Biology subjects

Berendsen, R. L.

Publications and source records attributed to Berendsen, R. L..

4 recordsLinked to original sources

bioRxiv2026

Root gene regulatory network analysis reveals roles for defense hormones and secondary metabolites in establishment of disease-suppressive soil

Plants recruit beneficial microbiota in their rhizosphere to alleviate stresses. In Arabidopsis thaliana, foliar infection by Hyaloperonospora arabidopsidis (Hpa) has been shown to establish a disease-suppressive microbiome that promotes protection against Hpa infection of the subsequent plant generation grown in this conditioned soil - a phenomenon known as soil-borne legacy (SBL). The root responses involved in SBL establishment have remained largely unclear. In this study, time-series RNA-seq of roots from Hpa-infected plants grown in natural soil was conducted over seven days post-inoculation. A gene regulatory network of the responding roots was constructed. The role of predicted key components was verified in follow-up assays. Root transcriptional reprogramming started within one day after foliar infection. Genes associated with salicylic acid (SA)-mediated defense were upregulated, while those linked to secondary metabolism and jasmonic acid (JA) responsiveness were downregulated. SA accumulation increased at 1 dpi, and JA decreased by 3 dpi. Transcriptional regulation occurred primarily in the tips of the roots. Mutant analyses confirmed that SA, JA, indole glucosinolates, camalexin, and flavonoids contribute to SBL establishment. Our findings reveal rapid systemic transcriptional reprogramming in roots upon foliar pathogen attack, uncovering novel roles of hormone signaling and secondary metabolism in shaping a disease-suppressive soil beyond their known defense functions.

plant biology↗

bioRxiv2025

Microbiome responses to natural Fusarium infection in field-grown soybean plants

The rhizosphere microbiome influences plant health by mediating plant-pathogen interactions. Plants can recruit protective microbes in response to disease, but the consistency of this process in field conditions is unclear. We examined the rhizosphere microbiome of field-grown soybean (Glycine max L.) naturally infected with root pathogens across three commercial fields in Kentucky, USA. Symptomatic and asymptomatic plants were sampled to assess disease-associated shifts in the rhizosphere microbiome. Amplicon sequencing identified a diverse Fusarium community, with one Fusarium solani amplicon sequence variant (ASV) consistently enriched in diseased plants, identifying it as the likely pathogen. While microbial communities differed between diseased and healthy plants, these shifts were largely field-specific. Several fungal ASVs with known biocontrol potential (Clonostachys rosea, Penicillium, and Trichoderma) were enriched in healthy plants, implying a role in disease suppression. A Sphingomonas ASV, a genus previously linked to plant protection, was more abundant in diseased plant rhizospheres in two fields, suggesting pathogen-triggered recruitment. Conversely, Macrophomina phaseolina, a generalist root pathogen, was enriched in the rhizosphere of diseased plants in all fields, indicating possible co-infection with F. solani. These findings reveal complex pathogen-microbe interactions in field conditions and emphasize the need for field-specific microbiome research to inform sustainable disease management strategies.

plant biology↗

bioRxiv2024

Seed tuber microbiome is a predictor of next-season potato vigor

Potato vigor, an important agronomic trait, is heavily influenced by the field of seed tuber production. Soil microbiota vary significantly between fields, impacting plant health and crop yield. Our study demonstrates that seed potato vigor can be predicted based on microbiota associated with seed tuber eyes, the dormant buds that grow out in the next season. By combining time-resolved drone-imaging of potato crop development with microbiome sequencing of seed tuber eyes from 6 varieties produced in 240 fields, we established correlations between microbiome fingerprints and potato vigor parameters. Employing Random Forest algorithms, we developed a predictive "Potato-Microbiome Informed" model, revealing variety-specific relationships between seed tuber microbiome composition and next seasons potato vigor in trial fields. The model accurately predicted vigor of seed tubers to which the model was naive and pinpointed key microbial indicators of potato vigor. By connecting variety-specific microbiome fingerprints to crop performance in the field, we pave the way for microbiome-informed breeding strategies.

microbiology↗

bioRxiv2023

Seed tuber imprinting shapes the next-generation potato microbiome

Potato seed tubers are colonized and inhabited by soil-borne microbes, some of which can positively or negatively impact the performance of the emerging daughter plant in the next season. In this study, we investigated the intergenerational inheritance of microbiota from seed tubers to next-season daughter plants by amplicon sequencing of bacterial and fungal microbiota associated with tubers and roots of two seed potato genotypes produced in six different fields. We observed that field of production and potato genotype significantly affected the seed tuber microbiome composition and that these differences persisted during winter storage of the seed tubers. When seed tubers from different production fields were planted in a single trial field, the microbiomes of daughter tubers and roots of the emerging plants could still be distinguished according to the field of origin of the seed tuber. Remarkably, we found little evidence of direct vertical inheritance of field-unique microbes from the seed tuber to the daughter tubers or roots. Hence, we hypothesize that this intergenerational "memory" is imprinted in the seed tuber, resulting in differential microbiome assembly strategies depending on the field of production of the seed tuber.

microbiology↗