Dagmar Tscherko

Abundance of narG, nirS, nirK, and nosZ Genes of Denitrifying Bacteria during Primary Successions of a Glacier Foreland

ABSTRACT Quantitative PCR of denitrification genes encoding the nitrate, nitrite, and nitrous oxide reductases was used to study denitrifiers across a glacier foreland. Environmental samples collected at different distances from a receding glacier contained amounts of 16S rRNA target molecules ranging from 4.9 × 105 to 8.9 × 105 copies per nanogram of DNA but smaller amounts of narG, nirK, and nosZ target molecules. Thus, numbers of narG, nirK, nirS, and nosZ copies per nanogram of DNA ranged from 2.1 × 103 to 2.6 × 104, 7.4 × 102 to 1.4 × 103, 2.5 × 102 to 6.4 × 103, and 1.2 × 103 to 5.5 × 103, respectively. The densities of 16S rRNA genes per gram of soil increased with progressing soil development. The densities as well as relative abundances of different denitrification genes provide evidence that different denitrifier communities develop under primary succession: higher percentages of narG and nirS versus 16S rRNA genes were observed in the early stage of primary succession, while the percentages of nirK and nosZ genes showed no significant increase or decrease with soil age. Statistical analyses revealed that the amount of organic substances was the most important factor in the abundance of eubacteria as well as of nirK and nosZ communities, and copy numbers of these two genes were the most important drivers changing the denitrifying community along the chronosequence. This study yields an initial insight into the ecology of bacteria carrying genes for the denitrification pathway in a newly developing alpine environment.

Structure and function of the soil microbial community in microhabitats of a heavy metal polluted soil

Abstract Particle-size fractionation of a heavy metal polluted soil was performed to study the influence of environmental pollution on microbial community structure, microbial biomass, microbial residues and enzyme activities in microhabitats of a Calcaric Phaeocem. In 1987, the soil was experimentally contaminated with four heavy metal loads: (1) uncontaminated controls; (2) light (300 ppm Zn, 100 ppm Cu, 50 ppm Ni, 50 ppm V and 3 ppm Cd); (3) medium; and (4) heavy pollution (two- and threefold the light load, respectively). After 10 years of exposure, the highest concentrations of microbial ninhydrin-reactive nitrogen were found in the clay (2–0.1 μm) and silt fractions (63–2 μm), and the lowest were found in the coarse sand fraction (2,000–250 μm). The phospholipid fatty acid analyses (PLFA) and denaturing gradient gel electrophoresis (DGGE) separation of 16S rRNA gene fragments revealed that the microbial biomass within the clay fraction was predominantly due to soil bacteria. In contrast, a high percentage of fungal-derived PLFA 18 : 2ω6 was found in the coarse sand fraction. Bacterial residues such as muramic acid accumulated in the finer fractions in relation to fungal residues. The fractions also differed with respect to substrate utilization: Urease was located mainly in the <2 μm fraction, alkaline phosphatase and arylsulfatase in the 2–63 μm fraction, and xylanase activity was equally distributed in all fractions. Heavy metal pollution significantly decreased the concentration of ninhydrin-reactive nitrogen of soil microorganisms in the silt and clay fraction and thus in the bulk soil. Soil enzyme activity was reduced significantly in all fractions subjected to heavy metal pollution in the order arylsulfatase >phosphatase >urease >xylanase. Heavy metal pollution did not markedly change the similarity pattern of the DGGE profiles and amino sugar concentrations. Therefore, microbial biomass and enzyme activities seem to be more sensitive than 16S rRNA gene fragments and microbial amino-sugar-N to heavy metal treatment.

