Environmental Biotechnology Theory and Application Gareth M. Evans Judith C. Furlong University of Durham, UK and Taeus Biotech Ltd Environmental. Environmental Biotechnology Principles and Applications Bioremediation: Principles and Applications (Biotechnology Research) · Read more. Request PDF on ResearchGate | On Jan 1, , B. E. Rittmann and others published Environmental Biotechnology: Principles and Applications.
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The C3 plants are therefore operating photosynthesis under suboptimal conditions especially when the oxygen tension is high and carbon dioxide tension is low. Why rubisco has not evolved to lose the oxidase activity is unclear: For the reasons indicated in the preceding section, C4 plants show little or no photorespiration due to their ability to channel carbon dioxide to rubisco by a method independent of oxygen tension. Balancing the light and the dark reactions in eukaryotes and cyanobacteria Using the six-carbon sugar, glucose, as an example, synthesis of one molecule requires six carbon dioxide molecules, 12 molecules of water, 12 protons, Microbes and Metabolism 45 18 molecules of ATP and 12 molecules of NADPH.
Since this may leave the dark reactions slightly short of ATP for carbohydrate synthesis, it is postulated that photosystem 2 passes through one extra cycle thus producing additional ATP molecules with no additional NADPH.
These combined processes are known collectively as the nitrogen cycle. The previous discussions have referred to the release of nitrogen during degradation of proteins and nucleic acid bases, either in the form of ammonia, the ammonium ion, urea or uric acid.
The fate of all these nitrogen species is to be oxidised to nitrite ion by Nitrosomas, a family of nitrifying bacteria. The nitrite ion may be reduced and released as atmospheric nitrogen, or further oxidised to nitrate by a different group of nitrifying bacteria, Nitrobacter.
The process of conversion from ammonia to nitrate is sometimes found as a tertiary treatment in sewage works to enable the nitrate consent to be reached. Closing Remarks The underpinning biochemistry and natural cycles described in this chapter form the basis of all environmental biotechnological interventions, and a thorough appreciation of them is an essential part of understanding the practical applications which make up most of the rest of this work.
Barrow, G. Cavalier-Smith, T. Demaneche, S. Ehlers, L. Horinouchi, M. Kreft, J. Lehninger, A. Mandelstam, J. McMaster, M. Michal, G. Round, F. Stackebrandt, E. Takai, K. Whittam, T. Woese, C. Case Study 2. This is particularly true when it is of microbial origin. Materials most commonly examined are from water originating from the sea, rivers, spa pools, swimming pools and drinking water.
They also analyse food in cases of suspected food poisoning and swabs from a variety of possibly contaminated surfaces. The laboratory insists that the specimens are transported in such a manner as to prevent bacterial multiplication. For some bacteria a resuscitation step is included to aid the recovery of damaged organisms.
This can be important to ensure that all microbes present in the original material remain viable and culturable at least until testing has been accomplished. These colonies are counted and the number of organisms in each millilitre of original sample, calculated.
The decision of which to use routinely, has been determined partly by constraints of time since a speedy warning is essential if pathogens or a particularly high microbial load is present. In addition, the tests are designed to look for the microbes which are specially problematic in given circumstances such as Pseudomonads in swimming and spa pools, or which are indicative of a particular contamination.
An example of the latter are faecal coliforms, such as Escherichia coli, which can indicate the presence of sewage. A rapid test for these involves incubation of a measured volume of sample with the colourless chemical orthonitrophenol galactoside ONPG.
This is one of many rapid tests which rely on colour change in response to the activity of an enzyme diagnostic of a group of organisms, and provides for a simple and reproducible method of scoring for the presence or absence of contamination.
If these initial tests prove positive within the guidelines set for Continued on page 48 48 Environmental Biotechnology Continued from page 47 public health, further detailed analyses are performed as necessary to determine the extent and identity of the contamination. Inevitably, much of routine testing seems rather dull, but this essential service offered by the PHLS is vital for an early warning of system malfunction, hopefully preventing a minor problem becoming a major incident.
As a result, most of the organisms used share many of our own needs and the majority of the relevant cycles are ones which are, at least, largely familiar. While other aspects of biotechnology may demand techniques of molecular biology and genetic manipulation, as has been discussed, the applications of biological science, certainly to questions of pollution and waste, generally do not.
