Fact sheet: Bioaugmentation—in situ

From: Public Services and Procurement Canada

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Bioaugmentation is an in situ bioremediation technique that consists of adding indigenous or exogenous (non-indigenous) microorganisms to contaminated soil or groundwater to enhance or supersede the existing microbial population. The microbial strain or consortium is introduced into the contaminated zone to improve contaminant biodegradation, which may be under aerobic (for example: diesel biodegradation) or anaerobic (for example: chlorinated solvent transformation) conditions. Biological activity may degrade contaminants, reduce their mobility and/or their toxicity.

Microbial consortia are prepared in laboratories, from contaminated soil and/or groundwater samples collected from the contaminated site, or from other sites where efficient biodegradation of the targeted contaminants is occurring. Cultures of microorganisms with known degradation capacities can also be used. The microorganisms from soil or groundwater samples can be isolated using a selective growth medium. Then the microorganisms are grown to high concentrations in a nutrient medium to obtain an inoculum. Once introduced into the subsurface, microorganisms must acclimatize, especially for exogenous microorganisms, to the geochemical conditions in the subsurface, before multiplying. 

In Canada, the injection of non-indigenous 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 Substances List (DSL) in order to be considered for the bioaugmentation remediation technique; few cultures are approved for use in Canada.

Internet links:

Implementation of the technology

Bioaugmentation projects may include:

  • Obtaining or cultivating an indigenous or allogenic bacterial consortium which will adapt to the site conditions and break down the target compounds.
  • Pre-treatment laboratory and/or pilot-scale trials
  • Mobilization, site access and temporary facilities
  • Reagent delivery, which could entail such measures as:
    • Groundwater well installation
    • Infiltration trench/drain construction
    • Injection or infiltration of aqueous treatment solutions
    • Injection of slurries
    • Injection of gasses below the water table
    • Deep soil mixing with solid or slurry reagents
    • Groundwater extraction, amendment and re-injection
  • Monitoring
  • Decommissioning of injection equipment

Microorganisms are normally introduced into shallow contaminated soil by surface spraying and into deep contaminated soil or groundwater by injection through injection wells. In specific cases, nutrients, electron donors (substrate) and/or electron acceptors, are also introduced below the water table to induce the destruction or transformation of contaminants of concern by enhancing the microbial degradation activity.

Issues with bioaugmentation are the distribution of treatment media in the subsurface and the selection adapted and efficient bacterial strains or bacterial consortium able to treat the targeted contaminants.

Bioaugmentation has seen extensive application for aerobically degradable fuel compounds and for anaerobically reduced chlorinated solvents.

Materials and storage

Injected materials vary widely according to contaminants, general groundwater composition and practitioners. The amendments to support microbial growth are similar to other aerobic or anaerobic bioremediation projects such as the nutrients and electron donor or acceptor substrates. 

On-site storage is primarily a function of the compounds being applied to the groundwater systems and the manner of application. Projects using periodic injections of material may bring materials to the site on an as-needed basis and avoid on-site storage. 

Waste and Discharges

  • If treatment is successful, the primary residual is microbial biomass (which decays over time).
  • System installation typically requires drilling or excavating in contaminated areas, resulting in the handling and disposal of contaminated soils, typically containerized and disposed of off-site.
  • Treated groundwater may transport bacteria, amendments, and degradation by-products out of the treatment zone. Hydraulic control may be required.

Recommended analyses for detailed characterization

Biological analysis

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

Chemical analysis

  • pH
  • Oxidation reduction potential (Eh)
  • Organic carbon content
  • Metals concentrations
  • Metabolite concentrations
  • Contaminant concentrations present in the following phases:
    • adsorbed
    • dissolved
    • free
  • Nutrient concentrations including:
    • ammonia nitrogen
    • total Kjeldahl nitrogen
    • nitrates
    • nitrites
    • total phosphorus
  • Electron acceptor concentrations/reaction by-products including:
    • dissolved oxygen
    • nitrate
    • sulfate
    • ferric and ferrous iron
    • methane
    • dissolved manganese

Physical analysis

  • Dissolved oxygen concentration
  • Temperature
  • Soil granulometry
  • Evaluation of biological conditions and ecological factors

Recommended trials for detailed characterization

Biological trials

  • Microcosm mineralization trial
  • Biodegradation trial

Hydrogeological trials

  • Tracer tests


Tests examining the effect of temperature change on hydraulic conductivity and establishing the zone of freezing with a pilot scale tubing system are recommended to properly design the full-scale containment system.

