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Biodegradation as a Remedial
"Naturally occurring biodegradation" means degradation of organic compounds by indigenous microbes without artificial enhancement. The terms "passive bioremediation" and "intrinsic bioremediation" are also used to describe utilization of naturally occurring biodegradation as a remedial action. Application of naturally occurring biodegradation as a remediation technique requires that a site be evaluated to ensure site conditions are appropriate and that a monitoring plan be developed.

Bioremediation Application
Bioremediation is a treatment process that uses naturally occurring microorganisms (yeast, fungi, or bacteria) to break down, or degrade, hazardous substances into less toxic or nontoxic substances. Microorganisms, just like humans, eat and digest organic substances for nutrients and energy. In chemical terms, “organic” compounds are those that contain carbon and hydrogen atoms. Certain microorganisms can digest organic substances such as fuels or solvents that are hazardous to humans.

Microbial genomes from the environment
Microbial communities are vital in the functioning of all ecosystems; however, most microorganisms are uncultivated, and their roles in natural systems are unclear. Here, using random shotgun sequencing of DNA from a natural acidophilic biofilm, we report reconstruction of near-complete genomes of Leptospirillum group II and Ferroplasma type II, and partial recovery of three other genomes. This was possible because the biofilm was dominated by a small number of species populations and the frequency of genomic rearrangements and gene insertions or deletions was relatively low. Because each sequence read came from a different individual, we could determine that single-nucleotide polymorphisms are the predominant
form of heterogeneity at the strain level.
Transgenic Plants and Microbes
The use of biotechnology to modify plants has become a common practice in agricultural and horticultural research. Unlike ordinary research materials used in laboratory, greenhouse, and field studies, transgenic (genetically engineered, genetically modified)1 organisms are subject to special rules intended to ensure that they are used in a way that does not pose an unacceptable risk to human health or the environment.
Microbial Enzymes and Their Applications
Enzymes are biocatalysts produced by living cells to bring about specific biochemical reactions generally forming parts of the metabolic processes of the cells. Enzymes are highly specific in their action on substrates and often many different enzymes are required to bring about, by concerted action, the sequence of metabolic reactions performed by the living cell. All enzymes which have been purified are protein in nature, and may or may not possess a nonprotein prosthetic group.
Naturally Occurring Biodegradation
"Naturally occurring biodegradation" means degradation of organic compounds by indigenous microbes without artificial enhancement. The terms "passive bioremediation" and "intrinsic bioremediation" are also used to describe utilization of naturally occurring biodegradation as a remedial action.

Cleaning up environmental pollution
Some pollutants, such as pesticides or fertilizers, are used to benefit agriculture and enter the environment intentionally. Others, such as solvents, are toxic by-products of industrial processes that yield medicines or other products for which there is consumer demand.

Bioremediation: Cost-effective Alternative to Clean Environmental Messes
Enormous quantities of organic and inorganic compounds are released into the environment each year as a result of human activities. In some cases, these releases are deliberate and well regulated (e.g., industrial emissions) while in other cases they are accidental (e.g., chemical or oil spills). Many of these compounds are both toxic and persistent in terrestrial and aquatic environments.

Despite the diminutive size of individual microbial cells, the high abundance of microorganisms in virtually all habitats ensures that they contribute significantly to global biomass. It has been estimated recently that the carbon biomass of prokaryotic microbes is 60-100% of that thought to occur in plants worldwide, and microbial nitrogen and phosphorus biomass exceeds that of all other organisms.

For intensive aquaculture to become a sustainable industry with minimal environmental impact microbial ecology is critically important as a scientific discipline; applications of microbial ecology are needed at the forefront of advances now being made. Water quality and the control of disease are interdependent and linked to the microbial, especially bacterial, activities in ponds.
New Approaches for Bioaugmentation as a Remediation Technology
Bioaugmentation is commonly employed as a remediation technology. However, numerous studies indicate that introduced microorganisms often do not survive in the environment and thus do not increase contaminant remediation. This review details several new approaches that may increase the persistence and activity of exogenous microorganisms and/or genes following introduction into the environment. These techniques include:
Bioremediation of Sewage Sludge by Compositing

