Eva-Maria Pfeiffer

Cultivation of a novel cold-adapted nitrite oxidizing betaproteobacterium from the Siberian Arctic

Permafrost-affected soils of the Siberian Arctic were investigated with regard to identification of nitrite oxidizing bacteria active at low temperature. Analysis of the fatty acid profiles of enrichment cultures grown at 4°C, 10°C and 17°C revealed a pattern that was different from that of known nitrite oxidizers but was similar to fatty acid profiles of Betaproteobacteria. Electron microscopy of two enrichment cultures grown at 10°C showed prevalent cells with a conspicuous ultrastructure. Sequence analysis of the 16S rRNA genes allocated the organisms to a so far uncultivated cluster of the Betaproteobacteria, with Gallionella ferruginea as next related taxonomically described organism. The results demonstrate that a novel genus of chemolithoautotrophic nitrite oxidizing bacteria is present in polygonal tundra soils and can be enriched at low temperatures up to 17°C. Cloned sequences with high sequence similarities were previously reported from mesophilic habitats like activated sludge and therefore an involvement of this taxon in nitrite oxidation in nonarctic habitats is suggested. The presented culture will provide an opportunity to correlate nitrification with nonidentified environmental clones in moderate habitats and give insights into mechanisms of cold adaptation. We propose provisional classification of the novel nitrite oxidizing bacterium as ‘Candidatus Nitrotoga arctica’.

Characterisation of microbial community composition of a Siberian tundra soil by fluorescence in situ hybridisation.

The bacterial community composition of the active layer (0-45 cm) of a permafrost-affected tundra soil was analysed by fluorescence in situ hybridisation (FISH). Arctic tundra soils contain large amounts of organic carbon, accumulated in thick soil layers and are known as a major sink of atmospheric CO(2). These soils are totally frozen throughout the year and only a thin active layer is unfrozen and shows biological activity during the short summer. To improve the understanding of how the carbon fluxes in the active layer are controlled, detailed analysis of composition, functionality and interaction of soil microorganisms was done. The FISH analyses of the active layer showed large variations in absolute cell numbers and in the composition of the active microbial community between the different horizons, which is caused by the different environmental conditions (e.g., soil temperature, amount of organic matter, aeration) in this vertically structured ecosystem. Universal protein stain 5-(4,6-dichlorotriazin-2-yl)aminofluorescein (DTAF) showed an exponential decrease of total cell counts from the top to the bottom of the active layer (2.3 x 10(9)-1.2 x 10(8) cells per gram dry soil). Using FISH, up to 59% of the DTAF-detected cells could be detected in the surface horizon, and up to 84% of these FISH-detected cells could be affiliated to a known phylogenetic group. The amount of FISH-detectable cells decreased with increasing depth and so did the diversity of ascertained phylogenetic groups.

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.

Methane production in aerated marshland and model soils : effects of microflora and soil texture

Under oxic conditions the importance of the indigenous microflora and the soil texture on methane production was investigated using marshland soils (clayey silt) and different textured model soils (clay, sand, gravel). Under an oxic partial pressure >2.5% O2, soil slurries had a low methane production rate over a period of 50–70 h with acetate (0.35±0.1 nmol g−1 h−1) as well as with hydrogen (2.43±0.51 nmol g−1 h−1) as substrate. The rates amounted to 1 and 5%, respectively, compared to methane production rates under anoxic conditions. As soon as the oxygen concentration decreased to 2.5% (microaerophilic conditions) the methane production increased significantly (9.5±3.3 nmol g−1 h−1 with acetate; 16.3±3.3 nmol g−1 h−1 with hydrogen). In the absence of the indigenous microflora, the inoculated culture of Methanosarcina mazei (DSM 2053) did not produce any methane in soil slurries under oxic conditions. To inhibit methane oxidation, all samples (oxic and anoxic) were supplied with 60 nl acetylene ml−1 headspace. Furthermore, methane production in different textured model soils demonstrated that a high amount of negative surface charges increased methane production under oxic as well as under anoxic conditions. Consequently the methane production rates increased in the following sequence: sand<gravel<clayey silt (marshland soil)≤clay. Our results show that the indigenous microflora in combination with the sorptive quality of soil particles (clay, silt, organic matter) enables methanogenic activity in the presence of oxygen, promoting microscale anoxia within the slurries.