Their position in respect of the third leg of the intervention tripod, shown in Figure 1. However, while this undoubtedly represents a contribution in terms of reduced pollution or the minimisation of waste, with regard to the express demands for environmental amelioration, their involvement is, at best, marginal. Using Biological Systems Consequently, a number of themes and similarities of approach exist, which run as common and repeated threads throughout the whole of the science.
Thus, optimisation of the activities of particular organisms, or even whole biological communities, to bring about any desired given end, typically requires manipulation of local conditions. Control of temperature, the accessibility of nutrients and the availability of oxygen are commonly the tools employed, especially when the target effectors are microbes or isolated biological derivatives.
The typical factors affecting 50 Environmental Biotechnology the use of biological systems in environmental engineering relate to the nature of the substances needing to be removed or treated and to the localised environmental conditions pertaining to the particular situation itself.
Thus, in respect of the former, the intended target of the bioprocessing must generally be both susceptible and available to biological attack, in aqueous solution, or at least in contact with water, and within a low to medium toxicity range. For land-based applications, especially in the remediation of contamination or as a component of integrated pollution control measures, there is an additional common constraint on the substrate.
Typically the soil types best suited to biotechnological interventions are sands and gravels, with their characteristically low nutrient status, good drainage, permeability and aeration. By contrast, biological treatments are not best suited to use in clays or peat or other soils of high organic content. In addition, generalised nutrient availability, oxygenation and the presence of other contaminants can all play a role in determining the suitability of biological intervention for any given application.
Extremophiles As has been previously mentioned, in general the use of biotechnology for environmental management relies on mesophilic micro-organisms which have roughly similar environmental requirements to ourselves, in terms of temperature, pressure, water requirement and relative oxygenation. Accordingly, ancient metabolic pathways can be very valuable tools for environmental biotechnology.
Thus, the selective advantages honed in Carboniferous coal measures and the Pleistocene tar pits have produced microbes which can treat spilled mineral oil products in the present and methanogenesis, a process developed by the Archae during the dawn of life on earth, remains relevant to currently commonplace biological interventions.
Moreover, some species living today tolerate extreme environments, like high salinity, pressures and temperatures, which might be of use for biotech applications requiring tolerance to these conditions. The Archaea the group formerly known as the archaebacteria and now recognised as forming a distinct evolutionary line rank amongst their numbers extreme thermophiles and extreme halophiles in addition to the methanogens previously mentioned.
To date, however, there has been little commercial interest in the extremophiles, despite their very obvious potential for exploitation.
The existence of microbes capable of surviving in extreme environments has been known since the s, but the hunt for them has taken on added impetus in recent years as possible industrial applications for their unique biological capabilities have been recognised. This often forces manufacturing processes that rely on them to introduce special steps to protect the proteins during either the active stage or storage.
The promise of extremozymes lies in their ability to remain functional when other enzymes cannot. In addition, their novel and distinct abilities in challenging environments allows them to be considered for use as the basis of entirely new enzyme-based approaches to processing. However, the widespread uptake and integration of biocatalytic systems as industrial production processes in their own right is not without obstacles which need to be overcome. Such procedures often irreversibly denature proteins, destroying enzymatic activity.
Unsurprisingly, the majority of them have been isolated from environments which have some association with volcanic activity. Now known as Thermus aquaticus, this bacterium would later make possible the widespread use of a revolutionary technology, the polymerase chain reaction PCR , which is returned to later in this chapter. Around 50 species are presently known. Although no one knows for certain at this time, it is widely thought that, higher than this, the chemical integrity of essential molecules will be unlikely to escape being compromised.
The potential for the industrial exploitation of the biochemical survival mechanisms which enable thermo- and hyperthermophiles to thrive under such hot conditions is clear. In this respect, the inactivation of thermophiles at temperatures which are still too hot for other organisms to tolerate may also have advantages in commercial processes.
Though an extreme example in a world of extremes, the previously mentioned P. A good understanding of the way in which extremophile molecules are able to function under these conditions is essential for any future attempt at harnessing the extremozymes for industrial purposes. In a number of heat-tolerant extremozymes, for example, the major difference appears to be no more than an increased prevalence of ionic bonds within the molecule.
Though the industrial use of extremophiles in general has been limited to date, it has notably given rise to polymerase chain reaction PCR , a major technique used in virtually every molecular biology laboratory worldwide. The original approach relied on mesophilic polymerases and since the reaction mixture is alternately cycled between low and high temperatures, enzymatic denaturation took place, requiring their replenishment at the end of each hot phase. Samples of T. Other extremophiles As was stated earlier, the thermophiles are amongst the best investigated of the extremophiles, but there are many other species which survive under equally challenging environmental conditions and which may also have some potential as the starting point for future methods of reduced pollution manufacturing.
