Christian Knoblauch

Community structure, cellular rRNA content, and activity of sulfate-reducing bacteria in marine Arctic sediments

ABSTRACT The community structure of sulfate-reducing bacteria (SRB) of a marine Arctic sediment (Smeerenburgfjorden, Svalbard) was characterized by both fluorescence in situ hybridization (FISH) and rRNA slot blot hybridization by using group- and genus-specific 16S rRNA-targeted oligonucleotide probes. The SRB community was dominated by members of the Desulfosarcina-Desulfococcus group. This group accounted for up to 73% of the SRB detected and up to 70% of the SRB rRNA detected. The predominance was shown to be a common feature for different stations along the coast of Svalbard. In a top-to-bottom approach we aimed to further resolve the composition of this large group of SRB by using probes for cultivated genera. While this approach failed, directed cloning of probe-targeted genes encoding 16S rRNA was successful and resulted in sequences which were all affiliated with the Desulfosarcina-Desulfococcus group. A group of clone sequences (group SVAL1) most closely related toDesulfosarcina variabilis (91.2% sequence similarity) was dominant and was shown to be most abundant in situ, accounting for up to 54.8% of the total SRB detected. A comparison of the two methods used for quantification showed that FISH and rRNA slot blot hybridization gave comparable results. Furthermore, a combination of the two methods allowed us to calculate specific cellular rRNA contents with respect to localization in the sediment profile. The rRNA contents of Desulfosarcina-Desulfococcus cells were highest in the first 5 mm of the sediment (0.9 and 1.4 fg, respectively) and decreased steeply with depth, indicating that maximal metabolic activity occurred close to the surface. Based on SRB cell numbers, cellular sulfate reduction rates were calculated. The rates were highest in the surface layer (0.14 fmol cell−1day−1), decreased by a factor of 3 within the first 2 cm, and were relatively constant in deeper layers.

Psychrophilic sulfate-reducing bacteria isolated from permanently cold Arctic marine sediments: description of Desulfofrigus oceanense gen. nov., sp. nov., Desulfofrigus fragile sp. nov., Desulfofaba gelida gen. nov., sp. nov., Desulfotalea psychrophila gen. nov., sp. nov. and Desulfotalea arctica sp. nov.

Five psychrophilic, Gram-negative, sulfate-reducing bacteria were isolated from marine sediments off the coast of Svalbard. All isolates grew at the in situ temperature of -1.7 degrees C. In batch cultures, strain PSv29T had the highest growth rate at 7 degrees C, strains ASv26T and LSv54T had the highest growth rate at 10 degrees C, and strains LSv21T and LSv514T had the highest growth rate at 18 degrees C. The new isolates used the most common fermentation products in marine sediments, such as acetate, propionate, butyrate, lactate and hydrogen, but only strain ASv26T was able to oxidize fatty acids completely to CO2. The new strains had growth optima at neutral pH and marine salt concentration, except for LSv54T which grew fastest with 1% NaCl. Sulfite and thiosulfate were used as electron acceptors by strains ASv26T, PSv29T and LSv54T, and all strains except PSv29T grew with Fe3+ (ferric citrate) as electron acceptor. Chemotaxonomy based on cellular fatty acid patterns and menaquinones showed good agreement with the phylogeny based on 16S rRNA sequences. All strains belonged to the delta subclass of Proteobacteria but had at least 9% evolutionary distance from known sulfate reducers. Due to the phylogenetic and phenotypic differences between the new isolates and their closest relatives, establishment of the new genera Desulfotalea gen. nov., Desulfofaba gen. nov. and Desulfofrigus gen. nov. is proposed, with strain ASv26T as the type strain of the type species Desulfofrigus oceanense sp. nov., LSv21T as the type strain of Desulfofrigus fragile sp. nov., PSv29T as the type strain of the type species Desulfofaba gelida sp. nov., LSv54T as the type strain of the type species Desulfotalea psychrophila sp. nov. and LSv514T as the type strain of Desulfotalea arctica sp. nov.

