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  • 1
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    The first day of the Cenozoic
    Proceedings of the National Academy of Sciences ; 2019
    In:  Proceedings of the National Academy of Sciences Vol. 116, No. 39 ( 2019-09-24), p. 19342-19351
    Details
    In: Proceedings of the National Academy of Sciences, Proceedings of the National Academy of Sciences, Vol. 116, No. 39 ( 2019-09-24), p. 19342-19351
    Abstract: Highly expanded Cretaceous–Paleogene (K-Pg) boundary section from the Chicxulub peak ring, recovered by International Ocean Discovery Program (IODP)–International Continental Scientific Drilling Program (ICDP) Expedition 364, provides an unprecedented window into the immediate aftermath of the impact. Site M0077 includes ∼130 m of impact melt rock and suevite deposited the first day of the Cenozoic covered by 〈 1 m of micrite-rich carbonate deposited over subsequent weeks to years. We present an interpreted series of events based on analyses of these drill cores. Within minutes of the impact, centrally uplifted basement rock collapsed outward to form a peak ring capped in melt rock. Within tens of minutes, the peak ring was covered in ∼40 m of brecciated impact melt rock and coarse-grained suevite, including clasts possibly generated by melt–water interactions during ocean resurge. Within an hour, resurge crested the peak ring, depositing a 10-m-thick layer of suevite with increased particle roundness and sorting. Within hours, the full resurge deposit formed through settling and seiches, resulting in an 80-m-thick fining-upward, sorted suevite in the flooded crater. Within a day, the reflected rim-wave tsunami reached the crater, depositing a cross-bedded sand-to-fine gravel layer enriched in polycyclic aromatic hydrocarbons overlain by charcoal fragments. Generation of a deep crater open to the ocean allowed rapid flooding and sediment accumulation rates among the highest known in the geologic record. The high-resolution section provides insight into the impact environmental effects, including charcoal as evidence for impact-induced wildfires and a paucity of sulfur-rich evaporites from the target supporting rapid global cooling and darkness as extinction mechanisms.
    Type of Medium: Online Resource
    ISSN: 0027-8424 , 1091-6490
    URL: Article
    DOI: 10.1073/pnas.1909479116
    RVK:
    TA 1000
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    Language: English
    Publisher: Proceedings of the National Academy of Sciences
    Publication Date: 2019
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  • 2
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    Biochemical diversity of glycosphingolipid biosynthesis as a driver of Coccolithovirus competitive ecology
    Wiley ; 2019
    In:  Environmental Microbiology Vol. 21, No. 6 ( 2019-06), p. 2182-2197
    Details
    In: Environmental Microbiology, Wiley, Vol. 21, No. 6 ( 2019-06), p. 2182-2197
    Abstract: Coccolithoviruses (EhVs) are large, double‐stranded DNA‐containing viruses that infect the single‐celled, marine coccolithophore Emiliania huxleyi . Given the cosmopolitan nature and global importance of E. huxleyi as a bloom‐forming, calcifying, photoautotroph, E. huxleyi –EhV interactions play a key role in oceanic carbon biogeochemistry. Virally‐encoded glycosphingolipids (vGSLs) are virulence factors that are produced by the activity of virus‐encoded serine palmitoyltransferase (SPT). Here, we characterize the dynamics, diversity and catalytic production of vGSLs in an array of EhV strains in relation to their SPT sequence composition and explore the hypothesis that they are a determinant of infectivity and host demise. vGSL production and diversity was positively correlated with increased virulence, virus replication rate and lytic infection dynamics in laboratory experiments, but they do not explain the success of less‐virulent EhVs in natural EhV communities. The majority of EhV‐derived SPT amplicon sequences associated with infected cells in the North Atlantic derived from slower infecting, less virulent EhVs. Our lab‐, field‐ and mathematical model‐based data and simulations support ecological scenarios whereby slow‐infecting, less‐virulent EhVs successfully compete in North Atlantic populations of E. huxleyi , through either the preferential removal of fast‐infecting, virulent EhVs during active infection or by having access to a broader host range.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2019.21.issue-6
