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Recovery of genomes from metagenomes via a dereplication, aggregation and scoring strategy

Microbial communities are critical to ecosystem function. A key objective of metagenomic studies is to analyse organism-specific metabolic pathways and reconstruct community interaction networks. This requires accurate assignment of assembled genome fragments to genomes. Existing binning methods often fail to reconstruct a reasonable number of genomes and report many bins of low quality and completeness…. [Read More]

Targeted in situ metatranscriptomics for selected taxa from mesophilic and thermophilic biogas plants

Biogas production is performed anaerobically by complex microbial communities with key species driving the process. Hence, analyses of their in situ activities are crucial to understand the process. In a previous study, metagenome sequencing and subsequent genome binning for different production-scale biogas plants (BGPs) resulted in four genome bins of special interest, assigned to the… [Read More]

Microbial life under ice: Metagenome diversity and in situ activity of Verrucomicrobia in seasonally ice-covered Lakes

Northern lakes are ice-covered for a large part of the year, yet our understanding of microbial diversity and activity during winter lags behind that of the ice-free period. In this study, we investigated under-ice diversity and metabolism of Verrucomicrobia in seasonally ice-covered lakes in temperate and boreal regions of Quebec, Canada using 16S rRNA sequencing,… [Read More]

Adaptations to marine versus terrestrial low temperature environments as revealed by comparative genomic analyses of the genus Psychrobacter

While cold-adapted bacteria isolated from marine or terrestrial low temperature environments share many similarities, cold-adapted bacteria from terrestrial environments usually grow over a broader range of temperatures suggesting different constraints of these two low temperature environments. The diversity of habitats from which Psychrobacter have been isolated (e.g. cold marine environments, frozen soils, permafrost and humans)… [Read More]

A mosaic monoploid reference sequence for the highly complex genome of sugarcane

Sugarcane (Saccharum spp.) is a major crop for sugar and bioenergy production. Its highly polyploid, aneuploid, heterozygous, and interspecific genome poses major challenges for producing a reference sequence. We exploited colinearity with sorghum to produce a BAC-based monoploid genome sequence of sugarcane. A minimum tiling path of 4660 sugarcane BAC that best covers the gene-rich… [Read More]

Coupled laboratory and field investigations resolve microbial interactions that underpin persistence in hydraulically fractured shales

Hydraulic fracturing is one of the industrial processes behind the surging natural gas output in the United States. This technology inadvertently creates an engineered microbial ecosystem thousands of meters below Earth’s surface. Here, we used laboratory reactors to perform manipulations of persisting shale microbial communities that are currently not feasible in field scenarios. Metaproteomic and… [Read More]

Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure

While prokaryotic pan-genomes have been shown to contain many more genes than any individual organism, the prevalence and functional significance of differentially present genes in eukaryotes remains poorly understood. Whole-genome de novo assembly and annotation of 54 lines of the grass Brachypodium distachyon yield a pan-genome containing nearly twice the number of genes found in… [Read More]

Genome-Scale Data Call for a Taxonomic Rearrangement of Geodermatophilaceae

Geodermatophilaceae (order Geodermatophilales, class Actinobacteria) form a comparatively isolated family within the phylum Actinobacteria and harbor many strains adapted to extreme ecological niches and tolerant against reactive oxygen species. Clarifying the evolutionary history of Geodermatophilaceae was so far mainly hampered by the insufficient resolution of the main phylogenetic marker in use, the 16S rRNA gene…. [Read More]

Comparative transcriptomics as a guide to natural product discovery and biosynthetic gene cluster functionality

Bacterial natural products remain an important source of new medicines. DNA sequencing has revealed that a majority of natural product biosynthetic gene clusters (BGCs) maintained in bacterial genomes have yet to be linked to the small molecules whose biosynthesis they encode. Efforts to discover the products of these orphan BGCs are driving the development of… [Read More]