Zooglea Ramigera


aNot necessarily all strains can carry out the indicated reaction.

aNot necessarily all strains can carry out the indicated reaction.

Nitrifying bacteria are aerobic autotrophs that oxidize reduced nitrogen in two separate steps. Ammonium oxidizers such as Nitrosomonas, Nitrosospira, and Nitrosococcus convert ammonium to nitrite. (The first two are p-Proteobacteria, the third a g-Protoebac-teria.) Nitrite oxidizers convert nitrite to nitrate; examples are Nitrobacter (a-Proteobac-teria) and Nitrococcus (g-Proteobacteria). (Another nitrite oxidizer, Nitrospira, is a member of the Xenobacteria.) There appear to be relatively few types of nitrifying bacteria, but they are widespread (soil, freshwater, and marine systems), common, and play a crucial role in the nitrogen cycle. They are relied on in most wastewater treatment systems that control ammonia, may exert a substantial oxygen demand on streams receiving ammonia in effluents, and play an important role in nitrate contamination of groundwater. All known nitrifiers prefer slightly alkaline, mesophilic conditions; they are inhibited by even moderately acidic pH, and none appear able to grow at temperatures much above 40°C.

Nonphototrophic prokaryotes able to oxidize various forms of reduced sulfur can be found among the Archaea and several bacterial kingdoms. Hydrogen sulfide is the most commonly used form, but elemental sulfur, metal sulfides, and thiosulfate also are used by many species. Some sulfur-oxidizing Proteobacteria, including members of the genus Thiobacillus, produce so much sulfate (sulfuric acid) from the oxidation of pyritic (metal sulfide) minerals that the pH may drop to below 2. This is a major cause of the environmental problem known as acid mine drainage (Section 13.4.3) and can also occur in clay soils containing pyrites if they are exposed to the air. Some hot springs and marine thermal vents also are sources of sulfides.

Other sulfur oxidizers prefer or require neutral pH. Many of these rely on the production of sulfide by the anaerobic sulfate-reducing bacteria (see later) growing on organic material (rather than release from minerals). Since they need oxygen (or in some cases nitrate), such bacteria tend to grow at the interface between aerobic and anaerobic environments (e.g., the surface sediments in salt marshes). One of these is the filamentous form Thiothrix, which may occasionally cause settling problems in activated sludge wastewater treatment plants if sufficient sulfide is present in the influent or generated in the process. Another, the gliding bacteria Beggiatoa (Figure 10.22), is the most common filamentous organism observed in rotating biological contactor (RBC) treatment plants, sometimes producing such heavy growths that the steel shafts collapse. Deeper layers of the biofilm become anaerobic in many such plants, so that hydrogen sulfide is then produced and released to the overlying aerobic portion of the film. It is thought that Beggiatoa's ability to glide helps it in remaining at the interface of the aerobic and anaerobic zones. Unlike many other lithotrophs, Thiothrix and Beggiatoa are also able to use small organic molecules as their carbon source and are thus referred to as mixotrophs.

Some bacteria are able to utilize the oxidation of ferrous (II) iron as a source of energy. For example, some of the acidophilic Thiobacillus (especially T. ferrooxidans) that grow on iron pyrites also are iron oxidizers. Ferrous iron is stable at low pH, allowing time for biochemical activity, but at neutral pH it is chemically oxidized to the ferric (III) form fairly rapidly. Interestingly, some bacteria, such as Gallionella and Leptothrix, can grow at the interface between oxic and anoxic zones and oxidize the iron before the chemical reactions occur. This is sometimes a problem when anaerobic well waters containing soluble ferrous iron are brought to the surface, as the growths (containing large amounts of insoluble ferric iron) can cause clogging. Similarly, some manganese-oxidizing bacteria can oxidize the manganous (II) to the manganic (IV) form.

Figure 10.22 Two species of Beggiatoa in samples from RBC wastewater treatment plants; a gliding filamentous sulfur-oxidizing proteobacteria. Note internally deposited sulfur granules.

Methanotrophs Methane (CH4) is a major product of the anaerobic degradation of organic material, especially in the absence of large amounts of sulfate. Methanotrophs (e.g., Methylomonas and Methylocystis) are a relatively specialized but environmentally widespread group of obligately aerobic Proteobacteria (mainly a and g groups) able to oxidize this methane. They are autotrophic, and some are also able to fix nitrogen. Most species produce a resting stage resistant to desiccation, either a cyst or an exospore (which is also quite heat resistant) produced by budding.

