Fact sheet: Biodegradation—Sediments

From: Public Services and Procurement Canada

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Biodegradation is a process by which organic contaminants in solid or liquid matrices are transformed by microorganisms to produce cell material, energy, organic compounds (generally less toxic than the parent compounds), CO2, and water. Under favourable conditions, microorganisms are capable of degrading a wide variety of organic compounds. The biodegradation of oil and polycyclic aromatic hydrocarbons (PAHs) (Ukiwe et al. 2013) in sediments has been clearly demonstrated, but biodegradation of polychlorinated biphenyls (PCBs) and chlorinated aliphatic hydrocarbons (CAHs) remains (for now) an emerging technology. The main advantage of biodegradation is the persistence of the biological reactions that can lead to complete transformation or mineralization of organic contaminants to a less-toxic or non-toxic form. This is also a method where the cost per unit of volume treated compares favourably with ex situ technologies and other in situ technologies.

Biodegradation may occur under aerobic or anaerobic conditions. Biodegradation occurs relatively easily for most petroleum hydrocarbons, PAHs (particularly low molecular-weight PAHs), PCBs and a small number of CAHs (dichloroethane [DCE], vinyl chloride) under aerobic conditions. If oxygen is not easily renewed, as is usually the case in sediments, the rapid reduction in dissolved oxygen concentrations due to microbial respiration creates anaerobic conditions. In such cases, anaerobic microorganisms can use electron acceptors other than oxygen, such as nitrate, sulfate, manganese (Mn) (IV), iron (Fe) (III), or CO2, to continue contaminant mineralization. Complex chlorinated compounds are easier to biodegrade under anaerobic conditions. Petroleum hydrocarbons, light PAHs and PCBs, and CAHs can be degraded under anaerobic conditions when electron acceptors other than oxygen are available for microorganisms.

Generally, two methods are used to promote the biological treatment of contaminated sediments: biostimulation and bioaugmentation.

Biostimulation is the introduction of additives (amendments) into sediments to stimulate the indigenous microorganisms and accelerate the biodegradation of specific contaminants (for instance, through oxidation or nutrient addition). Biostimulation can occur in both aerobic and anaerobic environments, provided the necessities are available for microbial life. It is often advantageous to focus on biostimulation under either aerobic or anaerobic conditions. The preferred environmental condition depends on the biodegradation potential of contaminants, access to biostimulants, and existing site conditions.

Bioaugmentation involves the introduction, directly on or into the contaminated sediment, of cultured microorganisms with specific catabolic abilities. This procedure enables or accelerates the biodegradation of target contaminants. The key factor in the success of bioaugmentation is selecting the appropriate bacterial strain. This selection must be made taking into account not only the ability of the strain to degrade the contaminants of concern, but also the ability of the strain to survive within the environmental conditions of the new habitat (e.g., pH, salinity, redox potential). It should be noted that, under real-world conditions, the effectiveness of bioaugmentation has not been conclusively demonstrated. This technology is still experimental, and there are significant challenges in applying it to underwater environments on a large-scale basis. In Canada, the injection of microorganisms into the environment is regulated by a federal agency, and must follow the 1999 Canadian Environmental Protection Act (CEPA 1999). The microorganisms must be registered on the Domestic Substance List (DSL) in order to be considered for the bioaugmentation remediation technique.

Internet Links

U.S. EPA, 1993. Guide for Conducting Treatability Studies under CERCLA: Biodegradation Remedy Selection.

Implementation of the technology

Biodegradation techniques are highly site-specific, and selecting an approach requires consideration of contaminant type, sediment grain size distribution, natural environmental conditions (e.g., anaerobic/aerobic conditions), site access, and location. The main issue implementing biodegradation remediation is the application and distribution of the treatment media (amendments) to the contaminated zone. Implementation includes achieving adequate surface coverage, reducing loss of amendments to suspension, and treating contaminants at depth. The process for selecting and implementing a biodegradation technique at a site may include the following:

