Scientific Publications
The scientific publications, conference papers,
and academic articles produced within the scope of
SoilBiom’s research activities are brought together on this page.
Understanding Soil Through Scientific Research
SoilBiom’s scientific publications consist of field studies conducted under different production conditions, laboratory analyses, and the outputs of academic research.
These studies address the biological, chemical, and physical processes of soil in an integrated manner, aiming to present the relationship between production, ecosystem health, and sustainability through scientific evidence.
Each published study is based on measurable results and comparative analyses.
Below, you can find scientific studies published by SoilBiom under different research themes.
Effects of Native Plant Growth-Promoting Rhizobacteria on Rhizome Development and Plant Growth of Trachystemon orientalis
Hatice Filiz Boyacı, Merve Erbil, Atakan Yıldız, Keziban Yazıcı, Umut Ferhat Başpınar
One of the key strategies for increasing agricultural productivity and sustainability is the use of plant growth-promoting rhizobacteria (PGPR) and their formulated microbial consortia.
This study aimed to determine the effects of PGPR on rhizome development and plant growth of Trachystemon orientalis, a species known for its capacity to enhance nutrient uptake from soil.
Eleven different rhobacteria isolated from the tea rhizosphere were evaluated, and six different microbial consortium combinations were prepared based on their beneficial effects. The consortia were applied to Trachystemon orientalis rhizomes planted in a 1:1 (v/v) peat-perlite medium.
The experiment was established in a randomized block design with three replications. Each replication included five rhizomes, and untreated rhizomes were used as controls.
Results showed that PGPR consortia had significant effects on 14 evaluated parameters related to rhizome development and plant growth. Correlation analysis revealed strong relationships among the examined parameters.
The highest performance was obtained from the P4 application, which included a mixture of Pseudomonas putida and Bacillus spp. The microbial mixture was found to be applicable in seedling cultivation of Trachystemon orientalis due to its beneficial and stable performance.
Keywords: Rhizobacteria, Quality, Microbial community, Sustainable agriculture, Bacillus spp., Pseudomonas spp.
Evaluation of Five Primer Pairs for Environmental DNA Metabarcoding of Central European Fish Species Using Mock Communities
Till-Hendrik Macher, Robin Schütz, Atakan Yıldız, Arne J. Beermann, Florian Leese
Environmental DNA (eDNA) metabarcoding has become a powerful tool for assessing fish communities. Before eDNA-based assessments can be widely implemented in regulatory monitoring contexts such as the EU Water Framework Directive, methodological standardization is required.
To ensure methodological accuracy and compatibility with regulatory standards, various sampling, laboratory, and bioinformatics workflows have been developed.
A critical prerequisite for comprehensive fish monitoring is the selection of appropriate primer pairs capable of accurately identifying fish species present in a given water body. Although several fish-specific primer pairs targeting different genetic marker regions have been published over the past decade, no dedicated study had systematically evaluated commonly used primer pairs for Central European fish species.
In this study, we constructed a mock community consisting of DNA from 45 Central European fish species and assessed the detection performance and repeatability of five primer pairs. We evaluated the effects of primer choice and bioinformatic filtering on eDNA metabarcoding outcomes.
Among the tested primer pairs, the tele02 (12S gene) primer pair showed the best overall performance for metabarcoding Central European freshwater fish. MiFish-U (12S) and SeaDNA-mid (COI) also demonstrated high detection performance and repeatability. In contrast, more general vertebrate-targeting primer pairs produced lower reliability and higher rates of false-positive and false-negative detections.
Our findings demonstrate that careful selection of primer pairs and bioinformatic analysis pipelines can substantially improve the reliability of eDNA metabarcoding for fish biomonitoring.
Keywords: 12S, 16S, biomonitoring, COI, environmental DNA (eDNA)
The Role of Soil Microbiota in Ecosystem Health and Sustainable Tea Cultivation: Insights from eDNA and Metagenomic Approaches
Atakan Yıldız
This study examines the composition of microbial communities in soils used for tea cultivation and their contribution to ecosystem functions through environmental DNA (eDNA) metabarcoding and metagenomic approaches.
Results obtained through culture-independent methods indicate that the dominant bacterial phyla in tea soils are Firmicutes, Proteobacteria, Actinobacteriota, Acidobacteriota, and Chloroflexi.
Seasonal comparisons revealed that the relative abundance of Proteobacteria and Actinobacteriota was higher in winter samples than in summer samples. These findings suggest that microbial community structure varies depending on environmental conditions and management practices.
Overall, the results highlight the critical importance of local microbial diversity for soil health, resilience, and sustainable agricultural production.
Unravelling the Role of Indigenous PGPB in Corm Development and Mineral Acquisition of Freesia hybrida: A Multivariate Perspective
Ümmü Özgül Karagüzel, Ergül Erkuş, Sümeyye İslam, Atakan Yıldız
This study investigated the effects of indigenous plant growth-promoting rhizobacteria (PGPB) consortia on corm development and mineral acquisition in Freesia hybrida grown under greenhouse conditions. Microbial consortia composed of bacterial strains isolated from the rhizosphere of tea plants were evaluated and compared with a chemical fertiliser treatment and a non-treated control.
Morphological and physiological parameters including corm number, corm weight, corm diameter, leaf area, chlorophyll content and mineral nutrient concentrations were analysed to determine the influence of microbial inoculations on plant growth and development. The results demonstrated that several bacterial consortia significantly enhanced plant growth, corm formation and nutrient uptake compared with the control treatment.
Multivariate statistical analyses revealed strong relationships between microbial applications and the measured plant development parameters. Overall, the findings highlight the potential of indigenous PGPB consortia as sustainable biofertiliser alternatives that can reduce reliance on chemical fertilisers in ornamental plant production systems.
Keywords: Plant growth-promoting rhizobacteria, PGPB, microbial consortia, Freesia hybrida, nutrient uptake, sustainable horticulture