Biology subjects

Weisskopf, L.

Publications and source records attributed to Weisskopf, L..

4 recordsLinked to original sources

bioRxiv2026

A scalable screening approach reveals phylogenetic patterns of bacterial antagonism against potato pathogens

Microbial biological control agents (mBCAs) offer a promising alternative to conventional disease management, but identifying effective strains requires screening large microbial collections against many pathogens. Here, we developed a scalable screening approach to characterize the antagonistic activity of potato-associated bacteria against multiple pathogens and investigated how bacterial origin and phylogeny relate to antagonistic phenotypes. A collection of 600 bacterial strains isolated from two potato cultivars, three plant compartments using four cultivation media was screened against six major potato pathogens: the bacteria Dickeya solani and Pectobacterium carotovorum, the fungi Alternaria solani and Rhizoctonia solani, and the oomycetes Phytophthora infestans and Pythium ultimum. A scalable confrontation method was developed for non-filamentous bacteria, while complementary lower-throughput assays were used for filamentous strains. This approach enabled successful assessment of 92% of non-filamentous and 97% of filamentous strain-pathogen combinations. Isolation cultivar, plant compartment and cultivation medium had only limited effects on the proportion of antagonistic strains. In contrast, pathogen sensitivity varied markedly: P. infestans was the most susceptible pathogen, whereas D. solani and P. carotovorum were generally resistant to bacterial antagonism. Antagonistic activity clustered phylogenetically, with Bacillus and Streptomyces containing many broad-spectrum inhibitors. In addition, several taxa showed preferential activity against the oomycetes, including P. infestans-specific antagonists from the Pseudomonas genus and P. ultimum-specific antagonists from the Frigoribacterium, Curtobacterium, Pedobacter and Phyllobacterium genera. Overall, multi-pathogen screening revealed distinct generalist and specialist antagonistic profiles and identified candidate strains and taxa for further evaluation as mBCAs.

microbiology↗

bioRxiv2026

Potato foliar infection with Phytophthora infestans drives strong, cultivar-specific shifts in rhizosphere communities

BackgroundPotato is an important crop worldwide, yet its production is severely threatened by Phytophthora infestans, the causal agent of late blight. Alternatives to the current control strategies are needed, as these rely heavily on environmentally harmful treatments. The recruitment of beneficial microbes by plants upon stress ("cry-for-help" mechanism) may represent an opportunity to find new biocontrol agents but this has not yet been reported for potato. The aim of this study was to analyse whether foliar late blight infection induces shifts in the phyllosphere, rhizosphere and soil bacterial communities associated with two potato cultivars of differing sensitivity to late blight. Moreover, we aimed at isolating members of the plant microbiota to test whether bacteria putatively recruited upon infection would be particularly active in protecting the plant against late blight. ResultsControlled foliar infection triggered substantial, cultivar-specific shifts in the rhizosphere communities across two successive generations. Despite the number of differentially abundant ASVs detected being ten times higher in the second generation than in the first one, the same taxonomic groups were concerned by the shifts: Burkholderiales, Flavobacteriales, and Bacillales. Furthermore, the communities linked to the susceptible cultivar consistently shifted more strongly than the communities linked to the resistant cultivar. The obtained ASV sequences were used to identify 163 corresponding isolates. The inhibition potential of these strains against P. infestans spores was assessed through biological assays, which revealed the biocontrol potential of strains otherwise not yet known to inhibit phytopathogenic organisms, such as Advenella, Nocardioides and Phyllobacterium strains. Although we found no correlation between the relative abundance shift of the ASVs upon infection and the activity of the corresponding strains, we observed that the overall activity of strains isolated from the resistant cultivar was higher than that of the strains isolated from the susceptible one. ConclusionTaken together, the higher activity of the strains isolated from the resistant cultivar, along with its comparatively modest microbiome shifts upon infection suggest that the investigated resistant cultivar might harbour specific microbiota enriched in strains with efficient protective abilities against their host plants pathogens, which possibly contribute to its higher resistance against P. infestans.

