Prokaryotes in Human Health, Agriculture, and the Environment

Nitrogen Fixation and Prokaryotes

• Prokaryotes are deeply involved in key global cycles and processes that support life on Earth: they participate in carbon and nitrogen cycles, digest and process nutrients in animals, contribute to food production, and aid in the degradation of hazardous materials.
• Although only a few species of prokaryotes are pathogenic, many interactions with humans and other organisms are beneficial.
• Nitrogen is essential because it is a building block of nucleotides and amino acids, but atmospheric N$2$ is not usable by eukaryotes as-is. Nitrogen can be fixed, meaning converted into a more accessible form such as ammonia (NH$3$). Abiotic fixation occurs via lightning or industrial processes; biological nitrogen fixation (BNF) is exclusively carried out by prokaryotes.
• Major BNF players: soil bacteria, cyanobacteria, and Frankia spp. (filamentous bacteria that interact with actinorhizal plants such as alder, bayberry, and sweet fern).
• After photosynthesis, BNF is the second most important biological process on Earth.
• The overall BNF process involves a series of redox reactions. A representative nitrogen fixation equation is:

\mathrm{N}2 + 16\,\mathrm{ATP} + 8\,\mathrm{e}^- + 8\,\mathrm{H}^+ \rightarrow 2\,\mathrm{NH}3 + 16\,\mathrm{ADP} + 16\,\mathrm{Pi} + \mathrm{H}2

• Total fixed nitrogen via BNF is about 100\text{--}180\ \text{million metric tons per year}, contributing roughly 65\% of nitrogen used in agriculture.
• Cyanobacteria are the most important nitrogen fixers in aquatic environments.
• In soil, free-living nitrogen-fixers include genera such as \text{Clostridium} and \text{Azotobacter}.
• Many bacteria live in symbiosis with legume plants, providing a crucial source of fixed nitrogen for the plant.
• Rhizobia (soil bacteria) symbiotically interact with legumes to form nodules, specialized structures where nitrogen fixation occurs.
• The enzyme nitrogenase fixes nitrogen; its activity requires a low-oxygen environment in the nodules.
• Oxygen is kept out of the nitrogen fixation zone by plant leghemoglobin, a plant hemoglobin that sequesters oxygen to protect nitrogenase while allowing enough oxygen for respiration.
• The nodules are thus oxygen-free enough for nitrogenase activity but still enable respiratory processes for the bacteria and plant.
• Nitrogen fixation is especially significant in soybeans and other legumes because it allows atmospheric nitrogen to be converted into forms usable by plants.
• Legumes and rhizobia create a sustainable plant–microbe partnership: plants provide carbohydrates synthesized by photosynthesis; bacteria fix nitrogen and convert it into ammonia used by the plant; soils gain added fertility, reducing the need for chemical fertilizers.
• Symbiotic nitrogen fixation can supply plants with nitrogen indefinitely from the atmosphere via the legume–rhizobia partnership; the symbiosis also benefits soil fertility and sustainability.
• Legume examples and their roles:
  • Soybean (Glycine max) interacts with the soil bacterium Bradyrhizobium japonicum to form nodules for nitrogen fixation (illustrated in Figure 22.27).
  • Other legumes include peanuts, peas, chickpeas, and beans; alfalfa is used as cattle feed.
• Benefits of the symbiosis:
  • Plants gain a renewable nitrogen source from the atmosphere.
  • Bacteria gain a protected niche and carbohydrates from the plant.
  • Soil benefits from natural fertilization, reducing the need for chemical fertilizers.
  • Rhizobia as biofertilizers are a sustainable agricultural practice.
• Legume importance and protein sources for humans:
  • Soybeans are a key agricultural protein source; other important legumes include peanuts, peas, chickpeas, and beans.
  • Alfalfa serves as cattle feed.
• Important legumes and bacteria:
  • Glycine max (soybean) interacts with Bradyrhizobium japonicum to form nodules on roots where nitrogen fixation occurs.
  • These nodules are described as providing an oxygen-free niche (thanks to leghemoglobin) conducive to nitrogen fixation.
• Practical implications:
  • Symbiotic nitrogen fixation provides a natural and inexpensive plant fertilizer and is a cornerstone of sustainable agriculture by converting atmospheric nitrogen into plant-usable ammonia.
  • This process reduces dependence on chemical nitrogen fertilizers and helps conserve natural resources.

Prokaryotes and the Human Body: The Microbiome

• Commensal bacteria inhabit our skin and gastrointestinal tract and perform beneficial roles:
  • Protect us from pathogens
  • Help digest food
  • Produce vitamins and other nutrients
• Recent evidence links these bacteria to broader physiological effects:
  • Potential regulation of mood and activity levels
  • Influence on weight, appetite, and absorption patterns
• The Human Microbiome Project aims to catalog the normal bacteria (and archaea) inhabiting humans to better understand these functions and their implications.
• Digestive tract example: antibiotic use can disrupt the normal gut microbiota, allowing a normally antibiotic-resistant species, Clostridium difficile (C. difficile), to overgrow and cause severe gastric problems, including chronic diarrhea.
  • Treating C. difficile overgrowth with antibiotics alone can worsen the problem.
  • Successful treatment has included fecal transplants from healthy donors to reestablish a normal intestinal microbial community; clinical trials are underway to assess safety and efficacy.
• Clostridium difficile (C. difficile): a Gram-positive, rod-shaped bacterium linked to antibiotic-associated diarrhea and severe infection, particularly in hospital settings (as depicted in Figure 22.28).
• Absence or imbalance of key gut microbes may contribute to various health issues: allergies, autoimmune disorders, and possibly autism; research is exploring whether adding selected microbes can help treat these problems.
• The microbiome’s broader role includes shaping the immune system; microbial balance is essential for proper immune development and function.
• The Human Microbiome Project and related research aim to map microbial communities, understand their functional roles, and explore potential therapeutic applications.