The response of soil microorganisms and roots to elevated CO2 and temperature in a terrestrial model ecosystem

We investigate the response of soil microorganisms to atmospheric CO2 and temperature change within model terrestrial ecosystems in the Ecotron. The model communities consisted of four plant species (Cardamine hirsuta, Poa annua, Senecio vulgaris, Spergula arvensis), four herbivorous insect species (two aphids, a leaf-miner, and a whitefly) and their parasitoids, snails, earthworms, woodlice, soil-dwelling Collembola (springtails), nematodes and soil microorganisms (bacteria, fungi, mycorrhizae and Protista). In two successive experiments, the effects of elevated temperature (ambient plus 2 °C) at both ambient and elevated CO2 conditions (ambient plus 200 ppm) were investigated. A 40:60 sand:Surrey loam mixture with relatively low nutrient levels was used. Each experiment ran for 9 months and soil microbial biomass (Cmic and Nmic), soil microbial community (fungal and bacterial phospholipid fatty acids), basal respiration, and enzymes involved in the carbon cycling (xylanase, trehalase) were measured at depths of 0–2, 0–10 and 10–20 cm. In addition, root biomass and tissue C:N ratio were determined to provide information on the amount and quality of substrates for microbial growth.Elevated temperature under both ambient and elevated CO2 did not show consistent treatment effects. Elevation of air temperature at ambient CO2 induced an increase in Cmic of the 0–10 cm layer, while at elevated CO2 total phospholipid fatty acids (PLFA) increased after the third generation. The metabolic quotient qCO2 decreased at elevated temperature in the ambient CO2 run. Xylanase and trehalase showed no changes in both runs. Root biomass and C:N ratio were not influenced by elevated temperature in ambient CO2. In elevated CO2, however, elevated temperature reduced root biomass in the 0–10 cm and 30–40 cm layers and increased N content of roots in the deeper layers. The different response of root biomass and C:N ratio to elevated temperature may be caused by differences in the dynamics of root decomposition and/or in allocation patterns to coarse or fine roots (i.e. storage vs. resource capture functions). Overall, our data suggests that in soils of low nutrient availability, the effects of climate change on the soil microbial community and processes are likely to be minimal and largely unpredicatable.

Microbial community composition and functional diversity in the rhizosphere of maize

This study investigates the small-scale stratification of bacterial community composition and functional diversity in the rhizosphere of maize. Maize seedlings were grown in a microcosm with a horizontal mesh (53 μM) creating a planar root mat and rhizosphere soil. An unplanted microcosm served as control. Thin slices of soil were cut at different distances from the mesh surface (0.2–5.0 mm) and analysed for bacterial community composition by PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) of 16S rDNA and tested for activities of different enzymes involved in C, N, P and S cycling. Bacterial community composition and microbial functional diversity were affected by the presence of the maize roots. The bacterial composition showed a clear gradient up to 2.2 mm from the root surface, while no such gradient was observed in the unplanted pot. Invertase and phosphatase activities were higher in the close vicinity of maize roots (0.2–0.8 mm), whereas xylanase activity was unaffected. This study shows that the changes in bacterial community composition and functional diversity induced by roots may extend several millimetres into the soil.

Microbial communities and activities in alpine and subalpine soils.

Soil samples were collected along two slopes (south and north) at subalpine (1500-1900 m, under closed vegetation, up to the forest line) and alpine altitudes (2300-2530, under scattered vegetation, above the forest line) in the Grossglockner mountain area (Austrian central Alps). Soils were analyzed for a number of properties, including physical and chemical soil properties, microbial activity and microbial communities that were investigated using culture-dependent (viable heterotrophic bacteria) and culture-independent methods (phospholipid fatty acid analysis, FISH). Alpine soils were characterized by significantly (P<0.01) colder climate conditions, i.e. lower mean annual air and soil temperatures, more frost and ice days and higher precipitation, compared with subalpine soils. Microbial activity (soil dehydrogenase activity) decreased with altitude; however, dehydrogenase activity was better adapted to cold in alpine soils compared with subalpine soils, as shown by the lower apparent optimum temperature for activity (30 vs. 37 degrees C) and the significantly (P<0.01-0.001) higher relative activity in the low-temperature range. With increasing altitude, i.e. in alpine soils, a significant (P<0.05-0.01) increase in the relative amount of culturable psychrophilic heterotrophic bacteria, in the relative amount of the fungal population and in the relative amount of Gram-negative bacteria was found, which indicates shifts in microbial community composition with altitude.