For example, cold environments are more common on earth than hot ones. Accordingly, in salty conditions, unprotected cells rapidly lose water from their cytoplasm and dehydrate. Halophilic microbes appear to deal with this problem by ensuring that their cytoplasm contains a higher solute concentration than is present in their surroundings. They seem to achieve this by two distinct mechanisms, either manufacturing large quantities of solutes for themselves or concentrating a solute extracted from external sources.
By the same token, many surface structural proteins in halophiles require severely elevated concentrations of sodium salts. Acidophiles thrive in the conditions of low pH, typically below 5, which occur naturally as a result of sulphurous gas production in hydrothermal vents and may also exist in residual spoils from coal-mining activity. Though they can tolerate an externally low pH, an acidic intra-cellular environment is intolerable to acidophilic organisms, which rely on protective molecules in, or on, their cell walls, membranes or outer cell coatings to exclude acids.
Extremozymes capable of functioning below pH1 have been isolated from these structures in some acidophile species. Like the previous acidophiles, alkaliphiles require more typically neutral internal conditions, again relying on protective chemicals on or near their surfaces or in their secretions to ensure the external environment is held at bay. Diverse degradative abilities Bacteria possessing pathways involved in the degradation of a number of organic molecules of industrial importance, have been acknowledged for some time.
One oft-quoted example is that for toluene degradation in Pseudomonas putida, which exhibits a fascinating interplay between the genes carried on the chromosome and the plasmids Burlage, Hooper and Sayler Bacteria are constantly being discovered which exhibit pathways involved in the degradation and synthesis of chemicals of particular interest to environmental biotechnologists. In very recent years, bacteria representing very diverse degradative abilities have been discovered in a variety of niches adding almost daily, to the pool of organisms of potential use to environmental biotechnology.
By illustration these include phenol-degrading Oceanomas baumannii isolated from estuarine mud from the mouth of the River Wear, UK Brown, Sutcliffe and Cummings , chloromethane utilising Hyphomicrobium and Methylobacterium from polluted soil near a petrochemical factory in Russia McDonald et al. Again, there is interest in this organism with regard to clean technology in the hope that it may Fundamentals of Biological Intervention 55 be used to convert cellulose into industrially useful substances.
A note of caution is that cellulose is a major product of photosynthesis and, being the most abundant biopolymer on this planet, has a vital role to play in the carbon cycle. Large-scale disturbance of this balance may have consequences to the environment even less welcome than the technologies they seek to replace.
However, judicious use of this biotechnology could reap rewards at many levels. Bacteria have also adapted to degrade man-made organics called xenobiotics.
They present a particular hazard if they are subject to bioaccumulation especially so if they are fat soluble since that enables them to be stored in the body fat of organisms providing an obvious route into the food chain. Consequently, cometabolism may be sustained only if a carbon source is supplied to the organism. The ability of a single compound to be degraded can be affected by the presence of other contaminants.
For example, heavy metals can affect the ability of organisms to grow, the most susceptible being Gram positive bacteria, then Gram negative. Fungi are the most resistant and actinomycetes are somewhere in the middle. Soil micro-organisms in particular are very versatile and may quickly adapt to a new food source by virtue of the transmission of catabolic plasmids.
Of all soil bacteria, Pseudomonads seem to have the most highly developed ability to adapt quickly to new carbon sources. In bacteria, the genes coding for degradative enzymes are often arranged in clusters, or operons, which usually are carried on a plasmid. This leads to very fast transfer from one bacterium to another especially in the case of Pseudomonas where many of the plasmids are self-transmissible.
The speed of adaptation is due in part to the exchange of plasmids but in the case of the archaeans particularly, the pathways they carry, which may have been latent over thousands of bacterial generations, owe their existence to previous exposure over millions of years to an accumulated vast range of organic molecules.
Even so, bioremediation may require that organisms are altered in some way to make them more suitable for the task and this topic is addressed in Chapter 9. There have been several cases reported where catabolic pathways have been expanded in the laboratory.
Hedlund and Staley isolated a strain of Vibrio cyclotrophicus from marine sediments contaminated with creosote. By supplying the bacteria with only phenanthrene as a carbon and energy source, the bacteria were trained to degrade several PAHs although some of these only by cometabolism with a supplied carbon source. Endocrine disrupters To date, there are chemicals, including xenobiotics, which still resist degradation in the environment.
