1. Introduction

BCRs can be designed to treat MIW at abandoned mine sites as well and active mining operations. A BCR can be suitable for remote sites and can potentially operate with minimal operation and maintenance for long periods of time. However, optimal performance of a BCR requires long-term monitoring and maintenance. Although BCRs can have various applications, this guidance emphasizes solid substrate BCRs for remediating MIW. Liquid substrates may be a design consideration in some instances. Additionally, MIW from a mine pool or pit lake could be pumped to an ex situ BCR in certain situations or a mine pool could be treated in situ using the same biochemical treatment processes. Like any treatment technology, proper influent characterization, testing, siting, design, monitoring and maintenance is required to minimize the risk of failure.

The advantages of using a BCR to treat MIW include:

• treatment for an wide variety of constituents
• low operational and maintenance (O&M) requirements
• low initial cost of material for construction, especially when using local material for substrate
• uses basic construction practices
• can be implemented in remote areas, can be self-sustaining for months without human intervention.

Disadvantages of using a BCR to treat MIW include:

• rarely a stand-alone treatment, often requiring pre- and posttreatment
• may not consistently meet water quality criteria
• uncertainty of the operation and maintenance costs,
• space may limit an effective design of a BCR

These advantages and limitations are discussed in more detail in this guidance and a decision tree is included to assist in determining the applicability of a BCR for particular sites. Limitations and possible design alternatives (pre- and posttreatment) are also included.

Although it is not a design manual, this guidance offers a decision tree that describes the features the user should consider when assessing the use of a BCR. The guidance outlines general design guidelines, testing protocols, cost elements, construction (scale-up considerations), troubleshooting, and maintenance. Case studies highlight the applications and challenges of BCRs.

This guidance can assist tribal, state, and federal regulators (including permit writers, compliance staff, and technical support staff), federal land managers, practitioners and consultants, industry (including site owners), public and private researchers, and the international mining industry. This guidance is also a valuable resource for community and public stakeholders (such as watershed groups), environmental protection and land resource nongovernment organizations, and educators.

Aerobic/anaerobic wetlands and some permeable reactive barriers used to treat MIW share many of the same technical features as BCRs and are now considered to be included under the broad term "biochemical reactor."

Because no single treatment unit type works in every situation or with every MIW geochemistry, a BCR treatment system often includes pre- or posttreatment units. For example, manganese in MIW is typically unaffected in a BCR unit; an aerobic polishing unit or similar post-BCR treatment unit is required to address manganese. Pretreatment may be required to reduce acidity or reduce metals loadingMass of something per time entering a volume (volumetric loading rate) or flowing into an area (areal loading rate)., specifically for iron and aluminum. An example (Nairn et al. 2010) of a multi-unit treatment system containing a BCR is the Tar Creek unit shown in Figure 1-1.

Figure 1-1. Tar Creek passive treatment system in 2009.

Source: Image used with permission from Nairn et al. 2010 (see Appendix B.2, Mayer Ranch Case Study).

This treatment system uses a sequence of five treatment unit types in series, with paired, parallel units for four of those steps:

1. The circumneutral (pH 6) MIW flows into an oxidation pond shown at the bottom of the image.
2. The water flows through parallel surface-flow aerobic wetlands (2N and 2S).
3. Water flows through a pair of parallel downflow BCRs (3N and 3S).
4. The water is aerated by surface flow and bubblers powered by solar and wind energy, through shallow ponds (4N and 4S).
5. The final unit is a pair of horizontal-flow limestone beds (5N and 5S).
6. The treated effluent then is combined into a pond/wetland (6) for polishing.

A BCR treatment system should function for years without organic substrate refurbishing or replacement and in most cases be able to function without electrical power. Beining and Ott (1997) described a volunteer passive system exhibiting BCR characteristics outside of an abandoned lead-zinc mine in Ireland that has apparently been functioning unattended for over 120 years. Ideally, these treatment systems should be designed to last for decades.

Each site and BCR has its own Eh-pH diagram. Since each site can be complex, the objective here is to provide a general overview. Each site will have its own unique combination of chemical species and microbiological reactions. Site specific treatment options can affect Eh-pH diagrams as well. For instance, the site water is often acidic and calcium carbonate (CaCO₃) is used in various unit configurations to raise and maintain the pH range to improve treatment efficiency in a BCR.

