Browsing by Subject "Soil enzymes"

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Carbon and nitrogen transformations in alpine ecosystems of the Eastern Alps, Austria
(2007) Koch, Oliver; Kandeler, Ellen
This thesis investigated net CH4 and net CO2 emissions from sites in the alpine region of the Eastern Alps, Austria. Four mature alpine sites (one dry meadow and three fen sites) were selected and the influence of abiotic (radiation, temperature, soil water conditions) and biotic (above-ground standing plant biomass) environmental controls on diurnal and seasonal emission patterns were studied. For a better understanding of the response of soil C- and N pools to global warming, the temperature sensitivity of activities involved in C- and N cycling were determined. The first part of the thesis dealt with net methane fluxes measured over a period of 24 months. During snow-free periods, average methane emissions of the fen sites ranged between 19 and 116 mg CH4 m-2 d-1. Mean emissions during snow periods were much lower, being 18 to 59% of annual fluxes. The alpine dry meadow functioned as a small methane sink during snow-free periods (-2.1 mg CH4 m-2 d-1 (2003); -1.0 mg CH4 m-2 d-1 (2004)). The diurnal and seasonal methane uptake of the dry meadow was positively related to soil temperature and negatively related to water-filled pore space (wfps). In the fen, the seasonal methane fluxes were related to soil temperature and groundwater table. The live above-ground standing plant biomass contributed to net methane fluxes only at those sites with higher water table positions. This study provided evidence that alpine fens acted as methane sources throughout the year, whereas an alpine meadow site acted as a net methane sink during snow-free periods. In the second part of the thesis the CO2 balance was estimated based on diurnal flux measurements and on the influence of photosynthetic active radiation (PAR), plant green area index (GAI), soil temperature and wfps. The daylight net ecosystem CO2 emission rate was influenced by PAR and GAI throughout snow-free seasons. The seasonal net CO2 emission rate at night was positively related to soil temperature, while low wfps reduced flux rates at the meadow and at the driest fen study site but reinforced carbon loss at the wetter fen sites. The daily average ecosystem net CO2 gain during snow-free periods at the meadow was 3.5 g CO2 m-2 d-1 and at the fen sites between 1.5 and 3.4 g CO2 m-2 d-1. The mean average daily CO2 emission during snow periods was low, being -0.9 g CO2 m-2 d-1 for the meadow and between -0.2 and -0.7 g CO2 m-2 d-1 for all fen sites. All sites function as significant annual net carbon sinks, with a net carbon gain from 50 to 121 g C m-2 a-1 (averaged over both years), irrespective of water balance. The results indicate that alpine fen sites, that have built up a large carbon stock in the past, are not expected to gain a further carbon surplus compared with meadows under the current climate. Temperature is important for regulating biological activities. The third part of the thesis focused on temperature sensitivity of soil C mineralization, N mineralization and potential enzyme activities involved in the C- and N cycle (ß-glucosidase, ß-xylosidase, N-acetyl-ß-glucosaminidase, tyrosine aminopeptidase, leucine aminopeptidase) over a temperature range of 0-30°C. The objective was to calculate Q10 values and relative temperature sensitivities (RTS) and to quantify seasonal (summer, autumn, winter) and site-specific factors. The Q10 values of C mineralization were significantly higher (average 2.0) than for N mineralization (average 1.7). The Q10 values of both activities were significantly negatively related to soil organic matter quality. In contrast, the chemical soil properties, microbial biomass and sampling date did not influence Q10 values. Analysis of RTS showed that the temperature sensitivity increased with decreasing temperature. The C- and N mineralization and potential aminopeptidase activities (tyrosine, leucine) showed an almost constant temperature dependence over 0-30°C. In contrast, ß-glucosidase, ß-xylosidase and N-acetyl-ß-glucosaminidase showed a distinctive increase in temperature sensitivity with decreasing temperature. Low temperature at the winter sampling date caused a greater increase in the RTS of all activities than in autumn and summer. Our results indicate a disproportion of the RTS for potential enzyme activities of the C- and N cycle and a disproportion of the RTS for easily degradable C compounds (ß-glucose, ß-xylose) compared with the C mineralization of soil organic matter. Thus, temperature may play an important role in regulating the decay of different soil organic matter fractions.
