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  • 1. Fernández-Gómez, Beatriz
    et al.
    Díez, Beatriz
    Polz, Martin F.
    Ignacio Arroyo, José
    Alfaro, Fernando D.
    Marchandon, Germán
    Sanhueza, Cynthia
    Farías, Laura
    Trefault, Nicole
    Marquet, Pablo A.
    Molina-Montenegro, Marco A.
    Sylvander, Peter
    Stockholms universitet, Institutionen för ekologi, miljö och botanik.
    Snoeijs-Leijonmalm, Pauline
    Stockholms universitet, Institutionen för ekologi, miljö och botanik.
    Bacterial community structure in a sympagic habitat expanding with global warming: brackish ice brine at 85-90 degrees N2019In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 13, no 2, p. 316-333Article in journal (Refereed)
    Abstract [en]

    Larger volumes of sea ice have been thawing in the Central Arctic Ocean (CAO) during the last decades than during the past 800,000 years. Brackish brine (fed by meltwater inside the ice) is an expanding sympagic habitat in summer all over the CAO. We report for the first time the structure of bacterial communities in this brine. They are composed of psychrophilic extremophiles, many of them related to phylotypes known from Arctic and Antarctic regions. Community structure displayed strong habitat segregation between brackish ice brine (IB; salinity 2.4-9.6) and immediate sub-ice seawater (SW; salinity 33.3-34.9), expressed at all taxonomic levels (class to genus), by dominant phylotypes as well as by the rare biosphere, and with specialists dominating IB and generalists SW. The dominant phylotypes in IB were related to Candidatus Aquiluna and Flavobacterium, those in SW to Balneatrix and ZD0405, and those shared between the habitats to Halomonas, Polaribacter and Shewanella. A meta-analysis for the oligotrophic CAO showed a pattern with Flavobacteriia dominating in melt ponds, Flavobacteriia and Gammaproteobacteria in solid ice cores, Flavobacteriia, Gamma- and Betaproteobacteria, and Actinobacteria in brine, and Alphaproteobacteria in SW. Based on our results, we expect that the roles of Actinobacteria and Betaproteobacteria in the CAO will increase with global warming owing to the increased production of meltwater in summer. IB contained three times more phylotypes than SW and may act as an insurance reservoir for bacterial diversity that can act as a recruitment base when environmental conditions change.

  • 2. Monteux, Sylvain
    et al.
    Weedon, James T.
    Blume-Werry, Gesche
    Gavazov, Konstantin
    Jassey, Vincent E. J.
    Johansson, Margareta
    Keuper, Frida
    Olid, Carolina
    Dorrepaal, Ellen
    Long-term in situ permafrost thaw effects on bacterial communities and potential aerobic respiration2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, p. 2129-2141Article in journal (Refereed)
    Abstract [en]

    The decomposition of large stocks of soil organic carbon in thawing permafrost might depend on more than climate change-induced temperature increases: indirect effects of thawing via altered bacterial community structure (BCS) or rooting patterns are largely unexplored. We used a 10-year in situ permafrost thaw experiment and aerobic incubations to investigate alterations in BCS and potential respiration at different depths, and the extent to which they are related with each other and with root density. Active layer and permafrost BCS strongly differed, and the BCS in formerly frozen soils (below the natural thawfront) converged under induced deep thaw to strongly resemble the active layer BCS, possibly as a result of colonization by overlying microorganisms. Overall, respiration rates decreased with depth and soils showed lower potential respiration when subjected to deeper thaw, which we attributed to gradual labile carbon pool depletion. Despite deeper rooting under induced deep thaw, root density measurements did not improve soil chemistry-based models of potential respiration. However, BCS explained an additional unique portion of variation in respiration, particularly when accounting for differences in organic matter content. Our results suggest that by measuring bacterial community composition, we can improve both our understanding and the modeling of the permafrost carbon feedback.

  • 3. Obermeier, Melanie Maria
    et al.
    Wicaksono, Wisnu Adi
    Taffner, Julian
    Bergna, Alessandro
    Poehlein, Anja
    Cernava, Tomislav
    Lindstaedt, Stefanie
    Lovric, Mario
    Müller Bogotá, Christina Andrea
    Berg, Gabriele
    Plant resistome profiling in evolutionary old bog vegetation provides new clues to understand emergence of multi-resistance2020In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370Article in journal (Refereed)
    Abstract [en]