This may be due to a dearth, at the site of contamination, of organisms able to degrade them fully or worse, microbial activity which changes them in such a way that they pose a bigger problem than they did previously. Natural oestrogens are deactivated in humans by glucuronidation, as shown in Figure 3. The enzyme catalysing this process is induced in response to prolonged exposure to the toxin thus imparting increased tolerance or even resistance to the chemical.
Returning to the problem of elevated levels of active hormones in the waterways, another aspect is that steroids do not occur in bacteria, although they are present in fungi, and so bacteria lack the necessary pathways to allow complete degradation of these hormones at a rate compatible with the dwell time in sewage treatment plants.
Such disturbances have been monitored by measuring the presence of the protein vitellogenin Sole et al. Many other chemicals, including polyaromatic hydrocarbons PAHs , dichlorodiphenyltrichloroethane DDT , alkyl phenols and some detergents may also mimic the activity of oestrogen.
There is general concern as to the ability of some organisms to accumulate these endocrine disrupters in addition to the alarm being raised as to the accumulative effects on humans of oestrogen-like activity from a number of xenobiotic sources. To date there is no absolute evidence of risk to human health but the Environmental Agency and Water UK are recommending the monitoring of environmental oestrogens in sewage treatment outfall.
Assays are being developed further to make these assessments Gutendorf and Westendorf and to predict potential endocrine disrupter activity of suspected compounds Takeyoshi et al Oestrogen and progesterone are both heat labile. In addition, oestrogen appears to be susceptible to treatment with ultra-violet light, the effects of which are augmented by titanium dioxide Eggins The oestrogen is degraded completely to carbon dioxide and water thus presenting a plausible method for water polishing prior to consumption.
Another method for the removal of oestrogens from water, in this case involving Aspergillus, has also been proposed Ridgeway and Wiseman Sulphation of the molecule by isolated mammalian enzymes, as a means of hormone inactivation is also being investigated Suiko Taken overall, it seems unlikely that elevated levels of oestrogen in the waterways will pose a problem 58 Environmental Biotechnology Figure 3.
New discoveries Almost daily, there are novel bacteria being reported in the literature which have been shown to have the capacity to degrade certain xenobiots. Presumably the mutation which occurred during the evolution of the organism conferred an advantage, and selective pressure maintained that mutation in the DNA, thus producing a novel strain with an altered phenotype.
Some example of such isolates are described here. This is in addition to some being toxic for other reasons and some being carcinogenic or teratogenic.
The PAHs are derived primarily from the petrochemicals industry and are polycyclic hydrocarbons of three or more rings which include as members, naphthalene and phenanthrene and historically have been associated Fundamentals of Biological Intervention 59 with offshore drilling, along with alkylphenols. Several genera of bacteria are now known to be able to degrade PAHs and recently, a novel strain of Vibrio cyclotrophicus able to digest naphthalene and phenanthrene, was isolated from creosote-contaminated marine sediments from Eagle Harbour, Washington, USA.
It would appear that bacteria isolated from the same marine or estuarine environments may vary quite considerably in their abilities to degrade certain PAHs. This observation is viewed as indicative of diverse catabolic pathways demonstrated by these organisms and awaiting our full understanding Hedlund and Staley Polycyclic hydrocarbons PCBs are xenobiotics which, due to their high level of halogenation, are substrates for very few pathways normally occurring in nature.
This was achieved by the bacterium employing two pathways encoded by two separate operons; the tod pathway employed in toluene degradation, and the cmt pathway which normally is responsible for the catabolism of p-cumate which is a substituted toluene.
The mutation which allowed this strain to utilise the cmt pathway was found to be a single base change to the promoter-operator sequence.
This allowed all the enzymes in this pathway to be expressed under conditions where their synthesis would normally be repressed. Thus, the two pathways could work in conjunction with each other to metabolise PCBs, a relationship described as mosaic Ohta et al In Chapter 2, and earlier in this chapter, homage has been paid to the resources of genetic capability exhibited by the archaeans.
In a recent analysis of anaerobic sewage sludge, a methanogenic consortium of over bacterial clones were found to have the capability to digest terephthalate. These two species are believed to be responsible for the degradation of terephthalic acid Wu et al During wastewater treatment, terepthalic acid is usually treated by aerobic processes. However, this consortium, or others like it provide an anaerobic alternative which, being methanogenic, may be structured to offset processing costs by the utilisation of the methane.
