In this chapter we focus on the role that microorganisms play in the cycling of elements important to life. Unlike the organisms themselves, these atoms never "die" or disappear. Instead, they continuously pass through a grand set of biogeochemical cycles whose mechanisms, although carried out at times on a minute scale, are vital to life. Quantitative aspects of these cycles, and their interactions with other parts of ecosystems, are described in Chapter 14.
These biogeochemical cycles include a variety of metabolic pathways as well as abiotic reactions that continuously replenish the chemical ingredients of life. Microbes are the agents of most of these reactions, often through adding electrons to and removing electrons from atoms within a sequence of redox reactions. Often, it is only microbes that can carry out a specific reaction. In some other cases, the reactions might still occur without microorganisms, but only at much lower rates.
Atoms found in living organisms, whether macro, micro, or trace ingredients, were at one time in inorganic, nonliving materials and eventually will be released from their assimilated organic forms and returned to an inorganic state. Thus, the microbial reactions not only create essential materials (e.g., reduced nitrogen compounds) but also eliminate unwanted, and potentially harmful, residuals (e.g., waste and decay products generated through the normal course of life and death).
In a few cases, essential elements occur almost entirely in one oxidation state. Phosphorus, which occurs almost solely (exceptions include some pesticides and nerve gases) in the form of phosphate, is a prime example. These elements are still potentially cycled between organic and inorganic forms, but through hydrolysis or other such reactions, not through oxidation or reduction.
Environmental Biology for Engineers and Scientists, by David A. Vaccari, Peter F. Strom, and James E. Alleman Copyright © 2006 John Wiley & Sons, Inc.
Biogeochemical cycles are not maintained by any single species; rather, they represent the collective effects of diverse, yet inherently coordinated, microbial consortia as well as interactions of microbes with higher organisms. In the following sections we examine the specific elements carbon, nitrogen, sulfur, iron, and manganese and their cyclic metabolic transitions, while also discussing oxygen and hydrogen.
In each case, these cycles provide an endless exchange of oxidation states through which these atoms are transformed, both oxidatively and reductively (Section 5.1.2). The oxidation state assumed by any given atom reflects the level and mode of electrons that it shares with its neighbors. For example, carbon has a range of oxidation states from —4 to +4, as dictated by its atomic number (AN), 6. This means that carbon has six protons (positive charge) in the nucleus (equal to its atomic number) and six electrons (negative charge) outside the nucleus, balancing the atom's charge.
The nucleus of an atom (except most hydrogen nuclei) also contains neutral particles, called neutrons. The sum of the protons and neutrons is the atomic weight of the atom. Carbon usually has six neutrons, so that its usual atomic weight is 12 (six protons + six neutrons). However, some forms, or isotopes, of carbon have seven or eight neutrons, so that they have an atomic weight of 13 or 14. These forms are relatively rare, so that on average, carbon typically has an atomic weight of 12.011.
The electrons surround an atom's nucleus in orbital shells. The first shell for any element can only have a maximum of two electrons, while the next can have a maximum of eight. (The third shell can have up to 18, but is also stable with only eight.) Therefore, after subtracting the two electrons allocated to its first shell, carbon's second orbital contains the four remaining electrons. In this configuration (six electrons along with the six protons in the nucleus), elemental carbon's net electrical charge (oxidation state) would then be zero. In fact, in elemental form, the oxidation state of all elements is zero. This oxidation state will change, though, as the outer shell either gains or loses electrons while bonding with adjacent atoms. For example (Figure 13.1), the carbon atom found in a methane molecule, CH4, effectively pulls four additional negatively charged electrons into its
Chemical Oxidation States
Chemical Oxidation States
outer shell (one from each of the four hydrogens), thereby changing its oxidation state to —4 (10 negatively charged electrons versus six positively charged protons). Conversely, the carbon found in carbon dioxide (CO2) essentially lends all four of its outer shell electrons to a pair of surrounding oxygen atoms, thereby shifting its oxidation state to +4.
Carbon, nitrogen, and sulfur are the three main elements of biological interest with a full eight-electron range in oxidation state. As shown in Figure 13.2, the ranges for these three elements (C, N, and S) are each, respectively, shifted one electron higher.
Table 13.1 shows the common oxidation states of some of the other elements of biological importance. Oxygen's (AN = 8) outer shell has six electrons, producing an aggressive tendency to add two additional electrons (thereby filling its outer shell) rather than releasing any to other adjacent atoms. This characteristic qualifies oxygen as having a high degree of electronegativity (Section 3.2). As a result, oxygen's metabolic range of oxidation states only includes —2 (e.g., H2O), besides 0 (diatomic oxygen, O2). Hydrogen (AN = 1) has possible states of —1, 0, and +1, since its single outer shell has only one electron of the two it would take to fill it. In living matter it typically donates its electron (thus, oxidation state = +1) to a more electronegative (e.g., oxygen, carbon, sulfur, nitrogen) receptor. Metabolic iron (AN = 26), occurs mainly in the +2 (ferrous) and +3 (ferric) oxidation states, while manganese (AN = 25) is found mainly as the +2 (manganous) and +4 (manganic) forms. Chlorine (AN = 17) as a disinfectant in water (HOCl, hypo-chlorous acid) has an oxidation state of +1, but as chloride or in organic compounds it is 1.
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