In addition to the pH adjustment by CaCO₃ addition, a carbon source is added to the BCR and often consists of complex organics such as wood chips or manure. This mixture slowly degrades over many years, providing bacteria with the necessary substrate and food to support the biochemical reaction required to precipitate metals. Microorganisms use the organic carbon and available electron acceptors, resulting in conditions that promote metal sulfide precipitation. The most energetically available electron acceptors are consumed first (such as oxygen, nitrate, nitrite, ferric iron) generating reducing conditionsA system in which the gain of electrons is energetically favored due to a low reduction potential. suitable for biological sulfate reduction to sulfide.

Often, and particularly in the case of uranium reduction, (see Appendix B.12, Uranium Remediation Case Study) the reduction in valence results in an insoluble species. See the biochemical reaction for uranium illustrated in Figure 1-3.

Figure 1-3. Biochemical reduction of uranium of soluble U⁺⁶ to insoluble U⁺⁴

Source: Dr. Eric Nuttall University of New Mexico Professor Emeritus.

The reactions of interest in a BCR are determined by the interactions of the organic substrate, the microbial consortium, and the water flowing through that substrate. Because BCRs may be applied to MIWs ranging widely in pH and containing various metals, the explanation could be exhaustive; instead, only the most commonly encountered mechanisms for various contaminants are presented here. Chemical equilibrium software such as MINTEQA2 (http://www.epa.gov/exposure-assessment-models/minteqa2), PHREEQC (http://wwwbrr.cr.usgs.gov/projects/GWC_coupled/phreeqc), or Geochemist’s Workbench (http://crustal.usgs.gov/projects/aqueous_geochemistry/geochemists_workbench.html), among others can be used to determine the likely species for a specific water composition as it is subjected to changes in pH and redox potential (Eh), as shown in Figure 1-4.  

Figure 1-4. Eh-pH diagram showing stability fields of common iron minerals (ferric iron, Fe³⁺, and ferrous iron, Fe²⁺]. Total activity of dissolved carbonate 1M and dissolved oxygen 10^-4 M. Solid boundaries represent 10^-4M iron: dashed lines 10^-4M.

Source: Robert Thomas, CH2M Hill.

Combining iron and uranium elements onto one Eh-pH diagram (see Figure 1-5) shows the formation of in soluble U⁺⁴ and at a lower Eh than the formation of FeS₂. These diagrams show the change in chemical minerals as the system become more anaerobic and as the pH shifts from low to high. As the system becomes more anaerobic, the Eh will decrease.

Figure 1-5. Eh-pH diagram for the combined case of iron and uranium.

Source: Dr. Eric Nuttall, Dankritz Case Study.

SRBsulfate-reducing bacteria respire anaerobically using sulfate as a terminal electron acceptorThe molecule which is reduced during metabolism. In aerobic metabolism, oxygen is the electron acceptor, accepting two electrons and two protons to form water. and a simple organic carbon source as an electron donor. Different genera of SRB use different carbon sources (for example; acetic acid, hydrogen, simple sugars), and a variety of genera are found in a typical BCR (Prieto et al. 2008). SRB are found within a number of taxonomic groups including Deltaproteobacteria (for instance, Desulfovibrio, Desulfomicrobium, and Desulfobacter) and spore-forming bacteria such as Desulfomaculum (Doshi 2006).

Figure 1-6. Microbial processes involved in BCRs.

Source: Logan et al. 2005.

Temperature affects the growth of SRBsulfate-reducing bacteria. Deltaproteobacteria are gram-negative mesophilic bacteria (optimal growth temperature range 20–40°C) with a variety of shapes and physiologic traits. Most bacterial species prefer a similar temperature range to Deltaproteobacteria although some can withstand higher temperature environments. Thermophilic SRBs thrive at the high temperatures found in environments such as geothermal vents; however, these bacteria are usually not present in BCR treatment systems.

Cellulose degraders are necessary for bioreactors because they degrade the substrate, which is typically a complex carbohydrate, into simple carbon compounds. SRBsulfate-reducing bacteria cannot degrade cellulose and depend on the cellulose degraders to provide the carbon source (Neculita et al. 2007). Cellulose degradation can be either aerobic or anaerobic, with fermentative anaerobes likely to predominate in a sulfate-reducing treatment system. Examples of bacteria that are cellulose degraders include members of the bacterial genera Clostridium, Ruminococcus, and Caldicellulosiruptor. A wide variety of fungi also degrade cellulose, including members of the groups Ascomycetes, Basidiomycetes, and Deuteromycetes.

