Nitrogen fixation in the context of Eubacteria

Bacteria are ubiquitous, mostly free-living organisms often consisting of one biological cell. They constitute a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria were among the first life forms to appear on Earth, and are present in most of its habitats. Bacteria inhabit the air, soil, water, acidic hot springs, radioactive waste, and the deep biosphere of Earth's crust. Bacteria play a vital role in many stages of the nutrient cycle by recycling nutrients and the fixation of nitrogen from the atmosphere. The nutrient cycle includes the decomposition of dead bodies; bacteria are responsible for the putrefaction stage in this process. In the biological communities surrounding hydrothermal vents and cold seeps, extremophile bacteria provide the nutrients needed to sustain life by converting dissolved compounds, such as hydrogen sulphide and methane, to energy. Bacteria also live in mutualistic, commensal and parasitic relationships with plants and animals. Most bacteria have not been characterised and there are many species that cannot be grown in the laboratory. The study of bacteria is known as bacteriology, a branch of microbiology.

Like all animals, humans carry vast numbers (approximately 10 to 10) of bacteria. Most are in the gut, though there are many on the skin. Most of the bacteria in and on the body are harmless or rendered so by the protective effects of the immune system, and many are beneficial, particularly the ones in the gut. However, several species of bacteria are pathogenic and cause infectious diseases, including cholera, syphilis, anthrax, leprosy, tuberculosis, tetanus and bubonic plague. The most common fatal bacterial diseases are respiratory infections. Antibiotics are used to treat bacterial infections and are also used in farming, making antibiotic resistance a growing problem. Bacteria are important in sewage treatment and the breakdown of oil spills, the production of cheese and yogurt through fermentation, the recovery of gold, palladium, copper and other metals in the mining sector (biomining, bioleaching), as well as in biotechnology, and the manufacture of antibiotics and other chemicals.

The nitrogen cycle is the biogeochemical cycle by which nitrogen is converted into multiple chemical forms as it circulates among atmospheric, terrestrial, and marine ecosystems. The conversion of nitrogen can be carried out through both biological and physical processes. Important processes in the nitrogen cycle include fixation, ammonification, nitrification, and denitrification. The majority of Earth's atmosphere (78%) is atmospheric nitrogen, making it the largest source of nitrogen. However, atmospheric nitrogen has limited availability for biological use, leading to a scarcity of usable nitrogen in many types of ecosystems.

The nitrogen cycle is of particular interest to ecologists because nitrogen availability can affect the rate of key ecosystem processes, including primary production and decomposition. Human activities such as fossil fuel combustion, use of artificial nitrogen fertilizers, and release of nitrogen in wastewater have dramatically altered the global nitrogen cycle. Human modification of the global nitrogen cycle can negatively affect the natural environment system and also human health.

A biogeochemical cycle, or more generally a cycle of matter, is the movement and transformation of chemical elements and compounds between living organisms, the atmosphere, and the Earth's crust. Major biogeochemical cycles include the carbon cycle, the nitrogen cycle and the water cycle. In each cycle, the chemical element or molecule is transformed and cycled by living organisms and through various geological forms and reservoirs, including the atmosphere, the soil and the oceans. It can be thought of as the pathway by which a chemical substance cycles (is turned over or moves through) the biotic compartment and the abiotic compartments of Earth. The biotic compartment is the biosphere and the abiotic compartments are the atmosphere, lithosphere and hydrosphere.

For example, in the carbon cycle, atmospheric carbon dioxide is absorbed by plants through photosynthesis, which converts it into organic compounds that are used by organisms for energy and growth. Carbon is then released back into the atmosphere through respiration and decomposition. Additionally, carbon is stored in fossil fuels and is released into the atmosphere through human activities such as burning fossil fuels. In the nitrogen cycle, atmospheric nitrogen gas is converted by plants into usable forms such as ammonia and nitrates through the process of nitrogen fixation. These compounds can be used by other organisms, and nitrogen is returned to the atmosphere through denitrification and other processes. In the water cycle, the universal solvent water evaporates from land and oceans to form clouds in the atmosphere, and then precipitates back to different parts of the planet. Precipitation can seep into the ground and become part of groundwater systems used by plants and other organisms, or can runoff the surface to form lakes and rivers. Subterranean water can then seep into the ocean along with river discharges, rich with dissolved and particulate organic matter and other nutrients.

Legumes are plants in the pea family Fabaceae (or Leguminosae), or the fruit or seeds of such plants. When used as a dry grain for human consumption, the seeds are also called pulses. Legumes are grown agriculturally, primarily for human consumption, but also as livestock forage and silage, and as soil-enhancing green manure. Legumes produce a botanically unique type of fruit – a simple dry fruit that develops from a simple carpel and usually dehisces (opens along a seam) on two sides.

