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  • 1
    Online Resource
    Online Resource
    Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
    Springer Science and Business Media LLC ; 2023
    In:  Nature Vol. 618, No. 7967 ( 2023-06-29), p. 992-999
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 618, No. 7967 ( 2023-06-29), p. 992-999
    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.
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/s41586-023-06186-2
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 2023
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    detail.hit.zdb_id: 1413423-8
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  • 2
    Online Resource
    Online Resource
    Biogeographical distribution and diversity of microbes in methane hydrate-bearing deep marine sediments on the Pacific Ocean Margin
    Proceedings of the National Academy of Sciences ; 2006
    In:  Proceedings of the National Academy of Sciences Vol. 103, No. 8 ( 2006-02-21), p. 2815-2820
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 103, No. 8 ( 2006-02-21), p. 2815-2820
    Abstract: The deep subseafloor biosphere is among the least-understood habitats on Earth, even though the huge microbial biomass therein plays an important role for potential long-term controls on global biogeochemical cycles. We report here the vertical and geographical distribution of microbes and their phylogenetic diversities in deeply buried marine sediments of the Pacific Ocean Margins. During the Ocean Drilling Program Legs 201 and 204, we obtained sediment cores from the Peru and Cascadia Margins that varied with respect to the presence of dissolved methane and methane hydrate. To examine differences in prokaryotic distribution patterns in sediments with or without methane hydrates, we studied 〉 2,800 clones possessing partial sequences (400–500 bp) of the 16S rRNA gene and 348 representative clone sequences (≈1 kbp) from the two geographically separated subseafloor environments. Archaea of the uncultivated Deep-Sea Archaeal Group were consistently the dominant phylotype in sediments associated with methane hydrate. Sediment cores lacking methane hydrates displayed few or no Deep-Sea Archaeal Group phylotypes. Bacterial communities in the methane hydrate-bearing sediments were dominated by members of the JS1 group, Planctomycetes, and Chloroflexi. Results from cluster and principal component analyses, which include previously reported data from the West and East Pacific Margins, suggest that, for these locations in the Pacific Ocean, prokaryotic communities from methane hydrate-bearing sediment cores are distinct from those in hydrate-free cores. The recognition of which microbial groups prevail under distinctive subseafloor environments is a significant step toward determining the role these communities play in Earth’s essential biogeochemical processes.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0511033103
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2006
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    detail.hit.zdb_id: 1461794-8
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  • 3
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    Online Resource
    Heterotrophic Archaea dominate sedimentary subsurface ecosystems off Peru
    Proceedings of the National Academy of Sciences ; 2006
    In:  Proceedings of the National Academy of Sciences Vol. 103, No. 10 ( 2006-03-07), p. 3846-3851
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 103, No. 10 ( 2006-03-07), p. 3846-3851
    Abstract: Studies of deeply buried, sedimentary microbial communities and associated biogeochemical processes during Ocean Drilling Program Leg 201 showed elevated prokaryotic cell numbers in sediment layers where methane is consumed anaerobically at the expense of sulfate. Here, we show that extractable archaeal rRNA, selecting only for active community members in these ecosystems, is dominated by sequences of uncultivated Archaea affiliated with the Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group, whereas known methanotrophic Archaea are not detectable. Carbon flow reconstructions based on stable isotopic compositions of whole archaeal cells, intact archaeal membrane lipids, and other sedimentary carbon pools indicate that these Archaea assimilate sedimentary organic compounds other than methane even though methanotrophy accounts for a major fraction of carbon cycled in these ecosystems. Oxidation of methane by members of Marine Benthic Group B and the Miscellaneous Crenarchaeotal Group without assimilation of methane–carbon provides a plausible explanation. Maintenance energies of these subsurface communities appear to be orders of magnitude lower than minimum values known from laboratory observations, and ecosystem-level carbon budgets suggest that community turnover times are on the order of 100–2,000 years. Our study provides clues about the metabolic functionality of two cosmopolitan groups of uncultured Archaea.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.0600035103