Controls on stable sulfur isotope fractionation during bacterial sulfate reduction in Arctic sediments

Abstract Sulfur isotope fractionation experiments during bacterial sulfate reduction were performed with recently isolated strains of cold-adapted sulfate-reducing bacteria from Arctic marine sediments with year-round temperatures below 2°C. The bacteria represent quantitatively important members of a high-latitude anaerobic microbial community. In the experiments, cell-specific sulfate reduction rates decreased with decreasing temperature and were only slightly higher than the inferred cell-specific sulfate reduction rates in their natural habitat. The experimentally determined isotopic fractionations varied by less than 5.8‰ with respect to temperature and sulfate reduction rate, whereas the difference in sulfur isotopic fractionation between bacteria with different carbon oxidation pathways was as large as 17.4‰. Incubation of sediment slurries from two Arctic localities across an experimental temperature gradient from −4°C to 39°C yielded an isotopic fractionation of 30‰ below 7.6°C, a fractionation of 14‰ and 15.5‰ between 7.6°C and 25°C, and fractionations of 5‰ and 8‰ above 25°C, respectively. In absence of significant differences in sulfate reduction rates in the high and low temperature range, respectively, we infer that different genera of sulfate-reducing bacteria dominate the sulfate-reducing bacterial community at different temperatures. In the Arctic sediments where these bacteria are abundant the isotopic differences between dissolved sulfate, pyrite, and acid-volatile sulfide are at least twice as large as the experimentally determined isotopic fractionations. On the basis of bacterial abundance and cell-specific sulfate reduction rates, these greater isotopic differences cannot be accounted for by significantly lower in situ bacterial sulfate reduction rates. Therefore, the remaining isotopic difference between sulfate and sulfide must derive from additional isotope effects that exist in the oxidative part of the sedimentary sulfur cycle.

Predicting long-term carbon mineralization and trace gas production from thawing permafrost of Northeast Siberia

The currently observed Arctic warming will increase permafrost degradation followed by mineralization of formerly frozen organic matter to carbon dioxide (CO2 ) and methane (CH4 ). Despite increasing awareness of permafrost carbon vulnerability, the potential long-term formation of trace gases from thawing permafrost remains unclear. The objective of the current study is to quantify the potential long-term release of trace gases from permafrost organic matter. Therefore, Holocene and Pleistocene permafrost deposits were sampled in the Lena River Delta, Northeast Siberia. The sampled permafrost contained between 0.6% and 12.4% organic carbon. CO2 and CH4 production was measured for 1200 days in aerobic and anaerobic incubations at 4 °C. The derived fluxes were used to estimate parameters of a two pool carbon degradation model. Total CO2 production was similar in Holocene permafrost (1.3 ± 0.8 mg CO2 -C gdw(-1) aerobically, 0.25 ± 0.13 mg CO2 -C gdw(-1) anaerobically) as in 34 000-42 000-year-old Pleistocene permafrost (1.6 ± 1.2 mg CO2 -C gdw(-1) aerobically, 0.26 ± 0.10 mg CO2 -C gdw(-1) anaerobically). The main predictor for carbon mineralization was the content of organic matter. Anaerobic conditions strongly reduced carbon mineralization since only 25% of aerobically mineralized carbon was released as CO2 and CH4 in the absence of oxygen. CH4 production was low or absent in most of the Pleistocene permafrost and always started after a significant delay. After 1200 days on average 3.1% of initial carbon was mineralized to CO2 under aerobic conditions while without oxygen 0.55% were released as CO2 and 0.28% as CH4 . The calibrated carbon degradation model predicted cumulative CO2 production over a period of 100 years accounting for 15.1% (aerobic) and 1.8% (anaerobic) of initial organic carbon, which is significantly less than recent estimates. The multiyear time series from the incubation experiments helps to more reliably constrain projections of future trace gas fluxes from thawing permafrost landscapes.