Early Biotechnology: Cheese, Bread, Wine, Beer, and Yogurt

• Biotechnology, per the United Nations Convention on Biological Diversity, is defined as “any technological application that uses biological systems, living organisms, or derivatives thereof, to make or modify products or processes for specific use” (i.e., a commercial application).
• Early biotechnology predates the term itself and relies on prokaryotes and other microbes:
  • Cheese and yogurt are produced using bacteria that ferment dairy substrates.
  • Bread, wine, and beer involve fermentation processes, with yeast (a fungus) playing a central role in bread, wine, and beer production.
• These early products demonstrate how microbial metabolism can be harnessed to preserve, transform, and create foods and beverages.
• The timeline of some traditional foods:
  • Cheese production began around 4,000–7,000 years ago when humans started domesticating animals and processing milk.
  • Fermentation to produce beer dates to about 6,000 years ago in Sumerian culture.
  • Wine has been produced for roughly 4,500 years.
  • Cultured dairy products like yogurt have existed for at least 4,000 years.

Bioremediation: Using Prokaryotes to Clean Up Our Planet

• Bioremediation is the use of prokaryotes (or microbial metabolism) to remove pollutants from the environment.
• Applications include:
  • Removal of agricultural chemicals (pesticides, fertilizers) that leach from soil into groundwater and subsurface environments.
  • Removal of toxic metals and oxides, such as selenium and arsenic compounds.
• Selenium remediation: reduction of SeO$_4^{2-}$ to elemental selenium Se(0) is used to remove selenium from water.
• Mercury remediation: bacteria can convert toxic Hg$^{2+}$ to nontoxic Hg$^0$; Pseudomonas aeruginosa is one example of bacteria that can participate in this transformation.
• Oil spill bioremediation is one of the most widely cited successes:
  • Notable spills include Exxon Valdez (1989), Prestige (2002), a Mediterranean spill (2006), and the BP Gulf of Mexico spill (2010).
  • Ocean environments contain oil-degrading bacteria even before spills, facilitating natural bioremediation.
  • In addition to natural processes, humans select and engineer bacteria with enhanced hydrocarbon-degrading capabilities and broader substrate ranges.
  • Bioremediation can be enhanced with inorganic nutrients to boost bacterial growth and activity.
  • Some hydrocarbon-degrading bacteria secrete surfactants that solubilize oil, making it more accessible for degradation (e.g., Alcanivorax borkumensis).
  • Degradation pathways include breaking down hydrocarbons into smaller subunits and eventually to carbon dioxide; under ideal conditions, up to about 80\% of nonvolatile components can be degraded within one year, although some fractions with aromatic or highly branched hydrocarbons persist longer.

Conceptual and Practical Connections

• Prokaryotes are foundational to life-support systems: they drive nitrogen and carbon cycles, support digestion and nutrition, enable sustainable agriculture, contribute to food production, and aid in environmental cleanup.
• The relationship between prokaryotes and eukaryotes often benefits both sides: plants gain nitrogen, microbes receive energy sources, and ecosystems gain resilience and sustainability.
• Ethical and practical implications for microbiome therapies include safety and regulatory considerations for interventions like fecal transplants; ongoing clinical trials aim to determine efficacy and safety for treating infections and potentially other conditions.
• The theme of symbiosis (e.g., rhizobia–legume interactions) highlights how co-evolved relationships expand ecological networks and support agriculture without heavy chemical inputs.
• The historical perspective shows that biotechnology has roots long before modern genetic engineering, rooted in fermentation and microbial metabolism that created staple foods and beverages.

Key Terms and Concepts to Remember

• Biological nitrogen fixation (BNF)
• Nitrogenase and nitrogen fixation enzyme system
• Nitrogen cycle: atmospheric N$2$ to plant-usable NH$3$/NH$_4^+$ forms
• Nodules and leghemoglobin in legume roots
• Rhizobia and their symbiotic relationship with legumes
• Free-living vs. symbiotic nitrogen-fixers (e.g., Clostridium, Azotobacter, cyanobacteria)
• Legumes as natural nitrogen sinks and biofertilizers
• The human microbiome and the Human Microbiome Project
• Clostridium difficile and fecal microbiota transplantation (FMT)
• Bioremediation: selenium, mercury, and oil spill cleanup
• Alcanivorax borkumensis and surfactant production in hydrocarbon degradation
• Early biotechnology: fermentation-based foods (cheese, yogurt, bread, beer, wine)
• Definitions of biotechnology with commercial applications

Quick Reference Equations and Figures

• Nitrogen fixation equation (BNF):
  
  \mathrm{N}2 + 16\,\mathrm{ATP} + 8\,\mathrm{e}^- + 8\,\mathrm{H}^+ \rightarrow 2\,\mathrm{NH}3 + 16\,\mathrm{ADP} + 16\,\mathrm{Pi} + \mathrm{H}2
  

• Fixed nitrogen contribution to agriculture: 100\text{--}180\ \text{million metric tons per year} and 65\%\$ of nitrogen used in agriculture.

• Bioremediation efficiency in oil degradation: up to \approx 80\% of nonvolatile components degraded within one year under ideal conditions.

• Selenium reduction: \mathrm{SeO}_4^{2-} \rightarrow \mathrm{Se}^0 (reduction to elemental selenium).

• Mercury reduction: \mathrm{Hg}^{2+} \rightarrow \mathrm{Hg}^0$$ (methyl mercury concerns addressed via bioremediation).