Biofilms – What? Where? Why?


Bacteria can be found in practically every part of the world, but while the common view is of individual species in relatively isolated colonies, they are often found in a mixed conglomeration known as a biofilm. Biofilms are present all around us, in almost every environment that humans encounter and also in many that we don’t. Like the analogous combined workforce of the human species, the worth of a biofilm can be greater than, and even very different from, the sum of its individual parts.

What are biofilms

Huq et al. (2008) define a biofilm as “an assemblage of microbial cells that is surrounded by a matrix of exopolysaccharide (EPS) secreted by those cells”. Most often they are found on a solid surface in contact with a fluid medium. Some biofilms exist as a simple monolayers consisting of a single species (rare), or as multiple species existing together in a dense, complex matrix (Prescott et al, 2005). A biofilm starts out as one or more individual bacterial cells that attach to a surface. As the number of bacteria increase – through replication and arrival of other bacteria – they join together adhering with the already present bacteria by a process called co-aggregation. Mature bacteria within a fully established biofilm will usually release back into the fluid and return to a planktonic state. By this process the bacteria spread and may go on to form another matrix, often expanding upon the initial structure. In this way, and by virtue of the benefits described below, biofilms can form and grow in almost any environment where there is a suitable solvent and surface for their initial formation.

The matrix of a biofilm is created by secretions from the bacteria themselves and consists primarily of proteins and polysaccharides. It may also include DNA and even component molecules from the surface to which it is attached (Wilson, 2005). A thin layer of molecules can exists between the host surface and the biofilm matrix proper – often composed of organic and inorganic molecules from the liquid medium –  and this is referred to as a conditioning film (Wilson, 2005), though in some cases such films can actually serve to prevent the formation of a biofilm (Palmer et al., 2007). While bacteria are microscopic, biofilms can grow to clearly visible, even huge, macroscopic scales.

The actual matrix of a biofilm may compose between 50-90% of a biofilm mass (Wilson, 2005) with the bacteria themselves forming the lesser portion. Much of the matrix structure is given over to water channels which transport oxygen and nutrients throughout the biofilm. It may also include void areas which contain fluids or gasses that serve in the formation of niches within the matrix (see Micro-Environments, below).

Where are Biofilms Found

Biofilms are encountered almost everywhere (Engelkirk and Burton, 2007) there is a solid surface to adhere to and suitable solvent for the bacteria. They also form on the surface of liquids such as the surface of a pond, though such films are often easily disrupted by water turbulence. Biofilms are very common in areas of flowing water where there is a constant replenishment of nutrients e.g. river beds, sewer walls etc. Sometimes they are obvious, e.g. pond scum or dental plaque. Very often they are visible, but not noticeable i.e. thin enough to appear transparent, especially in damp conditions. Indeed, many biofilms are ignored by humans in general unless they begin to cause problems. Most animals have biofilms that exist within or upon their person; the human gut is lined with a biofilm composed of our gut bacteria.

When found in unwanted locations, biofilms can cause problems. A build-up of biofilms within water pipes can lead to increased corrosion, reduced water flow and may even present a source of pathogens (Huq et al., 2008). Alternatively, biofilms are often harnessed by industry for their benefits. For example, in the treatment of waste water the natural nitrifying action of specific bacteria is utilised in place of chemicals.

Why Do Biofilms Exist

For the individual bacteria within it, a biofilm presents a multitude of benefits. Specific benefits and functions may vary dependent upon the species of bacteria present, but some factors are generic to all biofilms. While the adage of ‘safety in numbers’ may not apply to bacteria in the same sense as it does to, say, a school of fish, there are obvious benefits to being in a large colony.


Within a biofilm there exists many micro environments, usually along a gradient e.g. pH, O2 concentration, CO2 concentration. It is the manipulation of these gradients that allows the creation of specific niches (Hall-Stoodley and Stoodley, 2005) and thus allows resident bacteria to thrive in places they might not normally be found. This is arguably the key factor behind biofilm formation as a favourable growth environment is fundamental to the further proliferation of the bacteria.

Resource Management and Exchange

Distribution channels within the matrix ensure that even those members not actively involved in procurement of nutrients will still receive what they need to survive. It is not uncommon for a mix of trophic abilities to be present (Prescott, 2005) within a single biofilm. For example one member species may be photosynthetic, and be found at the upper surface of the biofilm to best utilise light. Another member may be a chemoautotroph and be found at the bottom of the biofilm – especially those attached to inorganic surfaces. In this way, the biofilm as a whole is capable of obtaining nutrients and energy from more sources than the individuals present within it could do so alone. As procured nutrients are shared throughout the biofilm, this is clearly a huge benefit to all members existing within a biofilm.