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

Phase III

  • Soil stratigraphy
  • Identification of preferential pathways for contaminant migration
  • Conceptual site model with hydrogeological and geochemical inputs
  • Characterization of the hydrogeological system including:
    • the direction and speed of the groundwater flow
    • the hydraulic conductivity
    • the seasonal fluctuations
    • the hydraulic gradient


  • Bioaugmentation allows for the treatment of residual and dissolved contamination;
  • Suitable for the treatment of organic contaminants under aerobic (with oxygen) or anaerobic (without oxygen) conditions;
  • pH value should ideally be between 6 and 8 to allow bacterial growth and activity.

Applications to sites in northern regions

In situ bioaugmentation, is potentially applicable to remote northern sites where impediments to material transport and injection equipment mobilization can be overcome. Cold temperatures can hamper biodegradation and microbial activity may only occur during the summer months, thus treatment time may take several years. Microbial activity may be possible in deep soil as temperatures (below permafrost) are relatively constant over the course of the year. 

Treatment type

Treatment type
Treatment typeApplies or Does not apply
In situ
Ex situ
Does not apply
Does not exist
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
Does not exist

Target contaminants

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

Long-term considerations (following remediation work)

Follow-up monitoring may be required to verify that the remediation objectives as well as applicable regulations are met once the groundwater system normalizes; after stimulation is withdrawn and excess biomass dies off.   

Secondary by-products and/or metabolites

Biodegradation of certain aliphatic chlorinated hydrocarbons could produce by-products or metabolites that are more toxic than the parent compound. In the case of (anaerobic) reductive dechlorination, the formation of chloroethane or vinyl chloride may warrant the use of an aerobic biostimulation step. Similar issues with toxic intermediates may occur in the degradation of some explosives and pesticides. Laboratory or pilot scale studies, as well as strict control of injected materials is typically required.

Limitations and Undesirable Effects of the Technology

  • Not suitable for free phase contaminants;
  • Not suitable for inorganic contaminant remediation;
  • Homogenous injection is difficult to achieve. Fractured or heterogeneous soil matrices could cause preferential pathways during injection;
  • Microorganisms that are not indigenous to the contaminated site may not adapt to survive under site conditions;
  • Possibility of deleterious metabolite(s) production;
  • High contaminant concentrations could be toxic for the microorganisms;
  • Low contaminant concentrations could limit bacterial activity (insufficient carbon source);
  • Important metal concentrations may reduce the efficiency of biodegradation;
  • In the presence of high-ferrous iron and manganese concentrations, microorganisms growth could induce clogging of the well-screen openings and of the aquifer formation around the screen.
  • If the treatment areas experience an incident or upset conditions, contaminated groundwater may escape untreated.
  • In Canada microorganisms must be registered on the Domestic Substances List (DSL) in order to be considered for bioaugmentation.

Complementary technologies that improve treatment effectiveness

  • Nutrient and oxygen addition may enhance the biodegradation process. Laboratory trials are recommended to verify the effectiveness of the bacterial consortium and nutrient formulation.

Required secondary treatments

Bioaugmentation requires no secondary treatment.

Application examples

Application examples are available at these addresses:


The treatment time for the remediation of a contaminated site by bioaugmentation varies according to contaminant type and concentration, the effectiveness of the bacterial population and the physical and chemical properties of the site.

Measures to improve sustainability or promote ecological remediation

  • Schedule optimization for resource sharing and fewer days of mobilization.
  • Use of renewable energy and energy-efficient equipment (such as geothermal or solar energy for reagent delivery).
  • Selection of amendments requiring less energy for their production
  • Use of local manufacturers of amendments
  • Use of groundwater recirculation to maximize the use of amendments and lower number of injection wells
  • Use of alternative sources of water for amendments/nutrients mix for injection.
  • Use of recyclable bulk solution containers.

Potential impacts of the application of the technology on human health

Unavailable for this fact sheet


Author and update

Composed by : Magalie Turgeon, National Research Council

Updated by : Karine Drouin, M.Sc., National Research Council

Updated Date : April 1, 2008

Latest update provided by : Marianne Brien, P.Eng., Christian Gosselin, P.Eng., M.Eng., Golder Associés Ltée

Updated Date : March 22, 2019