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  • 1.
    Lopez-Fernandez, Margarita
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Helmholtz Zentrum Dresden Rossendorf, Germany.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Turner, Stephanie
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Univ Copenhagen, Denmark.
    Bertilsson, Stefan
    Uppsala University.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Investigation of viable taxa in the deep terrestrial biosphere suggests high rates of nutrient recycling2018In: FEMS Microbiology Ecology, ISSN 0168-6496, E-ISSN 1574-6941, Vol. 94, no 8, article id fiy121Article in journal (Refereed)
    Abstract [en]

    The deep biosphere is the largest 'bioreactor' on earth, and microbes inhabiting this biome profoundly influence global nutrient and energy cycles. An important question for deep biosphere microbiology is whether or not specific populations are viable. To address this, we used quantitative PCR and high throughput 16S rRNA gene sequencing of total and viable cells (i.e. with an intact cellular membrane) from three groundwaters with different ages and chemical constituents. There were no statistically significant differences in 16S rRNA gene abundances and microbial diversity between total and viable communities. This suggests that populations were adapted to prevailing oligo trophic conditions and that non-viable cells are rapidly degraded and recycled into new biomass. With higher concentrations of organic carbon, the modem marine and undefined mixed waters hosted a community with a larger range of predicted growth strategies than the ultra-oligo trophic old saline water. These strategies included fermentative and potentially symbiotic lifestyles by candidate phyla that typically have streamlined genomes. In contrast, the old saline waters had more 16S rRNA gene sequences in previously cultured lineages able to oxidize hydrogen and fix carbon dioxide. This matches the paradigm of a hydrogen and carbon dioxide-fed chemolithoauto trophic deep biosphere.

  • 2.
    Ni, Gaofeng
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Simone, Domenico
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Swedish University of Agricultural Sciences.
    Palma, Daniela
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Broman, Elias
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Stockholm University.
    Wu, Xiaofen
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Turner, Stephanie
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    Dopson, Mark
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science.
    A novel inorganic sulfur compound metabolizing Ferroplasma-like population is suggested to mediate extracellular electron transfer2018In: Frontiers in Microbiology, ISSN 1664-302X, E-ISSN 1664-302X, article id 2945Article in journal (Refereed)
    Abstract [en]

    Mining and processing of metal sulfide ores produces waters containing metals and inorganic sulfur compounds such as tetrathionate and thiosulfate. If released untreated, these sulfur compounds can be oxidized to generate highly acidic wastewaters [termed 'acid mine drainage (AMD)'] that cause severe environmental pollution. One potential method to remediate mining wastewaters is the maturing biotechnology of 'microbial fuel cells' that offers the sustainable removal of acid generating inorganic sulfur compounds alongside producing an electrical current. Microbial fuel cells exploit the ability of bacterial cells to transfer electrons to a mineral as the terminal electron acceptor during anaerobic respiration by replacing the mineral with a solid anode. In consequence, by substituting natural minerals with electrodes, microbial fuel cells also provide an excellent platform to understand environmental microbemineral interactions that are fundamental to element cycling. Previously, tetrathionate degradation coupled to the generation of an electrical current has been demonstrated and here we report a metagenomic and metatranscriptomic analysis of the microbial community. Reconstruction of inorganic sulfur compound metabolism suggested the substrate tetrathionate was metabolized by the Ferroplasma-like and Acidithiobacillus-like populations via multiple pathways. Characterized Ferroplasma species do not utilize inorganic sulfur compounds, suggesting a novel Ferroplasma-likepopulation had been selected. Oxidation of intermediate sulfide, sulfur, thiosulfate, and adenylylsulfate released electrons and the extracellular electrontransfer to the anode was suggested to be dominated by candidate soluble electron shuttles produced by the Ferroplasma-like population. However, as the soluble electron shuttle compounds also have alternative functions within the cell, it cannot be ruled out that acidophiles use novel, uncharacterized mechanisms to mediate extracellular electron transfer. Several populations within the community were suggested to metabolize intermediate inorganicsulfur compounds by multiple pathways, which highlights the potential for mutualistic or symbiotic relationships. This study provided the genetic base for acidophilic microbial fuel cells utilized for the remediation of inorganic sulfur compounds from AMD.

  • 3.
    Turner, Stephanie
    et al.
    Linnaeus University, Faculty of Health and Life Sciences, Department of Biology and Environmental Science. Fed Inst Geosci & Nat Resources BGR, Germany.
    Mikutta, Robert
    Leibniz Univ Hannover, Germany;Martin Luther Univ Halle Wittenberg, Germany.
    Guggenberger, Georg
    Leibniz Univ Hannover, Germany.
    Schaarschmidt, Frank
    Leibniz Univ Hannover, Germany.
    Schippers, Axel
    Fed Inst Geosci & Nat Resources BGR, Germany.
    Distinct pattern of nitrogen functional gene abundances in top- and subsoils along a 120,000-year ecosystem development gradient2019In: Soil Biology and Biochemistry, ISSN 0038-0717, E-ISSN 1879-3428, Vol. 132, p. 111-119Article in journal (Refereed)
    Abstract [en]

    Soil microorganisms are key players of the nitrogen cycle and relevant for soil development. While the community structure of nitrogen-cycling microorganisms during initial soil development is already well investigated, knowledge about the patterns during long-term ecosystem development is limited. In this study, nitrogen functional genes of ammonia-oxidizers (amoA), nitrate-reducers (narG), and chitin-degraders (chiA) were determined via quantitative PCR and the functional community composition of archaeal ammonia-oxidizers was analyzed via clone libraries and DNA sequencing (amoA) in soil depth profiles along the 120,000-year Franz Josef chronosequence (New Zealand). The results show that absolute nitrogen functional gene abundances change significantly during long-term soil development. In organic layers, narG and chiA gene abundances were highest in young to intermediate-aged soils and then decreased following progressive and retrogressive development of the vegetation. While relative archaeal amoA gene abundance (proportional to total cell counts) decreased in the oldest phosphorus-limited topsoils, relative narG and chiA gene abundances remained constant. In subsoils, archaeal amoA and narG gene abundances also decreased with ecosystem retrogression that coincided with the increasing content of iron and aluminum oxides as well as other clay-sized minerals. In contrast, subsoil chiA gene abundances were hardly affected by soil age. The analysis of the archaeal amoA community revealed a compositional shift during long-term ecosystem development. Our study provides evidence that the community structure of nitrogen-cycling microorganisms in top- and subsoils is significantly affected by long-term ecosystem development and suggests an important role of the mineral phase in subsoils.

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