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biodegradation in soil

Decomposers of organic matter are found in the soils. These groups of living organismsm perform different functions:

• Microflora: certain types of bacteria and fungi are the major or primary decomposers; they are capable of digesting complex organic matter and transforming it into simpler substances that can be utilised by other organisms;

• Microfauna: certain types of protozoa and nematodes feed on or assimilate microbial tissues and excrete mineral nutrients;

• Mesofauna: includes a large number of organisms, ranging from small arthropods like mites (Acari) and springtails (Collembola) to potworms (Enchytraeidae). They break up plant detritus, ingest soil and organic matter or feed on primary decomposers thereby having a large influence on regulating the composition and activity of soil communities;

• Macrofauna: including ants, termites, millipedes and earthworms, contribute to organic matter decomposition by breaking up plant detritus and moving it down into the soil system thereby improving the availability of resources to microflora (through their nest building and foraging activities).

biodegradation of organic pollutants in soil

also called biological diversity; the relative number of species, diverse in form and function, at the genetic, organism, community, and ecosystem level. Loss of biodiversity − one of the global environmnatel problems − reduces an ecosystem's ability to recover from natural or man-induced disruption.

Source: https://www.cia.gov/library/publications/the-world-factbook


flavonoids (or bioflavonoids), also collectively known as Vitamin P and citrin, are a class of plant secondary metabolites.

They show anti-allergic, anti-inflammatory, anti-microbial and anti-cancer activity.

Flavonoids (both flavonols and flavanols) are most commonly known for their antioxidant activity in vitro. Their in vivo effect has not been proven yet, but the degradation of vitamin C can be hindered by flavonoids.

Flavonoids could also induce mechanisms that help kill cancer cells and inhibit tumor invasion.

Bioflavonoids like rutin, monoxerutin, diosmin, troxerutin and hidrosmin have vasoprotective proprieties.


material derived from living organisms. biogenic elements are the elements in the living organisms: C, H, O, N, S and P. biogenic amines are the biologically active amines of biological origin.


bioleaching is a type of leaching where the extraction of metal from solid minerals into a solution is facilitated by the metabolism of certain microbes - bioleaching microbes. Bioleaching is a process described as "the use of microorganisms to transform elements so that the elements can be extracted from a material when water is filtered trough it".

Source: BioMineWiki: http://wiki.biomine.skelleftea.se/wiki/index.php/Bioleaching

bioleaching based technology
biological immobilisation/stabilisation
biological pest control in organic farming

biological pest control in the organic agriculture is mainly against arthropods (e.g. insects, mites) and nematodes, as well as fungi and bacteria.

Insect pests are a common problem, and insecticides, both non-organic and organic, are controversial due to their environmental and health effects. One way to manage insects is to ignore them and focus on plant health, since plants can survive the loss of about a third of leaf area before suffering severe growth consequences.

To avoid using insecticides, one can select naturally resistant plants, put bags around the plants, remove dying material such as leaves, fruit, and diseased plants, cover plants with a solid barrier ("row cover"), wash them, encourage and release beneficial organisms and beneficial insects, plant companion plants and polycultures, install traps such as sticky cards (which can also be used to assess insect prevalence), and season extension. Biological pest control uses natural predators. Recommended beneficial insects include minute pirate bugs, big-eyed bugs, and to a lesser extent ladybugs (which tend to fly away), all of which eat a wide range of pests. Lacewings are also effective, but tend to fly away. Praying mantis tend to move more slowly and eat less heavily. Parasitoid wasps tend to be effective for their selected prey, but like all small insects can be less effective outdoors because the wind controls their movement. Predatory mites are effective for controlling other mites.

Several pesticides approved for organic use, such as spinosad and neem, have been called green pesticides. The main organic insecticides used in the US are Bt (a bacterial toxin) and pyrethrum. Surveys have found that fewer than 10% of organic farmers use these pesticides regularly. Nicotine sulfate may also be used although it is extremely toxic, but breaks down quickly. Less toxic but still effective organic insecticides include neem, spinosad, soaps, garlic, citrus oil, capsaicin (repellent), Bacillus popillae, Beauvaria bassiana, and boric acid. Pesticides should be rotated to minimize pest resistance.

