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Repeated migration, interbreeding and bottlenecking shaped the phylogeography of the selfing grass Brachypodium stacei

Brachypodium stacei is the most ancestral lineage in the genus Brachypodium, a model system for grass functional genomics. B. stacei shows striking and sometimes contradictory biological and evolutionary features, including a high selfing rate yet extensive admixture, an ancient Miocene origin yet with recent evolutionary radiation, and adaptation to different dry climate conditions in its narrow… [Read More]

Glacier-preserved Tibetan Plateau viral community probably linked to warm–cold climate variations

Glaciers archive time-structured information on climates and ecosystems, including microorganisms. However, the long-term ecogenomic dynamics or biogeography of the preserved viruses and their palaeoclimatic connections remain uninvestigated. Here we use metagenomes to reconstruct viral genomes from nine time horizons, spanning three cold-to-warm cycles over the past >41,000 years, preserved in an ice core from Guliya Glacier,… [Read More]

Orthophosphate uptake onto woodchips in denitrifying bioreactors is enhanced by anoxic-(anaerobic-)oxic cycling

Woodchips are widely used as a low-cost and renewable organic carbon source for denitrifying biofilms in passive nutrient removal systems. One limitation of wood-based biofiltration systems is their relatively poor removal of phosphorus (P) from subsurface drainage and stormwaters, necessitating the use of additional filter media when co-treatment of nitrogen (N) and P is required…. [Read More]

AraR plays a more dominant role than XlnR in plant biomass conversion in Penicillium subrubescens

Penicillium subrubescens is a promising candidate for industrial applications as its plant cell wall-degrading enzyme production levels and saccharification abilities are similar to that of the well-established industrial species Aspergillus niger. Interestingly, it has an expanded repertoire of hemicellulases, pectinases and inulinases in its genome compared to other Penicillia, that may enable a more targeted… [Read More]

Microorganisms Involved in Methylmercury Demethylation and Mercury Reduction are Widely Distributed and Active in the Bathypelagic Deep Ocean Waters

The ocean’s mercury (Hg) content has tripled due to anthropogenic activities, and although the dark ocean (>200 m) has become an important Hg reservoir, concentrations of the toxic and bioaccumulative methylmercury (MeHg) are low and therefore very difficult to measure. As a consequence, the current understanding of the Hg cycle in the deep ocean is… [Read More]

Time-series metagenomics reveals changing protistan ecology of a temperate dimictic lake

BackgroundProtists, single-celled eukaryotic organisms, are critical to food web ecology, contributing to primary productivity and connecting small bacteria and archaea to higher trophic levels. Lake Mendota is a large, eutrophic natural lake that is a Long-Term Ecological Research site and among the world’s best-studied freshwater systems. Metagenomic samples have been collected and shotgun sequenced from… [Read More]

Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales

DNA N6-adenine methylation (6mA) has recently gained importance as an epigenetic modification in eukaryotes. Its function in lineages with high levels, such as early-diverging fungi (EDF), is of particular interest. Here, we investigated the biological significance and evolutionary implications of 6mA in EDF, which exhibit divergent evolutionary patterns in 6mA usage. The analysis of two… [Read More]

Functional genomic screening in Komagataella phaffii enabled by high-activity CRISPR-Cas9 library

CRISPR-based high-throughput genome-wide loss-of-function screens are a valuable approach to functional genetics and strain engineering. The yeast Komagataella phaffii is a host of particular interest in the biopharmaceutical industry and as a metabolic engineering host for proteins and metabolites. Here, we design and validate a highly active 6-fold coverage genome-wide sgRNA library for this biotechnologically… [Read More]

High phenotypic and genotypic plasticity among strains of the mushroom-forming fungus Schizophyllum commune

Schizophyllum commune is a mushroom-forming fungus notable for its distinctive fruiting bodies with split gills. It is used as a model organism to study mushroom development, lignocellulose degradation and mating type loci. It is a hypervariable species with considerable genetic and phenotypic diversity between the strains. In this study, we systematically phenotyped 16 dikaryotic strains… [Read More]

Comparative transcriptomics provides insights into molecular mechanisms of zinc tolerance in the ectomycorrhizal fungus Suillus luteus

Zinc (Zn) is a major soil contaminant and high Zn levels can disrupt growth, survival, and reproduction of fungi. Some fungal species evolved Zn tolerance through cell processes mitigating Zn toxicity, although the genes and detailed mechanisms underlying mycorrhizal fungal Zn tolerance remain unexplored. To fill this gap in knowledge, we investigated the gene expression… [Read More]