Mobility of DNA Throughout this book, reference is made to the movement of genes within and between organisms. Plasmids may be transferred between bacteria by conjugation, of which there are several types, but all of which require direct cell to cell contact. Not only are genes transferred between bacteria on plasmids, but bacteriophages bacterial viruses are also vectors for intercellular transmission. Similarly, eukaryotic viruses are able to transfer genetic material between susceptible cells.
There is also considerable rearrangement of genomic material within an organism stimulated by the presence of transposons. There are many classes of transposable elements which are short pieces of DNA, able to excise themselves, or be excised, out of a genome. Often they take with them neighbouring pieces of DNA, and then reinsert themselves, sometimes with the assistance of other genes, into a second site distinct from the original location on the same genome.
Transposition normally requires replication of the original DNA fragment and so a copy of this transposon is transferred leaving the original behind. Transposition is widespread and occurs in virtually all organisms for which evidence of this process has been sought, both prokaryotic and eukaryotic.
Transposable elements are known to promote the fusion of plasmids within a bacterial cell, where more than one type of plasmid is present. They are often found at either end of a transposable element. Their presence enables various DNA rearrangements to take place leading to moderation of gene expression. Taking together the reorganisation of DNA within all types of organisms attributable to transposable elements and IS, with transfer of DNA between organisms by plasmids and transformation, in the case of prokaryotes, and viruses in the case of both prokaryotes and eukaryotes, the potential for DNA rearrangement within and between organisms is enormous.
It has been proposed Reanney , that such transfer is far more universal than had previously been voiced. Transfer of genes by extra chromosomal elements ECEs , which is the all-embracing name given to include plasmids and viruses, models the means by which molecular evolution takes place in the environment.
The proposal is that the evolutionary process occurs principally by insertions and deletions of the genome such as those caused by the activities of ECEs and transposable elements and not by point mutations more frequently observed in isolated cultures such as those maintained in laboratory conditions. It is further suggested that much of the phenotypic novelty seen in evolution is the result of rearrangement of existing structural genes into a different region Fundamentals of Biological Intervention 61 of the genome and therefore operating under different parameters affecting gene regulation.
Transfer of genes across wide taxonomic gaps is made possible by the mobile nature of ECEs many of which may cross species barriers often resulting in the insertion of all or part of the ECE into the recipient genome. Examples of such mobility are viruses which infect a wide host range, such as some retroviruses, the alfalfa mosaic virus, and the Ti plasmid of Agrobacterium tumefaciens which the bacterium introduces into plant cells.
They replicate in a manner which includes double-stranded DNA as an intermediate and so may integrate into the host cell genome. RNA viruses tend to be more susceptible than DNA viruses to mutation presumably due to the less chemically stable nature of the macromolecule.
They have been invoked by Reanney as being the likely agents for the spread of genetic information between unrelated eukaryotes. His observations led him to conclude that there is only a blurred distinction between cellular and ECE DNA both in eukaryotes and prokaryotes and further suggest that no organism lives in true genetic isolation as long as it is susceptible to at least one of the classes of ECEs described above.
Clearly, for the mutation to be stabilised, it must occur in inheritable DNA sequences, a situation reasonably easy to achieve in microbes and at least possible in multicellular organisms. The existence of genetic mobility has been accepted for many years, even though the extent and the mechanisms by which it operates are still being elucidated.
This topic is explored further in Chapters 9, 10 and Closing Remarks As has been seen, even within the brief discussion in this chapter, life on Earth is a richly varied resource and the functional reality of biodiversity is that many more metabolic pathways exist, particularly within the microbial melting pot, than might be commonly supposed.
As a result, a number of generally unfamiliar groups of chemicals and organisms have implications for the application of environmental biotechnology which exceed their most obvious contributions to a wider consideration of the life sciences.
There are many aspects of current environmental management for which there is no presently relevant biotechnological intervention. However, this is not a static science, either in terms of what can be done, or the tools available.
References Brown, G. Burlage, R. Byrns, G. Eggins, B.
Gutendorf, B. Hedlund, B. McDonald, I.
Monserrate, E. Ohta, Y. Reanney, D. Ridgeway, T. Nov Biochemical Society Transactions, 26 4: Fundamentals of Biological Intervention 63 Sole, M. Suiko, M. Takeyoshi, M. Wright, P. Wu, J. Case Study 3. In the UK, around a third of Continued on page 64 64 Environmental Biotechnology Continued from page 63 drinking water is abstracted from rivers and, in common with many other industrialised countries, human sperm counts are progressively dropping.
