| 1. |
- Nilsson, R. Henrik, 1976, et al.
(författare)
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Introducing guidelines for publishing DNA-derived occurrence data through biodiversity data platforms
- 2022
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Ingår i: Metabarcoding and Metagenomics. - : Pensoft Publishers. - 2534-9708. ; 6
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Tidskriftsartikel (refereegranskat)abstract
- DNA sequencing efforts of environmental and other biological samples disclose unprecedented and largely untapped opportunities for advances in the taxonomy, ecology, and geographical distributions of our living world. To realise this potential, DNA-derived occurrence data (notably sequences with dates and coordinates) – much like traditional specimens and observations – need to be discoverable and interpretable through biodiversity data platforms. The Global Biodiversity Information Facility (GBIF) recently headed a community effort to assemble a set of guidelines for publishing DNA-derived data. These guidelines target the principles and approaches of exposing DNA-derived occurrence data in the context of broader biodiversity data. They cover a choice of terms using a controlled vocabulary, common pitfalls, and good practices, without going into platform-specific details. Our hope is that they will benefit anyone interested in better exposure of DNA-derived occurrence data through general biodiversity data platforms, including national biodiversity portals. This paper provides a brief rationale and an overview of the guidelines, an up-to-date version of which is maintained at https://doi.org/10.35035/doc-vf1a-nr22. User feedback and interaction are encouraged as new techniques and best practices emerge.
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| 2. |
- Capo, Eric, et al.
(författare)
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Oxygen-deficient water zones in the Baltic Sea promote uncharacterized Hg methylating microorganisms in underlying sediments
- 2022
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Ingår i: Limnology and Oceanography. - : Wiley. - 1939-5590 .- 0024-3590. ; 67:1
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Tidskriftsartikel (refereegranskat)abstract
- Human-induced expansion of oxygen-deficient zones can have dramatic impacts on marine systems and its resident biota. One example is the formation of the potent neurotoxic methylmercury (MeHg) that is mediated by microbial methylation of inorganic divalent Hg (HgII) under oxygen-deficient conditions. A negative consequence of the expansion of oxygen-deficient zones could be an increase in MeHg production due to shifts in microbial communities in favor of microorganisms methylating Hg. There is, however, limited knowledge about Hg-methylating microbes, i.e., those carrying hgc genes critical for mediating the process, from marine sediments. Here, we aim to study the presence of hgc genes and transcripts in metagenomes and metatranscriptomes from four surface sediments with contrasting concentrations of oxygen and sulfide in the Baltic Sea. We show that potential Hg methylators differed among sediments depending on redox conditions. Sediments with an oxygenated surface featured hgc-like genes and transcripts predominantly associated with uncultured Desulfobacterota (OalgD group) and Desulfobacterales (including Desulfobacula sp.) while sediments with a hypoxic-anoxic surface included hgc-carrying Verrucomicrobia, unclassified Desulfobacterales, Desulfatiglandales, and uncharacterized microbes. Our data suggest that the expansion of oxygen-deficient zones in marine systems may lead to a compositional change of Hg-methylating microbial groups in the sediments, where Hg methylators whose metabolism and biology have not yet been characterized will be promoted and expand.
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| 3. |
- Broman, Elias, 1985-, et al.
(författare)
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Cyanophage Diversity and Community Structure in Dead Zone Sediments
- 2021
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Ingår i: mSphere. - : American Society for Microbiology. - 2379-5042. ; 6:2
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Tidskriftsartikel (refereegranskat)abstract
- Up to 20% of prokaryotic organisms in the oceans are estimated to die every day due to viral infection and lysis. Viruses can therefore alter microbial diversity, community structure, and biogeochemical processes driven by these organisms. Cyanophages are viruses that infect and lyse cyanobacterial cells, adding bioavailable carbon and nutrients into the environment. Cyanobacteria are photosynthesizing bacteria, with some species capable of N-2 fixation, which are known to form large blooms as well as resistant resting cells known as akinetes. Here, we investigated cyanophage diversity and community structure plus cyanobacteria in dead zone sediments. We sampled surface sediments and sequenced DNA and RNA, along an oxygen gradient-representing oxic, hypoxic, and anoxic conditions-in one of the world's largest dead zones located in the Baltic Sea. Cyanophages were detected at all stations and, based on partial genome contigs, had a higher alpha diversity and different beta diversity in the hypoxic-anoxic sediments, suggesting that cyanobacteria in dead zone sediments and/or environmental conditions select for specific cyanophages. Some of these cyanophages can infect cyanobacteria with potential consequences for gene expression related to their photosystem and phosphate regulation. Top cyanobacterial genera detected in the anoxic sediment included Dolichospermum/Anabaena, Synechococcus, and Cyanobium. RNA transcripts classified to cyanobacteria were associated with numerous pathways, including anaerobic carbon metabolism and N-2 fixation. Cyanobacterial blooms are known to fuel oxygen-depleted ecosystems with phosphorus (so-called internal loading), and our cyanophage data indicate the potential for viral lysis of cyanobacteria which might explain the high nutrient turnover in these environments. IMPORTANCE Cyanophages are viruses that target cyanobacteria and directly control their abundance via viral lysis. Cyanobacteria are known to cause large blooms in water bodies, substantially contributing to oxygen depletion in bottom waters resulting in areas called dead zones. Our knowledge of cyanophages in dead zones is very scarce, and so far, no studies have assembled partial cyanophage genomes and investigated their associated cyanobacteria in these dark and anoxic sediments. Here, we present the first study using DNA and RNA sequencing to investigate in situ diversity of cyanophages and cyanobacteria in dead zones. Our study shows that dead zone sediments contain different cyanophages compared to oxic sediments and suggest that these viruses are able to affect cyanobacterial photosystem and phosphate regulation. Furthermore, cyanophage-controlled lysis of cyanobacteria might also increase the turnover of carbon, phosphorus, and nitrogen in these oxygen-free environments at the bottom of the sea.