  • identify the native microorganisms present at the site as well as their ability to degrade the contaminants of concern. If native organisms are capable of optimizing the rate of biodegradation, biostimulation may be an effective treatment option. When native organisms are not capable of biodegrading the contaminants, yet the site provides all conditions necessary for microbial survival (e.g., pH, salinity, redox potential), bioaugmentation may be an effective treatment option
  • conduct a detailed analysis of site conditions, including characterization of the microbial and existing environmental conditions, such as temperature, pH, available nutrients, and dissolved oxygen content
  • determine if alterations to the site may be made to improve microbial performance, without having a detrimental effect on native benthic organisms. If alterations are feasible and will not negatively affect the benthic community (or if the negative effects are easily mitigated), the biodegradation pathway may be a viable option


  • Using knowledge of the existing microbial community and environmental conditions at the site, determine the deficiencies in site conditions and the optimal biodegradation pathway for optimal microbial performance.
  • Decide on the bacterial strain to be optimized, and obtain any amendments (e.g., nutrients) necessary to improve microbial performance.
  • Conduct on-site pilot scale testing with a variety of amendment doses to develop an accurate estimation of required amendment quantities, application techniques, and remediation timelines capable of meeting remediation objectives.
  • Apply amendments to contaminated sediments based on thickness and application techniques determined from pilot testing. Depending on site conditions and phase of amendment (i.e., solid, liquid, or gas), application may take the following forms:
    • Amendments may be placed on the water surface (similar to application of a sand cap, detailed in Capping-Sediment) and allowed to sink to the sediment surface. A mechanical bucket may be used for solid amendments, and a liquid sprayer for liquid amendments.
    • Deposit amendments below the water surface, directly above the sediment. This will reduce resuspension and loss of amendment due to flow within the water body, and improve accuracy of amendment applications for sediments at significant depth. Application may be conducted using a mechanical bucket for solid amendments or a hydraulic pump for liquid amendments (see Capping-Sediments for more application information).
    • Inject amendments directly into the sediments to reduce occurrences of resuspension and loss of amendment due to flow within the water body. Direct injection allows for effective treatment of subsurface contamination and targeted “hot spot” (e.g., discrete location of high contamination) treatment.
  • Monitor amendment dispersion, ensuring sufficient application to the contaminated area.
  • Implement a long-term monitoring plan to ensure that the site is moving toward remediation goals over time.


  • Determine the potential microorganism(s) capable of biologically degrading the target contaminant, along with the environmental necessities to optimize microbial performance.
  • Select and obtain the bacterial strain that is both capable of biodegrading the contaminant of concern and surviving in the existing site environment.
  • Conduct an on-site pilot test, with a variety of bacterial doses, to determine the quantity and application technique to optimize the rate of biodegradation.
  • Apply bacteria colonies to contaminated sediment based on the optimal mode derived from the pilot test. As the effectiveness of bioaugmentation has not been conclusively demonstrated, application techniques have yet to be developed for this remediation method.
  • Monitor bacterial dispersion during application to ensure sufficient coverage of the contaminated area.
  • Implement a long-term monitoring plan to ensure that the site is moving toward remediation goals. If monitoring results indicate that remediation goals are not being met, it may be necessary to reapply bacterial colonies or move to biostimulation techniques.

Long-term monitoring for biostimulation and bioaugmentation

  • Long-term monitoring should include parameters to quantify microbial activity and the availability of environmental factors (e.g., oxygen, nutrients) required for optimal microbial growth. Recurring amendment applications may be required to maintain the microbial activity necessary to achieve remediation objectives.
  • Long-term monitoring should occur on a regular, predetermined schedule.
  • Additional monitoring should take place following major weather events, such as flooding.
  • Site activities may require institutional controls or restricted site use during the remediation phase to prevent exposure of buried contaminants.

Materials and Storage

Amendments used in biodegradation vary greatly, depending on individual site conditions and needs. When biostimulation is used, amendments may include oxidizers, such as hydrogen peroxide, calcium nitrate, and sodium nitrate; nutrient fertilizers, such as nitrogen, phosphorus, and organic fertilizers; and products affecting the ionic balance, such as sodium chloride. Bioaugmentation materials include biodegraders and bacterial culture, such as KB-1, whereas inhibitors may consist of chemical or biological surfactants or dispersants, such as TritonX-100, bile salts, surfactin, sodium taurocholate, rhamolipid, and sophorolipid.