The first disease control strategy involves cleaning the area by removing diseased and dying plants and ensure that the plants are healthy by maintaining water and fertilization.

Compost tea can be effective, but there is concern over whether these are ineffective or even harmful when made incorrectly.

Polyculture and crop rotation reduce the ability of disease to spread. Disease-resistant cultivars can be purchased.

Organic fungicides include the bacteria Bacillus subtilis, Bacillus pumilus, and Trichoderma harzianum which are mainly effective for diseases affecting roots.

Bordeaux mixture contains copper, which can be used as an organic fungicide in various forms. Sulfur is effective against fungus as well as some insects.Lime sulfur is also available, but can damage plants if used incorrectly. Potassium and sodium bicarbonate are also effective against fungus.

Agricultural Research Service scientists have found that caprylic acid, a naturally-occurring fatty acid in milk and coconuts, as well as other natural plant extracts have antimicrobial characteristics that can help.

Source: http://en.wikipedia.org/wiki/Organic_farming

biological plant protection
biological sewage purufication
biological soil tretament in slurry phase reactor
biological treatment in slurry reactor
biological uptake

the transfer of substances from the environment to microorganisms, plants, animals, and humans.

biological waste-water treatment

biological methods of wastewater treatment aim the biodegradation of the organic and inorganic pollutants in the waste water or the elimination ot these by other biological processes. The biodegradable organic material content of the waste waters is expressed as BOD (Biological Oxigene Demand) which is too high to let the waste-water into living surface waters. That is why we can say, that the aim of biological waste-water treatment is to reduce the BOD content in the waste-waters before their discharge into surface waters. Wastewaters enter the treatment plant with a BOD higher than 200 mg/L, but primary settling has already reduced it to about 150 mg/L by the time it enters the biological component of the technology. It needs to exit with a BOD content no higher than about 20−30 mg/L, so that after dilution in the nearby receiving water body (river, lake), the BOD is less than 2−3 mg/L.

Main principle of biological waste-water treatment is that bacterial cells use the organic material present in the wastewater as substrates for energy production (respiration, mineralisation) accompanied with CO2 and NH3 production. Part of the organic and inorganic constituents of the waste-water is used for the biosynthesis of the same microbes; through their metabolism, the organic material is transformed into cellular mass, which is no longer in solution but can be precipitated at the bottom of a settling tank or retained as slime on solid surfaces or vegetation in the system. The outflow of water becomes much clearer than it was, when entered.

The bioengineer ensures the optimal conditionss for the microorganisms to be able to work most efficiently. A key factor is the operation of an aerobic biological system is an adequate supply of oxygen. Indeed, cells need not only organic material as food but also oxygen to breathe. Without an adequate supply of oxygen, the biological degradation of the waste is slowed down, thereby requiring a longer residency time of the water in the treatment technology.

Biological treatment, is also called secondary waste-water treatment is designed to substantially degrade the biologically degradable or modifiable content of the sewage which are derived from human waste, food waste, soaps and detergent, in some cases industrial wastes. The majority of municipal plants treat the settled sewage liquor using aerobic biological processes. The bacteria and protozoa consume biodegradable soluble organic contaminants (e.g. sugars, fats, organic short-chain carbon molecules, etc.) and bind much of the less soluble fractions into floc. Flocs consists of living and dead microbes, slime and sorbed, non.degradable pollutants and waste material. The flocs can be sedimented or otherwise separated from the water phase. Some pollutants are concentrated in the waste-water sludge; part of them are able to be slowly degraded, but an other part is persistent (metals, persistent organic substances). These persistent contaminants in waste-water sludges makes the unlimited utilisation of the sludge impossibel.

Biological waste-water treatment systems are classified as fixed-film or suspended-growth systems. Fixed-film or attached growth systems include trickling filters and rotating biological contactors, where the biomass grows on media and the sewage passes over its surface. Suspended-growth systems include activated sludge, where the biomass is mixed with the sewage and can be operated in a smaller space than fixed-film systems that treat the same amount of water. However, fixed-film systems are more able to cope with drastic changes in the amount of biological material and can provide higher removal rates for organic material and suspended solids than suspended growth systems (Wikipedia).

