22.5 Beneficial Prokaryotes

Nitrogen Fixation and Ecosystem Importance

Most organisms need nitrogen to build amino acids, proteins, and nucleic acids, but almost none can use the nitrogen gas ($N_2$) that makes up 78% of our atmosphere. Nitrogen fixation solves this problem by converting $N_2$ into biologically usable forms like ammonia ($NH_3$), making it one of the most important prokaryotic contributions to life on Earth.

Process of nitrogen fixation

Nitrogen-fixing bacteria carry out this conversion using the nitrogenase enzyme complex, which requires large amounts of ATP and is sensitive to oxygen. Because of that oxygen sensitivity, fixation happens in anaerobic or microaerobic environments like root nodules and soil aggregates.

Two key nitrogen-fixing genera to know:

• Rhizobium forms symbiotic relationships with legume roots (soybeans, alfalfa, peas). The plant provides sugars and a low-oxygen environment; the bacteria provide usable nitrogen.
• Azotobacter is a free-living soil bacterium that fixes nitrogen independently, without a plant partner.

Importance of nitrogen fixation in ecosystems

Nitrogen fixation is a critical step in the nitrogen cycle because it's the main way new usable nitrogen enters ecosystems.

• Plants absorb fixed nitrogen from the soil and incorporate it into their tissues. This is why legume crops can thrive in nitrogen-poor soils: their Rhizobium partners supply what the soil lacks.
• Herbivores obtain nitrogen by consuming nitrogen-rich plant material.
• When organisms die, decomposers break them down and release nitrogen back into the soil, where it can be reused.

This cycle keeps the usable nitrogen pool replenished. Without nitrogen-fixing prokaryotes, ecosystems would gradually run out of the nitrogen that all living things depend on.

Beneficial Bacteria in Human Microbiomes

Your body hosts trillions of prokaryotes, and many of them actively contribute to your health. The skin and gut harbor especially important microbial communities.

Bacteria in human skin microbiomes

Species like Staphylococcus epidermidis and Cutibacterium acnes (formerly Propionibacterium acnes) protect you by occupying space and resources that pathogens would otherwise use.

• S. epidermidis produces phenol-soluble modulins that inhibit pathogenic bacteria like S. aureus.
• C. acnes secretes bacteriocins, antimicrobial compounds that target closely related species.
• These bacteria produce lactic acid and other organic acids as metabolic byproducts, helping maintain the skin's acidic pH (around 4.7). That acidity discourages colonization by harmful microbes.
• Skin bacteria also stimulate your immune system to produce antimicrobial peptides such as defensins and cathelicidins.
• Some form biofilms on the skin surface, adding another physical layer of defense against pathogens.

Bacteria in human gut microbiomes

The gut microbiome is even more diverse, and genera like Bifidobacterium and Lactobacillus perform functions your own cells cannot.

Digestion and nutrition:

• They ferment dietary fiber and resistant starch, producing short-chain fatty acids (SCFAs) like acetate, propionate, and butyrate.
• SCFAs serve as an energy source for colonocytes (the cells lining your colon) and help maintain gut barrier integrity.
• Gut bacteria synthesize essential vitamins your body needs, including vitamin K (required for blood clotting and bone metabolism) and B vitamins like biotin and folate.

Immune support:

• They interact with gut-associated lymphoid tissue (GALT) to promote the maturation of immune cells.
• They stimulate production of secretory IgA antibodies, which neutralize pathogens and toxins in the gut lumen.

Pathogen defense:

• Beneficial bacteria compete with harmful species for nutrients and attachment sites, preventing colonization by organisms like Clostridium difficile.
• They produce bacteriocins and other antimicrobial substances that directly inhibit pathogen growth.

Many of these beneficial gut bacteria are classified as probiotics when consumed in foods or supplements to promote health.

Prokaryotes for Food Production

Humans have relied on microbial fermentation for thousands of years. Several prokaryotic (and one eukaryotic) species are central to food production.

Lactobacillus bacteria in food production

Lactobacillus species convert lactose into lactic acid, which lowers pH and causes milk proteins to coagulate into a gel-like structure. This is the basis of fermented dairy products.

• L. bulgaricus and L. acidophilus are commonly used in yogurt production.
• L. helveticus and L. casei are used in cheese production (Swiss cheese, Cheddar).
• These bacteria also produce flavor compounds like diacetyl and acetaldehyde, contributing to the distinct aroma and taste of fermented dairy.

