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  • 1.
    Bonaglia, Stefano
    et al.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Brüchert, Volker
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Vicenzi, Alessandra
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Chi Fru, Ernest
    Stockholm University, Faculty of Science, Department of Geological Sciences. Cardiff University, UK.
    Nascimento, Francisco J. A.
    Stockholm University, Faculty of Science, Department of Ecology, Environment and Plant Sciences.
    Methane fluxes from coastal sediments are enhanced by macrofauna2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, no 1, article id 13145Article in journal (Refereed)
    Abstract [en]

    Methane and nitrous oxide are potent greenhouse gases (GHGs) that contribute to climate change. Coastal sediments are important GHG producers, but the contribution of macrofauna (benthic invertebrates larger than 1 mm) inhabiting them is currently unknown. Through a combination of trace gas, isotope, and molecular analyses, we studied the direct and indirect contribution of two macrofaunal groups, polychaetes and bivalves, to methane and nitrous oxide fluxes from coastal sediments. Our results indicate that macrofauna increases benthic methane efflux by a factor of up to eight, potentially accounting for an estimated 9.5% of total emissions from the Baltic Sea. Polychaetes indirectly enhance methane efflux through bioturbation, while bivalves have a direct effect on methane release. Bivalves host archaeal methanogenic symbionts carrying out preferentially hydrogenotrophic methanogenesis, as suggested by analysis of methane isotopes. Low temperatures (8 °C) also stimulate production of nitrous oxide, which is consumed by benthic denitrifying bacteria before it reaches the water column. We show that macrofauna contributes to GHG production and that the extent is dependent on lineage. Thus, macrofauna may play an important, but overlooked role in regulating GHG production and exchange in coastal sediment ecosystems.

  • 2.
    Callac, Nolwenn
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Université de Brest, France; Ifremer, France; CNRS, France.
    Oger, Philippe
    Lesongeur, Francoise
    Rattray, Jayne E.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Vannier, Pauline
    Michoud, Gregoire
    Beauverger, Mickael
    Gayet, Nicolas
    Rouxel, Olivier
    Jebbar, Mohamed
    Godfroy, Anne
    Pyrococcus kukulkanii sp nov., a hyperthermophilic, piezophilic archaeon isolated from a deep-sea hydrothermal vent2016In: International Journal of Systematic and Evolutionary Microbiology, ISSN 1466-5026, E-ISSN 1466-5034, Vol. 66, p. 3142-3149Article in journal (Refereed)
    Abstract [en]

    A novel hyperthermophilic, piezophilic, anaerobic archaeon, designated NCB100(T), was isolated from a hydrothermal vent flange fragment collected in the Guaymas basin at the hydrothermal vent site named 'Rebecca's Roost' at a depth of 1997 m. Enrichment and isolation were performed at 100 degrees C under atmospheric pressure. Cells of strain NCB100(T) were highly motile, irregular cocci with a diameter of -1 mu m. Growth was recorded at temperatures between 70 and 112 degrees C (optimum 105 degrees C) and hydrostatic pressures of 0.1-80 MPa (optimum 40-50 MPa). Growth was observed at pH 3.5-8.5 (optimum pH 7) and with 1.5-7% NaCl (optimum at 2.5-3 %). Strain NCB100(T) was a strictly anaerobic chemo-organoheterotroph and grew on complex proteinaceous substrates such as yeast extract, peptone and tryptone, as well as on glycogen and starch. Elemental sulfur was required for growth and was reduced to hydrogen sulfide. The fermentation products from complex proteinaceous substrates were CO2 and H-2. The G+C content of the genomic DNA was 41.3 %. Phylogenetic analysis of the 16S rRNA gene sequence revealed that strain NCB100(T) belongs to the genus Pyrococcus, showing 99% similarity with the other described species of the genus Pyrococcus. On the basis of physiological characteristics, DNA G+C content, similarity level between ribosomal proteins and an average nucleotide identity value of 79 %, strain NCB100(T) represents a novel species for which the name Pyrococcus kukulkanii sp. nov. is proposed. The type strain is NCB100(T) (=DSM 101590(T) =Souchotheque de Bretagne BG1337(T)).