Sewage sludge used as soil organic amendment can positively affect soil physical, chemical, and biological properties. This organic material may be a solution for improving the low organic matter content of Mediterranean soils. However, the addition of sewage sludge to soils have not always shown positive effects, probably due to the particular characteristics of the residues concerned: high heavy metal or phytotoxic substance content, excess of labile organic matter, pathogenic microorganisms, etc:

Effects of Crude Oil, Oil Components, and Bioremediation on Plant Growth
The phytotoxic effects of crude oil and oil components on the growth of red beans (Phaseolus nipponesis OWH1) and corn (Zea mays) was investigated. In addition, the beneficial effects of bioremediation with the oil-degrading microorganism, Nocardia sp. H17-1, on corn and red bean growth in oil-contaminated soil was also determined. It was found that crude oil-contaminated soil (10,000 mg/kg) was phytotoxic to corn and red beans.

Multi-Species Ecotoxicity Assessment of Petroleum-Contaminated Soil
In 1992, a study was begun to compare the effect of landfarming vs. natural attenuation on the restoration of soil that had been contaminated with crude oil. Each of three lysimeters was filled with a sandy loam topsoil, and crude oil was applied to two of the lysimeters. One of the contaminated lysimeters was tilled, watered, and received a one-time application of fertilizer (N, P, K). No amendments were added to the second contaminated lysimeter, and the third was left uncontaminated. The lysimeters were monitored for 6 months and then left unattended.

Biodegradation of Natural Oils in Seawater
Spills of non-petroleum hydrocarbons including vegetable oils and fish oils are of environmental concern because of their potential to cause serious effects on marine life and coastal environments. Biodegradation by indigenous microorganisms is an important and potentially ubiquitous process affecting both the chemical composition and physical properties of contaminant oils. Data on the environmental persistence of non-petroleum oils is now required for risk assessments and decision making by spill responders. This article investigates the biodegradability of various vegetable and fishoils under the influence of natural bacteria in seawater.

Properties and Classification of Microorganisms
Just what are microorganisms? They are small living forms of life, which we cannot see with the naked eye. Bacteria, yeasts, and molds are three types of microorganisms. Some people often confuse, and almost always misunderstand, their functions, but they are just as real and alive as you are. They eat and grow. They reproduce and die. Have you ever wondered just how small microorganisms really are? Molds can be seen with only slight magnification and use of an ordinary magnifying glass. Yeasts must be viewed through a microscope that magnifies several hundred times. Bacteria can best be seen when studied with a more powerful microscope that enlarges 1,000 times.

Classification of Microorganism Taxonomy
By carbon and energy source, By cell structure, By genetic sequencing, By cell shape - morphology, By gram stain, By how they grow, By O2 requirements as electron acceptor, Other Classification Methods, Cell Chemistry, Parts of the Procaryotic Microbial Cell, Chemical Thermodynamics Review, Measurement of Organic Carbon, Microbial Metabolism, Respiration, Microbial Metabolism Review, Alternate Modes of Energy Metabolism, Measurement of Microbial Biomass, Genetics and Information Flow, Microbial Growth, Continuous growth of microbial cultures, CFSTR with Biomass Recycle: Activated Sludge.

Uptake of Heavy Metals by Microorganisms
Contamination in drinking water is the most common form of environmental problems encountered in water resources management. Some contaminants, present accidentally in drinking water, are very difficult to remove, such as heavy elements that are products of industrial waste. Lead is one of the most difficult-to-remove elements. This paper proposes a novel process for removal of lead compounds contaminants from water. The proposed method shows great efficiency.

Bacteria for Improvement of Oil Recovery
In microbial enhanced oil recovery (MEOR) technique, microorganisms and/or their products (gases, chemicals) are used in the enhancement of oil recovery. In the present study, MEOR is tested for Garzan (26° API) crude oil, produced from Southeast Turkey. This work consists of shut-in pressure tests and microbial water  ooding experiments. In shut-in pressure tests, the oil is placed in a stainless steel cell and a certain amount of microbial solution (Clostridium acetobutylicum) is introduced. During the soaking period, the pressure increase is monitored.
Anaerobic/aerobic treatment of colorants present in textile effluents
The operation of an anaerobic/aerobic process used to degrade the colorants present in textile wastewater is presented. The objective is to produce water that can be reused. Two particular cases were studied: the degradation of a synthetic wastewater containing the colorant disperse blue 79 (DB79) as a model compound and a real textile effluent containing reactive azo dyes. The biodegradation was achieved using a single tank operated as sequencing batch reactor. It was observed that the DB79 was biotransformed to amines in the anaerobic stage decolorizing the wastewater.