Spatial variability of soil gas concentration and methane oxidation capacity in landfill covers

In order to devise design criteria for biocovers intended to enhance the microbial oxidation of landfill methane it is critical to understand the factors influencing gas migration and methane oxidation in landfill cover soils. On an old municipal solid waste landfill in north-western Germany soil gas concentrations (10, 40, 90 cm depth), topsoil methane oxidation capacity and soil properties were surveyed at 40 locations along a 16 m grid. As soil properties determine gas flow patterns it was hypothesized that the variability in soil gas composition and the subsequent methanotrophic activity would correspond to the variability of soil properties. Methanotrophic activity was found to be subject to high spatial variability, with values ranging between 0.17 and 9.80 g CH(4)m(-2)h(-1)(.) Considering the current gas production rate of 0.03 g CH(4)m(-2)h(-1), the oxidation capacity at all sampled locations clearly exceeded the flux to the cover, and can be regarded as an effective instrument for mitigating methane fluxes. The methane concentration in the cover showed a high spatial heterogeneity with values between 0.01 and 0.32 vol.% (10 cm depth), 22.52 vol.% (40 cm), and 36.85 vol.% (90 cm). The exposure to methane raised the oxidation capacity, suggested by a statistical correlation to an increase in methane concentration at 90 cm depth. Methane oxidation capacity was further affected by the methanotroph bacteria pH optimum and nutrient availability, and increased with decreasing pH towards neutrality, and increased with soluble ion concentration). Soil methane and carbon dioxide concentration increased with lower flow resistance of the cover, as represented by the soil properties of a reduced bulk density, increase in air capacity and in relative ground level.

Assessment of the methane oxidation capacity of compacted soils intended for use as landfill cover materials.

The microbial oxidation of methane in engineered cover soils is considered a potent option for the mitigation of emissions from old landfills or sites containing wastes of low methane generation rates. A laboratory column study was conducted in order to derive design criteria that enable construction of an effective methane oxidising cover from the range of soils that are available to the landfill operator. Therefore, the methane oxidation capacity of different soils was assessed under simulated landfill conditions. Five sandy potential landfill top cover materials with varying contents of silt and clay were investigated with respect to methane oxidation and corresponding soil gas composition over a period of four months. The soils were compacted to 95% of their specific proctor density, resulting in bulk densities of 1.4-1.7 g cm(-3), reflecting considerably unfavourable conditions for methane oxidation due to reduced air-filled porosity. The soil water content was adjusted to field capacity, resulting in water contents ranging from 16.2 to 48.5 vol.%. The investigated inlet fluxes ranged from 25 to about 100g CH(4)m(-2)d(-1), covering the methane load proposed to allow for complete oxidation in landfill covers under Western European climate conditions and hence being suggested as a criterion for release from aftercare. The vertical distribution of gas concentrations, methane flux balances as well as stable carbon isotope studies allowed for clear process identifications. Higher inlet fluxes led to a reduction of the aerated zone, an increase in the absolute methane oxidation rate and a decline of the relative proportion of oxidized methane. For each material, a specific maximum oxidation rate was determined, which varied between 20 and 95 g CH(4)m(-2)d(-1) and which was positively correlated to the air-filled porosity of the soil. Methane oxidation efficiencies and gas profile data imply a strong link between oxidation capacity and diffusive ingress of atmospheric air. For one material with elevated levels of fine particles and high organic matter content, methane production impeded the quantification of methane oxidation potentials. Regarding the design of landfill cover layers it was concluded that the magnitude of the expected methane load, the texture and expected compaction of the cover material are key variables that need to be known. Based on these, a column study can serve as an appropriate testing system to determine the methane oxidation capacity of a soil intended as landfill cover material.

