Microbial Ecology

Microbes and Ecosystem Niches

Every ecosystem on Earth contains microorganisms that occupy unique niches based on their specific metabolic properties.

Learning Objectives

Evaluate microbes and the niches they occupy

Key Takeaways

Key Points

  • Microbes live in all parts of the biosphere where there is liquid water.
  • By virtue of their omnipresence, microbes impact the entire biosphere.
  • Each microbial species in an ecosystem is thought to occupy a unique niche, which is a complex description of the ways in which an organism uses its environment.
  • The precise ecological niche of a microbe is primarily determined by the specific metabolic properties of that organism.

Key Terms

  • bioremediation: The use of biological organisms, usually microorganisms, to remove contaminants, especially from polluted water.
  • niche: A function within an ecological system to which an organism is especially suited.
  • biosphere: The part of the Earth and its atmosphere capable of supporting life.

Microbes and Ecosystem Niches

Microbial life is amazingly diverse and microorganisms quite literally cover the planet. In fact, it has been estimated that there are 100,000,000 times more microbial cells on the planet than there are stars in the observable universe! Microbes live in all parts of the biosphere where there is liquid water, including soil, hot springs, the ocean floor, acid lakes, deserts, geysers, rocks, and even the mammalian gut.

By virtue of their omnipresence, microbes impact the entire biosphere; indeed, microbial metabolic processes (including nitrogen fixation, methane metabolism, and sulfur metabolism) collectively control global biogeochemical cycling. The ability of microbes to contribute substantially to the function of every ecosystem is a reflection their tremendous biological diversity.

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A Biofilm of Thermophilic Bacteria: Thermophiles, which thrive at relatively high temperatures, occupy a unique ecological niche. This image shows a colony of thermophilic bacteria at Mickey Hot Springs in Oregon, USA.

Microbes are vital to every ecosystem on Earth and are particularly important in zones where light cannot approach (that is, where photosynthesis cannot be the basic means to collect energy). Microorganisms participate in a host of fundamental ecological processes including production, decomposition, and fixation. They can also have additional indirect effects on the ecosystem through symbiotic relationships with other organisms. In addition, microbial processes can be co-opted for biodegradation or bioremediation of domestic, agricultural, and industrial wastes, making the study of microbial ecology particularly important for biotechnological and environmental applications.

Each species in an ecosystem is thought to occupy a separate, unique niche. The ecological niche of a microorganism describes how it responds to the distribution of resources and competing species, as well as the ways in which it alters those same factors in turn. In essence, the niche is a complex description of the ways in which a microbial species uses its environment.

The precise ecological niche of a microbe is primarily determined by the specific metabolic properties of that organism. For example, microbial organisms that can obtain energy from the oxidation of inorganic compounds (such as iron-reducing bacteria ) will likely occupy a different niche from those that obtain energy from light (such as cyanobacteria). Even among photosynthetic bacteria, there are various species that contain different photosynthetic pigments (such as chlorophylls and carotenoids) that allow them to take advantage of different portions of the electromagnetic spectrum; therefore, even microbes with similar metabolic properties may inhabit unique niches.

Organization of Ecosystems

Microorganisms serve essential roles in the complex nutrient exchange system that defines an ecological community.

Learning Objectives

Illustrate the organization of ecosystems

Key Takeaways

Key Points

  • An ecosystem is a unified system of exchange made up of autotrophic producers, heterotrophic consumers, and decomposers.
  • A food web depicts a collection of heterotrophic consumers that network and cycle the flow of energy and nutrients from a productive base of self-feeding autotrophs.
  • Microorganisms play a vital role in every ecological community by serving as both producers and decomposers.

Key Terms

  • autotroph: Any organism that can synthesize its food from inorganic substances, using heat or light as a source of energy.
  • heterotroph: An organism that requires an external supply of energy in the form of food as it cannot synthesize its own.

Although ecologists tend to regard ecosystems as basic structural units, it can be difficult (if not impossible) to formally define the boundaries of a given ecosystem. As such, ecosystems are better thought of as conceptual rather than actual geographical locations. Rarely are ecosystems isolated from one another; rather, they should be considered parts of a larger functioning whole that together comprise the biosphere (“the place on Earth’s surface where life dwells”).

Despite the fact that clear boundaries between ecosystems may be difficult to identify, the myriad interactions that take place within an ecological community can often be observed and defined. These interactions may be best described by detailing feeding connections (what eats what) among biota in an ecosystem, thereby linking the ecosystem into a unified system of exchange.

All life forms in an ecosystem can be broadly grouped into one of two categories (called trophic levels):

  • Autotrophs, which produce organic matter (food) from inorganic substances; and
  • Heterotrophs, which must feed on other organisms in order to obtain organic matter.