Streptococcus thermophilus in food production

S. thermophilus works alongside Lactobacillus in yogurt and cheese production. It produces lactic acid and breaks down milk proteins, which actually enhances the growth of Lactobacillus. It also generates exopolysaccharides that improve yogurt's texture and mouthfeel.

Acetobacter bacteria in food production

Acetobacter species oxidize ethanol to acetic acid, producing the characteristic sour taste of vinegar and kombucha.

• A. aceti and A. pasteurianus are commonly used in vinegar production. Acetic acid concentration in vinegar typically ranges from 4–8%.
• In kombucha, Acetobacter works in symbiosis with yeast to create a slightly acidic, effervescent beverage.

Saccharomyces cerevisiae (yeast) in food production

S. cerevisiae is a eukaryotic microorganism (not a prokaryote), but it's covered here because it often works alongside prokaryotes in fermentation.

• It ferments sugars to produce ethanol and carbon dioxide.
• In bread, the $CO_2$ gets trapped in the gluten network, causing dough to rise.
• In beer and wine, it converts sugars from grains or fruits into ethanol.
• Different strains (baker's yeast, brewer's yeast, wine yeast) have distinct characteristics that affect the flavor, aroma, and texture of the final product.

Prokaryotes in Bioremediation

Bioremediation uses living organisms to clean up environmental contaminants. Prokaryotes are especially useful because of their metabolic diversity: many can use pollutants as carbon or energy sources.

Hydrocarbon-degrading bacteria

When oil spills occur, bacteria like Pseudomonas and Alcanivorax can break down petroleum hydrocarbons into less harmful products ($CO_2$ and water).

• P. putida degrades a wide range of hydrocarbons, including benzene and toluene.
• A. borkumensis is a marine bacterium that thrives in oil-rich environments and efficiently degrades alkanes.
• The breakdown involves oxidation reactions catalyzed by enzymes like monooxygenases and dioxygenases. The bacteria use the hydrocarbons as a carbon and energy source.
• Bioremediation strategies include stimulating native hydrocarbon-degrading bacteria (by adding nutrients) or introducing engineered strains to the contaminated site.

Metal-reducing bacteria

Toxic metals like uranium and chromium can be managed by bacteria that convert them into less soluble, less toxic forms.

• Geobacter metallireducens reduces soluble U(VI) to insoluble U(IV), effectively immobilizing uranium so it can't spread through groundwater.
• Shewanella oneidensis reduces highly toxic Cr(VI) to less toxic Cr(III) through anaerobic respiration.
• The reduced metal forms precipitate out of solution and become trapped in sediment.
• To enhance this process, electron donors like acetate or lactate are added to stimulate bacterial activity at contaminated sites.

Plastic-degrading bacteria

Ideonella sakaiensis can break down polyethylene terephthalate (PET), the plastic used in beverage bottles and textile fibers. This is a relatively recent discovery with exciting potential.

The degradation happens in two enzymatic steps:

1. PETase breaks PET into an intermediate called MHET (mono(2-hydroxyethyl) terephthalate).
2. MHETase further degrades MHET into its monomers: terephthalic acid and ethylene glycol.

These monomers can be metabolized by the bacteria or potentially used to synthesize new plastics, opening up applications in recycling and waste management.

Prokaryotic Interactions and Genetic Exchange

Quorum sensing in prokaryotes

Quorum sensing is a cell-to-cell communication system that lets bacteria coordinate group behaviors based on population density. Bacteria produce and detect signaling molecules called autoinducers. As the population grows, autoinducer concentration rises. Once it hits a threshold, it triggers coordinated responses like biofilm formation, virulence factor production, or bioluminescence. This allows bacterial populations to act collectively rather than as isolated cells.

Horizontal gene transfer in prokaryotes

Unlike vertical gene transfer (parent to offspring), horizontal gene transfer (HGT) moves genetic material between organisms that aren't parent and child. There are three main mechanisms:

• Conjugation transfers DNA directly between two bacterial cells through a pilus.
• Transformation involves a bacterium picking up free DNA from its environment.
• Transduction occurs when a bacteriophage (virus) accidentally transfers bacterial DNA from one cell to another.

HGT is a major driver of bacterial evolution and adaptation. It's also how antibiotic resistance genes spread rapidly through bacterial populations, which is a significant public health concern.

Biodegradation by prokaryotes

Biodegradation is the breakdown of complex organic compounds by microorganisms. Beyond the bioremediation examples above, prokaryotes carry out biodegradation constantly in natural ecosystems. They decompose dead organic matter, recycle nutrients, and break down waste. Some can even degrade synthetic compounds (xenobiotics) that don't occur naturally, making them valuable tools for waste management and environmental cleanup.