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The trajectory of microbial single-cell sequencing

Over the past decade, it has become nearly routine to sequence genomes of individual microbial cells directly isolated from environmental samples ranging from deep-sea hydrothermal vents to insect guts, providing a powerful complement to shotgun metagenomics in microbial community studies. In this review, we address the technical aspects and challenges of single-cell genome sequencing and… [Read More]

Draft genome sequence of carbapenem-resistant Shewanella algae strain AC isolated from small abalone (Haliotis diversicolor)

OBJECTIVES: Shewanella algae is an environmental marine bacterium and an emerging opportunistic human pathogen. Moreover, there are increasing reports of strains showing multidrug resistance, particularly carbapenem-resistant isolates. Although S. algae has been found in bivalve shellfish aquaculture, there is very little genome-wide data on resistance determinants in S. algae from shellfish. The aim of this… [Read More]

Functional Diversity of Diterpene Synthases in the Biofuel Crop Switchgrass

Diterpenoids constitute a diverse class of metabolites with critical functions in plant development, defense, and ecological adaptation. Major monocot crops, such as maize (Zea mays) and rice (Oryza sativa), deploy diverse blends of specialized diterpenoids as core components of biotic and abiotic stress resilience. Here, we describe the genome-wide identification and functional characterization of stress-related… [Read More]

PlantSEED enables automated annotation and reconstruction of plant primary metabolism with improved compartmentalization and comparative consistency

Genome-scale metabolic reconstructions help us to understand and engineer metabolism. Next-generation sequencing technologies are delivering genomes and transcriptomes for an ever-widening range of plants. While such omic data can, in principle, be used to compare metabolic reconstructions in different species, organs and environmental conditions, these comparisons require a standardized framework for the reconstruction of metabolic… [Read More]

Complex Evolutionary History of Translation Elongation Factor 2 and Diphthamide Biosynthesis in Archaea and Parabasalids

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph)… [Read More]

Metagenomic insights into diazotrophic communities across Arctic glacier forefields

Microbial nitrogen fixation is crucial for building labile nitrogen stocks and facilitating higher plant colonization in oligotrophic glacier forefield soils. Here, the diazotrophic bacterial community structure across four Arctic glacier forefields was investigated using metagenomic analysis. In total, 70 soil metagenomes were used for taxonomic interpretation based on 185 nitrogenase (nif) sequences, extracted from assembled… [Read More]

Expressing the Thermoanaerobacterium saccharolyticum pforA in engineered Clostridium thermocellum improves ethanol production

Background: Clostridium thermocellum has been the subject of multiple metabolic engineering strategies to improve its ability to ferment cellulose to ethanol, with varying degrees of success. For ethanol production in C. thermocellum, the conversion of pyruvate to acetyl-CoA is catalyzed primarily by the pyruvate ferredoxin oxidoreductase (PFOR) pathway. Thermoanaerobacterium saccharolyticum, which was previously engineered to… [Read More]

Biogeochemical Cycling by a Low-Diversity Microbial Community in Deep Groundwater

Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for the storage of spent nuclear fuel. Microbially induced corrosion from the generation of sulphide is therefore a concern as it could potentially compromise the longevity of the copper waste canisters. Groundwater at Olkiluoto is geochemically stratified with depth and… [Read More]

Genomic Comparison of Two Family-Level Groups of the Uncultivated NAG1 Archaeal Lineage from Chemically and Geographically Disparate Hot Springs

Recent progress based on single-cell genomics and metagenomic investigations of archaea in a variety of extreme environments has led to significant advances in our understanding of the diversity, evolution, and metabolic potential of archaea, yet the vast majority of archaeal diversity remains undersampled. In this work, we coordinated single-cell genomics with metagenomics in order to… [Read More]

A compendium of geochemical information from the Saanich Inlet water column

Extensive and expanding oxygen minimum zones (OMZs) exist at variable depths in coastal and open ocean waters. As oxygen levels decline, nutrients and energy are increasingly diverted away from higher trophic levels into microbial community metabolism, resulting in fixed nitrogen loss and production of climate active trace gases including nitrous oxide and methane. While ocean… [Read More]