Browsing by Subject "Streu"

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Effects of resource availability and quality on soil microorganisms and their carbon assimilation
(2014) Kramer, Susanne; Kandeler, Ellen
Soil microorganisms play a pivotal role in decomposition processes and therefore influence nutrient cycling and ecosystem function. Availability and quality of resources determines activity, growth and identity of substrate users. In agricultural systems, availability of resources is dependent on, for example, crop type, management, season, and depth. At depth substrate availability and microbial biomass decrease. However, there remain gaps in our understanding of C turnover in subsoil and how processes in the topsoil may influence abundance, activity, and function of microorganisms in deeper soil layers. With respect to substrate quality it is thought that bacteria are the dominant users of high quality substrates and more labile components whereas fungi are more important for the degradation of low quality and more recalcitrant substrates (i.e. cellulose, lignin). Therefore, this thesis was designed to increase our understanding of C turnover and the influence of both availability and quality of substrates on microorganisms in an agricultural soil. In the first and second studies, a recently established C3-C4 plant exchange field experiment was used to investigate the C flow from belowground (root) and aboveground (shoot litter) resources into the belowground food web. Maize plants were cultivated to introduce a C4 signal into the soil both by plant growth (belowground / root channel) and also by applying shoot litter (aboveground litter channel). To separate C flow from the shoot litter versus the root channel, maize litter was applied on wheat cultivated plots, while on half of the maize planted plots no maize litter was returned. Wheat cultivated plots without additional maize litter application served as a reference for the calculation of incorporated maize-C into different soil pools. Soil samplings took place in two consecutive years in summer, autumn and winter. Three depths were considered (0-10 cm: topsoil, 40-50 cm: rooted zone beneath the plough layer, 60-70 cm: unrooted zone). In the third study a microcosm experiment with substrates of different recalcitrance and complexity was carried out to identify primary decomposers of different plant litter materials (leaves and roots) during early stages of decomposition (duration of 32 days) and to follow the C flow into the next higher trophic level (protozoa).
Microbial community structure and function is shaped by microhabitat characteristics in soil
(2016) Ditterich, Franziska; Kandeler, Ellen
Soil microorganisms play a key role in degradation processes in soil, such as organic matter decomposition and degradation of xenobiotics. Microbial growth and activity and therefore degradation processes are influenced by different ecological factors, such as substrate availability, pH and temperature. During soil development different microhabitats are formed which differ in their physiochemical properties. There is some evidence that mineral composition is a driver for specific microbial colonization. Thereby, the heterogeneity of soils with differences in mineral composition and substrate availability can lead to a spatial distribution of soil microorganisms. At the soil-litter interface, a biogeochemical hot spot in soil, the abundance and activity of soil microorganisms increases due to high substrate availability, and degradation processes such as pesticide degradation are enhanced. This thesis aimed to clarify the influence of habitat properties on the structure and function of the microbial community in soil. In particular, focus was on mineral-microbe interactions that result from the mineral composition and substrate availability in an artificial soils system. Furthermore this thesis was designed to increase our understanding of the bacterial and fungal roles in pesticide degradation at the soil-litter interface using 4-chloro-2-methylphenoxyacetic acid (MCPA) as a model xenobiotic. These two aspects of the thesis were examined in three studies. The first study focused on the succession of microbial communities and enzyme activities in an artificial soils system with varying mineral composition and substrate availability over a period of 18 months. In the second study a microcosm experiment was used to study the bacterial pathway of MCPA degradation at the soil-litter interface. Over a period of 27 days the succession of bacterial degraders was followed. The third study focused on the degradation of MCPA in soil by nonspecific fungal enzymes, through the addition of fungal laccases as well as litter during 42 days of incubation. Both studies indicated the involvement of fungi in MCPA degradation and the importance of the ecological behavior of different degraders as a function of substrate availability. Results of the first study indicated that the microbial community was affected by mineral properties under high substrate availability and by the availability of beneficial nutrients at the end of incubation when substrate had become limited. The measured enzyme activities provided clear evidence that microbial community structure was driven by nutrient limitation during incubation. In the presence of easily available organic substrates at the beginning of the experiment, the soil microbial community was dominated by copiotrophic bacteria (e.g. Betaproteobacteria), whereas under substrate limitation at the end of incubation, more recalcitrant compounds became important to oligotrophic bacteria (e.g. Acidobacteria), which then became dominant. The results of the second study indicated that the contribution of the potential degraders to degradation of MCPA differed, and this was also seen in the succession of specific bacterial MCPA degraders. Added litter stimulated MCPA degradation due to the availability of litter-derived carbon and induced a two-phase response of fungi. This was seen in the development of pioneer and late stage fungal communities. Both fungal communities were probably involved in MCPA degradation. Therefore, the third study focused on the fungal pathway. These results indicated that the fungal laccases used had no direct influence on degradation and were as efficient as litter in providing additional nutrient sources, increasing MCPA degradation by bacteria and fungi. The observed differences between litter and enzyme addition underscored the observation that the enzyme effect was short-lived and that substrate quality is an important factor in degradation processes. In conclusion, this thesis demonstrated that soil microbial communities and therefore degradation processes are driven by mineral composition as well as substrate availability and quality. In addition, this thesis extends our understanding of degradation processes such as the degradation of xenobiotics, with MCPA as model compound, in soil. The combined insights from all three studies suggest that the use of a simple system such as the artificial soil system can increase our understanding of complex mechanisms such as degradation of pesticides.
