Lithotrophs Lithotrophy, a type of metabolism that requires inorganic compounds as sources of energy. This metabolism is firmly established in both the Archaea and the Bacteria. The methanogens utilize H₂ as an energy source, and many extreme thermophiles use H₂S or elemental sulfur as a source of energy for growth. Lithotrophic Bacteria are typically Gram-negative species that utilize inorganic substrates including H₂, NH₃, NO₂, H₂S, S, Fe⁺⁺, and CO. Ecologically, the most important lithotrophic Bacteria are the nitrifying bacteria, Nitrosomonas and Nitrobacter that together convert NH₃ to NO₂, and NO₂ to NO₃, and the colorless sulfur bacteria, such as Thiobacillus, that oxidize H₂S to S and S to SO₄. Most lithotrophic bacteria are autotrophs, and in some cases, they may play an important role in primary production of organic material in nature. Lithotrophic metabolism does not extend to eucaryotes (unless a nucleated cell harbors lithotrophic endosymbiotic bacteria), and these bacteria are important in the biogeochemical cycles of the elements.

Pseudomonads. "Pseudomonad" is an informal term for bacteria which morphologically and physiologically resemble members of the genus Pseudomonas. They are unified only as Gram-negative rods with a strictly-respiratory mode of metabolism. The term has been applied to membersof the genera Pseudomonas, and Xanthomonas, which are Alpha Proteobacteria, and to plant and animal pathogens such as Burkholderia, Ralstonia and Acidovorax, which are Beta Proteobacteria although other related and nonrelated bacteria share their definitive characteristics, i.e., Gram-negative aerobic rods. The morphology and habitat of many pseudomonads sufficiently overlaps with the enterics (below) so that microbiologists must quickly learn how to differentiate these two types of Gram-negative motile rods. Pseudomonads move by polar flagella; enterics such as E. coli swim by means of peritrichous flagella. Enterics ferment sugars such as glucose; pseudomonads generally do not ferment sugars. And most pseudomonads have an unusual cytochrome in their respiratory electron transport chain that can be detected in colonies by a colorimetric test called the oxidase test. Pseudomonads are typically oxidase- positive.

Figure 13. Profile of a pseudomonad: Gram-negative rods motile by polar flagella. A. Electron micrograph, negative stain. B. Scanning electron micrograph. C. Gram stain.

Most pseudomonads are free-living organisms in soil and water; they play an important role in decomposition, biodegradation, and the C and N cycles. The phrase "no naturally-occurring organic compound cannot be degraded by some microorganism" must have been coined to apply to members of the genus Pseudomonas, known for their ability to degrade hundreds of different organic compounds including insecticides, pesticides, herbicides, plastics, petroleum substances, hydrocarbons and other of the most refractory molecules in nature. However, they are usually unable to degrade biopolymers in their environment, such as cellulose and lignin, and their role in anaerobic decomposition is minimal.

There are about 150 species of Pseudomonas, but, especially among the plant pathogens, there are many strains and biovars among the species. These bacteria are frequently found as part of the normal flora of plants, but they are one of the most important bacterial pathogens of plants, as well. Pseudomonas syringae and Xanthomonas species cause a wide variety of plant diseases as discussed below. One strain of Pseudomonas that lives on the surfaces of plants can act as an "ice nucleus" which causes ice formation and inflicts frost damage on plants at one or two degrees above the conventional freezing temperature of water (0 degrees C). One Pseudomonas species is an important pathogen of humans, Pseudomonas aeruginosa, the quintessential opportunistic pathogen, which is a leading cause of hospital-acquired (nosocomial) infections. Pseudomonas species are discussed elsewhere in the text at  Opportunistic Infections caused by Pseudomonas aeruginosa  and The Genus Pseudomonas.

Among some interesting or important ecologic relatives of the pseudomonads are Rhizobium and Bradyrhizobium, species that fix nitrogen in association with leguminous plants, and related Agrobacterium species that cause tumors ("galls") in plants. These bacteria are discussed later in this article because of their special relationships with plants. Relatives of the pseudomonads also include the methanotrophs that can oxidize methane and other one-carbon compounds, the azotobacters, which are very prevalent free-living (nonsymbiotic) nitrogen-fixing bacteria.

