@phdthesis{Holm2020,
  author    = {Holm, Stine},
  title     = {Methanogenic communities and metaplasmidome-encoded functions in permafrost environments exposed to thaw},
  school      = {Universit{\"a}t Potsdam},
  pages     = {VI, 243},
  year      = {2020},
  abstract  = {This thesis investigates how the permafrost microbiota responds to global warming. In detail, the constraints behind methane production in thawing permafrost were linked to methanogenic activity, abundance and composition. Furthermore, this thesis offers new insights into microbial adaptions to the changing environmental conditions during global warming. This was assesed by investigating the potential ecological relevant functions encoded by plasmid DNA within the permafrost microbiota. Permafrost of both interglacial and glacial origin spanning the Holocene to the late Pleistocene, including Eemian, were studied during long-term thaw incubations. Furthermore, several permafrost cores of different stratigraphy, soil type and vegetation cover were used to target the main constraints behind methane production during short-term thaw simulations. Short- and long-term incubations simulating thaw with and without the addition of substrate were combined with activity measurements, amplicon and metagenomic sequencing of permanently frozen and seasonally thawed active layer. Combined, it allowed to address the following questions. i) What constraints methane production when permafrost thaws and how is this linked to methanogenic activity, abundance and composition? ii) How does the methanogenic community composition change during long-term thawing conditions? iii) Which potential ecological relevant functions are encoded by plasmid DNA in active layer soils? The major outcomes of this thesis are as follows. i) Methane production from permafrost after long-term thaw simulation was found to be constrained mainly by the abundance of methanogens and the archaeal community composition. Deposits formed during periods of warmer temperatures and increased precipitation, (here represented by deposits from the Late Pleistocene of both interstadial and interglacial periods) were found to respond strongest to thawing conditions and to contain an archaeal community dominated by methanogenic archaea (40\% and 100\% of all detected archaea). Methanogenic population size and carbon density were identified as main predictors for potential methane production in thawing permafrost in short-term incubations when substrate was sufficiently available. ii) Besides determining the methanogenic activity after long-term thaw, the paleoenvironmental conditions were also found to influence the response of the methanogenic community composition. Substantial shifts within methanogenic community structure and a drop in diversity were observed in deposits formed during warmer periods, but not in deposits from stadials, when colder and drier conditions occurred. Overall, a shift towards a dominance of hydrogenotrophic methanogens was observed in all samples, except for the oldest interglacial deposits from the Eemian, which displayed a potential dominance of acetoclastic methanogens. The Eemian, which is discussed to serve as an analogue to current climate conditions, contained highly active methanogenic communities. However, all potential limitation of methane production after permafrost thaw, it means methanogenic community structure, methanogenic population size, and substrate pool might be overcome after permafrost had thawed on the long-term. iii) Enrichments with soil from the seasonally thawed active layer revealed that its plasmid DNA ('metaplasmidome') carries stress-response genes. In particular it encoded antibiotic resistance genes, heavy metal resistance genes, cold shock proteins and genes encoding UV-protection. Those are functions that are directly involved in the adaptation of microbial communities to stresses in polar environments. It was further found that metaplasmidomes from the Siberian active layer originate mainly from Gammaproteobacteria. By applying enrichment cultures followed by plasmid DNA extraction it was possible to obtain a higher average contigs length and significantly higher recovery of plasmid sequences than from extracting plasmid sequences from metagenomes. The approach of analyzing 'metaplasmidomes' established in this thesis is therefore suitable for studying the ecological role of plasmids in polar environments in general. This thesis emphasizes that including microbial community dynamics have the potential to improve permafrost-carbon projections. Microbially mediated methane release from permafrost environments may significantly impact future climate change. This thesis identified drivers of methanogenic composition, abundance and activity in thawing permafrost landscapes. Finally, this thesis underlines the importance to study how the current warming Arctic affects microbial communities in order to gain more insight into microbial response and adaptation strategies.},
  language  = {en}
}
@article{KleinLantuitHeimetal.2019,
  author    = {Klein, Konstantin P. and Lantuit, Hugues and Heim, Birgit and Fell, Frank and Doxaran, David and Irrgang, Anna Maria},
  title     = {Long-Term High-Resolution Sediment and Sea Surface Temperature Spatial Patterns in Arctic Nearshore Waters Retrieved Using 30-Year Landsat Archive Imagery},
  series = {Remote sensing},
  volume    = {11},
  journal   = {Remote sensing},
  number    = {23},
  publisher = {MDPI},
  address   = {Basel},
  issn      = {2072-4292},
  doi       = {10.3390/rs11232791},
  pages     = {21},
  year      = {2019},
  abstract  = {The Arctic is directly impacted by climate change. The increase in air temperature drives the thawing of permafrost and an increase in coastal erosion and river discharge. This leads to a greater input of sediment and organic matter into coastal waters, which substantially impacts the ecosystems, the subsistence economy of the local population, and the climate because of the transformation of organic matter into greenhouse gases. Yet, the patterns of sediment dispersal in the nearshore zone are not well known, because ships do not often reach shallow waters and satellite remote sensing is traditionally focused on less dynamic environments. The goal of this study is to use the extensive Landsat archive to investigate sediment dispersal patterns specifically on an exemplary Arctic nearshore environment, where field measurements are often scarce. Multiple Landsat scenes were combined to calculate means of sediment dispersal and sea surface temperature under changing seasonal wind conditions in the nearshore zone of Herschel Island Qikiqtaruk in the western Canadian Arctic since 1982. We use observations in the Landsat red and thermal wavebands, as well as a recently published water turbidity algorithm to relate archive wind data to turbidity and sea surface temperature. We map the spatial patterns of turbidity and water temperature at high spatial resolution in order to resolve transport pathways of water and sediment at the water surface. Our results show that these pathways are clearly related to the prevailing wind conditions, being ESE and NW. During easterly wind conditions, both turbidity and water temperature are significantly higher in the nearshore area. The extent of the Mackenzie River plume and coastal erosion are the main explanatory variables for sediment dispersal and sea surface temperature distributions in the study area. During northwesterly wind conditions, the influence of the Mackenzie River plume is negligible. Our results highlight the potential of high spatial resolution Landsat imagery to detect small-scale hydrodynamic processes, but also show the need to specifically tune optical models for Arctic nearshore environments.},
  language  = {en}
}