Biology subjects

Albertsen, M.

Publications and source records attributed to Albertsen, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Nation-scale recovery of complete environmental plasmids pushes the boundaries of plasmid diversity through long-read sequencing

Plasmids are important agents of prokaryotic evolution and yet existing reference databases remain biased towards cultivable species, limiting our knowledge of their function and ecology in the environment. Here we present a major expansion of known plasmid diversity, through curation and annotation of 8,744 topologically complete plasmids from 9,972 short- and 154 long-read metagenomes as part of the Microflora Danica project. These were found to increase plasmid taxonomic unit diversity by 15% and 99% relative to all and environmental plasmids, respectively, from public sources. In particular, we identify a novel lineage of plasmids in the genus Methanosarcina, encoding genes associated with methanogenesis and cell surface properties, expanding our understanding of chromosome-plasmid complementarity and its potential contribution to host biology. Combining our plasmids with public sources, we curated a set of 17 replication-associated proteins that could be found in 82% of known plasmids and can serve as hallmarks for future detection of plasmids. We present this resource, and a tool for confirming topological completeness of plasmid assemblies, as a toolkit for future plasmid discovery.

microbiology↗

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

Ecological specificity and interconnectivity in Danish environmental resistomes

The environment plays a critical role in "One Health", facilitating the evolution, persistence, and dissemination of antibiotic resistance genes (ARGs). However, environmental resistomes have primarily been characterized through scattered studies of individual habitats, limiting our understanding of baseline resistome structure and connectivity across landscapes at a national level. Here, we analyzed metagenomes from 7,000 Danish environmental samples (24 Tbp), collected from 21 distinct habitats including soils, sediments, aquatic environments and wastewater treatment plants (WWTPs). We identified core ARGs for establishing the environmental baseline, and habitat-associated indicator ARGs for facilitating source tracking. Using an additional 110 deep long-read metagenomes (9 Tbp data), we found a subset of cross-habitat commonly abundant ARGs was carried by diverse hosts and associated with mobile genetic elements, suggesting their potential role in resistome connectivity across ecosystems. Additionally, although natural habitats had much lower resistome relative abundance and transferability than human-associated habitats, some mobile environmental ARGs exhibited links to those in human pathogens. Our results support the implementation of environmental resistome surveillance by providing an environmental ARG baseline, enabling future ARG source-tracking and cross-habitat ARG dissemination assessment.

microbiology↗

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

Proposal of Patescibacterium danicum gen. nov., sp. nov. in the ubiquitous ultrasmall bacterial phylum Patescibacteriota phyl. nov.

Candidatus Patescibacteria is a diverse bacterial phylum that is notable for members with ultrasmall cell size, reduced genomes, limited metabolic capabilities and dependence on other prokaryotic hosts. Despite the prevalence of the name Ca. Patescibacteria in the scientific literature, it is not officially recognized under the International Code of Nomenclature of Prokaryotes (ICNP) and lacks a nomenclatural type. Here, we rectify this situation by describing two closely related circular metagenome-assembled genomes (MAGs) and by proposing one of them (ABY1TS) to serve as the nomenclatural type for the species Patescibacterium danicumTS gen. nov., sp. nov. according to the rules of the SeqCode. Rank-normalized phylogenomic inference confirmed the stable placement of P. danicumTS in the class ABY1 within Ca. Patescibacteria. Based on these results, we propose Patescibacterium gen. nov. to serve as the type genus for associated higher taxa, including the phylum Patescibacteriota phyl. nov. We complement our proposal with a genomic characterization, metabolic reconstruction, and biogeographical analysis of Patescibacterium. Our results confirm small genome sizes (< 1Mbp), low GC content (>36%), and the occurrence of long gene coding insertions in the 23S rRNA sequences, along with reduced metabolic potential, inferred symbiotic lifestyle, and a global distribution. In summary, this effort, focused on the fourth-largest phylum in the bacterial domain, aims to provide nomenclatural stability in the scientific literature.

microbiology↗

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↗

bioRxiv2024

Nanomotif: Identification and Exploitation of DNA Methylation Motifs in Metagenomes using Oxford Nanopore Sequencing

DNA methylation is found across all domains of life but is a rarely used feature in recovery of metagenome-assembled genomes (MAGs). Recently, Oxford Nanopore introduced all context methylation detection models. We leveraged this to develop Nanomotif, which identifies and exploits methylation motifs for enhanced MAG recovery. We demonstrate how Nanomotif enables database-independent contamination removal from high-quality MAGs and host association of plasmids directly from Nanopore sequencing data in complex metagenomes.