    DOI: 10.1111/1462-2920.14633
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2020213-1
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  • 3
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    Environmental paleomicrobiology: using DNA preserved in aquatic sediments to its full potential
    Wiley ; 2022
    In:  Environmental Microbiology Vol. 24, No. 5 ( 2022-05), p. 2201-2209
    Details
    In: Environmental Microbiology, Wiley, Vol. 24, No. 5 ( 2022-05), p. 2201-2209
    Abstract: In‐depth knowledge about spatial and temporal variation in microbial diversity and function is needed for a better understanding of ecological and evolutionary responses to global change. In particular, the study of microbial ancient DNA preserved in sediment archives from lakes and oceans can help us to evaluate the responses of aquatic microbes in the past and make predictions about future biodiversity change in those ecosystems. Recent advances in molecular genetic methods applied to the analysis of historically deposited DNA in sediments have not only allowed the taxonomic identification of past aquatic microbial communities but also enabled tracing their evolution and adaptation to episodic disturbances and gradual environmental change. Nevertheless, some challenges remain for scientists to take full advantage of the rapidly developing field of paleo‐genetics, including the limited ability to detect rare taxa and reconstruct complete genomes for evolutionary studies. Here, we provide a brief review of some of the recent advances in the field of environmental paleomicrobiology and discuss remaining challenges related to the application of molecular genetic methods to study microbial diversity, ecology, and evolution in sediment archives. We anticipate that, in the near future, environmental paleomicrobiology will shed new light on the processes of microbial genome evolution and microbial ecosystem responses to quaternary environmental changes at an unprecedented level of detail. This information can, for example, aid geological reconstructions of biogeochemical cycles and predict ecosystem responses to environmental perturbations, including in the context of human‐induced global changes.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.v24.5
    DOI: 10.1111/1462-2920.15913
    Language: English
    Publisher: Wiley
    Publication Date: 2022
    detail.hit.zdb_id: 2020213-1
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  • 4
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    Microbial biogeography of drinking water: patterns in phylogenetic diversity across space and time
    Wiley ; 2015
    In:  Environmental Microbiology Vol. 17, No. 7 ( 2015-07), p. 2505-2514
    Details
    In: Environmental Microbiology, Wiley, Vol. 17, No. 7 ( 2015-07), p. 2505-2514
    Abstract: In this study, we collected water from different locations in 32 drinking water distribution networks in the N etherlands and analysed the spatial and temporal variation in microbial community composition by high‐throughput sequencing of 16S rRNA gene amplicons. We observed that microbial community compositions of raw source and processed water were very different for each distribution network sampled. In each network, major differences in community compositions were observed between raw and processed water, although community structures of processed water did not differ substantially from end‐point tap water. End‐point water samples within the same distribution network revealed very similar community structures. Network‐specific communities were shown to be surprisingly stable in time. Biofilm communities sampled from domestic water metres varied distinctly between households and showed no resemblance to planktonic communities within the same distribution networks. Our findings demonstrate that high‐throughput sequencing provides a powerful and sensitive tool to probe microbial community composition in drinking water distribution systems. Furthermore, this approach can be used to quantitatively compare the microbial communities to match end‐point water samples to specific distribution networks. Insight in the ecology of drinking water distribution systems will facilitate the development of effective control strategies that will ensure safe and high‐quality drinking water.