Most methanotrophs are also able to utilize methanol (CH3OH) and many can utilize at least some other one-carbon compounds, such as formaldehyde (CH2O), formic acid (CHOOH), methyl amine (CH3NH2), or carbon monoxide (CO), or other compounds without carbon-carbon bonds such as dimethylamine [(CH3)2NH], dimethyl sulfide [(CH3)2S], or dimethyl ether [(CH3)2O]. The ability to utilize such compounds is referred to as methylotrophy and is more widespread (e.g., including some Bacillus, a grampositive bacteria) than growth on methane.

There has been recent interest in the use of methanotrophs for soil bioremediation systems. Their activity can be promoted by pumping methane into the subsurface environment, leading to increased generation of the enzyme methane monooxygenase (MMO). This enzyme can cometabolically convert a number of industrial contaminants, such as trichloroethylene, to less hazardous or harmless products (Section 16.7.2).

Nitrogen-Fixing Proteobacteria Nitrogen fixation, the conversion of elemental nitrogen (N2) to a more readily utilizable form, is an ability that is found scattered among many bacterial kingdoms (e.g., many of the Cyanobacteria and the gram-positives Clostridium and Frankia). Among the Proteobacteria this includes some methanotrophs, and most strains of the enteric bacteria Klebsiella. Rhizobium, and some similar species are of special importance because of the mutualistic (beneficial to both organisms) relationship they have with legumes (plants such as beans, peas, soybeans, alfalfa, clover, vetch, and mimosa). They are able to infect the plant roots to form special nodules in which they grow. Thereafter, they fix nitrogen (which is often in limited supply in soils), to the benefit of the plant, while they utilize organic substrates produced by the plant. Other important nitrogen fixers in soils (and water) are free-living, such as Azoto-bacter. Both the symbiotic (having a close relationship with another organism) and the free-living nitrogen fixers are aerobic, even though the required nitrogenase enzyme is sensitive to oxygen.

Proteobacteria with Special Morphologies: Appendaged, Sheathed, and Spiral

Forms A number of the Proteobacteria are known for their specialized morphologies, although these are not always indicative of phylogenetic relationships. Hyphomicrobium is a common aerobic soil and aquatic Proteobacteria whose prosthecae take the form of short hyphae from which buds are produced. Caulobacter is another common aerobic prosthecate bacteria; it uses its stalk for attachment. The chemolithotrophic iron oxidizer Gallionella also produces a stalk, but it consists of twisted exocellular fibrils coated with ferric hydroxide.

Sphaerotilus is a filamentous bacteria that produces a sheath (Figure 10.23). As part of its life cycle, single cells with polar flagella are formed that swim away to start new filaments. It is aerobic, but can still grow well at low dissolved oxygen concentrations (e.g., 0.5 mg/L). As a result, it is a common inhabitant of polluted streams and biological wastewater treatment systems. Large masses, commonly referred to as sewage fungus (although they are not fungi), sometimes form on rocks or other aquatic surfaces in such systems. Heavy growths in activated sludge wastewater treatment systems are one cause of the settling problem known as bulking. Leptothrix, mentioned above as an iron- and manganese-oxidizing organism, is a related species.

Spirillum is an example of a spiral Proteobacteria (not related to the spirochetes, Section 10.5.9). It is motile by tufts of flagella at both ends and is aerobic or microaer-ophilic.

Myxobacteria The fruiting myxobacteria do not appear to be particularly important in environmental engineering and science but are of great interest to some microbiologists because of their life cycle, the most complex of any known prokaryote. The single, usually rod-shaped vegetative cells have gliding motility and often leave a slime trail as they move about on solid surfaces. When nutrients become limiting, the cells "swarm," coming together to form a visible, often brightly colored fruiting body. Cells within the fruiting body develop into myxospores, which are resistant to drying and some other environmental stresses. These spores can later germinate to form new vegetative cells.

Figure 10.23 Sphaerotilus natans: (a) pure culture showing sheath and PHB granules; (b) branching filament in activated sludge sample.

Figure 10.23 Sphaerotilus natans: (a) pure culture showing sheath and PHB granules; (b) branching filament in activated sludge sample.

Myxobacteria are aerobic chemoorganotrophs found in soil. Many, such as Myxococ-cus, are bacteriolytic (they lyse, or rupture, bacteria to feed on their cellular constituents—particularly proteins), and commonly occur on animal dung (which includes a high percentage of bacteria). However, a number (including some species of Polyangium) are instead cellulolytic (digest cellulose), and grow on decaying vegetation.