Methanogenic community composition and anaerobic carbon turnover in submarine permafrost sediments of the Siberian Laptev Sea

The Siberian Laptev Sea shelf contains submarine permafrost, which was formed by flooding of terrestrial permafrost with ocean water during the Holocene sea level rise. This flooding resulted in a warming of the permafrost to temperatures close below 0 degrees C. The impact of these environmental changes on methanogenic communities and carbon dynamics in the permafrost was studied in a submarine permafrost core of the Siberian Laptev Sea shelf. Total organic carbon (TOC) content varied between 0.03% and 8.7% with highest values between 53 and 62 m depth below sea floor. In the same depth, maximum methane concentrations (284 nmol CH(4) g(-1)) and lowest carbon isotope values of methane (-72.2 per thousand VPDB) were measured, latter indicating microbial formation of methane under in situ conditions. The archaeal community structure was assessed by a nested polymerase chain reaction (PCR) amplification for DGGE, followed by sequencing of reamplified bands. Submarine permafrost samples showed a different archaeal community than the nearby terrestrial permafrost. Samples with high methane concentrations were dominated by sequences affiliated rather to the methylotrophic genera Methanosarcina and Methanococcoides as well as to uncultured archaea. The presented results give the first insights into the archaeal community in submarine permafrost and the first evidence for their activity at in situ conditions.

Methane oxidation following submarine permafrost degradation: Measurements from a central Laptev Sea shelf borehole

Submarine permafrost degradation has been invoked as a cause for recent observations of methane emissions from the seabed to the water column and atmosphere of the East Siberian shelf. Sediment drilled 52 m down from the sea ice in Buor Khaya Bay, central Laptev Sea revealed unfrozen sediment overlying ice-bonded permafrost. Methane concentrations in the overlying unfrozen sediment were low (mean 20 µM) but higher in the underlying ice-bonded submarine permafrost (mean 380 µM). In contrast, sulfate concentrations were substantially higher in the unfrozen sediment (mean 2.5 mM) than in the underlying submarine permafrost (mean 0.1 mM). Using deduced permafrost degradation rates, we calculate potential mean methane efflux from degrading permafrost of 120 mg m−2 yr−1 at this site. However, a drop of methane concentrations from 190 µM to 19 µM and a concomitant increase of methane δ13C from −63‰ to −35‰ directly above the ice-bonded permafrost suggest that methane is effectively oxidized within the overlying unfrozen sediment before it reaches the water column. High rates of methane ebullition into the water column observed elsewhere are thus unlikely to have ice-bonded permafrost as their source.Submarine permafrost degradation has been invoked as a cause for recent observations of methane emissions from the seabed to the water column and atmosphere of the East Siberian shelf. Sediment drilled 52 m down from the sea ice in Buor Khaya Bay, central Laptev Sea revealed unfrozen sediment overlying ice-bonded permafrost. Methane concentrations in the overlying unfrozen sediment were low (mean 20 µM) but higher in the underlying ice-bonded submarine permafrost (mean 380 µM). In contrast, sulfate concentrations were substantially higher in the unfrozen sediment (mean 2.5 mM) than in the underlying submarine permafrost (mean 0.1 mM). Using deduced permafrost degradation rates, we calculate potential mean methane efflux from degrading permafrost of 120 mg m−2 yr−1 at this site. However, a drop of methane concentrations from 190 µM to 19 µM and a concomitant increase of methane δ13C from −63‰ to −35‰ directly above the ice-bonded permafrost suggest that methane is effectively oxidized within the overlying unfrozen sediment before it reaches the water column. High rates of methane ebullition into the water column observed elsewhere are thus unlikely to have ice-bonded permafrost as their source.

Transformation of terrestrial organic matter along thermokarst-affected permafrost coasts in the Arctic.

