| 1. |
- Esser, Sarah P., et al.
(författare)
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A predicted CRISPR-mediated symbiosis between uncultivated archaea
- 2023
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Ingår i: Nature Microbiology. - : Nature Publishing Group. - 2058-5276. ; 8, s. 1619-1633
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Tidskriftsartikel (refereegranskat)abstract
- CRISPR spacers in DPANN archaea target putative essential genes in their episymbionts and could be a widespread occurrence across diverse archaeal lineages. CRISPR-Cas systems defend prokaryotic cells from invasive DNA of viruses, plasmids and other mobile genetic elements. Here, we show using metagenomics, metatranscriptomics and single-cell genomics that CRISPR systems of widespread, uncultivated archaea can also target chromosomal DNA of archaeal episymbionts of the DPANN superphylum. Using meta-omics datasets from Crystal Geyser and Horonobe Underground Research Laboratory, we find that CRISPR spacers of the hosts Candidatus Altiarchaeum crystalense and Ca. A. horonobense, respectively, match putative essential genes in their episymbionts' genomes of the genus Ca. Huberiarchaeum and that some of these spacers are expressed in situ. Metabolic interaction modelling also reveals complementation between host-episymbiont systems, on the basis of which we propose that episymbionts are either parasitic or mutualistic depending on the genotype of the host. By expanding our analysis to 7,012 archaeal genomes, we suggest that CRISPR-Cas targeting of genomes associated with symbiotic archaea evolved independently in various archaeal lineages.
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| 2. |
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| 3. |
- Treasure, Anne M., et al.
(författare)
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Marine Mammals Exploring the Oceans Pole to Pole A Review of the MEOP Consortium
- 2017
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Ingår i: Oceanography. - : The Oceanography Society. - 1042-8275. ; 30:2, s. 132-138
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Tidskriftsartikel (refereegranskat)abstract
- Polar oceans are poorly monitored despite the important role they play in regulating Earth's climate system. Marine mammals equipped with biologging devices are now being used to fill the data gaps in these logistically difficult to sample regions. Since 2002, instrumented animals have been generating exceptionally large data sets of oceanographic CTD casts (>500,000 profiles), which are now freely available to the scientific community through the MEOP data portal (http://meop.net). MEOP (Marine Mammals Exploring the Oceans Pole to Pole) is a consortium of international researchers dedicated to sharing animal-derived data and knowledge about the polar oceans. Collectively, MEOP demonstrates the power and cost-effectiveness of using marine mammals as data-collection platforms that can dramatically improve the ocean observing system for biological and physical oceanographers. Here, we review the MEOP program and database to bring it to the attention of the international community.
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| 4. |
- Bornemann, Till L., V, et al.
(författare)
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Genetic diversity in terrestrial subsurface ecosystems impacted by geological degassing
- 2022
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Ingår i: Nature Communications. - : Nature Publishing Group. - 2041-1723. ; 13:1
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Tidskriftsartikel (refereegranskat)abstract
- Earth's mantle releases 38.7 +/- 2.9 Tg/yr CO2 along with other reduced and oxidized gases to the atmosphere shaping microbial metabolism at volcanic sites across the globe, yet little is known about its impact on microbial life under non-thermal conditions. Here, we perform comparative metagenomics coupled to geochemical measurements of deep subsurface fluids from a cold-water geyser driven by mantle degassing. Key organisms belonging to uncultivated Candidatus Altiarchaeum show a global biogeographic pattern and site-specific adaptations shaped by gene loss and inter-kingdom horizontal gene transfer. Comparison of the geyser community to 16 other publicly available deep subsurface sites demonstrate a conservation of chemolithoautotrophic metabolism across sites. In silico replication measures suggest a linear relationship of bacterial replication with ecosystems depth with the exception of impacted sites, which show near surface characteristics. Our results suggest that subsurface ecosystems affected by geological degassing are hotspots for microbial life in the deep biosphere. Geological degassing can impact subsurface metabolism. Here, the authors describe microbial communities from a cold-water geyser are described and compared with other deep subsurface sites, finding a key role for an uncultivated archaeon.
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| 5. |
- Kataria, S., et al.
