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4.3.1: Prokaryote Habitats and Ecology

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    • Identify and describe unique examples of prokaryotes in various habitats on earth


    All living organisms are classified into three domains of life: Archaea, Bacteria, and Eukarya. In this chapter, we will focus on the domains Archaea and Bacteria. Archaea and bacteria are unicellular prokaryotic organisms. Unlike eukaryotes, they have no nuclei or any other membrane-bound organelles.

    Prokaryote Habitats and Functions

    Prokaryotes are ubiquitous. They can be found everywhere on our planet, even in hot springs, in the Antarctic ice shield, and under extreme pressure two miles under water. One bacterium, Paracoccus denitrificans, has even been shown to survive when scientists removed it from its native environment (soil) and used a centrifuge to subject it to forces of gravity as strong as those found on the surface of Jupiter.

    Prokaryotes also are abundant on and within the human body. According to a report by National Institutes of Health, prokaryotes, especially bacteria, outnumber human cells 10:1.1 More recent studies suggest the ratio could be closer to 1:1, but even that ratio means that there are a great number of bacteria within the human body.2 Bacteria thrive in the human mouth, nasal cavity, throat, ears, gastrointestinal tract, and vagina. Large colonies of bacteria can be found on healthy human skin, especially in moist areas (armpits, navel, and areas behind ears). However, even drier areas of the skin are not free from bacteria.

    The existence of prokaryotes is very important for the stability and thriving of ecosystems. For example, they are a necessary part of soil formation and stabilization processes through the breakdown of organic matter and development of biofilms. One gram of soil contains up to 10 billion microorganisms (most of them prokaryotic) belonging to about 1,000 species. Many species of bacteria use substances released from plant roots, such as acids and carbohydrates, as nutrients. The bacteria metabolize these plant substances and release the products of bacterial metabolism back to the soil, forming humus and thus increasing the soil’s fertility. In salty lakes such as the Dead Sea (Figure \(\PageIndex{1}\)), salt-loving halobacteria decompose dead brine shrimp and nourish young brine shrimp and flies with the products of bacterial metabolism.

    a) A photo of blue water and red sand. B) A micrograph of a cluster of rod shaped cells.
    Figure \(\PageIndex{1}\): (a) Some prokaryotes, called halophiles, can thrive in extremely salty environments such as the Dead Sea, pictured here. (b) The archaeon Halobacterium salinarum, shown here in an electron micrograph, is a halophile that lives in the Dead Sea. (credit a: modification of work by Jullen Menichini; credit b: modification of work by NASA)

    In addition to living in the ground and the water, prokaryotic microorganisms are abundant in the air, even high in the atmosphere. There may be up to 2,000 different kinds of bacteria in the air, similar to their diversity in the soil.

    Prokaryotes can be found everywhere on earth because they are extremely resilient and adaptable. They are often metabolically flexible, which means that they might easily switch from one energy source to another, depending on the availability of the sources, or from one metabolic pathway to another. For example, certain prokaryotic cyanobacteria can switch from a conventional type of lipid metabolism, which includes production of fatty aldehydes, to a different type of lipid metabolism that generates biofuel, such as fatty acids and wax esters. Groundwater bacteria store complex high-energy carbohydrates when grown in pure groundwater, but they metabolize these molecules when the groundwater is enriched with phosphates. Some bacteria get their energy by reducing sulfates into sulfides, but can switch to a different metabolic pathway when necessary, producing acids and free hydrogen ions.

    Prokaryotes perform functions vital to life on earth by capturing (or “fixing”) and recycling elements like carbon and nitrogen. Organisms such as animals require organic carbon to grow, but, unlike prokaryotes, they are unable to use inorganic carbon sources like carbon dioxide. Thus, animals rely on prokaryotes to convert carbon dioxide into organic carbon products that they can use. This process of converting carbon dioxide to organic carbon products is called carbon fixation.

