Final topic is to be determined together with the candidate.  

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For more details on our work. 

Topic: Microbial biocatalytic aggregated systems for improving interactions between microorganisms and plants

Scientific advisors: dr. Tomaž Rijavec (advisor), dr. Aleš Lapanje (co-advisor)

Aim:  Based on the analyses of natural structures, we assume that understanding the spatial arrangement of cells and their interactions with other cells in the consortium and other components of the artificially aggregated system is of key importance for studying any microbial activity. In the research program, the candidate will focus on constructing and studying different types of consortia and attempting to understand the parameters that influence microbial activity, thereby improving microbial interaction with the host plant.

Apart from scientific research work, the candidate will also learn important soft skills that are important for her/his future scientific work, such as the concept of scientific thinking and hypothesis generation, research planning and conducting laboratory experiments. During the training, she/he will learn how to prepare scientific publications, patents and project documentation and will become familiar with project management approaches.

Background: Microbial-based biocatalytic aggregated systems are artificially constructed consortia that can be obtained from natural samples or prepared by combining individual previously isolated strains. Artificially aggregated microbial cells can form three-dimensional aggregates suspended in a liquid or two-dimensional biofilms formed on surfaces. The functional properties of these structures can enable improved leaching of minerals necessary for plant growth, optimization of intercellular nutrient transfer in nitrogen fixation, faster and more efficient degradation of pollutants, valorization of biopolymers, and increased interspecific interactions, which, greatly contribute to the improved use of strains for the purposes of biocontrol of plant pathogens. In all cases, the spatial arrangement of cells needs to be properly evaluated from the perspective of understanding the activity of microorganisms and their interaction with plants. 

The research work will mainly be conducted in the Group for Colloid Biology (biocolloid.ijs.si) at the Department of Environmental Sciences (environment.si), Reactor Centre Podgorica, JSI. It will directly involve the use of different interdisciplinary methodologies, (i) methods in colloid biology (cell surface modification, immobilization, aggregation, biofilm construction, flow cytometry, particle size measurement), (ii) molecular biology techniques (nucleic acid isolation, PCR, sequencing), (iii) microscopy (time-resolved fluorescence, confocal, SEM) and (iv) chemical analyses, available to the candidate within the research group, the Department and the Institute, as well as the collaborative network of international partners (SurfBio Innovation Hub). 

Key words: bacteria, aggregate, plant-microbe interactions, artificial consortium

Topic: Spatial succession of bacterial communities.  

Background: Functional properties of bacterial communities enable them to be used in biotechnological, remediation or agricultural applications. Be it natural or synthetically prepared, the communities should be stable in order to be up-scaled and used in applications, to perform the function they were selected for, e.g. degradation of target compound/s or production or transformation of selected compound/s. Here, we hypothesize that quantitative parameters, not only ratio of strains and their activities, but more importantly, the parameters such as microgeograhic positioning of each of the members can importantly determine further succession of the community. 

Aim: We need to understand the stability of bacterial communities, particularly synthetic, over a longer period of time. It is crucial to understand whether the community structure changes during biomass growth and after it is applied in situ. Even more importantly, since the communities can be spatially structured in the form of aggregates or biofilms, we need to examine how these structures develop over a longer time period and how stable they are.   

Keywords: bacteria, cell aggregates, community succession

Topic: The physiology of physically entrapped bacterial cells

Background: Physical entrapment can change the physiology of a cell as it could theoretically prevent cell growth, division and exchange of nutrients. Preliminary experiments on bacterial encapsulation into rigid multi-layered nano-thick coatings have shown changes in cell morphology and metabolic activity, but it is not clear how the structure of the cell is changed or how the expression of genes is altered due to the physical pressure on the cell.

Aim: The study will focus on characterizing the morphological changes and changes in gene expression that arise due to the physical entrapment of bacterial cells. Physical entrapment of bacteria is also the natural state of bacteria in aggregates and biofilms present in the environments and this research will give important information of contribution of physical constraints solely on the physiological response in these conditions that microbes are faced with. 

Key words: cell encapsulation, gene expression, layer-by-layer encapsulation, nano-capsule