Pseudomonads The pseudomonads are a large group of aerobic (although a few can utilize nitrate or nitrite when oxygen is unavailable), nonfermentative, chemoorganotrophic (except that a few can grow on hydrogen or carbon monoxide), heterotrophic, non-spore-forming gram-negative rods with polar flagella. Pseudomonas (Figure 10.8) is the major genus; however, when it was realized that bacteria called Pseudomonas were members of the a- and ß- as well as the g-proteobacteria (based on 16S rRNA), it was split into several genera, including Sphingomonas, Burkholderia, and Ralstonia. Still, there is much diversity in this group and disagreement among characterization methods as to where the natural groupings lie.

Pseudomonads are common soil and water bacteria, and because of their metabolic diversity, many are important in biodegradation of a very wide variety of natural and human-made organic compounds (including for bioremediation applications). A few, such as Pseudomonas aeruginosa, are opportunistic pathogens of humans. Some Pseudomonas and most Xanthomonas are plant pathogens. Another pseudomonad, Zoogloea ramigera, is found in some activated sludge wastewater treatment systems, where it forms a special type of zoogloeal floc (randomly organized aggregations) that can lead to poor settling conditions (Figure 10.24).

Other Aerobic Proteobacteria Other aerobic proteobacteria include the nonflagellated species Neisseria, Moraxella, and Acinetobacter and the flagellated Acetobacter. Several Neisseria (including N. gonorrhoeae, the cause of gonorrhea; Section 12.6.2) and Moraxella (e.g., Section 12.7.4) are pathogenic to humans or other animals. Neisseria are cocci, whereas Moraxella are plump rods. Moraxella, which gives negative results for many classic biochemical tests, is of interest for another reason as well: Bacteria

Glitter Cells Wet Prep
Figure 10.24 Characteristic Zoogloea ramigera floc from activated sludge.

isolated from the environment are also often negative for these tests, and hence have been misidentified as Moraxella. Acinetobacter is unusual in that it is an aerobe that is oxidase negative. These rods are common in soil and water. It sometimes shows twitching moti-lity, as do some Moraxella.

Some Acinetobacter strains have been reported as phosphate accumulating organisms (PAOs) in activated sludge systems that achieve biological phosphorus removal (BPR). (This identification has since been challenged, and other aerobic proteobacteria using the same mechanism are now believed to be the major PAOs in these systems.) They contain metachromatic (volutin) granules composed of polyphosphate, which is used as a method of energy storage. This type of BPR is induced by having an anaerobic zone followed by an aerobic zone in the reactor. In the anaerobic zone, the PAOs utilize the stored polyphosphate for energy (releasing phosphate) to accumulate and store fermentation products. Subsequently, in the aerobic zone, they utilize the stored organics and remove phosphorus to very low levels (storing it again as polyphosphate). The low-P water is then separated and discharged, and the PAOs are recycled to the anaerobic zone to repeat the reaction. This is a fascinating application in which favoring a strictly aerobic organism in an ecosystem is accomplished by including a periodic anaerobic condition!

Acetic acid bacteria such as Acetobacter, although obligate aerobes, produce acetic acid from ethanol. This can lead to spoilage of alcoholic beverages but is also used commercially for vinegar production. Some Acetobacter are also able to produce a very pure form of cellulose.

The Family Enterobacteriaceae The Enterobacteriaceae includes many bacteria of importance to humans and hence has been studied extensively. They also form a relatively stable taxonomic grouping; although originally based on testing by traditional (phenoty-pic) methods, there has been little change after genotype testing was employed. These members of the g-proteobacteria are gram-negative, nonsporeforming rods that are typically facultatively anaerobic, capable of fermenting sugars. They either have peritrichous flagella or are nonmotile. Many live within the intestinal tract of warm-blooded animals (where they may play an important role in digestion) and hence are referred to as enteric bacteria. Some are important pathogens; others live in soil or water.

Escherichia coli (Figure 10.25) is probably the best known of all bacteria. E. coli is present in large numbers in the human intestines and is one of the coliforms used as indicator organisms to monitor fecal pollution of water (Section 12.9.2). A few strains are pathogenic (Section 12.3.2).

Important pathogenic members of this family include Salmonella, the cause of typhoid fever (S. typhi) and salmonellosis (but also used for testing chemical mutagenicity in the Ames test; Section 20.1.13); Shigella, which causes bacterial dysentery; and Yersinia (Y. pestis is the cause of plague). Other common species that may be intestinal or environmental (soil and water) include Enterobacter (formerly called Aerobacter), Citrobacter, and Klebsiella. K. pneumoniae, which is able to fix nitrogen, can also occasionally cause pneumonia. Proteus is well known to microbiologists because of the characteristic swarming of cells of some strains on the surface of agar plates. Serratia is also widely recognized in the lab because of the red colonies it often produces on plates.