    The expanding antibiotic resistance crisis calls for a more in depth understanding of the importance of antimicrobial resistance genes (ARGs) in pristine environments. We, therefore, studied the microbiome associated with Sphagnum moss forming the main vegetation in undomesticated, evolutionary old bog ecosystems. In our complementary analysis of culture collections, metagenomic data and a fosmid library from different geographic sites in Europe, we identified a low abundant but highly diverse pool of resistance determinants, which targets an unexpectedly broad range of 29 antibiotics including natural and synthetic compounds. This derives both, from the extraordinarily high abundance of efflux pumps (up to 96%), and the unexpectedly versatile set of ARGs underlying all major resistance mechanisms. Multi-resistance was frequently observed among bacterial isolates, e.g. in Serratia, Rouxiella, Pandoraea, Paraburkholderia and Pseudomonas. In a search for novel ARGs, we identified the new class A β-lactamase Mm3. The native Sphagnum resistome comprising a highly diversified and partially novel set of ARGs contributes to the bog ecosystem´s plasticity. Our results reinforce the ecological link between natural and clinically relevant resistomes and thereby shed light onto this link from the aspect of pristine plants. Moreover, they underline that diverse resistomes are an intrinsic characteristic of plant-associated microbial communities, they naturally harbour many resistances including genes with potential clinical relevance.

  • 4. Singleton, Caitlin M.
    et al.
    McCalley, Carmody K.
    Woodcroft, Ben J.
    Boyd, Joel A.
    Evans, Paul N.
    Hodgkins, Suzanne B.
    Chanton, Jeffrey P.
    Frolking, Steve
    Crill, Patrick M.
    Stockholms universitet, Institutionen för geologiska vetenskaper.
    Saleska, Scott R.
    Rich, Virginia
    Tyson, Gene W.
    Methanotrophy across a natural permafrost thaw environment2018In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 12, no 10, p. 2544-2558Article in journal (Refereed)
    Abstract [en]

    The fate of carbon sequestered in permafrost is a key concern for future global warming as this large carbon stock is rapidly becoming a net methane source due to widespread thaw. Methane release from permafrost is moderated by methanotrophs, which oxidise 20-60% of this methane before emission to the atmosphere. Despite the importance of methanotrophs to carbon cycling, these microorganisms are under-characterised and have not been studied across a natural permafrost thaw gradient. Here, we examine methanotroph communities from the active layer of a permafrost thaw gradient in Stordalen Mire (Abisko, Sweden) spanning three years, analysing 188 metagenomes and 24 metatranscriptomes paired with in situ biogeochemical data. Methanotroph community composition and activity varied significantly as thaw progressed from intact permafrost palsa, to partially thawed bog and fully thawed fen. Thirteen methanotroph population genomes were recovered, including two novel genomes belonging to the uncultivated upland soil cluster alpha (USCa) group and a novel potentially methanotrophic Hyphomicrobiaceae. Combined analysis of porewater delta C-13-CH 4 isotopes and methanotroph abundances showed methane oxidation was greatest below the oxic-anoxic interface in the bog. These results detail the direct effect of thaw on autochthonous methanotroph communities, and their consequent changes in population structure, activity and methane moderation potential.

  • 5. Waldrop, Mark P.
    et al.
    Chabot, Christopher L.
    Liebner, Susanne
    Holm, Stine
    Snyder, Michael W.
    Dillon, Megan
    Dudgeon, Steven R.
    Douglas, Thomas A.
    Leewis, Mary-Cathrine
    Walter Anthony, Katey M.
    McFarland, Jack W.
    Arp, Christopher D.
    Bondurant, Allen C.
    Taş, Neslihan
    Mackelprang, Rachel
    Permafrost microbial communities and functional genes are structured by latitudinal and soil geochemical gradients2023In: The ISME Journal, ISSN 1751-7362, E-ISSN 1751-7370, Vol. 17, no 8, p. 1224-1235Article in journal (Refereed)
    Abstract [en]

    Permafrost underlies approximately one quarter of Northern Hemisphere terrestrial surfaces and contains 25–50% of the global soil carbon (C) pool. Permafrost soils and the C stocks within are vulnerable to ongoing and future projected climate warming. The biogeography of microbial communities inhabiting permafrost has not been examined beyond a small number of sites focused on local-scale variation. Permafrost is different from other soils. Perennially frozen conditions in permafrost dictate that microbial communities do not turn over quickly, thus possibly providing strong linkages to past environments. Thus, the factors structuring the composition and function of microbial communities may differ from patterns observed in other terrestrial environments. Here, we analyzed 133 permafrost metagenomes from North America, Europe, and Asia. Permafrost biodiversity and taxonomic distribution varied in relation to pH, latitude and soil depth. The distribution of genes differed by latitude, soil depth, age, and pH. Genes that were the most highly variable across all sites were associated with energy metabolism and C-assimilation. Specifically, methanogenesis, fermentation, nitrate reduction, and replenishment of citric acid cycle intermediates. This suggests that adaptations to energy acquisition and substrate availability are among some of the strongest selective pressures shaping permafrost microbial communities. The spatial variation in metabolic potential has primed communities for specific biogeochemical processes as soils thaw due to climate change, which could cause regional- to global- scale variation in C and nitrogen processing and greenhouse gas emissions.

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