The domestic and industrial wastewater, solid wastes, hazardous wastes, and air contaminants that human activity produces are consumed or converted by microorganisms to innocuous forms. How do microorganisms do this? As an example, let’s take the case of human ("domestic" or municipal) wastewater. After your toilet is flushed, the wastewater flows to a septic tank (very common in Metro Manila) and/or through a series of sewer lines to a centralized wastewater treatment plant (e.g., the WWTP along Commonwealth Avenue in Quezon City serves the UP Diliman area). A common measure of "degree of pollution" or waste strength in wastewater is the amount of organic carbon present in the wastewater. Because it is very difficult and time-consuming to determine all the specific chemicals in human wastes as well as in many waste streams, we measure the waste strength in terms of the amount of oxygen needed to convert the organic carbon to CO2. We call this the "Biochemical Oxygen Demand" or BOD. The typical BOD of domestic waste is around 150-250 mg/L. Industrial wastewaters can have much higher BOD values, sometimes in the tens of thousands. Before discharging to receiving streams and rivers, the BOD should be as low as possible, around 10-20 mg/L (this depends on the applicable regulations). When high BOD wastewater is discharged into the river, microorganisms present in the river use up all the dissolved oxygen (DO) in the water. The river turns "septic"; it becomes black and starts to smell, as anaerobic processes take over. The Pasig River is the classic example of a river with depleted O2.
At the wastewater treatment plant, a variety of bacterial species (and some protozoa) are actively "grown" in tanks. These organisms consume the organics and lower the BOD. To do so, they have to be supplied with enough oxygen so they can perform the conversion of organics to CO2 and more bacterial cells. Some of the cells are retained in the system; some are excess, and have to be removed. The excess biomass, or "sludge" solids, should be treated (to reduce pathogens and degrade the volatile component), dewatered, and disposed of properly. Typically, the solids are land-applied to take advantage of the nutrients (nitrogen and phosphorus) present. Environmental engineers and WWTP operators design and operate wastewater treatment plants so that the different factors (e.g., biomass concentrations, reactor size, flow rates, oxygen levels, etc.) are in balance and optimized.
Aside from BOD, microorganisms transform nutrients such as nitrogen and phosphorus and decrease their concentrations in receiving water bodies. Nitrogen is an important nutrient, and high levels in lakes and rivers may lead to eutrophication, wherein high productivity causes algal blooms that then die and deplete the dissolved oxygen as organisms use up the organic carbon. Some cyanobacteria also produce algal toxins (for example, red tide poisoning is a manifestation of cyanobacterial growth). Nitrate in drinking water may lead to methemoglobinemia (blue-baby syndrome), where nitrate is converted in human saliva to nitrite, which then competes with oxygen in hemoglobin, thus reducing the O2 in the bloodstream.
In wastewater, nitrogen is usually in the form of ammonia or organic nitrogen, which is quickly converted to ammonia. Ammonia is used by autotrophic bacteria (e.g., Nitrosomonas and Nitrosospira) as an electron donor (substrate), and is oxidized in the presence of O2, to nitrite. This occurs at the wastewater treatment plant by giving these relatively slow-growing bacteria enough time to grow in the reactors. The nitrite produced is then subsequently oxidized by nitrite oxidizing bacteria (e.g., Nitrobacter and Nitrospira) to nitrate. The two-step process is collectively called nitrification. At this point, the nitrate is still dissolved in the wastewater. To remove nitrate, oxygen is removed from the reactors by turning off the air supply. Those heterotrophic bacteria that can denitrify then use the nitrate (instead of O2) as electron acceptor, and convert the nitrate to gaseous N2. Nitrogen gas is simply released to the atmosphere, which is 78 percent N2 anyway. There are other nitrogen transformation processes that occur in Nature and in wastewater treatment plants, but for the most part, nitrification-denitrification is the major route for nitrogen in wastewater treatment.