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2006
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 4
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    Online Resource
    Cable bacteria, living electrical conduits in the microbial world
    Proceedings of the National Academy of Sciences ; 2019
    In:  Proceedings of the National Academy of Sciences Vol. 116, No. 38 ( 2019-09-17), p. 18759-18761
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 116, No. 38 ( 2019-09-17), p. 18759-18761
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1913413116
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2019
    detail.hit.zdb_id: 209104-5
    detail.hit.zdb_id: 1461794-8
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  • 5
    Online Resource
    Online Resource
    Late Proterozoic rise in atmospheric oxygen concentration inferred from phylogenetic and sulphur-isotope studies
    Springer Science and Business Media LLC ; 1996
    In:  Nature Vol. 382, No. 6587 ( 1996-7), p. 127-132
    Details
    In: Nature, Springer Science and Business Media LLC, Vol. 382, No. 6587 ( 1996-7), p. 127-132
    Type of Medium: Online Resource
    ISSN: 0028-0836 , 1476-4687
    URL: Article
    DOI: 10.1038/382127a0
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    Language: English
    Publisher: Springer Science and Business Media LLC
    Publication Date: 1996
    detail.hit.zdb_id: 120714-3
    detail.hit.zdb_id: 1413423-8
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  • 6
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    Formation of ethane and propane via abiotic reductive conversion of acetic acid in hydrothermal sediments
    Proceedings of the National Academy of Sciences ; 2021
    In:  Proceedings of the National Academy of Sciences Vol. 118, No. 47 ( 2021-11-23)
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 118, No. 47 ( 2021-11-23)
    Abstract: A mechanistic understanding of formation pathways of low-molecular-weight hydrocarbons is relevant for disciplines such as atmospheric chemistry, geology, and astrobiology. The patterns of stable carbon isotopic compositions (δ 13 C) of hydrocarbons are commonly used to distinguish biological, thermogenic, and abiotic sources. Here, we report unusual isotope patterns of nonmethane hydrocarbons in hydrothermally heated sediments of the Guaymas Basin; these nonmethane hydrocarbons are notably 13 C-enriched relative to sedimentary organic matter and display an isotope pattern that is reversed relative to thermogenic hydrocarbons (i.e., δ 13 C ethane 〉 δ 13 C propane 〉 δ 13 C n -butane 〉 δ 13 C n -pentane). We hypothesized that this pattern results from abiotic reductive conversion of volatile fatty acids, which were isotopically enriched due to prior equilibration of their carboxyl carbon with dissolved inorganic carbon. This hypothesis was tested by hydrous pyrolysis experiments with isotopically labeled substrates at 350 °C and 400 bar that demonstrated 1) the exchange of carboxyl carbon of C 2 to C 5 volatile fatty acids with 13 C-bicarbonate and 2) the incorporation of 13 C from 13 C-2–acetic acid into ethane and propane. Collectively, our results reveal an abiotic formation pathway for nonmethane hydrocarbons, which may be sufficiently active in organic-rich, geothermally heated sediments and petroleum systems to affect isotopic compositions of nonmethane hydrocarbons.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.2005219118
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2021
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  • 7
    Online Resource
    Online Resource
    Global dispersion and local diversification of the methane seep microbiome
    Proceedings of the National Academy of Sciences ; 2015
    In:  Proceedings of the National Academy of Sciences Vol. 112, No. 13 ( 2015-03-31), p. 4015-4020
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 112, No. 13 ( 2015-03-31), p. 4015-4020
    Abstract: Methane seeps are widespread seafloor ecosystems shaped by the emission of gas from seabed reservoirs. The microorganisms inhabiting methane seeps transform the chemical energy in methane to products that sustain rich benthic communities around the gas leaks. Despite the biogeochemical relevance of microbial methane removal at seeps, the global diversity and dispersion of seep microbiota remain unknown. Here we determined the microbial diversity and community structure of 23 globally distributed methane seeps and compared these to the microbial communities of 54 other seafloor ecosystems, including sulfate–methane transition zones, hydrothermal vents, coastal sediments, and deep-sea surface and subsurface sediments. We found that methane seep communities show moderate levels of microbial richness compared with other seafloor ecosystems and harbor distinct bacterial and archaeal taxa with cosmopolitan distribution and key biogeochemical functions. The high relative sequence abundance of ANME (anaerobic methanotrophic archaea), as