The matrix of a biofilm acts as a shield to outside factors and can protect those within it from the external environment e.g. extremes of temperature, pH etc. In environments where there is a constant flow of water, the biofilm acts as an anchor for the member species, preventing them from being swept away.

A biofilm may also act as a barrier to unfavourable chemicals and toxins. For example, antibiotics may not be able to penetrate the matrix (Paolo et al., 2010). This, in particular, is an important concern in the medical profession; biofilms can form on almost any surface – especially within the human body. Control of biofilms as a possible pathogenic source is vital in the case of surgical implants such as artificial joints, catheters and heart valves.

Quorum Sensing

Within the natural world, bacteria exist either as part of a biofilm or in a planktonic (free floating) state. Very often they will transition between the two at various stages in their lifecycle (Paolo et al., 2010). It is not uncommon to find bacteria expressing a phenotype not encountered at any other time within the species, other than when it is part of a biofilm (Paolo et al., 2010). Such transformations are initiated through the phenomenon of quorum sensing; signal molecules are released by member bacteria and carried by the channels throughout the biofilm matrix. When the concentration of these molecules reaches a particular level, gene expression, and often phenotype, of the individual bacteria can change (Prescott, 2005).

Changes often result in the expression of specific enzymes that are only efficient in a biofilm environment. Quorum sensing can allow the bacteria within a biofilm to monitor the population size within the matrix and signal the appropriate time for mating, sporulation or the release of planktonic bacteria (Prescott, 2005).


Biofilm formation allows the contributing bacteria to fine tune and, even create, their perfect niche environment (Prescott et al., 2005) even in areas where it would perhaps not normally be possible for the bacteria to thrive. Ranging from simple layers of bacteria to complex, inter-related structures supporting many different bacterial species, they are a fundamental structure in bacterial life.

So successful are biofilms in enabling the proliferation of bacteria that they are regarded as a serious problem when they appear, as they so easily do, in areas that could pose a risk to humans. While a pathogenic bacterium introduced into the body in isolation might not pose a threat, the same bacterium as part of a biofilm – afforded the protection and opportunity to multiply to numbers constituting an infectious dose – can represent a serious problem.

Given the proliferation of biofilms throughout the environment, it is also important to consider them on a wider scale. The sheer biomass they represent comes into play when we consider them from an ecological standpoint. They act as primary producers for both invertebrates and, such is their scale, for some vertebrates, too (Tomohiro et al., 2008).

While the inner workings and mechanisms are still a subject of much study, it is clear that biofilms are an integral part of not just bacterial life, but of life on the planet as a whole.


Engelkirk, P.G. and Burton, G.R.W. (2007) Burton’s Microbiology For The Health Sciences. 8th Ed. USA: Lippincott Williams & Wilkins

Hall-Stoodley, L. and Stoodley, P. (2005) Biofilm formation and dispersal and the transmission of human pathogens. Trends in Microbiology. [e-journal] 13(1) Available through: Edinburgh Napier University website <; [Accessed 12th November 2012].

Huq, A., Whitehouse, C.A., Grim, C.J., Alam, M., Colwell, R.R. (2008)Biofilms in water, its role and impact in human disease transmission. Current Opinion in Biotechnology. [e-journal] 19, p.244-247. Available through: Edinburgh Napier University website < > [Accessed 12th November 2012].

Palmer, J., Flint, S., Brooks, J. (2007) Bacterial Cell Attachment, The Beginning of a Biofilm. Journal of Industrial Microbiology and Biotechnology. [e-journal] 34, p.577-588. Available through: Edinburgh Napier University website <; [Accessed 8th November 2012].

Paolo, L., Antoniani, D., Grant Burgess, J and Nijland, R. (2010) Molecular mechanisms of compounds affecting bacterial biofilm formation and dispersal. Applied Microbiology and Biotechnology. [e-journal] 86, Available through: Edinburgh Napier University website <; [Accessed 8th November 2012].

Prescott, L.M., Harley, J.P. and Klein, A.D. (2005) Microbiology. 6th Ed. New York: McGraw-Hill

Tomohiro, K., Beninger, P.G., Decottignies, P., Mathot, K.J., Lund, D.R., Elner, R.W., (2010) Biofilm Grazing in Higher Vertebrate: The Western Sandpiper, Calidris Mauri. Ecological Society of America.  [e-journal] 89(3), Available through: Edinburgh Napier University website <; [Accessed 1st November 2012].

Wilson, M. (2005) Microbial Inhabitants of Humans: Their ecology and Role in Health and Disease. USA: Cambridge University Press

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