Microbial regulation of pesticide degradation coupled to carbon turnover in the detritusphere
(2015) Pagel, Holger; Streck, Thilo
Many soil functions, such as nutrient cycling or pesticide degradation, are controlled by microorganisms. Dynamics of microbial populations and biogeochemical cycling in soil are largely determined by the availability of carbon (C). The detritusphere is a microbial “hot spot” of C turnover. It is characterized by a concentration gradient of C from litter (high) into the adjacent soil (lower). Therefore, this microhabitat is very well suited to investigate the influence of C availability on microbial turnover. My thesis aimed at the improved understanding of biochemical interactions involved in the degradation of the herbicide 4-chloro-2-methylphenoxyacetic acid (MCPA) coupled to C turnover. In the detritusphere gradients of organic matter turnover from litter into the adjacent soil could be identified. Increased C availability, due to the transport of dissolved organic substances from litter into soil, resulted in the boost of microbial biomass and activity as well as in the acceleration of MCPA degradation. Fungi and bacterial MCPA-degraders benefited most from litter-C input. Accelerated MCPA degradation was accompanied by increased incorporation of MCPA-C into soil organic matter. The experimental results show that the transport of dissolved organic substances from litter regulates C availability, microbial activity and finally MCPA degradation in the detritusphere. In general, litter-derived organic compounds provide energy and resources for microorganisms. The following possible regulation mechanisms were identified: i) Litter might directly supply the co-substrate alpha-ketoglutarate (or surrogates) required for enzymatic oxidation of MCPA by bacterial MCPA degraders. Alternatively it might provide additional energy and resources for production and regeneration of the needed co-substrate. ii) Additional litter-C might alleviate substrate limitation of enzyme production by bacteria and bacterial consortia resulting in an increased activity of specific enzymes attacking MCPA. iii) Litter-derived organic substances might stimulate MCPA degradation via fungal co-metabolism by unspecific extracellular enzymes, either directly by inducing enzyme production, or by supplying primary substrates that provide the energy consumed by co-metabolic MCPA transformation. A new biogeochemical model abstracts these regulation mechanisms in such a way that C availability controls physiological activity, growth, death and maintenance of microbial pools. Based on a global sensitivity analysis, 41% (n=33) of all considered parameters and input values were classified as “very important” and “important”. These mainly include biokinetic parameters and initial values. The calibration of the model allowed to validate the implemented regulation mechanisms of accelerated MCPA degradation. The Pareto-analysis showed that the model structure was adequate and the identified parameter values were reasonable to reproduce the observed dynamics of C and MCPA. The model satisfactorily matched observed abundances of gene-markers of total bacteria and specific MCPA degraders. However, it underestimated the steep increase of fungal ITS fragments, most probably because this gene-marker is only inadequately suited as a measure of fungal biomass. The model simulations indicate that soil fungi primarily benefit from low-quality C, whereas bacterial MCPA-degraders preferentially use high-quality C. According to the simulations, MCPA was predominantly transformed via co-metabolism to high-quality C. Subsequently, this C was primarily assimilated by bacterial MCPA-degraders. The highest turnover of litter-derived C occurred by substrate uptake for microbial growth. Input and microbial turnover of litter-C stimulated MCPA degradation mainly in a soil layer at 0-3 mm distance to litter. As a consequence of this, a concentration gradient of MCPA formed, which triggered the diffusive upward transport of MCPA from deeper soil layers into the detritusphere. The results of the three studies suggest: The detritusphere is a biogeochemical hot spot where microbial dynamics control matter cycling. The integrated use of experiments and mathematical modelling gives detailed insight into matter cycling and dynamics of microorganisms in soil. Microbial communities need to be explicitly considered to understand the regulation of soil functions.
