General Microbiology - Schlegel H. 1987

Microorganisms and the Environment
Microbial Ecology

In the preceding chapters, various microorganisms were described, grouped according to their PHYSIOLOGICAL AND BIOCHEMICAL properties. Their habitats were also mentioned. The insights gained now allow us to examine the interactions of microorganisms with their surrounding environment. We will first focus on the Basic Concepts and principles of ecology. This science studies The behavior of organisms in their natural habitats, their interrelationships with one another, and with their environment.

The earliest traces of life date back more than 3 billion years; these were microorganisms that dominated the Earth's biosphere until about 0.5 billion years ago. Thus, prokaryotes not only lie at the very origin of terrestrial life and gave rise to the entire diversity of eukaryotic forms, but they have also coexisted continuously ever since. Throughout their evolution, higher forms of life have never been alone; they have constantly been either crowded or supported by ubiquitous unicellular organisms. Among modern higher forms of life, some have established themselves not only in the struggle against their own kind, but also through interactions with microorganisms. In the course of evolution, many organisms have developed tolerant, cooperative relationships known as mutualistic Symbiosis. Part of this chapter (Section 17.2) will be specifically devoted to microorganisms as symbionts of other microorganisms, plants, and animals.

Microorganisms already existed when our planet's surface was taking on its present appearance; they were already present when continents shifted, sedimentary strata thousands of meters thick were formed, the Earth's crust repeatedly subsided and folded, and deposits of ores, coal, oil, and natural gas arose. Microorganisms actively participated in many of these processes (some issues of geomicrobiology will be discussed in Section 17.3).

For at least 80% of the entire period of organic evolution, the Earth was inhabited exclusively by microorganisms. While fossil remains of microbes are rarely found, comparative physiology and biochemistry provide a sufficient basis for classifying prokaryotes by their metabolic type. However, when reading the section on organismal evolution, one should keep in mind that this field still contains many gaps and assumptions.

17.1.1 Introduction

Considerable effort has been dedicated to isolating and describing individual microorganisms. Studies on pure cultures are essential because they help assess the potential capabilities and Functions of individual species in nature. For a time, taxonomic, physiological, biochemical, and genetic research diverted microbiologists from the primary goal of their science—The Study of microbial behavior in their natural habitats.

Ecology deals with the interrelationships among organisms and with their environment. Microbial ecology investigates only specific parts of holistic ecological systems. Ecology is a highly multifaceted science, and its problems are addressed by specialists across various biological disciplines and viewed from multiple Perspectives. Consequently, There is a lack of consensus even in The Use of basic ecological terms. We will first attempt to clarify some general terms applied in microbial ecology.

Ecosystem. The fundamental unit in ecology is the ecosystem. It comprises both biotic and abiotic components. The biotic components form a community of organisms, or biocenosis. As a rule, this refers to populations of microorganisms, where a population may consist of clones of a single species or several different species. Abiotic components are the Physical and Chemical conditions of the ecosystem in which organisms live. The sizes of microbial ecosystems vary widely. This can be, for example, a pond, a lake, or a tree ROOT system. Ecosystems can also be as small as the human Oral Cavity, the rumen of a ruminant, or a section of the intestine. The entire living space of our planet collectively—the biosphere—can be viewed as a giant ecosystem. METABOLISM/2.html">THE CONCEPT OF the "environment" is often associated with a particular ecosystem. This environment maintains the interactions of a given Organism (or population) with the surrounding biotic or abiotic Components of the ecosystem.

Habitat. Within an ecosystem, the habitat of each species can be described. This is the specific site or living space (locality) where a given organism (individual or population) typically lives. For every organism, one can identify at least one habitat where it commonly occurs, grows and develops successfully, and where it is most likely to be found again and isolated. Habitats may include marine benthic sediments, fertile humus-rich soil, or the human Nasal cavity or intestine. Within a given ecosystem, a microorganism generally has only a single habitat; however, broadly speaking, it may occupy several such sites, each in a separate ecosystem. For instance, Bacteria of the genus Rhizobium grow in both soil and plants; a specific methanogenic bacterium may inhabit marine sediments, the rumen of ruminants, or a sewage Treatment digester. In other words, a habitat is an organism's "street and house number"; some organisms may have multiple addresses.