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| 4. |
- Barnes, Paul W., et al.
(författare)
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Ozone depletion, ultraviolet radiation, climate change and prospects for a sustainable future
- 2019
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Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 2:7, s. 569-579
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Forskningsöversikt (refereegranskat)abstract
- © 2019, Springer Nature Limited. Changes in stratospheric ozone and climate over the past 40-plus years have altered the solar ultraviolet (UV) radiation conditions at the Earth’s surface. Ozone depletion has also contributed to climate change across the Southern Hemisphere. These changes are interacting in complex ways to affect human health, food and water security, and ecosystem services. Many adverse effects of high UV exposure have been avoided thanks to the Montreal Protocol with its Amendments and Adjustments, which have effectively controlled the production and use of ozone-depleting substances. This international treaty has also played an important role in mitigating climate change. Climate change is modifying UV exposure and affecting how people and ecosystems respond to UV; these effects will become more pronounced in the future. The interactions between stratospheric ozone, climate and UV radiation will therefore shift over time; however, the Montreal Protocol will continue to have far-reaching benefits for human well-being and environmental sustainability.
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| 5. |
- Drake, Henrik, Docent, 1979-, et al.
(författare)
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Fossilized anaerobic and possibly methanogenesis-fueling fungi identified deep within the Siljan impact structure, Sweden
- 2021
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Ingår i: Communications Earth & Environment. - : Springer Science and Business Media LLC. - 2662-4435. ; 2:1, s. 1-11
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Tidskriftsartikel (refereegranskat)abstract
- Recent discoveries of extant and fossilized communities indicate that eukaryotes, including fungi, inhabit energy-poor and anoxic environments deep within the fractured igneous crust. This subterranean biosphere may constitute the largest fungal habitat on our planet, but knowledge of abyssal fungi and their syntrophic interactions with prokaryotes and their concomitant metabolisms is scarce. Here we report findings of fossilized, chitin-bearing fungal hyphae at ~540 m depth in fractured bedrock of the Siljan impact structure, the largest crater in Europe. Strong 13C-enrichment of calcite precipitated with and on the fungi suggests formation following methanogenesis, and that the anaerobic fungi decomposed dispersed organic matter producing for example H2 that may have fueled autotrophic methanogens. An Eocene age determined for the calcite infers the first timing constraint of fossilized fungi in the continental igneous crust. Fungi may be widespread decomposers of organic matter and overlooked providers of H2 to autotrophs in the vast rock-hosted deep biosphere.
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| 6. |
- Drake, Henrik, 1979-, et al.
(författare)
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Ancient microbial activity in deep hydraulically conductive fracture zones within the Forsmark target area for deep geological nuclear waste disposal, Sweden
- 2018
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Ingår i: Geosciences. - : MDPI AG. - 2076-3263. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- Recent studies reveal that organisms from all three domains of life—Archaea, Bacteria, and even Eukarya—can thrive under energy-poor, dark, and anoxic conditions at large depths in the fractured crystalline continental crust. There is a need for an increased understanding of the processes and lifeforms in this vast realm, for example, regarding the spatiotemporal extent and variability of the different processes in the crust. Here, we present a study that set out to detect signs of ancient microbial life in the Forsmark area—the target area for deep geological nuclear waste disposal in Sweden. Stable isotope compositions were determined with high spatial resolution analyses within mineral coatings, and mineralized remains of putative microorganisms were studied in several deep water-conducting fracture zones (down to 663 m depth), from which hydrochemical and gas data exist. Large isotopic variabilities of 13Ccalcite (?36.2 to +20.2‰V-PDB) and 34Spyrite (?11.7 to +37.8‰V-CDT) disclose discrete periods of methanogenesis, and potentially, anaerobic oxidation of methane and related microbial sulfate reduction at several depth intervals. Dominant calcite–water disequilibrium of 18O and 87Sr/86Sr precludes abundant recent precipitation. Instead, the mineral coatings largely reflect an ancient archive of episodic microbial processes in the fracture system, which, according to our microscale Rb–Sr dating of co-genetic adularia and calcite, date back to the mid-Paleozoic. Potential Quaternary precipitation exists mainly at ~400 m depth in one of the boreholes, where mineral–water compositions corresponded.
