Bakteriální interakce a sekundární metabolity v rostlinném a půdním prostředí

Actinobacteriota představují jeden z nejvýznamnějších bakteriálních kmenů v rostlinném a půdním prostředí. Actinobacteriota jsou známá svou schopností produkovat sekundární metabolity, a proto mohou různými způsoby ovlivňovat jiné bakterie a rostliny. Táto práce byla zaměřena na posouzení souvislostí mezi produkcí sekundárních metabolitů a interakcemi aktinobakterií. V první části jsme hodnotili, jak aktinobakterie z kyselé půdy ovlivňují kultivovatelné půdní bakterie. Získali jsme sbírku kmenů aktinobakterií z kyselé půdy, ve které dominuje dříve nekultivovatelná skupina. Izolovali jsme zástupce této skupiny a popsali jsme novou čeleď Treboniaceae, ale také několik dalších potenciálně nových druhů známých rodů. Analýza genomu a metabolomu nového druhu Trebonia kvetii, sp.nov. gen.nov., prokázala jeho schopnost produkovat neobvyklé a potenciálně nové bioaktivní metabolity. Navrhli jsme pokus, ve kterém byl vždy jeden aktinobakteriální kmen pěstován společně s celým půdním bakteriálním společenstvem tak, aby byla umožněna volná výměna metabolitů. Pro tuto interakci byly vybrány tři kmeny pocházející z různých linií. Každý kmen významně a specificky ovlivňoval kultivovatelné bakterie a také produkci metabolitů, z nichž byla také část indukovana společnou kultivací. Ve druhé části práce jsme zkoumali...Phylum Actinobacteriota represents one of the major phyla in plant and soil environments. Known for the ability to produce numerous secondary metabolites, Actinobacteriota may affect other bacteria and plants in various ways. The thesis aimed at assessing the connection between the production of secondary metabolites and interactions of actinobacteria in plant and soil environments. In the first part, we assessed how rare actinobacteria from acid soil affect cultivable soil bacteria. We isolated a collection of actinobacteria from acid soil dominated by previously uncultivable lineage and isolated a representative described as a new family Treboniaceae and multiple other potentially novel species of known genera. The genome and metabolome analysis of Trebonia kvetii, sp.nov. gen.nov., demonstrated its ability to produce unusual and potentially novel bioactive metabolites. We designed an experiment where a single strain was co-cultivated with the total soil bacterial community of the same soil in a set up, where a free exchange of diffusible metabolites was allowed between them. Three actinobacteria strains coming from distinct lineages were selected for this interaction. Each strain significantly and specifically affected cultivable bacteria as well as the metabolite pool, part of which was induced...Katedra genetiky a mikrobiologieDepartment of Genetics and MicrobiologyPřírodovědecká fakultaFaculty of Scienc

Isolation of streptomycetes causing common scab from 3-years old potato samples from South America

In this paper, we aimed at assessing the best conditions for the isolation of actinobacteria from old potato samples. A set of media and pretreatments were tested. The optimal were chosen for the isolation of actinobacteria from potatoes from Peru, Chile and Argentina. Isolates were tested on the presence of thaxtomin phytotoxin by amplification of the respective gene. Phylogenetic position of strains was compared with their geographical origin, pathogenic potential and existence of common scab (CS) symptoms on potato sample. We demonstrated that RNAlater can be successfully used for the long-term preservation of potato peel for subsequent isolation of actinobacteria on R2A medium. Many streptomycetes were thaxtomin-positive, though they are distantly-related to described pathogens causing CS. Genus Nocardia was first reported to be thaxtomin-positive. Potentially pathogenic strains were isolated not only from infected potato but also from those lacking CS symptoms. Some strains from scabby potatoes were thaxtomin-negative.EEA BalcarceFil: Rapoport, Daria. Charles University in Prague. Faculty opf Science, República Checa. Crop Research Institute, Laboratory of Epidemiology and Ecology of Microorganisms, República Checa.Fil: Patrmanova, T. Crop Research Institute, Laboratory of Epidemiology and Ecology of Microorganisms, República Checa.Fil: Kopecky, J. Crop Research Institute, Laboratory of Epidemiology and Ecology of Microorganisms, República Checa.Fil: Mareckova, M. Crop Research Institute, Laboratory of Epidemiology and Ecology of Microorganisms, República Checa. Czech University of Life Sciences, Faculty of Agrobiology, Food, and Natural Resources, Department of Microbiology, República Checa.Fil: Clemente, Gladys. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina.Fil: Salvalaggio, Andrea Eugenia. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina

A Short-Term Response of Soil Microbial Communities to Cadmium and Organic Substrate Amendment in Long-Term Contaminated Soil by Toxic Elements

Two long-term contaminated soils differing in contents of Pb, Zn, As, Cd were compared in a microcosm experiment for changes in microbial community structure and respiration after various treatments. We observed that the extent of long-term contamination (over 200 years) by toxic elements did not change the total numbers and diversity of bacteria but influenced their community composition. Namely, numbers of Actinobacteria determined by phylum specific qPCR increased and also the proportion of Actinobacteria and Chloroflexi increased in Illumina sequence libraries in the more contaminated soil. In the experiment, secondary disturbance by supplemented cadmium (doses from double to 100-fold the concentration in the original soil) and organic substrates (cellobiose or straw) increased bacterial diversity in the less contaminated soil and decreased it in the more contaminated soil. Respiration in the experiment was higher in the more contaminated soil in all treatments and correlated with bacterial numbers. Considering the most significant changes in bacterial community, it seemed that particularly Actinobacteria withstand contamination by toxic elements. The results proved higher resistance to secondary disturbance in terms of both, respiration and bacterial community structure in the less contaminated soil

Bacterial interactions and secondary metabolites in plant and soil environment

Phylum Actinobacteriota represents one of the major phyla in plant and soil environments. Known for the ability to produce numerous secondary metabolites, Actinobacteriota may affect other bacteria and plants in various ways. The thesis aimed at assessing the connection between the production of secondary metabolites and interactions of actinobacteria in plant and soil environments. In the first part, we assessed how rare actinobacteria from acid soil affect cultivable soil bacteria. We isolated a collection of actinobacteria from acid soil dominated by previously uncultivable lineage and isolated a representative described as a new family Treboniaceae and multiple other potentially novel species of known genera. The genome and metabolome analysis of Trebonia kvetii, sp.nov. gen.nov., demonstrated its ability to produce unusual and potentially novel bioactive metabolites. We designed an experiment where a single strain was co-cultivated with the total soil bacterial community of the same soil in a set up, where a free exchange of diffusible metabolites was allowed between them. Three actinobacteria strains coming from distinct lineages were selected for this interaction. Each strain significantly and specifically affected cultivable bacteria as well as the metabolite pool, part of which was induced..

Development of a tool for digital terrain analysis

Component of many hydrological applications using digital terrain models is the calculation of flow accumulation and specific catchment area, which are broadly used conceptions in hydrological modelling. The goal of this diploma thesis was a proposal of tools for calculation of flow accumulation and specific catchment area by Multiple Flow Direction (MFD) algorithm as more appropriate for many hydrological applications then Single Flow Direction algorithm built-in in ArcGIS. The toolset should serve as an educational and research tool at the Faculty of Environmental Sciences, CULS, but not only there. The theoretical part of the thesis gives examples of digital terrain models applications in general and in hydrology, summarizes basic methods that define flow direction and flow accumulation of surface runoff in grid-based terrain models and their significance for hydrological modelling. Selected methods and their implementations are described in details in methodological part of the thesis. The tools were created in Python language and may be used in ArcGIS interface. The functionality of the toolset was tested on a coarse-resolution hydrologically correct digital terrain model of basin Moravian Dyje and simulation results has been extensively compared to those produced by Single Flow direction algorithm. It is suggested that created toolset would be developed further in direction of calculation of additional related terrain attributes (e.g.Topographic Wetness Index), river network extraction with MFD, dealing with flat and sink areas in input DEM, and other flow direction algorithms implementation

Micronutrients and Soil Microorganisms in the Suppression of Potato Common Scab

Nature-friendly approaches for crop protection are sought after in the effort to reduce the use of agrochemicals. However, the transfer of scientific findings to agriculture practice is relatively slow because research results are sometimes contradictory or do not clearly lead to applicable approaches. Common scab of potatoes is a disease affecting potatoes worldwide, for which no definite treatment is available. That is due to many complex interactions affecting its incidence and severity. The review aims to determine options for the control of the disease using additions of micronutrients and modification of microbial communities. We propose three approaches for the improvement by (1) supplying soils with limiting nutrients, (2) supporting microbial communities with high mineral solubilization capabilities or (3) applying communities antagonistic to the pathogen. The procedures for the disease control may include fertilization with micronutrients and appropriate organic matter or inoculation with beneficial strains selected according to local environmental conditions. Further research is proposed to use metagenomics/metabolomics to identify key soil–plant–microbe interactions in comparisons of disease-suppressive and -conducive soils