    Type of Medium: Online Resource
    ISSN: 1462-2912 , 1462-2920
    URL: Issue
    URL: Article
    DOI: 10.1111/emi.2015.17.issue-7
    DOI: 10.1111/1462-2920.12739
    Language: English
    Publisher: Wiley
    Publication Date: 2015
    detail.hit.zdb_id: 2020213-1
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  • 5
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    7000 Years of Emiliania huxleyi Viruses in the Black Sea
    American Association for the Advancement of Science (AAAS) ; 2011
    In:  Science Vol. 333, No. 6041 ( 2011-07-22), p. 451-452
    Details
    In: Science, American Association for the Advancement of Science (AAAS), Vol. 333, No. 6041 ( 2011-07-22), p. 451-452
    Abstract: A 7000-year record of Coccolithovirus and its host, the calcifying haptophyte Emiliania huxleyi , was reconstructed on the basis of genetic signatures preserved in sediments underlying the Black Sea. The data show that the same virus and host populations can persist for centuries. Major changes in virus and host populations occurred during early sapropel deposition, ~5600 years ago, and throughout the formation of the coccolith-bearing sediments of Unit I during the past 2500 years, when the Black Sea experienced dramatic changes in hydrologic and nutrient regimes. Unit I saw a reoccurrence of the same host genotype thousands of years later in the presence of a different subset of viruses. Historical plankton virus populations can thus be included in paleoecological and paleoenvironmental studies.
    Type of Medium: Online Resource
    ISSN: 0036-8075 , 1095-9203
    URL: Article
    DOI: 10.1126/science.1200072
    RVK:
    TA 1000
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    WA 15000
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2011
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    detail.hit.zdb_id: 2066996-3
    detail.hit.zdb_id: 2060783-0
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  • 6
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    Analysis of Subfossil Molecular Remains of Purple Sulfur Bacteria in a Lake Sediment
    American Society for Microbiology ; 1998
    In:  Applied and Environmental Microbiology Vol. 64, No. 11 ( 1998-11), p. 4513-4521
    Details
    In: Applied and Environmental Microbiology, American Society for Microbiology, Vol. 64, No. 11 ( 1998-11), p. 4513-4521
    Abstract: Molecular remains of purple sulfur bacteria ( Chromatiaceae ) were detected in Holocene sediment layers of a meromictic salt lake (Mahoney Lake, British Columbia, Canada). The carotenoid okenone and bacteriophaeophytin a were present in sediments up to 11,000 years old. Okenone is specific for only a few species of Chromatiaceae , including Amoebobacter purpureus , which presently predominates in the chemocline bacterial community of the lake. With a primer set specific for Chromatiaceae in combination with denaturing gradient gel electrophoresis, 16S rRNA gene sequences of four different Chromatiaceae species were retrieved from different depths of the sediment. One of the sequences, which originated from a 9,100-year-old sample, was 99.2% identical to the 16S rRNA gene sequence of A. purpureus ML1 isolated from the chemocline. Employing primers specific for A. purpureus ML1 and dot blot hybridization of the PCR products, the detection limit for A. purpureus ML1 DNA could be lowered to 0.004% of the total community DNA. With this approach the DNA of the isolate was detected in 7 of 10 sediment layers, indicating that A. purpureus ML1 constituted at least a part of the ancient purple sulfur bacterial community. The concentrations of A. purpureus DNA and okenone in the sediment were not correlated, and the ratio of DNA to okenone was much lower in the subfossil sediment layers (2.7 · 10 −6 ) than in intact cells (1.4). This indicates that degradation rates are significantly higher for genomic DNA than for hydrocarbon cell constituents, even under anoxic conditions and at the very high sulfide concentrations present in Mahoney Lake.
