Lecture No. 25. Special Topics III

Continuing with methods to predict acid mine drainage, we move on to methods that improve on acid-base accounting and are based more on actual measurements than are computational models.

C. More Empirical Methods

Pillard et al. (Pillard, David A., Thomas A. Doyle, Donald D. Runnells, and John Young, 1995, "Post-mining pit lakes: Predicting lake chemistry and assessing ecological risks," Tailings and Mine Waste '96 (Balkema, Rotterdam), 469-478.) reported a test method whereby net acid-producing potential was measured directly in a laboratory. Samples (5 kg) of crushed rock were packed into acrylic plastic tubes 2 ft long by 2 in. in diameter and inoculated with Thiobacillus ferrooxidans. A flow of humidified air was passed through the tubes for 20 weeks. The tubes were then flushed from the bottom with groundwater from the mine site. Each pore volume was analyzed separately for pH, dissolved iron, sulfate, and specific conductance. The first and eighth pore volumes were analyzed for the full suite of metallic constituents.

The authors used this method in an attempt to measure directly the net effect of oxidation and neutralization. Note that they used groundwater from the mine site rather than purified water, so they were able to allow automatically for the effects of alkaline groundwater.

If the rate of groundwater flow is known or can be predicted accurately by a hydrogeological model (e.g., MODFLOW), workers using this method can get a good idea of what to expect from drainage water or pit lake water on a time scale of months or years. There still may be other, gradual processes that take place on a time scale of decades.

Some Definitions

Acid mine drainage (AMD) is defined by Federal law (US CFR 1986) as the discharge of waters from mining sites at pH 6 or less, with total acidity greater than total alkalinity.

Acid rock drainage (ARD) is the component of AMD that comes from rocks. Another component of AMD comes from processed materials such as tailings.

These definitions are different from the way these words are used in everyday speech by people in the mining industry. Most mining folks avoid the term "acid mine drainage" and refer to any acid drainage as "acid rock drainage."

Geochemical Cycles of Soil Nutrients

Soil is a system consisting of a mineral matrix supporting life forms ranging from bacteria through fungi, algae, and protozoans to large plants and animals. (See overhead.) This collection of organisms participates in a very complex ecology. The energy source is photosynthesis carried on both by microphytes (cyanobacteria and true algae) and macrophytes (multicelled plants). This energy is passes on to the other soil organisms by dead plant matter, by organisms consuming live plants (such as grazers and parasites), and by photosynthate secreted by roots. Secreted photosynthate is very important to many soil microorganisms.

The only thing wrong with the overhead is that it tends to minimize the role of microorganisms like bacteria, actinomycetes, fungi, and protozoa. Without the microorganisms there is no soil. Many of the soil's chemical processes are only carried out by microorganisms.

Now for a matter of terminology: I made a distinction a moment ago between bacteria and actinomycetes. To most biologists, actinomycetes are bacteria; they have the general properties of eubacteria — they are single-celled prokaryotes. However, actinomycetes are bacteria that mimic fungi in many ways.

• They take long, threadlike forms (hyphae), apparently for the purpose of obtaining water and nutrients in environments unfriendly to bacteria, just as fungi do.
• They fill ecological niches at basic or near-neutral pH that would be filled by fungi in more acidic soils.
• They tend to produce antibiotics (e.g., streptomycin) the way many fungi do.
• They follow the growth laws followed by fungi rather than those followed by most bacteria.
• They are intermediate in size between bacteria and fungi — much larger than bacteria, somewhat smaller than true fungi.

Many soil microbiologists consider actinomycetes as a class separate from bacteria because of their ecological function and their other similarities to fungi.

The biogeochemical cycle is the chemically and biologically catalyzed cycling of elements among cellular, water soluble, gaseous, and mineral forms.

Cycling of nutrients is very important to the soil ecology. Today we will look at cycling of four important nutrient elements: carbon, nitrogen, sulfur, and phosphorus.

Carbon

Carbon is important from two viewpoints: as the fundamental building block of living tissue and as the main form of energy used by all heterotrophs.

Some definitions:

Autotroph: An organism that produces its own organic carbon from inorganic sources (bicarbonate and CO₂). The main autotrophs are certain bacteria and all photosynthesizers.