Fermenters are important in sulfate reducing treatment systems because they degrade amino acids, sugars, and fatty acids into simpler organic compounds (for example propionic acid and alcohols) that can also be used as carbon sources by SRBsulfate-reducing bacteria. Sometimes called "fermentative acidogens", these bacteria perform both fermentation and acidogenesis. Fermentation is an anaerobic metabolic process that does not depend on external electron donors or acceptors (unlike respiration) and in which the carbon source is both reduced, and a portion is oxidized, to produce the energy that the unit must have to thrive (Madigan et al. 2012). Acidogenesis is a stage in anaerobic digestion in which molecules such as sugars and amino acids are further broken down to simple fatty acids and alcohols (Figure 1-7).

Figure 1-7. Anaerobic digestion process.

Source: Waste To Energy Research and Technology, www.wtert.eu.

Hydrogen ion (H⁺) and molecular hydrogen are produced by a number of different fermentative bacteria in a bioreactor. Examples of hydrogen-producing fermentative reactions include the degradation of lactate to produce ethanol, carbon dioxide, and hydrogen ion by Lactobacillis and the degradation of glucose to butyrate, hydrogen gas, carbon dioxide, and hydrogen ion by Clostridium butyricum. Biological activity by fermenters has been found to significantly decrease as SRB activity increases in the initial stages of bench-scale passive treatment system operation (Logan et al. 2005).

Some microorganisms, including methanogens (a group of anaerobic Archaea) and a few genera of SRBsulfate-reducing bacteria, use molecular hydrogen as an electron donor. Studies have shown that SRB out-compete methanogens for available hydrogen, and methanogen activity is not expected to be high in a mature BCR (Logan et al. 2005).

If the BCR becomes exposed to oxygen, bacteria of the genus Thiobacillus (reclassified to Acidithiobacillus, Kelley and Wood 2000) can become more predominant (Hiibel et al. 2008). Thiobacilli are common bacteria in untreated MIW, are acidophilic, and aerobically oxidize ferrous iron to ferric iron.

Additionally microorganisms can be used to remove dissolved metals or other inorganic contaminants (such as uranium, tellurium, selenium, and chromium oxides). Microbes have the ability to incorporate metals into their structure. Contaminants are removed from the MIW and sorbed on the biomass within the bioreactor. The immobilized biomass is capable of ion exchange or chemical reduction. Microbe selection should be based on the organisms’ nutritional requirements available in the bioreactor (for example, sources of carbon, nitrogen, sulfur, and phosphorus), light requirements, and potential pathogenicity. The particular genus and species of the organisms are largely irrelevant, although organisms isolated from the site (or one similarly contaminated) would be most likely to carry out the desired reduction.

The physical, chemical, and biological mechanisms at work in each zone vary. These geochemical and biogeochemical reactions typically occur in an oxidizing environment in contact with air. When the percolating solutions encounter reducing conditions, sulfide minerals form in a steadily advancing enriched zone. At start-up, the oxide zone is relatively thin, as is the underlying transition zone. The sulfide zone extends from the bottom of the transition zone to the drainage collection layer that typically consists of crushed gravel and perforated pipes. This section first presents the general chemical and biochemical mechanisms occurring in a BCR. Then, these mechanisms are described as they occur in the reaction zones for a downflow BCR treating acidic and high iron and aluminum MIW. Portions of the chemistry identified in Table 1-2 (and explained further in Appendix A) are observed in each of the three zones of a BCR. A summary of zones and major reactions is also shown in Table 1-2.

A free water surface zone should evenly distribute MIW over the surface of a downflow BCR. Either a two to six inch layer of shallow standing water on the top of the BCR or, in place of standing water, gravel or plastic infiltration structures can be used to establish even distribution of MIW. Perforated pipes are not recommended for use in distributing MIW within the BCR because they are prone to plugging and causing short-circuiting within the BCR due to precipitation of ferric iron and aluminum oxyhydroxides (Gusek 2004).

MIW flowing into a BCR may have a pH less than 4.0 and could contain ferric iron (Fe⁺³) and aluminum (Al⁺³) in solution. If ferrous iron is present, it will likely oxidize to ferric iron:

1. 4Fe²⁺ + O₂ + 2H₂0 → 4Fe³⁺ + 4OH^-

As an example this reaction consumes hydrogen ions, so the pH tends to temporarily rise. If any aluminum is present in the mine water, a minor amount of aluminum hydroxide may precipitate:

2. Al³⁺ + 3H₂O → Al(OH)₃ [Gibbsite - amorphousHaving no crystalline form.] + 3H⁺

This reaction was observed in the lime-free aerobic wetland at the Wheal Jane site in Cornwall, England (see Appendix B.9).

