Biology subjects

Stefanic, P.

Publications and source records attributed to Stefanic, P..

9 recordsLinked to original sources

bioRxiv2025

An ERF transcription factor StPTI5, a novel regulator of endophyte community maintenance in potato

We have recently identified ERF transcription factor PTI5 as a susceptibility factor, negatively regulating immune response to diverse pathogens. Here we investigated the processes involved in colonisation of potato with beneficial organisms. RNAseq showed that at the time of Bacillus subtilis biofilm establishment, immune responses in interacting roots were attenuated, and complex transcriptional network was triggered, with ethylene signalling being a central module and PTI5 strongly induced. Interestingly, the response is intensified if plants are inoculated by two antagonistic B. subtilis strains. While PTI5 is not involved in the establishment of biofilm on roots, we show that bacterial abundance increases in PTI5-silenced plants. Remarkably, root colonization by the arbuscular mycorrhizal fungus Rhizophagus irregularis was also higher in the PTI5-silenced plants. PTI5 is thus involved both in blocking defence against harmful and blocking colonisation with beneficial microbes. Such mechanistic understanding of plant-microbe interaction paves the way for sustainable crop management.

plant biology↗

bioRxiv2024

Ecology of prophage-like elements in Bacillus subtilis at global and local geographical scale

Prophages account for a substantial part of most bacterial genomes, but the impacts on hosts remain poorly understood. Here, we combined computational and laboratory experiments to explore the abundance, distribution, and activity of prophage elements in Bacillus subtilis. NCBI database genome sequences and isolates from 1 cm3 riverbank soil samples were analyzed to provide insights at global and local geographical scales, respectively. Most prophages in wild B. subtilis isolates were related to mobile genetic elements previously identified in laboratory strains. Some large groups of prophages were closely related to completely uncharacterized yet functional Bacillus phages, or completely unknown. As certain prophage groups were unique to local isolates, we explored factors influencing prophages within a single genome. Phylogenetic relatedness was a slightly better predictor of host prophage repertoire than geographical origin. We show that cryptic phages can play a major role in acquisition and/or maintenance of other prophage elements both via strong antagonism or by co-dependence. Laboratory experiments showed that most predicted prophages may be cryptic, since they failed to induce under DNA-damaging stress conditions. Interestingly, the magnitude of stress responses remained proportional to the total number of prophage elements predicted, suggesting their importance in host physiology. This study highlights the diversity, integration patterns, and co-occurrence of prophages in B. subtilis and their potential impact on host evolution and physiology. Understanding these dynamics provides insight into bacterial genome evolution and prophage-host interactions, laying the groundwork for future experimental studies on the roles of phages in the ecology and evolution of this bacterial species.

microbiology↗

bioRxiv2024

The rise of cheats during experimental evolution is restricted by non-kin interactions between Bacillus subtilis soil isolates

Cooperative behaviors in human, animal, and even microbial societies are vulnerable to exploitation. Kin discrimination (KD) has been hypothesized to help stabilize cooperation. However, the mechanisms that sustain cooperative behavior remain poorly understood. We here investigate the role of KD in limiting the rise of cheats during surfactant dependent cooperative swarming over surfaces by bacterium Bacillus subtilis as a model organism. We show that mixing surfactant secreting cooperators and cheats that do not produce surfactants leads to cooperation collapse. However, when such mixed swarms transiently encounter non-kin B. subtilis swarms, the frequency of the surfactant nonproducers decreases, suggesting that kinship dependent interactions may limit cheats advantage. To further validate this hypothesis, we subjected wild-type co-operators to transient encounters with kin and non-kin swarms over 20 cycles of experimental evolution. Evolved populations exposed to non-kin swarms exhibited lower occurrences of genotypes with defective swarming phenotypes compared to those encountering kin swarms. These results provide compelling support for the prediction that the evolution of cheats in bacterial populations is impeded by kin discrimination providing experimental proof of its role in stabilizing cooperative behavior.

