Projects for Master Students


We are looking for motivated master's students to join ongoing research at the Department of Agricultural Ecology and Natural Resources (OKENV) of the Agricultural Institute of Slovenia. Our projects are grounded in long-term field experiments and real-world agricultural questions. Students can expect hands-on fieldwork and laboratory experience, mentorship, and the opportunity to contribute to publishable results.

Below you will find four open topics. If any of them resonates with you — or if you would like to discuss a related idea — get in touch.


Biodegradable mulch films and soil microbiomes

Single-use plastic in agriculture is a growing problem, and biodegradable mulch films are increasingly promoted as a solution. But do they actually break down in the field — and does the soil microbiome play a role in that process?

 

We have been running a multi-year field experiment since 2022 (Ptuj) and 2023 (Jable), comparing four PLA-based biodegradable films, a standard PE film, paper mulch, and bare soil across two pedologically distinct sites. The biodegradable films are incorporated into the soil at the end of each season; PE is removed. Soil samples have been collected every spring and are waiting for analysis.

 

What we want to understand: does repeated exposure to these films gradually enrich the soil with microorganisms capable of breaking them down — and if so, which ones?

 

This project might suit you if you are interested in:

–    soil microbiology, microbial ecology, or environmental microbiology

–    agricultural sustainability and the fate of materials in the environment

–    molecular methods (ddPCR) alongside classical cultivation-based approaches

 

What you can expect:

–    hands-on laboratory work: cultivation, isolation, and respirometry (IRGA)

–    experience with digital droplet PCR (ddPCR) for quantification of functional genes

–    access to a unique multi-site, multi-year sample archive

–    co-supervision with Dr. Kristina Ugrinović (Department of Plant Production, KIS)


Nutrient cycling in a 30-year fertilisation experiment

How does decades of different fertilisation practice shape the way soil microorganisms process carbon, nitrogen and phosphorus? This is the central question of this project, embedded in one of Slovenia's longest-running agricultural field experiments.

 

The IOSDV experiment at Jable (running since 1993) follows a three-year crop rotation — maize, winter wheat, oats — under three organic matter management systems: no organic fertilisation, farmyard manure, and straw incorporation with a catch crop. Each system is crossed with four mineral nitrogen rates. After more than 30 years, the soils in these treatments have diverged substantially, making this a rare platform for studying long-term agricultural impacts on soil function.

 

We want to quantify how microbial carbon use efficiency (CUE) — the fraction of assimilated carbon that ends up in biomass rather than CO₂ — differs across these systems, and what this means for nutrient availability and soil health.

 

This project might suit you if you are interested in:

–    biogeochemistry, soil ecology, or nutrient cycling

–    understanding how agricultural management shapes ecosystem function over time

–    combining field sampling with laboratory assays

 

What you can expect:

–    field sampling as part of the thesis — experience with long-term agronomic trial design

–    laboratory work: microbial biomass (fumigation-extraction), basal and substrate-induced respiration, enzyme assays (urease, phosphatase, β-glucosidase)

–    a clear applied question with policy relevance for sustainable fertilisation

 

Antimicrobial resistance genes in agricultural soils

Farmyard manure carries antimicrobial resistance genes (ARGs) into agricultural soils. Whether those genes persist, accumulate, or disappear over time depends on the soil environment — and remains poorly understood in long-term systems.

 

Using the same IOSDV experiment at Jable, we will compare soils that have received farmyard manure every three years for over 30 years against plots with no organic fertilisation. Fresh manure samples collected at the time of application will serve as the input reference. By tracking ARGs from manure into soil and across time, we aim to assess whether long-term manure application leads to a measurable and lasting enrichment of resistance genes — and what that might mean for environmental and human health.

 

This project might suit you if you are interested in:

–    microbiology, environmental health, or one health perspectives

–    molecular microbiology and the ecology of antibiotic resistance

–    connecting agricultural practice to public health questions

 

What you can expect:

–    fieldwork: soil and manure sampling within an active long-term experiment

–    laboratory work: environmental DNA extraction, quantification of ARGs and mobile genetic elements by qPCR or ddPCR

–    a topic at the intersection of agronomy, microbial ecology, and health sciences

 

Bioinformatics for soil microbiome data

Across our projects, we generate substantial metagenomic datasets — both amplicon sequencing (16S rRNA, ITS) and shotgun metagenomics. Each project has so far followed its own analytical path, which limits cross-project comparisons and reproducibility.

 

We are looking for a student with a bioinformatics background who would help us build a shared, standardised analytical foundation: evaluating and comparing established pipelines, running sensitivity analyses on processing decisions, and implementing a documented, reproducible workflow that can be applied across projects. The end product would become a working tool for the department — not just a thesis chapter.

 

This project might suit you if you are interested in:

–    bioinformatics, computational biology, or data science applied to ecology

–    microbiome analysis and the methodological choices behind it

–    building tools that others will actually use

 

What you can expect:

–    hands-on work with real, multi-project datasets (amplicon and/or shotgun)

–    experience with standard microbiome tools: QIIME2, DADA2, Kraken2, HUMAnN3, eggNOG-mapper

–    pipeline development in Snakemake or Nextflow

–    a concrete, infrastructure-level contribution to ongoing departmental research

 

Interested?

If any of these topics interests you, or if you would like to discuss a related idea before applying formally, feel free to reach out: nejc.stopnisek@kis.si

Please mention which project(s) you are interested in and include a brief description of your background. Applications from students across agronomy, biology, microbiology, biochemistry, bioinformatics and related fields are all welcome.


Wheat microbiome 

We recently launched a 3-year project, WHEATSHIELD, focused on exploring the wheat microbiome and its potential to enhance drought tolerance in this globally important crop. This project offers multiple opportunities for master’s students from diverse academic backgrounds to contribute and develop their theses. Here are a few examples:

If you are interested in any of these topics or would like to propose a project aligned with our research, feel free to contact us!