Browsing by Subject "Mikroorganismus"

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Bio-effectors for improved growth, nutrient acquisition and disease resistance of crops
(2017) Weinmann, Markus; Neumann, Günter
Recent scientific approaches to sustain agricultural production in face of a growing world food demand, limited natural resources, and ecological concerns have been focusing on biological processes to support soil fertility and healthy plant growth. In this context, the use of “bio-effectors”, comprising living (micro-) organisms and active natural compounds, has been receiving increasing attention. In contrast to conventional fertilizers and pesticides, the effectiveness of “bio-effectors” is essentially not based on the substantial direct input of mineral plant nutrients, neither in inorganic nor organic forms, nor of a-priori toxic compounds. Their direct or indirect effects on plant performance are rather based on the functional implementation or activation of biological mechanisms, in particular those interfering with soil-plant-microbe interactions. The general objective of the present research work was to improve the empirical and conceptual understanding concerning the utilization of bio-effectors in agricultural practice, following the principles of plant growth stimulation, bio-fertilization and bio-control. One main aspect of investigation was the application of bio-effectors to improve the efficiency of phosphorus (P) acquisition by the plant. Promising bio-preparations based on microbial inoculants (e.g. Bacillus, Pseudomonas, Trichoderma species) as well as natural compounds (e.g. algae extracts, humic acids) were tested in screening assays, greenhouse, and field experiments to characterize their potential effectiveness under varying environmental conditions. The most significant effects on plants appeared under severely low phosphate availability, but even under controlled conditions, bio-effectors required a narrow range of conductive environmental settings to reveal their potential effectiveness. Another focus of research was the application of bio-effectors to control soil borne pathogens, which typically appear in unsound crop rotations. Emphasis was set on take-all disease in wheat induced by the fungus Gaeumannomyces graminis. While the effectiveness of oat precrops to control take-all in subsequent wheat has been attributed to microbial changes and enhanced manganese (Mn) availability in soils, the take-all fungus is known to decrease the availability of Mn by oxidation. Against this background, the effectiveness of oat precrops and alternative crop management strategies to improve the Mn status and suppress the severity of take-all in wheat was investigated under controlled and field conditions. In conclusion, none of the tested supplemental treatments, such the application of microbial bio-effectors, stabilized ammonium or manganese fertilizers, could fully substitute for the multiple effectiveness of oat precrops, which was further confirmed by the results of a field experiment. Finally, some general conclusions and perspectives are summarized. Selected bio-effectors showed a strong capacity to improve the nutrient acquisition and healthy growth of crop plants under controlled conditions, but not in field experiments. However, even under controlled conditions the strongest effects occurred when plants were exposed to abiotic or biotic stresses, such as severely limited P availability or pathogen infestation of the soil substrate, still restricting plant growth to unproductive levels. Facing this situation, there is no perspective to improve the field efficiency of promising bio-effectors applications as a stand-alone approach. The only chance to develop viable alternatives to the conventional use of fertilizers or pesticides, for an ecological intensification of agriculture that maintains high yield levels, seems to be a reasonable integration of bio-effectors into the whole crop management of sound agricultural practice.
Bio-effectors for improved growth, nutrient acquisition and disease resistance of crops.- 2nd unrevised edition
(2019) Weinmann, Markus; Madora GmbH, Luckestr.1, D-79539 Lörrach; Raupp, Manfred G.
