Biology subjects

Friman, V. P.

Publications and source records attributed to Friman, V. P..

7 recordsLinked to original sources

bioRxiv2026

Detecting transcriptional responses and comparing the virulence of Pseudomonas aeruginosa cystic fibrosis isolates in a mung bean model

A mung bean infection model has previously been shown to differentiate between non-virulent and virulent Pseudomonas aeruginosa bacteria. However, it remains unclear how plant and bacteria adjust their gene expression during infection and whether the mung bean model can be used to compare the virulence of clinical cystic fibrosis (CF) P. aeruginosa lung isolates. Here, we first explored temporal transcriptomics of P. aeruginosa PAO1 and mung bean during an infection. We found that bacterial gene expression followed temporal changes, with an increase in the expression of O-antigen biosynthetic genes, chemotaxis, phosphate intake and phenazine production. Mung bean responded by upregulating genes associated with defence mechanisms and downregulating genes involved in the plant development. From the PAO1 perspective, the core-transcriptomic responses in the mung bean were similar to its responses previously observed in wound and excision and in in vitro media and sputum models, while differed from those observed in the bronchial cell model. Furthermore, we used the mung bean to assess the virulence of 119 clinical P. aeruginosa CF strains originating from the Copenhagen CF clinic. By quantifying bacterial virulence as a reduction in root and shoot growth and weight of the seeds, we found that CF strains isolated at later compared to early stages of lung infections showed higher virulence. This difference corresponded with the higher number of immune modulation-associated virulence genes and lower number of motility and effector genes, present in the genomes of late compared to early isolated CF strains. IMPORTANCEOur results demonstrate that based on PAO1 transcriptional profile, the mung bean model is similar to in vitro and wound infection models but differs from cell and bronchial models. Moreover, the mung bean model can detect virulence differences between clinical P. aeruginosa CF strains, making it a potentially useful high-throughput in vivo model for bacterial virulence screening.

microbiology↗

bioRxiv2026

Probiotic phage steering of disease suppressive rhizosphere microbiome

Current phage therapy approaches predominantly focus on targeting pathogenic bacteria, overlooking the vast potential of phages that interact with beneficial, plant growth-promoting (probiotic) bacteria. Here we tested if a single phage targeting a probiotic Stenotrophomonas maltophilia bacterium can steer the rhizosphere microbiome disease suppressiveness against Ralstonia solanacearum phytopathogen. We find that S. maltophilia quickly evolves resistance to its phage via mutations in ssb and TonB genes and by upregulating anti-phage defense systems. Crucially, evolution of phage resistance reprograms the bacterial transcriptome and metabolome, leading to unexpectedly enhanced antimicrobial activity against the R. solanacearum. Furthermore, exposing S. maltophilia to phage in the tomato rhizosphere increases the microbiota-wide disease suppressiveness by stabilizing bacterial diversity and facilitating pathogen suppression by other resident species. Our findings suggest that probiotic-specific phages could be used as ecological and evolutionary engineers to steer the rhizosphere microbiome disease suppressiveness through activation of antagonistic bacterial interactions.

evolutionary biology↗

bioRxiv2025

Normative assembly rule reveals fairness in microbial communities

Understanding and predicting how communities assemble is a paramount challenge in ecology. Here we address these questions normatively by comparing the ecological distribution of growth surplus to a game-theoretically fair distribution based on each species Shapley value. By analyzing in total 56 distinct community outcomes, we assess how fairly biomass is distributed in microbial communities displaying both competitive and cooperative interactions in different environmental conditions. We find examples of fair communities that closely follow their Shapley value across all environments as well as counterexamples where the true abundances deviate from the species objective contribution to community biomass. Our results give unique empirical insights into the distributive function of ecological dynamics and lay down the theoretical foundations of what might become a normative community assembly theory.

ecology↗

bioRxiv2025

Resistance mutation supply modulates the benefit of CRISPR immunity against virulent phages