Ecological niche. Unlike the term "habitat," the Concept of the "ecological niche" reflects not a spatial Location, but rather the function of a species or population within a community of organisms. The ecological niche characterizes the "profession" of a species. One can assume that each species (or population) performs a specific function determined by its nutritional requirements, mobility, mode reproduction, biochemical capabilities, structural features, and limits of tolerance to environmental conditions. Whether or not a given species can perform a specific function in a particular ecosystem depends on the aggregate of its properties. Typically, the actual distribution limits of a species or population are narrower than one might expect based solely on its properties. In other words, realized niches are generally narrower than fundamental ones. Whether a species will actually perform the function it is potentially capable of is often determined by secondary, incidental circumstances.

Let us illustrate this with an example. In the rumen of ruminants, only those cellulolytic bacteria that operate under anaerobic conditions and are capable of obtaining energy through Fermentation can grow and carry out the function of Cellulose breakdown. Furthermore, they must be tolerant to the internal Temperature of The Stomach, the presence of Fatty acids, Enzymes, ammonia, gases, and other products. Finally, the continuous removal of certain fermentation products, such as H₂, must be ensured. Thus, to perform a given function in a specific ecosystem, a species must possess a whole range of specific traits.

Ecosystem inhabitants. According to the concept proposed by Winogradsky in 1925, microorganisms found in an ecosystem can be subdivided into two categories: autochthonous and allochthonous. Autochthonous microorganisms are typical inhabitants of a given ecosystem (e.g., soil, intestine) and are always present there. They can invariably be found, say, in soil regardless of whether specific nutrients are introduced from the outside or not. The presence of such species is driven by the more or less constant presence of nutrients characteristic of that ecosystem. Allochthonous (or zymogenic) microorganisms are understood as those whose presence depends on a random increase in nutrient concentration or The addition of specific substances. Such species are, to a certain extent, foreign to the given ecosystem, present only temporarily, or existing in a resting state.

Autochthonous ecosystem inhabitants generally include highly specialized organisms, such as nitrifying bacteria, inhabitants of hot springs, and other extreme ecosystems. Zymogenic representatives include many ubiquitous soil and Water bacteria (ubiquists).

Abundance and diversity of microorganisms in ecosystems. Under normal conditions, A large number of species develop in soil or water. We consider "normal" conditions to be a neutral pH, an abundance of nutrients, and a high water content. The more ecosystem conditions deviate from normal—that is, the more extreme the chemical and physical CHARACTERISTICS OF THE environment—the lower the species diversity, but the higher the abundance of individuals belonging to the same species. Such relationships between the number of species and individuals on the one hand, and the degree of environmental extremity on the other, are observed in many ecosystems, such as hot springs, saline lakes, acidic mine drainage, the gut, and arid soils. Extreme ecosystems are dominated by organisms that are fully adapted to their habitat and fail to grow if the corresponding extreme factor is attenuated. This applies to extreme thermophiles, psychrophiles, halophiles, alkaliphiles, osmophiles, and other "extremophilic" microorganisms.

17.1.2 Aquatic Ecosystems

In many ecosystems of the Earth's biosphere, microorganisms occupy a crucial position or represent the sole life forms. Since it is impossible to consider all ecosystems, we must limit ourselves to only a few. This small Selection should include soil as an example of a terrestrial ecosystem, and oceans and seas as Examples of aquatic ecosystems. The study of fertile topsoil is extremely interesting, but due to the presence of a vast number of highly diverse organisms within a very small space, the soil ecosystem is immensely complex. Therefore, we will focus our attention on aquatic systems, especially since the majority of microbiological transformations take place in an aqueous environment. Typical aquatic ecosystems include oceans, seas, lakes, ponds, and flowing water bodies.

