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  • 1.
    Bengtson, Stefan
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology.
    Astolfo, Alberto
    Paul Scherrer Institute.
    Belivanova, Veneta
    Swedish Museum of Natural History, Department of Paleobiology.
    Broman, Curt
    Stockholm University.
    Marone, Federica
    Paul Scherrer Institute.
    Stampanoni, Marco
    ETH Zürich.
    Deep-biosphere consortium of fungi and prokaryotes in Eocene sub-seafloor basalts.2014In: Geobiology, ISSN 1472-4677, E-ISSN 1472-4669, Vol. 12, no 6, p. 489-496Article in journal (Refereed)
    Abstract [en]

    The deep biosphere of the subseafloor crust is believed to contain a significant part of Earth’s biomass, but because of the difficulties of directly observing the living organisms, its composition and ecology are poorly known. We report here a consortium of fossilized prokaryotic and eukaryotic microorganisms, occupying cavities in deep-drilled vesicular basalt from the Emperor Seamounts, Pacific Ocean, 67.5 meters below seafloor (mbsf). Fungal hyphae provide the framework on which prokaryote-like organisms are suspended like cobwebs and iron-oxidizing bacteria form microstromatolites (Frutexites). The spatial interrelationships show that the organisms were living at the same time in an integrated fashion, suggesting symbiotic interdependence. The community is contemporaneous with secondary mineralizations of calcite partly filling the cavities. The fungal hyphae frequently extend into the calcite, indicating that they were able to bore into the substrate through mineral dissolution. A symbiotic relationship with chemoautotrophs, as inferred for the observed consortium, may be a prerequisite for the eukaryotic colonization of crustal rocks. Fossils thus open a window to the extant as well as the ancient deep biosphere.

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  • 2. Büdel, B.
    et al.
    Colesie, C.
    Green, T.G.A.
    Grube, Martin
    Lázaro Suau, R.
    Loewen-Schneider, K.
    Maier, S.
    Peer, T.
    Pintado, A.
    Raggio, J.
    Ruprecht, U.
    Sancho, L. G.
    Schroeter, B.
    Türk, R.
    Weber, B.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Westberg, Martin
    Swedish Museum of Natural History, Department of Botany.
    Williams, L.
    Zheng, L.
    Improved appreciation of the functioning and importance of biological soil crusts in Europe – the Soil Crust International project (SCIN)2014In: Biodiversity and Conservation, ISSN 0960-3115, E-ISSN 1572-9710, Vol. 23, p. 1639-1658Article in journal (Refereed)
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  • 3. Chi Fru, Ernest
    et al.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology.
    Kilias, Stephanos P
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Belivanova, Veneta
    Swedish Museum of Natural History, Department of Paleobiology.
    Marone, Federica
    Paul Scherrer Institute.
    Fortin, Danielle
    Broman, Curt
    Stampanoni, Marco
    ETH Zürich.
    Fossilized iron bacteria reveal pathway to biological origin of banded iron formation.2013In: Nature Communications, ISSN 2041-1723, Vol. 4, no 2050, p. 1-7Article in journal (Refereed)
    Abstract [en]

    Debates on the formation of banded iron formations in ancient ferruginous oceans are dominated by a dichotomy between abiotic and biotic iron cycling. This is fuelled by difficulties in unravelling the exact processes involved in their formation. Here we provide fossil environmental evidence for anoxygenic photoferrotrophic deposition of analogue banded iron rocks in shallow marine waters associated with an Early Quaternary hydrothermal vent field on Milos Island, Greece. Trace metal, major and rare earth elemental compositions suggest that the deposited rocks closely resemble banded iron formations of Precambrian origin. Well-preserved microbial fossils in combination with chemical data imply that band formation was linked to periodic massive encrustation of anoxygenic phototrophic biofilms by iron oxyhydroxide alternating with abiotic silica precipitation. The data implicate cyclic anoxygenic photoferrotrophy and their fossilization mechanisms in the construction of microskeletal fabrics that result in the formation of characteristic banded iron formation bands of varying silica and iron oxide ratios.