    The most well-known biologica waste-water treatment technologies are the following:
    - Activated sludge treatmen
    - Surface-aerated basins (Lagoons)
    - Filter beds (oxidizing beds)
    - Soil Bio-Technology
    - Biological aerated filters
    - Rotating biological contactors
    - Membrane bioreactors
    - Secondary sedimentation
    - Lagooning
    - Constructed wetlands
    - Nitrogen removal
    - Phosphorus removal

    Technologies for the treatment of the waste-water sludge
    - Anaerobic digestion
    - Aerobic digestion
    - Composting
    - Incineration
    - Sludge disposal

    biological weathering

    living organisms contribute to the weathering process in many ways.

    Trees put down roots through joints or cracks in the rock in order to find moisture. As the tree grows, the roots gradually prize the rock apart.

    Even the tiniest bacteria, algae and lichens produce chemicals that help break down the rock on which they live, so they can get the nutrients they need.

    Many animals, such as these Piddock shells, bore into rocks for protection either by scraping away the grains or secreting acid to dissolve the rock.
    Source: http://www.geolsoc.org.uk/gsl/education/resources/rockcycle/page3568.html


    biomarkers of adverse effects are defined as any measurable biochemical, physiologic, or other alteration within an organism that, depending on magnitude, can be recognized as an established or potential health impairment or disease (NAS/NRC 1989). This definition encompasses biochemical or cellular signals of tissue dysfunction (e.g., increased liver enzyme activity or pathologic changes in female genital epithelial cells), as well as physiologic signs of dysfunction such as increased blood pressure or decreased lung capacity. Note that these markers are often not substance specific. They also may not be directly adverse, but can indicate potential health impairment (e.g., DNA adducts).

    Source: http://www.atsdr.cdc.gov/toxprofiles/tp140.pdf


    differentiation between biomarkers for exposures and adverse effects is done here and separately discussed the markers used for assessing and proving exposure and other ones for assessing the response of and organism or organ.

    A biomarker of exposure is a xenobiotic substance or its metabolites or the product of an interaction between a agent and some target molecule or cell that is measured within a compartment of an organism NAS/NRC 1989. The preferred biomarkers of exposure are generally the substance itself or substance-specific metabolites in readily obtainable body fluid or excreta. However, several factors can confound the use and interpretation of biomarkers of exposure. The body burden of a substance may be the result of exposures from more than one source. The substance being measured may be a metabolite of another xenobiotic e.g., high urinary levels of phenol can result from exposure to several different aromatic compounds. Depending on the properties of the substance e.g., biologic half-lifeand environmental conditions e.g., duration and route of exposure, the substance and all of its metabolites may have been eliminated from the body by the time biologic samples can be taken. It may be difficult to identify individuals exposed to hazardous substances that are commonly found in body tissues and fluids e.g., essential mineral nutrients such as copper, zinc and selenium.

    Biomarkers of effect are defined as any measurable biochemical,physiologic, or other alteration within an organism that, depending on magnitude, can be recognized as an established or potential health impairment or disease NAS/NRC 1989. This definition encompasses biochemical or cellular signals of tissue dysfunction e.g., increased liver enzyme activity or pathologic changes in female genital epithelial cells, as well as physiologic signs of dysfunction such as increased blood pressure or decreased lung capacity. Note that these markers are often not substance specific. They also may not be directly adverse,but can indicate potential health impairment e.g., DNA adducts.


    in general sense biomass is the mass of material built into living organisms.

    In bioengineering biomass is the mass of living cells or tissues growing during the propagation or fermentation process by utilising nutrients.

    In agriculture the useful mass of the plants: green leaves, wood, plant products, such as fruits, seeds, etc.

    In the moders environmnetal sciences we use the term biomnass in connection with renewable energy sources: the biological material from living, or recently living organisms, such as wood, waste, and alcohol fuels. Biomass is commonly plant matter grown to generate electricity or produce heat. For example, forest residues, yard clippings and wood chips may be used as biomass for energy production. However, biomass also includes plant or animal matter used for production of fibers or chemical substances.


    biomining is mining based on bioleaching.