Waste and Discharges

Biodegradation in sediments risks the loss of contaminants and/or amendments to suspension into the water column. Sediment contamination may be released when the water body is agitated, for example, by extreme weather events (e.g., flooding) or through human activities (e.g., construction). Loss of amendments may be mitigated through application techniques, such as application during periods of low energy (e.g., no current and wave action) and injection into sediment. Amendment application plans should be evaluated for their suspension potential, and preference should be given to products and/or techniques with little potential for loss into the water column. Sediment traps may be installed when contaminant or amendment loss is expected, to capture the fraction lost to suspension.

Materials and amendments should be safely stored to prevent accidental spills from contacting the water body or seeping into the groundwater. As a precautionary measure, sites should be equipped with spill kits and sorbent pads. Excess amendments may be returned to the supplier or disposed of in a manner acceptable to the local aut

Recommended analyses for detailed characterization

Biological analysis

  • Total heterotrophic and specific bacterial counts (according to the contaminants of interest)
  • Contaminant bioavailability

Chemical analysis

  • pH
  • Oxidation reduction potential (Eh)
  • Organic carbon content
  • Organic matter content
  • Dissolved salt concentration in water
  • Contaminant concentrations present in the following phases:
    • adsorbed
    • dissolved
    • free
  • Nutrient concentrations including:
    • ammonia nitrogen
    • total Kjeldahl nitrogen
    • nitrates
    • nitrites
    • total phosphorus

Physical analysis

  • Temperature
  • Soil granulometry
  • Contaminant physical characteristics including:
    • viscosity
    • density
    • solubility
    • vapour pressure
  • Evaluation of biological conditions and ecological factors
  • Characterization of sediments and interstitial water

Recommended trials for detailed characterization

Biological trials

  • Microcosm mineralization trial

Chemical trials

  • Evaluation of the matrix oxidant demand


On-site treatment trials will establish the efficiency of the technology and the parameters that influence the treatment time and cost (e.g. residence time, pump flow rate, requirements for pre-treatment, etc.).

Other information recommended for detailed characterization

Phase II

  • Contaminant delineation (area and depth)
  • Presence of receptors:
    • presence of potential environmental receptors
    • presence of above and below ground infrastructure
    • the risk of off-site migration
  • Regional climatic conditions (precipitation, temperature, etc.)
  • Characterization of hydrodynamic conditions includes:
    • current measurements
    • wave action
    • bed stability
    • etc.
  • Physical-chemical characterization of sediments and interstitial water
  • Bathymetry
  • Detailed evaluation of biological conditions and ecological factors
  • Characterization of the present and proposed surface water usage and the water body in general (including the required draft for vessels)


  • Biodegradation may be considered an appropriate remediation option under the following circumstances: contaminants of concern are not highly mobile, are adsorbed into the solid phase or dissolved in interstitial (pore) water, and are biodegradable under both aerobic and anaerobic conditions. The biodegradation of PAHs under anaerobic conditions has been demonstrated for low-molecular weight compounds only, such as naphthalene, methylnaphthalenes, phenanthrene, fluorene, and fluoranthese
  • The surface contamination is relatively uniform (i.e., no discrete locations of heavy contamination)
  • Sediments are stable with low erosion rates and high shear strength (the ability of the sediment to resist a slipping fault), capable of supporting the amendment application. They are located in low-energy environments, where strong currents and wave action are not a concern for resuspension during application
  • Water depth should not be so great as to hinder the settling of amendments. The optimal depth will vary with amendment characteristics and buoyancy, but may be assumed to be similar to sediment capping (less than 15 metres for non-buoyant material). Sediment slope stability must be sufficient to support the application of amendments
  • Locations with a healthy benthic and microbial community will better support the use of biodegradation. Benthic organisms should include those capable of providing bioturbation, which will naturally mix in the sediment amendments

Contaminants must be accessible at the surface of the sediment for amendment application, and be located at a reasonable distance from shore, to make application feasible and cost-effective. If contaminants are below the sediment surface, the depth to the contamination should be shallow enough to allow mechanical mixing-in of the amendments from the surface, or within the bioturbation zone (mixing of the sediments by benthic organisms at the sediment-water interface)

Applications to sites in northern regions

While biodegradation generally occurs more rapidly under warmer conditions, it has also been observed in Arctic environments. Biodegradation techniques that have been applied in northern environments include:

