Chapter 5
Minerals and the living world
When I was a student in the 1960s, apart from the fossil record, the geological and the biological domains were regarded as essentially separate. In our chemistry classes, we were not taught organic chemistry as it was largely regarded as irrelevant for our studies of minerals and rocks. Today the ‘geo-bio’ interface is one of the most active areas of research in the natural sciences with major research programmes and new journals with titles such as Geobiology, Geomicrobiology Journal, and Global Biogeochemical Cycles. There are no better examples of ‘modern mineralogy’ than those provided by the work being done on mineral–microbe interactions, biomineralization, minerals and the human body, and minerals and human health.
Minerals and microbes
The environmental electron microscope picture used in Chapter 2 to illustrate this method of studying minerals (Figure 8) shows several bacteria of the species Geobacter sulfurreducens on an iron oxide mineral substrate. These bacteria are not simply sitting on this mineral surface, they interact with it because it is their method of ‘respiration’, just as much as breathing in oxygen is ours. The transfer of electrons between the microbe and the mineral, in this case, brings about the reduction of the iron in this mineral from the ferric (Fe3+) to the ferrous (Fe2+) form. As illustrated in Figure 16, this can be done by this single-celled organism being directly in contact with the mineral or by an organic molecule (such as a humic compound) ‘shuttling’ back and forth between the mineral and the microbe, resulting in transfer of the electron. Also involved here is organic matter (in this case it is acetate) which is oxidized to CO2. This is in effect the ‘food’ consumed by this organism. A very important consequence of the microbial reduction of the iron in this oxide is that it releases the iron into solution (the ferrous iron is soluble unlike the highly insoluble ferric form). This also means that any contaminants trapped within the oxide or attached to its surface will also be released into the surrounding waters.
The reduction of iron by Geobacter is just one example of how important mineral–microbe interactions can be for the cycling of the elements in systems at or near the surface of the Earth. Other organisms can bring about the oxidation of ferrous iron in minerals, and there are numerous other examples of microorganisms controlling the reduction–oxidation (‘redox’) chemistry or other variables in a solution in contact with a mineral, such as the acidity. These changes may be responsible for the formation of minerals or their destruction. Good examples are provided by the iron sulphides. In estuaries or shelf areas just offshore where fine grained sediments have been deposited, a foot or so beneath the surface of the sediment, bacteria (such as the Thiobacilli) are active in reducing the dissolved sulphate (SO4 2−)—always present in seawater—to sulphide (S2−); this sulphide will then react to form very insoluble iron sulphide minerals. The first formed mineral is mackinawite (FeS) but, with time, the mackinawite reacts further with sulphur to form pyrite (FeS2). If other metals are present, such as copper or zinc, they will also react to form sulphides.
The reverse of this process can also be promoted by bacteria. In this case, metal sulphide minerals such as pyrite exposed at or near the Earth’s surface by uplift and weathering of a sulphide ore deposit may break down to form sulphates (such as FeSO4.7H2O, melanterite) in a process of bacterial oxidation that is greatly accelerated by the activities of other families of organisms (such as Acidithiobacillus ferrooxidans and Leptospirillum). For many years bacteria have been used in the mining industry to help in the breakdown of sulphide ores so as to release, and then recover, the metals.
16. A schematic diagram showing (top) direct reduction of a ferric oxide mineral through contact with a bacterium and (below) the same process using an electron shuttle
Minerals and life
We now live in what geologists call the Phanerozoic Era, a stretch of time which began at the start of the Cambrian Period 541 million years ago. The word Phanerozoic is derived from the Greek meaning ‘visible life’ and is a reference to the first clear appearance of fossils which is in the rocks of this age. Although for the early geologists, there was no evidence of life in rocks older than the Cambrian (i.e. the Precambrian) many scientists, including Charles Darwin, argued that such evidence must exist but just had not been found. Trilobites and other relatively advanced creatures were well known from rocks of Cambrian age, even in Darwin’s time, and must have evolved from ancestors of appreciably greater age. We now know that many organisms did exist before the Cambrian, but they were soft-bodied and were not preserved except under extremely rare conditions in rocks not known to the earlier workers.