    Type of Medium: Online Resource
    ISSN: 0099-2240 , 1098-5336
    URL: Article
    DOI: 10.1128/AEM.64.11.4513-4521.1998
    RVK:
    WA 15000
    Language: English
    Publisher: American Society for Microbiology
    Publication Date: 1998
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  • 7
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    Holocene paleodepositional changes reflected in the sedimentary microbiome of the Black Sea
    Wiley ; 2019
    In:  Geobiology Vol. 17, No. 4 ( 2019-07), p. 436-448
    Details
    In: Geobiology, Wiley, Vol. 17, No. 4 ( 2019-07), p. 436-448
    Abstract: Subsurface microbial communities are generally thought to be structured through in situ environmental conditions such as the availability of electron acceptors and donors and porosity, but recent studies suggest that the vertical distribution of a subset of subseafloor microbial taxa, which were present at the time of deposition, were selected by the paleodepositional environment. However, additional highly resolved temporal records of subsurface microbiomes and paired paleoenvironmental reconstructions are needed to justify this claim. Here, we performed a highly resolved shotgun metagenomics survey to study the taxonomic and functional diversity of the subsurface microbiome in Holocene sediments underlying the permanently stratified and anoxic Black Sea. Obligate aerobic bacteria made the largest contribution to the observed shifts in microbial communities associated with known Holocene climate stages and transitions. This suggests that the aerobic fraction of the subseafloor microbiome was seeded from the water column and did not undergo post‐depositional selection. In contrast, obligate and facultative anaerobic bacteria showed the most significant response to the establishment of modern‐day environmental conditions 5.2 ka ago that led to a major shift in planktonic communities and in the type of sequestered organic matter available for microbial degradation. No significant shift in the subseafloor microbiome was observed as a result of environmental changes that occurred shortly after the marine reconnection, 9 ka ago. This supports the general view that the marine reconnection was a gradual process. We conclude that a high‐resolution analysis of downcore changes in the subseafloor microbiome can provide detailed insights into paleoenvironmental conditions and biogeochemical processes that occurred at the time of deposition.
    Type of Medium: Online Resource
    ISSN: 1472-4677 , 1472-4669
    URL: Issue
    URL: Article
    DOI: 10.1111/gbi.2019.17.issue-4
    DOI: 10.1111/gbi.12338
    Language: English
    Publisher: Wiley
    Publication Date: 2019
    detail.hit.zdb_id: 2113509-5
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  • 8
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    Neoglacial climate anomalies and the Harappan metamorphosis
    Copernicus GmbH ; 2018
    In:  Climate of the Past Vol. 14, No. 11 ( 2018-11-13), p. 1669-1686
    Details
    In: Climate of the Past, Copernicus GmbH, Vol. 14, No. 11 ( 2018-11-13), p. 1669-1686
    Abstract: Abstract. Climate exerted constraints on the growth and decline of past human societies but our knowledge of temporal and spatial climatic patterns is often too restricted to address causal connections. At a global scale, the inter-hemispheric thermal balance provides an emergent framework for understanding regional Holocene climate variability. As the thermal balance adjusted to gradual changes in the seasonality of insolation, the Intertropical Convergence Zone migrated southward accompanied by a weakening of the Indian summer monsoon. Superimposed on this trend, anomalies such as the Little Ice Age point to asymmetric changes in the extratropics of either hemisphere. Here we present a reconstruction of the Indian winter monsoon in the Arabian Sea for the last 6000 years based on paleobiological records in sediments from the continental margin of Pakistan at two levels of ecological complexity: sedimentary ancient DNA reflecting water column environmental states and planktonic foraminifers sensitive to winter conditions. We show that strong winter monsoons between ca. 4500 and 3000 years ago occurred during a period characterized by a series of weak interhemispheric temperature contrast intervals, which we identify as the early neoglacial anomalies (ENA). The strong winter monsoons during ENA were accompanied by changes in wind and precipitation patterns that are particularly evident across the eastern Northern Hemisphere and tropics. This coordinated climate reorganization may have helped trigger the metamorphosis of the urban Harappan civilization into a rural society through a push–pull migration from summer flood-deficient river valleys to the Himalayan piedmont plains with augmented winter rains. The decline in the winter monsoon between 3300 and 3000 years ago at the end of ENA could have played a role in the demise of the rural late Harappans during that time as the first Iron Age culture established itself on the Ghaggar-Hakra interfluve. Finally, we speculate that time-transgressive land cover changes due to aridification of the tropics may have led to a generalized instability of the global climate during ENA at the transition from the warmer Holocene thermal maximum to the cooler Neoglacial.