(författare)
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Chemical vapor deposited graphene : From synthesis to applications
- 2014
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Ingår i: Physica Status Solidi (a) applications and materials science. - : Wiley. - 1862-6300 .- 1862-6319. ; 211:11, s. 2439-2449
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Forskningsöversikt (refereegranskat)abstract
- Graphene is a material with enormous potential for numerous applications. Therefore, significant efforts are dedicated to large-scale graphene production using a chemical vapor deposition (CVD) technique. In addition, research is directed at developing methods to incorporate graphene in established production technologies and process flows. In this paper, we present a brief review of available CVD methods for graphene synthesis. We also discuss scalable methods to transfer graphene onto desired substrates. Finally, we discuss potential applications that would benefit from a fully scaled, semiconductor technology compatible production process.
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| 6. |
- Nilsson, Måns, et al.
(författare)
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Interlinkages, Integration and Coherence
- 2022
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Ingår i: The Political Impact of the Sustainable Development Goals : Transforming Governance Through Global Goals? - Transforming Governance Through Global Goals?. - : Cambridge University Press. - 9781316514290 - 9781009082945 ; , s. 92-115
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Bokkapitel (refereegranskat)abstract
- This chapter focuses on the national level and studies interlinkages, institutional integration and policy coherence in the context of the 2030 Agenda for Sustainable Development and the Sustainable Development Goals. After defining key terms, the chapter reviews how perspectives on interlinkages have shaped a new discourse, followed by an analysis of the steering effects of the global goals on institutional integration and policy coherence. The chapter finds that some measures have been taken by national governments to advance institutional integration through coordination by central agencies and inter-ministerial exchanges. Growing policy coherence, however, is not clearly observable. Existing barriers in political-administrative systems preventing institutional integration and policy coherence have not vanished with the adoption of the Sustainable Development Goals. Although recent studies have considerably enhanced knowledge on the conceptual understanding of interlinkages, integration and coherence, empirical data about how these concepts play out in practice at national level is still very limited.
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| 7. |
- Rahlff, Janina, et al.
(författare)
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Host-Associated Phages Disperse across the Extraterrestrial Analogue Antarctica
- 2022
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Ingår i: Applied and Environmental Microbiology. - : American Society for Microbiology. - 0099-2240 .- 1098-5336. ; 88:10
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Tidskriftsartikel (refereegranskat)abstract
- Extreme Antarctic conditions provide one of the closest analogues of extraterrestrial environments. Since air and snow samples, especially from polar regions, yield DNA amounts in the lower picogram range, binning of prokaryotic genomes is challenging and renders studying the dispersal of biological entities across these environments difficult. Here, we hypothesized that dispersal of host-associated bacteriophages (adsorbed, replicating, or prophages) across the Antarctic continent can be tracked via their genetic signatures, aiding our understanding of virus and host dispersal across long distances. Phage genome fragments (PGFs) reconstructed from surface snow metagenomes of three Antarctic stations were assigned to four host genomes, mainly Betaproteobacteria, including Ralstonia spp. We reconstructed the complete genome of a temperate phage with nearly complete alignment to a prophage in the reference genome of Ralstonia pickettii 12D. PGFs from different stations were related to each other at the genus level and matched similar hosts. Metagenomic read mapping and nucleotide polymorphism analysis revealed a wide dispersal of highly identical PGFs, 13 of which were detected in seawater from the Western Antarctic Peninsula at a distance of 5,338 km from the snow sampling stations. Our results suggest that host-associated phages, especially of Ralstonia sp., disperse over long distances despite the harsh conditions of the Antarctic continent. Given that 14 phages associated with two R. pickettii draft genomes isolated from space equipment were identified, we conclude that Ralstonia phages are ideal mobile genetic elements to track dispersal and contamination in ecosystems relevant for astrobiology.IMPORTANCE Host-associated phages of the bacterium Ralstonia identified in snow samples can be used to track microbial dispersal over thousands of kilometers across the Antarctic continent, which functions as an extraterrestrial analogue because of its harsh environmental conditions. Due to the presence of these bacteria carrying genome-integrated prophages on space-related equipment and the potential for dispersal of host-associated phages demonstrated here, our work has implications for planetary protection, a discipline in astrobiology interested in preventing contamination of celestial bodies with alien biomolecules or forms of life.
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| 8. |
- Rahlff, Janina, et al.