Oceans. Marine microbiology constitutes a branch of marine biology and, as a science, is still very young. The primary producers in the sea are unicellular Algae—phytoplankton. The food chain includes bacteria, Protozoa, Arthropods, and fish. Although oceans absorb and store the largest amount of solar energy, they contribute very little to food production; only 5–10% of the protein produced on Earth is formed in the ocean. Productivity here is distributed very unevenly. This unevenness in Primary and secondary organic matter production can be illustrated by fish catch data. The open ocean, which covers 90% of our planet's water surface, yields only 0.7% of the total fish catch; coastal zones, accounting for about 10% of the area, account for 54% of the catch, while natural upwelling areas (0.1% of the surface) yield 44% of the total catch. The fish catch is obviously closely linked to total biomass production. Its distribution clearly shows the dependence of primary biomass formation on The amount of nutrients, mainly nitrates and phosphates. Therefore, the inflow of nutrient-rich wastewater into the global ocean does not lead to its pollution; moreover, it serves as a prerequisite for biomass production in the seas. Without a constant influx of such substances, even the seas cannot sustain large catches.

Bacteriologically interesting transformations occur in marginal marine areas, near river mouths (estuaries), in salt marshes, and in brackish water zones. The ubiquitous presence of sulfate in seawater leads to The formation of hydrogen sulfide in anaerobic zones and microhabitats through The activity of sulfate-reducing bacteria, which affects the entire remaining bacterial community.

Halophilic bacteria from coastal marine zones are not yet as thoroughly studied as they deserve to be. Both for cognitive purposes and for solving practical problems, it is essential to keep marine bacteria constantly in view. Currently, great attention is paid to wastewater MICROORGANISMS AND THE breakdown of recalcitrant substances in such waters. Wastewater is polluted not only by organic impurities, but also by significant amounts of salts, including sulfates. Thus, conditions similar to those of marine ecosystems are created therein. These considerations regarding wastewater biology emphasize the need to pay greater attention to microbiological transformations occurring in marine ecosystems.

Lakes. The science of lakes and ponds (limnology) has provided a better understanding of partial cycles and their integration. Lakes and smaller freshwater bodies represent well-delimited, easily describable aquatic ecosystems. They contain both aerobic and anaerobic zones. Such zones can also be found in most soils; however, whereas in soil they are clustered close together in a very confined space and are therefore difficult to study, in lakes these zones are quite extensive and easily investigated. Nevertheless, there are reasons to believe that the results of limnological research can, in principle, be extended to soil with its microheterogeneity.

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Fig. 17.1. Schematic vertical section of a eutrophic lake as an example of an aquatic ecosystem. The thermocline (or chemocline) separates the aerobic region from the anaerobic one. Primary organic matter production via Photosynthesis occurs in both regions. Anaerobic conditions begin to develop As a result of anaerobic decomposition in bottom sediments.

Biological processes in lakes and ponds are heavily influenced by the Physical Properties of water. Water has its maximum density at 4°C. Water temperature changes with depth; a more or less stable layering (stratification) may be observed depending on the season (Fig. 17.1). Stratification is characteristic of Two Types of lakes. One type includes freshwater lakes of temperate latitudes. In spring, the cold lake water is warmed by the sun; the surface water layer becomes warm, and its density decreases. This layer is called the epilimnion. It overlies a colder water layer—the hypolimnion. The layers are separated by a transition zone called the thermocline or metalimnion; this boundary between the layers is sometimes very sharp. In deep lakes, this Separation can persist throughout the entire summer. As a result of aerobic decomposition processes, dissolved oxygen in the water is consumed starting from the bottom layer, creating anaerobic conditions in the hypolimnion. The epilimnion is in contact with atmospheric oxygen, mixed by the wind, and therefore, as a rule, conditions here remain aerobic. This leads to the formation of redox potential and chemical gradients in the thermocline region, which is why the thermocline is also referred to as the chemocline. In autumn, the epilimnion cools. If the temperature of the epilimnion drops below that of the hypolimnion, both layers mix, aided by autumn gales. In the case of complete mixing, deep water layers rise to the surface and are re-oxygenated. Consequently, the uniform distribution of nutrients abundant in deep waters is restored annually. Lakes with complete water mixing are termed holomictic. In winter, reverse stratification may occur. The temperature at depth is 4°C, and above it lies a layer of colder water with lower density, sometimes capped by ice. When the temperature in the surface layer rises above 4°C in spring, stratification is disrupted once again.