    Type of Medium: Online Resource
    ISSN: 1814-9332
    URL: Article
    URL: Article
    DOI: 10.5194/cp-14-1669-2018
    DOI: 10.5194/cp-14-1669-2018-supplement
    Language: English
    Publisher: Copernicus GmbH
    Publication Date: 2018
    detail.hit.zdb_id: 2217985-9
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  • 9
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    Probing the hydrothermal system of the Chicxulub impact crater
    American Association for the Advancement of Science (AAAS) ; 2020
    In:  Science Advances Vol. 6, No. 22 ( 2020-05-29)
    Details
    In: Science Advances, American Association for the Advancement of Science (AAAS), Vol. 6, No. 22 ( 2020-05-29)
    Abstract: The ~180-km-diameter Chicxulub peak-ring crater and ~240-km multiring basin, produced by the impact that terminated the Cretaceous, is the largest remaining intact impact basin on Earth. International Ocean Discovery Program (IODP) and International Continental Scientific Drilling Program (ICDP) Expedition 364 drilled to a depth of 1335 m below the sea floor into the peak ring, providing a unique opportunity to study the thermal and chemical modification of Earth’s crust caused by the impact. The recovered core shows the crater hosted a spatially extensive hydrothermal system that chemically and mineralogically modified ~1.4 × 10 5 km 3 of Earth’s crust, a volume more than nine times that of the Yellowstone Caldera system. Initially, high temperatures of 300° to 400°C and an independent geomagnetic polarity clock indicate the hydrothermal system was long lived, in excess of 10 6 years.
    Type of Medium: Online Resource
    ISSN: 2375-2548
    URL: Article
    DOI: 10.1126/sciadv.aaz3053
    Language: English
    Publisher: American Association for the Advancement of Science (AAAS)
    Publication Date: 2020
    detail.hit.zdb_id: 2810933-8
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  • 10
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    Figure 6: Heatmap of top ten EnvO terms for determining ES.
    PeerJ ; 2016
    In:  PeerJ Vol. 4 ( 2016-12-20), p. e2690-
    Details
    In: PeerJ, PeerJ, Vol. 4 ( 2016-12-20), p. e2690-
    Abstract: Understanding the distribution of taxa and associated traits across different environments is one of the central questions in microbial ecology. High-throughput sequencing (HTS) studies are presently generating huge volumes of data to address this biogeographical topic. However, these studies are often focused on specific environment types or processes leading to the production of individual, unconnected datasets. The large amounts of legacy sequence data with associated metadata that exist can be harnessed to better place the genetic information found in these surveys into a wider environmental context. Here we introduce a software program, seqenv , to carry out precisely such a task. It automatically performs similarity searches of short sequences against the “nt” nucleotide database provided by NCBI and, out of every hit, extracts–if it is available–the textual metadata field. After collecting all the isolation sources from all the search results, we run a text mining algorithm to identify and parse words that are associated with the Environmental Ontology (EnvO) controlled vocabulary. This, in turn, enables us to determine both in which environments individual sequences or taxa have previously been observed and, by weighted summation of those results, to summarize complete samples. We present two demonstrative applications of seqenv to a survey of ammonia oxidizing archaea as well as to a plankton paleome dataset from the Black Sea. These demonstrate the ability of the tool to reveal novel patterns in HTS and its utility in the fields of environmental source tracking, paleontology, and studies of microbial biogeography. To install seqenv , go to: https://github.com/xapple/seqenv .
    Type of Medium: Online Resource
    ISSN: 2167-8359
    URL: Article
    URL: Article
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    URL: Article
    URL: Article
    URL: Article
    DOI: 10.7717/peerj.2690
    DOI: 10.7717/peerj.2690/fig-1
    DOI: 10.7717/peerj.2690/fig-2
    DOI: 10.7717/peerj.2690/fig-3
    DOI: 10.7717/peerj.2690/fig-4
    DOI: 10.7717/peerj.2690/fig-5
    DOI: 10.7717/peerj.2690/fig-6
    Language: English
    Publisher: PeerJ
    Publication Date: 2016
    detail.hit.zdb_id: 2703241-3
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