(författare)
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Lytic archaeal viruses infect abundant primary producers in Earth's crust
- 2021
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Ingår i: Nature Communications. - : Springer Nature. - 2041-1723. ; 12:1
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Tidskriftsartikel (refereegranskat)abstract
- The continental subsurface houses a major portion of life's abundance and diversity, yet little is known about viruses infecting microbes that reside there. Here, we use a combination of metagenomics and virus-targeted direct-geneFISH (virusFISH) to show that highly abundant carbon-fixing organisms of the uncultivated genus Candidatus Altiarchaeum are frequent targets of previously unrecognized viruses in the deep subsurface. Analysis of CRISPR spacer matches display resistances of Ca. Altiarchaea against eight predicted viral clades, which show genomic relatedness across continents but little similarity to previously identified viruses. Based on metagenomic information, we tag and image a putatively viral genome rich in protospacers using fluorescence microscopy. VirusFISH reveals a lytic lifestyle of the respective virus and challenges previous predictions that lysogeny prevails as the dominant viral lifestyle in the subsurface. CRISPR development over time and imaging of 18 samples from one subsurface ecosystem suggest a sophisticated interplay of viral diversification and adapting CRISPR-mediated resistances of Ca. Altiarchaeum. We conclude that infections of primary producers with lytic viruses followed by cell lysis potentially jump-start heterotrophic carbon cycling in these subsurface ecosystems. Little is known about viral-host interactions in the continental subsurface. Here, the authors use a combination of metagenomics, fluorescence in situ hybridization, and electron microscopy to show infections of abundant C-fixing subsurface archaea by lytic viruses.
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| 9. |
- Roth, Philipp J., et al.
(författare)
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Differentiation of charcoal, soot and diagenetic carbon in soil : method comparison and perspectives
- 2012
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Ingår i: Organic Geochemistry. - : Elsevier BV. - 0146-6380 .- 1873-5290. ; 46, s. 66-75
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Tidskriftsartikel (refereegranskat)abstract
- The various sources of pyrogenic and coalified carbon (black carbon, BC) in soil have considerable structural heterogeneity, making the quantification of BC a challenge. This study was aimed at evaluating the capability of different detection procedures to recover different types of BC from soil. We added defined quantities of urban dust (UD, NIST SRM1649a), diesel particulate matter (DPM, NIST SRM2975), charcoal, lignite, bituminous coal and wood to four topsoil samples. Mixtures were analyzed by way of chemothermal oxidation (CTO), thermal gradient oxidation (ThG), the benzene polycarboxylic acid method (BPCA) and mid-infrared spectroscopy (MIRS). CTO returned good quantification of soot BC in the pure DPM, yet the recovery of soot BC from soil was unsatisfactory (18-270%). ThG gave good precision but lower values for pure soot BC. It severely overestimated the BC content for all soil-standard mixtures. The BPCA method gave a low return for soot BC, but for the spiked soil it reliably detected charcoal and coalified C (69-107% avg. recovery) but underestimated soot BC (52-90% recovery of DPM). Linear coherence in specific MIR vibrations was found in one component soil-BC mixtures for each BC type. Applying these standard calibrations to multi-component mixtures allowed detecting charcoal and a quantification of soot BC (88% avg. recovery) via MIRS, but ignored the presence of diagenetic C. We see the greatest potential in differentiating soot from charcoal in soil by employing a combination of chemical and thermal oxidation and MIRS, while the differentiation from diagenetic C is not possible yet.
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| 10. |
- Schwank, Katrin, et al.
(författare)
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An archaeal symbiont-host association from the deep terrestrial subsurface
- 2019
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Ingår i: The ISME Journal. - : NATURE PUBLISHING GROUP. - 1751-7362 .- 1751-7370. ; 13:8, s. 2135-2139
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Tidskriftsartikel (refereegranskat)abstract
- DPANN archaea have reduced metabolic capacities and are diverse and abundant in deep aquifer ecosystems, yet little is known about their interactions with other microorganisms that reside there. Here, we provide evidence for an archaeal hostsymbiont association from a deep aquifer system at the Colorado Plateau (Utah, USA). The symbiont, Candidatus Huberiarchaeum crystalense, and its host, Ca. Altiarchaeum hamiconexum, show a highly significant co-occurrence pattern over 65 metagenome samples collected over six years. The physical association of the two organisms was confirmed with genome-informed fluorescence in situ hybridization depicting small cocci of Ca. H. crystalense attached to Ca. A. hamiconexum cells. Based on genomic information, Ca. H. crystalense potentially scavenges vitamins, sugars, nucleotides, and reduced redox-equivalents from its host and thus has a similar metabolism as Nanoarchaeum equitans. These results provide insight into host-symbiont interactions among members of two uncultivated archaeal phyla that thrive in a deep subsurface aquifer.
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| 11. |
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