In the oxide zone, acidic MIW attacks the cellulose in the organic substrate in a dehydration reaction in regions where limestone (a typical BCR substrate component) has been consumed. This may result in a small amount of hydrogen ion consumption which raises the local pH, allowing iron oxy-hydroxide to precipitate. Since most BCR is mixed with limestone (containing calcium carbonate, CaCO₃) to buffer acidity, the following reaction is likely to dominate in the oxide zone or the transition zone described below, which, depending on pH, produces bicarbonate (not shown) and carbonic acid.

This hydrogen ion consumption raises the local pH, allowing iron oxy-hydroxide to precipitate.

3. CH₂O → H₂O + C

4. CO₂:CaCO₃ + 2H⁺ → Ca⁺² + H₂CO₃ (H₂CO₃D H₂O + CO₂)

The presence of oxygen also allows cellulose-degrading bacteria to breakdown the organic matterStrictly defined, compounds in which carbon is bonded to hydrogen. Generally describes decomposed biological residues and other organic compounds synthesized by organisms. (see Figure 1-9).

Figure 1-9. Conceptual food chain in a BCR using woody substrate. CO₂ and H₂O omitted.

Source: Adapted from Seyler et al. (2003).

With the elevation of pH, iron oxyhydroxides should precipitate in accordance with the following equation:

5. Fe⁺³ + 3 H₂O → Fe(OH)₃ (s) + 3 H⁺

As the organic matter and limestone are consumed, the oxy-hydroxide zone expands downward. If the MIW is very acidic, the solid oxyhydroxides might actually be re-dissolved and re-deposited at the bottom of the oxidizing zone or in the transitional zone.

Plants are typically not part of a BCR design but can colonize the surface of the BCR and affect its chemistry. Oxygen diffuses from leaves to roots, creating a zone of oxidation surrounding the root surface known as an oxidized rhizosphereThe root zone of plants. (ITRC Phyto-3 2009). In addition, photosynthesis reactions drive ion uptake by roots, which can further increase the pH in the root zone because the use of carbon dioxide affects the carbonate equilibrium (Wildeman et al. 1993):

6. 6 HCO₃^- (aq) + 6 H⁺ → C₆H₁₂O₆ + 6 O₂

During the active growing season, the effects of oxygen diffusion and metabolic processes of the plant and fauna within the rhizosphere may dominate the oxidizing zone. These processes may convert narrow portions of the transitional and sulfide zones discussed below to oxide zone, liberating metals that had been precipitated there. At night plants use the sugar formed during photosynthesis, resulting in increases in CO₂ and possible diurnal pH swings in systems dominated by plant activity. When plants go dormant in the winter, lower portions of the oxide zone may revert to transitional and sulfide zone reactions over a period of weeks. Because of these effects, plant colonization on the top of a BCR should be carefully considered when designing or managing these systems.

Stripping of dissolved oxygen occurs in the transitional zone, primarily through biological decay of organic matter. Ferric iron (Fe³⁺) is reduced to ferrous iron (Fe⁺⁴) (Thomas et al. 2002):

7. Fe⁺³ + e^- → Fe⁺²

If a BCR is being overloaded, test evidence suggests the formation of the mineral siderite in accordance with the following reaction, where iron replaces calcium in the limestone:

8. Fe⁺² + CaCO₃ → FeCO₃ [siderite] + Ca⁺²

A similar phenomenon is possible if excess magnesium is present in the mine water:

9. Mg⁺² + CaCO₃ → MgCO₃ [dolomite] + Ca⁺²

A more common consequence of BCR overloading is the temporary removal of manganese. As discussed in Section 6, manganese removal in a BCR does not occur because of the reducing geochemistry. However, during overloading conditions, manganese removal often occurs. The mineral rhodochrosite is likely being formed in accordance with the following reaction:

10. Mn⁺² + CaCO₃ → MnCO₃ [rhodochrosite] + Ca⁺²

These three carbonate mineral phases are subject to subsequent dissolution from acidic BCR influent or, as in the case of the rhodochrosite, dissolution when overloading conditions abate, and the geochemistry surrounding the rhodochrosite grains becomes reducing.

