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The biofilm matrix: multitasking in a shared space

Abstract

The biofilm matrix can be considered to be a shared space for the encased microbial cells, comprising a wide variety of extracellular polymeric substances (EPS), such as polysaccharides, proteins, amyloids, lipids and extracellular DNA (eDNA), as well as membrane vesicles and humic-like microbially derived refractory substances. EPS are dynamic in space and time and their components interact in complex ways, fulfilling various functions: to stabilize the matrix, acquire nutrients, retain and protect eDNA or exoenzymes, or offer sorption sites for ions and hydrophobic substances. The retention of exoenzymes effectively renders the biofilm matrix an external digestion system influencing the global turnover of biopolymers, considering the ubiquitous relevance of biofilms. Physico-chemical and biological interactions and environmental conditions enable biofilm systems to morph into films, microcolonies and macrocolonies, films, ridges, ripples, columns, pellicles, bubbles, mushrooms and suspended aggregates — in response to the very diverse conditions confronting a particular biofilm community. Assembly and dynamics of the matrix are mostly coordinated by secondary messengers, signalling molecules or small RNAs, in both medically relevant and environmental biofilms. Fully deciphering how bacteria provide structure to the matrix, and thus facilitate and benefit from extracellular reactions, remains the challenge for future biofilm research.

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Fig. 1: The matrix of microbial biofilms.
Fig. 2: Interactions of extracellular polymeric substance components and their functions.
Fig. 3: Regulation of matrix synthesis.
Fig. 4: Mechanical properties of the biofilm matrix.

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Acknowledgements

The authors are grateful to I. C. H. Tan and C. Mayer for help with designing the drafts for Figs. 2 and 5a, respectively.

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H.-C.F., T.R.N., P.H.N., T.S. and P.S. researched data for the article. H.-C.F., E.D.v.H., T.R.N., P.H.N., T.S., P.S., J.W. and S.W. contributed substantially to discussion of the content. H.-C.F., T.R.N., P.H.N. and P.S. wrote the article. H.-C.F., T.R.N., J.W. and P.S. reviewed and/or edited the manuscript before submission. H.-C.F. assembled the team and coordinated the writing process.

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Correspondence to Hans-Curt Flemming.

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Glossary

Extracellular polymeric substances

(EPS). Microbial biopolymers such as polysaccharides, proteins, extracellular DNA (eDNA) and others, forming the biofilm matrix.

Extracellular matrix

The non-cellular component present within all tissues and organs, sometimes also used as an alternative to the term extracellular polymeric substances (EPS); frequently used in the medical context.

Amyloids

Aggregates of proteins in fibrillar morphology. Pathogenic amyloids form by misfolding of previously normal structures. In biofilms, amyloids fulfil many functions, including, for example, matrix stabilization, nutrient storage, desiccation resistance and others.

Humic-like microbially derived refractory substances

Remains of bacterial cells that are not readily degraded after cell death. As high molecular weight compounds they remain present within microbial communities, contributing to the polymeric matrix.

Humic substances

The organic components of humus. Humic substances are hetero-polycondensates based on a motif of aromatic nuclei with phenolic and carboxylic substituents linked together. They can form aggregates, provide cation complexation sites and regulate the bioavailability of metal ions.

Transparent exopolymer particles

Extracellular acidic polysaccharides produced by phytoplankton and bacteria in saltwater, freshwater and wastewater; they are extremely abundant and play a significant role in biogeochemical cycling of carbon and other elements in water.

Collective biological systems

Systems such as forests, beehives, coral reefs or kelp fields that show emerging properties which exceed those of the sum of the single individuals. Also known as ‘extended organisms’.

Psl

An extracellular polysaccharide of Pseudomonas aeruginosa and an important structural and functional feature of P. aeruginosa biofilms. Psl is rich in galactose and mannose.

Pel

An extracellular polysaccharide of Pseudomonas aeruginosa and an important structural and functional feature of P. aeruginosa biofilms. The structure of Pel is not fully characterized but it is a cationic polysaccharide, differing from Psl and alginate.

Ecotin

A protease inhibitor, formed in the periplasmic space of Gram-negative bacteria, inhibiting neutrophil elastase.

Anammox

(Ammonium oxidation). The reaction of nitrite and ammonium ions leading directly to dinitrogen and water.

Rhamnolipids

Amphiphilic glycolipids consisting of a monosaccharide or disaccharide connected by a glycosidic bond to a fatty acid; they act in various roles in the EPS matrix.

Necromass

The mass of dead biological material, including microorganisms.

Phenazine

The chemical description of the class of dibenzo annulated pyrazine; it embraces pyocyanine as a subclass in which one of the nitrogen atoms is substituted with a methyl group.

Glycomics

The study of all glycan structures in biology and a subset of glycobiology. Glycomics focuses on the identification of structure and function of the total collection of glycans (the glycome) produced by biological systems under specified conditions of time, space and environment.

Mesolens

A novel microscope objective lens that combines a high numerical aperture with a large field of view of up to 6 mm combined with high spatial resolution.

Nanoscopy

A term describing light microscopy techniques at a resolution across the diffraction limit of light. The techniques include localization or blink microscopy, stimulated emission depletion microscopy and, more recently, MinFlux. By exploiting switchable fluorochromes, achieving a resolution of 20–10 nm down to a few nanometres becomes possible.

Persisters

A subpopulation of transiently antibiotic-tolerant bacterial cells that are often slow growing or growth arrested, and are able to resume growth after a lethal stress.

Phoenix phenotypes

Phoenix colonies that grow out of the zone of clearance of antibiotic-loaded beads from lawn biofilms while there are still very high concentrations of antibiotic present, suggesting an antibiotic-resistant phenotype.

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Flemming, HC., van Hullebusch, E.D., Neu, T.R. et al. The biofilm matrix: multitasking in a shared space. Nat Rev Microbiol (2022). https://doi.org/10.1038/s41579-022-00791-0

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