bioinformatics↗

bioRxiv2024

Extracellular electron transfer genes expressed by candidate flocking bacteria in cable bacteria sediment

Cable bacteria, filamentous sulfide oxidizers that live in sediments, are at times associated with large flocks of swimming bacteria. It has been proposed that these flocks of bacteria transport electrons extracellularly to cable bacteria via an electron shuttle intermediate, but the identity and activity of these bacteria in freshwater sediment remains mostly uninvestigated. We coupled metagenomics and metatranscriptomics to 16S rRNA amplicon-based correlations with cable bacteria from two time series experiments up to 155 days. We identified bacteria expressing genes for extracellular electron transfer and motility, including synthesis genes for potential extracellular electron shuttles: phenazines and flavins. Of the 85 high quality MAGs (Metagenome Assembled Genomes >90% complete and <5% contaminated), 56 had genes encoding flagellar proteins, and of these 22 had genes encoding extracellular electron transport proteins. The candidate flockers constituted 21.4% of all MAGs and 42.1% of the proposed flocking bacteria expressed extracellular electron transfer genes. The proposed flockers belonged to a large variety of taxonomic groups: 18 genera spread across 9 phyla. Our data suggest that electric relationships in freshwater sediments between cable bacteria and other microbes likely help to generate and/or sustain cryptic element cycling and deep oxygen breathing, affecting more element cycles than sulfur, like metal- and in particular iron- and carbon cycles.

microbiology↗

bioRxiv2023

High-throughput DNA extraction and cost-effective miniaturized metagenome and amplicon library preparation of soil samples for DNA sequencing

Reductions in sequencing costs have enabled widespread use of shotgun metagenomics and amplicon sequencing, which have drastically improved our understanding of the microbial world. However, large sequencing projects are now hampered by the cost of library preparation and low sample throughput. Here, we benchmarked three high-throughput DNA extraction methods: ZymoBIOMICS 96 MagBead DNA Kit, MP BiomedicalsTM FastDNATM-96 Soil Microbe DNA Kit, and DNeasy(R) 96 PowerSoil(R) Pro QIAcube(R) HT Kit. The DNA extractions were evaluated based on length, quality, quantity, and the observed microbial community across five diverse soil types. DNA extraction of all soil types was successful for all kits, however DNeasy(R) 96 PowerSoil(R) Pro QIAcube(R) HT Kit excelled across all performance parameters. We further used the nanoliter dispensing robot I.DOT One to miniaturize Illumina amplicon and metagenomic library preparation volumes by a factor of 5 and 10, respectively, with no significant impact on the observed microbial communities. With these protocols, DNA extraction, metagenomic library preparation, or amplicon library preparation for one 96-well plate are approx. 3, 5, and 6 hours, respectively. Furthermore, the miniaturization of amplicon and metagenome library preparation reduces the chemical and plastic costs from 5.0 to 3.6 and 59 to 7.3 USD pr. sample.

microbiology↗

bioRxiv2023

Production of extracellular polymeric substances in granular sludge under selection for Accumulibacter and Competibacter