Heterotroph: An organism that obtains its organic matter from other organisms rather than synthesizing it from inorganics. Many bacteria, all fungi, and animals are obligate heterotrophs.

Facultative heterotroph: An organism that can obtain organics produced by other organisms or, in a pinch, can make it from inorganic carbon.

Phototroph: An organism that obtains its energy from light. Plants are autotrophic phototrophs.

Chemotroph: An organism that gets its energy from chemical reactions (rather than from light).

Lithotroph: For the purposes of this class, this term is synonymous with heterotroph.

The Carbon Cycle

The following box diagram shows the principal transformations in the carbon biogeochemical cycle.

Atmospheric carbon dioxide is converted to plant organic matter. This is a two-way street, since plants can respire and release CO₂. Animals get all their organic carbon from plants and convert some to CO₂. Atmospheric, soil, and dissolved CO₂ are interchanged, and carbonates in water and soil interchange with CO₂ in those compartments.

Plants and animals exude or excrete organic matter to the soil, and when they die their residues in general are transferred to the soil. Some of these residues become microbial biomass. Abiotic residues (e.g., cellulose, sugars, etc.) may decompose, be converted to inorganic carbon, or become humic substances.

Terms:

Mineralization is conversion to inorganic form — CO₂, nitrates, ammonia, sulfides, etc.

Immobilization is conversion to organic forms that are unavailable to plants.

Most of the carbon in the world is in oceans as dissolved carbon dioxide, carbonates, and marine humus. Most of the carbon in forests is in the trees; forest soils run about 1% organic matter. Most of the carbon in grasslands is in soil organic matter, and these soils run to 3-6% organic matter, sometimes even more. (This is one of the reasons that grassland soils are usually good for farming, while cleared forest soil is usually mediocre.)

The rate of carbon fixation into organic matter roughly balances the overall rate of mineralization. Microorganisms have carbon efficiencies — rates of carbon conversion to biomass — between 10% and 70%. The rest of the carbon gets metabolized and converted to CO₂. Fungi are generally more efficient than bacteria.

1. The initial breakdown of plant organic matter is by fungi and actinomycetes. Reason: their hyphal form is more efficient for this purpose. Fungi are the primary cellulose degraders. They break down macromolecules such as cellulose, hemicellulose, and lignin.
2. Then other organisms get involved. Bacteria and fungi oxidize released organics. Secondary attack on these intermediate compounds results in both anabolism (tissue formation) and CO₂ formation.
3. The final stage is slow degradation of "recalcitrant" compounds and formation of humic matter.

Soil organic matter consists of

• biomass
• non-humic material (~70-75% of dead matter)
• humic material — polymeric, stable, and pigmented.

We saw the classification of humic matter in an earlier lecture. In general, forest soils are dominated by fulvic acids, while prairie soils are dominated by humic acids.

Lignin (Think of it as the "glue" that holds cellulose and hemicellulose fibers together.) is the primary source of humus. It consists partly of phenols, which are refractory compared to other organics.

Mean residence times of fulvic acids in soil are around 500 years, while those of humic acids run over 1,000 years.

In humic matter, the ratio of organic C to organic N, organic P, and total (organic + inorganic) S is 140 : 10 : 1.3 : 1.3.

The Nitrogen Cycle

Nitrogen is very important in soil. Plants usually get it from soil microbes. In terms of the amount of the element needed for life, it comes right after C, H, and O.

What makes nitrogen special?

• It has multiple stable redox states — -3, 0, +3, and +5.
• With an eight-electron span in its redox states, the available energy is enormous.
• There are many organic compounds in which nitrogen's properties are used — proteins, nucleic acids, amino sugars, vitamins, etc.

Thus nitrogen is important both for its redox properties (as an oxidizing and a reducing agent) and for its usefulness as a molecular building block.

The geochemical distribution of nitrogen is:

About 1/3 of soil nitrogen is usually nitrate. Plants take up nitrate more readily than ammonia nitrogen. Here is why:

1. There is plenty of cation competition for ammonium: K⁺, Ca²⁺, Mg²⁺, etc.
2. At the same time, the cations have to be balanced with anions, and nitrate is a handy anion.
3. An anion like nitrate moves more readily, by mass flow, than a cation, which tends to get hung up in clays.

