1.4 Microbes in Our Environment

Microbes Support Natural Ecosystems

The first microbiologists to culture microbes in the laboratory selected the kinds of nutrients that feed humans, such as beef broth or potatoes. Some of Koch’s contemporaries, however, suspected that other kinds of microbes living in soil or wetlands existed on more exotic fare. Soil samples were known to oxidize hydrogen gas, and this activity was eliminated by treatment with heat or acid, suggesting microbial origin. Ammonia in sewage was oxidized to nitrate, and this process was eliminated by antibacterial treatment. These findings suggested the existence of microbes that “ate” hydrogen gas or ammonia instead of beef or potatoes, but no one could isolate these microbes in culture.

Among the first to study microbes in natural habitats was the Russian scientist Sergei Winogradsky (1856–1953). Winogradsky waded through marshes (wetlands) to discover new forms of microbes. In wetlands Winogradsky discovered microbes whose metabolism is very different from human digestion. For example, species of the bacterium Beggiatoa oxidize hydrogen sulfide (H₂S) to sulfuric acid (H₂SO₄). Beggiatoa fixes carbon dioxide into biomass without consuming any organic food. Organisms that feed solely on inorganic materials such as iron or ammonia are known as lithotrophs. Today, wetland microbes are known for their critical roles in environmental quality (Figure 1.19). Wetland microbes support the food web of animals and plants, and they filter the groundwater that we eventually drink.

Figure 1.19 Wetland Habitat for Microbes

The lithotrophs that Winogradsky studied could not be grown on Koch’s plate media containing agar or gelatin. The bacteria that Winogradsky isolated could grow only on inorganic minerals. For example, nitrifiers convert ammonia to nitrate, forming a crucial part of the nitrogen cycle in natural ecosystems. Winogradsky cultured nitrifiers on a completely inorganic solution containing ammonia and silica gel, which supported no other kind of organism. This experiment was an early example of enrichment culture, the use of selective growth media that support certain classes of microbial metabolism while excluding others (discussed in Chapter 6). Enrichment culture is important in clinical microbiology labs to help identify the specific microbes that cause disease. A kind of enrichment culture used today in hospitals is MacConkey agar, a formulation that permits growth of Gram-negative bacteria such as E. coli but excludes Gram-positive soil bacteria such as Bacillus species.

Winogradsky and later microbial ecologists showed that bacteria perform unique roles in the global interconversion of inorganic and organic forms of nitrogen, sulfur, phosphorus, and other minerals. Without these essential conversions (nutrient cycles), no plants or animals could live. Bacteria and archaea fix nitrogen (N₂) by reducing it to ammonia (NH₃), the form of nitrogen assimilated by plants. This process is called nitrogen fixation. Other bacterial species oxidize ammonium ions (NH₄⁺) in several stages back to nitrogen gas. (Global cycles of nutrients are presented in Chapter 27.)

Within plant cells, certain bacteria fix nitrogen as partners of a host organism, a relationship called mutualism. Mutualism is a form of symbiosis, growth of two species in intimate association; in mutualism, the partners receive essential benefits from each other. Bacteria that fix nitrogen in a mutualism within a plant cell are also called endosymbionts (meaning “inside symbionts”), organisms living inside a larger organism. Endosymbiotic bacteria provide nutrients to their host cell, which in turn provides protection and nutrients to the endosymbionts. Endosymbiotic bacteria known as rhizobia induce the roots of legumes (beans and lentils) to form special nodules to facilitate bacterial nitrogen fixation. Rhizobial endosymbiosis was first observed by Martinus Beijerinck.

Communities of bacteria serve animals as digestive endosymbionts (Figure 1.20). Such a community is known as a digestive microbiome. Animals such as cattle and termites require a digestive microbiome to break down cellulose and other plant polymers. Even we humans obtain as much as 15% of our nutrition from bacteria growing in our colon. Increasingly, the human digestive microbiome is considered an organ of the human body, with a role in medical conditions ranging from obesity to depression. Amazingly, bacteria from feces can actually cure a life-threatening disease. The transfer of fecal bacteria from one person to another, known as fecal microbiota transplant, was approved in 2013 by the FDA to treat infections of drug-resistant Clostridioides difficile.

