| 1. |
- Alneberg, Johannes, et al.
(author)
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Genomes from uncultivated prokaryotes : a comparison of metagenome-assembled and single-amplified genomes
- 2018
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In: Microbiome. - : BioMed Central. - 2049-2618. ; 6
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Journal article (peer-reviewed)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms. Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (average 99.51% sequence identity; range 98.77-99.84%) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs. Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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| 2. |
- Alneberg, Johannes, et al.
(author)
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Genomes from uncultivated prokaryotes: a comparison of metagenome-assembled and single-amplified genomes
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Other publication (other academic/artistic)abstract
- Background: Prokaryotes dominate the biosphere and regulate biogeochemical processes essential to all life. Yet, our knowledge about their biology is for the most part limited to the minority that has been successfully cultured. Molecular techniques now allow for obtaining genome sequences of uncultivated prokaryotic taxa, facilitating in-depth analyses that may ultimately improve our understanding of these key organisms.Results: We compared results from two culture-independent strategies for recovering bacterial genomes: single-amplified genomes and metagenome-assembled genomes. Single-amplified genomes were obtained from samples collected at an offshore station in the Baltic Sea Proper and compared to previously obtained metagenome-assembled genomes from a time series at the same station. Among 16 single-amplified genomes analyzed, seven were found to match metagenome-assembled genomes, affiliated with a diverse set of taxa. Notably, genome pairs between the two approaches were nearly identical (>98.7% identity) across overlapping regions (30-80% of each genome). Within matching pairs, the single-amplified genomes were consistently smaller and less complete, whereas the genetic functional profiles were maintained. For the metagenome-assembled genomes, only on average 3.6% of the bases were estimated to be missing from the genomes due to wrongly binned contigs; the metagenome assembly was found to cause incompleteness to a higher degree than the binning procedure.Conclusions: The strong agreement between the single-amplified and metagenome-assembled genomes emphasizes that both methods generate accurate genome information from uncultivated bacteria. Importantly, this implies that the research questions and the available resources are allowed to determine the selection of genomics approach for microbiome studies.
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| 3. |
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| 4. |
- Bäckström, Disa, et al.
(author)
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Virus Genomes from Deep Sea Sediments Expand the Ocean Megavirome and Support Independent Origins of Viral Gigantism
- 2019
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In: mBio. - 2161-2129 .- 2150-7511. ; 10:2
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Journal article (peer-reviewed)abstract
- The nucleocytoplasmic large DNA viruses (NCLDV) of eukaryotes (proposed order, “Megavirales”) include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified pithoviruses, pandoraviruses, molliviruses, and faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep sea sediments from the Loki’s Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high-quality genomic bins of novel NCLDV, 15 of which are related to pithoviruses, 5 to marseilleviruses, 1 to iridoviruses, and 2 to klosneuviruses. Some of the identified pithovirus-like and marseillevirus-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses, including putative giant members of the family Marseilleviridae, have a broad range of apparent genome sizes, in agreement with the multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the pithovirus-iridovirus-marseillevirus branch of the NCLDV. Similarly to other giant viruses, the pithovirus-like viruses from Loki’s Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than had been detected previously. Genome comparison suggests extensive gene exchange between members of the pithovirus-like viruses and Mimiviridae. Further exploration of the genomic diversity of Megavirales in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.Importance: Genomics and evolution of giant viruses are two of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diversity of the nucleocytoplasmic large DNA viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.
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| 5. |
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| 6. |
- Clement, Yves, et al.
(author)
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Evolutionary forces affecting synonymous variations in plant genomes
- 2017
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In: PLOS Genetics. - : PUBLIC LIBRARY SCIENCE. - 1553-7390 .- 1553-7404. ; 13:5
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Journal article (peer-reviewed)abstract
- Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.
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| 7. |
- Dharamshi, Jennah E., et al.
