Nutrition, Culture, and Metabolism of Microorganisms

4 Nutrition, Culture, and Metabolism of Microorganisms A microbial cell carries out a I Nutrition and Culture of IV Essentials of Catabolism 98 host of metabolic reactions to Microorganisms 86 4.8 Glycolysis 98 yield the energy necessary to 4.1 Nutrition and Cell Chemistry 86 4.9 Respiration and Electron Carriers 101 divide and form two cells. 4.2 Culture Media 88 4.10 The Proton Motive Force 103 Continued growth on a solid 4.3 Laboratory Culture 90 4.11 The Citric Acid Cycle 105 surface leads to visible II Energetics and Enzymes 92 4.12 Catabolic Diversity 106 masses of cells, called 4.4 Bioenergetics 92 V Essentials of Anabolism 108 colonies. 4.5 Catalysis and Enzymes 93 4.13 Biosynthesis of Sugars and III Oxidation–Reduction and Polysaccharides 108 4.14 Biosynthesis of Amino Acids and Energy-Rich Compounds 94 Nucleotides 109 4.6 Electron Donors and Electron 4.15 Biosynthesis of Fatty Acids and Acceptors 94 Lipids 110 4.7 Energy-Rich Compounds and Energy 4.16 Regulating the Activity of Biosynthetic Storage 97 Enzymes 111 86 UNIT 2 • Metabolism and Growth ecall from Chapter 2 that all cells require energy to drive life important as DNA is to a cell, it contributes a very small percent- Rprocesses. The requisite energy is obtained from organic age of a cell’s dry weight; RNA is far more abundant (Figure 4.1c). chemicals by chemoorganotrophs, from inorganic chemicals by The data shown in Figure 4.1 are from actual analyses of cells chemolithotrophs, and from light by phototrophs. In this chap- of E. coli; comparable data vary a bit from one microorganism to ter we explore how cells conserve and use their energy and the next. But in any microbial cell, carbon and nitrogen are nutrients. We assume that the reader has some background in important macronutrients, and thus we begin our study of cell chemistry and refer the reader who needs a refresher on the microbial nutrition with these key elements. chemical principles of life to an overview of this topic at www.microbiologyplace.com Carbon and Nitrogen All cells require carbon, and most prokaryotes require organic I Nutrition and Culture (carbon-containing) compounds as their source of carbon. Het- erotrophic bacteria assimilate organic compounds and use them of Microorganisms to make new cell material. Amino acids, fatty acids, organic acids, sugars, nitrogen bases, aromatic compounds, and count- efore a cell can replicate, it must coordinate many different less other organic compounds can be transported and catabo- Bchemical reactions and organize many different molecules lized by one or another bacterium. Autotrophic microorganisms into specific structures. Collectively, these reactions are called build their cellular structures from carbon dioxide (CO2) with metabolism. Metabolic reactions are either catabolic, which energy obtained from light or inorganic chemicals. means energy releasing, or anabolic, which means energy requir- A bacterial cell is about 13% nitrogen, which is present in pro- ing. Catabolism breaks molecular structures down, releasing teins, nucleic acids, and several other cell constituents. The bulk energy in the process, and anabolism uses energy to build larger of nitrogen available in nature is in inorganic form as ammonia 2 molecules from smaller ones. (NH3), nitrate (NO3 ), or nitrogen gas (N2). Virtually all prokary- We examine some of the key catabolic and anabolic reactions of otes can use NH3 as their nitrogen source, and many can also use 2 cells in this chapter. However, before we do, we consider how NO3 . By contrast, N2 can only be used by nitrogen-fixing microorganisms are grown in the laboratory and the nutrients they prokaryotes, discussed in detail in later chapters. Nitrogen in need for growth. Indeed, most of what we know about the metabo- organic compounds, for example, in amino acids, may also be lism of microorganisms has emerged from the study of laboratory available to microorganisms; if organic N is available and is taken cultures. Our initial focus is on chemoorganotrophs; later in the up, the compound can immediately enter the monomer pool for chapter we consider chemolithotrophs and phototrophs. biosynthesis or be catabolized as an energy source. 