Phosphorus is another nutrient that limits the productivity (read: eutrophication) of lakes and other water bodies. This is why phosphorus in the form of phosphates (P) has been removed as an ingredient in most detergents. However, domestic wastewater still has some P, and industrial cleaners (e.g., phosphoric acid) contribute phosphorus to waste streams. Phosphorus can be biologically removed by phosphate accumulating organisms (PAOs). These organisms apparently store polyphosphates (P polymers) as they are cycled through anaerobic and aerobic conditions. Under no oxygen conditions, these organisms take up volatile fatty acids (VFAs) such as acetate and release phosphate by cleaving polyphosphate molecules. However, in subsequent aerobic conditions, they take up more phosphate than they released, resulting in a net P removal from the liquid stream. The stored polyphosphates are removed when the solids is removed. When treated properly, the sludge can be used as fertilizer, and the accumulated phosphates can serve as plant nutrients.
In your backyard septic tank, the bioprocesses are slightly different. The deeper portions of the septic tank are anaerobic, and here fermentative bacteria convert the organics to reduced forms, such as volatile fatty acids. These VFAs are, in turn, converted to methane by methanogenic organisms that are members of the Archaea. If sulfate is present, the sulfate is reduced to sulfide by sulfate-reducing bacteria. Hydrogen sulfide is the gas that gives off the characteristic "rotten egg" smell. Most of the liquid flows out of the septic tank, ideally into a leachfield (a volume of soil of adequate proportions). Here, the organic material in wastewater is converted by soil bacteria to CO2. Over time, the solid byproducts of anaerobic digestion accumulate in the tank, and that is the time homeowners have to call in the folks who extract the solids for a fee. These extracted solids would also have to be disposed of properly.
In Metro Manila, septic tank overflows are typically connected to the sewer system infrastructure. Very old sewer lines are typically clogged with sediment, tree roots, and are most likely full of cracks and breaks, and leaking into the surrounding soil. Since groundwater wells are common, the possibility of contamination of water sources is high. In general, the deeper the well, the less chance there is for contamination from septic tanks. Still, most homeowners in Metro Manila relying on groundwater pumps should have their drinking water tested for coliform bacteria, the indicators of fecal contamination. There is a drastic need for upgrading the very old sewer system infrastructure in Metro Manila.
How about solid waste? In your backyard compost pile, Bacteria and Eukarya such as fungi break down the complex material to macromolecules and byproducts such as humus. The processes in compost piles are typically aerobic, and are simply "accelerated" processes of what would occur naturally (e.g., on forest floors). Typically, municipal solid waste is collected and hopefully disposed of in an engineered landfill. The landfill is really a giant anaerobic solid waste reactor, and anaerobic processes occur here. Complex material is broken down. For example, paper and other cellulose-based material are degraded by cellulolytic bacteria that ultimately convert the cellulose to fatty acids. Fermenting bacteria convert other complex carbohydrates, proteins, and fats to long chain and short chain fatty acids (such as acetate), hydrogen, and CO2. Methanogenic bacteria then use the acetate and CO2 to form methane. In properly designed landfills, the methane can be captured for energy, or at least burned to convert the methane to CO2. If left unburned, the released methane can act as a greenhouse gas (methane is 21 times deadlier as a greenhouse gas than CO2). Once filled to design capacity after many years of operation, landfills can be capped and converted to parks and golf courses. In non-engineered systems, such as open dumps, all you would get is a mountain of smoking (that’s the slowly burning methane) garbage. In either case, microorganisms are doing what they’ve been doing for a long time – simply eating to survive, grow, and produce more biomass. What engineers and scientists are doing, in both wastewater and solid waste treatment and disposal, is to harness these microorganisms to clean up our wastes in engineered, well-designed and operated systems. These waste treatment systems have to be designed, built, and operated properly. Without them, we will continue to have black, smelly rivers and smoking, open garbage dumps.