Granular sludge intensifies the removal of nutrients from wastewater. Granules structured by extracellular polymeric substances (EPS) can be recovered as biomaterial. Links between microbial selection and EPS formation during granulation need to get uncovered. We inoculated anaerobic-aerobic sequencing batch reactors with either flocs or granules to study the relationships between microbial selection, bioaggregation, exopolymer formation, and EPS composition. Selection for slow-growing organisms like the model polyphosphate- accumulating organism "Candidatus Accumulibacter" (max. 83% vs. amplicon sequencing read counts) and glycogen-accumulating organism "Ca. Competibacter" (max. 45%) sustained granulation. Gel-forming exopolymers were produced as high as above 40% of the volatile solids of the biomass by stepwise increase of the organic loading rate (0.3 to 2.0 g CODAc d-1 LR-1). Confocal laser scanning microscopy, FT-IR spectroscopy, and HPAE-PAD chromatography revealed the complex and dynamic chemical compositions of the structural EPS in relation to microbial population shifts along reactor regimes. The analysis of 20 representative genomes of "Ca. Accumulibacter" and "Ca. Competibacter" recovered from public databases revealed their functional potential to produce EPS among other representative wastewater microorganisms. The more than 40 functional gene categories annotated highlight the complexity of EPS metabolic networks from monomers processing to assembly, export, and epimerizations. The combination of ecological engineering principles and systems microbiology will help unravel and direct the production of EPS from wastewater, valorizing residual granular sludge into beneficial biomaterials for the circular economy. HighlightsO_LISelection for slow-growing organisms like PAOs and GAOs fostered a robust granulation. C_LIO_LIStructural EPS were produced above 40% of biomass volatile content under high loading. C_LIO_LIChemical composition of EPS evolved together with the microbial community composition. C_LIO_LIGenomic insights highlighted the genetic potential of PAOs and GAOs for EPS formation. C_LIO_LIMicrobial communities are complex; further are their EPS compositions and metabolisms. C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/534144v1_ufig1.gif" ALT="Figure 1"> View larger version (45K): org.highwire.dtl.DTLVardef@a163e2org.highwire.dtl.DTLVardef@1a4ab94org.highwire.dtl.DTLVardef@1fc93d4org.highwire.dtl.DTLVardef@14d4b7f_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Greengenes2 enables a shared data universe for microbiome studies

16S rRNA and shotgun metagenomics studies typically yield different results, usually attributed to biases in PCR amplification of 16S rRNA genes. Here, we introduce Greengenes2 and show that differences in reference phylogeny are more important. By inserting sequences into a whole-genome phylogeny, we show that 16S rRNA and shotgun metagenomic data generated from the same samples agree in principal coordinates space, taxonomy, and in phenotype effect size when analyzed with the same tree.

bioinformatics↗

bioRxiv2022

Closed genomes uncover a saltwater species of Candidatus Electronema and shed new light on the boundary between marine and freshwater cable bacteria

Cable bacteria of the Desulfobulbaceae family are centimeter-long filamentous bacteria, which are capable of conducting long-distance electron transfer. Currently, all cable bacteria are classified into two candidate genera: Candidatus Electronema, typically found in freshwater environments, and Candidatus Electrothrix, typically found in saltwater environments. This taxonomic framework is based on both 16S rRNA gene sequences and metagenome-assembled genome (MAG) phylogenies. However, most of the currently available MAGs are highly fragmented, incomplete, and thus likely miss key genes essential for deciphering the physiology of cable bacteria. To address this, we performed Nanopore long read (total 162.4 Gbp) and Illumina short read (total 148.3 Gbp) shotgun sequencing of selected environmental samples and a single-strain enrichment of Ca. Electronema aureum. We recovered multiple cable bacteria MAGs, including two circular and one single-contig. Phylogenomic analysis, also confirmed by 16S rRNA gene-based phylogeny, classified one circular MAG and the single-contig MAG as novel species of cable bacteria, which we propose to name Ca. Electronema halotolerans and Ca. Electrothrix laxa, respectively. The Ca. Electronema halotolerans, despite belonging to the previously recognized freshwater genus of cable bacteria, was retrieved from brackish-water sediment. Metabolic predictions showed several adaptations to a high salinity environment, similar to the "saltwater" Ca. Electrothrix species, indicating how Ca. Electronema halotolerans may be the evolutionary link between marine and freshwater cable bacteria lineages.

microbiology↗

bioRxiv2022

Taurine as a key intermediate for host-symbiont interaction in the tropical sponge Ianthella basta

Marine sponges are critical components of marine benthic fauna assemblages where their filter-feeding and reef-building capabilities provide bentho-pelagic coupling and crucial habitat. As potentially the oldest representation of a metazoan-microbe symbiosis, they also harbor dense, diverse, and species-specific communities of microbes, which are increasingly recognized for their contributions to dissolved organic matter (DOM) processing. Recent omics-based studies of marine sponge microbiomes have proposed numerous pathways of dissolved metabolite exchange between the host and symbionts within the context of the surrounding environment, but few studies have sought to experimentally interrogate these pathways. By using a combination of metaproteogenomics and laboratory incubations coupled with isotope-based functional assays, we showed that the dominant gammaproteobacterial symbiont Candidatus Taurinisymbion ianthellae residing in the marine sponge, Ianthella basta, expresses a pathway for the import and dissimilation of taurine, a ubiquitously occurring sulfonate metabolite in marine sponges. Candidatus Taurinisymbion ianthellae incorporates taurine-derived carbon and nitrogen while, at the same time, oxidizing the dissimilated sulfite into sulfate for export. Furthermore, we found that taurine-derived ammonia is exported by the symbiont for immediate oxidation by the dominant ammonia-oxidizing thaumarchaeal symbiont Candidatus Nitrosospongia ianthellae. Metaproteogenomic analyses also indicate that Candidatus Taurinisymbion ianthellae likely imports DMSP and possesses both pathways for DMSP demethylation and cleavage, enabling it to use this compound as a carbon and sulfur source for biomass, as well as for energy conservation. These results highlight the important role of biogenic sulfur compounds in the interplay between Ianthella basta and its microbial symbionts.