microbiology↗

bioRxiv2022

Bacillus velezensis SQR9 sways the rhizosphere community and its sociality toward cooperation and plant growth promotion

According to the Lotka-Volterra competition model, intraspecific competition in plant-associated microbial communities should be stronger than interspecific competition. However, there is limited information on whether microbial communities follow this pattern and how disturbance by a newcomer affects them. Given the increasing popularity of probiotics, filling this knowledge gap could help guide future coexistence research. Here, we show that inoculation with a known probiotic, B. velezensis SQR9 shifts species co-occurrence patterns by decreasing the diversity of more distant species and promoting the growth of more closely related species, especially within the Bacillus community. By testing the sociality of Bacillus rhizosphere isolates, we then demonstrated that SQR9 increases the frequency of cooperative interactions in the Bacillus community, which may contribute to the promotion of plant growth. Finally, we provide an ecosystem framework comprising the strains genetic relatedness, metabolic niche space and social compatibility for the efficient and reliable assembly of Bacillus consortia. These findings shed new light on the ecological mechanisms underlying the beneficial effects of probiotics on host fitness.

microbiology↗

bioRxiv2022

MuDoGeR: Multi-Domain Genome Recovery from metagenomes made easy

Several computational frameworks and workflows that recover genomes from prokaryotes, eukaryotes, and viruses from metagenomes exist. However, it is difficult for scientists with little bioinformatics experience to evaluate quality, annotate genes, dereplicate, assign taxonomy and calculate relative abundance and coverage of genomes belonging to different domains. MuDoGeR is a user-friendly tool accessible for non-bioinformaticians that make it easy to recover genomes of prokaryotes, eukaryotes, and viruses from metagenomes, either alone or in combination. We tested MuDoGer using 24 individual-isolated genomes and 574 metagenomes, demonstrating the applicability for a few samples and high throughput. MuDoGeR is open-source software available at https://github.com/mdsufz/MuDoGeR.

bioinformatics↗

bioRxiv2022

Housekeeping gene gyrA, a potential molecular marker for Bacillus ecology study

Bacillus is a ubiquitous microorganism and is one of the most commercially important species widely used in industry, agriculture and healthcare. Bacillus is relatively well understood at the single-cell level; however, molecular tools that determine diversity and ecology of Bacillus community are limited, which limits our understanding of how the Bacillus community works. In the present study, we investigated the potential of the housekeeping gene gyrA as a molecular marker for determining the diversity of Bacillus species. The amplification efficiency for Bacillus species diversity could be greatly improved by primer design. Therefore, we designed a novel primer pair gyrA3 that can detect at least 92 Bacillus species and related species. For Bacillus amyloliquefaciens, Bacillus pumilus, and Bacillus megaterium, we observed that the high variability of the gyrA gene allows for more detailed clustering at the subspecies level that cannot be achieved by the 16S rRNA gene. Since gyrA provides better phylogenetic resolution than 16S rRNA and informs on the diversity of the Bacillus community, we propose that gyrA gene may have broad application prospects in the study of Bacillus ecology.

microbiology↗

bioRxiv2021

Annulment of antagonism shifts properties that are beneficial to plants in two-member consortia of Bacillus velezensis

