This seminar series aims to provide a platform for early career researchers (including PhD candidates) to present their research and stimulate discussion on a diverse set of topics related to seed microbiomes.

Join us

The presentations take place online (~20 min + 10 min Q&A) via Teams, on the first Thursday of the month at 15:00-16:30 CET every three months (September, December, March and June). To stimulate discussion and allow for the presentation of ongoing work, the talks are not recorded.

Seminar organizers Carolina Lobato and Makrina Diakaki


Spinach Seed Microbiota and the Suppression of Globisporangium ultimum damping-off

Makrina Diakaki (Wageningen University & Research)

June 5, 2025 at 3 pm CET

Abstract:

Recently we demonstrated that the seed microbiome of certain spinach (Spinacia oleracea) seed lots can confer disease suppression against Globisporangium ultimum damping-off (previously known as Pythium ultimum). We hypothesized that differences in the microbial community composition of spinach seed lots correlate with the levels of damping-off suppressiveness of each seed lot. Here, we show that a large proportion of variance in seed-associated bacterial (16S) and fungal (Internal Transcribed Spacer 1) amplicon sequences was explained by seed lot identity, while 9.8% of bacterial and 7.1% of fungal community variance correlated with disease suppression. More specifically, a higher relative abundance of basidiomycetous dimorphic yeasts such as Vishniacozyma, Filobasidium, and Papiliotrema and of the bacterial genus Massilia was a key feature of suppressive seed microbiomes. We suggest that the abundance of these genera is indicative of seed lot suppressive potential. Seed processing and treatment can become more targeted with indicator taxa being used to evaluate the presence of beneficial seed-associated microbial functions. This process, in turn, could contribute to the sustainable management of seedling diseases. Finally, this study highlights the ubiquity of yeasts in spinach seed microbiota and their potential beneficial roles for seed health. For more info, please see our recent paper.”

About the presenter:

Makrina is a Plant Biologist with a specialization in sustainable cropping systems. She started her PhD in July 2020 studying the role of the seed microbiome in seed health and seed resilience against pathogens. Makrina holds a BSc Hons in Biological Sciences (Plant Science) from the University of Edinburgh (UK), and a Plant Health Erasmus Mundus Joint Master Degree from the University of Goettingen (Germany) and the Polytechnic University of Valencia (Spain). She also completed a one year traineeship at the European Food Safety Authority (Italy) as part of the Pest Surveillance Working Group of the Plant Health team. Her academic interests include the seed microbiome, phytopathology, disease suppression, microbial ecology and sustainable approaches in agriculture, especially in relation to plant health.

Unveiling the Seed Resistome: Dissemination Pathways and Environmental Influences

Xin-Yuan Li (Zhejiang University)

June 5, 2025 at 3 pm CET

Abstract:

Although evidence of antibiotic resistance spreading through the plant microbiome is growing, research on the antibiotic resistome in seeds, a key reproductive organ and food source, remains limited. We integrate findings from microcosm and field experiments to investigate how environmental factors, including long-term organic fertilization and elevated CO2, shape the seed resistome. We detected diverse antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in seed endophytes, with organic fertilization enhancing their numbers and abundance, and further impacted the relative abundance of ARGs in progeny rhizosphere. Furthermore, elevated CO2 significantly increased seed ARG abundance, altered bacterial and fungal communities, and strengthened bacteria–fungi interactions, further influencing resistome dynamics. Structural equation models revealed that seed resistomes play a pivotal role in ARG transmission to progeny rhizosphere soils, emphasizing their potential as resistome reservoirs. These findings highlight the overlooked contribution of plant seeds to antibiotic resistance dissemination and underscore the need for further research on their role in microbial resistance evolution within agroecosystems and under climate change. For more info, please see our papers on organic fertilization and free-air CO2 enrichment.

About the presenter:

Xin-Yuan Li is a PhD candidate in the labs of Yong-Guan Zhu and Xian-Yong Lin at Zhejiang University, as well as a guest researcher in Gabriele Berg’s lab at Graz University of Technology. Her research explores how environmental factors shapes plant health through plant microbiome, with a focus on seed microbiome and resistomes. Her long-term goal is to investigate how the assembly of seed microbial community is influenced by environmental factors, especially in the context of long-term climate change, and their implications for plant health and sustainable agriculture.

TBD

Verena Gschiel (University of Southampton)

September 18, 2025 at 3 pm CET

Abstract:

Not available

About the presenter:

Not available

TBD

Gillian Bergmann (University of California, Davis)

September 18, 2025 at 3 pm CET

Abstract:

Not available

About the presenter:

Gillian is an ecology PhD candidate in the labs of Johan Leveau and Rachel Vannette at UC Davis, as well as a visiting graduate researcher with the EmerSys team at INRAE-IRHS. She is particularly interested in how various processes can contribute to microbial transmission between floral stigmas and developing seeds across spatial scales. In the long-term, she aims to study microbial community assembly processes across the seed life cycle, document the microbial diversity of seed communities, and relate assembly outcomes to seedling health. She is an NSF Graduate Research Fellow and a UC Davis Dean’s Distinguished Graduate Fellow.