Biofilm
A biofilm is a syntrophic community of microorganisms in which cells stick to each other and often also to a surface. These adherent cells become embedded within a slimy extracellular matrix composed of extracellular polymeric substances produced by them, which are typically a polymeric combination of extracellular polysaccharides, proteins, lipids and DNA. Because they have a three-dimensional structure and represent a community lifestyle for microorganisms, they have been metaphorically described as "cities for microbes". The biofilm allows sharing of nutrients among its residents and serves as a physical barrier against harmful environmental interactions such as desiccation, toxins/antibiotics, bacterivory and attacks from a host body's immune system.
Biofilms may form on living or non-living surfaces and can be common in natural, industrial, and hospital settings. They may constitute a microbiome or be a portion of it. The microbial cells growing in a biofilm are physiologically distinct from planktonic cells of the same organism, which, by contrast, are single cells that may float or swim in a liquid medium. Biofilms can form on the teeth of most animals as dental plaque, where they may cause tooth decay and gum disease.
Microorganisms form a biofilm in response to a number of different factors, which may include cellular recognition of specific or non-specific attachment sites on a surface, nutritional cues, lack of light or in some cases, by exposure of planktonic cells to sub-inhibitory concentrations of antibiotics. A cell that switches to the biofilm mode of growth undergoes a phenotypic shift in behavior in which large suites of genes are differentially regulated.
A biofilm may also be considered a hydrogel, which is a complex polymer that contains many times its dry weight in water. Biofilms are not just bacterial slime layers but biological systems; the bacteria organize themselves into a coordinated functional community, and can begin to form when a free-swimming, planktonic bacterium attaches to a surface and then proliferates monoclonally. Biofilms can attach to a surface such as a tooth or rock, and may include a single species or a diverse group of microorganisms. Subpopulations of cells within the biofilm differentiate to perform various activities for motility, matrix production, and sporulation, supporting the overall success of the biofilm.
Origin and formation
Origin of biofilms
Biofilms are thought to have arisen during primitive Earth as a defense mechanism for prokaryotes, as the conditions at that time were too harsh for their survival. They can be found very early in Earth's fossil records as both Archaea and Bacteria, and commonly protect prokaryotic cells by providing them with homeostasis, encouraging the development of complex interactions between the cells in the biofilm.Formation of biofilms
The formation of a biofilm begins with the attachment of free-floating microorganisms to a surface. The first colonist bacteria of a biofilm may adhere to the surface initially by the weak van der Waals forces and hydrophobic effects. If the colonists are not immediately separated from the surface, they can anchor themselves more permanently using cell adhesion structures such as pili. A unique group of Archaea that inhabit anoxic groundwater have similar structures called hami. Each hamus is a long tube with three hook attachments that are used to attach to each other or to a surface, enabling a community to develop. Hyperthermophilic archaeon Pyrobaculum calidifontis produce bundling pili which are homologous to the bacterial TasA filaments, a major component of the extracellular matrix in bacterial biofilms, which contribute to biofilm stability. TasA homologs are encoded by many other archaea, suggesting mechanistic similarities and evolutionary connection between bacterial and archaeal biofilms.File:A114, Lava Beds National Monument, California, USA, Golden Dome Lava Tube Cave, 2004.jpg|thumb|Biofilm of golden hydrophobic bacteria; ceiling of Golden Dome Cave, a lava tube in Lava Beds National Monument
Hydrophobicity can also affect the ability of bacteria to form biofilms. Bacteria with increased hydrophobicity have reduced repulsion between the substratum and the bacterium. Some bacteria species are not able to attach to a surface on their own successfully due to their limited motility but are instead able to anchor themselves to the matrix or directly to other, earlier bacteria colonists. Non-motile bacteria cannot recognize surfaces or aggregate together as easily as motile bacteria.
During surface colonization bacteria cells are able to communicate using quorum sensing products such as N-acyl homoserine lactone. Once colonization has begun, the biofilm grows by a combination of cell division and recruitment. Polysaccharide matrices typically enclose bacterial biofilms. The matrix exopolysaccharides can trap QS autoinducers within the biofilm to prevent predator detection and ensure bacterial survival. In addition to the polysaccharides, these matrices may also contain material from the surrounding environment, including but not limited to minerals, soil particles, and blood components, such as erythrocytes and fibrin.
The development of a biofilm may allow for an aggregate cell colony to be increasingly tolerant or resistant to antibiotics. Cell-cell communication or quorum sensing has is involved in the formation of biofilm in several bacterial species.