Only a fraction of bacterial genomes encode CRISPR-Cas systems but the selective causes of this variation are unexplained. How naturally virulent bacteriophages (phages) select for CRISPR immunity has rarely been tested experimentally. Here, we show against a panel of genetically and functionally diverse virulent phages that CRISPR immunity was not universally beneficial, and its fitness effect varied strongly between phages in predictable ways. In addition to mechanisms known to alter the effectiveness of CRISPR immunity, such as encoding a matching spacer or a protective nuclear shell, we show that the fitness effect of CRISPR immunity negatively correlated with the probability of evolving receptor-based resistance to the phage via spontaneous mutation. Supply of resistance mutations differed strongly between very closely related lipopolysaccharide-binding phages and was associated with variation at the C-terminus of the tail fibre protein altering residues involved in hydrogen bonding and the predicted binding site. Our results show that CRISPR immunity is more beneficial against virulent phages that are harder to evolve resistance to via receptor mutations, suggesting that virulent phage community composition and diversity will be important drivers of the prevalence of CRISPR immunity.

microbiology↗

bioRxiv2025

Assembly and annotation of Solanum dulcamara and Solanum nigrum plant genomes, two nightshades with different susceptibilities to Ralstonia solanacearum

To understand why close wild plant relatives of crops, such as Solanum dulcamara, are resistant to Ralstonia solanacearum we need genetic resources to perform comparative studies and identify key genes and pathways. We de-novo assembled and annotated the genome of resistant S. dulcamara and susceptible Solanum nigrum plants using a hybrid approach including Oxford Nanopore Technologies and Illumina sequencing. Comparative genomic analysis was then performed to find differences between the genome of S. dulcamara and other susceptible Solanaceous species including potato, tomato, aubergine, and S. nigrum and one susceptible and one resistant S. americanum accession. We identified genes associated with auxin-transport only in S. dulcamara and a collection of pattern recognition receptors (PRRs) was identified in orthogroups only found in plant species with resistant/tolerant phenotype, suggesting novel plant receptors in these accessions that may improve recognition of pathogen-associated molecular patterns (PAMPs) associated with R. solanacearum. We also identified differences in methylation frequency across the gene bodies in both species, which may be associated with epigenetic regulation of resistance. Future work should assess the functional role of these PRRs during bacterial wilt development to determine if they could offer potential novel targets for breeding improved wilt resistance.

plant biology↗

bioRxiv2025

Spatiotemporal changes in soil properties predict plant health at continental scale

Abiotic and biotic soil properties are strong predictors of plant yield globally1-5, but they become unreliable over large areas when plant health is threatened by pathogen6-8. Here we present a novel approach to predict plant health based on spatiotemporal changes in soil chemical and biological properties. We first demonstrate that plant health and soil properties consistently respond to environmental change (organic fertilization) regardless of the soil type or geographical origin. Second, we experimentally show that trackable shifts in soil properties reliably explain soil suppressiveness to the Ralstonia solanacearum bacterial pathogen and that a scalable spatiotemporal model predicts plant health with 84% accuracy across multiple climatic zones and cropping systems. Our results suggest that this tight coupling between soil properties and plant health could facilitate the development of agricultural practices aimed at sustainably improving crop yields while safeguarding crop health.

ecology↗

bioRxiv2021

Introduction of probiotic bacterial consortia promotes plant growth via impacts on the resident rhizosphere microbiome

Plant growth depends on a range of functions provided by their associated rhizosphere microbiome, including nutrient mineralization, hormone co-regulation and pathogen suppression. Improving the ability of plant associated microbiome to deliver these functions is thus important for developing robust and sustainable crop production. However, it is yet unclear how beneficial effects of probiotic microbial inoculants can be optimised and how they are mediated. Here, we sought to enhance the tomato plant growth by targeted introduction of probiotic bacterial consortia consisting of up to eight plant-associated Pseudomonas strains. We found that the effect of probiotic consortium inoculation was richness-dependent: consortia that contained more Pseudomonas strains, reached higher densities in the tomato rhizosphere and had clearer beneficial effects on multiple plant growth characteristics. Crucially, these effects were best explained by changes in the resident community diversity, composition and increase in the relative abundance of initially rare taxa, instead of introduction of plant-beneficial traits into the existing community along with probiotic consortia. Together, our results suggest that beneficial effects of microbial introductions can be driven indirectly through effects on the diversity and composition of resident plant rhizosphere microbiome.

ecology↗