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  • 1
    Publication Date: 2019-02-25
    Description: Large, colorless sulfur-oxidizing bacteria (LSB) of the family Beggiatoaceae form thick mats at sulfidic sediment surfaces, where they efficiently detoxify sulfide before it enters the water column. The genus Thiomargarita harbors the largest known freeliving bacteria with cell sizes of up to 750 mm in diameter. In addition to their ability to oxidize reduced sulfur compounds, some Thiomargarita spp. are known to store large amounts of nitrate, phosphate and elemental sulfur internally. To date little is known about their energy yielding metabolic pathways, and how these pathways compare to other Beggiatoaceae. Here, we present a draft single-cell genome of a chain-forming “Candidatus Thiomargarita nelsonii Thio36”, and conduct a comparative analysis to five draft and one full genome of other members of the Beggiatoaceae. “Ca. T. nelsonii Thio36” is able to respire nitrate to both ammonium and dinitrogen, which allows them to flexibly respond to environmental changes. Genes for sulfur oxidation and inorganic carbon fixation confirmed that “Ca. T. nelsonii Thio36” can function as a chemolithoautotroph. Carbon can be fixed via the Calvin–Benson–Bassham cycle, which is common among the Beggiatoaceae. In addition we found key genes of the reductive tricarboxylic acid cycle that point toward an alternative CO2 fixation pathway. Surprisingly, “Ca. T. nelsonii Thio36” also encodes key genes of the C2- cycle that convert 2-phosphoglycolate to 3-phosphoglycerate during photorespiration in higher plants and cyanobacteria. Moreover, we identified a novel trait of a flavin-based energy bifurcation pathway coupled to a NaC-translocating membrane complex (Rnf). The coupling of these pathways may be key to surviving long periods of anoxia. As other Beggiatoaceae “Ca. T. nelsonii Thio36” encodes many genes similar to those of (filamentous) cyanobacteria. In summary, the genome of “Ca. T. nelsonii Thio36” provides additional insight into the ecology of giant sulfur-oxidizing bacteria, and reveals unique genomic features for the Thiomargarita lineage within the Beggiatoaceae.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Article , NonPeerReviewed
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  • 2
    Publication Date: 2018-05-27
    Description: Thawing submarine permafrost is a source of methane to the subsurface biosphere. Methane oxidation in submarine permafrost sediments has been proposed, but the responsible microorganisms remain uncharacterized. We analyzed archaeal communities and identified distinct anaerobic methanotrophic assemblages of marine and terrestrial origin (ANME-2a/b, ANME-2d) both in frozen and completely thawed submarine permafrost sediments. Besides archaea potentially involved in anaerobic oxidation of methane (AOM) we found a large diversity of archaea mainly belonging to Bathyarchaeota, Thaumarchaeota, and Euryarchaeota. Methane concentrations and δ13C-methane signatures distinguish horizons of potential AOM coupled either to sulfate reduction in a sulfate-methane transition zone (SMTZ) or to the reduction of other electron acceptors, such as iron, manganese or nitrate. Analysis of functional marker genes (mcrA) and fluorescence in situ hybridization (FISH) corroborate potential activity of AOM communities in submarine permafrost sediments at low temperatures. Modeled potential AOM consumes 72–100% of submarine permafrost methane and up to 1.2 Tg of carbon per year for the total expected area of submarine permafrost. This is comparable with AOM habitats such as cold seeps. We thus propose that AOM is active where submarine permafrost thaws, which should be included in global methane budgets.
    Repository Name: EPIC Alfred Wegener Institut
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  • 3
    Publication Date: 2018-07-05
    Description: Recent studies on permafrost organic matter (OM) suggest that a portion of previously frozen carbon will enter the active carbon cycle as high latitudes warm. Less is known about the fate of other OM components, including nutrients such as nitrogen (N). The abundance and availability of N following permafrost thaw will regulate the ability of plants to offset carbon losses. Additionally, lateral N losses could alter aquatic food webs. There is growing evidence that some N is lost vertically as N2O, a greenhouse gas 300 times stronger than CO2 over 100 years. Despite broad recognition of its role regulating both carbon and non-carbon aspects of the permafrost climate feedback, estimates of permafrost N remain uncertain. To address this knowledge gap, we quantified N content for different stratigraphic units, including yedoma, Holocene cover deposits, refrozen thermokarst deposits, taberal sediments, and active layer soils. The resulting N estimates from this one permafrost region were similar in magnitude to previous estimates for the entire permafrost zone. We conclude that the permafrost N pool is much larger than currently appreciated and a substantial pool of permafrost N could be mobilized after thaw, with continental-scale consequences for biogeochemical budgets and global-scale consequences.