Enterics. The Enteric Bacteria  are Gram-negative rods with facultative anaerobic metabolism that live in the intestinal tracts of animals. This group consists of Escherichia coli and its relatives, the members of the family Enterobacteriaceae. Enteric bacteria are related phenotypically to several other genera of bacteria such as Pseudomonas and Alcaligenes, but are physiologically quite unrelated. Generally, a distinction can be made on the ability to ferment glucose: enteric bacteria all ferment glucose to acid end products while similar Gram-negative bacteria cannot ferment glucose. Because they are consistent members of the normal flora of humans, and because of their medical importance, an extremely large number of enteric bacteria have been isolated and characterized.

Escherichia coli is, of course, the type species of the enterics. E. coli is such a regular inhabitant of the intestine of humans that it is used by public health authorities as an indicator of fecal pollution of drinking water supplies, swimming beaches, foods, etc. E. coli is the most studied of all organisms in biology because of its occurrence, and the ease and speed of growing the bacteria in the laboratory. It has been used in hundreds of thousands of experiments in cell biology, physiology, and genetics, and was among the first cells for which the entire chromosomal DNA base sequence was determined. In spite of the knowledge gained about the molecular biology and physiology of E. coli, surprisingly little is known about its ecology, for example why it consistently associates with humans, how it helps its host, how it harms its host, etc. A few strains of E. coli are pathogenic (one is notorious, strain 0157:H7, that keeps turning up in raw hamburger headed for a fast-food restaurants).  Pathogenic strains of E. coli cause intestinal tract infections (usually acute and uncomplicated, except in the very young ),  uncomplicated urinary tract infections and neonatal meningitis. See E. coli and Gastroenteritis, Urinary tract Infections and Neonatal Meningitis.

Figure 14. Left: Escherichia coli cells. Right: E. coli colonies on EMB Agar.

The enteric group also includes some other intestinal pathogens of humans such as Shigella dysenteriae, cause of bacillary dysentery (Shigella and Shigellosis), and Salmonella enterica, cause of gastroenteritis. Salmonella typhi, which infects via the intestinal route, causes typhoid fever (Salmonella and Salmonellosis). Some bacteria that don't have an intestinal habitat resemble E. coli in enough ways to warrant inclusion in the enteric group. This includes Proteus, a common saprophyte of decaying organic matter, Yersinia pestis, which causes bubonic plague, and Erwinia, an important pathogen of plants.

Gram-negative pathogens. Most, but not all, of the Gram negative bacteria that are important pathogens of humans are found scattered throughout the Proteobacteria. In the Alpha Proteobacteria, one finds the Rickettsias, a group of obligate intracellular parasites which are the cause of typhus and Rocky Mountain Spotted Fever.  In the Beta group, the agents of whooping cough (pertussis)  (Bordetella pertussis),  (Neisseria gonorrhoeae), and meningococcal meningitis (Neisseria meningitidis) are found. (Gonorrhea and Meningitis)  Among the Gamma group, Pseudomonas aeruginosa, the enterics, and Vibrio cholerae have already been mentioned. Likewise, the agents of Legionnaire's' pneumonia (Legionella pneumophilia), and childhood meningitis (Haemophilus influenzae) are Gamma Proteobacteria. Campylobacter and Helicobacter are Epsilon Proteobacteria. Most of these bacteria are discussed elsewhere in this article and/or in separate chapters which deal with their pathogenicity for humans.

Nitrogen-fixing organisms. This is a diverse group of procaryotes, reaching into phylogenetically distinct groups of Archaea and Bacteria. Members are unified only on the basis of their metabolic ability to "fix" nitrogen. Nitrogen fixation is the reduction of N₂ (atmospheric nitrogen) to NH₃ (ammonia). It is a complicated enzymatic process mediated by the enzyme nitrogenase. Nitrogenase is found only in procaryotes and is second only to RUBP carboxylase (the enzyme responsible for CO₂ fixation) as the most abundant enzyme on Earth.

