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2?Brief Description of Bioextraction Process

2?Brief Description of Bioextraction Process

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Bioextraction: The Interface of Biotechnology and Green Chemistry


relatively new and growing technology uses natural processes to break down,

stabilize, or accumulate pollutants and for extraction of metals [3]. It basically

incorporates two phenomena:

• Phytoextraction

• Biomining

Phytoextraction is the removal of pollutants by the roots of plants, followed by

translocation to aboveground plant tissues, which are subsequently harvested.

Biomining is the extraction of metals by the help of naturally growing thermal

sensitive microbes.

14.2.1 Phytoextraction

Contamination of soils with toxic metals has often resulted from human activities,

especially those related to mining, industrial emissions, disposal or leakage of

industrial wastes, application of sewage sludge to agricultural soils, manure, fertilizer, and pesticide use. Excessive metal concentration in soil poses significant

hazard to human, animal and plant health, and to the environment. The aim of

phytoextraction is to reduce the concentration of metals in contaminated soils to

regulatory levels within a reasonable time frame. This extraction process depends

on the ability of selected plants to grow and accumulate metals under the specific

climatic and soil conditions of the site being remediated.

It uses plants to remove metals from soils and to transport and concentrate them

in above-ground biomass [4]. In this process, plant roots sorb the contaminants

along with other nutrients and water. The contaminant mass is not destroyed but

ends up in the plant’s shoots and leaves. This method is used primarily for wastes

containing metals where water-soluble metals are taken up by plant species

selected for their ability to take up large quantities of metals. The metals stored in

the plant’s aerial shoots are harvested and smelted for potential metal recycling/

recovery which were earlier disposed off as a hazardous waste. As a general rule,

readily bio-available metals for plant uptake include cadmium, nickel, zinc,

arsenic, selenium, and copper. Moderately bio-available metals are cobalt,

manganese, and iron. They can be made much more bio-available by the addition

of chelating agents to soils.

Phytoextraction has been growing rapidly in popularity worldwide for the last

20 years or so. In general, this process has been tried more often for extracting

heavy metals than for organics. The plants absorb contaminants through the root

system and store them in the root biomass and/or transport them up into the stems

and/or leaves. A living plant may continue to absorb contaminants until it is

harvested. After harvest, a lower level of the contaminant will remain in the soil,

so the growth/harvest cycle must usually be repeated through several crops to

achieve a significant cleanup. After the process, the cleaned soil can support other



R. K. Sharma et al.

Fig. 14.1 Nickel hyperaccumulator (Alyssum


There are two main categories of plants to clean up toxic metals from soil:

• Metal hyper-accumulator plants

• High biomass plants Metal Hyper-Accumulator Plants

They take up significant amounts of metal from contaminated soil but their low

biomass production tends to limit their phytoextraction ability. As these plants

have natural ability to extract metal ions, so it is known as natural phytoextraction. Hyper-accumulating plants have natural ability to extract high amounts

of metals from soil, have efficient mechanism to translocate metals from roots to

shoots, and can accumulate and tolerate high metal concentrations due to inherent

mechanisms to detoxify metals in the tissues. Metal hyper-accumulators have the

extraordinary capacity to accumulate high concentrations of heavy metals in the

above-ground biomass. By virtue of this remarkable characteristic, phytoextraction

is economically viable alternative to the extreme expense of conventional remediation methods [5].

Example: Alyssum lesbiacum as Ni hyper-accumulator, Thlaspi caerulescens/

Alpine pennycress as Zn/Cd hyper-accumulator (Figs. 14.1, 14.2). High Biomass Plants

They are fast growing plants that can be easily cultivated using established

agronomic practices which compensate for their relatively low capacity of metal

accumulation. Their metal uptake capacity can further be enhanced by adding


Bioextraction: The Interface of Biotechnology and Green Chemistry


Fig. 14.2 a Zinc/Cadmium hyper-accumulator (Thlaspi caerulescens). b Fluorescence image of