Recent scientific approaches to sustain agricultural production in face of a growing world food demand, limited natural resources, and ecological concerns have been focusing on biological processes to support soil fertility and healthy plant growth. In this context, the use of “bio-effectors”, comprising living (micro-) organisms and active natural compounds, has been receiving increasing attention. In contrast to conventional fertilizers and pesticides, the effectiveness of “bio-effectors” is essentially not based on the substantial direct input of mineral plant nutrients, neither in inorganic nor organic forms, nor of a-priori toxic compounds. Their direct or indirect effects on plant performance are rather based on the functional implementation or activation of biological mechanisms, in particular those interfering with soil-plant-microbe interactions. The general objective of the present research work was to improve the empirical and conceptual understanding concerning the utilization of bio-effectors in agricultural practice, following the principles of plant growth stimulation, bio-fertilization and bio-control. One main aspect of investigation was the application of bio-effectors to improve the efficiency of phosphorus (P) acquisition by the plant. Promising bio-preparations based on microbial inoculants (e.g. Bacillus, Pseudomonas, Trichoderma species) as well as natural compounds (e.g. algae extracts, humic acids) were tested in screening assays, greenhouse, and field experiments to characterize their potential effectiveness under varying environmental conditions. The most significant effects on plants appeared under severely low phosphate availability, but even under controlled conditions, bio-effectors required a narrow range of conductive environmental settings to reveal their potential effectiveness. Another focus of research was the application of bio-effectors to control soil borne pathogens, which typically appear in unsound crop rotations. Emphasis was set on take-all disease in wheat induced by the fungus Gaeumannomyces graminis. While the effectiveness of oat precrops to control take-all in subsequent wheat has been attributed to microbial changes and enhanced manganese (Mn) availability in soils, the take-all fungus is known to decrease the availability of Mn by oxidation. Against this background, the effectiveness of oat precrops and alternative crop management strategies to improve the Mn status and suppress the severity of take-all in wheat was investigated under controlled and field conditions. In conclusion, none of the tested supplemental treatments, such the application of microbial bio-effectors, stabilized ammonium or manganese fertilizers, could fully substitute for the multiple effectiveness of oat precrops, which was further confirmed by the results of a field experiment. Finally, some general conclusions and perspectives are summarized. Selected bio-effectors showed a strong capacity to improve the nutrient acquisition and healthy growth of crop plants under controlled conditions, but not in field experiments. However, even under controlled conditions the strongest effects occurred when plants were exposed to abiotic or biotic stresses, such as severely limited P availability or pathogen infestation of the soil substrate, still restricting plant growth to unproductive levels. Facing this situation, there is no perspective to improve the field efficiency of promising bio-effectors applications as a stand-alone approach. The only chance to develop viable alternatives to the conventional use of fertilizers or pesticides, for an ecological intensification of agriculture that maintains high yield levels, seems to be a reasonable integration of bio-effectors into the whole crop management of sound agricultural practice.
Charakterisierung der Qualität von Blütenpollen in unterschiedlichen Regionen Baden-Württembergs
(2022) Friedle, Carolin Gertrud Maria; Hasselmann, Martin
Honey bees (Apis mellifera) collect nectar and pollen from plants to feed their brood. Pollen provides a wide range of nutrients, such as proteins and lipids, but also carbohydrates, vitamins and enzymes. Because of these ingredients, pollen is also attractive to humans and is used as a dietary supplement. However, honey bees collect pollen not only from wild plants, but also from flowering crops grown in agriculture. Accordingly, contamination from plant protection products can be found in bee pollen and bee bread. In order to get a deeper insight into the occurrence and distribution of pesticide residues during an entire season, a total of 102 daily pollen samples were collected from April to July 2018 using pollen traps in an orchard in southern Germany. Almost 90% of the pollen samples showed detectable levels of pesticide residues. A total of 29 pesticides were detected in the samples, with more than half being fungicides, followed by insecticides and herbicides. Maximum concentrations of up to 4500 ng/g could be measured at the end of April. Samples collected in early May and late June also showed high levels of pesticides. A general risk management was performed to assess the risk of the detected pesticide concentrations for honey bees. The microbial quality of bee pollen is highly dependent on its botanical and geographic origin, as well as climatic conditions and post-harvest processing steps by the beekeeper. If no processing steps such as freezing or drying follow after harvest, the growth of microorganisms can be promoted and the pollen quality can be influenced by negative side effects such as fermentation or the production of mycotoxins. Bacterial and fungal colonies can be determined both by culture-dependent methods such as colony counting on plates and by culture-independent methods such as 16-rRNA amplicon sequencing. Following the hypothesis that storage conditions influence the composition of microorganisms in bee pollen, freshly harvested bee pollen was stored for seven days in June 2018 and 2019 under defined conditions (cold, room temperature, warm) and analyzed by sequencing 16S and 18S PCR amplicons. The bacterial community varied slightly between the sites studied and showed no significant difference between the storage conditions. The fungal community showed significant differences both between the studied sites and between the different storage conditions. The dominant fungal genera in the pollen samples were Cladosporium, Aspergillus and Zygosaccharomyces. While Cladosporium was most dominant in freshly collected pollen and the percentage decreased during storage, Aspergillus and Zygosaccharomyces showed a significant increase especially under warm storage conditions. Other contaminants naturally produced by plants can also have negative impacts on human health. Pyrrolizidine alkaloids belong to a group of phytochemicals, of which more than 600 structures are known in around 3% of all flowering plants worldwide. PA are known to be able to cause both acute poisoning and chronic damage or cancer in animals and humans. In July 2019, pollen was collected at 57 locations in Baden-Württemberg and analyzed for 42 different PAs and their N-oxides in order to expand knowledge about PA contamination in pollen and to be able to estimate the risk of the concentrations. A total of 22 different PAs were detected in over 90% of all samples examined. Only 5% of the PA were obtained as PA from plants of Senecio sp. identified, while 95% of PAs with a botanical background are from Echium sp. and Eupatorium sp. could be identified. The maximum total concentration of PA per sample was determined to be 48,400 ng/g. According to the risk values calculated by the BfR, however, 42% of the samples represented an increased risk to human health.
