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Overexpression of REDUCED WALL ACETYLATION C increases xylan acetylation and biomass recalcitrance in Populus.

Plant lignocellulosic biomass, i.e., secondary cell walls of plants, is a vital alternative source for bioenergy. However, the acetylation of xylan in secondary cell walls impedes the conversion of biomass to biofuels. Previous studies have shown that REDUCED WALL ACETYLATION (RWA) proteins are directly involved in the acetylation of xylan, but the regulatory mechanism of… [Read More]

Highly diverse and unknown viruses may enhance Antarctic endoliths’ adaptability

BackgroundRock-dwelling microorganisms are key players in ecosystem functioning of Antarctic ice free-areas. Yet, little is known about their diversity and ecology, and further still, viruses in these communities have been largely unexplored despite important roles related to host metabolism and nutrient cycling. To begin to address this, we present a large-scale viral catalog from Antarctic… [Read More]

An HMM approach expands the landscape of sesquiterpene cyclases across the kingdom Fungi

Sesquiterpene cyclases (STC) catalyse the cyclization of the C15 molecule farnesyl diphosphate into a vast variety of mono- or polycyclic hydrocarbons and, for a few enzymes, oxygenated structures, with diverse stereogenic centres. The huge diversity in sesquiterpene skeleton structures in nature is primarily the result of the type of cyclization driven by the STC. Despite… [Read More]

Water mass age structures the auxiliary metabolic gene content of free-living and particle-attached deep ocean viral communities

BackgroundViruses play important roles in the ocean’s biogeochemical cycles. Yet, deep ocean viruses are one of the most under-explored fractions of the global biosphere. Little is known about the environmental factors that control the composition and functioning of their communities or how they interact with their free-living or particle-attached microbial hosts.ResultsWe analysed 58 viral communities… [Read More]

Terabase-Scale Coassembly of a Tropical Soil Microbiome

Petabases of environmental metagenomic data are publicly available, presenting an opportunity to characterize complex environments and discover novel lineages of life. Metagenome coassembly, in which many metagenomic samples from an environment are simultaneously analyzed to infer the underlying genomes’ sequences, is an essential tool for achieving this goal. We applied MetaHipMer2, a distributed metagenome assembler… [Read More]

Physiological and genomic evidence of cysteine degradation and aerobic hydrogen sulfide production in freshwater bacteria

The sulfur-containing amino acid cysteine is abundant in the environment, including in freshwater lakes. Biological cysteine degradation can result in hydrogen sulfide (H2S), a toxic and ecologically relevant compound that is a central player in biogeochemical cycling in aquatic environments. Here, we investigated the ecological significance of cysteine in oxic freshwater, using isolated cultures, controlled… [Read More]

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

In the ongoing debates about eukaryogenesis—the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors—members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes1. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved2–4. Here… [Read More]

Synthase-selected sorting approach identifies a beta-lactone synthase in a nudibranch symbiotic bacterium

BackgroundNudibranchs comprise a group of > 6000 marine soft-bodied mollusk species known to use secondary metabolites (natural products) for chemical defense. The full diversity of these metabolites and whether symbiotic microbes are responsible for their synthesis remains unexplored. Another issue in searching for undiscovered natural products is that computational analysis of genomes of uncultured microbes can result… [Read More]

Comparative Genomics Using the Integrated Microbial Genomes and Microbiomes (IMG/M) System: A Deinococcus Use Case

The Integrated Microbial Genomes and Microbiomes (IMG/M) system is a web-based platform that provides access to the wealth of public sequence data arising from diverse environments and enables the user to answer biological questions. In this review, we explore IMG’s tools and features using genome data for genus Deinococcus isolates as well as metagenome-assembled genomes… [Read More]