The conversion of nitrogen gas (which constitutes about 80 percent of the atmosphere) to ammonia introduces nitrogen into the biological nitrogen cycle. Living cells obtain their nitrogen in many forms, but usually from ammonia (NH₃) or nitrates (NO₃), and never from N₂. Nitrogenase extracts N₂ from the atmosphere and reduces it to NH₃ in a reaction that requires substantial reducing power (electrons) and energy (ATP). The NH₃ is immediately assimilated into amino acids and proteins by subsequent cellular reactions. Thus, nitrogen from the atmosphere is fixed into living (organic) material.

Although a widespread trait in procaryotes, nitrogen fixation occurs in only a few select genera. Outstanding among them are the symbiotic bacteria Rhizobium and Bradyrhizobium which form nodules on the roots of legumes. In this symbiosis the bacterium invades the root of the plant and fixes nitrogen which it shares with the plant. The plant provides a favorable habitat for the bacterium and supplies it with nutrients and energy for efficient nitrogen fixation. Rhizobium and Bradyrhizobium are Gram-negative aerobes related to the pseudomonads (above). An unrelated bacterium, an actinomycete (below), enters into a similar type of symbiosis with plants. The actinomycete, Frankia, forms nodules on the roots of several types of trees and shrubs, including alders (Alnus), wax myrtles (Myrica) and mountain lilacs (Ceanothus). They, too, fix nitrogen which is provided to their host in a useful form. This fact allows alder species to be "pioneer plants" (among the first to colonize) in newly-forming nitrogen-deficient soils. Still other bacteria live in regular symbiotic associations with plants on roots or leaves and fix nitrogen for their hosts, but they do not cause tissue hyperplasia or the formation of nodules.

Cyanobacteria are likewise very important in nitrogen fixation. Cyanobacteria provide fixed nitrogen, in addition to fixed carbon, for their symbiotic partners which make up lichens. This enhances the capacity for lichens to colonize bare areas where fixed nitrogen is in short supply. In some parts of Asia, rice can be grown in the same paddies continuously without the addition of fertilizers because of the presence of nitrogen fixing cyanobacteria. The cyanobacteria, especially Anabaena, occur in association with the small floating water fern Azolla, which forms masses on the paddies. Because of the nearly obligate association of Azolla with Anabaena,  paddies covered with Azolla remain rich in fixed nitrogen.

In addition to symbiotic nitrogen-fixing bacteria, there are various free-living nitrogen-fixing procaryotes in both soil and aquatic habitats. Cyanobacteria may be able to fix nitrogen in virtually all habitats that they occupy. Clostridia and some methanogens fix nitrogen in anaerobic soils and sediments, including thermophilic environments. A common soil bacterium, Azotobacter is a vigorous nitrogen fixer, as is Rhodospirillum, a purple sulfur bacterium. Even Klebsiella, an enteric bacterium closely related to E. coli, fixes nitrogen. There is great scientific interest, of course, in knowing how one might move the genes for nitrogen fixation from a procaryote into a eucaryote such as corn or some other crop plant. The genetically engineered plant might lose its growth requirement for costly ammonium or nitrate fertilizers and grow in nitrogen deficient soils.

Besides nitrogen fixation, bacteria play other essential roles in the processes of the nitrogen cycle. For example, saprophytic bacteria, decompose proteins releasing NH₃ in the process of ammoniafication. NH₃ is oxidized by lithotrophic Nitrosomonas species to NO₂ which is subsequently oxidized by Nitrobacter to NO₃. The overall conversion of NH₃ to NO₃ is called nitrification. NO₃ can be assimilated by cells as a source of nitrogen (assimilatory nitrate reduction), or certain bacteria can reduce NO₃ during a process called anaerobic respiration, wherein nitrate is used in place of oxygen as a terminal electron acceptor for a process analogous to aerobic respiration. In the case of anaerobic respiration, NO₃ is first reduced to NO₂, which is subsequently reduced to N₂O or N₂  (all gases). This process is called denitrification and it occurs in anaerobic environments where nitrates are present. If denitrification occurs in crop soils it may not be beneficial to agriculture if it converts utilizable forms of nitrogen (as in nitrate fertilizers) to nitrogen gases that will be lost into the atmosphere. A related process call dissimilatory nitrate reduction, conducted by certain Bacillus species, reduces NO₃ to NH₃. One rationale for tilling the soil is to keep it aerobic, in order to discourage these facultative processes in Pseudomonas and Bacillus, which are ubiquitous inhabitants.