The changing climate in the Arctic has a profound impact on permafrost coasts, which are subject to intensified thermokarst formation and erosion. Consequently, terrestrial organic matter (OM) is mobilized and transported into the nearshore zone. Yet, little is known about the fate of mobilized OM before and after entering the ocean. In this study we investigated a retrogressive thaw slump (RTS) on Qikiqtaruk - Herschel Island (Yukon coast, Canada). The RTS was classified into an undisturbed, a disturbed (thermokarst-affected) and a nearshore zone and sampled systematically along transects. Samples were analyzed for total and dissolved organic carbon and nitrogen (TOC, DOC, TN, DN), stable carbon isotopes (δ13C-TOC, δ13C-DOC), and dissolved inorganic nitrogen (DIN), which were compared between the zones. C/N-ratios, δ13C signatures, and ammonium (NH4-N) concentrations were used as indicators for OM degradation along with biomarkers (n-alkanes, n-fatty acids, n-alcohols). Our results show that OM significantly decreases after disturbance with a TOC and DOC loss of 77 and 55% and a TN and DN loss of 53 and 48%, respectively. C/N-ratios decrease significantly, whereas NH4-N concentrations slightly increase in freshly thawed material. In the nearshore zone, OM contents are comparable to the disturbed zone. We suggest that the strong decrease in OM is caused by initial dilution with melted massive ice and immediate offshore transport via the thaw stream. In the mudpool and thaw stream, OM is subject to degradation, whereas in the slump floor the nitrogen decrease is caused by recolonizing vegetation. Within the nearshore zone of the ocean, heavier portions of OM are directly buried in marine sediments close to shore. We conclude that RTS have profound impacts on coastal environments in the Arctic. They mobilize nutrients from permafrost, substantially decrease OM contents and provide fresh water and nutrients at a point source.

Regional, seasonal and interspecific variation in 15N and 13C in sympatric mouse lemurs.

Madagascar provides some of the rare examples where two or more primate species of the same genus and with seemingly identical niche requirements occur in sympatry. If congeneric primate species co-occur in other parts of the world, they differ in size in a way that is consistent with Hutchinson’s rule for coexisting species, or they occupy different ecological niches. In some areas of Madagascar, mouse lemurs do not follow these “rules” and thus seem to violate one of the principles of community ecology. In order to understand the mechanisms that allow coexistence of sympatric congeneric species without obvious niche differentiation, we studied food composition of two identical sized omnivorous mouse lemur species, Microcebus griseorufus and M. murinus with the help of stable isotope analyses (δ15N and δ13C). The two species are closely related sister species. During the rich season, when food seems abundant, the two species do not differ in their nitrogen isotope composition, indicating that the two species occupy the same trophic level. But they differ in their δ13C values, indicating that M. griseorufus feeds more on C4 and CAM (Crassulacean-acid-metabolism) plants than M. murinus. During the lean season, M. murinus has lower δ15N values, indicating that the two species feed at different trophic levels during times of food shortage. Hybrids between the two species showed intermediate food composition. The results reflect subtle differences in foraging or metabolic adaptations that are difficult to quantify by traditional observations but that represent possibilities to allow coexistence of species.

Anaerobic methanotrophic communities thrive in deep submarine permafrost

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.

Methane production as key to the greenhouse gas budget of thawing permafrost

Permafrost thaw liberates frozen organic carbon, which is decomposed into carbon dioxide (CO2) and methane (CH4). The release of these greenhouse gases (GHGs) forms a positive feedback to atmospheric CO2 and CH4 concentrations and accelerates climate change1,2. Current studies report a minor importance of CH4 production in water-saturated (anoxic) permafrost soils3–6 and a stronger permafrost carbon–climate feedback from drained (oxic) soils1,7. Here we show through seven-year laboratory incubations that equal amounts of CO2 and CH4 are formed in thawing permafrost under anoxic conditions after stable CH4-producing microbial communities have established. Less permafrost carbon was mineralized under anoxic conditions but more CO2–carbon equivalents (CO2–Ce) were formed than under oxic conditions when the higher global warming potential (GWP) of CH4 is taken into account8. A model of organic carbon decomposition, calibrated with the observed decomposition data, predicts a higher loss of permafrost carbon under oxic conditions (113 ± 58 g CO2–C kgC−1 (kgC, kilograms of carbon)) by 2100, but a twice as high production of CO2–Ce (241 ± 138 g CO2–Ce kgC−1) under anoxic conditions. These findings challenge the view of a stronger permafrost carbon-climate feedback from drained soils1,7 and emphasize the importance of CH4 production in thawing permafrost on climate-relevant timescales.An organic carbon decomposition model, calibrated with laboratory incubations, indicates a greater production rate of CO2-C equivalents from waterlogged (compared to drained) permafrost soils, when the higher global warming potential of methane is factored in.