Bacterial metabolisms

Bacteria. Bacteria and fungi are the non-photosynthesizing organisms at the base of the food web. They are the decomposers at the end of the downswing and  are also grazed upon by the primary grazers. They are the main source of all the B-vitamins in the food web; no vertebrate can manufacture its own.
 
All bacteria are aquatic, even if their watery environment is no more than a wet film upon a surface, yet few bacteria are found living free in water. In a laboratory, bacteria can be cultured free in a broth of nutrient, but in natural waters and in the aquarium, most of any apparently "free-floating" planktonic bacteria are actually attached to minute particles of organic flotsam, or "floc." And they are not alone, ever, nor even normally to be found in a colony of just one kind. No bacteria live alone— a "bacterium" can be only temporarily isolated on a sterile glass slide under a microscope.
 
Characteristically bacteria live in a richly mixed community of populations, thriving on the exhalations and "waste"— or metabolic byproducts— of their neighbors. "Waste" isn't a very useful word, when you're thinking about food webs, and "waste" scarcely applies to the microbial world, where all "waste" is a resource for some organism. Even free oxygen, when it first appeared in the atmosphere eons ago, was a toxic pollutant exhaled as a metabolic end product by cyanobacteria, until some other bacteria found a way to harness this waste for energy.
 
All the bacterial communities are intermixed with algal cells and algal colonies, and with fungi and sessile protists, all bound within the polysaccharide floc that bacteria exude, which covers every natural underwater surface. We call this mix the biofilm.
 
Bacteria power and manage all the nutrient cycles in the aquarium. The nitrogen cycle is the one we are thinking of when we say the aquarium has "cycled," but there are several other bacterial processes keeping the aquarium in ecological balance besides the metabolisms that convert ammonia eventually to nitrate.
 
Bacterially-generated biofilm coats every submerged surface, not just plant leaves and gravel grains. It makes the filter stem slimy and would even coat the glass with a film, if we let it, within a couple of days. Bacteria also mineralize organic forms of phosphate, making it available to plants and algae. Whatever "waste" the system produces provides a resource for some bacteria, in a feedback system that keeps the aquarium in balance.
 
Aerobic and anaerobic bacteria. Bacteria can be grouped according to their metabolisms. The aerobic bacteria all respire oxygen and give off carbon dioxide. (This is true even of the cyanobacteria, though the oxygen they produce in photosynthesis overwhelms the effects of their cellular respiration.)
 
Oxygen is the electron receptor that keeps the current of aerobic metabolisms flowing. But when there isn't enough available oxygen to get by on, some bacteria are able to switch metabolisms; they find a different electron receptor and keep going. They are called "facultative" anaerobes because they have this handy faculty. Other bacteria are "obligate" anaerobes, in the sense that they are obliged to live in anoxic micro-environments, for oxygen is deadly poison to them.
 
Aerobic forms of bacteria. Populations of aerobic bacteria are the overwhelming majority in our well-oxygenated environments. Many aerobic bacteria make a living by decomposing organic molecules, breaking them down into simple molecules that can pass through the bacterial membrane by osmosis— or that may be co-opted and taken up by plants. Aerobic decomposition is fast and efficient; it oxidizes organic carbon into things like ammonia (NH₃/NH₄) , it strips off phosphate groups(PO₄), and, perhaps surprisingly, even produces a little hydrogen sulfide (H₂S). Aerobic metabolisms break down proteins into their component amino acids, releasing energy in the process and producing ammonia as a by-product. And always aerobic metabolism produces CO₂ and molecules of H₂O.
 
These are the bacteria you'll hear characterized as "heterotrophs," because their nutrition depends on "other" (hetero) living or once-living organisms. Another large important group of aerobic bacteria are "autotrophs" that make their food themselves. Chemotrophic bacteria are kinds of autotrophs that make a living chemically, for instance by metabolizing ammonia— some of it produced by the decomposers— to form nitrite, or by metabolizing nitrite to nitrate.
 
These metabolisms require lots of oxygen. Two smaller groups of aerobic bacteria establish a narrow zone within the substrate (unless you're constantly disturbing it), where they oxidize bacterial byproducts produced by obligate anaerobes in the anoxic zones below them. These byproducts include hydrogen sulfide, which they turn to harmless sulfate, and methane, which they oxidize to carbon dioxide, deriving their own energy in the process. Truly, in the bacterial world there is no "waste."
 
Anaerobic bacteria. The anaerobic metabolisms of bacteria are less familiar and quite various, though all of them must take place where local supplies of oxygen are too low to interfere. Two separate kinds of bacteria are involved, the "facultative" anaerobes that are able to switch from a metabolism that requires oxygen to one that doesn't, and the "obligate" anaerobes, which require anoxic conditions.
 
An important service is provided by anaerobic "de-nitrifying" bacteria. De-nitrification is the hidden side of the nitrogen cycle, in which nitrates are metabolized through several possible pathways, to nitrogen gas. Some bacteria metabolize nitrate back to nitrite, some to nitrous oxide and eventually to N₂. When any nitrogen gas dissolved in water is diffused out into the atmosphere, that completes the nitrogen cycle. Whenever de-nitrification is inadequate, or if it's disturbed, then nitrates can build up, a signal that the nitrogen cycle is incomplete.
 
A useful link. Now only an abstract is available of a densely technical but readable 19-page handbook "Prokaryotes and their habitats" by Hans G. Schlegel and Holger W. Jannasch, which is  a chapter of The Prokaryotes (2006). The chapter provides a fundamental introduction to the microecosystems of bacteria, which encourages you to consider bacteria in their natural microenvironments, to define their habitats and ecological niches. Schlegel and Hannasch briefly describe the versatility of prokaryote metabolisms in relation to a few basic principles, and the ecology of the microcosm community, including those in anaerobic conditions or those using inorganic compounds (such as ammonia)— some in environments more extreme than you'd find in the aquarium. This document is primarily geared to college biology students, but don't be daunted. In a couple of evenings' reading, it will give you some sound background in the aquarium's prokaryotes: aerobic and anaerobic bacterial lifestyles, cyanobacteria, biofilm. etc.