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  • 1.
    Eiler, Alexander
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Mondav, Rhiannon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Sinclair, Lucas
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Fernandez-Vidal, Leyden
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Scofield, Douglas G.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Evolutionary Biology.
    Schwientek, Patrick
    Martinez-Garcia, Manuel
    Torrents, David
    McMahon, Katherine D.
    Andersson, Siv G. E.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology, Molecular Evolution. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Stepanauskas, Ramunas
    Woyke, Tanja
    Bertilsson, Stefan
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. Uppsala University, Science for Life Laboratory, SciLifeLab.
    Tuning fresh: radiation through rewiring of central metabolism in streamlined bacteria2016In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 10, no 8, p. 1902-1914Article in journal (Refereed)
  • 2.
    McCalley, Carmody
    et al.
    Department of Ecology and Evolutionary Biology, University of Arizona.
    Woodcroft, Ben
    Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland.
    Hodgkins, Suzanne
    Department of Earth, Ocean and Atmospheric Science, Florida State University.
    Wehr, Richard
    Department of Ecology and Evolutionary Biology, University of Arizona.
    Kim, Eun-Hae
    Department of Soil, Water and Environmental Science, University of Arizona,.
    Mondav, Rhiannon
    Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland.
    Crill, Patrick
    Department of Geological Sciences, Stockholm University.
    Chanton, Jeffrey
    epartment of Earth, Ocean and Atmospheric Science, Florida State University.
    Rich, Virginia
    Department of Soil, Water and Environmental Science, University of Arizona.
    Tyson, Gene
    Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, University of Queensland.
    Saleska, Scott
    Department of Ecology and Evolutionary Biology, University of Arizona.
    Methane dynamics regulated by microbial community response to permafrost thaw2014In: Nature, ISSN 0028-0836, E-ISSN 1476-4687, Vol. 514, no 7523, p. 478-481Article in journal (Refereed)
    Abstract [en]

    Permafrost contains about 50% of the global soil carbon1. It is thought that the thawing of permafrost can lead to a loss of soil carbon in the form of methane and carbon dioxide emissions2, 3. The magnitude of the resulting positive climate feedback of such greenhouse gas emissions is still unknown3 and may to a large extent depend on the poorly understood role of microbial community composition in regulating the metabolic processes that drive such ecosystem-scale greenhouse gas fluxes. Here we show that changes in vegetation and increasing methane emissions with permafrost thaw are associated with a switch from hydrogenotrophic to partly acetoclastic methanogenesis, resulting in a large shift in the δ13C signature (10–15‰) of emitted methane. We used a natural landscape gradient of permafrost thaw in northern Sweden4, 5 as a model to investigate the role of microbial communities in regulating methane cycling, and to test whether a knowledge of community dynamics could improve predictions of carbon emissions under loss of permafrost. Abundance of the methanogen Candidatus ‘Methanoflorens stordalenmirensis6 is a key predictor of the shifts in methane isotopes, which in turn predicts the proportions of carbon emitted as methane and as carbon dioxide, an important factor for simulating the climate feedback associated with permafrost thaw in global models3, 7. By showing that the abundance of key microbial lineages can be used to predict atmospherically relevant patterns in methane isotopes and the proportion of carbon metabolized to methane during permafrost thaw, we establish a basis for scaling changing microbial communities to ecosystem isotope dynamics. Our findings indicate that microbial ecology may be important in ecosystem-scale responses to global change.

  • 3.
    Mondav, Rhiannon
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Development of an environmental functional gene microarray for soil microbial communities2010In: Applied and Environmental Microbiology, ISSN 0099-2240, E-ISSN 1098-5336, Vol. 76, no 21, p. 7161-7170Article in journal (Refereed)
    Abstract [en]

    Functional attributes of microbial communities are difficult to study, and most current techniques rely on DNA- and rRNA-based profiling of taxa and genes, including microarrays containing sequences of known microorganisms. To quantify gene expression in environmental samples in a culture-independent manner, we constructed an environmental functional gene microarray (E-FGA) consisting of 13,056 mRNA-enriched anonymous microbial clones from diverse microbial communities to profile microbial gene transcripts. A new normalization method using internal spot standards was devised to overcome spotting and hybridization bias, enabling direct comparisons of microarrays. To evaluate potential applications of this metatranscriptomic approach for studying microbes in environmental samples, we tested the E-FGA by profiling the microbial activity of agricultural soils with a low or high flux of N₂O. A total of 109 genes displayed expression that differed significantly between soils with low and high N₂O emissions. We conclude that mRNA-based approaches such as the one presented here may complement existing techniques for assessing functional attributes of microbial communities.