  • modified biodegraders (Roberg et al., 2007), where the researchers utilized a modified cold-climate version of the well-known biodegradation agent Inipol EAP 22 to increase hydrocarbon degrader counts and thus the rate of hydrocarbon removal from the Arctic intertidal sediments
  • enhanced biodegradation (Horowitz and Atlas, 1977), where a natural shift in microbial populations toward leaded-gasoline-tolerant microorganisms was observed after a fuel spill in a freshwater lake. Biodegradation was enhanced by adding nutrients and bacterial inoculation resulting in significantly reduced residual hydrocarbons
  • increased salinity on crude oil degradation (Sharma and Schiewer, 2016). This study found that increased salinity had a positive impact on crude oil degradation in sediment due to enhanced formation of oil-mineral aggregates

Treatment type

Treatment type
Treatment typeApplies or Does not apply
In situ
Ex situ
Does not exist
Dissolved contamination
Free Phase
Does not exist
Does not exist
Residual contamination
Does not exist

State of technology

State of technology
State of technologyExist or Does not exist

Target contaminants

Target contaminantsApplies, Does not apply or With restrictions
Aliphatic chlorinated hydrocarbons
With restrictions
Does not apply
Monocyclic aromatic hydrocarbons
With restrictions
Non metalic inorganic compounds
Does not apply
With restrictions
Petroleum hydrocarbons
Phenolic compounds
With restrictions
Policyclic aromatic hydrocarbons
Polychlorinated biphenyls
With restrictions

Treatment time

Treatment time
Treatment timeApplies or Does not apply
Less than 1 year
Does not apply
1 to 3 years
3 to 5 years
More than 5 years


Biodegradation techniques remain in the developmental phase. They are heavily studied and discussed in the scientific research literature. However, technical reviews and case studies are seldom available.

Treatment time can vary from one to many years, dependent on the contaminant type, quantity, site conditions, and amendment/technique used. Following the initial treatment, regular monitoring is required to demonstrate that contaminant levels are trending toward remediation objectives over time. Additional amendment applications may be required.

Long-term considerations (following remediation work)

In theory, biodegradation treatments are permanent if they result in the complete destruction of contaminants. However, there have been no long-term (30–50 years) monitoring studies completed to date.

Secondary by-products and/or metabolites

In most cases, biodegradation by-products are water, carbon dioxide and, in the case of chlorinated compounds, inorganic chlorine. However, in cases where bacterial catabolic activities are not present, incomplete degradation of the target molecule may occur. For example, the incomplete biodegradation of some PCBs (dihydrodiols and dihydroxybiphenyls) may lead to breakdown products that are significantly higher in toxicity to bacteria, even in short incubation periods. Trichloroethene (TCE) and perchloroethene (PCE) lead to the production of dichloroethene (DCE), and the incomplete biodegradation of DCE can lead to vinyl chloride (VC) production, which is more toxic than the parent compounds.

Addition of amendments and increased biological activity may lead to a change in the geochemical conditions within the sediment, for example a change in pH. These changes may result in increased bioavailability and mobilization for certain metals and other contaminants.

Surfactants may increase contaminant solubility, allowing them to be more available for microbial uptake. Care must be taken when using surfactants to ensure that they do not inhibit biodegradation, which can occur if the surfactant is toxic to the native bacteria or if there is competition for substrate utilization (Liu et al., 2001).

Limitations and Undesirable Effects of the Technology

  • The technology is not suitable
    • for inorganic contaminants such as metals or free-phase contamination,
    • in deep water or high-energy environments,
    • at sites where there is significant in-water and shoreline infrastructure that makes it challenging to access the sediments and evenly distribute the nutrients, microorganisms, or other amendments
    • Pyrogenic PAHs (derived from incomplete combustion) are more difficult to biodegrade than petrogenic PAHs (derived from crude oil and its refined products). (Lei et al, 2005)
    • It is difficult to predict the behaviour of microorganisms with respect to the level and rate of attainable contaminant biodegradation. For example, the rate of biodegradation of PCBs may be several orders of magnitude slower in situ than in the laboratory, because of the shortage of one or more essential nutrients, preferential metabolism of other more easily degraded substrates, or the presence of microbial predators or toxins. (Agarwal et al, 2007)
    • Biodegradation can require long time frames, depending on the level of contamination, the contaminants present, the bioavailability of the contaminants, sediment type, temperature, and other factors.
    • Few technical reviews and case studies exist for examples of successful biodegradation projects. The effectiveness of biostimulation has been demonstrated under real-world conditions, but to date bioaugmentation has been effective only under laboratory conditions. The absence of full-scale, completed projects for bioaugmentation may limit the public acceptability of biodegradation as a remedial option.

