Biology subjects

Burmolle, M.

Publications and source records attributed to Burmolle, M..

7 recordsLinked to original sources

bioRxiv2026

Biofilm compactness and spatial community composition determine bacterial phage-susceptibility

Bacteriophages (phages) are viruses that infect bacteria, often posing a threat to their survival. In recent years, research has shifted from studying bacteria-phage interactions in homogeneous, well-mixed environments to investigating more complex heterogeneous, structured communities, thereby more accurately reflecting bacterial life in natural and disease-associated settings. So far, these studies predominantly tested interactions of phages and single-species biofilms, despite the dominance of highly diverse biofilm communities in nature. Here, we investigated how different lytic phages spread in and infect a synthetic community composed of Escherichia coli, Kluyvera cryocrescens, and Vibrio anguillarum. We found that E. coli was protected from eradication by the T7-coliphage when embedded in a multispecies biofilm and covered by the two other species, where the V. anguillarum biofilm matrix was essential for protection of E. coli. The protective nature of the V. anguillarum matrix also ensured survival of K. cryocrescens exposed to the lytic kluyveraphage Lyn. V. anguillarum mutants lacking the matrix synthesis genes vpsMNOP or rbmC failed to protect E. coli despite forming biofilms. Labelling of phages indicated that these were not trapped in the matrix of the wildtype. Instead, advanced image analysis revealed that the mutants displayed biofilms with lower cell density, resulting in the E. coli clusters being less tightly surrounded by V. anguillarum cells, which opened gaps for phage entry. These findings highlight that community context and matrix composition play a major role in phage-bacteria dynamics.

microbiology↗

bioRxiv2026

Carbon substrate type shapes spatial self-organization in a multi-species biofilm community

Spatial organization is a defining feature of multispecies biofilms and critically influences microbial interactions and emergent community properties. However, understanding and manipulating how microbes assemble into spatially structured biofilms remains challenging because most experimental frameworks emphasize species composition and pairwise interactions, while often overlooking the spatial constraints on biofilms imposed by the environment. In this study, we focus on how carbon substrate type, distinguishing between diffusible sugars and polymeric substrates, affects biofilm self-organization in a four-member synthetic bacterial community (SynCom). Across all tested conditions, the SynCom consistently formed more biofilm biomass than any of its subsets, indicating a robust synergistic phenotype. Using chemically defined, 3D-printed hydrogel substrates with consistent physical properties, we varied carbon source composition to identify its impact on biofilm assembly. Microscopic imaging showed that carbon substrate type strongly influenced biofilm self-organization with diffusible simple carbon substrates yielding relatively intermixed communities, whereas polymer-rich carbon substrates promoted a highly structured biofilm organization characterized by the dominance and peripheral localization of polymer-degrading species. Bioinformatic analyses of carbohydrate-active enzymes (CAZymes) annotation and genome-scale metabolic modeling suggested that metabolite exchange networks in the SynCom may drive more complex metabolic interactions beyond the commonly observed degrader-exploiter-scavenger relationship within planktonic microbial communities. Together, our findings demonstrate carbon substrate type as an important ecological determinant of biofilm self-organization, highlighting the need to integrate environmental factors alongside species composition and metabolic potential to fully understand and manipulate natural and engineered multispecies biofilms.

microbiology↗

bioRxiv2023

Evolution of genotypic and phenotypic diversity in multispecies biofilms

Bacterial fitness and adaptability in microbial communities are influenced by interspecies interactions and spatial organization. This study investigated how these factors shape the evolutionary dynamics of Bacillus thuringiensis. A distinct phenotypic variant of B. thuringiensis emerged consistently under both planktonic and biofilm conditions, as well as in monospecies and mixed-species settings, but was strongly selected in biofilms and during coexistence with Pseudomonas defluvii and/ or Pseudomonas brenneri. Compared to its ancestor, the variant exhibited shorter generation times, reduced sporulation, auto-aggregation, and lower biomass in mixed-species biofilms. Mutations in the spo0A regulator, which controls sporulation and biofilm matrix production, were identified in all variants. Proteomics revealed a reduction in TasA, a key matrix protein, in the variant but increased levels in co-culture with P. brenneri. These findings highlight how interspecies interactions drive B. thuringiensis diversification, promoting traits like reduced matrix production and species coexistence, with implications for microbial consortia applications in agriculture and biopesticides.

microbiology↗

bioRxiv2023

Fundamentals of biofilm formation in soil: From functionalized self-assembled monolayers to rewilding