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| 7. |
- Andersson, Martin O., et al.
(författare)
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Molecular detection of Babesia capreoli and Babesia venatorum in wild Swedish roe deer, Capreolus capreolus
- 2016
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Ingår i: Parasites & Vectors. - : Springer Science and Business Media LLC. - 1756-3305. ; 9:1
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Tidskriftsartikel (refereegranskat)abstract
- Background: The epidemiology of the zoonotic tick-transmitted parasite Babesia spp. and its occurrence in wild reservoir hosts in Sweden is unclear. In European deer, several parasite species, including Babesia capreoli and the zoonotic B. venatorum and B. divergens has been reported previously. The European roe deer, Capreolus capreolus, is an important and common part of the indigenous fauna in Europe, as well as an important host for Ixodes ricinus ticks, the vector of several Babesia spp. in Europe. Here, we aimed to investigate the occurrence of Babesia spp. in roe deer in Sweden. Findings: Roe deer (n = 77) were caught and sampled for blood. Babesia spp. was detected with a PCR assay targeting the 18S rRNA gene. The prevalence of Babesia spp. was 52 %, and two species were detected; B. capreoli and B. venatorum in 44 and 7.8 % of the individuals, respectively. Infection occurred both in summer and winter. Conclusions: We showed that roe deer in Sweden, close to the edge of their northern inland distributional range, are infected with Babesia spp. The occurrence of B. venatorum in roe deer imply that it is established in Sweden and the zoonotic implication of this finding should be regarded to a greater extent in future.
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| 8. |
- Hassellöv, Ida-Maja, et al.
(författare)
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Effekter på havsmiljön av att flytta över transporter från vägtrafik till sjöfart
- 2019
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Rapport (refereegranskat)abstract
- Antagandet av en nationell godstransportstrategi 2018 innebär att Sverige strävar efter att ”främja en överflyttning av godstransporter från väg till järnväg och sjöfart”. Ett delmål är att minska negativ miljöpåverkan från godstransporter. Men, om en överflyttning av gods från väg till sjöfart innebär ökat antal fartyg, eller ökad tillryggalagd distans med fartyg, innebär överflyttningen en ökad belastning på havsmiljön. Här föreligger därför en målkonflikt mellan transportpolitiska mål och flera miljömål. Tillståndet i havsmiljön runt Sveriges kuster uppnår idag inte god miljöstatus med avseende på exempelvis näringsämnen, miljögifter och främmande arter; för samtliga dessa belastningar bidrar sjöfarten till den negativa situationen. För att nå god miljöstatus behöver istället den totala belastningen på den marina miljön minska. Vid en eventuell överflyttning av godstransport från väg till sjöfart, är det därför angeläget att säkerställa att den ökade belastningen på den marina miljön minimeras. Ett sätt är att visa geografisk hänsyn genom att undvika sjöfart inom miljömässigt känsliga havsområden. Ett annat sätt är att ställa hårdare krav på fartygens prestanda. Miljöpåverkan från fartyg varierar framför allt mellan, men också inom, olika fartygstyper. Men att skapa nya regelverk med syfte att förbättra fartygens prestanda är en långsam process eftersom sjöfarten primärt regleras genom internationella konventioner där tillämpning av regionala eller nationella särregler undviks. Några förslag till åtgärder för att säkerställa att havsmiljön kring Sverige inte försämras till följd av överflyttning av godstransporter från väg till sjöfart är: Tillse att det skapas högkvalitativt och jämförbart underlag för sjö- och landtransporters påverkan på havsmiljön. Analysera och kommunicera samtliga typer av utsläpp, inte bara utsläpp av koldioxid. Utsläppsmängder och påverkan bör anges och jämföras i absoluta tal och relevanta enheter. Minimera antalet transporter genom att öka fyllnadsgraden. Optimera fartygens hastighet för att minimera drivmedelsförbrukningen och emissioner. Dagens fartygstrafik i Sveriges mest känsliga och skyddade havsområden måste minska. När- och kustsjöfart bör kanaliseras bort från havs- och kustområden med höga naturvärden. Skapa tydliga incitament så att fraktköpare enbart anlitar fartyg som har högsta miljöprestanda avseende såväl utsläpp av växthusgaser som av andra förorenande eller övergödande ämnen till luft och vatten. Säkerställ att införandet av ett NECA (kvävekontrollområde) i Östersjön och Nordsjön innebär att fler fartyg installerar kväverening och att införandet inte leder till att fler äldre fartyg utan regelstadgad effektiv kväverening trafikerar området. • Stärk samordningen mellan myndigheter så att framtidsfrågor som rör sjöfart och dess miljöpåverkan behandlas och åtgärdas i linje med ekosystembaserad förvaltning. Relaterat till sjöfartens striktare svavelregler som träder i kraft 2020-01-01: Förbjud utsläpp av skrubbervatten till havet då utsläppen innebär en stor risk för försämrad miljöstatus och överskridna miljökvalitetsnormer enligt vattendirektivet, med avseende på exempelvis koppar och zink. Utred konsekvenserna av den förväntade ökade användningen av lågsvavliga hybridoljor som fartygsbränsle. Då befintlig saneringsutrustning är mindre effektiv för hybridoljor innebär detta en ökad risk vid kommande olyckor och oljeutsläpp.