Zn hyperaccumulation in leaf of Thlaspi caerulescens

Fig. 14.3 Indian Mustard

conditioning fluid containing a chelator or another agent to soil to upsurge metal

solubility or mobilization so that the plants can absorb them more easily. This is

known as chemically induced/assisted phytoextraction. Afterwards, the soluble

metal (desorbed from soil particles) is easily transported to roots surface via

diffusion and translocated from roots to shoots. Complexing with organic

ligands, which may occur at any point along the transport pathway, converts the

metal into less toxic form thus conferring high metal tolerance in biomass plants

[5]. A wide range of synthetic chelates [e.g.Ethylenediaminetetraacetic acid

(EDTA), 1,2-cyclohexylenedinitrilotetraacetic acid (CDTA), diethylenetriaminepentaacetic acid (DTPA), EGTA, EDHA, hydroxyethylethylenediaminetriacetic

acid (HEDTA), nitriloacetic acid (NTA), and organic acids (e.g. citric acid,

oxalic acid, malic acid) are used for enhancing root uptake and translocation of

metal contaminants from soil to biomass plants, thereby improving phytoextraction [6] (Fig. 14.3, 14.4, 14.5).


R. K. Sharma et al.

Fig. 14.4 Willows

Fig. 14.5 Poplars

Example: Indian mustard, sunflower, and maize as high biomass crop plants,

willows, and poplars as high biomass trees

Advantages. The main advantage of phytoextraction is environmental friendliness. Traditional methods that are used for cleaning up heavy metal contaminated

soil disrupt the soil structure and reduce its productivity, whereas phytoextraction

can clean up the soil without causing any kind of harm to soil quality. Add on

benefit of phytoextraction is that it is less expensive than any other clean-up

process (Fig. 14.6) (Table 14.1).


Bioextraction: The Interface of Biotechnology and Green Chemistry


Fig. 14.6 Phytoextraction

Table 14.1 Main characteristics of the two categories of plants for phytoextraction of metals [4]:

Chemically assisted phytoextraction

Natural phytoextraction

Plants are normally metal excluders

Fast growing, high biomass plants

Synthetic chelators and organic acids are used

to enhance metal uptake

Efficient translocation of metals from roots to


Low tolerance to metals, the increase in

absorption leads to plant death

Risk of leaching of metal chelates to


Plants naturally hyper-accumulate metals

Slow growing, low biomass production

Natural ability to extract high amount of metals

from soils

Chemical amendments increase the metal

transfer from roots to shoots

High tolerance, survival with high

concentrations of metals in tissues

No environmental drawback regarding leaching

of metals

14.2.2 Biomining

For centuries people have been using microbes to their advantage, turning grapes

into wine, milk into cheese, and cabbage into sauerkraut. People benefit from what

microbes do naturally: They eat and digest organic compounds, changing the

chemical makeup of one product and turning it into a completely different yet tasty

food or drink. Now microbes, in form of biomining, are providing efficient helping

hand for extraction of heavy metals from sub-graded ores and minerals (Fig. 14.7).

Biomining is the interaction between metals and microbes with the specific aim

of converting insoluble metal sulfides to soluble metal sulfates. Bioleaching has

been defined as the dissolution of metals from their mineral sources by certain

naturally occurring microorganisms or the use of microorganisms to transform

elements so that the elements can be extracted from a material when water is

filtered through it. So, it is the application of microbial process in the mining

industry for economic recovery on a large scale [7] (Fig. 14.8).


R. K. Sharma et al.

Mineral Ores








H 2 O/O 2




Solubilized metals

PO 43SO32Nutrients for the Microbes

Fig. 14.7 Biomining

In short, biomining is a term that describes the processing of metal containing

ores and concentrates of metal containing ores using microbiological technology.

It is often called bioleaching.