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    ChiFru_etal_2013_BIF_MS
  • 4. Cunningham, J. A.
    et al.
    Thomas, C.-W.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Marone, Federica
    Paul Scherrer Institute.
    Stampanoni, Marco
    ETH Zürich.
    Turner, F. R.
    Bailey, J. V.
    Raff, R. A.
    Raff, E. C.
    Donoghue, Philip C.J.
    University of Bristol.
    Experimental taphonomy of giant sulphur bacteria: implications for the interpretation of the embryo-like Ediacaran Doushantuo fossils.2012In: Proceedings of the Royal Society of London. B. Biological Sciences, ISSN 0962-8452, Vol. 279, no 1734, p. 1857-1864Article in journal (Refereed)
    Abstract [en]

    The Ediacaran Doushantuo biota has yielded fossils interpreted as eukaryotic organisms, either animal embryos or eukaryotes basal or distantly related to Metazoa. However, the fossils have been interpreted alternatively as giant sulphur bacteria similar to the extant Thiomargarita. To test this hypothesis, living and decayed Thiomargarita were compared with Doushantuo fossils and experimental taphonomic pathways were compared with modern embryos. In the fossils, as in eukaryotic cells, subcellular structures are distributed throughout cell volume; in Thiomargarita, a central vacuole encompasses approximately 98 per cent cell volume. Key features of the fossils, including putative lipid vesicles and nuclei, complex envelope ornament, and ornate outer vesicles are incompatible with living and decay morphologies observed in Thiomargarita. Microbial taphonomy of Thiomargarita also differed from that of embryos. Embryo tissues can be consumed and replaced by bacteria, forming a replica composed of a threedimensional biofilm, a stable fabric for potential fossilization. Vacuolated Thiomargarita cells collapse easily and do not provide an internal substrate for bacteria. The findings do not support the hypothesis that giant sulphur bacteria are an appropriate interpretative model for the embryo-like Doushantuo fossils. However, sulphur bacteria may have mediated fossil mineralization and may provide a potential bacterial analogue for other macroscopic Precambrian remains.

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    Cunningham_etal_2012_Experimental
  • 5. Drake, Henrik
    et al.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Heim, Christine
    Siljeström, Sandra
    Whitehouse, Martin
    Swedish Museum of Natural History, Department of Geology.
    Broman, Curt
    Belivanova, Veneta
    Swedish Museum of Natural History, Department of Paleobiology.
    Åström, Mats E.
    Anaerobic consortia of fungi and sulfate reducing bacteria in deep granite fractures2017In: Nature Communications, E-ISSN 2041-1723, Vol. 8, no 55, p. 1-9Article in journal (Refereed)
    Abstract [en]

    The deep biosphere is one of the least understood ecosystems on Earth. Although most microbiological studies in this system have focused on prokaryotes and neglected microeukaryotes, recent discoveries have revealed existence of fossil and active fungi in marine sediments and sub-seafloor basalts, with proposed importance for the subsurface energy cycle. However, studies of fungi in deep continental crystalline rocks are surprisingly few. Consequently, the characteristics and processes of fungi and fungus-prokaryote interactions in this vast environment remain enigmatic. Here we report the first findings of partly organically preserved and partly mineralized fungi at great depth in fractured crystalline rock (-740 m). Based on environmental parameters and mineralogy the fungi are interpreted as anaerobic. Synchrotron-based techniques and stable isotope microanalysis confirm a coupling between the fungi and sulfate reducing bacteria. The cryptoendolithic fungi have significantly weathered neighboring zeolite crystals and thus have implications for storage of toxic wastes using zeolite barriers.