  • 3.
    Callac, Nolwenn
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Posth, Nicole R.
    Rattray, Jayne E.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Yamoah, Kweku K. Y.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Wiech, Alan
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Ivarsson, Magnus
    Hemmingsson, Christoffer
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Kilias, Stephanos P.
    Argyraki, Ariadne
    Broman, Curt
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Skogby, Henrik
    Smittenberg, Rienk H.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Chi Fru, Ernest
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Modes of carbon fixation in an arsenic and CO2-rich shallow hydrothermal ecosystem2017In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 7, article id 14708Article in journal (Refereed)
    Abstract [en]

    The seafloor sediments of Spathi Bay, Milos Island, Greece, are part of the largest arsenic-CO2-rich shallow submarine hydrothermal ecosystem on Earth. Here, white and brown deposits cap chemically distinct sediments with varying hydrothermal influence. All sediments contain abundant genes for autotrophic carbon fixation used in the Calvin-Benson-Bassham (CBB) and reverse tricaboxylic acid (rTCA) cycles. Both forms of RuBisCO, together with ATP citrate lyase genes in the rTCA cycle, increase with distance from the active hydrothermal centres and decrease with sediment depth. Clustering of RuBisCO Form II with a highly prevalent Zetaproteobacteria 16S rRNA gene density infers that ironoxidizing bacteria contribute significantly to the sediment CBB cycle gene content. Three clusters form from different microbial guilds, each one encompassing one gene involved in CO2 fixation, aside from sulfate reduction. Our study suggests that the microbially mediated CBB cycle drives carbon fixation in the Spathi Bay sediments that are characterized by diffuse hydrothermal activity, high CO2, As emissions and chemically reduced fluids. This study highlights the breadth of conditions influencing the biogeochemistry in shallow CO2-rich hydrothermal systems and the importance of coupling highly specific process indicators to elucidate the complexity of carbon cycling in these ecosystems.

  • 4.
    Callac, Nolwenn
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Université de Bretagne Occidentale, France.
    Rouxel, Olivier
    Lesongeur, Francoise
    Liorzou, Celine
    Bollinger, Claire
    Pignet, Patricia
    Cheron, Sandrine
    Fouquet, Yves
    Rommevaux-Jestin, Celine
    Godfroy, Anne
    Biogeochemical insights into microbe-mineral-fluid interactions in hydrothermal chimneys using enrichment culture2015In: Extremophiles, ISSN 1431-0651, E-ISSN 1433-4909, Vol. 19, no 3, p. 597-617Article in journal (Refereed)
    Abstract [en]

    Active hydrothermal chimneys host diverse microbial communities exhibiting various metabolisms including those involved in various biogeochemical cycles. To investigate microbe-mineral-fluid interactions in hydrothermal chimney and the driver of microbial diversity, a cultural approach using a gas-lift bioreactor was chosen. An enrichment culture was performed using crushed active chimney sample as inoculum and diluted hydrothermal fluid from the same vent as culture medium. Daily sampling provided time-series access to active microbial diversity and medium composition. Active archaeal and bacterial communities consisted mainly of sulfur, sulfate and iron reducers and hydrogen oxidizers with the detection of Thermococcus, Archaeoglobus, Geoglobus, Sulfurimonas and Thermotoga sequences. The simultaneous presence of active Geoglobus sp. and Archaeoglobus sp. argues against competition for available carbon sources and electron donors between sulfate and iron reducers at high temperature. This approach allowed the cultivation of microbial populations that were under-represented in the initial environmental sample. The microbial communities are heterogeneously distributed within the gas-lift bioreactor; it is unlikely that bulk mineralogy or fluid chemistry is the drivers of microbial community structure. Instead, we propose that micro-environmental niche characteristics, created by the interaction between the mineral grains and the fluid chemistry, are the main drivers of microbial diversity in natural systems.