However, such public health concerns aside, the persistence and potency of synthetic oestrogens remains a clear example of the environmental importance of xenobiotic contamination.
However, the diverse nature of potentially polluting substances can lead to some confusion. It is important to realise that not all pollutants are manufactured or synthetic, that under certain circumstances, many substances may contribute to pollution and that, perhaps most importantly for our purposes, any biologically active substance has the potential to give rise to a pollution effect.
EPA, Introduction. Despite these limitations, there is considerable value in having some method, if only as a predictive environmental management tool, for considerations of likely pollutant effect. Figure 4. This may include factors such as: Toxicity Toxicity represents the potential damage to life and can be both short and long term.
It is related to the concentration of pollutant and the time of exposure to it, though this relationship is not an easy one. Intrinsically highly toxic substances can kill in a short time, while less toxic ones require a longer period of exposure to do damage.
This much is fairly straightforward. However, some pollutants which Figure 4. Persistence This is the duration of effect.
Environmental persistence is a particularly important factor in pollution and is often linked to mobility and bioaccumulation. Highly toxic chemicals which are environmentally unstable and break down rapidly are less harmful than persistent substances, even though these may be intrinsically less toxic. Mobility The tendency of a pollutant to disperse or dilute is a very important factor in its overall effect, since this affects concentration.
Others spread readily and can cause widespread contamination, though often the distribution is not uniform. Whether the pollution is continuous or a single event, and if it arose from a single point or multiple sources, form important considerations.
Clearly, control at source is the most effective method, since it removes the problem at its origin. However, this is not always possible and in such cases, containment may be the solution, though this can itself lead to the formation of highly concentrated hot-spots.
For some substances, the dilute and disperse approach, which is discussed more fully later in this chapter, may be more appropriate, though the persistence of the polluting substances must obviously be taken into account when making this decision.
Bioaccumulation As is widely appreciated, some pollutants, even when present in very small amounts within the environment, can be taken up by living organisms and become concentrated in their tissues over time. This tendency of some chemicals to be taken up and then concentrated by living organisms is a major consideration, since even relatively low background levels of contamination may accumulate up the food chain.
This is of particular relevance to the present discussion, since the principle underlying much of practical bioremediation in general involves the break down of pollutants to form less harmful products. Accordingly, both synergism and antagonism are possible.
In the former, two or more substances occurring together produce a combined pollution outcome which is greater than simply the sum of their individual effects; in the latter, the combined pollution outcome is smaller than the sum of each acting alone. The Pollution Environment There is sometimes a tendency for contamination to be considered somewhat simplistically, in isolation from its context. It is important to remember that pollution cannot properly be assessed without a linked examination of the environment in which it occurs.
The nature of the soil or water which harbours the pollution can have a major effect on the actual expressed end-result. Hence, the depth of soil, its texture, type, porosity, humus content, moisture, microbial complement and biological activity can all have a bearing on the eventual pollution outcome. It should be obvious that, in general terms, the postpollution survival of a given environment depends on the maintenance of its natural cycles. In principle, it involves the attenuation of pollutants by permitting them to become physically spread out, thereby reducing their effective point concentration.
It may take place, with varying degrees of effectiveness, in air, water or soil. Air In general terms, air movement gives good dispersal and dilution of gaseous emissions. Water Typically, there is good dispersal and dilution potential in large bodies of water or rivers, but smaller watercourses clearly have a correspondingly lower capacity.
Stoichiometry and Bacterial Energetics 3. Microbial Kinetics 4. Biofilm Kinetics 5. Reactors 6. The Activated Sludge Process 7. Lagoons 8. Aerobic Biofilm Processes 9. Nitrification Denitrification Phosphorus Removal Drinking-Water Treatment Anaerobic Treatment by Methanogenesis However, the picture is not entirely rosy. Typically the sector comprises a number of relatively small, specialist companies and the market is, as a consequence, inevitably fragmented.
The fact remains that one of the major barriers to the wider uptake of biological approaches is the high perceived cost of these applications. Part of the reason for this lies in historical experience. For many years, the solutions to all environmental problems were seen as expensive and for many, particularly those unfamiliar with the multiplicity of varied technologies available, this has remained the prevalent view.