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  • 6. Drake, Henrik
    et al.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology.
    Heim, Christine
    Snoeyenbos-West, Oona
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Belivanova, Veneta
    Swedish Museum of Natural History, Department of Paleobiology.
    Whitehouse, Martin
    Swedish Museum of Natural History, Department of Geology.
    Fossilized anaerobic and possibly methanogenesis-fueling fungi identified deep within the Siljan impact structure, Sweden2021In: Communications Earth & Environment, E-ISSN 2662-4435, Vol. 2, no 1, p. 1-11Article in journal (Refereed)
    Abstract [en]

    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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  • 7.
    Fernández-Brime, Samantha
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Muggia, Lucia
    Maier, S.
    Grube, Martin
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Bacterial communities in an optional lichen symbiosis are determined by substrate, not algal photobionts2019In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 95, article id fiz012Article in journal (Refereed)
  • 8. Grube, Martin
    et al.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Lichenized fungi and the evolution of symbiotic organization.2016In: Microbiology Spectrum, E-ISSN 2165-0497, Vol. 4, no 6, article id FUNK-0011-2016Article in journal (Refereed)
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  • 9.
    Hammarlund, Emma
    et al.
    University of Southern Denmark.
    Canfield, Donald E.
    University of Southern Denmark.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Leth, Peter Mygind
    Schillinger, Burkhard
    Calzada, Elbio
    The influence of sulfate concentration on soft-tissue decay and preservation.2011In: Palaeontographica Canadiana, ISSN 0821-7556, Vol. 31, p. 141-156Article in journal (Refereed)
    Abstract [en]

    To explore how seawater chemistry might influence exceptional Burgess Shale-type preservation, freshly-killed shrimp and annelids were covered in clay and exposed to high and low sulfate concentrations for up to six weeks of anaerobic decay. Decay was monitored by carbon mass balance calculations and non-destructive imaging. Decay rates and visual distortion of shrimp cuticle and muscle appear slower in environments without sulfate, compared to environments with normal marine sulfate concentrations. By means of X-ray and neutron tomography, the carapace and tail muscle of shrimp was observed to pass from seemingly intact after three weeks of decay to distorted after six weeks of decay. The distortion of the annelids was more rapid. Preservation of detailed structures must occur within this short time span, in order to produce exceptional fossils. When sulfate is absent, methanogenesis is the dominant pathway of carbon re-mineralization. We argue that a slight inefficiency of methanogenic carbon oxidation, also indicated in other studies, could widen the time frame for initial preservation and enhance the likelihood of labile tissue being preserved, as well as play a role in the formation of Burgess Shale-type carbonaceous compressions.

  • 10.
    Ivarsson, Magnus
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Oceanbottnarnas hemliga liv.2017In: Havsutsikt, ISSN 1104-0513, Vol. 2017, no 2, p. 16-18Article in journal (Other (popular science, discussion, etc.))
    Abstract [sv]

    Berggrunden under havens bottensediment är en vidsträckt men svårtillgänglig och outforskad del av vår planet, särskilt när det gäller liv. Paradoxalt nog är det, förutom haven, världens volymmässigt största livsmiljö för mikroorganismer. Med nya metoder har forskare från Naturhistoriska riksmuseet vänt upp och ner på den gängse vetenskapliga uppfattningen. I den spruckna berggrunden under havssedimenten bor inte bara de förväntade extremt tåliga bakterierna och arkéerna – de har även gott sällskap av svampar.

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  • 11.
    Ivarsson, Magnus
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Belivanova, Veneta
    Swedish Museum of Natural History, Department of Paleobiology.
    Stampanoni, Marco
    ETH Zürich.
    Marone, Federica
    Paul Scherrer Institute.
    Tehler, Anders
    Swedish Museum of Natural History, Department of Botany.
    Fossilized fungi in subseafloor Eocene basalts.2012In: Geology, ISSN 0091-7613, Vol. 40, no 2, p. 163-166Article in journal (Refereed)
    Abstract [en]