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| 9. |
- Ivarsson, Magnus, et al.
(författare)
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Introducing palaeolithobiology
- 2021
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Ingår i: GFF. - London : Taylor & Francis. - 1103-5897 .- 2000-0863. ; 143:2-3, s. 305-319
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Tidskriftsartikel (refereegranskat)abstract
- A growing literature of deep but also surficial fossilized remains of lithobiological life, often associated with igneous rocks, necessitates the unfolding of a sub-discipline within paleobiology. Here, we introduce the term paleolithobiology as the new auxiliary sub-discipline under which fossilized lithobiology should be handled. We present key criteria that distinguish the paleolithobiological archive from the traditional one and discuss sample strategies as well as scientific perspectives. A majority of paleolithobiological material consists of deep biosphere fossils, and in order to highlight the relevance of these, we present new data on fungal fossils from the Lockne impact crater. Fungal fossils in the Lockne drill cores have been described previously but here we provide new insights into the presence of reproductive structures that indicate the fungi to be indigenous. We also show that these fungi frequently dissolve and penetrate secondary calcite, delineating the role lithobionts plays in geobiological cycles. We hope that the formalization of the sub-discipline paleolithobiology will not only highlight an overlooked area of paleobiology as well as simplify future studies of endo- and epilithic fossil material, but also improve our understanding of the history of the deep biosphere.
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| 10. |
- Lorenz, Henning, Dr. 1972-, et al.
(författare)
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COSC-2 – drilling the basal décollement and underlying margin of palaeocontinent Baltica in the Paleozoic Caledonide Orogen of Scandinavia
- 2022
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Ingår i: Scientific Drilling. - Göttingen : Copernicus Publications. - 1816-8957 .- 1816-3459. ; 30, s. 43-57
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Tidskriftsartikel (refereegranskat)abstract
- Abstract.The Collisional Orogeny in the Scandinavian Caledonides (COSC) scientific drilling project aims to characterise the structure and orogenic processes involved in a major collisional mountain belt by multidisciplinary geoscientific research. Located in western central Sweden, the project has drilled two fully cored deep boreholes into the bedrock of the deeply eroded Early Paleozoic Caledonide Orogen. COSC-1 (2014) drilled a subduction-related allochthon and the associated thrust zone. COSC-2 (2020, this paper) extends this section deeper through the underlying nappes (Lower Allochthon), the main Caledonian décollement, and the upper kilometre of basement rocks. COSC-2 targets include the characterisation of orogen-scale detachments, the impact of orogenesis on the basement below the detachment, and the Early Paleozoic palaeoenvironment on the outer margin of palaeocontinent Baltica. This is complemented by research on heat flow, groundwater flow, and the characterisation of the microbial community in the present hard rock environment of the relict mountain belt. COSC-2 successfully, and within budget, recovered a continuous drill core to 2276 m depth. The retrieved geological section is partially different from the expected geological section with respect to the depth to the main décollement and the expected rock types. Although the intensity of synsedimentary deformation in the rocks in the upper part of the drill core might impede the analysis of the Early Paleozoic palaeoenvironment, the superb quality of the drill core and the borehole will facilitate research on the remaining targets and beyond. Protocols for sampling in the hard rock environment and subsequent sample preservation were established for geomicrobiological research and rock mechanical testing. For the former, a sparse sample series along the entire drill core was taken, while the target of the latter was the décollement. COSC-2 was surveyed by a comprehensive post-drilling downhole logging campaign and a combined borehole/land seismic survey in autumn 2021. This paper provides an overview of the COSC-2 (International Continental Scientific Drilling Project – ICDP 5054_2_A and 5054_2_B boreholes) operations and preliminary results. It will be complemented by a detailed operational report and data publication.
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