Permafrost-Affected Soils of the Russian Arctic and their Carbon Pools

Permafrost-affected soils have accumulated enormous pools of organic matter during the Quaternary period. The area occupied by these soils amounts to more than 8.6 million km2, which is about 27 % of all land areas north of 50 ◦ N. Therefore, permafrost-affected soils are considered to be one of the important cryosphere elements within the climate system. Due to the cryopedogenic processes that form these particular soils and the overlying vegetation that is adapted to the arctic climate, organic matter has accumulated to the present extent of up to 1024 Pg (1 Pg = 1015 g = 1 Gt) of soil organic carbon stored within the uppermost 3 m of ground. Considering the observed progressive climate change and the projected polar amplification, permafrost-affected soils will undergo fundamental property changes. Higher turnover and mineralisation rates of the organic matter are consequences of these changes, which are expected to result in an increased release of climate-relevant trace gases into the atmosphere. The controversy of whether permafrost regions continue accumulating carbon or already function as a carbon source remains open until today. An increased focus on this subject matter, especially in underrepresented Siberian regions, could contribute to a more robust estimation of the soil organic carbon pool of permafrost regions and at the same time improve the understanding of the carbon sink and source functions of permafrost-affected soils.

Temporal variability of soil gas composition in landfill covers.

In order to assess the temporal variability of the conditions for the microbial oxidation of methane in landfill cover soils and their driving variables, gas composition at non-emissive and strongly emissive locations (hotspots) was monitored on a seasonal, daily and hourly time scale on an old, unlined landfill in northern Germany. Our study showed that the impact of the various environmental factors varied with the mode of gas transport and with the time scale considered. At non-emissive sites, governed by diffusive gas transport, soil gas composition was subject to a pronounced seasonal variation. A high extent of aeration, low methane concentrations and a high ratio of CO(2) to CH(4) were found across the entire depth of the soil cover during the warm and dry period, whereas in the cool and moist period aeration was less and landfill gas migrated further upward. Statistically, variation in soil gas composition was best explained by the variation in soil temperature. At locations dominated by advective gas transport and showing considerable emissions of methane, this pattern was far less pronounced with only little increase in the extent of aeration during drier periods. Here, the change of barometric pressure was found to impact soil gas composition. On a daily scale under constant conditions of temperature, gas transport at both types of locations was strongly impacted by the change in soil moisture. On an hourly scale, under constant conditions of temperature and moisture, gas migration was impacted most by the change in barometric pressure. It was shown that at diffusion-dominated sites complete methane oxidation was achieved even under adverse wintry conditions, whereas at hotspots, even under favorable dry and warm conditions, aerobic biological activity can be limited to the upper crust of the soil.

Microbial Life in Terrestrial Permafrost: Methanogenesis and Nitrification in Gelisols as Potentials for Exobiological Process

The comparability of environmental and climatic conditions of the early Mars and Earth is of special interest for the actual research in astrobiology. Martian surface and terrestrial permafrost areas show similar morphological structures, which suggests that their development is based on comparable processes. Soil microbial investigations of adaptation strategies of microorganisms from terrestrial permafrost in combination with environmental, geochemical and physical analyses give insights into early stages of life on Earth. The extreme conditions in terrestrial permafrost soils can help to understand the evolution of life on early Mars and help searching for possible niches of life on present Mars or in other extraterrestrial permafrost habitats [1, 2].

Studies of Methane Production and Emission in Relation to the Microrelief of a Polygonal Tundra in Northern Siberia

Methane production and emission in a polygonal tundra on Taimyr Peninsula in North Siberia (75°N, 98°E) were investigated during summer 1996. The in situ methane emission was measured several times per day between July and September at a typical polygonal tundra site. Additionally, measurements were carried out at different plots along a transsect through the investigated valley to determine the variability of methane emissions of the whole polygon area. CH4 emission rates showed high response on microrelief, which influences water table and soil temperatures. No diurnal variations in methane emissions were found. The emission rates ranged from 0-160 mg CH4-d-1-m-2. Based on detailed mapping of soils and surface structures (patterned grounds) a projection on total methane emission from the investigated polygonal tundra is possible. The mean daily emission rate between July and September is about 50 mg CH4*d-l*-m-2, which is about 4% of total gaseous carbon loss from soil to atmosphere. Isotope investigations proof the reduction of CO2/H2 to be the major pathway of methane production and fermentation being negligible. At the end of the thawing season methane emissions and methane content of the pore water decrease. Methane oxidation is very effective even when the water table is only a few centimeters below the surface.