BSc 2nd Year Environmental Microbiology Notes Study Material
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BSc 2nd Year Environmental Microbiology Notes Study Material
Human activities create vast amounts of various wastes and pollutants. The release of these materials into the environment causes serious health problems as they make undesirable changes to our land and water resources making them unfit for use. Proper treatment of such wastes and is necessary, using microbial biodegradation/detoxification.
In this post, we would discuss some of the methods which make environmental use of microorganisms to maintain environmental quality and safe disposal of waste and pollutants. The chief wastes and pollutants of concern are : (i) solid wastes, (ii) liquid (water) waste, i.e. sewage, and (iii) industrial wastes, such as pesticides, oil spills, etc.
Solid Waste Disposal
Besides the inert part such as glass, metal, and plastic, the solid wastes also contain degradable organic waste such as kitchen scraps, paper, and other household and industrial garbage. Sewage sludge derived from the treatment of liquid wastes, animal waste from cattle feed lots, and poultry and swine farms are also major sources of solid organic waste. In rural areas, these may be recycled into the land as fertilizer. However, in urban areas, they pose an environmental problem.
Following microbiological methods have been developed to treat the organic part of these wastes by the use of microbial biodegradation.
[I] Sanitary landfills
The material is placed in a landfill to allow it to decompose. Both, organic and inorganic solid wastes are deposited together in low-lying land. To avoid, foul odour and attraction of insects and rodents, each day’s waste deposit is covered over with a layer of soil, creating a sanitary landfill. A developed landfill can be used for construction and recreation purposes. For 30-50 years, the organic matter undergoes slow, anaerobic microbial decomposition, and the products which result include CO2, H2O CH4, and low mol. wt. alcohols, and acids diffuse in the surrounding air and water. Thus landfill settles down.
Various methods for making sanitary landfills are used. These are, the GN area methods where a bulldozer spreads and compacts solid waste; cover material is hauled in and spread at the end of the operation, (ii) trench method in which the waste collection truck deposits its load in a trench where it is spread and compacted, and (iii) ramp variation, where solid wastes are spread and compacted on a slope.
[II] Composting
Here the organic part of the waste is biodegraded by composting. In this process, the waste is degraded by aerobic, mesophilic, and thermophilic microbes. Inorganic fraction is separated either at the source or by using magnetic separators. Organic fraction is ground up, mixed with sewage sludge and/or bulking agents (shredded newspaper, wood chips), and then composted. This balances the C: N balance. Microbial composting converts the waste into a stable, sanitary, humus-like product. Various composting methods are used. These include the following:
1. Window method. Solid waste is arranged in long rows and covered to allow decomposition. Material is turned over repeatedly.
2. Aerated pile method. Here composting rates can be enhanced. Waste is arranged in piles and forced aeration is used to supply extra O2. Perforated pipes are buried inside the compost pile and the air is then pumped.
3. Continuous-feed composting. It uses a reactor that permits control of the environmental parameters. A reactor is like an industrial fermentor. Here composting is complete in 2-4 days. But this method is expensive.
In compost of domestic garbage and sludge, several microbial species that come from the soil, water, and human fecal matter are present. The high moisture content of the compost favours the growth of bacteria more than fungi. Mesophiles are the first to appear and as the temperature rises, thermophiles begin to grow.
Thermophiles that are dominant in compost are bacteria like Bacillus stearothermophilus, Thermomonospora spp, Thermoactinomyces spp, and Clostridium thermocellum, and the fungi, such as Geotrichum candidum, Aspergillus fumigatus, Mucor pusillus, Chaetomium thermophile, Thermoascus auranticus, and Torula thermophila. The reactor is maintained at thermophilic temperatures. Maximum composting occurs at 50-60°C, moisture should be 50-60°% water content, the C: N ratio must not exceed 40: 1, and the lower nitrogen will not allow the growth of enough microbial biomass. (BSc 2nd Year Environmental Microbiology Notes Study Material)
Liquid Waste Treatment
Agricultural and industrial operations – along with everyday human activities – produce liquid wastes, including domestic sewage. These enter into natural water bodies through different routes depending upon the living conditions and habits of the local population. Fortunately, self-purification is an inherent capability of natural waters, based on biogeochemical cycling.