Conversions of nitrogen

1. Assimilatory nitrate reduction

Plants and microorganisms can reduce nitrate and convert the nitrogen into ammonium and from there into organic forms — amino acids, nucleic acids, etc.

NO₃^– ¨ R–NH₂

where R–NH₂ is organic amino nitrogen. This is an especially important process in forest soils because, with the low organic content of the soil, there is little organic nitrogen present.

2. Dissimilatory nitrate reduction

NO₃^– + 2 CH₂O + 2 H⁺ ¨ NH₄⁺ + 2 CO₂ + H₂O

This is what many nitrate reducers and facultative anaerobes do; nitrate is for them an electron acceptor.

3. Denitrification

NO₃^– ¨ N₂

This can be a source of energy or just a way for organisms to get rid of nuisance nitrate. It is the main way in which nitrogen is lost from most soils. It takes place in several steps.

NO₃^– ¨ HNO₂ ¨ NO ¨ N₂O ¨ N₂

Any of the last 3 compounds can escape to the atmosphere as a gas.

Note that denitrification is an anaerobic process that consumes a compound made by aerobic processes. Thus it cannot be a continuous process. It happens when soil E_h drops, especially when the soil becomes saturated by rain or snowmelt or when the top layer of soil freezes and cuts off atmospheric oxygen. Dissimilatory reduction is similarly limited to times when E_h is low.

On the other hand, assimilatory nitrate reduction can be a continuous process because it takes place in the interior of a plant, in the chloroplasts (the plant's photosynthetic organs). Thus it is independent of soil E_h.

4. Nitrogen fixation

N₂ ¨ NH₄⁺

This is the main way by which nitrogen gets into soil by natural processes. It is a very energy-consumptive process. It is done exclusively by microorganisms — "blue-green algae" (which are actually cyanobacteria), Azotobacter species, Clostridium species, and various other bacteria, and actinomycetes. Some bacteria, such as Rhizobium species, live in pea-sized root nodules on plants and trade photosynthate for fixed nitrogen. Actinomycetes like Frankia do the same thing with other plants, only their nodules are the size of a potato. With this process being so energy-consumptive, it is a little surprising that Clostridium species, which are all strict anaerobes and in fact are fermenters, can fix nitrogen. (Fermentation is a very low-energy class of reactions.)

Lightning, atmospheric fallout from industry, volcanic inputs, acid rain, and synthetic fertilizers are other sources of soil nitrogen. Lightning makes nitric oxide in the atmosphere, which reaches the soil dissolved in rain.

N₂ + O₂ ¨ 2 NO

5. Nitrification

This is the energy source for a group of autotrophic aerobic bacteria as well as for some heterotrophic fungi.

In neutral to alkaline soils, this is a two-step process. The first step is mediated by Nitrosomonas species:

NH₄⁺ + 3/2 O₂ ¨ HNO₂ + H⁺ + H₂O

The next step is mediated by Nitrobacter species:

HNO₂ + 1/2 O₂ ¨ NO₃^– + H⁺

In acidic soils, especially forest soils, a similar process is carried out by heterotrophic ammonia oxidizers, mostly fungi. They do it two electrons at a time and start with organic N rather than ammonium:

R–NH₂ ¨ NH₂OH ¨ NOH ¨ HNO₂ ¨ NO₃^–

Some of the nitroxyl is lost as nitrous oxide:

2 NOH ¨ N₂O + H₂O

This may be a bypass mechanism used to avoid a buildup of nitrite. The last step, oxidation of nitrite to nitrate, is slow and is the most sensitive to O₂ limitations.

6. Nitrogen immobilization

This is the conversion of inorganic reduced nitrogen to organic nitrogen such as protein nitrogen:

NH₄⁺ ¨ R–NH₂

Plants and many microorganisms can do this.

7. Ammonia volatilization

This happens in alkaline soils:

NH₄⁺ + OH^– ¨ NH₃Ð + H₂O

8. Nitrogen mineralization

Organic nitrogen is converted to inorganic nitrogen, normally ammonia or ammonium N:

R–NH₂ ¨ NH₄⁺

This happens frequently in the process of decomposition of dead organisms and in the decomposition of organic waste matter such as excrement. For example, urea is decomposed by enzymes called ureases.