Natural clean-up for oil-spill soils
Oil spills from tankers or simply your local garage could soon be cleaned up using specially-selected bacteria, according to research presented today (Wednesday, 06 April 2005) at the Society for General Microbiology's 156th Meeting at Heriot-Watt University, Edinburgh. Millions of gallons of crude oil and its derivates used by the plastics and chemical industries are transported vast distances around the world every day, and inevitably some of it gets spilled. Scientists from University College Dublin are studying how natural bacteria can be used to tackle these pollutants.

Global warming plus natural bacteria could release vast carbon deposits

Increasing concentrations of carbon dioxide in the atmosphere will make global temperatures rise. By studying soil cores from the Arctic, scientists have discovered that this rise in temperature stimulates the growth of microorganisms that can break down long-term stores of carbon, releasing them into the atmosphere as carbon dioxide. This will lead to further increases in global temperatures. Carbon is held in soil either in material that is easily degraded by chemical and bacterial action (labile soil carbon), or in material that is less easily degraded by microorganisms (resistant soil carbon). About one third of the world's soil carbon is located in high latitudes such as the Arctic, and much of this effectively locked away in recalcitrant stores.

Home composting and its role in waste management
Composting is the aerobic microbial degradation of bulky organic waste, which usually generates heat, to produce a stabilized residue with significant value as a soil conditioner. The advantages of this natural process for treating biodegradable waste have placed it in a priority role for delivering the Government's target reductions in household waste disposal to landfill. Many householders with horticultural interests have traditionally composted and re-used their garden waste (Fig. 1). Encouraging and developing participation in home composting schemes also has major potential advantages in providing a low-cost approach to waste management and facilitating the sustainable recycling of biodegradable organic waste (Fig. 2).

Bugs within bugs: symbiotic bacteria in garden insects

Macrobiologists would give a microbefree answer to this question. The animals consuming garden plants - mostly insects - are kept in check by a combination of plant defences which make the plants unpalatable or downright toxic, and natural enemies such as ladybirds and other predatory beetles, parasitic wasps and fungal pathogens. This approach neglects a key weapon of phytophagous (plantfeeding) insects in their fight back against the near-inedible plants and army of natural enemies: symbiotic micro-organisms. Many of the microbes requisitioned by phytophagous insects in their unending war with plants and natural enemies cannot be cultured by traditional laboratory methods. However, the recent development of molecular techniques to study unculturable forms is permitting many new discoveries to be made about these micro-organisms.

Soil microbes and the war on garden weeds
Weeds have been associated with human activity from the very beginnings of society, when man evolved from a hunter-gatherer mindset and began to domesticate plants and animals and cultivate the land on which he settled. Why have weeds continued to persist as problems in our gardens, lawns, fields, meadows, and roadsides to this day? What is the nature of weeds that causes them to be opportunistic in almost any environmental situation and pose problems ranging from competition with man's desirable plants, to production of allergens, production of complex chemicals often toxic to man and animal, contamination of foods, feed and fibre, and harbouring other pests? In today's society it seems to be easier to find a 'quick fix' for problems rather than try to understand why the problem exists and derive a management plan based on knowledge.

Bacterial and fungal diseases of garden plants
The main reason is that seedlings are fleshy and juicy whereas seeds contain reserves of carbohydrates and other stored food reserves used in germination. Many seedlings are either killed or incapacitated by a mixed group of micro-organisms which cause damping-off and foot rots. The protozoan oomycete 'pseudofungi', in the genus Pythium, are often the chief culprits, causing damping off. The disease is worse in damp or wet soils. The closely related oomycete Phytophthora spp. behave similarly, but also attack the fleshy newly emerged roots and stem collars on much more mature plants, including a number of trees.
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