    Repository Name: EPIC Alfred Wegener Institut
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  • 4
    Publication Date: 2018-08-24
    Description: Introduction: Thawing arctic subsea permafrost is a source of organic carbon in deep sediment layers. The permafrost that is at its thermal equilibrium releases biologically produced methane and a deep sulfate-methane transition zone (SMTZ) is formed due to sulfate-rich overlaying marine sediment layers. The process of methane oxidation in this anaerobic environment has been suggested1 but AOM associated microbial communities remain to be identified. Objectives: We aimed at providing evidence for anaerobic methanotrophic (ANME) archaeal communities at the deep SMTZ of the north-east Siberian Laptev Sea shelf. Material and methods: Two sediment cores were retrieved (77 m and 47.4 m deep) from the coastal shelf north of Cape Mamontov Klyk ‘C2’ (11.5 km offshore) and west to the Buor Khaya Peninsula ‘BK2’ (800 m offshore), respectively. Methane and sulfate concentrations as well as 13C isotope values of CH4 were measured and correlated with molecular analysis of microbial communities along the thaw front. Results: At the thaw front of BK2, at 23.7 meters below sea floor (mbsf) biologically produced methane (13 C= -70‰ VPDB) gets oxidized (13C= -29.8 ‰ VPDB)1. At the same depth, we found an increase in functional genes of methanogenic archaea (mcrA) and sulfate reducing bacteria (dsrB) analysed by quantitative PCR. Massive parallel tag-sequencing of the 16S rRNA gene showed an increase of ANME-2a/2b and ANME-2d sequences towards the thaw front in both cores. At the thaw front of the BK2 core, typical ANME-2 partners of the Desulfobacterales2were found to dominate the sulfate reducing bacterial community, whereas Desulfobaccasequences dominate in all samples of the C2 core. Theoretical methane oxidation rates (0.4-6 nmol cm-3d-1)1based on estimated methane fluxes showed higher values than typically found in subsurface sediments and are more similar to rates of margin SMTZs3. Conclusion: Our data indicate that active anaerobic methane oxidizer communities at the thaw front of subsea permafrost prevent methane from being released into the water column and subsequently to the atmosphere. Further analyses on lipid biomarkers and 14C-CH4isotopic rate measurements will determine how active these communities are in situ. 1. Overduin, P. P. et al.Methane oxidation following submarine permafrost degradation: Measurements from a central Laptev Sea shelf borehole. J. Geophys. Res. Biogeosciences2014JG002862 (2015). 2. Schreiber, L., Holler, T., Knittel, K., Meyerdierks, A. & Amann, R. Identification of the dominant sulfate-reducing bacterial partner of anaerobic methanotrophs of the ANME-2 clade. Environ. Microbiol.12, 2327-2340 (2010). 3. Knittel, K. & Boetius, A. Anaerobic Oxidation of Methane: Progress with an Unknown Process. Annu. Rev. Microbiol. 63, 311-334 (2009).
    Repository Name: EPIC Alfred Wegener Institut
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  • 5
    Publication Date: 2018-08-28
    Description: Thermokarst lakes are widespread features of changing periglacial environments. In this study, we analyze total organic carbon content (TOC), C/N, stable carbon isotopes and methane concentration in pore water from sediments of 18 tundra lakes in West Alaska and 11 boreal lakes in Central Alaska in order to discuss differences in carbon accumulation, sources of organic matter and their role in the carbon cycle. While a wide range of TOC content was measured in West Alaska with highest TOC in lakes that initiated in drained lake basins, some boreal lakes in Central Alaska, like Goldstream Lake show surprisingly low TOC. Similar finding in CH4 concentration suggest that state of permafrost, the age of the lakes and the catchment characteristics have an important influence on sources of organic carbon and, thus, different potential of thermokarst lakes to contribute to the global carbon cycle.
    Repository Name: EPIC Alfred Wegener Institut
    Type: Conference , NonPeerReviewed , info:eu-repo/semantics/conferenceObject
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  • 6
    Publication Date: 2017-10-24
    Repository Name: EPIC Alfred Wegener Institut
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  • 7
    Publication Date: 2016-12-14
    Description: Fossil organic matter (OM) stored in permafrost is an important subject in climate research. Such OM represents a huge reservoir of carbon (C). Multiple studies suggest its source potential for C release into the active C cycle through permafrost thaw and subsequent microbial turnover in a warming Arctic. However, net ecosystem OM balance in the permafrost region depends on more than just carbon. The abundance and availability of nitrogen (N) following permafrost thaw will influence plant growth, nutrient delivery to aquatic and estuarine ecosystems, and N oxide (N2O) emissions. Despite its central importance to predicting permafrost impacts and feedbacks to climate change, relatively little is known about permafrost N stocks and composition. In this study, we present the most extensive dataset to date of permafrost N in the Siberian and Alaskan Yedoma domain. The Yedoma domain comprises decameter thick ice-rich silts intersected by syngenetic ice wedges, which formed in late Pleistocene tundra-steppe environments, as well as other deposits resulting from permafrost degradation during the Holocene. Together, the deposits in this region constitute a large C inventory storing several hundred Gt C, but are also known to be nutrient-rich due to rapid burial and freezing of plant remains. Hitherto, the total organic C pool of the Yedoma region was quantified, while the total N inventory is lacking so far. Based on the most comprehensive data set of N content in permafrost to date, our study aims to estimate the present pool of N stored in the different stratigraphic units of the Yedoma domain: 1) late Pleistocene Yedoma deposits, 2) in-situ thawed and diagenetically altered Yedoma deposits (taberite), 3) Holocene thermokarst deposits, 4) Holocene cover deposits on top of Yedoma, and 5) the modern active layer of soils. To quantify measurement uncertainty, we estimated nitrogen stocks with bootstrapping techniques. We show that the deposits of the Yedoma region store a substantial pool of N that is expected to get mobilized after thaw and, at least partially, affecting biogeochemical budgets of thawing warming permafrost ecosystems.