(author)
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Marine Sediments Illuminate Chlamydiae Diversity and Evolution
- 2020
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In: Current Biology. - : Elsevier BV. - 0960-9822 .- 1879-0445. ; 30:6, s. 1032-1048.e7
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Journal article (peer-reviewed)abstract
- The bacterial phylum Chlamydiae is so far composed of obligate symbionts of eukaryotic hosts. Well known for Chlamydiaceae, pathogens of humans and other animals, Chlamydiae also include so-called environmental lineages that primarily infect microbial eukaryotes. Environmental surveys indicate that Chlamydiae are found in a wider range of environments than anticipated previously. However, the vast majority of this chlamydial diversity has been underexplored, biasing our current understanding of their biology, ecological importance, and evolution. Here, we report that previously undetected and active chlamydial lineages dominate microbial communities in deep anoxic marine sediments taken from the Arctic Mid-Ocean Ridge. Reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic units, these Chlamydiae represent important community members. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, expanding by over a third the known genomic diversity in this phylum. Phylogenomic analyses revealed several novel clades across the phylum, including a previously unknown sister lineage of the Chlamydiaceae, providing new insights into the origin of pathogenicity in this family. We were unable to identify putative eukaryotic hosts for these marine sediment chlamydiae, despite identifying genomic features that may be indicative of host-association. The high abundance and genomic diversity of Chlamydiae in these anoxic marine sediments indicate that some members could play an important, and thus far overlooked, ecological role in such environments and may indicate alternate lifestyle strategies.
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| 8. |
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| 9. |
- Eme, Laura, et al.
(author)
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Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
- 2023
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In: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 992-
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Journal article (peer-reviewed)abstract
- In the ongoing debates about eukaryogenesis-the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors-members of the Asgard archaea play a key part as the closest archaeal relatives of eukaryotes(1). However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved(2-4). Here we analyse distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably a thermophilic chemolithotroph and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
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| 10. |
- Hammond, Maria, et al.
(author)
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Picodroplet partitioned whole genome amplification of low biomass samples preserves genomic diversity for metagenomic analysis
- 2016
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In: Microbiome. - : BioMed Central. - 2049-2618. ; 4
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Journal article (peer-reviewed)abstract
- Background: Whole genome amplification (WGA) is a challenging, key step in metagenomic studies of samples containing minute amounts of DNA, such as samples from low biomass environments. It is well known that multiple displacement amplification (MDA), the most commonly used WGA method for microbial samples, skews the genomic representation in the sample. We have combined MDA with droplet microfluidics to perform the reaction in a homogeneous emulsion. Each droplet in this emulsion can be considered an individual reaction chamber, allowing partitioning of the MDA reaction into millions of parallel reactions with only one or very few template molecules per droplet. Results: As a proof-of-concept, we amplified genomic DNA from a synthetic metagenome by MDA either in one bulk reaction or in emulsion and found that after sequencing, the species distribution was better preserved and the coverage depth was more evenly distributed across the genomes when the MDA reaction had been performed in emulsion. Conclusions: Partitioning MDA reactions into millions of reactions by droplet microfluidics is a straightforward way to improve the uniformity of MDA reactions for amplifying complex samples with limited amounts of DNA.
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| 11. |
- Sjöberg, Susanne, et al.
(author)
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Bubble biofilm : Bacterial colonization of air-air interface
- 2020
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In: Biofilm. - : Elsevier. - 2590-2075. ; 2
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Journal article (peer-reviewed)abstract
- Microbial mats or biofilms are known to colonize a wide range of substrates in aquatic environments. These dense benthic communities efficiently recycle nutrients and often exhibit high tolerance to environmental stressors, characteristics that enable them to inhabit harsh ecological niches. In some special cases, floating biofilms form at the air-water interface residing on top of a hydrophobic microlayer. Here, we describe biofilms that reside at the air-air interface by forming gas bubbles (bubble biofilms) in the former Ytterby mine, Sweden. The bubbles are built by micrometer thick membrane-like biofilm that holds enough water to sustain microbial activity. Molecular identification shows that the biofilm communities are dominated by the neuston bacterium Nevskia. Gas bubbles contain mostly air with a slightly elevated concentration of carbon dioxide. Biofilm formation and development was monitored in situ using a time-lapse camera over one year, taking one image every second hour. The bubbles were stable over long periods of time (weeks, even months) and gas build-up occurred in pulses as if the bedrock suddenly exhaled. The result was however not a passive inflation of a dying biofilm becoming more fragile with time (as a result of overstretching of the organic material). To the contrary, microbial growth lead to a more robust, hydrophobic bubble biofilm that kept the bubbles inflated for extended periods (several weeks, and in some cases even months).