Soil microbial assimilation and turnover of carbon depend on resource quality and availability
(2017) Müller, Karolin; Kandeler, Ellen
The decomposition of soil organic carbon (SOC), which is predominantly performed by soil microorganisms, is an important process in global carbon (C) cycling. Despite the importance of microbial activity to the global C budget, the effects of resource quality and availability on soil microorganisms are little understood. Most of this plant-derived C enters the soil organic C pool via incorporation into soil microorganisms, but the subsequent fate of C is rarely reported. Therefore, soil microbial biogeochemistry is still highly uncertain in earth system models. The study presented in Chapter 5 used a field experiment established in 2009 to investigate C flow at three soil depths over five consecutive years after a C3 to C4 crop exchange. Root-derived C (belowground pathway) was introduced by the cropping of maize plants, whereas shoot-derived C (aboveground pathway) was introduced by application of shoot litter to the soil surface. The proportion of maize-derived C varied between the different soil pools with lower incorporation into SOC and EOC (extractable organic C) and higher incorporation ratios of maize C into microbial groups. Although root-C input was three times higher than shoot-C input, similar relative amounts of maize-C were found in microorganisms. Both root and shoot C were transferred to a depth of 70 cm. At all three depths, fungi utilized the provided maize C to a greater extent than did either Gram-positive or Gram-negative bacteria. Fungal biomass was labeled with maize-C to 78% after the fifth vegetation period, indicating preferential utilization of litter-derived C by saprotrophic fungi. The second study investigated, in a microcosm experiment, the effects of decreasing resource quality on microorganisms during plant residue decomposition at the soil-litter interface. Reciprocal transplantation of labeled 13C and unlabeled 12C maize litter to the surface of soil cores allowed us to follow C transfer and subsequent C turnover from residues into microbial biomass of fundamental members (bacteria and fungi) of the detritivore food web during three stages of the litter decomposition process. Quality (i.e. age) of the maize litter influenced C incorporation into bacteria and fungi. Labile C from freshly introduced litter was incorporated by both groups of microorganisms, whereas saprotrophic fungi additionally used complex C in the intermediate stage of decomposition. Bacteria responded differentially to the introduced litter; either by turnover of litter C in their phospholipid fatty acids (PLFAs) over time, or by storage and/or reuse of previous microbially released C. Saprotrophic fungi, however, showed a distinct litter C turnover in the fungal PLFA. The mean residence time of C in the fungal biomass was 32 to 46 days; the same or shorter time than in bacterial PLFAs. In the third study, presented in Chapter 7, another field experiment was conducted to distinguish herbivore- from detritus-based food chain members over two consecutive years. Three treatments were established: maize as crop plant, maize shoot litter application, and fallow without C input. This provided root-derived C, shoot-derived C, and autochthonous organic matter, respectively, as the main C resource. The altered C supply due to plant removal had less severe effects on the micro-food web structure than expected. In the first growing season, nematode abundance under plant cultivation was similar to that under litter and fallow conditions. After the second harvest, the abundance of detritivore food chain members increased, reflecting the decomposition of root residues. Bacteria and fungi showed a marked resilience to changed C availability. Results of this experiment suggest considerable micro-food web resilience to altered C and nutrient availability, and indicate that organic matter from previous vegetation periods was successfully utilized to overcome C deprivation. In conclusion, this thesis provides new insights into microbially mediated decomposition processes at different time scales and at different soil depths. Stable isotope probing combined with biomarker analysis enabled us to study C fluxes between biotic and soil C pools to separate the contributions of bacteria and fungi to soil C cycling. These results can be used as a basis for an empirical model of C flow through the entire soil food web.