    Bioleaching is a preparatory step to metal recovery. In subsequent processes, different from bioleaching, the metal is recovered from the leachate. Bacterial oxidation such as bioleaching or biooxidation on a commercial scale has been done on sulfide metal bearing materials such as arsenopyrite, pyrite, pyrrhotite, covellite and chalcocite ores and concentrates, the one exception to this processing being the oxidation of chalcopyrite ores and concentrates.

    Gold and copper are the dominating valuable metals that are commercially extracted:

    • Copper from low-grade secondary copper sulfide ores by heap bioleaching.
    • Gold from refractory gold concentrates by stirred tank leaching as a pretreatment step. The biooxidation residue is further treated by cyanide leaching to recover gold.
    • Co is also commercially extracted. Ni and Zn may become so in the future.

    Heap leaching is the most common method for bioleaching and is mainly used for secondary copper ores. Stirred tank leaching is used for refractory gold concentrates where gold is locked into the pyrite/arsenopyrite matrix. As the microbes do not necessarily need to contact the valuable metal-bearing material that is bioleached, they can be physically separated from it:

    • Direct bioleaching. The microbes are kept together with the valuable metal-bearing material
    • Indirect bioleaching. The microbes are kept in a pond external to the valuable metal-bearing material and provide the leaching chemicals at a distance.

    Bioleaching involves abiotic and biotic reactions, often with different physicochemical requirements. Indirect bioleaching is a way of satisfying the requirements independently by separating the biotic and abiotic reactions. In direct bioleaching the challenge is to select microbes whose living conditions are as close to the optimal conditions of the abiotic leaching reactions as possible.

    Advantages of biomining:

    • Ores and concentrates of lower metal concentration can be treated economically. Therefore the concentrating process can stop earlier, before the concentrate is sent for leaching. This means that loss of metal value during concentration is avoided.
    • "Difficult" - refractory - concentrates can be processed.
    • Concentrates with contaminants like arsenic, bismuth and magnesia are often expensive to treat in conventional metal-production. Mining companies often have to pay penalties for these difficult-to-treat contaminants when they sell concentrate to a smelter.
    • The arsenic in the concentrates can be removed in an environmentally stable form.
    • Possible to make use of existing SX/EW plant capacaties once the oxidic ore cap has been mined out.
    • Economic exploitation of smaller deposits, in remote locations, becomes viable because of reduced infrastructural costs.
    • Rapid start-up. Easy and reliable process when it comes to maintenance.
    • The process takes place at atmospheric pressure and low temperatures.
    • Water-based process means less dust.
    • No emissions of sulfur dioxide. Therefore, purification of smoke gas and sulfuric acid plants are superfluous.

    Despite the advantages with bioleaching it is not always easy to choose among the different methods of metal extraction in order to explore a potential mine. The Techno-Economic factors of a resource need to be evaluated from case to case.

    A list of Biomining Plants are given here: http://wiki.biomine.skelleftea.se/wiki/index.php/List_of_bioleaching_or_biooxidation_plants

    Source: BioMineWiki: http://wiki.biomine.skelleftea.se/wiki/index.php/Bioleaching


    biorefinery is a complex plant that integrates biomass conversion processes and technologies to produce fuels, power, heat, and value-added chemicals from biomass. The term biorefinery is analogous to petroleum refinery, which produce multiple fuels and products from petroleum.

    Biorefining is the processing of biomass into a wide range of bio-based products, such as food, feed, chemicals, materials and bioenergy, including biofuels, power and/or heat.

    Fully equipped biorefineries − similar to ptroleum refineries − do not exist yet, but combined heat and power (CHP) technologies generating electricity and process heat for smaller communities are more and more widespread in Europe (1).

    The biomass to be converted into heat, energy, fuel or materials can be of plant or microbial as well as organic waste origin. There are many individual ‘enabling technologies’ behind a biorefinery process. These include mechanical pretreatment, heat treatment, chemical/enzymatic cell wall degradation, fermentation, isolation/purification, conversion etc.

    The total chain of processing events is always tailor-made and optimized for a given biomass source and the applications aimed at. For unicellular organisms like algae, the first steps in the total biorefinery process differ strongly from that for plant-based material. Instead of mechanical harvesting and pretreatment of the crude plant material, efficient isolation of dispersed cells from the production medium is required. No lignin or hemicellulose is present, but many algae have cell walls that need to be broken down to allow efficient isolation of compounds of interest. In the later stages where individual compounds are isolated and converted, processes are more similar.