Many providers, particularly in the UK, have cited a lack of marketing expertise as one of the principal barriers to their exploitation of novel opportunities. Good education, in the widest sense, of customers and potential users of biological solutions will be one major factor in any future upswing in the acceptance and utilisation of these technologies.
Neither the nature of the biological system, nor of the application method itself, play anything like so relevant a role. Accordingly, what may make abundant sense as a biotech intervention in one region or country, may be totally unsuited to use in another.
While environmental biotechnology must, inevitably, be viewed as contextually dependent, as the previous example shows, contexts can change. Again as has been discussed, the legal framework is another aspect of undeniable importance in this respect.
There is a natural tendency to delineate, seeking to characterise technologies into particular categories or divisions. However, the essence of environmental biotechnology is such that there are many more similarities than differences.
Though it is, of course, often helpful to view individual technology uses as distinct, particularly when considering treatment options for a given environmental problem, there are inevitably recurrent themes which feature throughout the whole topic.
Moreover, this is a truly applied science. While the importance of the laboratory bench cannot be denied, the controlled world of research translates imperfectly into the harsh realities of commercial implementation. Thus, there can often be a dichotomy between theory and application and it is precisely Introduction to Biotechnology 9 this fertile ground which is explored in the present work. Thus, this science stands on a foundation of fundamental biology and biochemistry.
To understand the application, the biotechnologist must simply examine the essential elements of life, living systems and ecological circulation sequences.
However engineered the approach, this fact remains true. In essence, all of its applications simply encourage the natural propensity of the organisms involved, while seeking to enhance or accelerate their action. Integrated Approach Integration is an important aspect for environmental biotechnology.
One theme that will be developed throughout this book is the potential for different biological approaches to be combined within treatment trains, thereby producing an overall effect which would be impossible for any single technology alone to achieve.
In some spheres, traditional biology has become rather unfashionable and the emphasis has shifted to more exciting sounding aspects of life science. The fundamentals of living systems are the stuff of this branch of science and, complex though the whole picture may be, at its simplest the environmental biotechnologist is principally concerned with a relatively small number of basic cycles.
Unsurprisingly, then, these basic processes appear throughout this book, either explicitly or tacitly accepted as underpinning the context of the discussion.
The intent here has been neither to insult the readership by parading what is already well known, nor gloss over aspects which, if left unexplained, at least in reasonable detail, might only serve to confuse.
Practitioners come into the profession from a wide variety of disciplines and by many different routes. Thus, amongst their ranks are agronomists, biochemists, biologists, botanists, enzymologists, geneticists, microbiologists, molecular biologists, process engineers and protein technologists, all of whom bring their own particular skills, knowledge base and experiences.
The applied nature of environmental biotechnology is obvious. While the science underlying the processes themselves may be as pure as any other, what distinguishes this branch of biological technology are the distinctly real-life purposes to which it is put. Hence, part of the intended function of this book is to attempt to elucidate the former in order to establish the basis of the latter.
At times, anything more than an approximation to the expected results may be counted as something of a triumph of environmental engineering. This approach is particularly valid for environmental biotechnology. With new developments in treatment technologies appearing all the time, the list of what can be processed or remediated by biological means is ever changing. By the same token, the applications for which biotechnological solutions are sought are also subject to alteration. This is the basis of innovation; the inventiveness of an industry is often a good measure of its adaptability and commercial robustness.
Walker P. Metabolic pathways Michal are interlinked to produce what can develop into an extraordinarily complicated network, involving several levels of control. However, they are fundamentally about the interaction of natural cycles and represent the biological element of the natural geobiological cycles. These impinge on all aspects of the environment, both living and nonliving.
Using the carbon cycle as an example, carbon dioxide in the atmosphere is returned by dissolution in rainwater, and also by the process of photosynthesis to produce sugars, which are eventually metabolised to liberate the carbon once more. In addition to constant recycling through metabolic pathways, carbon is also sequestered in living and nonliving components such as in trees in the relatively short term, and deep ocean systems or ancient deposits, such as carbonaceous rocks, in the long term.
Cycles which involve similar principles of incorporation into biological molecules and subsequent re-release into the environment operate for nitrogen, phosphorus and sulphur. All of these overlap in some way, to produce the metabolic pathways responsible for the synthesis and degradation of biomolecules.
Superimposed, is an energy cycle, ultimately driven by the sun, and involving constant consumption and release of metabolic energy. To appreciate the biochemical basis and underlying genetics of environmental biotechnology, at least an elementary grasp of molecular biology is required. The Immobilisation, Degradation or Monitoring of Pollutants from a Biological Origin Removal of a material from an environment takes one of two routes: it is either degraded or immobilised by a process which renders it biologically unavailable for degradation and so is effectively removed.
