Extracellular DNA Dynamics in Bacterial Biofilms

Bacterial biofilms are structured communities enveloped in an extracellular matrix that confers mechanical stability, environmental resilience and enhanced resistance to antimicrobial agents. A central component of this matrix is extracellular DNA (eDNA), which is released via cell lysis, active secretion and vesicle shedding. Once outside the cell, eDNA interacts with polysaccharides and proteins to form a hydrated, viscoelastic network that binds cells together, facilitates nutrient capture and mediates horizontal gene transfer. Recent advances have revealed that eDNA adopts diverse higher-order conformations and engages in dynamic interactions with extracellular RNA and matrix-associated proteins to fine-tune biofilm architecture. Non-canonical structures such as G-quadruplexes and left-handed Z-DNA emerge under ionic and mechanical stress, protecting the matrix from enzymatic degradation. In some species, eDNA even acts as a catalytic scaffold, exhibiting peroxidase-like activity. Beyond structural roles, eDNA chelates cations, modulates local microenvironments and serves as a template for mineral deposition in biomineralizing communities. The multifaceted dynamics of eDNA underlie biofilm development, maturation and dispersal, with broad implications for chronic infection control, environmental remediation and industrial biofouling management.

Research from Nature Portfolio

Recent studies have uncovered the intimate partnership between extracellular RNA (eRNA) and eDNA in Pseudomonas aeruginosa biofilms. Specific mRNA transcripts co-localise with eDNA to form fibrous networks that impart viscoelastic properties to the matrix. Degradation of associated RNAs disrupts eDNA fibre assembly and diminishes biofilm elasticity. Single-molecule imaging techniques reveal that virulence-associated transcripts, including those encoding extracellular enzymes, are enriched within the matrix, suggesting that RNA–DNA interactions stabilise structural scaffolds and may influence matrix composition in clinical settings.

Extracellular DNA Dynamics in Bacterial Biofilms publication trend

The graph below shows the total number of articles in extracellular dna dynamics in bacterial biofilms across all publications each year (not limited to Nature Index journals).

Technical terms

Extracellular DNA (eDNA): DNA located outside living cells, released by lysis or secretion and integral to biofilm structure.

Extracellular RNA (eRNA): RNA fragments present in the biofilm matrix that interact with eDNA to stabilise matrix fibres.

Biofilm matrix: A hydrated, polymeric network of nucleic acids, polysaccharides and proteins that encases biofilm cells.

G-quadruplex: A four-stranded DNA secondary structure formed by guanine-rich sequences, stabilised by cations.

Z-DNA: A left-handed helical form of DNA that can arise under physiological conditions of supercoiling and high ionic strength.

DNAzyme: A DNA molecule with catalytic activity, in this context exhibiting peroxidase-like function when complexed with hemin.

Viscoelasticity: The property of a material that exhibits both viscous and elastic characteristics when deformed, crucial for biofilm mechanical resilience.

References

1. Mechanisms and Regulation of Extracellular DNA Release and Its Biological Roles in Microbial Communities. Frontiers in Microbiology (2017).
2. RNA is a key component of extracellular DNA networks in Pseudomonas aeruginosa biofilms. Nature Communications (2023).
3. Extracellular G-quadruplexes and Z-DNA protect biofilms from DNase I, and G-quadruplexes form a DNAzyme with peroxidase activity. Nucleic Acids Research (2024).
4. Matrix is everywhere: extracellular DNA is a link between biofilm and mineralization in Bacillus cereus planktonic lifestyle. npj Biofilms and Microbiomes (2023).