    In case of an algal biomass biorefinery technology consists of the the following steps (2):

    • Isolation is necessary unless direct milking of a desired algal product is possible. The first step in microalgae value creation is the isolation (harvesting) thereof from the production medium. There are several techniques available for this.
    • Purification strategies for individual components from algal biomass are highly diverse, as a direct consequence of the complexity and diversity of the algae biomass ‘matrices’ and the physico-chemical properties of the compounds of interest therein.
    • Conversion: many isolated algal components will need to be (bio) chemically converted to match the exact application needs, e.g. conversion by transesterification.

    The tactical biorefinery (3) first separates organic food material from residual trash, such as paper, plastic, Styrofoam and cardboard. The food waste goes to a bioreactor where industrial yeast ferments it into ethanol, a "green" fuel. Residual materials go to a gasifier where they are heated under low-oxygen conditions and eventually become low-grade propane gas and methane. The gas and ethanol are then combusted in a modified diesel engine that powers a generator to produce electricity.

    (1) http://en.wikipedia.org/wiki/Biorefinery
    (2) http://www.algae.wur.nl/UK/technologies/biorefinery/
    (3) http://news.uns.purdue.edu/x/2007a/070201LadischBio.html


    bioremediation uses microorganisms to degrade organic contaminants in soil, sludge, and solids either excavated or in situ. The microorganisms break down contaminants by using them as a food source or cometabolizing them with a food source. Aerobic processes require an oxygen source, and the end products typically are carbon dioxide and water.

    Anaerobic processes are conducted in the absence of oxygen, and the end products can include methane, hydrogen gas, sulfide, elemental sulfur, and dinitrogen gas.

    Ex situ bioremediation includes slurry-phase bioremediation, in which the soils are mixed in water to form a slurry to keep solids suspended and microorganisms in contact with the soil contaminants, and solid-phase bioremediation, in which the soils are placed in a cell or building and tilled with added water and nutrients.

    Land farming, biopiles, and composting are examples of ex situ, solid-phase bioremediation. In situ bioremediation is bioremediation in place, rather than ex situ. In situ techniques stimulate and create a favorable environment for microorganisms to grow and use contaminants as a food and energy source. Generally, this means providing some combination of oxygen, nutrients, and moisture, and controlling the temperature and pH. Sometimes, microorganisms that have been adapted for degradation of specific contaminants are applied to enhance the process.

    Source: US-EPA, Clu-In: http://www.clu-in.org/techfocus/default.focus/sec/Bioremediation_of_Chlorinated_Solvents/cat/Overview/

    bioremediation based on anaerobic oxidation
    bioremediation based on anaerobic reduction
    aeration of the saturated soil zone combined with nutrient supplement for the intensification of aerobic microbial activity in the saturated soil zone.

    biostimulation, the addition of nutrients to encourage the growth of indigenous contaminant-degrading microorganisms, is one of the most mature methods of bioremediation. It is applicable to both chlorinated and unchlorinated dissolved hydrocarbons.

    Biostimulation is dependent on indigenous organisms and thus requires that they are present and that their environment can be altered in a way that will have the desired bioremediation effect. In addition to an explanation of the concept of biostimulation, this chapter discusses critical aspects of site biogeochemistry, characterization and monitoring, combined biological technologies, and research needs.

    Source: US-EPA, Clu-In: http://www.clu-in.org/techfocus/default.focus/sec/Bioremediation_of_Chlorinated_Solvents/cat/Overview/

    biotechnology based on biodegradation

    biotin is also called vitamin H or coenzyme R. It belongs to the group of vitamin B. Biotin is necessary for cell growth, the production of fatty acids, and the metabolism of fats and amino acids. It plays a role in the Krebs-cycle (citric acid cycle), where the biochemical energy is generated during aerobic respiration. Biotin also helps to transfer carbon dioxide.

    Biotin may also be helpful in maintaining a steady blood sugar level and is often recommended for strengthening hair and nails. Consequently, it is found in many cosmetics and health products for the hair and skin, though it cannot be absorbed through the hair or skin itself.