Immobilisation can be achieved by chemicals excreted by an organism or by chemicals in the neighbouring environment which trap or chelate a molecule thus making it insoluble. Since virtually all biological processes require the substrate to be dissolved in water, chelation renders the substance unavailable. In some instances 12 Environmental Biotechnology this is a desirable end result and may be viewed as a form of remediation, since it stabilises the contaminant.
In other cases it is a nuisance, as digestion would be the preferable option. Degradation is achieved by metabolic pathways operating within an organism or combination of organisms, sometimes described as consortia. These processes are the crux of environmental biotechnology and thus form the major part of this chapter. Biological monitoring utilises proteins, of which enzymes are a subset, produced by cells, usually to identify, or quantify contaminants.
Who are the biological players in these processes, what are their attributes which are so essential to this science and which types of biological material are being addressed here?
The answers to these questions lie throughout this book and are summarised in this chapter. The players Traditionally, life was placed into two categories — those having a true nucleus eukaryotes and those that do not prokaryotes. It is primarily to the archaea, which typically inhabit extreme niches with respect to temperature, pressure, salt concentration or osmotic pressure, that a great debt of gratitude is owed for providing this planet with the metabolic capability to carry out processes under some very odd conditions indeed.
The importance to environmental biotechnology of life in extreme environments is addressed in Chapter 3.
The relevance of this becomes obvious when genetic engineering is discussed later in this book in Chapter 9. However, it is interesting to examine the potentially prokaryotic Microbes and Metabolism 13 origins of the eukaryotic cell.
There are many theories but the one which appears to have the most adherents is the endosymbiotic theory. These included an aerobic bacterium, which became a mitochondrion, endowing the cell with the ability to carry out oxidative phosphorylation, a method of producing chemical energy able to be transferred to the location in the cell where it is required. Similarly, the chloroplast, the site of photosynthesis in higher plants, is thought to have been derived from cyanobacteria, the so-called blue-green algae.
Chloroplasts are a type of plastid. These are membrane-bound structures found in vascular plants. Nuclei may well have similar origins but the evidence is still awaited. No form of life should be overlooked as having a potential part to play in environmental biotechnology. However, the organisms most commonly discussed in this context are microbes and certain plants.
They are implicated either because they are present by virtue of being in their natural environment or by deliberate introduction. Microbes Microbes are referred to as such, simply because they cannot be seen by the naked eye.
In addition, there are some microscopic multicellular organisms, such as rotifers, which have an essential role to play in the microsystem ecology of places such as sewage treatment plants. Although bacterial cells occur in a variety of shapes and sizes, depending on the species, typically a bacterial cell is rod shaped, measuring approximately one micron in width and two microns in length.
At its simplest visualisation, a cell, be it a unicellular organism, or one cell in a multicellular organism, is a bag, bounded by a membrane, containing an aqueous solution in which are all the molecules and structures required to enable its continued survival. Survival requires cell growth, replication of the DNA and then division, usually sharing the contents into two equal daughter cells.
Under ideal conditions of environment and food supply, division of some bacteria may occur every 20 minutes, however, most take rather longer. However, the result of many rounds of the binary division just described, is a colony of identical cells. This may be several millimetres across and can be seen clearly as a contamination on a solid surface, or if in a liquid, it will give the solution a cloudy appearance.
Other forms of replication include budding off, as in some forms of yeast, or the formation of spores as in other forms of yeast and some bacteria. This is a type of DNA storage particularly resistant to environmental excesses of heat and pH, for example.
When the environment becomes more hospitable, the spore can develop into a bacterium or yeast, according to its origins, and the life cycle continues. Micro-organisms may live as free individuals or as communities, either as a clone of one organism, or as a mixed group. Models for their organisation have been proposed Kreft et al. Such consortia can increase the habitat range, the overall tolerance to stress and metabolic diversity of individual members of the group.
It is often thanks to such communities, rather than isolated bacterial species, that recalcitrant pollutants are eventually degraded due to combined contributions of several of its members. Another consequence of this close proximity is the increased likelihood of bacterial transformation. This is a procedure whereby a bacterium may absorb free deoxyribonucleic acid DNA , the macromolecule which stores genetic material, from its surroundings released by other organisms, as a result of cell death, for example.