Below-ground microbial community development in a high temperature world

The response of above-ground plant and ecosystem processes to climate change are likely to be influenced by both direct and indirect effects of elevated temperature on soil biota and their activities. This study examined the effects of elevated atmospheric temperature on the development of the soil microbial community in a model terrestrial ecosystem facility. The model system was characterized by a soil of low nutrient availability, a condition that simulates most native terrestrial plant communities. The experiment was run over three plant generations, broadly mimicking the early stages of a plant succession, and showed that microbial biomass, measured using phospholipid fatty acid (PLFA) analysis, increased significantly in response to elevated temperature during the first generation only. This increase was unrelated to changes in plant productivity or soil C-availability, and was largely due to a direct effect of elevated temperature on fast-growing Gram-positive bacteria. Slow growing soil micoorganisms such as fungi and actinomycetes were unaffected by elevated temperature throughout the experimental period. Measures of microbial biomass, microbial respiration and N-mineralization were also unaffected by elevated atmospheric temperature over the three generations. The lack of effects on the soil microbial community is thought to be due to the fact that elevated temperature did not influence root biomass or soil C-availability. We suggest that the observed reductions in above-ground plant productivity, in response to elevated temperature, will become apparent in the longer term when litter decomposition pathways are more established. The temporal measures of PLFA and microbial biomass indicated that over the experimental period rapid initial changes occurred in most soil biological characteristics, followed by periods of stabilization during later plant succession. These changes were associated with increases in above-ground plant productivity and amounts of available C in the soil. In contrast, total microbial biomass declined during the last plant generation. Reductions in the diversity of PLFAs in later plant generations appeared to be associated with an increase in the proportion of fatty acids associated with fungi, relative to those from bacteria. These changes are likely to be related to increased competition for resources within the soil, and an associated reduction in N- and C-availability. These changes appear to be broadly consistent with those reported for other studies on the successional development of soil microbial and plant communities. Overall, our data suggest that elevated atmospheric temperature has little effect on the development of below-ground microbial communities and their activities in soils of low nutrient status.

Distribution of High Bacterial Taxa Across the Chronosequence of Two Alpine Glacier Forelands

Little is known about the changes in abundance of microbial taxa in relation to the chronosequence of receding glaciers. This study investigated how the abundances of ten bacterial phyla or classes varied along successional gradients in two glaciers, Ödenwinkelkees and Rotmoosferner, in the central Alps. Quantitative PCR was used to estimate the abundance of the different bacterial taxa in extended glacier chronosequences, including 10- to 160-year-old successional stages, the surface of the glacier, and a fully established soil. Actinobacteria (15–30%) was the dominant group within the chronosequences. Several taxa showed significant differences in the number of taxa-specific 16S rRNA gene copies per nanogram of DNA and/or in the ratio of taxa-specific to the total bacterial 16S rRNA gene copies (i.e., the relative abundance of the different taxa within the bacterial community) between the established soils or the glacier surface and the 10- to 160-year-old successional stages. A significantly higher proportion of Βetaproteobacteria (20%) was observed on the surface of both glaciers. However, no differences were observed between the 10- to 160-year-old successional stages in the number of taxa-specific 16S rRNA gene copies per nanogram of DNA or in the ratio of taxa-specific to the total bacterial 16S rRNA gene copies for the different taxa. Nevertheless, when the relative abundance data from all the studied taxa were combined and analyzed altogether, most of the sites could be distinguished from one other. This indicates that the overall composition of the bacterial community was more affected than the abundance of the targeted taxa by changes in environmental conditions along the chronosequences.