Most legumes have symbiotic nitrogen-fixing bacteria, Rhizobia, in structures called root nodules. Some of the fixed nitrogen becomes available to later crops, so legumes play a key role in crop rotation.

A bean is the seed of plants in many genera of the legume family (Fabaceae) used as a vegetable for human consumption or animal feed. The seeds are sold fresh or preserved through drying (a pulse). Beans have been cultivated since the seventh millennium BCE in Thailand, and since the second millennium BCE in Europe and in Peru. Most beans, with the exception of peas, are summer crops. As legumes, the plants fix nitrogen and form seeds with a high protein content. They are produced on a scale of millions of tons annually in many countries; India is the largest producer.

Dried beans are traditionally soaked and boiled, and used in traditional dishes throughout the world including salads, soups, and stews such as chili con carne. Some are processed into tofu; others are fermented to form tempeh. Guar beans are used for their gum. The unripe seedpods of some varieties are also eaten whole as green beans or edamame (immature soybean). Some types are sprouted to form beansprouts.

Human impact on the nitrogen cycle is diverse. Agricultural and industrial nitrogen (N) inputs to the environment currently exceed inputs from natural N fixation. As a consequence of anthropogenic inputs, the global nitrogen cycle (Fig. 1) has been significantly altered over the past century. Global atmospheric nitrous oxide (N₂O) mole fractions have increased from a pre-industrial value of ~270 nmol/mol to ~319 nmol/mol in 2005. Human activities account for over one-third of N₂O emissions, most of which are due to the agricultural sector. This article is intended to give a brief review of the history of anthropogenic N inputs, and reported impacts of nitrogen inputs on selected terrestrial and aquatic ecosystems.

The Three Sisters (Spanish: tres hermanas) are the three main agricultural crops of various indigenous people of Central and North America: squash, maize ("corn"), and climbing beans (typically tepary beans or common beans). Traditionally, several Native American groups planted sunflowers on the north edges of their gardens as a "fourth sister." In a technique known as companion planting, the maize and beans are often planted together in mounds formed by hilling soil around the base of the plants each year; squash is typically planted between the mounds. The cornstalk serves as a trellis for climbing beans, the beans fix nitrogen in their root nodules and stabilize the maize in high winds, and the wide leaves of the squash plant shade the ground, keeping the soil moist and helping prevent the establishment of weeds.

Indigenous peoples throughout North America cultivated different varieties of the Three Sisters, adapted to varying local environments.The individual crops and their use in polyculture originated in Mesoamerica, where squash was domesticated first, followed by maize and then beans, over a period of 5,000–6,500 years. European records from the sixteenth century describe highly productive Indigenous agriculture based on cultivation of the Three Sisters throughout what are now the Eastern United States and Canada, where the crops were used for both food and trade.Geographer Carl O. Sauer described the Three Sisters as "a symbiotic plant complex of North and Central America without an equal elsewhere".

In agriculture, polyculture is the practice of growing more than one crop species together in the same place at the same time, in contrast to monoculture, which had become the dominant approach in developed countries by 1950. Traditional examples include the intercropping of the Three Sisters, namely maize, beans, and squashes, by indigenous peoples of Central and North America, the rice-fish systems of Asia, and the complex mixed cropping systems of Nigeria.

Polyculture offers multiple advantages, including increasing total yield, as multiple crops can be harvested from the same land, along with reduced risk of crop failure. Resources are used more efficiently, requiring less inputs of fertilizers and pesticides, as interplanted crops suppress weeds, and legumes can fix nitrogen. The increased diversity tends to reduce losses from pests and diseases. Polyculture can yield multiple harvests per year, and can improve the physical, chemical and structural properties of soil, for example as taproots create pores for water and air. Improved soil cover reduces soil drying and erosion. Further, increased diversity of crops can provide people with a healthier diet.

Cycads /ˈsaɪkædz/—constituting the division Cycadophyta—are seed plants with a stout, woody cylindrical trunk with a crown of large, hard, stiff, evergreen and usually pinnate (feather-shaped) leaves. The species are dioecious, that is, individual plants of a species are either male or female. Cycads vary in size from having trunks only a few centimeters to several meters tall. They typically grow slowly and have long lifespans. They superficially resemble palms or ferns, but are not closely related to either group. Cycads are gymnosperms. Cycads have specialized pollinators, usually a specific beetle, and more rarely a thrips or a moth.