The formation of iron, magnesium, or manganese carbonates is reversible, which can affect BCR effluent concentrations. When these mineral phases re-dissolve, the concentrations of manganese, iron, or magnesium in the BCR effluent may temporarily be higher than the respective concentrations in the influent. This condition may persist for weeks, until the carbonate minerals are consumed (Reisman et al. 2003). Some of the increase in concentrations may also be due to freeing of adsorbed (physically bound) compounds from the substrate.

11. 2 NO₃- + 10e^- + 12H⁺ →N₂ + 6H₂O

Nitrate is reduced to nitrogen gas in a BCR as the dissolved oxygen decreases.

In the sulfide zone, the SRBsulfate-reducing bacteria produce sulfide and bicarbonate (which can also raise the pH of the BCR effluent) in accordance with the following approximate reactions shown as equations (Wildeman et al. 2005):

11. SO₄^-2 + 2CH₂O → HS^- + 2 HCO₃^- + H⁺

The dissolved sulfide ion can precipitate metals as sulfides, essentially reversing the reactions that occurred to produce MIW. For example, the following reaction occurs for dissolved zinc, typically forming amorphous zinc sulfide (ZnS):

12. Zn⁺² + HS^- → ZnS (s)  + H⁺

These sulfides are thought to precipitate in the void spaces between the particles of limestone and organic matter in the substrate, but can form and infill the cells of the cellulose as shown in Figure 1-10 (Thomas 2002).

Figure 1-10. Cellulose cell infilling by metal sulfide precipitates.

Source: Thomas and Romanek (2002).

While aluminum does not form a sulfide, it is commonly removed in BCR environments. In one case, instead of aluminum hydroxide, Al(OH)₃, typically formed in SAPSsuccessive alkalinity producing systems, zones of insoluble aluminum hydroxyl-sulfate precipitates occurred in portions of a limestone buffered organic substrate (LBOS)A solid media containing limestone. Term is often used to describe the substrate used in vertical flow ponds.-filled units, similar to BCRs. The following reactions may apply (Thomas and Romanek 2002):       

13. Al³⁺ + H₂O + SO₄^2-D Al(SO₄)(OH) + H⁺

14. 3Al³⁺ +K⁺ + 6H₂O + 2SO₄^2- → KAl₃(OH)₆(SO₄)₂ [Alunite] + 6H⁺

15. 6Ca²⁺ + 2Al³⁺ + 38H₂O + 3SO₄^2- → Ca₆Al₂(SO₄)₃(OH)₁₂:26H₂O [Ettringite] + 12H⁺

The formation of such aluminum hydroxyl-sulfates may be related to a replacement reaction with limestone as suggested by the limestone fragment ghost observed by Thomas and Romanek (2002) and shown in Figure 1-11.

Figure 1-11. Limestone fragment containing gypsum ghosts.

Source: Thomas and Romanek (2002).

Exhumation of bench and pilot scale BCR units in test programs typically reveals a deep zone of “relatively fresh” organic substrate deeper in the sulfide zone. This layer often exhibits the appearance and fabric of recently placed substrate despite the likelihood that some organic degradation has occurred. Gusek (personal communication 2011) reported observing green hay in the relatively fresh zone of the BCR at the Ferris-Haggerty mine site in Wyoming that exhibited the appearance similar to the substrate placed on the day the BCR was constructed (see Appendix B.4). This layer often exhibits the appearance and fabric of recently-placed substrate despite the likelihood that some organic degradation has occurred. During operation of a BCR, by the time the water reaches this zone, virtually all the metals have been precipitated into oxides, hydroxy-sulfates, sulfides, or carbonates. If the precipitates are formed in the pore space of the sulfide zone, ultrafine, colloidal-sized precipitates may attach to the surfaces of the organic materials and be retained. The extent of this phenomenon may vary from BCR to BCR and may increase with BCR maturity.

Gusek (personal communication 2011) measured metal concentrations in substrate exhumed from two locations in a pilot BCR at the Haile Gold Mine (unpublished data) in 2004 (see Appendix B.3). The unit had operated for about two years (Gusek and Schneider 2010). Substrate samples from the lower portions of this unit typically did not contain elevated levels of the parameters of interest (such as Al, As, Cd, Cu, Mn, and Zn). In fact, the concentrations of these parameters were typically less than the concentrations in a baseline, fresh archival sample of substrate. Only iron levels appeared to be elevated in the relatively fresh substrate layer compared to the baseline in one of the two sample locations (baseline = 7,380 mg/kg Fe; zone 18 to 24 inches = 10,100 mg/kg Fe).