    The deep biosphere of subseafl oor basalts is thought to consist of mainly prokaryotes (bacteria and archaea). Here we report fossilized fi lamentous microorganisms from subseafl oor basalts interpreted as fossilized fungal hyphae, probably Dikarya, rather than fossilized prokaryotes. The basalts were collected during the Ocean Drilling Program Leg 197 at the Emperor Seamounts, North Pacifi c Ocean, and the fossilized fungi are observed in carbonate-fi lled veins and vesicles in samples that represent a depth of ~150 m below the seafl oor. Three-dimensional visualizations using synchrotron-radiation X-ray tomographic microscopy show characteristic fungal morphology of the mycelium-like network, such as frequent branching, anastomosis, and septa. Possible presence of chitin in the hypha walls was detected by staining with Wheat Germ Agglutinin conjugated with Fluorescein Isothiocyanate and examination using fl uorescence microscopy. The presence of fungi in subseafl oor basalts challenges the present understanding of the deep subseafl oor biosphere as being exclusively prokaryotic.

  • 12.
    Ivarsson, Magnus
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Skogby, Henrik
    Swedish Museum of Natural History, Department of Geology.
    Belivanova, Veneta
    Swedish Museum of Natural History, Department of Paleobiology.
    Marone, Federica
    Paul Scherrer Institute.
    Fungal colonies in open fractures of subseafloor basalt.2013In: Geo-Marine Letters, ISSN 0276-0460, E-ISSN 1432-1157, Vol. 33, no 4, p. 233-234Article in journal (Refereed)
    Abstract [en]

    The deep subseafloor crust is one of the few great frontiers of unknown biology on Earth and, still today, the notion of the deep biosphere is commonly based on the fossil record. Interpretation of palaeobiological information is thus central in the exploration of this hidden biosphere and, for each new discovery, criteria used to establish biogenicity are challenged and need careful consideration. In this paper networks of fossilized filamentous structures are for the first time described in open fractures of subseafloor basalts collected at the Emperor Seamounts, Pacific Ocean. These structures have been investigated with optical microscopy, environmental scanning electron microscope, energy dispersive spectrometer, X-ray powder diffraction as well as synchrotron-radiation X-ray tomographic microscopy, and interpreted as fossilized fungal mycelia.Morphological features such as hyphae, yeastlike growth and sclerotia were observed. The fossilized fungi are mineralized by montmorillonite, a process that probably began while the fungi were alive. It seems plausible that the fungi produced mucilaginous polysaccharides and/or extracellular polymeric substances that attracted minerals or clay particles, resulting in complete fossilization by montmorillonite. The findings are in agreement with previous observations of fossilized fungi in subseafloor basalts and establish fungi as regular inhabitants of such settings. They further show that fossilized microorganisms are not restricted to pore spaces filled by secondary mineralizations but can be found in open pore spaces as well. This challenges standard protocols for establishing biogenicity and calls for extra care in data interpretation.

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    Ivarsson_etal_2013_Fungal
  • 13.
    Ivarsson, Magnus
    et al.
    Swedish Museum of Natural History, Department of Paleobiology.
    Broman, Curt
    Sturkell, Erik
    Ormö, Jens
    Siljeström, Sandra
    van Zuilen, Mark
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Fungal colonization of an Ordovician impact-induced hydrothermal system.2013In: Scientific Reports, E-ISSN 2045-2322, Vol. 3, no 3487, p. 1-6Article in journal (Refereed)
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    Ivarsson et al. 2013
  • 14. Klawonn, I.
    et al.
    Nahar, N.
    Walve, J.
    Andersson, B.
    Olofsson, M.
    Svedén, J.B.
    Littmann, S.
    Whitehouse, Martin J.
    Swedish Museum of Natural History, Department of Geology.
    Kuypers, M.M.M.
    Ploug, H.
    Cell-specific nitrogen- and carbon-fixation of cyanobacteria in a temperate marine system (Baltic Sea).2016In: Environmental Microbiology Reports, ISSN 1758-2229, E-ISSN 1758-2229Article in journal (Refereed)
    Abstract [en]