When nutrient-rich deep waters reach the surface, a massive proliferation of cyanobacteria and green algae ("water bloom") ensues. The scale of substance transformations and biomass production depends on the nutrient content in the water body: in nutrient-rich (eutrophic) lakes these transformations are very intense, whereas in nutrient-poor (oligotrophic) ones they are barely perceptible.

Holomictic lakes are distinguished from meromictic and amictic lakes, in which mixing is only partial or absent altogether, resulting in a stable anaerobic hypolimnion ("monimolimnion") that persists regardless of the season. Such permanence of stratification is characteristic mainly of tropical lakes, where the surface water temperature rarely drops below that of the deep layer. However, meromictic lakes are also found in temperate latitudes. The stability of stratification in them is most commonly maintained by the high salinity of deep water (in fjord branches) or special geographical conditions.

Biological processes leading to summer stratification, which lasts for several months, can be illustrated using the example of a holomictic lake. In the light-drenched epilimnion, phytoplankton (diatoms, flagellates, green algae, cyanobacteria) produce biomass. Typically, additional organic material enters the lake from the surrounding environment. A portion of this organic matter—especially cellulose-containing particles—settles to the lake bottom and undergoes decomposition. During the initial aerobic stage of decomposition, oxygen is consumed, creating anaerobic conditions at the bottom. As a result of anaerobic breakdown, organic fermentation products such as H₂, H₂S, CH₄, and CO₂ are formed. Since convection does not occur, these products migrate from the bottom sediments into the water Column very slowly. Methane alone—the primary product of the anaerobic food chain in bottom sediments—is released in the form of gas bubbles. On its way to the water surface, some of the methane dissolves and is oxidized by aerobic bacteria that utilize this gas. The rapid consumption of oxygen in the hypolimnion is driven by the accelerated distribution of methane and the proliferation of methane-oxidizing bacteria. Eventually, anaerobic conditions become established throughout the entire hypolimnion.

As soon as oxygen disappears from the hypolimnion, transformations mediated by anaerobic microorganisms resume. Primary fermentation products are utilized for the reduction of nitrate and sulfate. The bulk of hydrogen sulfide is produced via sulfate reduction within the water column (Fig. 17.2). The hypolimnion and thermocline serve as a true paradise for anaerobic bacteria. In the presence of H₂S and sufficient light intensity below the thermocline, Purple and green sulfur bacteria thrive, forming a secondary layer with high primary biomass production. In this zone, one can find forms possessing gas vacuoles, such as Lamprocystis, Amoebobacter, Thiodictyon, Thiopedia, Pelodictyon, and Ancalochloris, as well as flagellated species like Chromatium and Thiospirillum. Biomass production via anoxygenic photosynthesis is substantial; this is evidenced by the abundance of Ciliates, copepods, and cladocerans that inhabit the water directly above the thermocline and feed on phototrophic bacteria. The sulfate produced by purple sulfur bacteria is rapidly reduced back to H₂S, with exudates from the phototrophic bacteria likely serving as hydrogen Donors for sulfate-reducing bacteria.