    Repository Name: EPIC Alfred Wegener Institut
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  • 8
    Publication Date: 2018-08-24
    Description: Introduction: Submarine arctic permafrost was formed when sea level rise flooded terrestrial permafrost and warmed the frozen sediments during the Holocene. This thawing permafrost may play a major role in global warming as it stores huge amounts of organic carbon. Hitherto, the extent and importance of microbial activity on carbon transformations as well as the reactions of microorganisms to the environmental changes accompanying the inundation of permafrost by sea water are poorly understood. Objectives: We investigated the impact of sea level rise on methane cycle associated microbial communities in degrading permafrost of the western and central Laptev Sea shelf, Siberian. Material and methods: Two sediment cores were retrieved (77 m and 52 m deep) from the coastal shelf north of Cape Mamontov Klyk ‘C2’ (11.5 km offshore) and west of Buor Khaya Peninsula ‘BK2’ (800 m offshore), respectively. Chemical parameters such as total organic carbon (TOC), methane concentrations and 13 C isotope values were measured and correlated with molecular analysis of microbial communities along the cores. Results: Frozen sediment was encountered at 35.5 (C2) and 28 (BK2) meters below sea level (mbsl), respectively. Methane concentrations varied between 0.21 and 284.31 nmol g-1with highest values in the frozen permafrost and lowest values in the overlaying unfrozen sediments. Low methane concentrations in the unfrozen sediments of BK2 (16.25-28.20 mbsl) correlated with the highest carbon isotope values of methane (-29.8 ‰ VPDB) indicating microbial oxidation of methane under in situ conditions in the thawing permafrost. Bacterial cell numbers (16S rRNA) and functional genes (mcrA) of methanogenic archaea and sulphate reducing bacteria (dsrB) analysed by quantitative PCR often peaked at high methane or TOC concentrations in the frozen permafrost and showed specific 13CH4isotopic values indicating distinct methanogenic populations. Conclusion : Our data give first insights into how the inundation of permafrost by sea water influences the abundance of active members of the microbial methane cycle both along thawed and still frozen sediments. Further analysis of amplicon sequencing and quantitative analysis by fluorescence in situ,hybridization will give a better overview of these highly dynamic microbial populations.
    Repository Name: EPIC Alfred Wegener Institut
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  • 9
    Publication Date: 2018-12-23
    Repository Name: EPIC Alfred Wegener Institut
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  • 10
    Publication Date: 2019-12-06
    Description: Warming of the Arctic led to an increase in permafrost temperatures by about 0.3 �C during the last decade. Permafrost warming is associated with increasing sediment water content, permeability, and diffusivity and could in the long term alter microbial community composition and abundance even before permafrost thaws. We studied the long-term effect (up to 2500 years) of submarine permafrost warming on microbial communities along an onshore–offshore transect on the Siberian Arctic Shelf displaying a natural temperature gradient of more than 10 �C. We analysed the in situ development of bacterial abundance and community composition through total cell counts (TCCs), quantitative PCR of bacterial gene abundance, and amplicon sequencing and correlated the microbial community data with temperature, pore water chemistry, and sediment physicochemical parameters. On timescales of centuries, permafrost warming coincided with an overall decreasing microbial abundance, whereas millennia after warming microbial abundance was similar to cold onshore permafrost. In addition, the dissolved organic carbon content of all cores was lowest in submarine permafrost after millennial-scale warming. Based on correlation analysis, TCC, unlike bacterial gene abundance, showed a significant rank-based negative correlation with increasing temperature, while bacterial gene copy numbers showed a strong negative correlation with salinity. Bacterial community composition correlated only weakly with temperature but strongly with the pore water stable isotopes �18O and �D, as well as with depth. The bacterial community showed substantial spatial variation and an overall dominance of Actinobacteria, Chloroflexi, Firmicutes, Gemmatimonadetes, and Proteobacteria, which are amongst the microbial taxa that were also found to be active in other frozen permafrost environments. We suggest that, millennia after permafrost warming by over 10 �C, microbial community composition and abundance show some indications for proliferation but mainly reflect the sedimentation history and paleoenvironment and not a direct effect through warming.
    Repository Name: EPIC Alfred Wegener Institut
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