Doctoral Thesis

Encapsulation of microorganisms for application in agriculture

Final Thesis 9.85 MB

Author of thesis: Ing. Diana Černayová, Ph.D.

Acad. year: 2025/2026

Supervisor: prof. Ing. Stanislav Obruča, Ph.D.

Reviewers: Assoc. Prof. Wojciech Bialas, PhD., Prof. Dr.-Ing. Jochen Schmid

Abstract:

Plant Growth-Promoting Rhizobacteria (PGPR) serve as effective bioinoculants that stimulate plant growth and enhance soil fertility. Encapsulating PGPR within hydrogel matrices provides a protective environment that improves their survival, stability and overall bioactivity in agricultural applications. This dissertation presents a novel self-encapsulation method employing Azotobacter vinelandii, a bacterium capable of synthesizing its own alginate, a natural exopolysaccharide that forms a stable gel upon Ca2+ crosslinking. Six A. vinelandii strains from German and Czech microbial collections were investigated for their growth performance, alginate yield and plant growth-promoting traits. Among them, strains DSM 87, DSM 720 and CCM 289 produced the alginate concentrations (4.9 ± 0.6 g/L, 3.5 ± 0.5 g/L and 2.2 ± 0.3 g/L, respectively) with easy ability to form strong gels. These strains also demonstrated strong PGPR activities, including indole-3-acetic acid production (up to 10.5 μg/mL), siderophore synthesis and phosphate solubilization. Further experiments focused on different gelation possibilities including multivalent ions, organic acids and gelation in the whole volume by dissolving insoluble CaCO3 presented in the cultivation media. Focusing on application and industrial potential of this process for biofertilizer production, the entire procedure was up-scaled to bioreactors, where the effects of agitation speed and filling volume were tested for strain DSM 87. To evaluate the plant growth-stimulation properties of the obtained bacterial gels, lettuce plants were cultivated under different treatment conditions. The results demonstrated that bacterial gelled cultures positively influenced plant growth and improved plant survival under drought stress.
This work demonstrates a cost-effective and environmentally sustainable approach to bioinoculant production by using A. vinelandii’s alginate-forming capacity, providing a promising alternative to conventional biofertilization methods.

Keywords:

Plant growth-promoting rhizobacteria, PGPR, alginate, polyhydroxyalkanoates, biopolymers, bioinoculants, agriculture, cultivation experiments

Date of defence

22.01.2026

Result of the defence

Defended (thesis was successfully defended)

znamkaPznamka

Process of defence

Obhajoba probíhala v angličtině. Jeden ze zahraničních oponentů prof. Schmid se připojil prostřednictvím MS Teams. Předsedkyně komise představila doktorandku a předala jí slovo. Ing. Černayová absolvovala v roce 2023 pedagogické minimum. V roce 2023 absolvovala stáž ve Švédsku. Již nyní má určité pracovní zkušenosti. Je spoluautorkou 3 článků v časopisech s impakt faktorem. Je také spoluautorkou celé řady konferenčních příspěvků. Language of a defence was English. One of the foreign reviewers, Prof. Schmid, joined via MS Teams. The chairwoman of the committee introduced the doctoral student and gave her the floor. Ing. Černayová completed her pedagogical minimum in 2023. In 2023, she also completed an internship in Sweden. She already has some work experience. She is a co-author of three articles in journals with an impact factor. She is also a co-author of numerous conference papers.

Language of thesis

English

Faculty

Department

Study programme

Biophysical Chemistry (DKCP_BCH)

Composition of Committee

prof. RNDr. Ivana Márová, CSc. (předseda)
doc. Ing. Barbora Branská, PhD. (člen)
doc. Mgr. Pavel Dvořák, Ph.D. (člen)
prof. Mgr. Marek Koutný, Ph.D. (člen)
doc. Ing. Petr Sedláček, Ph.D. (člen)
Prof. Dr.-Ing. Jochen Schmid (člen)
Assoc. Prof. Wojciech Bialas, PhD. (člen)

Ing. Diana Černayová prepared her doctoral dissertation as part of full-time study in the PhD programme Biophysical Chemistry at the Faculty of Chemistry, Brno University of Technology. She commenced her doctoral studies in September 2020 and submitted her dissertation in October 2025.

During her PhD studies, the doctoral candidate successfully completed all required examinations and passed the state doctoral examination. An integral part of her training also included an international research internship – in 2023, she completed a six-month research stay at Lund University in Sweden.

In addition to her dissertation work, the student actively participated in the implementation of several research projects throughout her doctoral studies. One of the GAČR projects was largely based on her experimental work and results, and her research has provided a foundation for follow-up studies which have continued to develop and expand upon her findings.

Furthermore, she made a significant contribution to teaching activities at the Faculty of Chemistry, Brno University of Technology, particularly through student consultations and by supervising a number of bachelor’s and master’s theses. As part of her doctoral training, she also completed a certified course in pedagogical fundamentals required for secondary school teaching.

The achieved results were published in three papers in internationally recognised journals with a high impact factor. The candidate is the first author of one publication and the second author of the remaining two. Ing. Diana Černayová is also the author or co-author of several conference contributions presented at both national and international conferences. Notably, she received the Best Poster Award at the International Conference on Chemical Technology held in Mikulov in 2023.

Within her dissertation research, the student focused on a novel concept for the preparation of microbial inoculants for agricultural applications. This new approach is based on the encapsulation of bacteria within a gel matrix, where gelation is achieved using extracellular polysaccharides produced directly by plant growth-promoting bacteria (so-called self-encapsulation). Within this concept, the student carried out all key experimental activities, including the screening of suitable bacterial strains, optimisation of cultivation conditions and the gelation process of microbial suspensions, as well as the verification of the effectiveness of the prepared formulations through pilot pot experiments.

The student summarised the most important experimental results achieved during her doctoral studies in a well-prepared dissertation written in English. The Results and Discussion section is divided into several thematic chapters and is complemented by parts outlining the contribution of the submitted work to the current state of knowledge as well as future perspectives in the field.

Ing. Diana Černayová is a well-rounded individual who, during her studies and international research internship, achieved a high level of professional independence and demonstrated the ability to conduct both independent and collaborative scientific research. She repeatedly proved her strong motivation, work ethic, and responsible approach to assigned tasks. Her friendly and positive attitude towards colleagues and students, as well as her willingness to provide support, also deserve special recognition.

In view of the above and in accordance with the applicable legislation, I recommend that the dissertation be accepted for defence and, upon its successful defence, that Ing. Diana Černayová be awarded the academic degree Ph.D.
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Posudek oponenta [.pdf] 801,50 kB

Reviewer’s report
Prof. Dr.-Ing. Jochen Schmid

File inserted by the reviewer Size
Posudek oponenta [.pdf] 549,85 kB

Responsibility: Mgr. et Mgr. Hana Odstrčilová