  • 5.
    Chi Fru, Ernest
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Swedish Museum of Natural History, Sweden.
    Arvestal, Emma
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    El Albani, Abderrazak
    Kilias, Stephanos
    Argyraki, Ariadne
    Jakobsson, Martin
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Arsenic stress after the Proterozoic glaciations2015In: Scientific Reports, ISSN 2045-2322, E-ISSN 2045-2322, Vol. 5, article id 17789Article in journal (Refereed)
    Abstract [en]

    Protection against arsenic damage in organisms positioned deep in the tree of life points to early evolutionary sensitization. Here, marine sedimentary records reveal a Proterozoic arsenic concentration patterned to glacial-interglacial ages. The low glacial and high interglacial sedimentary arsenic concentrations, suggest deteriorating habitable marine conditions may have coincided with atmospheric oxygen decline after similar to 2.1 billion years ago. A similar intensification of near continental margin sedimentary arsenic levels after the Cryogenian glaciations is also associated with amplified continental weathering. However, interpreted atmospheric oxygen increase at this time, suggests that the marine biosphere had widely adapted to the reorganization of global marine elemental cycles by glaciations. Such a glacially induced biogeochemical bridge would have produced physiologically robust communities that enabled increased oxygenation of the ocean-atmosphere system and the radiation of the complex Ediacaran-Cambrian life.

  • 6.
    Chi Fru, Ernest
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences. Cardiff University, UK.
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Posth, Nicole R.
    Argyraki, Ariadne
    Ling, Yu-Chen
    Ivarsson, Magnus
    Broman, Curt
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Kilias, Stephanos P.
    Arsenic and high affinity phosphate uptake gene distribution in shallow submarine hydrothermal sediments2018In: Biogeochemistry, ISSN 0168-2563, E-ISSN 1573-515X, Vol. 141, no 1, p. 41-62Article in journal (Refereed)
    Abstract [en]

    The toxicity of arsenic (As) towards life on Earth is apparent in the dense distribution of genes associated with As detoxification across the tree of life. The ability to defend against As is particularly vital for survival in As-rich shallow submarine hydrothermal ecosystems along the Hellenic Volcanic Arc (HVA), where life is exposed to hydrothermal fluids containing up to 3000 times more As than present in seawater. We propose that the removal of dissolved As and phosphorus (P) by sulfide and Fe(III)(oxyhydr)oxide minerals during sediment-seawater interaction, produces nutrient-deficient porewaters containing<2.0ppb P. The porewater arsenite-As(III) to arsenate-As(V) ratios, combined with sulfide concentration in the sediment and/or porewater, suggest a hydrothermally-induced seafloor redox gradient. This gradient overlaps with changing high affinity phosphate uptake gene abundance. High affinity phosphate uptake and As cycling genes are depleted in the sulfide-rich settings, relative to the more oxidizing habitats where mainly Fe(III)(oxyhydr)oxides are precipitated. In addition, a habitat-wide low As-respiring and As-oxidizing gene content relative to As resistance gene richness, suggests that As detoxification is prioritized over metabolic As cycling in the sediments. Collectively, the data point to redox control on Fe and S mineralization as a decisive factor in the regulation of high affinity phosphate uptake and As cycling gene content in shallow submarine hydrothermal ecosystems along the HVA.

  • 7.
    Chi Fru, Ernest
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Hemmingsson, Christoffer
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Pérez, Nathalie
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Panova, Elena G.
    Broman, Curt
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    El Albani, Abderrazzak
    Atmospheric weathering of Scandinavian alum shales and the fractionation of C, N and S isotopes2016In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 74, p. 94-108Article in journal (Refereed)
    Abstract [en]

    Subaerial exposure and oxidation of organic carbon (C-org)-rich rocks is believed to be a key mechanism for the recycling of buried C and S back to Earth's surface. Importantly, processes coupled to microbial C-org oxidation are expected to shift new biomass delta C-13(org) composition towards more negative values relative to source. However, there is scarcity of information directly relating rock chemistry to oxidative weathering and shifting delta C-13(org) at the rock-atmosphere interface. This is particularly pertinent to the sulfidic, C-org-rich alum shale units of the Baltoscandian Basin believed to constitute a strong source of metal contaminants to the natural environment, following subaerial exposure and weathering. Consistent with independent support, we show that atmospheric oxidation of the sulfidic, C-org-rich alum shale sequence of the Cambrian-Devonian Baltoscandian Basin induces intense acid rock drainage at the expense of progressive oxidation of Fe sulfides. Sulfide oxidation takes priority over microbial organic matter decomposition, enabling quantitative massive erosion of C-org without producing a delta C-13 shift between acid rock drainage precipitates and shale. Moreover, C-13 enrichment in inorganic carbon of precipitates does not support microbial C-org oxidation as the predominant mechanism of rock weathering upon exposure. Instead, a Delta S-34 = delta S-34(shale) - delta S-34(precipitates) approximate to 0, accompanied by elevated S levels and the ubiquitous deposition of acid rock drainage sulfate minerals in deposited efflorescent precipitates relative to shales, provide strong evidence for quantitative mass oxidation of shale sulfide minerals as the source of acidity for chemical weathering. Slight delta N-15 depletion in the new surface precipitates relative to shale, coincides with dramatic loss of N from shales. Collectively, the results point to pyrite oxidation as a major driver of alum black shale weathering at the rock-atmosphere interface, indicating that quantitative mass release of C-org, N, S, and key metals to the environment is a response to intense sulfide oxidation. Consequently, large-scale acidic weathering of the sulfide-rich alum shale units is suggested to influence the fate and redistribution of the isotopes of C, N, and S from shale to the immediate environment.

