A5008685503- Microbial Community Ecology and Physiology
- Genomics and Phylogenetic Studies
- Gut microbiota and health
- Environmental DNA in Biodiversity Studies
- Marine and coastal ecosystems
- Methane Hydrates and Related Phenomena
- Scientific Computing and Data Management
- Research Data Management Practices
- Bacteriophages and microbial interactions
- Probiotics and Fermented Foods
- Gene expression and cancer classification
- Atmospheric and Environmental Gas Dynamics
- CO2 Sequestration and Geologic Interactions
- Wastewater Treatment and Nitrogen Removal
- Analog and Mixed-Signal Circuit Design
- Anodic Oxide Films and Nanostructures
- Advanced Proteomics Techniques and Applications
- Algorithms and Data Compression
- Scientific Research and Discoveries
- Pharmaceutical and Antibiotic Environmental Impacts
- Ichthyology and Marine Biology
- Isotope Analysis in Ecology
- Reservoir Engineering and Simulation Methods
- Semiconductor materials and devices
- Climate change and permafrost
Science for Life Laboratory
2014-2022
KTH Royal Institute of Technology
2014-2022
Stockholm University
2019
Microbes are main drivers of biogeochemical cycles in oceans and lakes. Although the genome is a foundation for understanding metabolism, ecology evolution an organism, few bacterioplankton genomes have been sequenced, partly due to difficulties cultivating them. We use automatic binning reconstruct large number from metagenomic time-series Baltic Sea, one world's largest brackish water bodies. These represent novel species within typical freshwater marine clades, including clades not...
We introduce DESMAN for De novo Extraction of Strains from Metagenomes. Large multi-sample metagenomes are being generated but strain variation results in fragmentary co-assemblies. Current algorithms can bin contigs into metagenome-assembled genomes unable to resolve strain-level variation. identifies variants core genes and uses co-occurrence across samples link haplotypes abundance profiles. These then searched against non-core determine the accessory genome each strain. validated on a...
Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for most part limited minority that has been successfully cultured. Molecular techniques now allow obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses may ultimately improve understanding these key organisms. We compared results from two culture-independent strategies recovering bacterial genomes: single-amplified...
Abstract The genome encodes the metabolic and functional capabilities of an organism should be a major determinant its ecological niche. Yet, it is unknown if niche can predicted directly from genome. Here, we conduct metagenomic binning on 123 water samples spanning environmental gradients Baltic Sea. resulting 1961 metagenome-assembled genomes represent 352 species-level clusters that correspond to 1/3 metagenome sequences prokaryotic size-fraction. By using machine-learning, placement...
Abstract Microbial life is widespread in the terrestrial subsurface and present down to several kilometers depth, but energy sources that fuel metabolism deep oligotrophic anoxic environments remain unclear. In crystalline bedrock of Fennoscandian Shield at Olkiluoto, Finland, opposing gradients abiotic methane ancient seawater-derived sulfate create a sulfate-methane transition zone (SMTZ). We used chemical isotopic data coupled genome-resolved metaproteogenomics demonstrate active and, for...
Metagenomics enables the reconstruction of microbial genomes in complex communities without need for culturing. Since assembly typically results fragmented grouping genome fragments (contigs) belonging to same genome, a process referred as binning, remains major informatics challenge. Here we present CONCOCT, computer program that combines three types information - sequence composition, coverage across multiple sample, and read-pair linkage automatically bin contigs into genomes. We...
Abstract The standardization, portability, and reproducibility of analysis pipelines is a renowned problem within the bioinformatics community. Most are designed for execution on-premise, associated software dependencies tightly coupled with local compute environment. This leads to poor pipeline portability ensuing results - both which fundamental requirements validation scientific findings. Here, we introduce nf-core : framework that provides community-driven, peer-reviewed platform...
Olkiluoto, an island on the south-west coast of Finland, will host a deep geological repository for storage spent nuclear fuel. Microbially induced corrosion from generation sulphide is therefore concern as it could potentially compromise longevity copper waste canisters. Groundwater at Olkiluoto geochemically stratified with depth and elevated concentrations are observed when sulphate-rich methane-rich groundwaters mix. Particularly high in groundwater fracture 530.6 mbsl, where mixing...
Abstract The Baltic Sea is one of the world’s largest brackish water bodies and characterised by pronounced physicochemical gradients where microbes are main biogeochemical catalysts. Meta-omic methods provide rich information on composition of, activities within, microbial ecosystems, but computationally heavy to perform. We here present Reference Metagenome (BARM), complete with annotated genes facilitate further studies much less computational effort. assembly constructed using 2.6...
Abstract Bacterioplankton are main drivers of biogeochemical cycles and important components aquatic food webs. While sequencing-based studies have revealed how bacterioplankton communities structured in time space, relatively little is known about intraspecies diversity patterns their ecological relevance. Here, we use the newly developed software POGENOM (POpulation GENomics from Metagenomes) to investigate genomic differentiation metagenome-assembled genomes Baltic Sea, variation using...
Urban sewer systems consist of wastewater and stormwater sewers, which only is processed before being discharged. Occasionally, misconnections or damages in the network occur, resulting untreated entering natural water bodies via system. Cultivation faecal indicator bacteria (e.g. Escherichia coli; E. coli) current standard for tracing contamination. This method cheap but has limited specificity mobility. Here, we compared coli culturing approach with two sequencing-based methodologies...
ABSTRACT Heterotrophic bacteria are important drivers of nitrogen (N) cycling and the processing dissolved organic matter (DOM). Projected increases in precipitation will potentially cause increased loads riverine DOM to Baltic Sea likely affect composition function bacterioplankton communities. To investigate this, effects from two different catchment areas (agricultural forest) on natural assemblages contrasting sites were examined. Two microcosm experiments carried out, where community...
Summary Bacteria are major drivers of biogeochemical nutrient cycles and energy fluxes in marine environments, yet how bacterial communities respond to environmental change is not well known. Metagenomes allow examination genetic responses the entire microbial community change. However, it challenging link metagenomes directly process rates. Here, we investigate metagenomic natural bacterioplankton simulated stressors Baltic Sea, including increased river water input, concentration, reduced...
Abstract Microbes are main drivers of biogeochemical cycles in oceans and lakes, yet surprisingly few bacterioplankton genomes have been sequenced, partly due to difficulties cultivating them. Here we used automatic binning reconstruct a large number from metagenomic time-series the Baltic Sea. The represent novel species within freshwater marine clades, including clades not previously genome-sequenced. Their seasonal dynamics followed phylogenetic patterns, but with fine-grained lineage...
Bacteria are ubiquitous and live in complex microbial communities. Due to differences physiological properties niche preferences among community members, communities respond specific ways environmental drivers, potentially resulting distinct fingerprints for a given state. As proof of the principle, our goal was assess opportunities limitations machine learning detect indicating presence munition compound 2,4,6-trinitrotoluene (TNT) southwestern Baltic Sea sediments. Over 40 variables...
Abstract Background We introduce DESMAN for De novo Extraction of Strains from MetAgeNomes. Metagenome sequencing generates short reads throughout the genomes a microbial community. Increasingly large, multi-sample metagenomes, stratified in space and time are being generated communities with thousands species. Repeats result fragmentary co-assemblies potentially millions contigs. Contigs can be binned into metagenome assembled (MAGs) but strain level variation will remain. identifies...
Abstract Background Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for most part limited minority that has been successfully cultured. Molecular techniques now allow obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses may ultimately improve understanding these key organisms. Results We compared results from two culture-independent strategies recovering bacterial...