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The use of the herbicide glyphosate and its formulations on protein-rich feedstuff for cattle leads to a considerable intake of glyphosate into the rumen of the animals, where glyphosate may potentially impair the 5-enolpyruvylshikimate-3-phosphate pathway of the commensal microbiota, which could cause dysbiosis or proliferation of pathogenic microorganisms. Here, we evaluated the effects of pure glyphosate and the formulations Durano TF and Roundup® LB plus in different concentrations on the fermentation pattern, community composition and metabolic activity of the rumen microbiota using the Rumen Simulation Technique (RUSITEC). Application of the compounds in three concentrations (0.1mg/l, 1.0mg/l or 10mg/l, n=4 each) for 9days did not affect fermentation parameters such as pH, redox potential, NH3-N concentration and production of short-chain fatty acids compared to a control group. Microbial protein synthesis and the degradation of different feed fractions did not vary among the treatments. None of the used compounds or concentrations did affect the microbial diversity or abundance of microbial taxa. Metaproteomics revealed that the present metabolic pathways including the shikimate pathway were not affected by addition of glyphosate, Durano TF or Roundup® LB plus. In conclusion, neither pure glyphosate, nor its formulations Durano TF and Roundup® LB plus did affect the bacterial communities of the rumen.

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No description available.

Hansson, L. Detektion av makrolidresistens hos Mycoplasma genitalium med Panther Fusion. Examensarbete i biomedicinsk laboratorievetenskal 15 högskolepoäng. Malmö universitet: Fakulteten för hälsa och samhälle, institutionen för Biomedicinsk Vetenskap, 2023.   Mycoplasma genitalium är en sexuellt överförbar mikroorganism som infekterar både män och kvinnor, som behandlas oftast med azitromycin med ett ökande problem av antibiotikaresistens. För M. genitalium är makrolidresistens det främsta hotet mot behandling, och har kopplats till fyra punktmutationer i region V i 23S rRNA-genen: A2071G, A2072G, A2072C samt A2071T (M. genitalium G-37, GenBank NR_077054.1). Projektet har undersökt möjligheten att ersätta nuvarande in house realtids-PCR metod för makrolidresistensbestämning med ett integrerat nukleinsyra-reningssteg och realtids-PCR med Panther Fusion (Hologic) hos Klinisk mikrobiologi i Lund. Under projektet analyserades 55 patientprover som samlades under perioden januari-februari 2023 i Region Skåne, som blivit positiva vid M. genitalium testning. Dessa prover har därefter analyserats av personal med nuvarande ABI-metod för resistensbestämning och sedan analyserats på Panther Fusion. Nuvarande ABI-metod resulterade i positiv signal för 91% (50/55) av patientprover positiva vid M. genitalium analys och makrolidresistensmutation hos 25 % (14/55), medan Panther Fusion metoden resulterade i positiv signal för 81 % (45/55) av positiva M. genitalium prover och påvisade resistensmutation hos 20 % (11/55) av proverna.

Despite the wealth of research into strategies for microbiome modulation, studies of microbiome management in pig hosts have found mixed results. A refined understanding of the patterns of microbiome assembly during the host’s early life, when management strategies are most commonly applied, is necessary for the development of successful management practices. Here, we study the development of the pig gut microbial community in a monitoring experiment, sampling the microbiome of pigs in a commercial farm intensively during the first month of life. We found that the community’s taxonomic richness increased linearly with host age. Furthermore, rapid changes across communities occurred in stages, and non-linear patterns in relative abundance were commonly observed among dominant taxa across host age, consistent with primary succession. Our results highlight the importance of understanding the patterns of microbiome assembly during host development, and identify successional stages as windows of opportunity for future research.

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No description available.