But rising population, large-scale agricultural operations, and industrialization result in the production of liquid waste on a scale that routinely overwhelms the self-purification capacity of aquatic ecosystems. A prominent feature of river water receiving sewage is the presence of the filamentous aerobic bacterium, Sphaerotilus natans, known as the “sewage fungus”. A heterogeneous microbial community also develops amid the filaments of this bacterium below a sewage outfall. This bacterium and the associated microbial community are efficient degraders of organic matter. (BSc 2nd Year Environmental Microbiology Notes Study Material)
Sewage Treatment (Microbiology of Sewage)
Sewage is the used water supply containing domestic waste together with human excrement and washes water and industrial waste, including acids, greases, oils, animal matter, vegetable matter, and storm waters. The basic Principle in sewage treatment is that water is separated from the waste while the solid organic matter is biodegraded by microorganisms to simple compounds like nitrates, sulphates, carbonates, carbon dioxide, methane, etc. (BSc 2nd Year Environmental Microbiology Notes Study Material)
Sewage treatment is managed on small scale as in individual homes and rural areas as well as on a large scale in towns by municipal bodies. We shall consider the most common methods of sewage treatment at these levels.
Small-scale sewage treatment
This is managed by the following two common methods.
1. Cesspools. In many homes, human waste is dumped into cesspools. A cesspool is an underground construction, consisting of concrete cylindrical rings with pores in the walls of the ring. Water passes out the bottom and through the pores into the surrounding sand, whereas solid waste accumulates at the bottom.
Anaerobic bacteria in the compacted sludge layer at the bottom of the cesspool digest the organic matter. The breakdown products diffuse into the ground. After a few years, it may become necessary to pump out the sludge layer (if it becomes thicker) and clean it with strong acid. Chemicals that can digest the grease should also be added to avoid blockage of the pores. Dried bacterial spores such as those of Bacillus subtilis are available in stores. These may be added to accelerate sludge digestion. The addition of yeasts at intervals is also useful.
2. Septic tanks. These are also used in some homes. A septic tank is an enclosed concrete box into which waste flows from the house.
The organic matter accumulates at the bottom of the tank whereas the water rises to the outlet pipe to flow to a distribution box. The box is then separated into pipes that empty into the surrounding area. The tank is to be pumped out regularly as there is no absorption of the digested organic matter into the earth. Small towns collect the sewage into large ponds called oxidation lagoons. The sewage is left in the lagoon for a couple of months during which aerobic bacteria digest the organic matter in the water and anaerobic organisms break down the sedimented material. (BSc 2nd Year Environmental Microbiology Notes Study Material)
Large-scale sewage treatment by municipal bodies
Municipal plants are equipped with a mechanized sewage treatment that handles massive amounts of waste and garbage generated daily. A simplified view of such a waste treatment facility is shown in Figure. The overall process can be divided into three steps: the primary, secondary, and tertiary treatments. These different treatments to sewage depend on the quality of the effluent deemed necessary to be achieved to permit the maintenance of acceptable water quality.
Primary treatments rely on physical separation procedures to lower the BOD; secondary treatments rely on microbial biodegradation to further reduce the concentration of organic compounds in the effluent, and tertiary treatments use chemical methods to remove inorganic compounds and pathogenic microorganisms. Municipal treatment plants are not capable of dealing with industrial wastes containing toxicants, such as heavy metals. (BSc 2nd Year Environmental Microbiology Notes Study Material)
1. Primary treatment. This removes suspended solids in settling tanks or basins. Solids are drawn off. Raw sewage is piped into huge open tanks where it is screened to remove solid fractions. This solid material is then subjected to anaerobic digestion in landfill or composting. The liquid portion is then passed into sludge tanks for further treatment. Flocculating materials such as aluminium or iron sulphate are also added to raw sewage to trap microbes and debris to the bottom as in the sedimentation process of water purification. These materials are added to sludge tanks also. (BSc 2nd Year Environmental Microbiology Notes Study Material)
2. Secondary treatment (microbial biodegradation). To achieve an acceptable reduction in the BOD, secondary treatment by a variety of means is necessary.
