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Microbial Ecology

Nitrogen Cycle

Nitrogen is a major component of biological systems, and its cycling through the biosphere is dependent on several microbial transformations.

Nitrogen is a critical component of DNA, the genetic material of all organisms, and protein, the main structural material in all organisms. By dry mass, it is the second most abundant element in biological organisms, second only to carbon. The primary reservoir of nitrogen is the atmosphere, which is composed of 78% nitrogen, primarily as diatomic nitrogen (N2) gas, composed of two nitrogen atoms bonded together by a triple covalent bond. Nitrogen gas cannot be used as a source of nitrogen by most organisms because this triple bond is stable and unreactive.

Nitrogen fixation is the natural conversion of nitrogen gas to a form that is usable by organisms, and is performed by bacteria and archaea. Most natural nitrogen fixation is performed by bacteria that break the triple bond between nitrogen (N) atoms in atmospheric nitrogen gas molecules (N2) and combine the nitrogen (N) atoms with hydrogen to yield ammonia (NH3) and ammonium (NH4+).

In the ocean, photosynthetic cyanobacteria are the primary nitrogen fixers. On land, nitrogen fixation is performed in the soil by free-living bacteria and bacteria that have symbiotic relationships with certain plants, as well as in the atmosphere when lightning strikes. These bacteria live in the rhizosphere—the soil ecosystem adjacent to plant roots that is affected by the roots, their secretions, and the microorganisms that are present. Tiny root hairs grow around and internalize these bacteria. Communication between the bacteria and the plant creates a root nodule, which is a specialized bulbous, tumorlike growth on the root that contains the nitrogen-fixing bacteria. The bacteria in root nodules fix nitrogen gas that they supply to their plant host, which in turn supplies the bacteria with energy.

Plants are able to assimilate nitrogen in the form of ammonium or nitrate (NO3-) into organic compounds. Soil bacteria perform nitrification, which is the conversion of ammonium to the intermediate product nitrite (NO2-) and the final product nitrate (NO3-). Other soil bacteria use nitrate as an electron acceptor in cellular respiration, converting it eventually into nitrogen (N2) gas in the process of denitrification. The major source of nitrogen for most soil organisms is organic nitrogen from dead and decomposing organisms. Conversion of organic compounds into inorganic nutrients in the soil by bacteria or fungi is mineralization. Mineralization of organic nitrogen into ammonium is ammonification.

Nitrogen Cycle

The nitrogen cycle involves several molecular conversions by many soil and water microorganisms, and is substantially modified by human activity.
Today nitrogen fixation occurs on a massive industrial scale to produce nitrogen fertilizer to increase agricultural output. Some of this fertilizer enters groundwater through agricultural runoff. People also release large quantities of nitrogen into the environment through the burning of fossil fuels, such as gasoline and coal, and nitrogen oxides from fossil fuel use can return to Earth's surface in the form of acid rain. Together, industrial nitrogen fixation and nitrogen released from fossil fuels have approximately doubled the amount of biologically available nitrogen in the world.

An excess release of nutrients that serve as limiting factors to the growth of photosynthetic organisms has become a dominant form of human pollution. Unrestrained growth of plants, algae, and cyanobacteria resulting from increased availability of nutrients required by photosynthesis is called eutrophication. The primary limiting factor nutrients include nitrogen and phosphorus. These two nutrients can enter bodies of water through point-source pollution, such as sewage discharges, or as nonpoint source discharges, such as fertilizer runoff from lawns or agricultural fields. Lawns and crops are regularly overfertilized, and the excess nutrients make their way into bodies of water. Most sewage is still only treated to remove pathogens, and the nutrients in sewage are released directly into bodies of water. Together, sewage and fertilizer runoff add excess and unnatural quantities of limiting nutrients into bodies of water all around the world.

Oligotrophic bodies of water contain relatively low levels of plant and algae nutrients and have abundant oxygen at depth, providing good support to aquatic organisms. Low-level eutrophication can be desirable. It can increase the quantity of food sources at the bottom of food chains, which can ripple up through the ecosystem, increasing the populations of valuable sport or commercial fish species. A body of water's ability to absorb excess nutrients is quickly overwhelmed, though, with negative consequences for all organisms in the water.

When algae or cyanobacteria are overfertilized, for example, they grow and reproduce more rapidly than they can be consumed, causing an algal bloom. Blooms reduce light penetration into the water to the detriment of photosynthetic organisms that reside deeper in the water column. They alter the water's acidity, causing the starvation of organisms that rely on chemical signals to find prey.

The most consequential effect of algal blooms occurs when they die. Mass die-offs of algal blooms cause a feeding frenzy by decomposer bacteria in the water that rapidly grow and reproduce themselves. All of the decomposer growth depletes oxygen in the water, creating dead zones where conditions are unlivable for most aquatic organisms. Dead zones are annual phenomena in many bodies of water around the world. Recurrent dead zones are found in the Baltic Sea, the Chesapeake Bay, the Gulf of Mexico, Lake Erie, and the estuaries of the Yangtze and Yellow Rivers of China. In 2018, Florida beaches experienced a red tide, an algal bloom that lasted for over nine months and killed dozens of marine animals, including fish, sharks, dolphins, manatees, eels, and turtles.

Nutrient Pollution

With less vegetation, oligotrophic lakes are clearer than eutrophic lakes, which have more nutrients. Unrestrained growth of plants, algae, and cyanobacteria in eutrophic lakes can inhibit photosynthesis and kill other organisms.