BTX biodegradation rates, biochemical expression patterns and microbial ecology were studied under anoxic (denitrifying), anoxic/microaerobic/aerobic, and anoxic/microaerobic conditions in activated sludge sequencing batch reactors. The studies showed that toluene and m-xylene were denitrified via benzoyl-CoA reductase. Although benzene, o-, and p-xylene were recalcitrant under denitrifying conditions, they were biodegraded under microaerobic (< 0.2 mg/L dissolved oxygen) and nitrate or nitrite (NOx)-supplemented microaerobic conditions. The patterns of the specific enzymes associated with BTX biodegradation under microaerobic conditions indicated that the three compounds were metabolized by oxygen-dependent pathways. The expression levels of catechol 1, 2-dioxygenase and catechol 2, 3-dioxygenase under microaerobic conditions were induced to levels as high as under aerobic conditions (> 4 mg/L dissolved oxygen). Benzene, o-, and p-xylene biodegradation rates were twice as fast under NO_x-supplemented compared to NO_x-free microaerobic conditions, and the specific biodegradation rates under aerobic and NO_x-supplemented microaerobic conditions were comparable. 16S rRNA probes targeting representative toluene-degraders were used to investigate the microbial communities in the three sequencing batch reactors by using a dot blot hybridization technique. The hybridization results suggest that multiple redox environments fostered a more diverse microbial community and the activities of the target organisms in the reactors with multiple redox environments were higher than in the single redox reactor. Additionally, facultative toluene-degraders appeared to play a less significant role than the strict anoxic and aerobic toluene-degraders in all three SBRs. / Ph. D.

Loss of nitrogen (N) from dairy manure during storage is an issue of economic, environmental, and social concern for farming communities. The lost N 1) decreases the value of manure as a fertilizer and is an economic loss because supplemental inorganic N fertilizer is purchased to meet N needs on farms; 2) produces the potential pollution for water and air systems, thereby damaging the associated ecosystems; 3) causes challenges to human health. Thus, it is vital to manage and use N in an efficient and eco-friendly manner. N mineralization is a pathway in the N cycle, which converts organic N to inorganic N that is more susceptible to loss. The objective of this study was to conduct lab-scale experiments to assess the effects of temperature, manure solids content, using manure seed and autoclave sterilization operation at the start of storage, and storage time on the N mineralization and the associated microbial community during the storage of liquid dairy manure. Manure scrapped from the barn floor of a commercial dairy farm and diluted to make experimental stocks with high (46 to 78 g/L) and low (19 to 36 g/L) total solids (TS), to simulate what is typically transported to the manure storage pit was used. The manure was incubated in the laboratory at three temperatures (10, 20, and 30°C) for two storage periods (60 and 180 days). Manure samples were taken at different storage time for analyses. The results showed that temperature and using sterilization operation at the start of storage had significant effects on N mineralization for both storage periods (p < 0.05). The highest N mineralization rate occurred at 30℃, which rate constant (k) was 0.096 week-1. While, the lowest N mineralization occurred at 10℃, and its corresponding k was 0.013 week-1. The concentrations of mineralized N (Nm) with non-sterilized (R) manure were significantly higher than that with sterilized (R0) manure (p < 0.05). Compared to that with high TS (H) manure, the concentrations of Nm were significantly higher with low TS (L) manure after 180-d storage (p < 0.05). Raw manure augmented with manure seed (MS) had significantly higher Nm than the manure seed only (SO) (p < 0.05). In order to investigate the changes of microbial community in manure, samples were collected on days 0, 30, 90, and 180 for the 180-d storage experiment, and days 0, 30, and 60 for the 60-d storage experiment, and then manure DNA under different condition was successfully extracted from collected samples and used for 16S rRNA sequencing. This study provided a more comprehensive understanding of the impact factors for manure storage, and was expected to clarify the relationship between N mineralization and the associated microbial community. / Master of Science / Loss of nitrogen (N) from dairy manure during storage is rooted in the process of degradation via microbial activities. During storage of dairy manure, up to 60% of N can be lost to the environment (the air, rivers, groundwater, etc.), causing damages such as global warming and water pollution. However, it is challenging to manage and reduce the N lost during manure storage because of lack of comprehensive knowledge of the complex microbial activities in manure storage structures. Thus, the long-term goal of this study is to discern the interactions of the physical, chemical, and microbial processes that affect the N transformation. The generated information will help to mitigate/minimize the loss of nitrogenous gases during storage of dairy manure. The specific objectives included: 1) to evaluate the effects of selected factors (including storage time, temperature, manure solids content, using manure seed and sterilization operation at the beginning of storage) on N mineralization during storage of liquid dairy manure and determine the associated N mineralization rate; 2) to reveal the microbial communities in stored liquid dairy manure under different conditions (listed above). The outcome of this study could be used to refine N mineralization input parameter of manure storage submodules of the process-based models such as Manure DeNitrification-DeComposition model (Manure-DNDC) and Integrated Farm System Model (IFSM) with the goal to improve their accuracy of estimating or accounting for the fate or cycling of N in dairy manure during storage.