In this treatment, a small portion of the dissolved organic matter is mineralized, and the large portion is converted to removable solids. By now the original sewage BOD is reduced to 80-90 percent. Secondary treatment relies on microbial activity, may be aerobic or anaerobic, and is conducted in a large variety of devices. Since this step is a microbial process, the accidental introduction of a toxic chemical is very dangerous. Various devices used in this treatment are as follows:
(a) Oxidation ponds. Oxidation ponds or stabilization ponds and lagoons are used for simple secondary treatment in rural areas or industrial units. Heterotrophic bacteria degrade sewage organic matter within ponds, producing cellular material and mineral products that support the growth of algae. Oxygen produced by algae compensates for the poor O2 conditions created by heterotrophic bacteria. The pond should be shallow, 10 feet deep, to maximize the euphotic zone for algal growth. Bacterial and algal cells settle at the bottom of the pond. Effluents containing oxidized products are periodically removed.
(b) Trickling filter. This system is a simple and inexpensive film-flow type of aerobic sewage treatment device. Sewage is distributed by a revolving sprinkler suspended over a bed of porous material. The sewage slowly percolates through this porous bed and the effluent collected at the bottom. The porous material of the filter bed becomes coated with a dense, slimy bacterial growth, mainly composed of Zooglea ramigera and similar slime-forming bacteria. (BSc 2nd Year Environmental Microbiology Notes Study Material)
This slimy matrix thus generated harbors a heterogeneous microbial community, including bacteria, fungi, protozoa, nematodes, and rotifers. The most frequent bacteria are Beggiatoa alba, Sphaerotilus natans, Achromobacter spp, Flavobacterium spp, Pseudomonas spp, and Zooglea spp. (BSc 2nd Year Environmental Microbiology Notes Study Material)
This community absorbs and mineralizes dissolved organic nutrients in the sewage reducing the BOD of the effluent. A porous bed allows aeration. Sewage may be passed through two or more trickling filters or recirculated through the same filter.
(c) Biodisc system. The bio-disc system or rotating biological contactor is a more advanced type of aerobic film-flow treatment system. Here, closely spaced discs, usually made of plastic are rotated in a trough containing the sewage effluent. The discs are partially submerged and become coated with a microbial slime similar to that developing in trickling filters. Continuous rotation of the discs keeps the slime well aerated and in contact with the sewage. Microbial growth on the disc surfaces is sloughed off gradually and removed by subsequent settling.
When the film becomes so thick that O2 and nutrients fail to reach the inner portion of the film, the innermost microbes die, causing detachment of the film. The system is used in communities for the treatment of domestic and industrial sewage effluents.
(d) Activated sludge. This process is very widely used in aerobic suspension type of liquid waste treatment system. After primary settling, the sewage is introduced into an aeration tank. Air injection and/or mechanical stirring provides aeration. The rapid development of microbes is also stimulated by the reintroduction of most of the settled sludge from a previous run, and the process derives its name from this inoculation with activated sludge. The vigorous development of heterotrophic microbes has taken place during the holding period.
The populations include Gram-negative rods, predominantly Escherichia, Enterobacter, Pseudomonas, Achromobacter, Flavobacterium, and Zooglea spp; other bacteria including Micrococcus, Arthrobacter, various coryneform and mycobacteria; Sphaerotilus and other large filamentous bacteria; and low numbers of filamentous fungi, yeasts, and protozoa. Bacteria occur in free suspension and as flocs. The flocs are microbial biomass held together by slime. (BSc 2nd Year Environmental Microbiology Notes Study Material)
Due to the extensive microbial metabolism of the organic compounds in sewage, a large proportion of dissolved organic substrates is mineralized and another portion is converted to microbial biomass. In the advanced stage, biomass associated with flocs is removed by Poor settling may cause bulking of sewage sludge caused by proliof filamentous bacteria like Sphaerotilus, Beggiatoa, Thiothrix, and Bacillus and filamentous fungi like Geotrichum, Cephalosporium, Cladom, and Penicillium. A portion of the settled sewage sludge is recycled for use as the inoculum for the incoming raw sewage, but the rest goes for additional treatment by composting or anaerobic digestion.