(NH₂)₂CO ¨ NH₄⁺ + other products

9. Nitrogen leaching

Ammonia and nitrate nitrogen can both be removed from the soil and transferred to surface and ground waters by leaching.

Summary of Nitrogen Conversions

• Nitrogen is fixed (converted from N₂ to inorganic N) by various biota and by some abiotic processes.
• It is mineralized through the processes of decay.
• It is oxidized by nitrifying organisms.
• It is reduced by assimilatory and dissimilatory reducers and by denitrifiers.
• It is lost to the atmosphere by the processes of denitrification, ammonia volatilization, and some side reactions involved in heterotrophic nitrification. (Fire also converts organic and inorganic nitrogen to N₂).
• It is lost to the hydrosphere by leaching.

All of these processes except leaching also take place in aquatic systems.

Nitrogen Pollution

The main problem is methemoglobinemia, a kind of poisoning similar to poisoning by carbon monoxide or cyanide. Nitrite is actually the toxic agent, but nitrates are reduced to nitrite in the intestine. Humans are susceptible to methemoglobinemia during the first three months of life, when they do not yet have the ability to destroy nitrite.

About the time the synthetic nitrogen fertilizers first came into use (1945), powdered baby formula also was on the market. In Des Moines, Iowa, a number of babies died from something called the "blue baby" condition. This was methemoglobinemia. Large amounts of nitrate had been leached from local soils into the surface water. The Des Moines River, which supplies drinking water for Des Moines, carried high levels of nitrate. Many babies fed with formula made up using city water died. This is the reason for the current MCL of 10 ppm nitrate in drinking water.

Some drinking water wells on the west side of Missoula had to be shut down a few years ago as septic tank effluents created high nitrate levels in the ground water.

Among domestic animals, ruminants and horses are susceptible to nitrate poisoning. Nitrate-rich water can kill them, as can green oats, which often contain high nitrate levels. Some green vegetables also can present a problem if grown in high-nitrate soils.

Other problems that stem from high nitrate and nitrite levels are nitrosamine formation in foods (which can cause cancer) and hemolytic anemia among kidney patients whose dialysis machines run with municipal water high in nitrate.

The Sulfur Cycle

For a long time many people in agriculture were not fully aware of sulfur's role as a plant nutrient. Two reasons for this:

• Many nitrogen and potassium fertilizers contained sulfate as a counterion (e.g., (NH₄)₂SO₄ and K₂SO₄), so their crops were getting sulfur anyway.
• Farms near large cities were receiving sulfur in the form of atmospheric fallout from coal and fuel oil combustion.

Sulfur is similar to nitrogen in having a wide range of possible redox states and in having an atmospheric component to its geochemical cycle. Common oxidation states for sulfur in the environment are -2, -1, 0, +4, and +6. Like nitrogen, sulfur is used by organisms both as a source of energy and as a molecular building block. Almost all proteins require sulfur in the form of the amino acids cysteine and/or methionine. Sulfate esters are also essential in many organisms.

Sulfur occurs in many mineral forms; pyrite and gypsum are two important ones. Plants can only take up sulfur as soluble sulfates.

Organic sulfur tends to be turned over quickly in soils; microbes use it or convert it. It consists of C-bonded S (such as S in proteins) and non-C-bonded S in which the sulfur is in sulfate esters of organic acids.

Inorganic sulfur is either soluble (as sulfate) or in "reservoirs" like pyrite and gypsum.

Atmospheric forms of sulfur that can be transported to soil include sulfur dioxide and hydrogen sulfide.

• SO₂ from volcanoes and industry rains out as sulfurous acid, H₂SO₃. Soil microbes quickly oxidize it to sulfate.
• Marshes, hot springs, and other low-E_h environments release H₂S to the air; it also enters the soil in rain.

Sulfur is lost from the soil mainly by

• leaching,
• gaseous emission of H₂S from anoxic soils,
• gaseous emission of organosulfur compounds like CS₂, dimethylsulfide, methyl mercaptan, etc.,
• crop removal, and
• fire.

Available sulfur in soil is commonly 200-500 m g S/g soil. Plants are 0.2%-0.5% sulfur. Sulfur is thus a macronutrient comparable to phosphorus.

Sulfur Transformations

1. Mineralization

Organic S is converted to inorganic sulfate. This is mostly a microbial process.

2. Immobilization (assimilatory reduction)

Inorganic S is converted to organic S.

