H

Sulfate reduction (assimilatory)

Sulfur oxidation

Mineralization

Sulfur oxidation

Sulfate reduction (assimilatory)

Mineralization

Organic sulfur

Alteromonas Clostridium Desulfovibrio Desulfotomaculum

Organic sulfur

Sulfur oxidation Thiobacillus Beggiatoa Thiothrix } Aerobic

Aerobic anoxygenic | phototrophs

Figure 28.21 The Basic Sulfur Cycle. Photosynthetic and chemosynthetic microorganisms contribute to the environmental sulfur cycle. Sulfate and sulfite reductions carried out by Desulfovibrio and related microorganisms, noted with purple arrows, are dissimilatory processes. Sulfate reduction also can occur in assimilatory reactions, resulting in organic sulfur forms. Elemental sulfur reduction to sulfide is carried out by Desulfuromonas, thermophilic archaea, or cyanobacteria in hypersaline sediments. Sulfur oxidation can be carried out by a wide range of aerobic chemotrophs and by aerobic and anaerobic phototrophs.

Chlorobium Chromatium

Anaerobic

Assimilatory nitrate reduction

(Many genera)

Organic N

(Many genera)

Dissimilation and Mineralization

Assimilatory nitrate reduction

(Many genera)

Organic N

(Many genera)

Dissimilation and Mineralization

Nitrification (Nitrobacter, Nitrococcus)

Geobacter metallireducens

Desulfovibrio

Clostridium

Nitrification

(Nitrosomonas,

Nitrosococcus)

Nitrification (Nitrobacter, Nitrococcus)

Geobacter metallireducens

Desulfovibrio

Clostridium

Nitrification

(Nitrosomonas,

Nitrosococcus)

Figure 28.22 The Basic Nitrogen Cycle. Flows that occur predominantly under aerobic conditions are noted with open arrows. Anaerobic processes are noted with solid bold arrows. Processes occurring under both aerobic and anaerobic conditions are marked with cross-barred arrows. The anammox reaction of NO2~ and NH4+ to yield N2 is shown. Important genera contributing to the nitrogen cycle are given as examples.

result of chemical reactions in the absence of microorganisms. An important example of such an abiotic process is the oxidation of sulfide to elemental sulfur. This takes place rapidly at a neutral pH, with a half-life of approximately 10 minutes for sulfide at room temperature.

Nitrogen Cycle

Several important aspects of the basic nitrogen cycle will be discussed: the processes of nitrification, denitrification, and nitrogen fixation (figure 28.22). It should be emphasized that this is a "basic" nitrogen cycle. Although not mentioned in the figure, the het-erotrophs can carry out nitrification, and some of these het-erotrophs combine nitrification with anaerobic denitrification, thus oxidizing ammonium ion to N2O and N2 with depressed oxy gen levels. The occurrence of anoxic ammonium ion oxidation (anammox is the term used for the commercial process) means that nitrification is not only an aerobic process. Thus as we learn more about the biogeochemical cycles, including that of nitrogen, the simple cycles of earlier textbooks are no longer accurate representations of biogeochemical processes.

Nitrification is the aerobic process of ammonium ion (NH4+) oxidation to nitrite (NO2~) and subsequent nitrite oxidation to nitrate (NO3_). Bacteria of the genera Nitrosomonas and Ni-trosococcus, for example, play important roles in the first step, and Nitrobacter and related chemolithoautotrophic bacteria carry out the second step. Recently Nitrosomonas eutropha has been found to oxidize ammonium ion anaerobically to nitrite and nitric oxide (NO) using nitrogen dioxide (NO2) as an oxidant in a denitrifica-tion-related reaction. In addition, heterotrophic nitrification by

616 Chapter 28 Microorganism Interactions and Microbial Ecology bacteria and fungi contributes significantly to these processes in more acidic environments. Nitrification and nitrifiers (p. 193)

The process of denitrification requires a different set of environmental conditions. This dissimilatory process, in which nitrate is used as an oxidant in anaerobic respiration, usually involves het-erotrophs such as Pseudomonas denitrificans. The major products of denitrification include nitrogen gas (N2) and nitrous oxide (N2O), although nitrite (NO2~) also can accumulate. Nitrite is of environmental concern because it can contribute to the formation of carcinogenic nitrosamines. Finally, nitrate can be transformed to ammonia in dissimilatory reduction by a variety of bacteria, including Geobacter metallireducens, Desulfovibrio spp., and Clostridium. Denitrification and anaerobic respiration (pp. 190-91)

