Biofilm covers every underwater surface. In a newly set-up aquarium, within hours of first filling the tank, the first bacterial colonists and germinating algal and fungal spores have already begun settling on every available surface, plant, leaf litter, root, rock, gravel, or glass. With them, the processes that build up the living biofilm community have begun. The community is based on its bacteria and algae, and, where leaf litter is present (introduced in the aquarium by you), on the concentration of proteins in the fungal mycelium that quickly covers the surfaces of dead leaves that have washed into the stream and penetrates their largely inert structure.
Bacteria on surfaces. Few bacteria remain free in the water column, many fewer than there are in the moist films in soils, for instance. Solid surfaces present the only secure sites for making a microscopic living. Any bacteria present in the water tend to be drawn to surfaces and adhere to them. Several forces are involved in this. Even in very still waters, isolated bacteria are unlikely to settle on horizontal surfaces by sedimentation alone. Brownian motion, caused by the random buffeting of molecules, is ordinarily involved in bacterial settling, and once bacteria have come very near to surfaces, various fluid dynamic forces take effect: van der Waals forces and electrostatic interactions. Bacteria become irreversibly bound to surfaces, in processes broadly analogous to adsorption of molecules to surfaces. So all the surfaces in the aquarium tend to "pull" the bacteria from the water. Bacterial populations in open water are likely to be adhering to free-floating particles of organic floc or colloidal silt.
The accumulation of bacteria on surfaces isn't just passive, either. Nutrients also tend to bind to surfaces, and bacteria actively move towards nutrients, a reaction that bacteriologists call chemotaxis.
Once attached to a surface, bacteria have mastered the art of clinging. They exude coatings made of sticky proteins assembled from amino acids and starches built of linked-up sugars, and their communal life-processes are continually renewing these exudations. The polysaccharide matrix bears a light negative charge, which tends to attract positively-charged cations, including some nutrients. The stringy, sticky, spongy, flaky, water-penetrated polysaccharides accumulate into a highly-structured labyrinthine protective environment in which mutually beneficial bacterial communities thrive. Additional bacterial nutrients are adsorbed to these gummy surfaces. Anti-bacterials, even chlorine, are rendered much less effective by this protective sugar-based envelope, which bacteriologists like to call the glycocalyx, which is Greek for, um, "sugar-based envelope." The spongy structure continues to build up, maintained by an interactive web of bacterial signals, eventually becoming hundreds of times thicker than the size of a single bacterium. Deep within a matured biofilm, where surface oxygen becomes rapidly depleted, even anaerobic bacteria find microzones that are secure from the damaging effects of oxygen.
Aufwuchs. This structure and the community that lives on it and within it is called the benthos when it's accumulated in and on the bottom sediment, or more generally the biofilm. This is the stuff German aquarists call Aufwuchs, which could be translated "overgrowth." The bacterial communities in the biofilm and in water trapped within the substrate provide the energy that drives all the recycling of organic and inorganic substances within the aquarium's ecosystem. This same biofilm forms in the woven crimped fibers of the rotating biowheel, so you'll find the description of bio-filtration relevant here. If you think that a biofilm structure built out of simple sugars linked into polysaccharide chains has a nutritious sound to it, well, you're right. Our snails and otocinclus are more omnivorous than their "algae-eater" titles suggest. A snail passing across what looks to us like a simple algal film is also ingesting a whole community of organisms founded on the bacterial polysaccharides.
"The greatest population of bacteria is in the gravel" is a familiar statement that you often hear when the bacteria at work in filter media are being discussed, but don't forget that even older statement, "A rolling stone gathers no moss." A more nurturing location for those nitrifying bacteria and the others said to be "in the gravel" must be in the floc, or humic compost that is lodged among the grains. If your substrate started out purely gravel, with all silt carefully rinsed out of it, it could take months for this floc to develop. Some additives to substrates for planted tanks are expressly designed to substitute for floc: laterite and colloidal clay and humic compost. Floc and biofilm in the interstitial water of the substrate work like humus in an undisturbed forest soil; they provide homes for most of the bacterial energy that runs the whole cycling system. So, you won't be surprised to hear that I scarcely ever vacuum my gravel, just siphon off loose surface detritus.
Bacterial communism. In a natural environment, no solitary species of bacteria exists in an isolated culture for long. Bacteria forever thrive in consortium with other bacteria, metabolizing each other's wastes and even trading packets of genetic information. The familiar image of an evolutionary tree— or more often nowadays of a densely twiggy evolutionary bush— which is employed to describe the genealogy of animal life, doesn't fully apply to bacteria. Their "tree of life" can only be pictured in the form of a network, more like a fungal mycelium than a tree, with packets of genetic material not only inherited from forebears, which you'd picture lying back towards the center of the network, but also transferred "side-to-side" between unrelated but neighboring strains. As far as bacteria are concerned, DNA is more like a fund of community capital than the individual DNA bank accounts we animals maintain.
So when you're trying to disentangle the bacteria, even the concept of "species" begins to break down, and scientists resort to exotic categories. They may sort out bacteria according to their reactions to staining, into "Gram-positive" and "Gram-negative" types. Or they pigeonhole them according to their characteristic shapes: rods or spirals or balls offer handy categories, which are embodied in familiar names ending in -bacillus or -spirochæte or -coccus. Or scientists sort bacteria according to their metabolisms. When you're considering the biofilm in your tanks, it's the metabolisms of bacteria, which fix their roles in the community, that will probably concern you most.
Diatoms. The bacterial/fungal co-op isn't alone in the benthos, of course. Among those first colonizers in the community will also be diatoms: as photosynthesizers, they get a more general discussion among algae. Diatoms, too, may secrete mucilage. Some kinds of diatoms grow on the end of mucilaginous stalks or within mucilaginous tubes. Mucilage may bind other kinds of diatoms together into chains or colonies. So diatoms can also contribute to the gummy, porous biofilm structure. Cyanobacteria won't lag behind, but they mostly have to make room for green algae, as the biofilm matures (see next page).
Link. Biofilms: The Hypertextbook
offers an introduction to biofilms in its Chapter 1, available online.
To get a sense of the dense, richly varied population of floc and biofilm, look at Micrographia's directory of color photos of freshwater microorganisms.