Other Facultatively Anaerobic Proteobacteria Other facultative bacteria include Vibrio, Photobacterium, Aeromonas, and Chromobacterium. These species differ from the Enterobacteriaceae in that they are polarly flagellated (Chromobacterium may have

Figure 10.25 Escherichia coli. (SEM image courtesy of the University of Iowa Central Microscopy Research Facility.)

other flagella as well) and usually oxidase positive. They differ from Pseudomonas in that they are capable of fermentative metabolism. They are common soil and/or water organisms but include a few pathogens, such as Vibrio cholerae (cause of cholera) and V para-haemolyticus (a marine species that can cause enteritis, usually from eating raw fish). V fischeri and Photobacterium are marine species that are luminescent: They emit blue-green light (at ^490 nm) through reactions similar to those of the firefly. Some live in the specialized light-emitting organs of certain fish; others live freely and give some sea-waters their luminescence. They are also utilized in the Microtox (Azur Environmental, Strategic Diagnostics Inc., Newark, Delaware, www.azurenv.com) toxicity test. Aeromo-nas sometimes gives false-positive results in the coliform test. It is an aquatic organism sometimes associated with diseases of fish and frogs. Chromobacterium produces a violet pigment (violacein), so that colonies on agar plates are very noticeable.

Sulfur-Reducing Proteobacteria Some strictly anaerobic proteobacteria, such as Desulfovibrio (Figure 10.26), are able to utilize oxidized forms of sulfur, especially sulfate and elemental sulfur, as the terminal electron acceptor for respiratory metabolism. As their energy source they use fermentation products (such as hydrogen, lactate, and pyru-vate) produced by other bacteria in the same ecosystem. Sulfate reducers are very common in habitats containing organic material and sulfate, such as salt marsh sediments and animal intestinal tracts. They may also be active in anaerobic digesters used for sewage sludge treatment, and in the deeper layers of the biofilms in wastewater treatment processes such as trickling filters and rotating biological contactors. The hydrogen sulfide produced may be released, giving the characteristic rotten egg odor, and/or may combine with iron or some other metals to give the black color characteristic of such anaerobic systems. In confined spaces, hydrogen sulfide can build up to toxic levels. In sewers with inadequate flushing, the hydrogen sulfide released can cause odor problems and also dissolve in the moist films that form on the aerobic, unsubmerged surfaces; there the sulfide may undergo biological oxidation by chemolithotrophic bacteria, resulting in production of sulfuric acid and crown corrosion of the sewer.

Figure 1G.26 Desulfovibrio. Note the bent rods (vibrios).

Rickettsias Rickettsias are obligate intracellular parasites—they grow within the cells of their hosts. Rickettsia species are responsible for typhus (Section 12.5.4) and Rocky Mountain spotted fever (Section 12.5.5). They are typically spread by fleas, lice, and ticks.

e-Proteobacteria Campylobacter (Figure 10.10) and Helicobacter are microaerophilic, motile, spiral, and usually, pathogenic. Campylobacter can cause serious cases of enteritis and has been responsible for some waterborne outbreaks (Section 12.2.5). H. pylori has been found to be responsible for many cases of stomach ulcers.

Other Proteobacteria In addition to the Proteobacteria described briefly above, there are many other interesting and important species. For example, several bacteria, such as the marine Magnetospirillum, contain organelles with small magnetic mineral deposits that enable them to detect magnetic fields. Bdellovibrio hunts and feeds on other bacteria, growing inside the cell wall of its prey. Legionella grows in relatively clean, warm aquatic systems, including cooling towers and commercial hot-water and air-conditioning systems. If L. pneumophila becomes airborne and is inhaled, it can cause a severe form of pneumonia known as Legionnaires' Disease (Section 12.2.3).

10.5.7 Firmicutes: Gram Positives

This large kingdom is often broken into two broad groups based on G + C content (low G + C and high G + C) and then further subdivided (Table 10.7). It contains many bacteria of interest to the environmental engineer and scientist, including common soil organisms and normal inhabitants of our skin, mucous membranes, and digestive tract, as well as important pathogens. Members of the Firmicutes are also utilized in producing many foods, in industrial processes, and as sources of antibiotics. They are chemoorganic heterotrophs, including both aerobes and anaerobes.

Some of the Clostridia and Bacilli form endospores, specialized resting structures that are very resistant to heat, drying, and other environmental stresses. Many actinomycetes (high G + C) also produce spores, but these are not formed in the same way, nor are they

TABLE 10.7 Kingdom Firmicutes: The Gram-Positive Bacteriaa

Low G + C

High G + C

Class 1. Clostridia

Class 4. Actinobacteria


Order Actinomycetales











Class 2. Mollicutes




Class 3. Bacilli


Order Bacillales








Order Lactobacillales








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