3. Dissimilatory sulfur oxidation

This is the familiar set of reactions catalyzed by bacteria of the genus Thiobacillus and by a few other autotrophic genera. The bacteria are aerobic autotrophs that favor acid conditions. There are also many heterotrophic sulfur oxidizers active in soils, including both bacteria and fungi.

4. Dissimilatory sulfate reduction

These are the familiar reactions promoted by a set of anaerobic heterotrophs such as Desulfovibrio, Desulfotomaculum, and others. There are also a few anaerobic autotrophs that can perform this trick.

5. Leaching of soluble sulfates from soil.

This is a slower process than nitrogen leaching because sulfates in tend to be less soluble and because calcium tends to precipitate gypsum.

6. Sulfur volatilization

This happens by emission of H₂S and organic sulfides by microorganisms and plants and by emission of SO₂ and SO₃ through fire.

As with nitrogen, all of the above transformations except leaching also take place in aquatic systems.

Sulfur Pollution

Most of the time sulfur pollution is really acid pollution, as from acid rock drainage. Hydrogen sulfide is poisonous to all aerobic organisms, and localized H₂S emissions from industry or from anoxic waters and soils can be a health hazard at high concentrations and an aesthetic nuisance at low parts per billion. Sulfides in soil are poisonous to most plants. High sulfate levels in drinking water are mostly an aesthetic problem (hence the Secondary MCL of 250 mg./L) but fish and other aquatic life are not bothered much by sulfate.

The Phosphorus Cycle

Lithospheric abundance of phosphorus is about 1200 ppm. In soils its average abundance is 600 ppm.

Unlike C, N, and S, phosphorus has no gaseous component to its soil cycle, and it also has no redox component. Its only stable oxidation state in soil is +5, as phosphate minerals and phosphate esters.

Phosphorus is not very soluble under either acidic or basic conditions. Calcium tends to precipitate it in basic soils, and iron and aluminum do the same in acidic soils. Part of soil phosphorus is tightly bound to soil organic matter, and some is in very insoluble minerals. Mycorrhizal associations are very important in making phosphorus available.

Phosphorus is regarded as existing in several pools in soil that vary in their availability to plants and other organisms. These include

• the solution pool,
• the calcium phosphate pool,
• the iron and aluminum phosphate pool,
• the surface adsorbed pool,
• the microbial biomass pool, and
• the organic phosphorus pool.

The solution pool is normally a very small part of the total soil phosphorus. As a result, unlike N and S, phosphorus is very seldom lost by leaching. It is lost by erosion, however.

Between pH 5.5 and pH 7.9, calcium controls phosphate solubility. Soluble phosphate goes through a cascade of decreasingly soluble minerals until it finally forms apatite, the most stable calcium phosphate.

Brushite (also known as dicalcium phosphate), CaHPO₄ á 2 H₂O

ø

"Octacalcium phosphate" Ca₄H(PO₄)₃ á 2.5 H₂O

ø

b -Tricalcium phosphate Ca₃(PO₄)₂

ø

Apatite Ca₅(PO₄)₃X, X=F, Cl, Br, OH

In acidic oxisols (laterites), aluminum usually controls phosphorus solubility as variscite (AlPO₄ á 2 H₂O). In acidic but less weathered soils, iron (III) controls phosphorus as strengite (FePO₄ á 2 H₂O). In poorly drained (and thus low-E_h) acidic soils, vivianite (Fe₃(PO₄)₂ á 8 H₂O) can control P solubility.

At high pH, carbon dioxide starts to control phosphate solubility! Calcium phosphates are less stable than calcium carbonate above pH 7.9. If carbonate is abundant, phosphate is more soluble. If there is not enough carbonate to precipitate all the calcium, then apatite forms.

Phosphorus Pollution

Phosphorus is not toxic. Phosphorus pollution is a matter of having too much of a good thing. If too much phosphorus is present in a lake or river, an algal population explosion takes place, since phosphorus is often the limiting nutrient for algae. The great increase in organic matter can cause parts of a lake to go anoxic as dead algae use up oxygen. Phosphorus is a key player in eutrophication of lakes.

To previous lecture: Lecture No. 24. Special Topics II

To next lecture: Lecture No 26. Chlorinated Organics in Groundwater

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