Fig. 17.2. Model representation of the vertical profile of a temperate freshwater lake, showing concentrations, turnover rates, and biomasses. This scheme is based on data by Yu. I. Sorokin (1970), V. M. Gorlenko, G. A. Dubinina, and S. I. Kuznetsov (1977), as well as J. Overbeck (1972). T - temperature, °C; 1 - light-driven CO₂ fixation via oxygenic photosynthesis; 2 - dark CO₂ fixation; 3 - light-driven CO₂ fixation via anoxygenic photosynthesis; 4 and 5 - sulfate reduction; 6-10 - biomass (mg/mL); 6 - algae and cyanobacteria; 7 - total bacterial mass; 8 - phototrophic bacteria; 9 - protozoa; 10 - cladocerans and copepods.

High biological activity is also characteristic of the thermocline zone. Certain cyanobacteria capable of tolerating the presence of hydrogen sulfide and the absence of O₂ develop here, including Oscillatoria limnetica.

The described interrelationships are illustrated in Figs. 17.1 and 17.2. These diagrams clearly show that a stratified lake contains two types of aquatic environments where primary biomass production occurs via photosynthesis: in the layers near The surface of the epilimnion, oxygenic photosynthesis takes place, whereas in the upper layer of the hypolimnion, anoxygenic photosynthesis occurs.

Flowing waters. In natural, unpolluted flowing water bodies, unicellular organisms are often so scarce that the water appears crystal clear. It is worth recalling, however, that a suspension containing 10⁶ bacteria per 1 mL remains visually clear. As long as water pollution was minimal, a stream or river stretch just a few kilometers long could mineralize all the easily degradable organic material originating from riparian settlements. The composition of microflora and microfauna in a flowing water body serves as a reliable indicator of its pollution level. If Daphnia are still present, the water is clean. The presence of the "sewage fungus" Sphaerotilus natans indicates heavy organic pollution, while the odor of hydrogen sulfide points to anaerobic sulfate reduction, thus serving as an alarm signal.

Wastewater treatment. A treatment plant is essentially a flowing water body in which organic substances are decomposed through the action of Fungi and bacteria (both aerobic and anaerobic). Wastewater contaminants can vary depending on whether the discharge consists solely of human waste and domestic refuse, or also includes manure, slaughterhouse wastewater, or other industrial effluents. In many cases, wastewater contains heavy metals or persistent Organic compounds. The goal of wastewater treatment is to free the water of solid, liquid, mineral, and organic substances before it enters streams and rivers. Special efforts are required to mineralize organic material microbiologically.

The concentration of microbially degradable organic substances is assessed by the so-called "biological oxygen demand" (BOD). This is the amount of oxygen required by microorganisms to oxidize organic material during Respiration. For example, BOD₅ is the amount of oxygen (in mg) consumed by microorganisms during the decomposition of organic substances over a period of 5 days. "Chemical oxygen demand" (COD) refers to the amount of oxygen required for the complete chemical oxidation of these same substances to CO₂ and H₂O.

Various technical Methods are used for wastewater treatment in treatment systems, yet they fundamentally follow the same basic stages:

1) removal of relatively easily settleable solids in a grit chamber and primary clarifier;

2) microbiological oxidation of dissolved organic substances using activated sludge or a biological filter;

3) anaerobic incubation of sludge removed from the primary and secondary clarifiers in an anaerobic digester, where methane is produced as a result and sludge precipitates. After dewatering, this sludge can be composted and used as fertilizer or incinerated (Fig. 17.3).

Fig. 17.3. Schematic diagram of a mechanical and biological wastewater treatment plant.

Subsequently, the treated, clarified water is discharged into rivers—either directly or via a receiving basin. This water still contains mineralization products such as phosphate, nitrate, ammonium ions, and others. Its discharge into a river may induce such an excess of nutrients that it triggers an increase in primary production. To prevent such eutrophication of water bodies, one can either utilize treated wastewater for field irrigation or forest soil Fertilization, or add an extra treatment step to the conventional Procedure—namely denitrification—to rid the wastewater of at least bound nitrogen. Additionally, they can be purified via chemical clarification, specifically the precipitation of phosphate ions using iron salts. Other wastewater treatment measures may also be implemented.