Function and composition of the soil microbial community in calcareous grassland exposed to elevated atmospheric carbon dioxide
(2003) Ebersberger, Diana; Kandeler, Ellen
Terrestrial ecosystems generally respond to rising atmospheric carbon dioxide (CO2) concentrations with increased net primary productivity and increased water use efficiency. This may change the amount and quality of organic substances entering the soil and fuelling microbial metabolism. Soil microorganisms and their activity might also be affected by increased soil moisture at elevated CO2. This thesis was designed to analyse the response of the soil microbial community in a species-rich calcareous grassland in the Swiss Jura Mountains, which had been exposed to ambient and elevated CO2 concentrations (365 and 600 ppm) for six growing seasons. In the first study, laboratory incubation experiments were conducted to explore the relationship between litter quality under elevated carbon dioxide and enzymes involved in carbon cycling. Naturally senescent, mixed litter from the long-term field experiment was incubated with soil material for 10, 30 and 60 days. Soil samples were then obtained close to the litter layer using a microtome cutting device. Litter and soil samples were analysed for invertase and xylanase activity. The lower litter quality produced under elevated CO2, i.e. wider C/N ratio, yielded lower invertase and xylanase activities of litter. Litter addition stimulated activities in adjacent soil. Invertase activities of adjacent soil were not affected by litter quality, while soil xylanase activity was higher in soil compartments adjacent to litter from elevated CO2 plots. The reduced enzyme activities of litter produced under elevated CO2 can slow decomposition, at least during the initial stages. Since the effects of litter quality on enzyme activities in adjacent soil were small, we conclude that CO2-induced belowground C-inputs (e.g. increased root mass) and altered moisture conditions are more important controls of enzyme activities than altered litter quality. In the second study, functional diversity of the soil microbial community was assessed by analysing N-mineralisation and activities of enzymes of the C-, N-, P- and S-cycle of soil samples taken in spring and summer 1999, in the 6th season of CO2 exposure. In spring, N-mineralisation increased significantly by 30% at elevated CO2, while there was no significant difference between treatments in summer. The response of soil enzymes to CO2 enrichment was also more pronounced in spring, when alkaline phosphatase and urease activities were increased most strongly, by 32% and 21%, respectively. In summer, activity differences between CO2 treatments were greatest in the case of urease and protease (+21% and +17% at elevated CO2). The significant stimulation of N-mineralisation and enzyme activities at elevated CO2 was probably caused by higher soil moisture and/or increased root biomass. In the third study, soil microbial community structure of soil samples taken in spring and summer 1999 was analysed by means of PLFA profiles and 16S rDNA fingerprints obtained by PCR-DGGE. PLFA profiles were not affected by elevated CO2. Ordination analysis of DNA fingerprints revealed a significant relation between CO2 enrichment and variation in DNA fingerprints. This variation must be attributed to low intensity bands because dominant bands did not differ between treatments. Diversity of the bacterial community (number of bands in DNA fingerprints and Shannon indices) was not affected. The observed minute, but significant changes in the structure of the soil bacterial community might be caused by changes in the quality of rhizodeposits at elevated CO2. These could either result from altered rhizodeposition of individual plants or from altered species composition of the calcareous grassland.The 4th part of the thesis compiles data on soil microorganisms, soil fauna, soil structure and nitrogen cycle of calcareous grassland after CO2 exposure for six growing seasons. Microbial biomass, soil basal respiration and the metabolic quotient were not altered significantly. PLFA analysis revealed no significant shift in the ratio of fungi to bacteria. Protozoans, bacterivorous and fungivorous nematodes, acarians, collembolans, and root-feeding nematodes were not affected by elevated CO2. Total nematode numbers averaged slightly lower (-16%) and nematode mass was significantly reduced (by 43%) due to fewer large-diameter nematodes classified as omnivorous and predacious. CO2 exposure resulted in a shift towards smaller aggregate sizes; this was caused by higher soil moisture. Reduced aggregate sizes result in reduced pore neck diameters. This can confine the locomotion of large-diameter nematodes and possibly accounts for their decrease. The CO2 enrichment also affected the nitrogen cycle. N stocks in living plants and surface litter increased, but N in soil organic matter and microorganisms remained unaltered. N mineralisation increased considerably, but microbial N did not differ between treatments, indicating that net N immobilization rates were unaltered.