  • 8.
    Neubeck, Anna
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Sjöberg, Susanne
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Price, Alex
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Schnürer, Anna
    Effect of Nickel Levels on Hydrogen Partial Pressure and Methane Production in Methanogens2016In: PLoS ONE, ISSN 1932-6203, E-ISSN 1932-6203, Vol. 11, no 12, article id e0168357Article in journal (Refereed)
    Abstract [en]

    Hydrogen (H-2) consumption and methane (CH4) production in pure cultures of three different methanogens were investigated during cultivation with 0, 0.2 and 4.21 mu M added nickel (Ni). The results showed that the level of dissolved Ni in the anaerobic growth medium did not notably affect CH4 production in the cytochrome-free methanogenic species Methanobacterium bryantii and Methanoculleus bourgensis MAB1, but affected CH4 formation rate in the cytochrome-containing Methanosarcina barkeri grown on H-2 and CO2. Methanosarcina barkeri also had the highest amounts of Ni in its cells, indicating that more Ni is needed by cytochrome-containing than by cytochrome-free methanogenic species. The concentration of Ni affected threshold values of H-2 partial pressure (pH(2)) for all three methanogen species studied, with M. bourgensis MAB1 reaching pH(2) values as low as 0.1 Pa when Ni was available in amounts used in normal anaerobic growth medium. To our knowledge, this is the lowest pH(2) threshold recorded to date in pure methanogen culture, which suggests that M. bourgensis MAB1 have a competitive advantage over other species through its ability to grow at low H-2 concentrations. Our study has implications for research on the H-2-driven deep subsurface biosphere and biogas reactor performance.

  • 9.
    Sjöberg, Susanne
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Allard, Bert
    Rattray, Jayne E.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Grawunder, Anja
    Ivarsson, Magnus
    Sjöberg, Viktor
    Karlsson, Stefan
    Skelton, Alasdair
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Dupraz, Christophe
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Rare earth element enriched birnessite in water-bearing fractures, the Ytterby mine, Sweden2017In: Applied Geochemistry, ISSN 0883-2927, E-ISSN 1872-9134, Vol. 78, p. 158-171Article in journal (Refereed)
    Abstract [en]

    Characterization of a black substance exuding from fractured bedrock in a subterranean tunnel revealed a secondary manganese oxide mineralisation exceptionally enriched in rare earth elements (REE). Concentrations are among the highest observed in secondary ferromanganese precipitates in nature. The tunnel is located in the unsaturated zone at shallow depth in the former Ytterby mine, known for the discovery of yttrium, scandium, tantalum and five rare earth elements.

    Elemental analysis and X-ray diffraction of the black substance establish that the main component is a manganese oxide of the birnessite type. Minor fractions of calcite, other manganese oxides, feldspars, quartz and about 1% organic matter were also found, but no iron oxides were identified. The Ytterby birnessite contains REE, as well as calcium, magnesium and traces of other metals. The REE, which constitute 1% of the dry mass and 2% of the metal content, are firmly included in the mineral structure and are not released by leaching at pH 1.5 or higher. A strong preference for the trivalent REE over divalent and monovalent metals is indicated by concentration ratios of the substance to fracture water. The REE-enriched birnessite has the general formula Mx(Mn3+,Mn4+)(2)O-4 center dot(H2O)(n) with M = (0.37-0.41) Ca + 0.02 (REE + Y), 0.04 Mg and (0.02-0.03) other metals, and with [Mn3+]/[Mn4+] = 0.86-1.00.