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| 12. |
- Sjöberg, Susanne, et al.
(author)
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Microbiomes in a manganese oxide producing ecosystem in the Ytterby mine, Sweden : impact on metal mobility
- 2020
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In: FEMS Microbiology Ecology. - : Oxford University Press. - 0168-6496 .- 1574-6941. ; 96:11
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Journal article (peer-reviewed)abstract
- Microbe-mediated precipitation of Mn-oxides enriched in rare earth elements (REE) and other trace elements was discovered in tunnels leading to the main shaft of the Ytterby mine, Sweden. Defining the spatial distribution of microorganisms and elements in this ecosystem provide a better understanding of specific niches and parameters driving the emergence of these communities and associated mineral precipitates. Along with elemental analyses, high-throughput sequencing of the following four subsystems were conducted: (1) water seeping from a rock fracture into the tunnel, (2) Mn-oxides and associated biofilm; referred to as the Ytterby Black Substance (YBS) biofilm (3) biofilm forming bubbles on the Mn-oxides; referred to as the bubble biofilm, and (4) fracture water that has passed through the biofilms. Each subsystem hosts a specific collection of microorganisms. Differentially abundant bacteria in the YBS biofilm were identified within the Rhizobiales (e.g. Pedomicrobium), PLTA13 Gammaproteobacteria, Pirellulaceae, Hyphomonadaceae, Blastocatellia and Nitrospira. These taxa, likely driving the Mn-oxide production, were not detected in the fracture water. This biofilm binds Mn, REE and other trace elements in an efficient, dynamic process, as indicated by substantial depletion of these metals from the fracture water as it passes through the Mn deposit zone. Microbe-mediated oxidation of Mn(II) and formation of Mn(III/IV)-oxides can thus have considerable local environmental impact by removing metals from aquatic environments.
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| 13. |
- Sjöberg, Susanne, 1969-, et al.
(author)
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Mn oxide precipitation by epilithic biofilms in the Ytterby mine, Sweden : formation of an YREE-enriched birnessite
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Other publication (other academic/artistic)abstract
- Biofilms scavenge and bind reduced Mn(II) as well as stabilize highly reactive Mn(III), favouring formation of Mn oxides. Mn oxidation and precipitation involve closely connected and concomitant abiotic and biotic biogeochemical mechanisms, often making the biogenicity of the mineral product difficult to determine. In order to use these precipitates as potential biosignatures, profound knowledge of the formation pathways is required. Here we have access to an underground Mn oxide producing ecosystem in which epilithic biofilms precipitate yttrium and rare earth element enriched birnessite-type Mn oxides. Microbial community composition combined with elemental data is investigated to provide insight into how different subsystems of this ecosystem (fracture water, Mn oxide producing biofilm, and bubble biofilm) interact with each other to form the birnessite. We find that the microbial assembly of the feeding water has little impact on the derived biofilms, in which the signature microbial groups rather results from water chemistry and environmental conditions. In the Mn oxide producing biofilm, bacteria are adapted to the emerging extreme environment (low temperature, no light, high metal concentration) which is generated by the biofilm itself. Microstructural characterizations show that the birnessite has a dendritic/shrublike or spherulitic/botryoidal growth pattern. Nucleation occurs in close association to the biofilm and Mn encrustations of cells and other organic structures serve as stable nuclei for further growth. The influence of organics decrease in importance as precipitates grow. In more evolved crystals, a repetitive pattern, Liesegang-type of rings, implies that abiotic factors dominate. Grown on a solid substrate, four bacterial (Hydrogenophaga sp., Pedobacter sp., Rhizobium sp. and Nevskia sp.) and one fungal species (Cladosporium sp.) are involved in Mn oxide production. Hydrogenophaga and Pedobacter oxidize Mn independently while Rhizobium needs a synergistic relationship with selected species (e.g., Nevskia). Members of the Pedobacter and Nevskia genera are previously not known Mn oxidizers. The onset of Mn precipitaiton takes place at different locations with respect to the cells for the different species. Precipitates are located intracellularly (possibly post mortem), on the bacterial cell walls, at the outer edges of more well developed crystals, within the extracellular organic matter (EOM) and on hyphal surfaces.
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