The start of the Cambrian saw the evolutionary development of organisms with hard parts that were readily preserved in the fossil record. Then, around 520 million years ago, there was a development of life forms over a period of 10 million years of rapid evolution known as the ‘Cambrian Explosion’. Much of this ‘explosion’ had to do with the evolutionary development of organisms with hard parts, with factors such as the development of predation leading to ‘arms races’ with some hard parts evolving as a defensive armour (shells) and others for attack (teeth). These hard parts were composed of minerals as they still are in the evolutionary descendants of those first shelly creatures or those with external skeletons. The minerals used by organisms in this way form some extraordinarily complex structures. These are biominerals and the remarkable processes by which living organisms produce them we call biomineralization. A relatively small number of minerals are formed in this way; mainly they are forms of calcium carbonate (calcite, aragonite), of calcium phosphate (apatite), and of silica, but they can be responsible for vast rock formations. Many of the limestones found through much of the geological column are the remains of great coral reefs similar in scale to the present-day Great Barrier Reef off the coast of Australia. Other limestones are largely composed of beds of shells: the ancestors of present day oysters.
A remarkable example of the capacity of living organisms to produce biominerals on a large scale is provided by coccoliths. The chalk rock familiar from the south of England, responsible for the ‘White Cliffs of Dover’, is 95–99 per cent composed of these microscopic plates of calcite which were used to form a protective armour around unicellular planktonic algae (coccolithophorids). As this example shows, as well as relatively large organisms, biomineralization is responsible for the hard parts of numerous microorganisms, many of which have delicate structures of great beauty. A good example is provided by the radiolaria (see Figure 17) which have skeletons of poorly crystalline (‘opaline’) silica. These free-floating single-celled organisms are found in the upper few hundred metres of the water column in the oceans, seaward of the continental slope. After death, their skeletal remains sink through the water column to contribute to the siliceous radiolarian oozes found on the ocean floors in equatorial latitudes. The fossilized remains of radiolaria are preserved in cherts and flints, which are rocks comprised of a microcrystalline variety of quartz. The key question in the study of biominerals is: ‘How could these elaborate structures be produced by the organisms concerned’. Here, once again, the mineral and living worlds are intimately associated.
Two distinct mechanisms are proposed for biomineralization. In ‘biologically induced biomineralization’, the minerals form without apparent regulatory control, and as incidental by-products of the interactions between an organism and its environment. The minerals produced are very similar in their chemistries and crystal habits to those formed without any biological involvement. By contrast, there is ‘biologically controlled biomineralization’ in which the organism precipitates minerals that have specific physiological and structural roles. In this case, minerals can be formed within the organism even when the overall conditions in the solution surrounding it are not favourable for their formation.
17. The ‘opaline’ silica skeleton of a radiolarian
Biologically controlled mineralization is a complex topic of great current research interest and one where we still have much to learn. For example, it seems that the formation of mineralized tissues is often closely linked to organic compounds that are concentrated in specialized regions (‘compartments’) within the organism during mineral formation. However, isolating those organics and assigning each one a particular function is problematic, particularly as isolating and removing any particular molecule may actually disrupt its function. Here, methods need to be developed for studying the relevant systems within the living organism (i.e. ‘in vivo’). The roles of amorphous and transient metastable mineral phases during biomineralization are important areas of investigation, as it appears that many organisms use amorphous precursors to mineralization. There is much to be learnt about how biomolecules promote the transition from amorphous to crystalline mineral whilst controlling the development of particular crystalline forms, habits, and faces.