Development
Biofilms are the product of a microbial developmental process. The process is summarized by five major stages of biofilm development, as shown in the diagram below:Dispersal
Dispersal of cells from the biofilm colony is an essential stage of the biofilm life cycle. Dispersal enables biofilms to spread and colonize new surfaces. Enzymes that degrade the [|biofilm extracellular matrix], such as dispersin B and deoxyribonuclease, may contribute to biofilm dispersal. Enzymes that degrade the biofilm matrix may be useful as anti-biofilm agents. Evidence has shown that a fatty acid messenger, cis-2-decenoic acid, is capable of inducing dispersion and inhibiting growth of biofilm colonies. Secreted by Pseudomonas aeruginosa, this compound induces cyclo heteromorphic cells in several species of bacteria and the yeast Candida albicans.Nitric oxide has also been shown to trigger the dispersal of biofilms of several bacteria species at sub-toxic concentrations. Nitric oxide has potential as a treatment for patients that have chronic infections caused by biofilms.
It was generally assumed that cells dispersed from biofilms immediately go into the planktonic growth phase. However, studies have shown that the physiology of dispersed cells from Pseudomonas aeruginosa biofilms is highly different from that of planktonic and biofilm cells. Hence, the dispersal process is a unique stage during the transition from biofilm to planktonic lifestyle in bacteria. Dispersed cells are found to be highly virulent against macrophages and Caenorhabditis elegans, but highly sensitive towards iron stress, as compared with planktonic cells.
Furthermore, Pseudomonas aeruginosa biofilms undergo distinct spatiotemporal dynamics during biofilm dispersal or disassembly, with contrasting consequences in recolonization and disease dissemination. Biofilm dispersal induced bacteria to activate dispersal genes to actively depart from biofilms as single cells at consistent velocities but could not recolonize fresh surfaces. In contrast, biofilm disassembly by degradation of a biofilm exopolysaccharide released immotile aggregates at high initial velocities, enabling the bacteria to recolonize fresh surfaces and cause infections in the hosts efficiently. Hence, biofilm dispersal is more complex than previously thought, where bacterial populations adopting distinct behavior after biofilm departure may be the key to survival of bacterial species and dissemination of diseases.
Properties
Biofilms are usually found on solid substrates submerged in or exposed to an aqueous solution, although they can form as floating mats on liquid surfaces and also on the surface of leaves, particularly in high humidity climates. Given sufficient resources for growth, a biofilm will quickly grow to be macroscopic. Biofilms can contain many different types of microorganism, e.g. bacteria, archaea, protozoa, fungi and algae; each group performs specialized metabolic functions. However, some organisms will form single-species films under certain conditions. The social structure within a biofilm depends highly on the different species present.Extracellular matrix
The EPS matrix consists of exopolysaccharides, proteins and nucleic acids. A large proportion of the EPS is more or less strongly hydrated, however, hydrophobic EPS also occur; one example is cellulose which is produced by a range of microorganisms. This matrix encases the cells within it and facilitates communication among them through biochemical signals as well as gene exchange. The EPS matrix also traps extracellular enzymes and keeps them in close proximity to the cells. Thus, the matrix represents an external digestion system and allows for stable synergistic microconsortia of different species. Some biofilms have been found to contain water channels that help distribute nutrients and signalling molecules. This matrix is strong enough that under certain conditions, biofilms can become fossilized.Bacteria living in a biofilm usually have significantly different properties from free-floating bacteria of the same species, as the dense and protected environment of the film allows them to cooperate and interact in various ways. One benefit of this environment is increased resistance to detergents and antibiotics, as the dense extracellular matrix and the outer layer of cells protect the interior of the community. In some cases antibiotic resistance can be increased up to 5,000 times. Lateral gene transfer is often facilitated within bacterial and archaeal biofilms and can lead to a more stable biofilm structure. Extracellular DNA is a major structural component of many different microbial biofilms. Enzymatic degradation of extracellular DNA can weaken the biofilm structure and release microbial cells from the surface.
However, biofilms are not always less susceptible to antibiotics. For instance, the biofilm form of Pseudomonas aeruginosa has no greater resistance to antimicrobials than do stationary-phase planktonic cells, although when the biofilm is compared to logarithmic-phase planktonic cells, the biofilm does have greater resistance to antimicrobials. This resistance to antibiotics in both stationary-phase cells and biofilms may be due to the presence of persister cells.