By convention bioleaching has been divided into two approaches:

• Direct bioleaching

• Indirect bioleaching

Direct bioleaching entails an enzymatic attack by the bacteria on components of

the mineral that are susceptible to oxidation. In the process of obtaining energy

from the inorganic material the bacteria cause electrons to be transferred from iron

or sulfur to oxygen. In many cases the more oxidized product is more soluble. It

should be noted that the inorganic ions never enter the bacterial cell; the electrons

released by the oxidation reaction are transported through a protein system in the

cell membrane and then (in aerobic organisms) to oxygen atoms, forming water.

The transferred electrons give up energy, which is coupled to the formation of

adenosine triphosphate (ATP), the energy currency of the cell.

Indirect bioleaching, in contrast, does not proceed through a frontal attack by

the bacteria on the atomic structure of the mineral. Instead the bacteria generate

ferric iron by oxidizing soluble, ferrous iron; ferric iron in turn is a powerful

oxidizing agent that reacts with other metals, transforming them into the soluble

oxidized form in a sulfuric acid solution. In this reaction ferrous iron is again

produced and is rapidly reoxidized by the bacteria. Indirect bioleaching is usually

referred to as bacterially assisted leaching. In an acidic solution without the

bacteria, ferrous iron is stable and leaching mediated by ferric iron would be slow.

T ferrooxidans can accelerate such an oxidation reaction by a factor of more than a



Bioextraction: The Interface of Biotechnology and Green Chemistry


Fig. 14.8 Electron micrographs of typical bacteria used in biomining a Leptospirillum

ferrooxidans. b Thiobacillus ferrooxidans [7]

Biomining is applied using four different engineered methods:

Dump bioleaching

Heap bioleaching

Heap minerals biooxidation

Stirred-tank bioleaching

Minerals biooxidation

Dump bioleaching extracts copper from sulfide ores that are too low grade to

process by any other method. This process has been used since the mid-1950s.

Heap bioleaching, which has been used since the 1980s, extracts copper from

crushed sulfide minerals placed on engineered pads.

Heap minerals biooxidation pretreats gold ores in which the gold particles are

locked in sulfide minerals, significantly enhancing gold recovery.

Stirred-tank bioleaching extracts base metals from concentrates of metal

containing sulfide ores.

Stirred-tank minerals biooxidation enhances gold recovery from mineral

concentrates in which the gold is locked in sulfide minerals [8].


The advantages of biomining process over chemical leaching are:

(i) Biomining is a way to exploit low grade ores and mineral resources located in

remote areas that would otherwise be too expensive to mine.

(ii) It is more environmentally friendly than the conventional (smelting) method,

since it uses less energy and does not produce SO2 emissions. This also

translates into profit, as the companies have to spend huge sums finding ways

of limiting their SO2 emissions.

(iii) Less landscape damage occurs, since the bacteria grow naturally. Native

bacteria can operate over a wide temperature range between 20 and 55°C.

Other materials for the process are also natural such as air and water.


R. K. Sharma et al.

(iv) The bacteria breed on their own, i.e. they are self-sustaining. Since there is no

need to pay for heating and chemicals required in a conventional operation,

companies may be able to reduce the price of metal production by nearly a half.

(v) It is a less energy intensive process.

(vi) It is simpler and therefore cheaper to operate and maintain, as no technical

specialist is needed to operate complex chemical plants [9].

(vii) Even the dumps left behind after traditional mining processes can be

reprocessed to extract residual metal [10].

So, biomining is the process of extracting valuable metals from ores and mine

tailings with the assistance of microorganisms. It is a green technology that can

help mine valuable metals with minimal impact on the environment. It requires

low energy, causes low gaseous emission and is not labor intensive.

14.3 Contribution of Microbes/Microorganisms

in Bioextraction

The microbes are single-celled organisms that multiply by simple cell division and

derive energy for growth and cell functioning by oxidizing iron and sulfur. Oxidation involves the removal of electrons from a substance. In biomining process,

the microbes remove electrons from dissolved iron (ferrous iron) converting it to

another form of iron (ferric iron); electrons are removed from sulfur converting it

to sulfuric acid. They obtain carbon for their cellular bodies from carbon dioxide

(CO2) in the atmosphere and also require a sulfuric acid environment to grow. This

acidic environment is helpful in growth of these microorganisms but acidity must

be less than pH 2.5, which is more acidic than vinegar.