18. A double chain of magnetite crystals in a magnetotactic bacterium
Amongst the most remarkable examples of organisms producing a mineral to serve a specific function are the magnetotactic bacteria. Here, the bacterium concerned produces a chain of perfect crystals (see Figure 18), most commonly of magnetite (Fe3O4), which make use of the magnetic properties of that mineral. It seems that these organisms use the magnetite to become aligned in relation to the Earth’s magnetic field and, therefore, in the most ‘advantageous’ position in relation to the environment at the sediment–water interface. The mineral greigite (Fe3S4) is found in other magnetotactic bacteria. It has very similar magnetic properties to magnetite but is stable in oxygen-poor, sulphur-rich sedimentary environments. The use of magnetic minerals for a specific function is also well known in a number of much larger organisms; birds in particular are known to use ‘bio-magnetite’ for navigation purposes.
Minerals and human health
Minerals, or rather the chemical elements from which they are made, are essential for humans but can also pose some of the greatest threats to health. Out of the 90 naturally occurring chemical elements on Earth, 22 are needed by a healthy human body and the great majority of those come originally from mineral sources. Deficiencies in the supply of such elements can lead to arrested development in children or pathological conditions in adults. Some of these requirements are widely appreciated, such as the need for calcium and phosphorous to form hydroxylapatite, Ca5(PO4)3(OH), the main mineral matter of bones and teeth. As well as the 22 essential chemical elements, more than 20 biominerals have been identified within the human body, with apatite being the most common. The rest include other calcium phosphates, along with carbonates and oxalates, again mostly of calcium and, in some cases, magnesium. Calcite, the mineral that dominates as a biomineral in so many organisms, does occur in the human body, but only in one very specialized site, in the maculae portion of the inner ear. Human biominerals can be divided into those which are an essential part of the body’s systems, such as the material found in bones and teeth, and those which are unexpected and undesired (‘pathological’) mineral deposits. Although we talk of bone matter being dominantly hydroxylapatite, various substitutions for the calcium, phosphate, and hydroxyl ions in the structure leads to a much more complex chemistry, as suggested by a formula for ‘bioapatite’ of:
(Ca,Na,H2O,ϒ )10(PO4,HPO4,CO3)6(OH,F,Cl,H2O,CO3,O,ϒ)2
where ϒ signifies a site in the crystal that would normally contain an atom but is empty (or ‘vacant’). Bioapatite may deposit in soft tissues or organs throughout the body, particularly causing problems in the cardiovascular system. Deposits of mineral matter can also build up in other parts of the body where they cause serious health problems. Examples of this are the ‘stones’ which can grow in human organs such as the kidneys or the gall bladder. In the kidneys, the stones are composed of the calcium oxalate minerals whewellite and weddellite and their formation has been linked to high levels of calcium in the urine. There are also examples of non-calcareous renal stones causing the pain in about 10 per cent of cases, and associated with the magnesium ammonium phosphate mineral struvite. These are related, in turn, to urinary infections caused by bacteria such as Escherichia coli. Pancreatic ‘stones’ or calcifications are mainly calcite, which blocks ducts leading to and away from this organ. Other pathogenic deposits include the crystals of monosodium urate monohydrate, which can form in the joint spaces of the extremities, causing gout, whereas crystalline deposits of three types (apatites, uric acids, and pyrophosphates) are associated with osteoarthritis.
Mineral derived materials can pose a serious threat to human health through their release into the food chain from poorly controlled mining or industrial waste disposal practices, or from abandoned industrial sites and mines. The materials involved can be toxic metals such as lead, cadmium, or mercury, or metalloids such as arsenic, antimony, or selenium. Our discussion in Chapter 4 of the release and transport of contaminants as part of the cycling of minerals at the Earth’s surface is important here, and the extraordinary story of arsenic is described in Box 4. Three other special cases are worth discussing. One centres on the chemical property of radioactivity and the other two on the physical properties of particle size and shape. The health issues regarding radioactivity are associated with long-standing debates about the safety of nuclear power installations, the safe disposal of nuclear wastes, and the control of ‘legacy’ wastes from the former mining and processing of uranium ores.