The activated sludge process reduces the BOD of the effluent to 10-15% of that of the raw sewage. Intestinal pathogens are also reduced. Non-pathogenic bacteria proliferate in number. (BSc 2nd Year Environmental Microbiology Notes Study Material)
(e) Septic tank. This is the simplest anaerobic treatment system, used extensively in homes and rural areas with no proper sewerage systems. A septic tank acts largely as a settling tank within which organic wastes undergo limited anaerobic digestion.
(f) Anaerobic digesters. Large-scale anaerobic digesters are used for further processing of the sewage sludge produced by primary and secondary treatments. In practice, these digesters are used only for processing settled sewage sludge and the treatment of very high BOD industrial effluents. Anaerobic digesters are large fermentation tanks designed for continuous operation under anaerobic conditions.
There are provisions for mechanical mixing, heating, gas collection, sludge addition, and drawing off of established sludge. They contain high amounts of suspended organic matter, much of which is bacterial biomass (109-1010/ml). A complex bacterial community is involved in the degradation, with the number of anaerobes, 2-3 times more than that of aerobes.
Anaerobic digestion of wastes is a two-step process in which a large variety of non-methanogenic, obligately or facultatively anaerobic bacteria participate. In the first step, complex organic materials, including microbial biomass are depolymerized and converted to fatty acids, CO2 and H2. In the next step, methane is generated either by the direct reduction of methyl groups to CH4 or by reduction of Co2 to CH4 by molecular hydrogen or other reduced products of fermentation.(Microbiology Environmental Quality Notes Study Material)
The final products obtained in the digester are a gas mixture, approx. 70% CH4 and 30% CO2, microbial biomass, and a non-biodegradable residue. The gas can be used within the treatment plant to drive the pumps and/or to provide heat.
3. Tertiary treatment. This is designed to remove non-biodegradable organic pollutants and mineral nutrients, especially N2 and P salts. Activated carbon filters are normally used in their removal from secondary-treated effluents. To prevent eutrophication, phosphate is removed from sewage by precipitation as calcium, aluminum, or iron phosphate. Breakpoint chlorination is a process to remove NH3. In big cities, a highly advanced tertiary water treatment system integrates several of the tertiary treatment processes.
Biodegradation of Industrial Wastes
[I] Pesticide waste
We have already referred to the biodegradation of pesticides used in agriculture in the preceding topics. Besides physical and chemical methods, there are also biological methods for pollution control. Microorganisms have been found very effective in the disposal of pesticide waste through biodegradation. The excess pesticide wastes generated from pesticide industries’ effluents, and washings of pesticide containers are environmental problems. Microbes detoxify/degrade these wastes and thus present a safe method of their disposal.
Instead of whole cells, cell extracts or enzymes of microbes have been recommended. Parathion hydrolase obtained from Flavobacterium ATCC 27551 and Pseudomonas diminuta can hydrolyze a number of organophosphates, such as methyl parathion, diazinon, fenitrothion, cyanephos, and coumaphos. The process is very fast and requires no cofactors. Pseudomonas cepacia is used to clean up soil containing 20,000 ppm of 2, 4, and 5-T.(BSc 2nd Year Environmental Microbiology Notes Study Material)
[II] Toxic heavy metals
Wastes from thermal power stations, metal and refining industries, electroplating units, sewage sludge, tanneries, etc. contain toxic heavy metals. These can be removed by physicochemical means, such as ion exchange, precipitation, activated carbon adsorption, and electrolysis. But each of these has some drawbacks and limitations. Therefore, microbial biomass has been all of heavy metals. Microbes are being exploited for the removal and recovery of these metals. Microbes adsorb these metals actively or passively. Biomass produced from Zooglea ramigera, a polysaccharide-secreting organism adsorbs copper and cadmium up to the levels of 300 and 100 mg of metal/g dry wt. respectively.