microbiology↗

bioRxiv2022

Metagenomic binning with assembly graph embeddings

Despite recent advancements in sequencing technologies and assembly methods, obtaining high-quality microbial genomes from metagenomic samples is still not a trivial task. Current metagenomic binners do not take full advantage of assembly graphs and are not optimized for long-read assemblies. Deep graph learning algorithms have been proposed in other fields to deal with complex graph data structures. The graph structure generated during the assembly process could be integrated with contig features to obtain better bins with deep learning. We propose GraphMB, which uses graph neural networks to incorporate the assembly graph into the binning process. We test GraphMB on long-read datasets of different complexities, and compare the performance with other binners in terms of the number of High Quality (HQ) genome bins obtained. With our approach, we were able to obtain unique bins on all real datasets, and obtain more bins on most datasets. In particular, we obtained on average 17.5% more HQ bins when compared to state-of-the-art binners and 13.7% when aggregating the results of our binner with the others. These results indicate that a deep learning model can integrate contig-specific and graph-structure information to improve metagenomic binning. GraphMB is available from https://github.com/MicrobialDarkMatter/GraphMB.

bioinformatics↗

bioRxiv2021

Assessing long-read sequencing with Nanopore R9, R10, and PacBio CCS to obtain high-quality metagenome assembled genomes from complex microbial communities

Long-read Oxford Nanopore sequencing has democratized microbial genome sequencing and enables the recovery of highly contiguous microbial genomes from isolates or metagenomes. However, to obtain near-perfect genomes it has been necessary to include short-read polishing to correct insertions and deletions derived from homopolymer regions. Here, we show that Oxford Nanopore R10.4 can be used to generate near-perfect microbial genomes from isolates or metagenomes without shortread or reference polishing.

microbiology↗

bioRxiv2021

MiDAS 4: A global catalogue of full-length 16S rRNA gene sequences and taxonomy for studies of bacterial communities in wastewater treatment plants

Biological wastewater treatment and an increased focus on resource recovery is fundamental for environmental protection, human health, and sustainable development. Microbial communities are responsible for these processes, but our knowledge of their diversity and function is still poor, partly due to the lack of good reference databases and comprehensive global studies. Here, we sequenced more than 5 million high-quality, full-length 16S rRNA gene sequences from 740 wastewater treatment plants (WWTPs) across the world and used the sequences to construct MiDAS 4, a full-length amplicon sequence variant resolved 16S rRNA gene reference database with a comprehensive taxonomy from the domain to species-level for all references. Using a study-independent amplicon dataset from the Global Water Microbiome Consortium project (269 WWTPs), we showed that the MiDAS 4 database provides much better coverage for bacteria in WWTPs worldwide compared to commonly applied universal references databases, and greatly improved the rate of genus and species-level classification. Hence, MiDAS 4 provides a unifying taxonomy for the majority of prokaryotic diversity in WWTPs globally, which can be used for linking microbial identities with their functions across studies. Taking advantage of MiDAS 4, we carried out an amplicon-based, global-scale microbial community profiling of activated sludge plants using two common sets of primers targeting the V1-V3 and V4 region of the 16S rRNA gene. We found that the V1-V3 primers were generally best suited for this ecosystem, and revealed how environmental conditions and biogeography shape the activated sludge microbiota. We also identified process-critical taxa (core and conditionally rare or abundant taxa), encompassing 966 genera and 1530 species. These represented approximately 80% and 50% of the accumulated read abundance, respectively, and represent targets for further investigations. Finally, we showed that for well-studied functional guilds, such as nitrifiers or polyphosphate accumulating organisms, the same genera were prevalent worldwide, with only a few abundant species in each genus.

microbiology↗