    The influence of microorganisms on the accumulation of this REE enriched substance is demonstrated by electron paramagnetic resonance spectroscopy. Results show that it is composed of two or more manganese phases, one of which has a biogenic signature. In addition, the occurrence of C-31 to C-35 extended side chain hopanoids among the identified lipid biomarkers combined with the absence of ergosterol, a fungal lipid biomarker, indicate that the in-situ microbial community is bacterial rather than fungal.

  • 10.
    Sjöberg, Susanne
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences. Swedish Museum of Natural History, Sweden.
    Allard, Bert
    Smittenberg, Rienk H.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Dupraz, Christophe
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Microbial Communities Inhabiting a Rare Earth Element Enriched Birnessite-Type Manganese Deposit in the Ytterby Mine, Sweden2018In: Geomicrobiology Journal, ISSN 0149-0451, E-ISSN 1521-0529, Vol. 35, no 8, p. 657-674Article in journal (Refereed)
    Abstract [en]

    The dominant initial phase formed during microbially mediated manganese oxidation is a poorly crystalline birnessite-type phyllomanganate. The occurrence of manganese deposits containing this mineral is of interest for increased understanding of microbial involvement in the manganese cycle. A culture independent molecular approach is used as a first step to investigate the role of microorganisms in forming rare earth element enriched birnessite-type manganese oxides, associated with water bearing rock fractures in a tunnel of the Ytterby mine, Sweden. 16S rRNA gene results show that the chemotrophic bacterial communities are diverse and include a high percentage of uncultured unclassified bacteria while archaeal diversity is low with Thaumarchaeota almost exclusively dominating the population. Ytterby clones are frequently most similar to clones isolated from subsurface environments, low temperature milieus and/or settings rich in metals. Overall, bacteria are dominant compared to archaea. Both bacterial and archaeal abundances are up to four orders of magnitude higher in manganese samples than in fracture water. Potential players in the manganese cycling are mainly found within the ferromanganese genera Hyphomicrobium and Pedomicrobium, and a group of Bacteroidetes sequences that cluster within an uncultured novel genus most closely related to the Terrimonas. This study strongly suggest that the production of the YBS deposit is microbially mediated.

  • 11.
    Yamoah, Kweku Afrifa
    et al.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Callac, Nolwenn
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Chi Fru, Ernest
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Wohlfarth, Barbara
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Wiech, Alan
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    Chabangbor, Akkaneewut
    Smittenberg, Rienk H.
    Stockholm University, Faculty of Science, Department of Geological Sciences.
    A 150-year record of phytoplankton 1 community succession controlled by hydroclimatic variability in a tropical lake2016In: Biogeosciences, ISSN 1726-4170, E-ISSN 1726-4189, Vol. 13, no 13, p. 3971-3980Article in journal (Refereed)
    Abstract [en]

    Climate and human-induced environmental change promotes biological regime shifts between alternate stable states, with implications for ecosystem resilience, function and services. While this has been shown for recent microbial communities, the long-term response of microbial communities has not been investigated in detail. This study investigated the decadal variations in phytoplankton communities in a ~150 year long sedimentary archive of Lake Nong Thale Prong (NTP), southern Thailand using a combi nation of DNA and lipid biomarkers techniques. Reconstructed drier climate from ~1857-1916 Common Era (CE) coincided with oligotrophic lake water conditions and dominance of the green algae Botryococcus braunii, producing characteristic botryococcene lipids. A change to higher silica (Si) input ~1916 CE, which was related to increased rainfall concurs with an abrupt takeover by diatom blooms lasting for 50 years. Since the 1970s more eutrophic conditions prevailed, which was likely caused by increased levels of anthropogenic phosphate (P), aided by increased lake stratification caused by somewhat dryer conditions. The eutrophic conditions led to increased primary productivity consisting again of a Botryococcus sp., though this time not producing the botryococcene lipids. Moreover, Cyanobacteria became dominant. Our results indicate that a combined DNA and lipid biomarker approach provides an efficient way to allow tracking centennial-scale hydroclimate and anthropogenic feedback processes in lake ecosystems.

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