Nitrogen assimilation occurs when inorganic nitrogen is used as a nutrient and incorporated into new microbial biomass. Ammonium ion, because it is already reduced, can be directly incorporated without major energy costs. However, when nitrate is assimilated, it must be reduced with a significant energy expenditure. In this process nitrite may accumulate as a transient intermediate. The biochemistry of nitrogen assimilation (pp. 210-14)

Nitrogen fixation can be carried out by aerobic or anaerobic procaryotes and does not occur in eucaryotes. Under aerobic conditions a wide range of free-living microbial genera (Azotobacter, Azospirillum) contribute to this process. Under anaerobic conditions the most important free-living nitrogen fixers are members of the genus Clostridium. Nitrogen fixation by cyanobacteria such as Anabaena and Oscillatoria can lead to the enrichment of aquatic environments with nitrogen. These nutrient-enrichment processes are discussed in chapter 29. In addition, nitrogen fixation can occur through the activities of bacteria that develop symbiotic associations with plants. These associations include Rhizobium and Bradyrhizobium with legumes, Frankia in association with many woody shrubs, and Anabaena, with Azolla, a water fern important in rice cultivation. The establishment of the Rhizobium-legume association (pp. 675-78)

The nitrogen-fixation process involves a sequence of reduction steps that require major energy expenditures. Ammonia, the product of nitrogen reduction, is immediately incorporated into organic matter as an amine. Reductive processes are extremely sensitive to O2 and must occur under anaerobic conditions even in aerobic microorganisms. Protection of the nitrogen-fixing enzyme is achieved by means of a variety of mechanisms, including physical barriers, as occurs with hetero-cysts in some cyanobacteria (see section 21.3), O2 scavenging molecules, and high rates of metabolic activity. The biochemistry of nitrogen fixation (pp. 212-14)

As shown in figure 28.22, microorganisms have been isolated that can couple the anaerobic oxidation of NH4+ with the reduction of NO2~, to produce gaseous nitrogen, in what has been termed the anammox process (anoxic ammonia oxidation). This may provide a means by which nitrogen can be removed from sewage plant effluents to decrease nitrogen flow to sensitive freshwater and marine ecosystems. It has been suggested that chemolithotrophic members of the planctomycetes (see section 21.4) play a role in this process.

1. What are the major oxidized and reduced forms of sulfur and nitrogen?

2. Diagram a simple sulfur cycle.

3. Why is dimethylsulfide (DMS), considered to be a "minor" part of the sulfur cycle, of such environmental importance?

4. What is aerobic anoxygenic photosynthesis?

5. What are nitrification, denitrification, nitrogen fixation, and the anammox process?

Iron Cycle

The iron cycle (figure 28.23) includes several different genera that carry out iron oxidations, transforming ferrous ion (Fe2+) to ferric ion (Fe3+). Thiobacillus ferrooxidans carries out this process under acidic conditions, Gallionella is active under neutral pH conditions, and Sulfolobus functions under acidic, thermophilic conditions. Much of the earlier literature suggested that additional genera could oxidize iron, including Sphaerotilus and Leptothrix. These two genera are still termed "iron bacteria" by many nonmi-crobiologists. Confusion about the role of these genera resulted from the occurrence of the chemical oxidation of ferrous ion to ferric ion (forming insoluble iron precipitates) at neutral pH values, where microorganisms also grow on organic substrates. These microorganisms are now classified as chemoheterotrophs.

Recently microbes have been found that oxidize Fe2+ using nitrate as an electron acceptor. This process occurs in aquatic sediments with depressed levels of oxygen and may be another route by which large zones of oxidized iron have accumulated in environments with lower oxygen levels.

Iron reduction occurs under anaerobic conditions resulting in the accumulation of ferrous ion. Although many microorganisms can reduce small amounts of iron during their metabolism, most iron reduction is carried out by specialized iron-respiring microorganisms such as Geobacter metallireducens, Geobacter sul-furreducens, Ferribacterium limneticum, and Shewanella putre-faciens, which can obtain energy for growth on organic matter using ferric iron as an oxidant.

In addition to these relatively simple reductions to ferrous ion, some magnetotactic bacteria such as Aquaspirillum magneto-tacticum (see section 3.3) transform extracellular iron to the mixed valence iron oxide mineral magnetite (Fe3O4) and construct intra-cellular magnetic compasses. Furthermore, dissimilatory iron-reducing bacteria accumulate magnetite as an extracellular product.

