Browsing by Subject "Fungi"

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Biological regulation of subsoil C-cycling
(2019) Preußer, Sebastian; Kandeler, Ellen
Soils are the largest terrestrial reservoir of organic carbon (OC). Substantial proportions of the stored OC are found in stabilized form in deeper soil layers. Beside the quality and quantity of C input from plant biomass, C storage in soil is primarily controlled by the microbial decomposition capacity. Various physical, chemical and biological factors (e.g., substrate availability, temperature, water content, pH, texture) vary within soil profiles and directly or indirectly influence the abundance, composition and activity of microbial communities and thus the microbial C turnover. While soil microbiological research has so far focused mainly on processes in topsoil, the mechanisms of C storage and turnover in subsoil are largely unknown. The objective of the present thesis was therefore to investigate the specific influence of substrate availability and different environmental factors as well as their interactions on microbial communities and their regulatory function in subsoil C-cycling. This objective was addressed in three studies. In the first and second study, one-year field experiments were established in which microbial communities from different soil depths were exposed to altered habitat conditions to identify crucial factors influencing the spatial and temporal development of microbial abundance and substrate utilization within soil profiles. This was achieved by reciprocal translocation of soils between subsoil horizons (first study) and topsoil and subsoil horizons (second study) in combination with addition of 13C-labelled substrates and different sampling dates. In the third study, a flow cascade experiment with soil columns from topsoil and subsoil horizons and soil minerals (goethite) coated with 13C-labelled organic matter (OM) was established. This laboratory experiment investigated the importance of exchange processes of OM with reactive soil minerals for the quality and quantity of dissolved OM and the influence of these soil micro-habitats on microbial abundance and community composition with increasing soil depth. In the first study, the reciprocal translocation of subsoils from different soil depths revealed that due to comparable micro-climatic conditions and soil textures within the subsoil profile, no changes in microbial biomass, community composition and activity occurred. Moreover, increasing microbial substrate utilization in relation to the quantity of added substrate indicated that deep soil layers exhibit high potential for microbial C turnover. However, this potential was constrained by low soil moisture in interplay with the coarse soil texture and the resulting micro-scale fragmentation of the subsoil environment. The bacterial substrate utilization was more affected by this spatial separation between microorganisms and potentially available substrate than that of fungi, which was further confirmed by the translocation experiment with topsoil and subsoil in the second study. While the absolute substrate utilization capacity of bacteria decreased from the more moist topsoil to the drier subsoil, fungi were able to increase their substrate utilization and thus to partially compensate the decrease in C input from other sources. Furthermore, the addition of root litter as a preferential C source of fungal decomposer communities led to a pronounced fungal growth in subsoil. The third study demonstrated the high importance of reactive soil minerals both in topsoil and in subsoil for microbial growth due to extensive exchange processes of OM and the associated high availability of labile C. In particular copiotrophic bacteria such as Betaproteobacteria benefited from the increased C availability under non-limiting water conditions leading to a pronounced increase in bacterial dominance in the microbial communities of these soil micro-habitats. In conclusion, this thesis showed that subsoil exhibits great potential for both bacterial and fungal C turnover, albeit this potential is limited by various factors. This thesis, however, allowed to determine the specific effects of these factors on bacteria and fungi and their function in subsoil C-cycling and thus to identify those factors of critical importance. The micro-climate in subsoil, in particular soil moisture, was the primary factor limiting bacterial growth and activity, whereas fungi were more strongly restricted by substrate limitations.
Microbial regulation of soil organic matter decomposition at the regional scale
(2018) Ali, Rana Shahbaz; Kandeler, Ellen
The fate of soil organic carbon (SOC) is one of the greatest uncertainties in predicting future climate. Soil microorganisms, as primary decomposers of SOC, control C storage in terrestrial ecosystems by mediating feedbacks to climate change. Even small changes in microbial SOC decomposition rates at the regional scale have the potential to alter land-atmospheric feedbacks at the global scale. Despite their critical role, the ways in which soil microorganisms may change their abundances and functions in response to the climate change drivers of soil temperature and moisture is unclear. Additionally, most existing C models do not consider soil microorganisms explicitly as drivers of decomposition, one consequence of which is large variability in predicted SOC stock projections. This demonstrates the need for a better mechanistic understanding of microbial SOC decomposition at large scales. This thesis was designed to clarify the role of microbial SOC decomposition dynamics in response to climate change factors in two geographically distinct areas and land-use types. The hypothesis was that microbial communities would be adapted to climatic and edaphic conditions specific to each area and to the SOC organic quality in each land-use and would therefore exhibit distinct responses to soil temperature and moisture variations. Three studies were performed to address the goals of this thesis. The first study aimed to clarify temporal patterns of degradation in C pools that varied in complexity by modelling in situ potentials of microbially produced extracellular enzymes. Temperature and moisture sensitivity patterns of C cycling enzymes were followed over a period of thirteen months. The second study investigated group-specific temperature responses of bacteria and fungi to substrate quality variations through an additional incubation experiment. Here, complex environments were mimicked in order to determine the dependence of microbial responses not only on environmental conditions, but also under conditions of inter- and intra-specific community competition. Changes in microbial community composition, abundance, and function were determined at coarse (phospholipid fatty acid – PLFA, ergosterol) and relatively fine resolutions (16S rRNA, taxa-specific