Substrate availability affects abundance and function of soil microorganisms in the detritusphere
(2008) Poll, Christian; Kandeler, Ellen
Plant litter is the major source of soil organic carbon (SOC). Its decomposition plays a pivotal role in nutrient recycling and influences ecosystem functioning and structure. Soil microorganisms are the main protagonists of litter decomposition. Among other factors, their activity is controlled by the physicochemical conditions of the soil. This interaction is strongly influenced by the soil structure, resulting in a heterogeneous distribution of microorganisms, substrates and physicochemical conditions at the small-scale. Due to this heterogeneity, microhabitats differ in their decomposition rate of organic C. Considering microhabitat diversity is therefore important for understanding C turnover. In the detritusphere, plant litter closely interacts with the soil by releasing soluble C into the adjacent soil and providing new sites for microorganisms. The abundant readily available substrates characterise the detritusphere as a hot spot of microbial activity and C turnover. Despite the important role of this microhabitat, the interaction of physicochemical conditions with soil microorganisms remains unclear. This thesis was designed to clarify the effect of litter C transport on the spatial and temporal availability of substrates and therefore on microbial abundance and activity in the detritusphere. This goal was addressed in three studies. The first study focused on the influence of solute transport conditions on microbial activity and substrate utilisation by the microbial community. In two 2-week microcosm experiments, diffusion and convection were considered as transport mechanisms; both mechanisms were studied at two different water contents. The second study aimed to identify temporal patterns of diffusive solute transport and microbial activity at two water contents during an 84-day incubation. Both studies emphasised the important role of fungi in the detritusphere. The third study therefore identified fungi that benefit from freshly added litter. The three studies combined classical soil biological methods and modern techniques. Analysis of microbial biomass, ergosterol content, CO2 production, and enzyme activities provided general information on the mineralisation of litter C as well as on microbial activity and abundance. A convective-diffusive solute transport model with a first-order decay was used to interpret enzyme activity profiles. This allowed the underlying factors determining the spatial dimension of the detritusphere to be identified. By adding plant residues with a different 13C signature than the SOC, it was possible to quantify the transport of litter C into different C pools. The incorporation litter C into different microbial groups, for example, was traced by coupling of phospholipid fatty acid (PLFA) extraction with 13C analysis. Fungal species were identified by constructing clone libraries based on 18S rDNA and subsequent sequencing. The results of the first study indicated that the transport rate of soluble substrates determines the spatial dimension of the detritusphere, with an enlarged detritusphere after convective versus diffusive transport. The isotopic ratios of bacterial and fungal PLFAs differed under both transport mechanisms, indicating different substrate utilisation strategies: bacteria relied on the small-scale transport of substrates, whereas fungi assimilated new C directly in the litter layer. Water content affected only diffusive C transport and modified the temporal pattern of microbial activity by enhancing transport at higher soil water content. The expected chronological order of C transport, microbial growth and enzyme release was verified in the second and third study. During the first two weeks, mainly easily available and soluble litter compounds were mineralised and transported into the adjacent soil. After this initial phase, depolymerisation of complex litter compounds started. During the initial phase, enhanced C transport induced greater microbial biomass and activity, and increased fungal diversity. During the later phase, however, substrate availability and microbial activity were reduced. Measurements of microbial biomass C and ergosterol indicated that the initial phase was dominated by bacterial r strategists, whereas fungal K strategists dominated the later phase. Sequencing of fungal 18S rDNA detected a shift in the fungal community during the initial phase, pointing to growth of pioneer colonisers, especially Mortierellaceae. These fungi do not produce ergosterol and therefore were not detected by the ergosterol measurements. Accordingly, the r strategists consist of both bacteria and fungi. During the later phase, the fungal community was dominated by the cellulose-degrading fungus Trichocladium asperum. Based on these results, the original concept was modified and a two-phase conceptual model of litter C turnover and microbial response in the detritusphere was developed. In conclusion, this thesis yields new insight into litter decomposition at the small-scale. Combining classical methods with modern techniques enabled the development of a conceptual model of litter C turnover and microbial response in the detritusphere. This provides a useful basis for future studies addressing, for example, the impact of global change on the interaction of decomposition and soil microorganisms.