Magnetite has been detected in sediments, where it is present in particles similar to those found in bacteria, indicating a longer-term contribution of bacteria to iron cycling processes. Genes for magnetite synthesis have been cloned into other organisms, creating new magnetically sensitive microorganisms. Magnetotactic bacteria are now described as magneto-aerotactic bacteria, due to their using magnetic fields to migrate to the position in a bog or swamp where the oxygen level is best suited for their functioning. In the last decade new microorganisms have been discovered that use ferrous ion as an electron donor in anoxygenic photosynthesis. Thus, with production of ferric ion in lighted

Aerobic

Neutral pH = Gallionella

Acidic = Leptospirillum, Thiobacillus ferrooxidans Acidic, thermophilic = Sulfolobus

Ferribacterium limneticum Geobacter metallireducens Geobacter sulfurreducens Geovibrio ferrireducens Desulfuromonas acetoxidans Pelobacter carbinolicus Shewanella putrefaciens

Aerobic

Neutral pH = Gallionella

Acidic = Leptospirillum, Thiobacillus ferrooxidans Acidic, thermophilic = Sulfolobus

Anaerobic

Anaerobic purple phototrophic bacteria

Anaerobic

Figure 28.23 The Basic Iron Cycle. A

simplified iron cycle with examples of microorganisms contributing to these oxidation and reduction processes. In addition to ferrous ion (Fe2+) oxidation and ferric ion (Fe3+) reduction, magnetite (Fe3O4), a mixed valence iron compound formed by magnetotactic bacteria is important in the iron cycle. Different microbial groups carry out the oxidation of ferrous ion depending on environmental conditions.

Anaerobic purple phototrophic bacteria anaerobic zones by iron-oxidizing bacteria, the stage is set for subsequent chemotrophic-based iron reduction, such as by Geobacter and Shewanella, creating a strictly anaerobic oxidation/reduction cycle for iron.

Manganese Cycle

The importance of microorganisms in manganese cycling is becoming much better appreciated. The manganese cycle (figure 28.24) involves the transformation of manganous ion (Mn2+) to MnO2 (equivalent to manganic ion [Mn4+]), which occurs in hydrothermal vents, bogs, and as an important part of rock varnishes. Leptothrix, Arthrobacter, Pedomicrobium, and the incompletely characterized "Metallogenium"" are important in Mn2+ oxidation. Shewanella, Geobacter, and other chemoorganotrophs can carry out the complementary manganese reduction process.

Other Cycles and Cycle Links

Microorganisms can use a wide variety of additional metals as electron acceptors. Metals such as europium, tellurium, selenium, and rhodium can be reduced. Important microorganisms that reduce these metals include the photoorganotrophs Rhodobacter, Rho-dospirillum and Rhodopseudomonas. For selenium, Pseudomonas stutzeri, Thauera selenatis, and Wolinella succinogenes are active. Such reductions can decrease the toxicity of a metal.

The microbial transformation of phosphorus involves primarily the transformation of phosphorus (+5 valence) from simple orthophosphate to various more complex forms, including polyphosphates found in metachromatic granules (see p. 52). A unique (and possibly microbial) product is phosphine (PH3) with a —3 valence, which is liberated from swamps, soils, and marine regions and which ignites when exposed to air. This can then ignite methane

Aerobic

Leptothrix discophora Arthrobacter "Metallogenium" Pedomicrobium

Aerobic

Leptothrix discophora Arthrobacter "Metallogenium" Pedomicrobium

Figure 28.24 The Basic Manganese Cycle. Microorganisms make important contributions to the manganese cycle. Manganous ion (2+) is oxidized to manganic oxide (valence equivalent to 4+). Manganous oxide reduction is noted with a maroon arrow. Examples of organisms carrying out these processes are given.

Figure 28.24 The Basic Manganese Cycle. Microorganisms make important contributions to the manganese cycle. Manganous ion (2+) is oxidized to manganic oxide (valence equivalent to 4+). Manganous oxide reduction is noted with a maroon arrow. Examples of organisms carrying out these processes are given.

produced in the same environment! The production of methane by anaerobic microorganisms will be discussed in the next chapter.

Having described the sulfur, iron, and manganese cycles as functioning independently, it is important to again emphasize that many microorganisms metabolically link these cycles by using

618 Chapter 28 Microorganism Interactions and Microbial Ecology

Table 28.6

Examples of Microorganism-Metal Interactions and Relations to Effects on Microorganisms and Homeothermic Animals

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