Bacillus spp. strains that are beneficial to plants are widely used in commercial biofertilizers and biocontrol agents for sustainable agriculture. Generally, functional Bacillus strains are applied as single strain communities since the principles of synthetic microbial consortia constructed with Bacillus strains remain largely unclear. Here, we demonstrated that the mutual compatibility directly affects the survival and function of two-member consortia composed of B. velezensis SQR9 and FZB42 in the rhizosphere. A mutation in the global regulator Spo0A of SQR9 markedly reduced the boundary phenotype with wild-type FZB42, and the combined use of the SQR9{triangleup}spo0A mutant and FZB42 improved biofilm formation, root colonization and the production of secondary metabolites that are beneficial to plants. We further confirmed the correlation between the swarm discrimination phenotype between the two consortia members and the effects that are beneficial to plants in a greenhouse experiment. Our results provide evidence that social interactions among bacteria could be an influencing factor in achieving a desired community-level function. IMPORTANCEBacillus velezensis is one of the most widely applied bacteria in biofertilizers in China and Europe. Additionally, the molecular mechanisms of plant growth promotion and disease suppression by representative model strains are well established, such as B. velezensis SQR9 and FZB42. However, it remains extremely challenging to design efficient consortia based on these model strains. Here, we showed that swarm discrimination phenotype is one of the major determinants affects the performance of two-member Bacillus consortia in vitro and in the rhizosphere. Deletion in global regulatory gene spo0A of SQR9 reduced the strength of boundary formation with FZB42, result in the improved plant growth promotion performance of dual consortium. This knowledge provides new insights into efficient probiotics consortia design in Bacillus.

microbiology↗

bioRxiv2019

Quorum sensing in Bacillus subtilis slows down biofilm formation by enabling sporulation bet hedging

1.2The ComQXPA quorum sensing (QS) system of Bacillus subtilis, a Gram-positive, industrially relevant, endospore forming bacterium, promotes surfactin production. This lipopeptide increases transcription of several genes involved in biofilm matrix synthesis via the Spo0A-P master regulator. We hypothesized that the inactivation of the QS system will therefore result in decreased rates of floating biofilm formation. We find that this is not the case and that the QS deficient mutant forms pellicles with a faster rate and produces more biofilm matrix components than the wild type. As Spo0A-P is the master regulator of sporulation initiation we hypothesized that the ComQXPA dependent signaling promotes sporulation and consequently slows the growth rate of the wild type strain. Indeed, our results confirm that cells with the inactive QS initiate endospore formation in biofilms later and more synchronously than the wild type, as evidenced by spore frequencies and the PspoIIQ promoter activity. We argue, that the QS system acts as a switch that promotes stochastic sporulation initiation and consequently bet hedging behavior. By committing a subpopulation of cells to sporulation early during growth, wild type population grows slower and produces thinner biofilms but also assures better survival under stressful conditions.\n\n1.1 IMPORTANCEBacillus subtilis is widely employed model organism to study biofilm formation and sporulation in Gram-positive bacteria. The ComQXPA quorum sensing (QS) system indirectly increases the transcription of genes involved in biofilm matrix formation, which predicts a positive role of this QS in biofilm development Here we show that QS mutants actually form more matrix components per pellicle than the wild type and that their pellicles are thicker and form with a faster rate. We explain this, by showing that cells with an inactive QS exhibit a delay in sporulation entry, which is also more synchronous relative to the wild type. We argue, that the ComQXPA QS system acts as a switch that contributes to the stochastic sporulation initiation and though this path promotes bet hedging behavior. This finding is important in terms of \"quorum quenching\" strategies aiming to down modulate biofilm development through inhibition of QS signaling and underscores the richness of QS regulated phenotypic outcomes among bacterial species.

microbiology↗

bioRxiv2019

Intra-species DNA exchange: Bacillus subtilis prefers sex with less related strains

B. subtilis is a surface-dwelling bacterium that is competent for natural transformation. Genetically distinct B. subtilis swarms form a boundary upon encounter, mediated by a fast-evolving molecular kin discrimination (KD) system. We here demonstrate that KD-mediated swarm antagonisms in B. subtilis promote transformation-mediated horizontal gene transfer between strains of low relatedness. Gene transfer is largely uni-directional and the result of the induction of competence of the recipient strain by the donor strain is linked to a sigW-mediated stress response. More closely related strains, which in theory would experience more efficient recombination due to increased sequence homology, did not upregulate transformation upon encounter, demonstrating that social interactions can override mechanistic barriers to horizontal gene transfer. KD-mediated competence in response to the encounter of distinct neighbouring strains could maximize the probability of efficient incorporation of novel alleles and genes that have proved to function in a genomically and ecologically similar context.

microbiology↗