well as aerobic Methylococcales , sulfate-reducing Desulfobacterales , and sulfide-oxidizing Thiotrichales , matches the most favorable microbial metabolisms at methane seeps in terms of substrate supply and distinguishes the seep microbiome from other seafloor microbiomes. The key functional taxa varied in relative sequence abundance between different seeps due to the environmental factors, sediment depth and seafloor temperature. The degree of endemism of the methane seep microbiome suggests a high local diversification in these heterogeneous but long-lived ecosystems. Our results indicate that the seep microbiome is structured according to metacommunity processes and that few cosmopolitan microbial taxa mediate the bulk of methane oxidation, with global relevance to methane emission in the ocean.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1421865112
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2015
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  • 8
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    Online Resource
    Comment on “A Persistent Oxygen Anomaly Reveals the Fate of Spilled Methane in the Deep Gulf of Mexico”
    American Association for the Advancement of Science (AAAS) ; 2011
    In:  Science Vol. 332, No. 6033 ( 2011-05-27), p. 1033-1033
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 332, No. 6033 ( 2011-05-27), p. 1033-1033
    Abstract: Kessler et al . (Reports, 21 January 2011, p. 312) reported that methane released from the 2010 Deepwater Horizon blowout, approximately 40% of the total hydrocarbon discharge, was consumed quantitatively by methanotrophic bacteria in Gulf of Mexico deep waters over a 4-month period. We find the evidence explicitly linking observed oxygen anomalies to methane consumption ambiguous and extension of these observations to hydrate-derived methane climate forcing premature.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1203307
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2011
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  • 9
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    Online Resource
    Distributions of Microbial Activities in Deep Subseafloor Sediments
    American Association for the Advancement of Science (AAAS) ; 2004
    In:  Science Vol. 306, No. 5705 ( 2004-12-24), p. 2216-2221
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 306, No. 5705 ( 2004-12-24), p. 2216-2221
    Abstract: Diverse microbial communities and numerous energy-yielding activities occur in deeply buried sediments of the eastern Pacific Ocean. Distributions of metabolic activities often deviate from the standard model. Rates of activities, cell concentrations, and populations of cultured bacteria vary consistently from one subseafloor environment to another. Net rates of major activities principally rely on electron acceptors and electron donors from the photosynthetic surface world. At open-ocean sites, nitrate and oxygen are supplied to the deepest sedimentary communities through the underlying basaltic aquifer. In turn, these sedimentary communities may supply dissolved electron donors and nutrients to the underlying crustal biosphere.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1101155
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2004
    detail.hit.zdb_id: 128410-1
    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 10
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    Cryptic Links in the Ocean
    American Association for the Advancement of Science (AAAS) ; 2010
    In:  Science Vol. 330, No. 6009 ( 2010-12-03), p. 1326-1327
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 330, No. 6009 ( 2010-12-03), p. 1326-1327
    Abstract: Oxygen depletion in the ocean water column, in stratified basins such as the Santa Barbara and Cariaco basins, and in enclosed anoxic oceans such as the Black Sea provide vivid examples of a type of marine habitat where multicellular life gradually disappears with depth as oxygen is consumed by respiration and not replenished. Only bacteria and archaea with anaerobic metabolisms persist, controlling the microbial cycling of nitrogen, sulfur, metals, and carbon. Genuine fondness for these environments and their anaerobic microbial inhabitants, although possibly an acquired taste, is widespread among marine microbiologists and geochemists who are tracing the path of key elements and the role of microbes in the ocean's biogeochemical economy. On page 1375 of this issue, Canfield et al. ( 1 ) analyze the microbial cycling of nitrogen and sulfur in the oxygen minimum zone offshore of northern Chile. They show that our working hypotheses on microbial interactions and processes of stratified marine water columns have overlooked a critical component: the contribution of the “cryptic” microbial sulfur cycle.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1198400
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    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2010
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