In general, trophic levels are used to describe the way in which a particular organism within an ecosystem gets its food. Using this description, we can restate and reorganize the categories above to define the three basic ways organisms acquire their food:

  • Producers (autotrophs) do not usually eat other organisms but pull nutrients from the soil or the ocean and manufacture their own food using photosynthesis. In this way, it is the energy from the sun that usually powers the base of the food chain.
  • Consumers (heterotrophs) cannot manufacture their own food and need to consume other organisms.
  • Decomposers break down dead plant and animal material and wastes and release them into the ecosystem as energy and nutrients for recycling.

Within ecosystems, the biotic factors that comprise the categories above can be organized into a food chain in which autotrophic producers use materials and nutrients recycled by decomposers to make their own food; the producers are in turn eaten by heterotrophic consumers. In real world ecosystems, there are multiple food chains for most organisms (since most organisms eat more than one kind of food or are eaten by more than one type of predator). Additionally, the movement of mineral nutrients in the food chain is cyclic rather than linear. As a consequence, the intricate network of intersecting and overlapping food chains for an ecosystem is more commonly represented as a food web. A food web depicts a collection of heterotrophic consumers that network and cycle the flow of energy and nutrients from a productive base of self-feeding autotrophs.

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A simplified food web: This image shows a simplified food web model of energy and mineral nutrient movement in an ecosystem. Energy flow is unidirectional (noncyclic) and mineral nutrient movement is cyclic.

Microorganisms play a vital role in every ecological community by serving both as producers and as decomposers. Although plants are the most common primary producers, autotrophic photosynthetic microbes (such as cyanobacteria and algae) can harness light energy to generate organic matter. Additionally, in zones where light cannot penetrate (and thus photosynthesis cannot be the basic means to produce energy), chemosynthetic microbes provide energy and carbon to the other organisms in the ecosystem. Other microbes are decomposers, with the ability to recycle nutrients from dead organic matter and other organisms’ waste products. Decomposition is critical as most of the carbon and energy incorporated into plant tissues during photosynthesis remains uneaten when the plant tissue dies (and therefore must be broken down before it can be made available for recycling).

Role of Microbes in Biogeochemical Cycling

Microbes form the backbone of every ecological system by controlling global biogeochemical cycling of elements essential for life.

Learning Objectives

Explain the role microbes play in biogeochemical cycling

Key Takeaways

Key Points

  • A biogeochemical cycle is a pathway by which a chemical element (such as carbon or nitrogen) circulates through and is recycled by an ecosystem.
  • Microorganisms play a primary role in regulating biogeochemical systems in virtually all of our planet ‘s environments.
  • Microbes participate in essential biogeochemical cycling events such as carbon and nitrogen fixation.

Key Terms

  • photosynthesis: The process by which plants and other photoautotrophs generate carbohydrates and oxygen from carbon dioxide, water, and light energy in chloroplasts.
  • biogeochemistry: The scientific study of biological, geological, and chemical processes in the natural environment and especially of their mutual relationships.
  • nitrogenase: The enzyme, in nitrogen-fixing bacteria, that catalyzes the conversion of atmospheric nitrogen into ammonia.

Microbial Role in Biogeochemical Cycling

Nutrients move through the ecosystem in biogeochemical cycles. A biogeochemical cycle is a pathway by which a chemical element (such as carbon or nitrogen) circulates through the biotic (living) and the abiotic (non-living) factors of an ecosystem. The elements that move through the factors of an ecosystem are not lost but are instead recycled or accumulated in places called reservoirs (or “sinks”) where they can be held for a long period of time. Elements, chemical compounds, and other forms of matter are passed from one organism to another and from one part of the biosphere to another through these biogeochemical cycles.

Ecosystems have many biogeochemical cycles operating as a part of the system. A good example of a molecule that is cycled within an ecosystem is water, which is always recycled through the water cycle. Water undergoes evaporation, condensation, and then falls back to Earth as rain (or other forms of precipitation). This typifies the cycling that is observed for all of the principal elements of life.

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The Water Cycle: Water is recycled in an ecosystem through the water cycle.

Although biogeochemical cycles in a given ecosystem are coordinated by the full complement of living organisms and abiotic factors that make up that system, microorganisms play a primary role in regulating biogeochemical systems in virtually all of our planet’s environments. This includes extreme environments such as acid lakes and hydrothermal vents, and even includes living systems such as the human gut. The key collective metabolic processes of microbes (including nitrogen fixation, carbon fixation, methane metabolism, and sulfur metabolism) effectively control global biogeochemical cycling. Incredibly, production by microbes is so immense that global biogeochemistry would likely not change even if eukaryotic life were totally absent!

Microbes comprise the backbone of every ecological system, particularly those in which there is no light (i.e. systems in which energy cannot be collected through photosynthesis ). Two key examples of critical biogeochemical processes carried out by microorganisms are discussed below.