When loaded biomass is exposed to acid treatment it results in rapid desorption of metals. Pseudomonas putida, Arthrobacter viscous, and Citrobacter spp are employed to remove several toxic metals from industrial effluents. Recently BIOCHEM- a wastewater treatment and metal recovery technology has been developed in which granulated, non-living biosorbent of microbial origin is used for absorption of Cd, Cu, Pb, Zn, and Ag with 98% efficiency. (BSc 2nd Year Environmental Microbiology Notes Study Material)
Radioactive metals can also be removed by using microbial biomass. The biomass of Rhizopus arrhizus can accumulate about 180 mg/g dry wt. of uranium and thorium. Penicillium chrysogenum biomass is used for radium removal. Saccharomyces cerevisiae, the common yeast can accumulate uranium from dilute metal solution. Thiobacillus ferrooxidans is used in leaching of iron from pyrite. Thiobacillus thiooxidans brings about bioleaching of cobalt, nickel, and zinc from their sulphide ores. T. ferrooxidans can also be used in the recovery of gold and silver. (BSc 2nd Year Microbiology Environmental Quality Notes Study Material)
[III] Petrol and petroleum products (oil spills causing pollution)
More than 10 million metric tons of oil pollutants enter the marine environment each year due to accidental spillages and disposal of oily wastes. Most of the oil pollution infact comes not from major oil spills, but from minor spills associated with routine operations. After evaporation of volatile fraction of petroleum waste, the residue is dissipated mainly by microbial degradation and to a lesser degree by autooxidation and photooxidation. There are two steps in hydrocarbon oxidation. (i) conversion of an initial hydrocarbon to the suitable substrate for next step, by specialized activities, and (ii) methyl group oxidation to carboxylic acid.
Petroleum is a complex mixture composed primarily of aliphatic, alicyclic, and aromatic hydrocarbons. There are hundreds of individual compounds in every crude oil. Thus the fate of oil pollutants in the environment is complex. The challenge for microbes to degrade all of the components of a petroleum mixture is immense. Nevertheless, microbial biodegradation of petroleum is a major process and that’s why oceans are not covered with oil today. In the 1978 wreck of the supertanker Amoco Cadiz off the coast of France, microbes biodegraded 10 tons of oil every day in the affected area. Bacteria and yeasts can grow on several fractions of hydrocarbons e.g. heptane, decane, hexadecane, etc.
The structure and molecular weight of the hydrocarbon molecule determine its susceptibility to biodegradation, n-alkanes of intermediate chain length (C10-C24) are degraded most rapidly. As the length of the chain increases, so does resistance to biodegradation. Aromatic compounds are degraded more slowly than alkanes. (BSc 2nd Year Environmental Microbiology Notes Study Material)
The successful biodegradative removal of petroleum hydrocarbons from the sea depends on the enzymatic capacities of microbes and various abiotic factors. Microbial biodegradation needs suitable temperature and available supplies of fixed forms of nitrogen, PO4, and O2. In oceans, low concentrations of N2 and PO4 limit petroleum biodegradation. Although many microorganisms can metabolize petroleum hydrocarbons no sing microbe possesses the enzymatic capability to degrade all, or even most, of the compounds in a petroleum mixture.
Recombinant DNA technology has created a “superbug” that is able to degrade many hydrocarbon structures, which is potentially useful in oil pollution abatement programmes. This hydrocarbon-degrading microbe is the first organism for which a patent has been granted in the U.S.A. (BSc 2nd Year Environmental Microbiology Notes Study Material)
BSc 2nd Year Microbiology Environmental Quality Notes Study Material
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