General Microbiology - Schlegel, H. 1987

The place of microorganisms in nature
Participation in the nutrient cycle

Depending on their role and function in the balance of nature, organisms are divided into three groups. Green plants synthesize organic substances using solar energy and carbon dioxide, which is why they are called producers. Animals act as consumers (heterotrophs); they expend a significant portion of primary biomass to build their own bodies. Eventually, the remains of both animals and plants undergo decomposition, during which organic matter is converted into mineral, Inorganic Compounds. This process, known as mineralization, is carried out primarily by Fungi and Bacteria, which serve as the decomposers in nature's balance. Thus, bioelements participate in cyclic processes. At this point, it is appropriate to briefly examine the biogeochemical cycles of carbon, nitrogen, phosphorus, and sulfur.

The Carbon Cycle. Microorganisms play a vital role in the carbon cycle, which is essential for sustaining life on Earth. They drive the mineralization of carbon previously converted by green plants into Organic compounds, thereby maintaining a highly delicate equilibrium (Fig. 1.1). Atmospheric air contains just over 0.03% carbon dioxide (12 µM/L). However, the photosynthetic productivity of green plants is so immense that the atmospheric reserve of СО₂ would be depleted in roughly 20 years. This is a relatively short timeframe on a human scale; after all, the Earth's energy and coal reserves are estimated to last between 1,000 and 3,000 years. Even accounting for the СО₂ dissolved in the oceans, this gas would suffice for only about 2,000 years.

Class="center">

Fig. 1.1. The carbon cycle in the biosphere. Numbers near the arrows indicate the annual turnover of СО₂ (fixation, formation, exchange). Photosynthetic fixation of carbon dioxide by green plants would rapidly exhaust its atmospheric reserves if organic compounds were not decomposed by microorganisms and oxidized back into СО₂, thus replenishing the carbon dioxide supply in the air. The combustion of carbon-based fossil fuels (oil, natural gas, coal) leads to a gradual increase in atmospheric СО₂ levels.

Green plants would soon be forced to cease СО₂ fixation if lower animals and microorganisms did not ensure the return of this gas to the atmosphere through the continuous Mineralization of organic material. In the global balance of matter, soil bacteria and fungi play a role no less significant than that of photosynthetic green plants. The interdependence of all living creatures on Earth finds its most vivid expression in the carbon cycle.

Another characteristic of the mineralization process deserves mention: a small fraction of the mineralized carbon (1–1.5%) enters the atmosphere not as СО₂, but in the form of methane. This gas is produced from organic matter in oxygen-depleted environments (such as tundra soils, rice paddies, and the rumen of ruminants), subsequently escaping into the atmosphere where it is oxidized by OH radicals via carbon monoxide (СО) to СО₂. The production of methane, as well as other trace gases (Н₂, СО, N₂О, NО₂), is mediated primarily by bacteria.

At first glance, the oceans appear to be a massive reservoir of carbon dioxide. However, it must be considered that The rate of exchange between atmospheric СО₂ and oceanic СО₂—where over 90% of the substance exists as HCO^-₃—is very slow; only one-tenth of the atmospheric Carbon dioxide is exchanged in this manner over the course of a year. Moreover, only a thin surface layer of Water participates in gas exchange between the ocean and the atmosphere. Vast quantities of СО₂ located below the thermocline in the oceans reach the surface in only a few regions (such as West Africa and Chile), where they enrich the atmosphere (up to 0.05%). For many years, the concentration of carbon dioxide in the air has been steadily rising. On the one hand, this is attributed to the combustion of oil and coal; in 1976, approximately 3.2 ∙ 10⁹ tons of oil were consumed (primarily burned) worldwide. On the other hand, the increase in atmospheric СО₂ concentration is likely linked to a reduction in Photosynthetic Carbon Fixation resulting from large-scale deforestation and soil degradation. It should be emphasized that the World Ocean acts as a powerful buffer system striving to maintain atmospheric СО₂ levels at a stable level.

Photosynthetic fixation of СО₂ by green plants primarily yields sugars and related compounds. The bulk of fixed carbon in both woody and herbaceous plants is temporarily stored in the form of polymeric CARBOHYDRATES. Approximately 60% of the carbon dioxide fixed on land goes into wood formation. Wood consists of 75% Polysaccharides (Cellulose, hemicelluloses, starch, Pectins, and arabinogalactans) and contains little more than 20% Lignin and Lignans, with a very low protein content (1%). In grasses and other herbaceous plants, the polysaccharide content is even higher.

