Over the past few months, Rebecca Philp, a PhD student from the Pirbright Institute, has been working at the Microbiology Society as our Public Affairs intern. While researching for a policy briefing, Rebecca learnt a lot about bioremediation. She explains a little about it in this blog.
Bioremediation uses micro-organisms to reduce pollution through the biological degradation of pollutants into non-toxic substances. This can involve either aerobic or anaerobic micro-organisms that often use this breakdown as an energy source. There are three categories of bioremediation techniques: in situ land treatment for soil and groundwater; biofiltration of the air; and bioreactors, predominantly involved in water treatment.
Sewage treatment plants are the largest and most important bioremediation enterprise in the world. In the UK, 11 billion litres of wastewater are collected and treated everyday. Major components of raw sewage are suspended solids, organic matter, nitrogen and phosphorus.
Terry Hazen who was primarily responsible for the discussion of the BP Deepwater Horizon spill was funded by a subcontract from the University of California at Berkeley, Energy Biosciences Institute (EBI), to Lawrence Berkeley National Laboratory. EBI receives funds from BP. Ronald Atlas who was primarily responsible for the discussion of the Exxon Valdez spill serves as a consultant to Exxon-Mobil on bioremediation; he also is a consultant to BP on oil biodegradation.
In situ bioremediation of oily sludge-contaminated soil by biostimulation of indigenous microbes through adding manure was conducted at the Shengli oilfield in northern China. After bioremediation for 360 days, total petroleum hydrocarbon (TPH) content was reduced by 58.2% in the treated plots compared with only 15.6% in the control plot. Moreover, bioremediation significantly improved the physicochemical properties of the soil in the treated plot. Soil microbial counts and community-level physiological profiling were also examined. Manure addition increased TPH degraders and polycyclic aromatic hydrocarbon (PAH) degraders in the contaminated soil by one to two orders of magnitude. The activity and biodiversity of soil microbial communities also increased markedly in the treated plot compared with that of the control. Finally, biotoxicity was used to evaluate the soils and a sharp increase in the EC50 of the soil after bioremediation was observed, indicating that bioremediation had reduced the toxicity of the soil.
Fungi possess the biochemical and ecological capacity to degrade environmental organic chemicals and to decrease the risk associated with metals, metalloids and radionuclides, either by chemical modification or by influencing chemical bioavailability. Furthermore, the ability of these fungi to form extended mycelial networks, the low specificity of their catabolic enzymes and their independence from using pollutants as a growth substrate make these fungi well suited for bioremediation processes. However, despite dominating the living biomass in soil and being abundant in aqueous systems, fungi have not been exploited for the bioremediation of such environments. In this Review, we describe the metabolic and ecological features that make fungi suited for use in bioremediation and waste treatment processes, and discuss their potential for applications on the basis of these strengths.
Bioremediation refers to the use of microorganisms to degrade contaminants that pose environmental and human risks. Bioremediation processes typically involve the actions of many different microbes acting in parallel or sequence to complete the degradation process. Both in situ (in place) and ex situ (removal and treatment in another place) remediation approaches are used. The versatility of microbes to degrade a vast array of pollutants makes bioremediation a technology that can be applied in different soil conditions . Though it can be inexpensive and in situ approaches can reduce disruptive engineering practices, bioremediation is still not a common practice .
A widely used approach to bioremediation involves stimulating naturally occurring microbial communities, providing them with nutrients and other needs, to break down a contaminant. This is termed biostimulation. Biostimulation can be achieved through changes in pH, moisture, aeration, or additions of electron donors, electron acceptors or nutrients. Another bioremediation approach is termed bioaugmentation, where organisms selected for high degradation abilities are used to inoculate the contaminated site . These two approaches are not mutually exclusive- they can be used simultaneously.