Both male and female cycads bear cones (strobili) containing their seeds, somewhat resembling conifer cones. Cycads fix nitrogen in association with cyanobacteria living in the plants' roots. Some species are used as narcotics, while in Vanuatu the plant symbolizes peace and appears on the national flag. Cycads all over the world are in decline, with four species on the brink of extinction and seven species each with fewer than 100 plants left in the wild.

In agriculture, cover crops are plants that are planted to cover the soil rather than for the purpose of being harvested. Cover crops manage soil erosion, soil fertility, soil quality, water, weeds, pests, diseases, biodiversity and wildlife in an agroecosystem—an ecological system managed and shaped by humans. Cover crops can increase microbial activity in the soil, which has a positive effect on nitrogen availability, nitrogen uptake in target crops, and crop yields. Cover crops reduce water pollution risks and remove CO₂ from the atmosphere. Cover crops may be an off-season crop planted after harvesting the cash crop. Cover crops are nurse crops in that they increase the survival of the main crop being harvested, and are often grown over the winter.

Rhizobia are diazotrophic bacteria that fix nitrogen after becoming established inside the root nodules of legumes (Fabaceae). To express genes for nitrogen fixation, rhizobia require a plant host; they cannot independently fix nitrogen. In general, they are gram negative, motile, non-sporulating rods.

Rhizobia are a "group of soil bacteria that infect the roots of legumes to form root nodules". Rhizobia are found in the soil and, after infection, produce nodules in the legume where they fix nitrogen gas (N₂) from the atmosphere, turning it into a more readily useful form of nitrogen. From here, the nitrogen is exported from the nodules and used for growth in the legume. Once the legume dies, the nodule breaks down and releases the rhizobia back into the soil, where they can live individually or reinfect a new legume host.

Soil microbiology is the study of microorganisms in soil, their functions, and how they affect soil properties. It is believed that between two and four billion years ago, the first ancient bacteria and microorganisms came about on Earth's oceans. These bacteria could fix nitrogen, in time multiplied, and as a result released oxygen into the atmosphere. This led to more advanced microorganisms, which are important because they affect soil structure and fertility. Soil microorganisms can be classified as bacteria, actinomycetes, fungi, algae and protozoa. Each of these groups has characteristics that define them and their functions in soil.

Up to 10 billion bacterial cells inhabit each gram of soil in and around plant roots, a region known as the rhizosphere. In 2011, a team detected more than 33,000 bacterial and archaeal species on sugar beet roots.

Root nodules are found on the roots of plants, primarily legumes, that form a symbiosis with nitrogen-fixing bacteria. Under nitrogen-limiting conditions, capable plants form a symbiotic relationship with a host-specific strain of bacteria known as rhizobia. This process has evolved multiple times within the legumes, as well as in other species found within the Rosid clade. Legume crops include beans, peas, and soybeans.

Within legume root nodules, nitrogen gas (N₂) from the atmosphere is converted into ammonia (NH₃), which is then assimilated into amino acids (the building blocks of proteins), nucleotides (the building blocks of DNA and RNA as well as the important energy molecule ATP), and other cellular constituents such as vitamins, flavones, and hormones. Their ability to fix gaseous nitrogen makes legumes an ideal agricultural organism as their requirement for nitrogen fertilizer is reduced. Indeed, high nitrogen content blocks nodule development as there is no benefit for the plant of forming the symbiosis. The energy for splitting the nitrogen gas in the nodule comes from sugar that is translocated from the leaf (a product of photosynthesis). Malate as a breakdown product of sucrose is the direct carbon source for the bacteroid. Nitrogen fixation in the nodule is very oxygen sensitive. Legume nodules harbor an iron containing protein called leghaemoglobin, closely related to animal myoglobin, to facilitate the diffusion of oxygen gas used in respiration.

Azolla filiculoides (water fern) is a species of aquatic fern. It is native to warm temperate and tropical regions of the Americas, and has been introduced to Europe, North and sub-Saharan Africa, China, Japan, New Zealand, the Caribbean, and Hawaii.

It is a floating aquatic fern with very fast growth, capable of spreading over the surfaces of lakes to give complete coverage of the water in only a few months. Each individual plant is 1–2 cm across, green tinged pink, orange, or red at the edges, branching freely, and breaking into smaller sections as it grows. It is not tolerant of cold temperatures; in temperate regions it largely dies back in winter, surviving by means of submerged buds. It harbors the diazotrophic organism Anabaena azollae in specialized leaf pockets. This ancient symbiosis allows A. azollae to fix nitrogen from the air and contribute to the fern's metabolism.