| 1. |
- Baker, Brett J., et al.
(författare)
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Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
- 2016
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Ingår i: Nature Microbiology. - 2058-5276. ; 1:3
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Tidskriftsartikel (refereegranskat)abstract
- The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H-2 oxidation (or H-2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.
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| 2. |
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| 3. |
- Eme, Laura, et al.
(författare)
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Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
- 2023
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Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 992-
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Tidskriftsartikel (refereegranskat)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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| 4. |
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| 5. |
- Guy, Lionel, et al.
(författare)
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The Archaeal Legacy of Eukaryotes : A Phylogenomic Perspective
- 2014
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Ingår i: Cold Spring Harbor Perspectives in Biology. - : Cold Spring Harbor Laboratory. - 1943-0264. ; 6:10, s. a016022-
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Tidskriftsartikel (refereegranskat)abstract
- The origin of the eukaryotic cell can be regarded as one of the hallmarks in the history of life on our planet. The apparent genomic chimerism in eukaryotic genomes is currently best explained by invoking a cellular fusion at the root of the eukaryotes that involves one archaeal and one or more bacterial components. Here, we use a phylogenomics approach to reevaluate the evolutionary affiliation between Archaea and eukaryotes, and provide further support for scenarios in which the nuclear lineage in eukaryotes emerged from within the archaeal radiation, displaying a strong phylogenetic affiliation with, or even within, the archaeal TACK superphylum. Further taxonomic sampling of archaeal genomes in this superphylum will certainly provide a better resolution in the events that have been instrumental for the emergence of the eukaryotic lineage.
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| 6. |
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| 7. |
- Richert, Inga, et al.
(författare)
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Bacterial communities in a tar-contaminated lake sediment
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- Organic anthropogenic pollutants, such as polycyclic aromatic hydrocarbons (PAHs) are widespread in nature and even low concentrations can be harmful for many organisms. To assess if also microbiota residing in freshwater sediments respond to such contaminants a lake sediment adjacent to the former discharge of a factory that conducted tar distillation in the early 20th century in central Sweden were studied. We compared the bacterial community composition (BCC) at sites affected by high tar loads to BCC in a linked, but pristine sediment, and a downstream site that is likely influenced by regular diffusive loads of PAHs. PAH and VOC (Volatile Organic Carbon) concentrations were analyzed whereas sediment aliquots were used for molecular identification of the local BCC. Here we took the opportunity to compare the bacteria abundance-data retrieved from two distinct approaches; two OTU tables were generated based on either paired-end MiSeq Illumina 16S rRNA gene amplicon sequencing or direct HiSeq Illumina-based metagenome sequencing of sediment DNA extracts. Both methods revealed that the high PAH loads adjacent to the tar factory significantly alters the BCC compared to the less affected sites, even though they both partly result in contrasting outcome. The highly contaminated sediments hosted a bacterial community that was low in richness, featuring taxa known to colonize habitats with high PAH loads. For instance the relative abundance of Sphingomonadales and Burkhoderiales, both orders, within the phylum Proteobacteria, increased relative to the pristine site as well as Acidimicrobiales, one subclass of Actinobacteria. Interestingly the sediment downstream of the former factory outlet was colonized by bacteria which were very similar in community composition to the pristine site upstream of the factory outlet, implying a capacity of the natural sediment microbiota to cope with low levels of PAH contamination.
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| 8. |
- Saw, Jimmy H., et al.
(författare)
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Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
- 2015
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Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 370:1678
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Tidskriftsartikel (refereegranskat)abstract
- The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteo-bacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.
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| 9. |
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| 10. |
- Spang, Anja, et al.
(författare)
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Close Encounters of the Third Domain : The Emerging Genomic View of Archaeal Diversity and Evolution
- 2013
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Ingår i: Archaea. - : Hindawi Limited. - 1472-3646 .- 1472-3654. ; 2013, s. 202358-
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Forskningsöversikt (refereegranskat)abstract
- The Archaea represent the so-called Third Domain of life, which has evolved in parallel with the Bacteria and which is implicated to have played a pivotal role in the emergence of the eukaryotic domain of life. Recent progress in genomic sequencing technologies and cultivation-independent methods has started to unearth a plethora of data of novel, uncultivated archaeal lineages. Here, we review how the availability of such genomic data has revealed several important insights into the diversity, ecological relevance, metabolic capacity, and the origin and evolution of the archaeal domain of life.
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