Activity of microorganisms in the rhizosphere of herbicide treated and untreated transgenic glufosinate-tolerant and wildtype oilseed rape grown in containment

An experiment was carried out with plants grown in containment in order to determine potential effects on metabolically active microbial populations as well as on soil enzyme activities in the rhizosphere of genetically modified Basta-tolerant oilseed rape. Transgenic as well as isogenic wild-type plants were grown in combination with the associated herbicide Basta (active ingredient glufosinate) or the herbicide Butisan S (active ingredient metazachlor), respectively. In control treatments, weeds were mechanically removed. Rhizosphere soil was sampled at the early and late flowering stage as well as at senescence. RNA was isolated and 16S rRNA was amplified by reverse transcription and PCR. Amplicons were subjected to denaturating gradient gel electrophoresis in order to generate community fingerprints of metabolically highly active bacteria. Additionally, RNA was hybridized with group-specific probes. Furthermore, bacterial biomass and activities of invertase, alkaline phosphatase, urease and arylsulfatase were determined. Results showed that oilseed rape rhizosphere bacteria were affected by the genetic modification as well as by the herbicide application, however, these effects were minor compared to the influence of the plant growth stage. At senescence, invertase, urease and alkaline phosphatase activities were significantly enhanced in the rhizospheres of transgenic plants as compared to wild-type plants propably due to an altered root exudation in comparison to the wildtype plant. Dot blot hybridizations indicated altered activities and/or abundances of various phylogenetic groups at all sampling times. The transformation process may have unintentionally altered the physiology of plants (e.g. root exudation) leading to changes in rhizosphere community structures and bacterial activities.

Biomass and Enzyme Activity of Two Soil Transects at King George Island, Maritime Antarctica

Abstract Soil microbial properties were investigated to assess the potential of organic matter dynamics in mineral and ornithogenic soils in a cold climate. Microbial biomass, respiration, N-mineralization, and enzyme activities were measured along two catenary transects crossing penguin rookeries and seabird colonies. Ornithogenic excrements, total organic carbon (TOC), and phosphorus accumulation were major factors controlling microbial properties in Antarctic soils. Multivariate approaches (cluster and discriminant analysis) clearly distinguished the ornithogenic soils from the mineral soils based on their microbial characteristics. Microbial biomass, respiration, and N-mineralization were gradually inhibited by increasing P-inputs by penguins. The metabolic quotient (qCO2) was negatively correlated to P-content, whereas all other microbial properties (microbial biomass, respiration, N-mineralization, enzyme activities) followed the patterns of TOC. Urease, xylanase, phosphatase, and arylsulfatase activities were significantly favored by penguin and seabird excrements in the ornithogenic soils compared to the mineral soils. Microbial biomass-to-enzyme activity ratios were substantially higher at sites influenced by penguin guano than by other seabird excrement. We show that enzymes are active in antarctic soils, and that high levels of biomass-based specific activity in the ornithogenic soils, compared to those of mineral soils, result from continuous input of large quantities of enzyme-rich penguin guano.

Seasonal and Diurnal Net Methane Emissions from Organic Soils of the Eastern Alps, Austria: Effects of Soil Temperature, Water Balance, and Plant Biomass

ABSTRACT Although the contribution of methane emission to global change is well recognized, analyses of net methane emissions derived from alpine regions are rare. Therefore, three fen sites differing in water balance and plant community, as well as one dry meadow site, were used to study the importance of soil temperature, water table, and plant biomass as controlling factors for net methane emission in the Eastern Alps, Europe, during a period of 24 months. Average methane emissions during snow-free periods in the fen ranged between 19 and 116 mg CH4 m−2 d−1. Mean wintertime emissions were much lower and accounted for 18 to 59% of annual flux. The alpine dry meadow functions as a methane sink during snow-free periods, with mean flux of −2.1 mg CH4 m−2 d−1 (2003) and −1.0 mg CH4 m−2 d−1 (2004). Seasonal methane emissions of the fen were related to soil temperature and groundwater table. During the snow-free periods the water table was the main control for seasonal methane emission. The net methane flux related to water table was much higher for the distinctly drier year 2003 than for the wetter year 2004. Methane emissions differed diurnally at sites where the water table position was high or very low. The influence of total above-ground plant biomass on methane emission was apparent only for those sites with high water table positions. Seasonal and diurnal methane uptake of the dry meadow was related to soil temperature and water-filled pore space, whereas plant biomass did not significantly influence methane fluxes. Our studies gave evidence that fens in the Eastern Alps act as a source of methane throughout the whole year and that a dry meadow site acts as a net methane sink during snow-free periods.