    We analysed N2- and carbon (C) fixation in individual cells of Baltic Sea cyanobacteria by combining stable isotope incubations with secondary ion mass spectrometry (SIMS). Specific growth rates based on N2- and C-fixation were higher for cells of Dolichospermum spp. than for Aphanizomenon sp. and Nodularia spumigena. The cyanobacterial biomass, however, was dominated by Aphanizomenon sp., which contributed most to total N2-fixation in surface waters of the Northern Baltic Proper. N2-fixation by Pseudanabaena sp. and colonial picocyanobacteria was not detectable. N2-fixation by Aphanizomenon sp., Dolichospermum spp. and N. spumigena populations summed up to total N2-fixation, thus these genera appeared as sole diazotrophs within the Baltic Sea's euphotic zone, while their mean contribution to total C-fixation was 21%. Intriguingly, cell-specific N2-fixation was eightfold higher at a coastal station compared to an offshore station, revealing coastal zones as habitats with substantial N2-fixation. At the coastal station, the cell-specific C- to N2-fixation ratio was below the cellular C:N ratio, i.e. N2 was assimilated in excess to C-fixation, whereas the C- to N2-fixation ratio exceeded the C:N ratio in offshore sampled diazotrophs. Our findings highlight SIMS as a powerful tool not only for qualitative but also for quantitative N2-fixation assays in aquatic environments.

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  • 15.
    Little, Crispin T. S.
    et al.
    School of Earth and Environment University of Leeds Leeds UK.
    Johannessen, Karen C.
    Department of Earth Science University of Bergen Bergen Norway.
    Bengtson, Stefan
    Swedish Museum of Natural History, Department of Paleobiology.
    Chan, Clara S.
    Department of Earth Sciences University of Delaware Newark USA.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology.
    Slack, John F.
    U.S. Geological Survey (Emeritus), National Center Reston USA.
    Broman, Curt
    Department of Geological Sciences Stockholm University Stockholm Sweden.
    Thorseth, Ingunn H.
    Department of Earth Science University of Bergen Bergen Norway.
    Grenne, Tor
    Geological Survey of Norway Trondheim Norway.
    Rouxel, Olivier J.
    Marine Geosciences Research Unit IFREMER Plouzané France.
    Bekker, Andrey
    Department of Earth and Planetary Sciences University of California Riverside USA;Department of Geology University of Johannesburg Johannesburg South Africa.
    A late Paleoproterozoic (1.74 Ga) deep-sea, low-temperature, iron-oxidizing microbial hydrothermal vent community from Arizona, USA2021In: Geobiology, ISSN 1472-4677, E-ISSN 1472-4669, Vol. 19, no 3, p. 228-249Article in journal (Refereed)
    Abstract [en]

    Modern marine hydrothermal vents occur in a wide variety of tectonic settings and are characterized by seafloor emission of fluids rich in dissolved chemicals and rapid mineral precipitation. Some hydrothermal systems vent only low-temperature Fe-rich fluids, which precipitate deposits dominated by iron oxyhydroxides, in places together with Mn-oxyhydroxides and amorphous silica. While a proportion of this mineralization is abiogenic, most is the result of the metabolic activities of benthic, Fe-oxidizing bacteria (FeOB), principally belonging to the Zetaproteobacteria. These micro-organisms secrete micrometer-scale stalks, sheaths, and tubes with a variety of morphologies, composed largely of ferrihydrite that act as sacrificial structures, preventing encrustation of the cells that produce them. Cultivated marine FeOB generally require neutral pH and microaerobic conditions to grow. Here, we describe the morphology and mineralogy of filamentous microstructures from a late Paleoproterozoic (1.74 Ga) jasper (Fe-oxide- silica) deposit from the Jerome area of the Verde mining district in central Arizona, USA, that resemble the branching tubes formed by some modern marine FeOB. On the basis of this comparison, we interpret the Jerome area filaments as having formed by FeOB on the deep seafloor, at the interface of weakly oxygenated seawater and low-temperature Fe-rich hydrothermal fluids. We compare the Jerome area filaments with other purported examples of Precambrian FeOB and discuss the implications of their presence for existing redox models of Paleoproterozoic oceans during the “Boring Billion.”

