihood (ML) that has been used to compute ML trees on two of the largest alignments to date.
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