Bioremediation in the context of Mycoremediation

An extremophile (from Latin extremus 'extreme' and Ancient Greek φιλία (philía) 'love') is an organism that is able to live (or in some cases thrive) in extreme environments, i.e., environments with conditions approaching or stretching the limits of what known life can adapt to, such as extreme temperature, pressure, radiation, salinity, or pH level.

Since the definition of an extreme environment is relative to an arbitrarily defined standard, often an anthropocentric one, these organisms can be considered ecologically dominant in the evolutionary history of the planet. Extremophiles have continued to thrive in the most extreme conditions, making them one of the most abundant lifeforms. The study of extremophiles has expanded human knowledge of the limits of life, and informs speculation about extraterrestrial life. Extremophiles are also of interest because of their potential for bioremediation of environments made hazardous to humans due to pollution or contamination.

Biomining refers to any process that uses living organisms to extract metals from ores and other solid materials. Typically these processes involve prokaryotes, however fungi and plants (phytoextraction also known as phytomining) may also be used. Biomining is one of several applications within biohydrometallurgy with applications in ore refinement, precious metal recovery, and bioremediation. The largest application currently being used is the treatment of mining waste containing iron, copper, zinc, and gold allowing for salvation of any discarded minerals. It may also be useful in maximizing the yields of increasingly low grade ore deposits. Biomining has been proposed as a relatively environmentally friendly alternative and/or supplementation to traditional mining. Current methods of biomining are modified leach mining processes. These aptly named bioleaching processes most commonly includes the inoculation of extracted rock with bacteria and acidic solution, with the leachate salvaged and processed for the metals of value. Biomining has many applications outside of metal recovery, most notably is bioremediation which has already been used to clean up coastlines after oil spills. There are also many promising future applications, like space biomining, fungal bioleaching and biomining with hybrid biomaterials.

A plasmid is a small, extrachromosomal DNA molecule within a cell that is physically separated from chromosomal DNA and can replicate independently. They are most commonly found as small circular, double-stranded DNA molecules in bacteria and archaea; however plasmids are sometimes present in eukaryotic organisms as well. Plasmids often carry useful genes, such as those involved in antibiotic resistance, virulence, secondary metabolism and bioremediation. While chromosomes are large and contain all the essential genetic information for living under normal conditions, plasmids are usually very small and contain additional genes for special circumstances.

Artificial plasmids are widely used as vectors in molecular cloning, serving to drive the replication of recombinant DNA sequences within host organisms. In the laboratory, plasmids may be introduced into a cell via transformation. Synthetic plasmids are available for procurement over the internet by various vendors using submitted sequences typically designed with software, if a design does not work the vendor may make additional edits from the submission.

The capillary fringe is the subsurface layer in which groundwater seeps up from a water table by capillary action to fill pores. Pores at the base of the capillary fringe are filled with water due to tension saturation. This saturated portion of the capillary fringe is less than the total capillary rise because of the presence of a mix in pore size. If the pore size is small and relatively uniform, it is possible that soils can be completely saturated with water for several feet above the water table. Alternately, when the pore size is large, the saturated portion will extend only a few inches above the water table. Capillary action supports a vadose zone above the saturated base, within which water content decreases with distance above the water table. In soils with a wide range in pore size, the unsaturated zone can be several times thicker than the saturated zone.

Some workers restrict their definition of the capillary fringe only to the tension-saturated base portion and exclude it wholly from the vadose zone. This is more common among workers addressing solute transport and water flow. Others define the capillary fringe as including both the tension-saturated and unsaturated portions. This is the preferred definition among workers dealing with the remediation of salt affected soils as well as those dealing with the vapor phase of soil processes and bioremediation. It is not uncommon to see the capillary fringe treated as a boundary condition separating the water table from the unsaturated zone, without defining it as a significant part of either.

Genetically modified crops (GM crops) are plants used in agriculture, the DNA of which has been modified using genetic engineering methods. Plant genomes can be engineered by physical methods or by use of Agrobacterium for the delivery of sequences hosted in T-DNA binary vectors. In most cases, the aim is to introduce a new trait to the plant which does not occur naturally in the species. Examples in food crops include resistance to certain pests, diseases, environmental conditions, reduction of spoilage, resistance to chemical treatments (e.g. resistance to a herbicide), or improving the nutrient profile of the crop. Examples in non-food crops include genetically modified trees for silviculture, and production of pharmaceutical agents, biofuels, and other industrially useful goods, as well as for bioremediation.

Farmers have widely adopted GM technology. Acreage increased from 1.7 million hectares in 1996 to 185.1 million hectares in 2016, some 12% of global cropland. As of 2016, major crop (soybean, maize, canola and cotton) traits consist of herbicide tolerance (95.9 million hectares) insect resistance (25.2 million hectares), or both (58.5 million hectares). In 2015, 53.6 million ha of Genetically modified maize were under cultivation (almost 1/3 of the maize crop). GM maize outperformed its predecessors: yield was 5.6 to 24.5% higher with less mycotoxins (−28.8%), fumonisin (−30.6%) and thricotecens (−36.5%). Non-target organisms were unaffected, except for lower populations some parasitoid wasps due to decreased populations of their pest host European corn borer; European corn borer is a target of Lepidoptera active Bt maize. Biogeochemical parameters such as lignin content did not vary, while biomass decomposition was higher.

Nitratidesulfovibrio vulgaris (formerly Desulfovibrio vulgaris) is a species of Gram-negative sulfate-reducing bacteria in the Desulfovibrionaceae family. It is also an anaerobic bacterium that is an important organism involved in the bioremediation of heavy metals in the environment. N. vulgaris is often used as a model organism for sulfur-reducing bacteria and was the first of such bacteria to have its genome sequenced. It is ubiquitous in nature and has also been implicated in a variety of human bacterial infections, although it may only be an opportunistic pathogen. This microbe also has the ability to endure high salinity environments, which is done through the utilization of osmoprotectants and efflux systems.

Drug metabolism is the metabolic breakdown of drugs by living organisms, usually through specialized enzymatic systems. More generally, xenobiotic metabolism (from the Greek xenos "stranger" and biotic "related to living beings") is the set of metabolic pathways that modify the chemical structure of xenobiotics, which are organic compounds that are foreign to an organism's normal biochemistry, such as any drug, pollutant, or poison. These pathways are a form of biotransformation that are present in all major groups of organisms, a fact which may allude to an ancient origin. These reactions often act to detoxify poisonous compounds (although in some cases the intermediates in xenobiotic metabolism may cause toxic effects). The study of drug metabolism is one of the tenets of pharmacokinetics (PK) as metabolism (M), the fourth stage of LADME (a drug's transit through the body), involves the enzymatic biotransformation and non-enzymatic biotransformation of a drug, thereby leading to the fifth stage, excretion (E).

The metabolism of pharmaceutical drugs is an important aspect of pharmacology and medicine. For example, the rate of metabolism determines the duration and intensity of a drug's pharmacologic action. Drug metabolism also affects multidrug resistance in infectious diseases and in chemotherapy for cancer, and the actions of some drugs as substrates or inhibitors of enzymes involved in xenobiotic metabolism are a common reason for hazardous drug interactions. These pathways are also important in environmental science, with the xenobiotic metabolism of microorganisms determining whether a pollutant will be broken down during bioremediation, or persist in the environment. The enzymes of xenobiotic metabolism, particularly the glutathione S-transferases are also important in agriculture, since they may produce resistance to pesticides and herbicides.