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Insights into the phylogeny and coding potential of microbial dark matter
TLDR
This study applies single-cell genomics to target and sequence 201 archaeal and bacterial cells from nine diverse habitats belonging to 29 major mostly uncharted branches of the tree of life and provides a systematic step towards a better understanding of biological evolution on the authors' planet. Expand
Community Genomics Among Stratified Microbial Assemblages in the Ocean's Interior
TLDR
Genomic analyses of planktonic microbial communities in the North Pacific Subtropical Gyre, from the ocean's surface to near–sea floor depths, suggested depth-variable community trends in carbon and energy metabolism, attachment and motility, gene mobility, and host-viral interactions. Expand
Pathways of Carbon Assimilation and Ammonia Oxidation Suggested by Environmental Genomic Analyses of Marine Crenarchaeota
TLDR
Analysis of fosmid sequences derived from the uncultivated marine crenarchaeote, Cenarchaeum symbiosum, focused on the reconstruction of carbon and energy metabolism substantiate the likely global metabolic importance of Cren archaeal importance with respect to key steps in the biogeochemical transformation ofcarbon and nitrogen in marine ecosystems. Expand
Genomic analysis of the uncultivated marine crenarchaeote Cenarchaeum symbiosum
TLDR
The C. symbiosum genome was remarkably distinct from those of other known Archaea and shared many core metabolic features in common with its free-living planktonic relatives. Expand
Identification of Methyl Coenzyme M Reductase A (mcrA) Genes Associated with Methane-Oxidizing Archaea
TLDR
The existence and genomic conservation of methyl coenzyme M reductase (MCR), the enzyme catalyzing the terminal step in methanogenesis, was studied in AN ME-1 and ANME-2 archaea isolated from various marine environments, providing a basis for identifying methanotrophic archaea with mcrA sequences and defining a functional genomic link between methanogenic and methanosynthetic archaea. Expand
Microbial ecology of expanding oxygen minimum zones
TLDR
Current efforts to explore the fundamental factors that control the ecological and microbial biodiversity in oxygen-starved regions of the ocean, termed oxygen minimum zones are described and new insights into coupled biogeochemical processes in the ocean are provided. Expand
Reverse Methanogenesis: Testing the Hypothesis with Environmental Genomics
TLDR
Genetic analyses of methane-oxidizing Archaea from deep-sea sediments show that nearly all genes typically associated with methane production are present in one specific group of archaeal methanotrophs, which supports previous hypotheses and provides an informed foundation for metabolic modeling of anaerobic methane oxidation. Expand
Metagenome of a Versatile Chemolithoautotroph from Expanding Oceanic Dead Zones
TLDR
Analysis of a ubiquitous and abundant but uncultivated oxygen minimum zone microbe related to chemoautotrophic gill symbionts of deep-sea clams and mussels provides a genomic foundation for understanding the ecological and biogeochemical role of pelagic SUP05 in oxygen-deficient oceanic waters and its potential sensitivity to environmental changes. Expand
Minimum information about a single amplified genome (MISAG) and a metagenome-assembled genome (MIMAG) of bacteria and archaea
TLDR
Two standards developed by the Genomic Standards Consortium (GSC) for reporting bacterial and archaeal genome sequences are presented, including the Minimum Information about a Single Amplified Genome (MISAG) and the Minimum information about a Metagenome-Assembled Genomes (MIMAG), including estimates of genome completeness and contamination. Expand
A communal catalogue reveals Earth’s multiscale microbial diversity
TLDR
A meta-analysis of microbial community samples collected by hundreds of researchers for the Earth Microbiome Project is presented, creating both a reference database giving global context to DNA sequence data and a framework for incorporating data from future studies, fostering increasingly complete characterization of Earth’s microbial diversity. Expand
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