Figure 1.20 Biofilm of Digestive Bacteria in the Human Intestine

Animals and Plants Evolved through Endosymbiosis

Microbial endosymbiosis, in many diverse forms, is widespread in all ecosystems. Many interesting cases involve animal or human hosts. The endosymbiotic origin of eukaryotic cells was proposed by Lynn Margulis (1938–2011), of the University of Massachusetts, Amherst (Figure 1.21). Margulis tried to explain how it is that eukaryotic cells contain mitochondria and chloroplasts, membranous organelles that possess their own chromosomes. She proposed that eukaryotes evolved by merging with bacteria to form composite cells by intracellular endosymbiosis, in which one cell internalizes another that grows within it. The endosymbiosis may ultimately generate a single organism whose formerly independent members are now incapable of independent existence.

Figure 1.21 Lynn Margulis and the Serial Endosymbiosis Theory

Margulis proposed that, early in the history of life, respiring bacteria similar to E. coli were engulfed by pre-eukaryotic cells, where they evolved into mitochondria, the eukaryote’s respiratory (energy-generating) organelle. Similarly, a phototroph related to cyanobacteria was taken up by a eukaryote, giving rise to the chloroplasts of phototrophic algae and plants. Ultimately, DNA sequence analysis produced compelling evidence of the bacterial origin of mitochondria and chloroplasts. Both these classes of organelles contain circular molecules of DNA, whose sequences show unmistakable homology (similarity) to those of modern bacteria. DNA sequences and other evidence established the common ancestry between mitochondria and respiring bacteria and between chloroplasts and cyanobacteria.

The endosymbiotic origin of mitochondria has medical importance because mitochondria still share key properties with bacteria. Such properties include the structure and function of the respiratory complex. Mitochondrial defects cause human diseases, including a form of epilepsy associated with malformed muscle fibers (myoclonic epilepsy with ragged-red fibers, or MERRF). The similarity between mitochondria and bacteria also limits the use of certain antibiotics, such as those that kill bacteria by inhibiting respiratory proteins embedded in the membrane. Bacteria have the respiratory proteins in their cell membrane, whereas human mitochondria have similar proteins in the mitochondrial inner membrane.

New Microbes Continue to Emerge

We continue to discover surprising new kinds of microbes deep underground and in places previously thought uninhabitable, such as the hot springs of Yellowstone National Park (Figure 1.22A). Microbes shape our biosphere and provide new tools that impact human society. For example, a bacterial DNA polymerase (a DNA-replicating enzyme) from a Yellowstone hot spring is used for the PCR technology that identifies pathogens in ill patients.

Figure 1.22 Archaea, a Newly Discovered Form of Life

In 1977, Carl Woese (1928–2012), of the University of Illinois (Figure 1.22B), discovered that some of the microbes from Yellowstone hot springs have genomes very different from those of all other known life forms. The genomes of these microbes had diverged so far from that of any known bacteria that the newly discovered prokaryotes were seen as a distinct form of life—the archaea (discussed in Section 1.1). Archaea living in extreme environments produce exceptionally sturdy enzymes that can be used for biotechnology.

SECTION SUMMARY

• Sergei Winogradsky first developed a system of enrichment culture to grow microbes from natural environments.
• Lithotrophs metabolize inorganic minerals, such as ammonia, instead of the organic nutrients used by the microbes isolated by Koch.
• Endosymbionts are microbes that live within a larger organism. Some endosymbionts are mutualists that provide essential functions for their host, such as nitrogen fixation for a legume plant.
• Martinus Beijerinck first demonstrated that nitrogen-fixing rhizobia grow as endosymbionts within leguminous plants.
• The human body has a microbiome, a community of associated bacteria that play important roles in human health.
• Lynn Margulis proposed that eukaryotic organelles such as mitochondria and chloroplasts evolved by endosymbiosis from prokaryotic cells engulfed by pre-eukaryotes.
• Carl Woese discovered a domain of life, Archaea, whose genetic sequences diverge equally from those of bacteria and those of eukaryotes.

Thought Question 1.4 Suppose a microbiologist isolates microbes from 2 miles below Earth’s surface. Would these microbes be likely to cause disease in humans?