Biology subjects

Knudsen, K. S.

Publications and source records attributed to Knudsen, K. S..

5 recordsLinked to original sources

bioRxiv2026

The MiDAS global genome catalog: 53,501 long-read MAGs representing all core prokaryotic genera in the global activated sludge microbiome

Wastewater treatment relies on complex microbial communities, yet existing genome-resolved references for this essential engineered ecosystem remain dominated by short-read assemblies, limiting genome contiguity and linkage between taxonomic and metabolic function. We applied long-read sequencing to activated sludge from 83 globally distributed plants, reconstructing 53,501 metagenome-assembled genomes to establish the Microbial Database of Activated Sludge (MiDAS) global genome catalog. The catalog encompasses high-quality genomes for 12,047 prokaryotic species, 82% of which are not represented in GTDB release 226, and provides a median of 32 high-quality genomes for each of the 250 core prokaryotic genera previously defined in our MiDAS global 16S rRNA gene survey. This enables analyses of predicted functional traits and their ecological context, for example, we identified two sparsely represented Nitrospiraceae genera with conserved nitrite-oxidation genes that are abundant in higher-temperature wastewater treatment plants. In summary, the MiDAS genome catalog provides a framework for linking taxonomy, metabolism and ecological roles in wastewater treatment systems globally.

microbiology↗

bioRxiv2026

From soil to sea: unravelling the metabolic versatility and social dynamics of Myxococcota bacteria from different Danish environments

Myxococcota are globally distributed bacteria renowned for their remarkable ecological and biotechnological significance due to their complex lifestyles, social behaviour, and secondary metabolite production. Despite their ubiquity in diverse environments, including soil, marine, and extreme habitats, their diversity and ecological roles remain underexplored. Here, we utilized the Microflora Danica dataset, encompassing >10,000 metagenomes and >400 rRNA gene datasets from various environments in Denmark, to investigate the distribution, diversity, and metabolic potential of Myxococcota. We show that Myxococcota are ubiquitous but strongly structured by environment, with soil-associated lineages enriched in predatory and multicellular development traits, whereas aquatic-associated taxa exhibit alternative lifestyles, including anaerobic metabolism and phototrophy. Comparative genomic analysis reveals widespread potential for secondary metabolite production, hydrocarbon degradation, and organohalide transformation, alongside diverse contribution to carbon and nutrient cycling. Together, these findings redefine Myxococcota as a functionally diverse and ecologically differentiated phylum, extending beyond canonical predation and multicellularity, and underscore their promise as large reservoir of unexplored functional potential for biotechnological applications in drug discovery and environmental remediation.

ecology↗

bioRxiv2026

A national baseline for methane sink habitats and methanotroph diversity

Methane emissions account for nearly a third of the Earths effective radiative forcing, with methanotrophs playing a critical role in mitigating emissions by oxidising methane in diverse environments1. Despite their ecological importance, methanotrophic diversity and environmental distribution remain incompletely characterised due to cultivation challenges, incomplete or low-quality metagenome-assembled genomes, and limited taxonomic resolution in marker gene surveys. Here, we present a national study of the biogeography of novel and known methanotrophs across Denmarks major natural, urban and agricultural habitats, using genome-resolved classification of 10,683 metagenomes2 and 102 new methanotrophic species3. By linking metabolic potential to habitat-specific distributions, we reveal uncharacterised methanotrophs as dominant in natural ecosystems. These findings provide a comprehensive baseline of methanotroph diversity, reveal clear contrasts between natural and disturbed habitats, and highlight candidate species and habitats for future methane-mitigation strategies.

microbiology↗

bioRxiv2024

Recovery of highly contiguous genomes from complex terrestrial habitats reveals over 15,000 novel prokaryotic species and expands characterization of soil and sediment microbial communities

Genomes are fundamental to understanding microbial ecology and evolution. The emergence of high-throughput, long-read DNA sequencing has enabled recovery of microbial genomes from environmental samples at scale. However, expanding the microbial genome catalogue of soils and sediments has been challenging due to the enormous complexity of these environments. Here, we performed deep, long-read Nanopore sequencing of 154 soil and sediment samples collected across Denmark and through an optimised bioinformatics pipeline, we recovered genomes of 15,314 novel microbial species, including 4,757 high-quality genomes. The recovered microbial genomes span 1,086 novel genera and provide the first high-quality reference genomes for 612 previously known genera, expanding the phylogenetic diversity of the prokaryotic tree of life by 8 %. The long-read assemblies also enabled the recovery of thousands of complete rRNA operons, biosynthetic gene clusters and CRISPR-Cas systems, all of which were underrepresented and highly fragmented in previous terrestrial genome catalogues. Furthermore, the incorporation of the recovered MAGs into public genome databases significantly improved species-level classification rates for soil and sediment metagenomic datasets, thereby enhancing terrestrial microbiome characterization. With this study, we demonstrate that long-read sequencing and optimised bioinformatics, allows cost-effective recovery of high-quality microbial genomes from highly complex ecosystems, which remain the largest untapped source of biodiversity for expanding genome databases and filling in the gaps of the tree of life.

bioinformatics↗

bioRxiv2024

Microflora Danica: the atlas of Danish environmental microbiomes

The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes in natural and human associated environments. Recent large-scale metagenome surveys record the variety of microbial life in the oceans1, wastewater2, human gut3,4, and earth5,6, with compilations encompassing thousands of public datasets7-13. So far, large-scale microbiome studies either miss functional information or consistency in sample processing, and although they may cover thousands of locations, these are missing resolution, sparsely located, or lacking metadata. Here, we present Microflora Danica, an atlas of Danish environmental microbiomes, encompassing 10,686 shotgun metagenomes and 449 full-length 16S and 18S rRNA datasets linked to a detailed 5 level habitat classification scheme. We determine that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.

microbiology↗