Åsa Lankinen

Biological control agents (BCAs) offer a potential sustainable alternative to fungicides for crop disease management, but their effects on resident plant microbiomes and microbial interactions remain poorly understood. Here, we investigated the effects of the BCA Pythium oligandrum on disease control and the rhizosphere microbiome of starch potato cv. Kuras in a field trial. We compared a laboratory strain and a commercial formulation (Polygandron) with commonly used fungicides during early blight development. The laboratory strain suppressed early blight at plant senescence, but this effect did not persist until harvest, whereas fungicide treatment provided near-complete disease suppression throughout the growing season. P. oligandrum caused transient changes in rhizosphere fungal community composition at flowering, while bacterial community richness varied among sampling times in untreated controls. However, bacterial co-occurrence network analysis revealed pronounced treatment-specific changes in microbial connectivity. Application of the laboratory strain increased network connectivity, resulting in almost a threefold increase in mean degree and greater interconnectedness among bacterial taxa. In contrast, Polygandron and fungicide treatments reduced mean degree, indicating reduced connectivity within the bacterial network. Fungicide treatment additionally altered network organisation, including increased betweenness centrality and changes in modularity. Together, our results show that P. oligandrum can modify microbial interactions in the potato rhizosphere without substantially altering overall bacterial community composition, highlighting the value of integrating microbial network structure with community-level analyses when evaluating the ecological effects of BCAs. Lay summary: Biological control agents offer a more sustainable alternative to fungicides for managing crop diseases, but their effects on beneficial and resident microbes are not fully understood. We investigated how Pythium oligandrum , a potential biological control agent, affected early blight and the microbial communities around the roots of starch potato plants grown in a field trial. We compared a laboratory strain and a commercial formulation (Polygandron) with conventional fungicide treatment. The laboratory strain reduced early blight symptoms towards the end of the growing season, but this effect did not persist until harvest. Fungicides provided more consistent disease control throughout the season. While treatments had limited effects on the overall composition of bacterial communities, they changed the patterns of associations between bacterial groups. The laboratory strain almost tripled the average number of associations per bacterial group, whereas Polygandron and fungicide treatments reduced this connectivity. Fungicides also changed how these associations were organised. These findings show that biological control agents can influence relationships among root-associated microbes even when the overall bacterial community changes little. Understanding these microbial networks alongside community composition could help improve the evaluation of biological control strategies and support the development of more sustainable crop protection practices. Teaser text: Biological control with Pythium oligandrum reshapes bacterial network connectivity in the potato rhizosphere, revealing microbial changes that remain hidden when community composition is considered alone.

Fungicides are intended to control fungal diseases in agricultural production systems in a target‐specific manner. However, in an open‐field experiment in garden strawberry ( Fragaria × ananassa ), in which the fungicide Switch 62.5 WG (cyprodinil and fludioxonil) was applied for the control of grey mould ( Botrytis cinerea ), we found that fungicide application was associated with a strong reduction in herbivory damage by sawflies ( Cladius spp. Hymenoptera: Symphyta). Three years of field data showed a consistent reduction in leaf damage in fungicide‐treated plants compared with the control, with up to a 94% reduction in leaf damage, along with improved fruit quality and increased fruit weight. To further investigate how fungicide treatment of individual plants affects the plant community, fungicide‐treated and non‐treated control plants were grown in close proximity in an alternating pattern. We observed that fungicide non‐target effects could spill over from fungicide‐treated plants and reduce herbivory damage in their non‐treated neighbours by 46%. This finding broadens the concept of associational resistance, which has previously been reported for mixtures of resistant and susceptible crop cultivars, but not for heterogeneous pesticide treatments. Our study provides new field‐based evidence for non‐target effects of a synthetic fungicide from the anilinopyrimidine and phenylpyrrole class on leaf‐dwelling insect pests and opens possibilities for novel pest management strategies via heterogeneous pesticide application.

While we are beginning to understand that the plant microbiome is important for plant health, we still lack information about how plant microbiomes are shaped across environments and how they influence plant performance, in particular, in wild study species. Here, we examined the root microbiota of the perennial vine Solanum dulcamara , a wild relative of potato with an unusually wide ecological amplitude. Using amplicon sequencing, we characterized root communities of bacteria, fungi, and arbuscular mycorrhizal fungi in eight populations across four habitat types (beach, forest, rural, urban) and investigated the link with habitat and plant performance. We found significant differences in the composition and diversity of the root microbiota across habitats and populations, but a core set of taxa (61% of all bacterial and 73% of all fungal) made up the majority of the root microbiome. The microbiome composition was connected to soil pH and plant nutrients. Even though the investigated populations differed in herbivory and plant performance, the association between plant performance and microbial composition was weak. In conclusion, our results suggest that wild species can have similar root microbiomes across widely different habitats, and that plant performance is not always directly linked to the plant microbiome.