Impact of age and weaning time on the gut microbiome and the potential host-microbe interactions in calves
(2021) Amin, Nida; Seifert, Jana
The period from birth until the end of weaning is critical for calves as they undergo extreme stress caused by maternal separation, transportation, and weaning related dietary shifts, that can cause long-lasting effects on animal behaviour, health as well as future production parameters. Monitoring the development of microbial ecosystem throughout the gastrointestinal tract of calves and host-microbe interactions during the challenging life periods such as perinatal and weaning is essential for sustainable ruminant production. The present thesis provided new insight on the suitability of buccal swabs as an alternative to complex stomach tubing method for predictive analysis of rumen microbial communities. The changes in oral, rumen and faecal microbial community structure of female German Holstein calves from 8-days to 5-months of age as well as during early- and late-weaning event were identified. The oral microbiota plays a crucial role in animal health. A high dominance of oral pathogens was observed during the first 11-weeks of calves’ life. Similar to the oral microbiota, faeces of 8-day-old calves also showed high abundances of certain opportunistic pathogenic bacteria. Both oral and faecal pathogens showed a decrease in abundance with age and after weaning event in the earlyC group, indicating the age and weaning-dependent maturation of the host immune system. The establishment of dense microbial communities in the faeces of 8-day-old (experimental day 1) pooled herd milk and milk replacer fed Holstein calves was shown and it was dominated by phyla Firmicutes and Actinobacteria and potential lactose- and starch-degrading bacterial species, but as the calves aged and became more mature (5-months of age), their rumen and faecal bacterial communities were dominated by potential fibre-utilizing bacterial genera. The weaning related dietary transitions are critical for calves as their gastrointestinal tract undergoes several modifications, enabling them to digest plant-based diet during the postweaning period. Thus, it was proposed that the age at which animals should be weaned must be carefully considered as it clearly impacted the gastrointestinal tract microbial communities and plasma metabolic profiles of calves in the present study. Early introduction of roughages in the diet of 7-week-old calves increased the abundances of plant fiber degrading bacteria and decreased the abundances of potential lactose- and starch-degrading bacteria in the buccal cavity, rumen and faeces, indicating the weaning-related increase in fiber ingestion and the decrease in milk consumption of the early-weaned group. However, when roughages were introduced in the diet of late-weaned calves at 17-weeks of age, no significant modifications in the structure of gastrointestinal tract microbial communities were observed. Similar to the microbiome, plasma metabolic profiles of early-weaned calves during days 42–112, showed lower concentrations of most of the amino acids, few biogenic amines, and sphingomyelins as compared to the late-weaned calves, suggesting that the liquid diet could provide certain metabolites that can be transported into the bloodstream through gastrointestinal tract. Similarly, the weaning-dependent changes in the quantity of dietary protein, fat and carbohydrates resulted in substantial changes in amino acid metabolism of the early-weaned group. The early-weaning event not only impacted the host microbiome and metabolome but also the host-microbe metabolic interactions as the abundances of potential lactose- and starch degrading bacteria and plasma concentrations of amino acid, biogenic amines and sphingomyelins were strongly positively correlated, both were negatively impacted by the early-weaning event. Thus, it can be concluded that late-weaning was beneficial as it allowed better adaptability of microbes to weaning-related dietary shifts, perhaps due to the greater maturation of their gastrointestinal tract with age as compared to the early-weaning group.