Uranium and thorium are the important radioactive elements that occur in nature as minerals, and it is uranium that is mined for use in power generation, particularly as the oxide mineral uraninite (UO2). Uranium has a complex chemistry that leads to a large number of minerals being formed by the alteration (especially the weathering) of uraninite. There are also the products of the radioactive decay of uranium from its ores such as the radioactive gas, radon. The damage to health caused by the exposure to radioactive minerals or their breakdown products comes both from exposure to the radiation and ingestion of material into the lungs or via the food chain. However, the evaluation of the health risk is complicated by the wide variation in decay times of different radioactive isotopes. Some, like the isotopes of uranium, remain radioactive for millions of years, whereas others are no longer a threat after a few weeks or even days.
Box 4 Arsenic—the great poisoner
Throughout history, arsenic has been the poison of choice for murderers and assassins. Long before forensic analysis could detect even minute amounts of arsenic in a body, it featured in the power struggles of Imperial Rome and Renaissance Italy. One might imagine that arsenic poisoning leading to sickness and death is a fate no longer suffered by humans, but arsenic is currently responsible for what has been described as the ‘greatest poisoning of a population in history’. In countries including Bangladesh, India (Bengal), and Vietnam, millions of people are affected through drinking water that contains arsenic concentrations above the World Health Organization ‘acceptable’ maximum level of 10 parts in a billion. The problem with arsenic is that it can accumulate in the body over many years. So where does this arsenic come from?
The story here is one of ‘good intentions’. In attempts to reduce the occurrence of water-borne diseases, such as cholera, arising from the use of surface waters for human consumption in large areas of Bangladesh and Bengal, numerous wells were sunk to tap the water available in shallow aquifers. The water trapped in the aquifer sediments, consisting of fine grained mineral matter brought down to densely populated regions from the rapidly eroding Himalayas in great rivers like the Ganges, are the source of the arsenic. Arsenic was probably transported sorbed to surfaces or incorporated within very fine grained minerals such as iron oxides and hydroxides. Release of this arsenic appears to be associated with the microbial reduction of insoluble ferric iron to the soluble ferrous iron form, and of reduction of arsenic (from the As5+ ion to the more mobile As3+). This microbial activity also requires a supply of organic carbon. Much recent research has been aimed at remediation. Strategies have included drilling into deeper aquifers, manipulating the chemistry and microbiology within the aquifer, or using the iron hydroxides formed on corroding metallic iron filings to treat the water and remove the arsenic at the well-head.
Although many dangerous radioactive elements such as plutonium, neptunium, and technetium occur only as products of the nuclear industries, they can interact with common minerals such as clays and iron oxides, becoming incorporated in their structures in ways that may lead either to their concentration or their dispersal. The nuclear metals participate in the cycling of minerals at the Earth’s surface, particularly being involved in sorption and desorption processes, as described in Chapter 4.
There are two great concerns over human health in the context of the nuclear industries. First, there are the dangers posed by natural (or human-made, such as acts of terror) disasters, as happened at Fukushima, Japan, in 2011 when the power plant was severely damaged by a tsunami. Secondly, there is safe disposal of the most toxic of the nuclear wastes. It is sobering to recall that just one litre of such ‘high-level’ wastes in liquid form, if distributed evenly throughout the global population would inflict a lethal dose of radiation on every person on the planet. High-level wastes, defined as those in which the level of radioactivity is over a million times that regarded as acceptable for human exposure, contribute only one-tenth of 1 per cent of the volume of wastes generated, whilst contributing 95 per cent of the radioactivity.
The problems involved in the safe disposal of radioactive wastes involve minerals in two particular ways. The first is concerned with transformation of the waste into a form where it is immobilized, i.e. held in a solid material that is as resistant as possible to being broken down to release radioactive material into the environment. This ‘wasteform’ needs to be resistant to attack from solutions of widely varying chemistries. Although synthetic glasses are commonly used in this way, an alternative strategy involves incorporating the radioactive elements into synthetic minerals of the kind known to accommodate such elements into their crystal structures. For example, Australian scientists have developed a synthetic rock (known as SYNROC) composed of a group of titanium-bearing minerals such as zirconolite (CaZrTi2O7) and perovskite (CaTiO4). The former can act as a host for uranium, thorium, plutonium, and related metals, and the latter as host for radioactive strontium, sodium, and rare earth elements.