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  • 16. Muggia, Lucia
    et al.
    Fernández-Brime, Samantha
    Swedish Museum of Natural History, Department of Botany.
    Grube, Martin
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Schizoxylon as an experimental model for studying interkingdom symbiosis.2016In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 92, article id fiw165Article in journal (Refereed)
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  • 17. Olofsson, Malin
    et al.
    Kourtchenko, Olga
    Zetsche, Eva-Maria
    Marchant, Hannah K.
    Whitehouse, Martin J.
    Swedish Museum of Natural History, Department of Geology.
    Godhe, Anna
    Ploug, Helle
    High single-cell diversity in carbon and nitrogen assimilations by a chain-forming diatom across a century2019In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 21, no 1, p. 142-151Article in journal (Refereed)
    Abstract [en]

    Summary Almost a century ago Redfield discovered a relatively constant ratio between carbon, nitrogen and phosphorus in particulate organic matter and nitrogen and phosphorus of dissolved nutrients in seawater. Since then, the riverine export of nitrogen to the ocean has increased 20 fold. High abundance of resting stages in sediment layers dated more than a century back indicate that the common planktonic diatom Skeletonema marinoi has endured this eutrophication. We germinated unique genotypes from resting stages originating from isotope-dated sediment layers (15 and 80 years old) in a eutrophied fjord. Using secondary ion mass spectrometry (SIMS) combined with stable isotopic tracers, we show that the cell-specific carbon and nitrogen assimilation rates vary by an order of magnitude on a single-cell level but are significantly correlated during the exponential growth phase, resulting in constant assimilation quota in cells with identical genotypes. The assimilation quota varies largely between different clones independent of age. We hypothesize that the success of S. marinoi in coastal waters may be explained by its high diversity of nutrient demand not only at a clone-specific level but also at the single-cell level, whereby the population can sustain and adapt to dynamic nutrient conditions in the environment.

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  • 18. Pokharel, Rasesh
    et al.
    Gerrits, Ruben
    Schuessler, Jan
    Frings, Patrick J
    Swedish Museum of Natural History, Department of Geology.
    Sobotka, Roman
    Gorbushina, Anna
    von Blanckenburg, Friedhelm
    Magnesium Stable Isotope Fractionation on a Cellular Level Explored by Cyanobacteria and Black Fungi with Implications for Higher Plants2018In: Environmental Science and Technology, ISSN 0013-936X, E-ISSN 1520-5851, Vol. 52, p. 12216-12224Article in journal (Refereed)
    Abstract [en]

    In a controlled growth experiment we found that the cyanobacterium Nostoc punctiforme has a bulk cell 26Mg/24Mg ratio (expressed as δ26Mg) that is −0.27‰ lower than the growth solution at a pH of ca. 5.9. This contrasts with a recently published δ26Mg value that was 0.65‰ higher than growth solution for the black fungus Knufia petricola at similar laboratory conditions, interpreted to reflect loss of 24Mg during cell growth. By a mass balance model constrained by δ26Mg in chlorophyll extract we inferred the δ26 Mg value of the main Mg compartments in a cyanobacteria cell: free cytosolic Mg (−2.64‰), chlorophyll (1.85‰), and the nonchlorophyll-bonded Mg compartments like ATP and ribosomes (−0.64‰). The lower δ26Mg found in Nostoc punctiformewould thus result from the absence of significant Mg efflux during cell growth in combination with either (a) discrimination against 26Mg during uptake by desolvation of Mg or transport across protein channels or (b) discrimination against 24Mg in the membrane transporter during efflux. The model predicts the preferential incorporation of 26Mg in cells and plant organs low in Mg and the absence of isotope fractionation in those high in Mg, corroborated by a compilation of Mg isotope ratios from fungi, bacteria, and higher plants.