quantitative PCR, fungal ITS fragment). A third study investigated 1) the spatial variability of temperature sensitivity of microbial processes, and 2) the scale-specificity and relative significance of their biotic and physicochemical controls at landscape (two individual areas, each ca. 27 km2) and regional scales (pooled data of two areas). Strong seasonal dependency was observed in the temperature sensitivities (Q10) of hydrolytic and oxidative enzymes, whereas moisture sensitivity of β-glucosidase activities remained stable over the year. The range of measured enzyme Q10 values was similar irrespective of spatial scale, indicating a consistency of temperature sensitivities of these enzymes at large scales. Enzymes catalyzing the recalcitrant SOC pool exhibited higher temperature sensitivities than enzymes catalyzing the labile pool; because the recalcitrant C pool is relatively large, this could be important for understanding SOC sensitivity to predicted global warming. Response functions were used to model temperature-based and temperature and moisture-based in situ enzyme potentials to characterize seasonal variations in SOC decomposition. In situ enzyme potential explained measured soil respiration fluxes more efficiently than the commonly used temperature-respiration function, supporting the validity of our chosen modelling approach. As shown in the incubation experiment, increasing temperature stimulated respiration but decreased the total biomass of bacteria and fungi irrespective of substrate complexity, indicating strong stress responses by both over short time scales. This response did not differ between study areas and land-uses, indicating a dominant role of temperature and substrate quality in controlling microbial SOC decomposition. Temperature strongly influenced the responses of microbial groups exhibiting different life strategies under varying substrate quality availability; with soil warming, the abundance of oligotrophs (fungi and gram-positive bacteria) decreased, whereas copiotrophs (gram-negative) increased under labile C substrate conditions. Such an interactive effect of soil temperature and substrate quality was also visible at the taxon level, where copiotrophic bacteria were associated with labile C substrates and oligotrophic bacteria with recalcitrant substrates. Which physicochemical and biological factors might explain the observed alterations in microbial communities and their functions in response to climate change drivers at the regional scale was investigated in the third study. Here, it was shown that the soil C:N ratio exerted scale-dependent control over soil basal respiration, whereas microbial biomass explained soil basal respiration independent of spatial scale. Factors explaining the temperature sensitivity of soil respiration also differed by spatial scale; extractable organic C and soil pH were important only at the landscape scale, whereas soil texture as a control was independent of spatial scale. In conclusion, this thesis provides an enhanced understanding of the response of microbial C dynamics to climate change at large scales by combining field measurements with innovative laboratory assays and modelling tools. Component specific degradation rates of SOC using extracellular enzyme measurements as a proxy, group-specific temperature sensitivities of microbial key players, and the demonstrated scale-specificity of factors controlling microbial processes could potentially improve the predictive power of currently available C models at regional scale.
Occurrence of mycotoxins in pulses
(2022) Acuña‐Gutiérrez, Catalina; Jiménez, Víctor M.; Müller, Joachim
Pulses, dry grains of the Fabaceae family used for food and feed, are particularly important agricultural products with increasing commercial and nutritional relevance. Similar to other plant commodities, pulses can be affected by fungi in the field and during postharvest. Some of these fungi produce mycotoxins, which can seriously threaten human and animal health by causing acute poisoning and chronic effects. In this review, information referring to the analysis and occurrence of these compounds in pulses is summarized. An overview of the aims pursued, and of the methodologies employed for mycotoxin analysis in the different reports is presented, followed by a comprehensive review of relevant articles on mycotoxins in pulses, categorized according to the geographical region, among other considerations. Moreover, special attention was given to the effect of climatic conditions on microorganism infestation and mycotoxin accumulation. Furthermore, the limited literature available was considered to look for possible correlations between the degree of fungal infection and the mycotoxin incidence in pulses. In addition, the potential effect of certain phenolic compounds on reducing fungi infestation and mycotoxin accumulation was reviewed with examples on beans. Emphasis was also given to a specific group of mycotoxins, the phomopsins, that mainly impact lupin. Finally, the negative consequences of mycotoxin accumulation on the physiology and development of contaminated seeds and seedlings are presented, focusing on the few reports available on pulses. Given the agricultural and nutritional potential that pulses offer for human well-being, their promotion should be accompanied by attention to food safety issues, and mycotoxins might be among the most serious threats.
Previtamin D2, vitamin D2, and vitamin D4 amounts in different mushroom species irradiated with ultraviolet (UV) light and occurrence of structurally related photoproducts
(2024) Sommer, Katrin; Hillinger, Marissa; Vetter, Walter
Mushrooms are rich in ergosterol and ergosta‐5,7‐dienol, which can be partly converted into vitamin D2 and D4 through ultraviolet (UV) light exposure. Typically, mushrooms have very low vitamin D contents, but it can be increased by UV irradiation. This process generates additional photoisomers scarcely studied in mushrooms due to analytical challenges. Here, we developed a new solid phase extraction (SPE) method to separate vitamin D2, vitamin D4, and other tri‐ and pentacyclic photoisomers from the much higher abundant ergosterol. Subsequent GC/MS analysis enabled the detection of ten photoisomers in eight UV‐treated mushroom species, including vitamin D2 (previtamin D2, tachysterol2, two suprasterol2 and trans‐vitamin D2 isomers) and vitamin D4 (previtamin D4). Quantitated vitamin D2 contents of 10–540 µg/100 g dry weight agreed well with the sparse literature data available for the investigated mushroom species. In addition, previtamin D2 (nd–1950 µg/100 g dry weight) and vitamin D4 (10–140 µg/100 g dw) were quantified in the samples. The content and photoproduct compositions varied considerably between different mushroom species. Practical applications: The novel SPE method can be applied to study the vitamin D and photoisomer content of mushrooms.