The second role minerals can play arises if the wasteform does break down and release its highly toxic components. Commonly it involves surrounding the wasteform, contained within stainless steel canisters, with mineral matter of the kind that would readily take up toxic contaminants from any escaping solutions. Candidates here include various clay minerals and zeolites; minerals known to have high capacities for sorption of metals from solution.
These first lines of defence against the escape of radioactive materials are called ‘near field’; beyond that, the ‘far field’ is determined by the geology (and hence mineralogy) of any disposal site where wastes are buried. The minerals present will be critical for the choice of a suitable site and likely dominated by those impervious to fluids, or able to take up any escaping contaminants.
Knowledge of the behaviour of key radioactive species in all of the near- and far-field systems is essential information for assessing (and minimizing) the risks involved in any radioactive waste disposal strategy. This includes modelling the interactions between possible contaminants and any minerals they may encounter, so as to properly understand the potential mobility of any escaping contaminants.
The health impact of another group of minerals is entirely to do with the shape (more correctly termed ‘habit’) of the crystals involved. ‘Asbestos’ is not itself a mineral name but a term used to label a small number of minerals that occur with a very distinctive habit (called ‘asbestiform’): individual crystals of the minerals grow as fibres because they are so elongated along one axis. In the extreme case, they resemble other fibrous materials such as cotton. Indeed, some mined asbestos has been woven so as to make heat and flame resistant fabrics used for gloves or suits.
Although there are six minerals that can be asbestiform, over 90 per cent of the asbestos mined is so-called ‘white asbestos’ and made up of a mineral named chrysotile, which is a hydrate magnesium silicate member of a clay mineral family called the serpentines. (An electron microscope image of a cross-section through a chrysotile fibre is shown in Figure 7c.) Other forms of asbestos which are also mined are fibrous members of the amphibole family referred to as ‘blue asbestos’ (crocidolite) and ‘brown asbestos’ (amosite).
The dangers to health posed by asbestos are mainly associated with ingestion into the lungs. There are three diseases associated with asbestos exposure: lung cancer, mesothelioma (cancer of the pleural and peritoneal membranes), and asbestosis, where the lung tissue becomes fibrous and ceases to function properly. The precise roles of the different kinds of asbestos (and other ‘elongate’ minerals) in causing lung disease have long been controversial. However, it does seem that the ‘white asbestos’ (crysotile) is less hazardous than the other (amphibole family) types. It also seems that the dangers posed by low-level exposure (for example, to the occupants where asbestos has been used in a building, such as a school) are negligible compared to the exposure suffered by miners and mineral processors in the asbestos industry.
The dangers posed by asbestos have been known for decades and legislation limiting human exposure is now widespread. One other example of a health impact that I will discuss has only come to public attention in the last few years. It concerns nanomaterials and nanotechnology, a topic we touched upon in Chapter 4. Various scare stories began to appear in the popular press once the industrial production of synthetic nanomaterials got under way. One story, inaccurately attributed to HRH Prince Charles, heir to the British throne, was that nanoscale robots would take over the world and transform everything into ‘grey goo’. Such ideas may have a place in science fiction stories but show no signs whatever of becoming a reality. There is some concern, however, arising from the limited knowledge we have of the properties of many nanomaterials, and their possible impact on the environment including biological systems and, ultimately, on human health.
The health and safety issues mainly concern ‘free’ manufactured nanoparticles rather than those incorporated into new materials or devices. As discussed in Chapter 4, the properties of nanoparticles are commonly very different from their larger grain-size equivalents. So, the absence of any possible adverse effects cannot be inferred from the behaviour of macro-sized equivalents. The extremely small size of nanomaterials means that they are much more likely to be taken up by the human body. However, much remains to be learnt about their behaviour and interaction with biological processes in all living organisms. To properly assess the health hazards posed by manufactured nanoparticles, the whole lifecycle of these particles, from fabrication to ultimate disposal, needs to be evaluated. This includes, for example, their interactions with the surfaces of minerals when, if released into the environment, they become part of the cycling discussed in Chapter 4.