Surface energy and surface charges play crucial roles in bacterial adhesion and biofilm formation, however the mechanisms underlying the bacteria-surface interaction, particularly on the formation of soil biofilms, remain unclear. In spite of considering the spatiotemporal dynamics of biofilm formation on different soil surfaces, we compared the impact of four different substrates on bacterial attachment and biofilm formation. The substrates were constituted of gold layer covered by NH2+, CH3, COO- and OH-terminated self-assembled monolayers (SAMS). Two soil habitat bacteria with different Gram barriers, Bacillus subtilis and Acinetobacter baylyi, were grown with incubation times of 6-72 h on each type of surfaces. Bacterial attachment and biofilm formation was assessed using metabolic activity of the cells adhered to the surfaces. The spatial distribution of adhere bacteria was visualized by scanning electron microscopy and confocal laser scanning microscopy. We also investigated whether the surface impacts the biofilm matrix composition. A general view of our results suggests a major influence of the surface chemistry on bacterial potential to form biofilms. The hydrophobic or positively charged substrates attract bacteria while a lack of attachment and biofilm formation on hydrophilic and negatively charged surfaces. This work points out the potential of surface treatments in the environment where it is intended to either repel or attract bacteria.

microbiology↗

bioRxiv2020

Adaptive evolution of phenotypic switching during environmental change

Microbes are faced with environmental fluctuations and it is therefore important to understand how change affects bacterial evolution and population dynamics. Here, we evolved a model bacterium, Pseudomonas aeruginosa PA14, under both constant and changing conditions where settlement by biofilm formation or migration by swimming motility was induced. In changing environments, a heterogeneous population evolved with both specialists and generalists. Interestingly, over time, generalists were outcompeted despite being better at both phenotypes compared to the ancestor. However, generalists became dominant when faced with local competition after resettlement. Reintroduction into a burn wound model, the environment PA14 originally was isolated from, further suggested a tradeoff between niche breadth and peak fitness in agreement with the evolution experiments. Mutations in the c-di-GMP system were key for adaptation of the phenotypes. No mutants lost their ability to regulate c-di-GMP, but generalists acquired mutations that optimized their phenotypic response by efficiently adjusting c-di-GMP levels.

evolutionary biology↗

bioRxiv2018

In vitro community synergy between bacterial soil isolates can be facilitated by pH stabilisation of the environment

Composition and development of naturally occurring microbial communities is defined by a complex interplay between the community and the surrounding environment and by interactions between community members. Intriguingly, these interactions can in some cases cause community synergies where the community is able to outperform it single species constituents. However, the underlying mechanisms driving community interactions are often unknown and difficult to identify due to high community complexity. Here we show how pH stabilisation of the environment through the metabolic activity of specific community members acts as a positive inter-species interaction driving in vitro community synergy in a model consortium of four co-isolated soil bacteria: Microbacterium oxydans, Xanthomonas retroflexus, Stenotrophomonas rhizophila and Paenibacillus amylolyticus. Using micro-sensor pH measurements to show how individual species change the local pH micro-environment, and how co-cultivation leads to a stabilised pH regime over time. Specifically, in vitro acid production from Paenibacillus amylolyticus and alkali production primarily from Xanthomonas retroflexus lead to an overall pH stabilisation of the local environment over time, which in turn resulted in enhanced community growth. This specific type of interspecies interaction was found to be highly dependent on media type and media concentration, however similar pH drift from the individual species could be observed across media variants.\n\nImportanceWe show that in vitro metabolic activity of individual members of a synthetic, co- isolated model community presenting community synergistic growth arises through the inter-species interaction of pH stabilization of the community micro-environment. The observed inter-species interaction is highly media specific and most pronounced under high nutrient availability. This adds to the growing diversity of identified community interactions leading to enhanced community growth.

microbiology↗

bioRxiv2018

DAtest: a framework for choosing differential abundance or expression method

DAtest is an R package for directly comparing different statistical methods for differential abundance and expression analysis on a dataset of interest; be it data from RNA-seq, proteomics, metabolomics or a microbial marker-gene survey. A myriad of statistical methods exists for conducting these analyses, and with this tool we give the analyst an empirical foundation for choosing a method suitable for a specific dataset. The package supports categorical and quantitative variables, paired/block experimental designs, and the inclusion of covariates. It is freely available at GitHub: https://github.com/Russel88/DAtest along with detailed instructions.

bioinformatics↗