    Plants and animals also rely heavily on prokaryotes for nitrogen fixation, the conversion of atmospheric nitrogen into ammonia, a compound that some plants can use to form many different biomolecules necessary to their survival. Bacteria in the genus Rhizobium, for example, are nitrogen-fixing bacteria; they live in the roots of legume plants such as clover, alfalfa, and peas (Figure \(\PageIndex{2}\)). Ammonia produced by Rhizobium helps these plants to survive by enabling them to make building blocks of nucleic acids. In turn, these plants may be eaten by animals—sustaining their growth and survival—or they may die, in which case the products of nitrogen fixation will enrich the soil and be used by other plants.

    A) photo of roots with small nodules labeled root nodules. A micrograph of a root nodule. A thick cell wall is on the outside. Lines inside are labeled endoplasmic reticulum. Large ovals in clear structures are labeled bacteroids.
    Figure \(\PageIndex{2}\): (a) Nitrogen-fixing bacteria such as Rhizobium live in the root nodules of legumes such as clover. (b) This micrograph of the root nodule shows bacteroids (bacterium-like cells or modified bacterial cells) within the plant cells. The bacteroids are visible as darker ovals within the larger plant cell. (credit a: modification of work by USDA)

    Another positive function of prokaryotes is in cleaning up the environment. Recently, some researchers focused on the diversity and functions of prokaryotes in manmade environments. They found that some bacteria play a unique role in degrading toxic chemicals that pollute water and soil.3

    Despite all of the positive and helpful roles prokaryotes play, some are human pathogens that may cause illness or infection when they enter the body. In addition, some bacteria can contaminate food, causing spoilage or foodborne illness, which makes them subjects of concern in food preparation and safety. Less than 1% of prokaryotes (all of them bacteria) are thought to be human pathogens, but collectively these species are responsible for a large number of the diseases that afflict humans.

    Besides pathogens, which have a direct impact on human health, prokaryotes also affect humans in many indirect ways. For example, prokaryotes are now thought to be key players in the processes of climate change. In recent years, as temperatures in the earth’s polar regions have risen, soil that was formerly frozen year-round (permafrost) has begun to thaw. Carbon trapped in the permafrost is gradually released and metabolized by prokaryotes. This produces massive amounts of carbon dioxide and methane, greenhouse gases that escape into the atmosphere and contribute to the greenhouse effect.

    Exercise \(\PageIndex{2}\)

    1. In what types of environments can prokaryotes be found?
    2. Name some ways that plants and animals rely on prokaryotes.

    ented by approaches based on molecular genetics.


    1. 1 Medical Press. “Mouth Bacteria Can Change Their Diet, Supercomputers Reveal.” August 12, 2014. Accessed February 24, 2015.
    2. 2 A. Abbott. “Scientists Bust Myth That Our Bodies Have More Bacteria Than Human Cells: Decades-Old Assumption about Microbiota Revisited.” Nature. Accessed June 3, 2016.
    3. 3 A.M. Kravetz “Unique Bacteria Fights Man-Made Chemical Waste.” 2012. Accessed March 9, 2015.
    4. 4 E.M. Bik et al. “Bacterial Diversity in the Oral Cavity of 10 Healthy Individuals.” The ISME Journal 4 no. 8 (2010):962–974.
    5. 5 C.C. Booijink et al. “High Temporal and Intra-Individual Variation Detected in the Human Ileal Microbiota.” Environmental Microbiology 12 no. 12 (2010):3213–3227.
    6. 6 National Institutes of Health. “Human Microbiome Project. Overview.” Accessed June 7, 2016.
    7. 7 Q. Dong et al. “Diversity of Bacteria at Healthy Human Conjunctiva.” Investigative Ophthalmology & Visual Science 52 no. 8 (2011):5408–5413.
    8. 8 F.E. Dewhirst et al. “The Human Oral Microbiome.” Journal of Bacteriology 192 no. 19 (2010):5002–5017.
    9. 9 J.C. Lagier et al. “Microbial Culturomics: Paradigm Shift in the Human Gut Microbiome Study.” Clinical Microbiology and Infection 18 no. 12 (2012):1185–1193.


    • Nina Parker, (Shenandoah University), Mark Schneegurt (Wichita State University), Anh-Hue Thi Tu (Georgia Southwestern State University), Philip Lister (Central New Mexico Community College), and Brian M. Forster (Saint Joseph’s University) with many contributing authors. Original content via Openstax (CC BY 4.0; Access for free at