4.1 Nutrition and Cell Chemistry Other Macronutrients: P,S, K, Mg, Ca, Na In this section we learn how to care for and feed microorganisms. In addition to C, N, O, and H, many other elements are needed Nutrition is the part of microbial physiology that deals with the by cells, but in smaller amounts (Figure 4.1b). Phosphorus is a key element in nucleic acids and phospholipids and is typically nutrients required for growth. Different organisms need different 2 supplied to a cell as phosphate (PO 2 ). Sulfur is present in the complements of nutrients, and not all nutrients are required in 4 amino acids cysteine and methionine and also in several vita- the same amounts. Some nutrients, called macronutrients,are mins, including thiamine, biotin, and lipoic acid. Sulfur can be required in large amounts, while others, called micronutrients, 2 supplied to cells in several forms, including sulfide (HS ) and are required in just trace amounts. 2 sulfate (SO 2 ). Potassium (K) is required for the activity of sev- All microbial nutrients are compounds constructed from the 4 eral enzymes, whereas magnesium (Mg) functions to stabilize chemical elements. However, just a handful of elements domi- ribosomes, membranes, and nucleic acids and is also required for nate living systems and are essential: hydrogen (H), oxygen (O), the activity of many enzymes. Calcium (Ca) is not required by all carbon (C), nitrogen (N), phosphorus (P), sulfur (S), and selenium cells but can play a role in helping to stabilize microbial cell walls, (Se). In addition to these, at least 50 other elements, although not and it plays a key role in the heat stability of endospores. Sodium required, are metabolized in some way by microorganisms (Na) is required by some, but not all, microorganisms, and its (Figure 4.1). An approximate chemical formula for a cell is requirement is typically a reflection of the habitat. For example, CH O N , indicating that C, H, O, and N constitute the bulk 1 2 0.5 0.15 seawater contains relatively high levels of Na , and marine of a living organism. 1 microorganisms typically require Na for growth. By contrast, Besides water, which makes up 70–80% of the wet weight of a 1 - freshwater species are usually able to grow in the absence of Na . microbial cell (a single cell of Escherichia coli weighs just 10 12 g), cells consist primarily of macromolecules—proteins, nucleic K, Mg, Ca, and Na are all supplied to cells as salts, typically as acids, lipids, and polysaccharides. The essential elements make chloride or sulfate salts. up the building blocks (monomers) of these macromolecules, the amino acids, nucleotides, fatty acids, and sugars. Proteins domi- Micronutrients: Iron and Other Trace Metals Microorganisms require several metals for growth (Figure 4.1a). nate the macromolecular composition of a cell, making up 55% of Chief among these is iron (Fe), which plays a major role in cellu- total cell dry weight. Moreover, the diversity of proteins exceeds lar respiration. Iron is a key component of cytochromes and of that of all other macromolecules combined. Interestingly, as iron–sulfur proteins involved in electron transport reactions CHAPTER 4 • Nutrition, Culture, and Metabolism of Microorganisms 87 Group 12345678910 11 12 13 14 15 16 17 18 Period 1 Essential for all microorganisms 2 1 H Essential cations and anions for most microorganisms He 3 4 Trace metals, some essential for some microororganisms 5 6 7 8910 Used for special functions 2 Li Be B C N O F Ne UNIT 2 Unessential, but metabolized 11 12 Unessential, not metabolized 13 14 15 16 17 18 3 Na Mg Al Si P S Cl Ar 1920 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 4 K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 5 Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe 55 56 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 6 Cs Ba Lu Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn (a) Essential elements as a percent of cell dry weight Macromolecular composition of a cell Macromolecule Percent of dry weight C 50% P 2.5% Protein 55 O 17% S 1.8% Lipid 9.1 Polysaccharide 5.0 N 13% Se <0.01% Lipopolysaccharide 3.4 H 8.2% DNA 3.1 RNA 20.5 (b) (c) Figure 4.1 Elemental and macromolecular composition of a bacterial cell. (a) A microbial periodic table of the elements. With the exception of uranium, which can be metabolized by some prokaryotes, elements in period 7 or beyond in the complete periodic table of the elements are not known to be metabolized. (b) Contributions of the essential elements to cell dry weight. (c) Relative abundance of macromolecules in a bacterial cell. Data in (b) from Aquat. Microb. Ecol. 10: 15–27 (1996) and in (c) from Escherichia coli and Salmonella typhimurium: Cellular and Molecular Biology. ASM, Washington, DC (1996). (Section 4.9). Under anoxic conditions, iron is generally in the many lactic acid bacteria such as species of Lactobacillus do not 1 ferrous (Fe2 ) form and soluble. However, under oxic conditions, contain detectable iron and grow normally in its absence.

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