Microbial Roles in Ecology

Microorganisms (microbes) are life-forms that are too small to be seen without magnification. Microbes such as bacteria, protozoa, fungi, algae, and nonliving viruses are present in and exert effects on every ecosystem on the planet. Microbes are found in soils, water, the deep ocean, floating in the air, beneath the ice in Antarctica, on top of mountains, and in valleys. They are present on every square millimeter of human skin or external plant leaf tissue and are in the digestive tracts of all animals—trillions live in human intestines. Microbial action influences the composition of the atmosphere and the breakdown of rock at Earth's surface. Chemical transformations, movements, and recycling are largely microbial processes. Microbes evolved billions of years ago and have inhabited and forever changed Earth long before multicellular life evolved. It is believed that microbial metabolism was responsible for drastic changes in Earth’s atmosphere. Early microbes produced oxygen as a byproduct of their metabolic processes, and released it into the atmosphere. The development of photosynthesis by ancient cyanobacteria contributed to the accumulation of oxygen in the atmosphere.

Microbial ecology, also called environmental microbiology, is the study of microorganisms and their interactions with one another, with other organisms, and with their environments. All nonmicrobial organisms have symbiotic relationships with microbes, ecological relationships between two or more organisms that live in direct contact with one another. Some of these relationships are parasitic, with microbes such as bacteria gaining a benefit at a cost to their host. In others, the host is not affected by the microbe. Most symbiotic relationships are mutualistic, benefiting both the microbe and their hosts. By occupying space on or in animal bodies, mutualistic microbes prevent more harmful species from colonizing. Microbes within a digestive tract communicate with their host's immune system during development and help train it. They also break down foods that their hosts lack enzymes to digest, thus increasing the nutritive value of food. Bacteria and fungi both assist plants in obtaining nutrients from the environment and provide protection from invading pathogens. In some insects, relationships with microbes have persisted for such long periods of time that both host and microbe have transferred genes to their partners, or lost them entirely, and neither is able to survive without its partner. The pea aphid, for example, hosts Buchnera aphidicola bacteria that transfer amino acids to their aphid host that are not present in its diet.

Increased understanding of microbial ecology is important for understanding how ecosystems function. It also provides opportunities for controlling and utilizing the diverse actions of microbes to improve the environment and human existence. Microbes are critical to ecosystem functioning, agriculture, and disease. People use microbes to create products and medicines industrially. They are also used to clean environmental pollution, a process called bioremediation. Microbial ecology provides a framework for continuing to exist successfully in a microbial world.

Environmental microbiology is the study of the microbes in an environment. Specifically, it examines the composition and physiology of the microbial communities in the environment. Increasingly, understanding the complex interactions among microbial communities and their environment is becoming an essential tool in combating disease and protecting natural resources on which all organisms depend.

Organisms, their natural habitats, and their relationships with one another are organized in hierarchical structures. An interbreeding group of individuals of the same species is a population. Examples of microbial populations include pure cultures of a single species of microbe being grown in a lab and E. coli living inside the human intestines. A community—the set of all organisms living in a given area—includes many different populations. Microbial communities are often referred to as a microbiome. For example, humans have a gut microbiome that is distinct from their skin microbiome. The physical area where an organism lives is its habitat. An ecosystem is composed of a community and all the habitats of all species in the community. It includes the surrounding physical and chemical factors in the environment where the community lives. The collection of all living things and their ecosystems on Earth constitute the biosphere.

The ways that organisms obtain their food are also used to categorize them. These are known as trophic levels, and the energy in food moves from one level to the next. An organism that can make its own food is an autotroph. Plants are the primary autotrophs on land. Likewise, the main autotrophs in the oceans are phytoplankton, microscopic, aquatic, photosynthetic organisms that drift with currents. Another group, called chemoautotrophs, extracts energy from chemical reactions and uses it to make food from carbon dioxide. For example, a methanogen is an archaeon that uses carbon dioxide and hydrogen gas for energy during anaerobic respiration. it also produces methane, as its name implies. Methanogens are found in the human gut, where they produce methane. Additionally, they give marshes their distinctive odor, and form the base of the food chain in deep-sea hydrothermal vents.

Autotrophs are the basis of all life in the biosphere.The energy in all consumer and decomposer organisms began with autotrophs. A consumer (or heterotroph) is an organism that consumes (eats) other organisms for food. For example, amoebas and other protists consume cyanobacteria, bacteria that conduct photosynthesis and produce oxygen. A decomposer breaks down dead materials and organic wastes and then uses them for food. There are many microbial decomposers, including fungi and bacterial populations.

The relationship between different organisms based on which organism eats or is eaten by another organism is a food chain. A specific food chain is a linear pathway of feeding relationships. For example, in a basic food chain, a photosynthetic autotroph such as a cyanobacterium synthesizes its own food and is eaten by a consumer, such as a paramecium. Later, the paramecium dies, and a decomposer, perhaps the bacteria Bacillus subtilis, breaks down the paramecium and uses it for sustenance. In contrast, a food web is a combination of food chains interacting with each other within an ecosystem.