Microbial consortia as inoculants for improvedcrop performance
(2020) Bradácová, Klára; Neumann, Günter
The use of microbial consortia products (MCP) based on combinations of different strains of plant growth-promoting microorganisms (PGPM) and frequently also on non-microbial bio-stimulants (BS) with complementary beneficial properties, is discussed as a strategy to increase the efficiency and the flexibility of BS-based crop production strategies under variable environmental conditions. Moreover, MCP application aims at the restoration of plant-beneficial, soil biological processes disturbed by soil degradation and intensive use of agro-chemicals. This PhD thesis was initiated to characterize the modes of action and the potential advantages of a representative commercial MCP formulation over selected single strain PGPM inoculants, with documented effects on plant growth promotion and pathogen suppression. In total, nine pot and field experiments were conducted with three crops (maize, spring wheat, tomato) on seven different soils with three organic and inorganic fertilization regimes. Only in one out of nine experiments conducted in this thesis, clear evidence for superior MCP performance was detectable in a drip-irrigated tomato field experiment conducted under the challenging environmental conditions of the Negev desert in Israel (Bradáčová et al., 2019c). This finding demonstrates that MCP inoculants can exhibit an advantage over single strain inoculants but not as a general feature. Selective interactions with the type and dosage of the selected fertilizers, as well as avoidance of inhibitory effects on root growth during MCP rhizosphere establishment, have been identified as critical factors. A further characterization of the conditions, promoting beneficial plant-MCP interactions is mandatory for a more targeted and reproducible MCP application.
Microplastics interactions with soil organisms
(2022) Schöpfer, Lion; Kandeler, Ellen
Microplastics (MP) are plastic particles from 100 nm to 5 mm with different shapes and chemical compositions. In aquatic ecosystems, MP have proven to affect the biological fitness of aquatic organisms, enter the food web, and act as vectors of pollutants. Agricultural soils are sinks for MP due to inputs via sewage sludges, plastic mulches, and organic fertilizers. However, ecological consequences of MP in agricultural soils are unknown. This doctoral thesis aimed to evaluate the risk of conventional and biodegradable MP for soil organisms in agricultural soils. A microcosm study was combined with a field study and a nematode study to investigate background concentrations, the persistence, and the biodegradation of MP in the soil, and effects of MP on soil microorganisms and nematodes. In the microcosm study, the influence of plastic type, particle size, and soil moisture on the biodegradation of MP in the soil and on effects on soil microorganisms were examined under controlled conditions (25 °C, 230 days). The abundance and composition of the main soil microbial groups was analyzed via phospholipid fatty acids (PLFAs) as biomarkers; activities of C cycling enzymes driving the decomposition of differently complex substances were analyzed as proxies for C turnover. To understand better the role of MP as an interface for specific microbial processes in the soil, e.g. the enzymatic hydrolysis of MP, enzyme activities of individual MP particles extracted from the soil were measured. The site of the field study was a conventionally managed agricultural soil (silt-loam Luvisol) of the Heidfeldhof, University of Hohenheim. No practices associated with significant inputs of MP have been conducted at the site in the past (sewage sludge, organic fertilizers, plastic mulch). In a randomized complete block design, the effects of MP, organic fertilizers (digestate and compost), and their interactions on soil microbiological indicators (microbial biomass, soil enzymes) were studied. Before the setup of the field study, MP background concentrations (particle-based) in the soil were analyzed. The persistence of added MP in the soil was evaluated by comparing MP concentrations in the soil after 1 month and 17 months with initial MP concentrations after addition. In the nematode study, the soil-dwelling nematode Caenorhabditis elegans was exposed to MP feed suspensions on agar plates. The uptake of MP through nematodes and the influence of plastic type and concentration on MP effects on nematode reproduction and body length were examined. In all studies, artificially fragmented MP from a conventional polymer (low-density polyethylene, LDPE) and a biodegradable polymer blend (poly(lactic acid) and poly(butylene adipate-co-terephtalate), PLA/PBAT) were used. The occurrence of both LDPE- and PLA/PBAT-MP is likely in agricultural soils because these are used for plastic mulches and compost bags. Results from this thesis suggest that (1) agricultural soils, including those without management practices related to significant MP entry, contain various MP, indicating diffuse MP inputs via atmospheric deposition, littering, and the abrasion of machinery coatings (a possible newly identified pathway), (2) also biodegradable MP persist and are slowly biodegraded in the soil implying a long term exposure risk for soil organisms to MP, (3) MP have no acute negative effects on microorganisms and C turnover, (4) MP form a specific habitat in the soil, the plastisphere, where MP-specific processes take place, e.g. the enzymatic hydrolysis of PLA/PBAT, (5) MP can enter the soil food web via nematodal uptake and affect nematode reproduction, which could destabilize the soil food web.