  • 4.
    Mondav, Rhiannon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology. School of Chemistry and Molecular Biosciences, University of Queensland, Brisbane, QLD 4072, Australia.
    McCalley, Carmody K
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH 03824, USA.
    Hodgkins, Suzanne B
    Department of Earth Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306-4320, USA.
    Frolking, Steve
    Institute for the Study of Earth, Oceans, and Space, University of New Hampshire, Durham, NH 03824, USA.
    Saleska, Scott R
    Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, USA.
    Rich, Virginia I
    Department of Soil, Water and Environmental Science, University of Arizona, Tucson, AZ 85721, USA.
    Chanton, Jeff P
    Department of Earth Ocean and Atmospheric Science, Florida State University, Tallahassee, FL 32306-4320, USA.
    Crill, Patrick M
    Department of Geology and Geochemistry, Stockholm University, Stockholm 10691, Sweden.
    Microbial network, phylogenetic diversity and community membership in the active layer across a permafrost thaw gradient2017In: Environmental Microbiology, ISSN 1462-2912, E-ISSN 1462-2920, Vol. 19, no 8, p. 3201-3218Article in journal (Refereed)
    Abstract [en]

    Biogenic production and release of methane (CH4 ) from thawing permafrost has the potential to be a strong source of radiative forcing. We investigated changes in the active layer microbial community of three sites representative of distinct permafrost thaw stages at a palsa mire in northern Sweden. The palsa site (intact permafrost and low radiative forcing signature) had a phylogenetically clustered community dominated by Acidobacteria and Proteobacteria. The bog (thawing permafrost and low radiative forcing signature) had lower alpha diversity and midrange phylogenetic clustering, characteristic of ecosystem disturbance affecting habitat filtering. Hydrogenotrophic methanogens and Acidobacteria dominated the bog shifting from palsa-like to fen-like at the waterline. The fen (no underlying permafrost, high radiative forcing signature) had the highest alpha, beta and phylogenetic diversity, was dominated by Proteobacteria and Euryarchaeota and was significantly enriched in methanogens. The Mire microbial network was modular with module cores consisting of clusters of Acidobacteria, Euryarchaeota or Xanthomonodales. Loss of underlying permafrost with associated hydrological shifts correlated to changes in microbial composition, alpha, beta and phylogenetic diversity associated with a higher radiative forcing signature. These results support the complex role of microbial interactions in mediating carbon budget changes and climate feedback in response to climate forcing.

  • 5.
    Mondav, Rhiannon
    et al.
    Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Ecology and Genetics, Limnology.
    Woodcroft, Ben J.
    Kim, Eun-Hae
    McCalley, Carmody K.
    Hodgkins, Suzanne B.
    Crill, Patrick M.
    Chanton, Jeffrey
    Hurst, Gregory B.
    VerBerkmoes, Nathan C.
    Saleska, Scott R.
    Hugenholtz, Philip
    Rich, Virginia I.
    Tyson, Gene W.
    Discovery of a novel methanogen prevalent in thawing permafrost2014In: Nature Communications, ISSN 2041-1723, E-ISSN 2041-1723, Vol. 5, article id 3212Article in journal (Refereed)
    Abstract [en]

    Thawing permafrost promotes microbial degradation of cryo-sequestered and new carbon leading to the biogenic production of methane, creating a positive feedback to climate change. Here we determine microbial community composition along a permafrost thaw gradient in northern Sweden. Partially thawed sites were frequently dominated by a single archaeal phylotype, Candidatus ‘Methanoflorens stordalenmirensis’ gen. nov. sp. nov., belonging to the uncultivated lineage ‘Rice Cluster II’ (Candidatus ‘Methanoflorentaceae’ fam. nov.). Metagenomic sequencing led to the recovery of its near-complete genome, revealing the genes necessary for hydrogenotrophic methanogenesis. These genes are highly expressed and methane carbon isotope data are consistent with hydrogenotrophic production of methane in the partially thawed site. In addition to permafrost wetlands, ‘Methanoflorentaceae’ are widespread in high methane-flux habitats suggesting that this lineage is both prevalent and a major contributor to global methane production. In thawing permafrost, Candidatus ‘M. stordalenmirensis’ appears to be a key mediator of methane-based positive feedback to climate warming.

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