From an ecological point of view, bioremediation depends on the various interactions between three factors: substrate (pollutant), organisms, and environment, as shown in the figure at right . The interactions of these factors affect biodegradability, bioavailability, and physiological requirements, which are important in assessing the feasibility of bioremediation . Biodegradability, or whether a chemical can be degraded or not, is determined by the presence or absence of organisms that are able to degrade a chemical of interest and how widespread these organisms are in the site . The substrate (pollutant) can interact with its surrounding environment to change its bioavailability, or availability to organisms that are capable of degrading it; for example, substrate has low bioavailability if it is tightly bound to soil organic matter or trapped inside aggregates . Physiological requirements, or set of conditions required by organisms to carry out bioremediation in the environment, include nutrient availability, optimal pH, and availability of electron acceptors, such as oxygen and nitrate . Also, the environment needs to be habitable for organisms involved in bioremediation .
While organic pollutants are causing both environmental and health problems, bioremediation offers an effective solution to the pollution . The table below lists some of the organic pollutants and microorganisms that are found to be able to degrade them.
As stated previously, bioremediation involves various microorganisms that are able to degrade and reduce toxicity of environmental pollutants . Therefore, the interactions of microbes with the environment and pollutants are significant in determining effectiveness of bioremediation . Those microbes can be either naturally present in the site of bioremediation or isolated from other sites and inoculated artificially . Biodegradation often occurs as part of microbial metabolism and in some cases, microbes are able to directly harvest carbon and energy by breaking down pollutants . Sections below go over bacteria and fungi, the commonly used organisms in bioremediation, and archaea, the more recently discovered group of organisms with unique potential in bioremediation.
Bacteria are widely diverse organisms, and thus make excellent players in biodegradation and bioremediation. There are few universal toxins to bacteria, so there is likely an organism able to break down any given substrate, when provided with the right conditions (anaerobic versus aerobic environment, sufficient electron donors or acceptors, etc.). Below are several specific bacteria species known to participate in bioremediation.
Pseudomonas putida is a gram-negative soil bacterium that is involved in the bioremediation of toluene, a component of paint thinner. It is also capable of degrading naphthalene, a product of petroleum refining, in contaminated soils. 
Dechloromonas aromatica is a rod-shaped bacterium which can oxidize aromatics including benzoate, chlorobenzoate, and toluene, coupling the reaction with the reduction of oxygen, chlorate, or nitrate. It is the only organism able to oxidize benzene anaerobically. Due to the high propensity of benzene contamination, especially in ground and surface water, D. aromatic is especially useful for in situ bioremediation of this substance. 
Industrial bioremediation is used to clean wastewater. Most treatment systems rely on microbial activity to remove unwanted mineral nitrogen compounds (i.e. ammonia, nitrite, nitrate). The removal of nitrogen is a two stage process that involves nitrification and denitrification. During nitrification, ammonium is oxidized to nitrite by organisms like Nitrosomonas europaea.Then, nitrite is further oxidized to nitrate by microbes like Nitrobacter hamburgensis.
Deinococcus radiodurans is a radiation-resistant extremophile bacterium that is genetically engineered for the bioremediation of solvents and heavy metals. An engineered strain of Deinococcus radiodurans has been shown to degrade ionic mercury and toluene in radioactive mixed waste environments .
Methylibium petroleiphilum (formally known as PM1 strain) is a bacterium capable of methyl tert-butyl ether (MTBE) bioremediation. PM1 degrades MTBE by using the contaminant as the sole carbon and energy source .
Current bioremediation applications primarily utilize bacteria, with comparatively few attempts to use fungi. Fungi have fundamentally important roles because of their participation in the cycling of elements through decomposition and transformation of organic and inorganic materials. These characteristics can be translated into applications for bioremediation which could break down organic compounds and reduce the risks of metals. In some cases, fungi have an advantage over bacteria not just in metabolic versatility but also their environmental resilience.They are able to oxidize a diverse amount of chemicals and survive in harsh environmental conditions such as low moisture and high concentrations of pollutants. Therefore, fungi are potentially an extremely powerful tool in soil bioremediation and some versatile species such as White Rot Fungi have been a hot topic of research. [16,17] 153554b96e