    Biotin deficiency is rare, as intestinal bacteria generally produce an excess of the body's recommended daily requirement. For that reason, statutory agencies in many countries do not prescribe a recommended daily intake of biotin.

    Biotin is consumed from a wide range of food sources in the diet, however there are few particularly rich sources. Foods with a relatively high biotin content include egg yolk, liver, and some vegetables. The dietary biotin intake in Western populations has been estimated to be 35 to 70 μg/d (143–287 nmol/d).

    biotransformation, bioconversion

    bioventing is a promising new technology that stimulates the natural in situ biodegradation of any aerobically degradable compounds in soil by providing oxygen to existing soil microorganisms. In contrast to soil vapor vacuum extraction, bioventing uses low air flow rates to provide only enough oxygen to sustain microbial activity. Oxygen is most commonly supplied through direct air injection into residual contamination in soil. In addition to degradation of adsorbed fuel residuals, volatile compounds are biodegraded as vapors move slowly through biologically active soil.

    The U.S. Air Force has produced a technical memorandum which summarizes the results of bioventing treatability studies of fuels conducted at 145 US Air Force sites. The memorandum discusses overall study results and presents cost and performance data and lessons learned.

    Regulatory acceptance of this technology has been obtained in 30 states and in all 10 EPA regions, and the use of this technology in the private sector is growing rapidly following USAF leadership.

    Bioventing is a medium to long-term technology. Cleanup ranges from a few months to several years.

    Bioventing techniques have been successfully used to remediate soils contaminated by petroleum hydrocarbons, nonchlorinated solvents, some pesticides, wood preservatives, and other organic chemicals.

    While bioremediation cannot degrade inorganic contaminants, bioremediation can be used to change the valence state of inorganics and cause adsorption, uptake, accumulation, and concentration of inorganics in micro or macroorganisms. These techniques, while still largely experimental, show considerable promise of stabilizing or removing inorganics from soil.

    Factors that may limit the applicability and effectiveness of the process include:

    * The water table within several feet of the surface, saturated soil lenses, or low permeability soils reduce bioventing performance.

    * Vapors can build up in basements within the radius of influence of air injection wells. This problem can be alleviated by extracting air near the structure of concern.

    * Extremely low soil moisture content may limit biodegradation and the effectiveness of bioventing.

    * Monitoring of off-gases at the soil surface may be required.

    * Aerobic biodegradation of many chlorinated compounds may not be effective unless there is a co-metabolite present, or an anaerobic cycle.

    * Low temperatures may slow remediation, although successful remediation has been demonstrat

    Source: US-EPA, Clu-In: http://www.frtr.gov/matrix2/section4/4_1.html


    biphenyl is an aromatic hydrocarbon with a molecular formula (C6H5)2.

    CAS number 92-52-4

    PubChem 7095

    ChemSpider 6828 Yes

    Molecular formula: C12H10

    Molar mass: 154.21 g mol−1

    Appearance: colorless crystals

    Density: 1.04 g/cm3[1]

    Melting point: 69.2 °C, 342 K, 157 °F

    Boiling point: 255 °C, 528 K, 491 °F

    Solubility in water: 4.45 mg/L

    Flash point: 113 °C (235 °F)


    temperature: 540 °C (1,004 °F)[


    EU Index 601-042-00-8

    EU classification: Irritant (Xi), Dangerous for the environment (N)

    R-phrases R36/37/38 R50/53

    S-phrases (S2) S23 S60 S61

    It is notable as a starting material for the production of polychlorinated biphenyls (PCBs), which were once widely used as dielectric fluids and heat transfer agents. Biphenyl is also an intermediate for the production of a host of other organic compounds such as emulsifiers, optical brighteners, crop protection products, and plastics.

    bit, informatics

    a bit is a specific amount of information found in computers. It is abreviation of Binary Unit.

    Bytes, kilobytes, megabytes and gigabytes are all increasing levels of bits. A bit is the smallest piece of computer memory. It is either 1 or 0, meaning on or off. It is exactly one-eighth.

    bizonyítási teher
    black earth

    the term black earth is synonymous with Chernozem used (e.g. in Australia) to describe self-mulching black clays.

    blending zone
    blog, weblog, IT