The biomining microorganisms do not cause diseases in humans, animals, or

plants. Because their food source is inorganic (sulfur and iron) and because they

must live in a sulfuric acid environment, they cannot survive in or on plants and

animals. These microbes are conveniently grouped within temperature ranges at

which they grow and where they are found in the natural environment:

• Ambient temperature bacteria (mesophiles)

• Moderately-thermophilic (heat-loving) bacteria

• Extremely-thermophilic (heat-loving) bacteria

Ambient temperature bacteria (mesophiles). These cylindrical-shaped biomining

bacteria are about 1 lm long and ‘ lm in diameter (1 lm is 4/100,000 of an inch).

About 1,500 of these bacteria could lay end-to-end across a pin head. They only

grow and function from 10 to 40°C (50 to 104°F). If the temperature is too low,

these bacteria become dormant. If the temperature exceeds 45°C (113°F), the

organisms die as their proteins coagulate similar to cooking an egg. Acidithiobacillus ferrooxidans belong to this group of bacteria. Others include Leptospirillum ferrooxidans and species of Ferroplasma.


Bioextraction: The Interface of Biotechnology and Green Chemistry


Moderately-thermophilic (heat-loving) bacteria. These bacteria are similar to

the ‘‘mesophilic’’ biomining bacteria, except they are somewhat larger in length —

about 2–5 lm long and they only grow and perform when the temperature exceeds

40°C (104°F). The moderate thermophiles die when the temperature exceeds 60°C

(140°F). Examples of moderate thermophiles are species of Sulfobacillus and

Acidithiobacillus caldus.

Extremely-thermophilic Archaea. While similar in size (one micrometer in

diameter) to ambient temperature bacteria, Archaea have a different molecular

organization. In the tree of life, Archaea occupy the lowest branch and are extant

members of an offshoot of primitive microbes. They have a spherical shape and

characteristically lack a rigid cell wall, rather the contents of the single cell are

enclosed by a membrane. These microbes, nevertheless, are extremely robust

growing and performing only at temperatures between 60 (140°F) and 85°C

(185°F). Examples of extremely-thermophilic Archaea used in biomining are

Acidianus brierleyi, Sulfolobus metallicus and Metallosphaera sedula [8].

14.3.1 Role of Microbes in Biomining

Some microbes float freely in the solution around the minerals and some attach

themselves to the mineral particles forming a biofilm. The microbes, whether they

are freely floating or whether they are in the biofilm, continuously devour their

food sources—iron (chemically represented as Fe2+) and sulfur. The product of the

microbial conversion of iron is ‘‘ferric iron’’, chemically represented as ‘‘Fe3+’’.

Ferric iron is a powerful oxidizing agent, corroding metal sulfide minerals

(for example, pyrite, arsenopyrite, chalcocite, and sphalerite) and degrading them

into a dissolved metal, such as copper, zinc, and more iron—the latter is the food

source for the microbes.

The reaction of the biological oxidation involved in leaching of a mineral

sulfide is

MS ỵ 2O2 ! MSO4

where, M is a bivalent metal.

There are two major mechanisms involved in microbial metal solubilization of

sulfide minerals. One is a direct mechanism that involves physical contact of the

organism with the insoluble sulfide.

Microorganisms oxidize the metal sulfides obtaining electrons directly from the

reduced minerals. Another, indirect mechanism, involves the ferric-ferrous cycle.

The oxidation of reduced metals is mediated by the ferric (III) ion and this is

formed by microbial oxidation of ferrous (II) ion present in the minerals. Ferric

(III) ion acts as an oxidant and oxidizes metal sulfides and is reduced to ferrous (II)

ion that, in turn, can be microbially oxidized. Both direct and indirect mechanisms

of bacterial leaching are shown schematically in Fig. 14.9.

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2?Brief Description of Bioextraction Process

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