Biofilm metabolism

In order to understand current approaches for prevention and control of biofilms, we must first consider the reasons for the failure of conventional antimicrobial protocols. There are thought to be three main reasons as to why biofilm bacteria out-survive their planktonic counterparts during antimicrobial treatments (reviewed by McBain et a/.16).These are i) poor penetration of antimicrobial compounds due to the presence and turn-over of exopolymer slime (glycocalyx) ii) the imposition of extreme nutrient limitation within the depths of the biofilm community and the co-incident expression of metabolically-dormant, recalcitrant phenotypes and (iii) the expression of attachment-specific phenotypes that are radically different and intrinsically less susceptible than unattached ones. 

Among the wide choice of reactor designs, the biofilm reactor is one of the best suited for azo-dye conversion as it meets two important process requisites. The first is related to the hindered growth feature of bacterial metabolism under anaerobic conditions. The second is related to the necessity to increase cell densities (see previous section) with respect to those commonly harvested in liquid broths [55, 56]. Except for bacteria that forms aggregates spontaneously, immobilization of cells on granular carriers and membrane reactor technology are the two common pathways to achieve high-density confined cell cultures in either discontinuous or flow reactors. 

Metabolic and physiological approaches in the detection of cause-effect relationships may be useful in the early assessment of stressors on biofilms. Physiological responses may be much faster and might reflect transient effects on the biofilms, while those that are more persistent may be reflected in the structural components (Fig. 10). 

General descriptors may be related to the metabolism responses in the biofilm. Biofilm algae have several mechanisms to counterbalance the damage caused by the toxicants. Environmental stress produces oxidative damage in the cells, which can be tracked down by means of the analysis of many enzymes (superoxide dismutase, catalase, peroxidase, etc.) that function as effective quenchers of reactive oxygen species (ROS). 

In spite of all of this variety of approaches, covering a wide array of metabolism pathways, limitations also exist. Differences in the vulnerability of biofilms have been found to depend on the age, community composition and succession status of the community. In dense biofilms the transfer of contaminants may be limited, resulting in decreased bioavailable concentrations of nutrients or toxicants for the algae. Biofilms show an inverse relationship between metal toxicity and biomass accrual [26], and a similar relationship has been established with nutrients. Therefore, the colonisation time or biofilm thickness are relevant factors to be included in the procedure uses. 

Marquis RE (1995) Oxygen metabolism, oxidative stress and acid-base physiology of dental plaque biofilms. J Ind Microbiol 15, 198-207. 

The presence of S. mutans and other cariogenic bacteria contributes towards the formation of a biofilm known as dental plaque, and their metabolism of fermentable carbohydrates in the diet leads to the formation of acids [12]. Dental caries has been described as a complex imbalance in physiologic equilibrium between tooth mineral and biofilm [13]. Biofilms imply the involvement of microbiological species [14], but the key concept included within this definition is that the bacteria involved are native to the body, not a group of specific invasive bacteria causing infection [14]. 

Figure 8.1. Biofilms are microbial communities that are made up of several species and often possess a distinct spatial structure. It has been found that living in a biofilm can offer significant protection to individuals, with sterilisation agents and even antibiotics being less potent against individuals if they are found in a biofilm. This is significant because it has been estimated that nearly three quarters of bacterial infections involve microbes that live in biofilm communities. Although there is a growing literature on the effects of NPs on biofilms, there is currently little knowledge of the production and metabolism of NPs in biofilms.

The pore wall consists of metal oxides. Its reactive part is consumed in proportion to depth because of metabolic activity within a biofilm. The biofilm separates the bulk solution from the pore wall. The horizontal biofilm concentration profiles on the left side of Figure 6 correspond to the center of each of the five boxes. (Concentration is on the vertical axis and biofilm thickness is on the horizontal axis.) Excess organic matter is assumed within the upper few centimeters. The arrows indicate net flux densities of various substances in and out of the biofilm. 

Substances in the bulk solution diffuse into the biofilm, where they are consumed (such as oxygen, point 1 in Figure 6) or recycled (such as sulfate through stepwise reoxidation of H2S from sulfate reduction, point 5). Within the biofilm, very steep gradients exist for oxygen or hydrogen sulfide and also for ferrous iron from reductive dissolution of ferric oxides. These gradients result from the coexistence of anaerobic and aerobic metabolisms such as aerobic respiration (point 1), reduction of ferric oxides (point 3), and sulfate... 

Fletcher, M., 1992. Bacterial metabolism in biofilms. In Biofilms — Science and Technology (L. E. Melo et ah, Eds.), pp. 113-124. Kluwer Academic, Dordrecht, the Netherlands. 

Biofilms enhance bacteria-DOM interactions by several means. Their spatial and chemical heterogeneity provides additional sorption sites for DOM compared with clean surfaces. Their loose architecture with interstitial voids and channels increases diffusivity and to some extent allows convective flow within biofilm structures. Because bacteria metabolize organic matter sorbed to the biofilm, a diffusion flux from the free water to the biofilm is maintained. Large proportions of organic matter sorbed to the biofilm are not instantly turned over but remain in the biofilm as a reservoir, which buffers direct effects of DOM depletion in the water column. 

Because of the high area of solid surfaces covered with biofilms, these biofilms dominate the heterotrophic metabolism in many aquatic ecosystems. In streams, rivers, and shallow lakes, bacterial activity in epilithic and epiphytic biofilms may be several times higher on an areal basis than the activity of free living bacteria. By the differential use of specific DOM fractions, biofilm bacteria influence the biogeochemical composition of DOM in these ecosystems. Biofilms thus can control biogeochemical fluxes of DOM and are important sinks of organic matter. 

Battin, T. J., A. Butturini, and F. Sabater. 1999. Immobilization and metabolism of dissolved organic carbon by natural sediment biofilms in a Mediterranean and temperate stream. Aquatic Microbial Ecology 19 297-305. 

Romani, A. M., and S. Sabater. 1999. Effect of primary producers on the heterotrophic metabolism of a stream biofilm. Freshwater Biology 41 729—736. 

Aside from adding defined compounds, experimental additions of natural DOM mixtures suspected to vary in lability have helped test ideas about the contribution of various DOM sources to aquatic ecosystems. In a nice example using manipulation of natural DOM sources, Battin et al. (1999) used flowthrough microcosms to measure the relative uptake rates of allochthonous and autochthonous DOM by stream sediments. They documented greater than fivefold differences or more in uptake and respiration, depending on whether the DOM was extracted from soil or periphyton. Moreover, they were able to show, via transplant experiments, several cases where prior exposure to a particular source of DOM increased the ability of that community to metabolize the DOM supplied. There appears to be some preadaptation of microbial catabolic capacity when these stream biofilms were re-exposed to a familiar type of DOM. Similarly, the response of heterotrophic bacteria to carbon or nutrient addition was greatest when the source community was particularly active (Foreman et al., 1998). Kaplan et al. (1996) showed that fixed film bioreactors, colonized on one water source, were unable to rapidly metabolize DOC in water from another source. 

In freshwater ecosystems, particularly streams and wetlands, biofilms account for a large portion of heterotrophic metabolism, as well as primary production (Edwards etal., 1990 see Chapter 12), acting as both sources and sinks for DOM. As the depth of the overlying water in the system increases, attached communities account for a declining share of system metabolism. 

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