  • 19.
    Réblová, Martina
    et al.
    Department of Taxonomy, Institute of Botany of the Czech Academy of Sciences, 252 43, Pruhonice, Czech Republic.
    Hubka, Vit
    Department of Botany, Faculty of Science, Charles University in Prague, Benatska 2, 128 01 Prague 2, Czech Republic.
    Thureborn, Olle
    Institutionen för ekologi miljö och botanik, Stockholms Universitet.
    Lundberg, Johannes
    Swedish Museum of Natural History, Department of Botany.
    Sallstedt, Therese
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    From the tunnels into the treetops: new lineages of black yeasts from biofilm in the Stockholm metro system and their relatives among ant-associated fungi in the Chaetothyriales2016In: PLOS ONE, E-ISSN 1932-6203, Vol. 11, no 10, p. e0163396-, article id e0163396Article in journal (Refereed)
    Abstract [en]

    Rock-inhabiting fungi harbour species-rich, poorly differentiated, extremophilic taxa of polyphyletic origin. Their closest relatives are often well-known species from various biotopes with significant pathogenic potential. Speleothems represent a unique rock-dwelling habitat, whose mycobiota are largely unexplored. Isolation of fungi from speleothem biofilm covering bare granite walls in the Kungsträdgården metro station in Stockholm yielded axenic cultures of two distinct black yeast morphotypes. Phylogenetic analyses of DNA sequences from six nuclear loci, ITS, nuc18S and nuc28S rDNA, rpb1, rpb2 and β-tubulin, support their placement in the Chaetothyriales (Ascomycota). They are described as a new genus Bacillicladium with the type species Blobatum, and a new species Bradymyces graniticolaBacillicladium is distantly related to the known five chaetothyrialean families and is unique in the Chaetothyriales by variable morphology showing hyphal, meristematic and yeast-like growth in vitro. The nearest relatives of Bacillicladium are recruited among fungi isolated from cardboard-like construction material produced by arboricolous non-attine ants. Their sister relationship is weakly supported by the Maximum likelihood analysis, but strongly supported by Bayesian inference. The genus Bradymyces is placed amidst members of the Trichomeriaceae and is ecologically undefined; it includes an opportunistic animal pathogen while two other species inhabit rock surfaces. ITS rDNA sequences of three species accepted in Bradymyces and other undescribed species and environmental samples were subjected to phylogenetic analysis and in-depth comparative analysis of ITS1 and ITS2 secondary structures in order to study their intraspecific variability. Compensatory base change criterion in the ITS2 secondary structure supported delimitation of species in Bradymyces, which manifest a limited number of phenotypic features useful for species recognition. The role of fungi in the speleothem biofilm and relationships of Bacillicladium and Bradymyces with other members of the Chaetothyriales are discussed.

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  • 20.
    Sallstedt, Therese
    et al.
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE); Department of Biology, University of Southern Denmark.
    Ivarsson, Magnus
    Swedish Museum of Natural History, Department of Paleobiology. Nordic Center for Earth Evolution (NordCEE).
    Lundberg, Johannes
    Swedish Museum of Natural History, Department of Botany.
    Sjöberg, Rabbe
    Vidal Romaní, Juan Ramón
    University of Coruña, Campus de Elviña, ES-15071 Coruña, Spain.
    Speleothem and biofilm formation in a granite/dolerite cave, Northern Sweden2014In: International Journal of Speleology, ISSN 0392-6672, E-ISSN 1827-806X, Vol. 43, no 3, p. 305-313Article in journal (Refereed)
    Abstract [en]