The Carbon Cycle

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Cyanobacteria: Cyanobacteria, also known as blue-green bacteria, blue-green algae, and Cyanophyta, is a phylum of bacteria that obtain their energy through photosynthesis

Carbon is critical for life because it is the essential building block of all organic compounds. Plants and animals utilize carbon to produce carbohydrates, fats, and proteins, which can then be used to build their internal structures or to obtain energy.

Carbon in the form of carbon dioxide (CO2) is readily obtained from the atmosphere, but before it can be incorporated into living organisms it must be transformed into a usable organic form. The transformative process by which carbon dioxide is taken up from the atmospheric reservoir and “fixed” into organic substances is called carbon fixation. Perhaps the best known example of carbon fixation is photosynthesis, a process by which energy derived from sunlight is harnessed to form organic compounds. Photosynthesis depends on the activity of microorganisms such as cyanobacteria; indeed, the fact that there is oxygen in the Earth’s atmosphere at all is a consequence of the photosynthetic activity of ancient microbes.

The Nitrogen Cycle

Nitrogen is essential for all forms of life because it is required for synthesis of the basic building blocks of life (e.g., DNA, RNA, and amino acids). The Earth’s atmosphere is primarily composed of nitrogen, but atmospheric nitrogen (N2) is relatively unusable for biological organisms. Consequently, chemical processing of nitrogen (or nitrogen fixation) is necessary to convert gaseous nitrogen into forms that living organisms can use. Almost all of the nitrogen fixation that occurs on the planet is carried out by bacteria that have the enzyme nitrogenase, which combines N2 with hydrogen to produce a useful form of nitrogen (such as ammonia). Thus, microorganisms are absolutely essential for plant and animal life forms, which cannot fix nitrogen on their own.

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The Role of Microbes in the Nitrogen Cycle: The processing of nitrogen into a biologically useful form requires the activity of microorganisms.

Microbial Environments and Microenvironments

The extraordinary biological diversity among microbes reflects their ability to occupy every habitable environment on the planet.

Learning Objectives

Define microenvironments

Key Takeaways

Key Points

  • Microorganisms are found in practically every habitat present on the planet.
  • Microorganisms have evolved to survive in extraordinarily diverse environments, including extreme, hostile, or otherwise intolerant ecological systems.
  • In addition to occupying a unique niche within an ecosystem, microbes adapt to microenvironments (or microhabitats) that can be distinguished from the immediate surroundings by such factors as the amount of incident light, the degree of moisture, and the range of temperatures.

Key Terms

  • microenvironment: The very small environment in the immediate vicinity of an organism.
  • extremophilic: Of or pertaining to the extremophiles, a class of organism that thrives under extreme conditions of temperature, salinity, and so on; commercially important as a source of enzymes that operate under similar conditions.
  • ubiquitous: Being everywhere at once: omnipresent.

Microorganisms are found on practically every habitable square inch of the planet. They live and thrive in all parts of the biosphere where there is liquid water, including hostile environments such as the poles, deserts, geysers, rocks, and the deep sea. Additionally, while microbes are often free-living, many have intimate symbiotic relationships with other larger organisms. Clearly, microbes have adapted to extreme and intolerant conditions, and it is this adaptation that has yielded tremendous biological diversity among microorganisms.

Like all extant organisms, microbes have evolved to thrive within a given environmental context. Microorganisms are ubiquitous despite the fact that the planet is host to extraordinarily diverse environments. Therefore, microbes have adapted to fill every ecological niche on the planet. For example, extremophilic species have been found that can tolerate the following environmental extremes:

  • Temperatures as high as 130 °C (266 °F) and as low as −17 °C (1 °F)
  • Highly alkaline (pH 0) and highly acidic (pH 11.5) environments
  • Extremely saline environments (including those in which the salt concentration is saturating)
  • Extremely high (1,000-2,000 atm) and low (0 atm) pressures (some bacteria can survive for prolonged periods in a pressure-less vacuum, meaning they might even survive in space)
  • High ionizing radiation (up to 15,000 Gy; as a reference, a mere 5 Gy would kill a human! )

These evolutionary adaptations have allowed microbial life to extend into much of the Earth’s atmosphere, crust, and hydrosphere (the water found over, under, and on the surface of a planet).

In addition to occupying a unique niche within an ecosystem, microbes are potentially sensitive to subtle environmental differences between adjacent areas. These differences define so-called microenvironments (or microhabitats) that can be distinguished from the immediate surroundings by such factors as the amount of incident light, the degree of moisture, and the range of temperatures. For example, the side of a tree that is shaded from sunlight is a microenvironment that typically supports a somewhat different community of microorganisms than would be found on the side that receives regular light. Microbes, therefore, are not only adapted to their habitat, but also to the immediate environment, thus promoting increased diversity among microbial species within an ecosystem.