Fitness costs of plant disease defence are often subtle and difficult to quantify. In this study, we therefore used comparative high-throughput phenotyping in two independent facilities to assess growth, morphology and physiology of potato (cv. Désirée) with high time-resolution monitoring different defence mechanisms under pathogen-free conditions. Plants were either treated weekly with the resistance inducers β-aminobutyric acid (BABA; 10 mM) or potassium phosphite (KPhi; 36 mM) or comprised six transgenic lines expressing late blight resistance genes (single Rpi genes or a three-gene stack) or reduced jasmonate perception (StCOI1-RNAi). Over four weeks, image-derived traits revealed consistent cross-facility effects for plant height and colour: BABA treatment increased plant height but reduced canopy area and induced a paler greenness signature, whereas KPhi caused minimal and transient growth effects. Chlorophyll fluorescence at the NaPPI facility indicated reduced vitality (Rfd_Lss) in BABA-treated plants and increased Rfd_Lss following KPhi, while maximum PSII efficiency was largely unchanged. Several transgenic lines showed somewhat reduced above-ground biomass. Enzyme activity profiling produced distinct treatment and genotype signatures, but was strongly modulated by facility conditions that overrode these specificities. Overall, high-throughput phenotyping robustly detected subtle growth–defence trade-offs across platforms. Highlight: High-throughput optical phenotyping validated across two independent research facilities reveals that stacked resistance genes and resistance inducers in potato trigger subtle growth trade-offs. Graphical abstracts: Experimental timeline for high-throughput plant phenotyping platforms. Created in BioRender. Poque, S. (2026) https://BioRender.com/nmkve7g

While we are beginning to understand that the plant microbiome is important for plant health, we still lack information about how plant microbiomes are shaped across environments and how they influence plant performance, in particular, in wild study species. Here, we examined the root microbiota of the perennial vine Solanum dulcamara , a wild relative of potato with an unusually wide ecological amplitude. Using amplicon sequencing, we characterized root communities of bacteria, fungi and arbuscular mycorrhizal fungi in eight populations across four habitat types (beach, forest, rural, urban) and investigated the link with habitat and plant performance. We found significant differences in the composition and diversity of the root microbiota across habitats and populations, but a core set of taxa (61% of all bacterial and 73% of all fungal) made up the majority of the root microbiome. The microbiome composition was connected to soil pH and plant nutrients. Even though the investigated populations differed in herbivory and plant performance, the association between plant performance and microbial composition was weak. In conclusion, our results suggest that wild species can have similar root microbiomes across widely different habitats, and that plant performance is not always directly linked to the plant microbiome.

Integrated pest management (IPM) is an important tool for sustainable crop production. IPM includes a diversity of methods, e.g., the use of biological control agents (BCAs) for disease control or growth promotion. While there is an increasing interest in the use of BCAs, less is known about their environmental costs and benefits on wild species, such as wild crop relatives. For example, a BCA may have the positive effect of controlling disease in wild relatives, but could also have the negative effect of growth promotion on wild relatives that act as weeds. In this study, we investigated if three wild potato relatives—the perennial climber Solanum dulcamara , and the annual weeds S. nigrum and S. physalifolium —could be infected by Alternaria solani , the causal agent of early potato blight in Sweden, and studied how two BCAs, Pythium oligandrum (a laboratory strain) and Bacillus amyloliquefaciens (Serenade), affected the disease and growth promotion in a series of greenhouse and field experiments. Our studies confirmed the semantic knowledge that A. solani can infect all three wild species, in particular the two annual species often growing as weeds in potato fields. We also found a disease-controlling effect of B. amyloliquefaciens , but not P. oligandrum , in the greenhouse. Some growth effects were found for both BCAs, but whether these were positive or negative varied with trait, plant species, and genotype. In conclusion, BCAs can confer both environmental costs and benefits on the three wild relatives of potato investigated in the current study, which should be taken into consideration for development of sustainable potato cultivation.

Integrated pest management (IPM) is an important tool for sustainable crop production. IPM includes a diversity of methods, e.g. the use of biological control agents (BCAs) for disease control or growth promotion. While there is an increasing interest in the use of BCAs, less is known about their environmental costs and benefits on wild species, such as wild crop relatives. For example, a BCA may have the positive effect of controlling disease in wild relatives, but could also have the negative effect of growth promotion on wild relatives that act as weeds. In this study we investigated if three wild potato relatives – the perennial climber Solanum dulcamara, and the annual weeds S. nigrum and S. physalifolium – could be infected by Alternaria solani, the causal agent of early potato blight in Sweden, and studied how two BCAs, Pythium oligandrum (a lab strain) and Bacillus amyloliquefaciens (Serenade®), affected the disease and growth promotion in a series of greenhouse and field experiments. Our studies confirmed the semantic knowledge that A. solani can infect all three wild species, in particular the two annual species often growing as weeds in potato fields. We also found a disease controlling effect of B. amyloliquefaciens, but not P. oligandrum, in the greenhouse. Some growth effects were found for both BCAs, but whether these were positive or negative varied with trait, plant species and genotypes. In conclusion, BCAs can confer both environmental costs and benefits on wild plants, which should be taken into consideration for development of sustainable agriculture.