Strain-resolved analysis of the human intestinal microbiota
(2022) Podlesny, Daniel; Fricke, Florian W.
The gut microbiota is ascribed a crucial role in human health, particularly in regulating immune and inflammatory responses, which is why it is being associated with a wide range of diseases, including obesity, diabetes, and cancer. Nonetheless, fundamental ecological questions of microbiome establishment, stability and resilience, as well as its transmission across hosts and generations remain incompletely understood, partly due to the lack of methods for high-resolution microbiome profiling. New insights in this field can therefore directly contribute to the development of bacterial and microbiota-based therapies. This work introduces SameStr, a novel bioinformatic program for strain-resolved metagenomics that allows for the specific tracking of microbes across samples, enabling the detection and quantification of microbial transmission and persistence, as well as the observation of direct strain competition. Deployed across cohorts to process over 4200 metagenomes, SameStr enabled analysis of the microbiome with unprecedented phylogenetic resolution. The data included both publicly available metagenomes and sequence data generated in collaboration with our research partners, and was examined using multivariate statistics and machine learning frameworks. First, the establishment and development of the neonatal microbiota was studied, revealing a birth mode-dependent vertical transmission of the maternal microbiota. The microbiota of neonates born by cesarean section was characterized by increased relative abundance of oxygen-tolerant and atypical organisms and showed signs of a delayed establishment of a strictly anaerobic gut environment in these children. Such birth mode-dependent differences diminished over time, yet were measurable within the first two years of life. Furthermore, strain analysis verified the transmission and colonization of parental microbes, which indicated a possible lifelong colonization by microbes from selected species. The temporal persistence of microbes was also characterized in healthy adults, revealing similar taxonomy-dependent patterns of stability. For some species, persistence has been demonstrated both in children and in adults over a period of at least two years. These species are known for their capability to metabolize host-derived glycans found both in breastmilk and intestinal mucus, pointing to a potential strategy for effective cross-generational microbiota transmission, and warranting additional research to assess the implications of their disturbed transfer for long-term health. Since their specificity allows assignment to individual hosts, fingerprints of individual microbial strains offer the potential to be used in forensics and data quality control applications. Finally, to gain new insights into the microbiota dynamics during Fecal Microbiota Transplantation (FMT), microbial strain transmission was analyzed in the context of a diverse set of patient, microbiome, and clinical conditions. In the analyzed studies, FMT was used for the experimental treatment of a variety of diseases, including colonization with drug-resistant and pathogenic microbes, metabolic and inflammatory bowel diseases, and as an adjunct to the immunotherapeutic treatment of cancer. Analyses uncovered what appear to be the universal drivers of post-FMT microbiota assembly, including clinical and ecological factors that are important for successful transplantation of donor strains. In particular, the relevance of the microbiota dysbiosis of the recipient was emphasized, which was inducible by pre-treating the patient with antibiotics or laxatives. Presumably, this can open up ecological niches in the patients intestines, which favors colonization with donor strains. Colonization rates did not play a role for the treatment success of recurrent C. difficile infections and inflammatory bowel disease, but indicated a trend associated with an improved immune response in cancer patients. Concerningly, the transfer of an atypical and potentially pro-inflammatory microbial community from one donor was also observed, calling for further investigations into the immediate and long-term clinical consequences of FMT. These analyses demonstrate the advantages of a strain-based microbiome analysis. Due to the achieved methodological accuracy, strain-resolved microbial dynamics could be precisely disentangled when comparing longitudinal samples from healthy adults as well as parent-child and patient-donor pairs. This revealed taxonomic, clinical, and ecological factors that are critical to microbiome assembly, including microbial transmission, persistence, and competition. Together, these findings lay the groundwork for future developments of precision personalized microbiota modulation therapies.