Adverse Impacts

  • As contamination remains in place, the release of subsurface contamination is a potential concern. Future site activities (e.g., construction) or extreme events (e.g., flooding) may release contaminants into the water body.
  • Geochemical conditions may be altered by chemical biodegradation; for example, increased biological activity may lead to increased bioavailability and mobilization of certain metals, increasing the direct toxicity of the sediment. Biodegradation may also generate products more toxic than the parent compounds.

Complementary technologies that improve treatment effectiveness

  • Biodegradation can be used in conjunction with other in situ technologies, such as dredging, excavating, or capping, to further reduce the availability of contaminants.
  • Amendments can also be incorporated into capping designs to stimulate biodegradation as an active in situ remediation process for contaminated sediments.
  • Biodegradation can be used as a secondary treatment to degrade the residual contamination remaining in the sediment after environmental dredging.
  • One study found that coupling biodegradation techniques with an electro-kinetic process allowed for greater bioavailability and therefore removal of phthalate esters in river sediment (Yang et al., 2015).

Required secondary treatments

No secondary treatment is required if the target contaminant concentrations are reached.

Application examples

University of Alaska Fairbanks, 2015. Biodegradation and Transport of Crude Oil in Sand and Gravel Beaches of Arctic Alaska.

Environment Canada, 1995. in situ Treatment of Hamilton Harbour Sediment. Injection of Calcium Nitrate and Nutrients to Degrade Organic Compounds (PAHs) within Freshwater Sediments.


The performance of biodegradation systems in sediments, reported in the literature during pilot scale testing or remediation projects, can achieve up to a 90% reduction in sulphide concentrations and a 50% to 80% reduction in concentrations of PAHs, petroleum hydrocarbons, and BTEX. The dechlorination of PCBs or halogenated hydrocarbons in the laboratory has demonstrated that it is possible to eliminate all contamination. It is important to note that achieving this level of biodegradation in situ is highly unlikely due to the intrinsic heterogeneity of sediment and the difficulty in controlling all parameters, as can be done in the laboratory. The efficacy of biodegradation may be compromised by groundwater advection and tidal action, which may carry sediment and amendments out of the treatment zone. However, the laboratory results demonstrate the potential of the technology, which can be exploited in the future due to improved understanding and control of the processes.

Measures to improve sustainability or promote ecological remediation

Biodegradation is one of the most sustainable in situ technologies and has fewer environmental impacts than more invasive remedial options, such as dredging or excavation. Sustainability and overall success may be improved by developing a site-specific plan that reduces consumption of energy, material, and water, minimizes harmful air emissions and waste generation, and protects human health and ecosystems during monitoring. For example, to the extent possible,

  • use local services and service providers,
  • use appropriate institutional controls to minimize site-wide human health risks and displacement of native materials,
  • implement sustainable site-monitoring methods, such as passive sampling devices, on-site analytical techniques and telemetry or remote data collection, and
  • follow site-specific timing restrictions to manage and protect fish and fish habitat.

Potential impacts of the application of the technology on human health

Exposure Pathway Triggers (Remediation stages) Residency or Transport Media Public Exposure Routes (On-site and Off-site) Monitoring, Action Levels, and Mitigation Approaches
In situ treatment Amendments (e.g., nutrients, microbes) Skin contact, inhalation of particulates and gaseous discharges, incidental ingestion Select benign amendments, where possible. Educate staff on safety and provide appropriate personal protective equipment (PPE) and reactionary materials (e.g., sorbent pads), as necessary. Follow measures for safe storage and handling to minimize exposure, as outlined in MSDS sheets.
Monitoring Increased microbial activity, potentially causing change in chemical concentrations, temperature increase Physical contact during recreational activities Institutional controls may be required to prevent the public from accessing the remediation zone during active remediation.


Author and update

Composed by : Bruno Vallée M.Sc, LVM Inc.

Latest update provided by : Bruno Vallée, M.SC. (1), Sharilyn Hoobin, M.Sc. (2) and Ashley Hosier, Ing. (2), LVM Inc. (1) and Royal military college royal (2), respectively

Updated Date : November 24, 2016