microbiology↗

bioRxiv2025

Phyllosphere microbiome-based biocontrol solution against the filamentous pathogens Botrytis cinerea and Plasmopara viticola in grapevine

Plants harbor different microbial communities in their different organs. This difference is due to the various conditions to which the different parts of the plant are subjected. Consequently, the phyllosphere microbiota can differ strongly from root-associated communities. We hypothesize that the grapevine phyllosphere is a valuable source of biocontrol bacteria, whose adaptation to the aerial plant environment may enable them to reach their full protective potential against foliar pathogens. In previous work, we isolated phyllosphere bacteria and showed that many strains were very effective against such pathogens in vitro, inhibiting their mycelial and spore development. This work investigates the biocontrol ability of these phyllosphere bacteria in leaf disc assays against two foliar pathogens: Botrytis cinerea (gray mold) and Plasmopara viticola (downy mildew). Our results show that 40 strains out of 46 affected at least one pathogen by altering their spore physiology and/or reducing disease progression. Among these strains, 27 strains could impact both pathogens and 20 were also capable of stimulating plant defenses. Because bacterial consortia might perform better than single strains, we also compared the protection conferred by individual bacteria and associations of up to three strains. When combined, bacteria showed improved efficacy in vitro against B. cinerea and in planta against P. viticola, resulting in a much stronger protection than that obtained by the application of the strains alone. These data suggest that phyllosphere bacteria could be a promising tool to help winegrowers manage grapevine diseases by providing an effective and sustainable protection of their crops.

plant biology↗

bioRxiv2021

Much more than a toxin: hydrogen cyanide is a volatile modulator of bacterial behaviour

Bacterial volatile compounds have emerged as important chemical messengers between bacteria themselves as well as in their interactions with other organisms. One of the earliest examples of bioactive volatiles emitted by bacteria is hydrogen cyanide (HCN), which was long considered a mere respiratory toxin conferring competitive advantage to cyanogenic strains. Using cyanide-deficient mutants in two Pseudomonas strains and global transcriptome analysis, we demonstrate that the impact of HCN is much more global than previously thought. We first observed that the lack of cyanogenesis in emitting strains led to massive transcriptome reprogramming affecting diverse traits such as motility and biofilm formation (respectively inhibited vs. promoted by HCN), or the production of siderophores, phenazines and other antimicrobial compounds (repressed by HCN). We then exposed non-cyanogenic strains to biogenically emitted HCN from neighboring cells and observed similar transcriptome modulations and phenotypic changes, suggesting that HCN not only acts endogenously but also exogenously, remotely manipulating important traits involved in competition and virulence, e.g. siderophore production, in other organisms. Cyanogenesis in Pseudomonas has long been known to play a role in both the virulence of opportunistic pathogens and the efficient biocontrol activity of plant-beneficial strains, however this impact was so far thought to occur solely through the inhibition of respiration. We demonstrate here new ecological roles for a small and fast-diffusing volatile compound, which opens novel avenues in our understanding of and ability to interfere with important processes taking place in pathogenic and beneficial Pseudomonas strains. ImportanceBacteria communicate by exchanging chemical signals, some of which are volatile and can remotely reach other organisms. Hydrogen cyanide (HCN) was one of the first volatiles discovered to severely impact exposed organisms by inhibiting their respiration. Using HCN-deficient mutants in two Pseudomonas strains, we demonstrate that HCNs impact goes beyond the sole inhibition of respiration and affects both emitting and receiving bacteria in a global way, modulating their motility, biofilm formation and production of antimicrobial compounds. Our data suggest that bacteria could use HCN not only to control their own cellular functions, but also to remotely influence the behavior of other bacteria sharing the same environment. Since HCN emission occurs in both clinically and environmentally relevant Pseudomonas, these findings are important to better understand or even modulate the expression of bacterial traits involved in both virulence of opportunistic pathogens and in biocontrol efficacy of plant-beneficial strains.

microbiology↗