The functional role of phosphorus-mobilizing bacteria in the rhizosphere of tomato and maize
(2017) Nassal, Dinah; Kandeler, Ellen
Phosphorus (P) is an essential plant nutrient. However, global P reserves are being increasingly exploited and surplus P applied by P fertilization is steadily accumulating in the form of plant-unavailable P compounds in arable soils. Future plant production will therefore require a more effective and sustainable P fertilization regime. One promising approach is the use of phosphorus-mobilizing bacteria (PMB), which are able to mobilize P in soil through mineralization or solubilization so effectively that plant P supply is improved. Increases in plant growth and P uptake by the addition of PMB have been reported several times, but PMB’s functional mechanisms in soils and plants are still poorly understood. However, an understanding of PMB’s functional mechanisms is necessary to evaluate both the potential and limitations of their use as well as to develop practical application recommendations. This thesis aimed to provide a better understanding of PMB’s functional mechanisms in soil; the foci here were mechanisms and interactions of P mineralization with indigenous soil microorganisms. We aimed to identify P mineralization-dependent and -independent as well as direct and indirect mechanisms of PMB on soil and plants. To this end, three rhizobox experiments were performed in the greenhouse using tomato and maize as the test plants and Pseudomonas sp. RU47 (RU47) as the PMB. To identify effective P mineralization beyond the level of endogenous microbial activity, a treatment using unselectively cultivated soil bacteria for inoculation was included. Furthermore, the addition of devitalized RU47 cells provided the opportunity to identify indirect mechanisms. In all three rhizobox experiments the activities of acid and alkaline phosphomonoesterases in rhizosphere and bulk soil were determined, as the latter could be clearly identified as being of microbial origin. Effects on microbial community structure in soil were estimated by denaturing gradient gel electrophoresis (DGGE) and/or phospholipid fatty acid analysis. For deeper investigations of potential effects on microbial population composition and possible dependencies on soil conditions, a fourth experiment was performed using maize, three different Pseudomonas strains possessing PMB abilities, and three different soils varying in parameters which included organic C, pH, and P content. Microbiome shifts in soil were quantitatively determined via quantitative PCR using domain- (bacteria, archaea, fungi) and six bacterial phylum-specific primers. Our experiments showed that tomato plants grown under low P availability soil conditions improved in both growth and P uptake when viable RU47 cells were added. This effect was accompanied by increased alkaline phosphatase activity (PA) in the rhizosphere. We also observed plant growth-promotion effects and a trend of increased PA by the addition of dead RU47 cells. Based on DGGE results, which indicated the promotion of indigenous rhizobacteria, we assume a priming effect induced by the addition of C sources in the form of bacterial residues (dead RU47), which resulted in increased indigenous microbial activity in the rhizosphere. In each rhizobox experiment viable RU47 cells were able to colonize the rhizosphere at high abundances, persisting up to 50 days after sowing. We found indications of phytohormonal influences with the addition of both viable and dead RU47 cells, but this was more pronounced in dead than in viable RU47 treatments. Increasing P availability in soil by mineral P fertilization seemed to improve RU47’s ability to colonize and persist, which was shown by an increased RU47 abundance in both rhizosphere and bulk soils. However, despite an observable slight tendency, strengthened plant growth-promotion that positively correlated with improved RU47 abundance in the rhizosphere could not be detected. In general, colonization by viable RU47 cells did not significantly affect microbial community structure, either in the rhizosphere or in bulk soil. Using three different PMB strains, including RU47, in three contrasting soils, inoculation effects on the microbial community occurred heterogeneously, differing between the strains, soils, and time. Changes at the domain level were due primarily to nutrient availability in the soil, which differed between the soils and over time. Individual shifts in microbial community structure occurred more frequently in the rhizosphere than in bulk soil, but colonizing PMB neither increased bacterial abundance in rhizosphere bacteria, nor displaced copiotrophic rhizobacteria (indicative of C competition).