    Tjuv-Antes grotta (Tjuv-Ante's Cave) located in northern Sweden is a round-abraded sea cave ('tunnel cave'), about 30 m in length, formed by rock-water abrasion in a dolerite dyke in granite gneiss. Abundant speleothems are restricted to the inner, mafic parts of the cave and absent on granite parts. The speleothems are of two types: cylindrical (coralloid, popcorn-like), and flowstone (thin crusts). Coralloids correspond to terrestrial stromatolite speleothems in which layers of light calcite alternate with dark, silica-rich laminae. The dark laminae are also enriched in carbon and contain incorporated remains of microorganisms. Two types of microbial communities can be distinguished associated with the speleothems: an Actinobacteria-like biofilm and a fungal community. Actinobacteria seem to play an important role in the formation of speleothem while the fungal community acts as both a constructive and a destructive agent. A modern biofilm dominated by Actinobacteria is present in the speleothem-free parts of the dolerite and located in cave ceiling cracks. These biofilms may represent sites of early speleothem formation. Because of its unusual position in between two types of host rock, Tjuv-Ante's Cave represents a unique environment in which to study differences in microbe-rock interactions and speleothem genesis between the granite and dolerite host rock. Our study shows that the mafic rock is superior to the granite in hosting a microbial community and to support formation of speleothems.

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    Sallstedt et al 2014 Int J Speleology
  • 21. Singh, Abhijeet
    et al.
    Nylander, Johan A A
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics. NBIS.
    Schnürer, Anna
    Bongcam-Rudloff, Erik
    Müller, Bettina
    High-Throughput Sequencing and Unsupervised Analysis of Formyltetrahydrofolate Synthetase (FTHFS) Gene Amplicons to Estimate Acetogenic Community Structure.2020In: Frontiers in Microbiology, E-ISSN 1664-302X, Vol. 11, article id 2066Article in journal (Refereed)
    Abstract [en]

    The formyltetrahydrofolate synthetase (FTHFS) gene is a molecular marker of choice to study the diversity of acetogenic communities. However, current analyses are limited due to lack of a high-throughput sequencing approach for FTHFS gene amplicons and a dedicated bioinformatics pipeline for data analysis, including taxonomic annotation and visualization of the sequence data. In the present study, we combined the barcode approach for multiplexed sequencing with unsupervised data analysis to visualize acetogenic community structure. We used samples from a biogas digester to develop proof-of-principle for our combined approach. We successfully generated high-throughput sequence data for the partial FTHFS gene and performed unsupervised data analysis using the novel bioinformatics pipeline "AcetoScan" presented in this study, which resulted in taxonomically annotated OTUs, phylogenetic tree, abundance plots and diversity indices. The results demonstrated that high-throughput sequencing can be used to sequence the FTHFS amplicons from a pool of samples, while the analysis pipeline AcetoScan can be reliably used to process the raw sequence data and visualize acetogenic community structure. The method and analysis pipeline described in this paper can assist in the identification and quantification of known or potentially new acetogens. The AcetoScan pipeline is freely available at https://github.com/abhijeetsingh1704/AcetoScan.

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  • 22.
    Tuovinen, Veera
    et al.
    Department of Ecology and Genetics Uppsala University Uppsala Norbyvägen 18D, 752 36 Sweden;Department of Botany Swedish Museum of Natural History Stockholm P.O. Box 50007, SE‐104 05 Sweden.
    Millanes, Ana Maria
    Departamento de Biología y Geología, Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles E‐28933 Spain.
    Freire‐Rallo, Sandra
    Departamento de Biología y Geología, Física y Química Inorgánica Universidad Rey Juan Carlos Móstoles E‐28933 Spain.
    Rosling, Anna
    Department of Ecology and Genetics Uppsala University Uppsala Norbyvägen 18D, 752 36 Sweden.
    Wedin, Mats
    Swedish Museum of Natural History, Department of Botany.
    Tremella macrobasidiata and Tremella variae have abundant and widespread yeast stages in Lecanora lichens2021In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 23, p. 2484-2498Article in journal (Refereed)
  • 23.
    Wedin, Mats
    et al.
    Swedish Museum of Natural History, Department of Botany.
    Maier, S.
    Fernández-Brime, Samantha
    Swedish Museum of Natural History, Department of Botany.
    Cronholm, Bodil
    Swedish Museum of Natural History, Department of Bioinformatics and Genetics.
    Westberg, Martin
    Swedish Museum of Natural History, Department of Botany.
    Grube, Martin
    Microbiome change by symbiotic invasion in lichens2016In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 18, p. 1428-1439Article in journal (Refereed)
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