The predominance of polysaccharides among green plant assimilation products makes sugars crucial for the Nutrition of All living organisms requiring organic food. Glucose and other sugars in polymeric form are the quantitatively dominant substrates for mineralization processes in nature; as monomers, they serve as the preferred nutrients for most heterotrophic microorganisms. The Nitrogen Cycle (Fig. 1.2). Ammonium occupies a central place in the nitrogen cycle. It is a product of the decomposition of Proteins AND AMINO acids entering the soil with animal and plant remains. In well-aerated soils, ammonium undergoes nitrification; bacteria of the genera Nitrosomonas and Nitrobacter oxidize it to nitrite and nitrate. Plants can utilize and assimilate both ammonium and nitrate as nitrogen sources. In the absence of oxygen, molecular nitrogen is formed from nitrate (denitrification). Bacteria involved in this process use nitrate as an oxidizing agent (hydrogen acceptor)—that is, they "respire" using NO^-₃ instead of О₂, a phenomenon known as "nitrate Respiration." Denitrification leads to a loss of nitrogen from the soil. Along with this, bacteria are also capable of MOLECULAR Nitrogen Fixation. Nitrogen-fixing bacteria live either freely in the soil (non-symbiotically) or in Symbiosis with higher plants (symbiotic diazotrophs). Alongside animals and plants, bacteria play a fundamental role in the nitrogen cycle.

Fig. 1.2. The nitrogen cycle.

The phosphorus cycle. In the biosphere, phosphorus is found almost exclusively in the form of phosphates. In living organisms, phosphoric acid occurs in the form of esters. Following Cell death, these esters are rapidly degraded, leading to the release of phosphoric acid ions. The form of phosphorus available to plants in soil is free orthophosphoric acid ions (Н₃РО₄). Their concentration is often very low; plant growth is typically limited not by an overall shortage of phosphate, but by The formation of its sparingly soluble compounds, such as apatite and complexes with heavy metals. Phosphate reserves in deposits suitable for mining are large, and in the foreseeable future, agricultural production will not be constrained by a lack of phosphorus; however, phosphate must be converted into a soluble form. In many places, agricultural fertilizers introduce phosphates into flowing waters and lakes. Since the concentration of iron, calcium, and aluminum ions in aquatic environments is low, phosphate remains in a dissolved state, leading to eutrophication—a process particularly favorable for the proliferation of nitrogen-fixing cyanobacteria. In soils, conversely, phosphates rapidly become unavailable for uptake due to the formation of insoluble salts.

The sulfur cycle (Fig. 1.3). In living Cells, sulfur is represented primarily by sulfhydryl groups within Sulfur-Containing Amino Acids (Cysteine, Methionine, homocysteine). Sulfur accounts for 1% of the dry weight of organisms. During the anaerobic decomposition of organic matter, sulfhydryl groups are cleaved by desulfurases; the production of hydrogen sulfide during mineralization under anaerobic conditions is also referred to as desulfurization. However, the largest quantities of naturally occurring hydrogen sulfide are generated via dissimilatory sulfate reduction carried out by sulfate-reducing bacteria (see Section 9.2 and Fig. 9.4).

This hydrogen sulfide, produced in the absence of molecular oxygen in aquatic sediments, can be oxidized to elemental sulfur and sulfate by anaerobic phototrophic bacteria (Chromatiaceae, Sections 12.1; 12.1.2). When hydrogen sulfide diffuses into zones containing O₂, it is oxidized to sulfate either abiotically or by aerobic sulfur bacteria (Section 11.2). Plants and a subset of microorganisms obtain the sulfur required for the synthesis of sulfur-containing amino acids through assimilatory sulfate reduction, whereas animals acquire reduced sulfur compounds via their diet.

Fig. 1.3. The sulfur cycle. 1. Sulfate is reduced to sulfide during assimilatory sulfate reduction, and sulfur is temporarily accumulated in living organisms in organically bound form within proteins. 2. Sulfur is released during protein degradation and the Cleavage of S^2- from amino acids. 3 and 4. Under aerobic conditions, sulfide can be oxidized either abiotically to sulfur or sulfate, or bacterially (Beggiatoa, Thiothrix) via sulfur to sulfate. Elemental sulfur is oxidized to sulfate by thiobacilli under aerobic conditions (4). Under anaerobic conditions, sulfide can be oxidized to sulfur by phototrophic bacteria (Chlorobium) or to sulfate (Chromatium). Under anaerobic conditions, dissimilatory reduction of sulfate to sulfide (by sulfate-reducing bacteria such as Desulfovibrio and Desulfotomaculum) (5) and of sulfur to sulfide (by Desulfuromonas bacteria) (6) can also take place.

Table 1.1. Distribution of bioelements in seawater (Kalle K., "Das Meerwasser als Mineralstoffquelle der Pflanzen," Handbuch der Pflanzenphysiologie, Bd. IV. Springer, Berlin, 1958, abridged)

Phosphorus and nitrogen as biomass-limiting factors. The elements that restrict plant growth, and consequently biomass production, are phosphorus and nitrogen. They play this limiting role in both terrestrial and marine ecosystems, with precise data available for seawater. Based on the data in Table 1.1, one can calculate how much biomass (in grams of dry weight) can be produced from the elements contained in one cubic meter of seawater. From 28 g of carbon (C), 60–100 g of biomass can be formed; from 0.3 g of nitrogen (N), 6 g; and from 0.03 g of phosphorus (P), only 5 g. It follows that biomass production is ultimately limited by phosphates. Consequently, even nitrogen-fixing cyanobacteria hold no selective advantage over other organisms in seawater.