Microbial biodegradation
Encyclopedia
Interest in the microbial biodegradation of pollutant
s has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments. These bioremediation
and biotransformation
methods endeavour to harness the astonishing, naturally occurring ability of microbial xenobiotic metabolism
to degrade, transform or accumulate a huge range of compounds including hydrocarbon
s (e.g. oil), polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds (such as pyridine
or quinoline
), pharmaceutical substances, radionuclide
s and metals. Major methodological breakthroughs in recent years have enabled detailed genomic, metagenomic, proteomic, bioinformatic and other high-throughput analyses of environmentally relevant microorganism
s providing unprecedented insights into key biodegradative pathways and the ability of organisms to adapt to changing environmental conditions.
The elimination of a wide range of pollutants and wastes from the environment
is an absolute requirement to promote a sustainable development of our society with low environmental impact. Biological processes play a major role in the removal of contaminants and they take advantage of the astonishing catabolic versatility of microorganisms to degrade or convert such compounds. New methodological breakthroughs in sequencing
, genomics
, proteomics
, bioinformatics
and imaging are producing vast amounts of information. In the field of Environmental microbiology
, genome
-based global studies open a new era providing unprecedented in silico views of metabolic and regulatory networks, as well as clues to the evolution of degradation pathways and to the molecular adaptation strategies to changing environmental conditions. Functional genomic and metagenomic approaches are increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds and they will certainly accelerate the development of bioremediation technologies and biotransformation processes.
s. Aromatic compounds are among the most recalcitrant of these pollutants and lessons can be learned from the recent genomic studies of Burkholderia xenovorans
LB400 and Rhodococcus
sp. strain RHA1, two of the largest bacterial genomes completely sequenced to date. These studies have helped expand our understanding of bacterial catabolism
, non-catabolic physiological adaptation to organic compound
s, and the evolution of large bacterial genome
s. First, the metabolic pathway
s from phylogenetically diverse isolates are very similar with respect to overall organization. Thus, as originally noted in pseudomonads, a large number of "peripheral aromatic" pathways funnel a range of natural and xenobiotic
compounds into a restricted number of "central aromatic" pathways. Nevertheless, these pathways are genetically organized in genus-specific fashions, as exemplified by the b-ketoadipate and Paa pathways. Comparative genomic studies further reveal that some pathways are more widespread than initially thought. Thus, the Box and Paa pathways illustrate the prevalence of non-oxygenolytic ring-cleavage strategies in aerobic aromatic degradation processes. Functional genomic studies have been useful in establishing that even organisms harboring high numbers of homologous enzymes seem to contain few examples of true redundancy. For example, the multiplicity of ring-cleaving dioxygenases in certain rhodococcal isolates may be attributed to the cryptic aromatic catabolism of different terpenoids and steroids. Finally, analyses have indicated that recent genetic flux appears to have played a more significant role in the evolution of some large genomes, such as LB400's, than others. However, the emerging trend is that the large gene repertoires of potent pollutant degraders such as LB400 and RHA1 have evolved principally through more ancient processes. That this is true in such phylogenetically diverse species is remarkable and further suggests the ancient origin of this catabolic capacity.
microbial mineralization of recalcitrant organic pollutant
s is of great environmental significance and involves intriguing novel biochemical reactions. In particular, hydrocarbon
s and halogenated compounds have long been doubted to be degradable in the absence of oxygen, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria
during the last decades provided ultimate proof for these processes in nature. Many novel biochemical reactions were discovered enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was rather slow, since genetic systems are not readily applicable for most of them. However, with the increasing application of genomics
in the field of environmental microbiology
, a new and promising perspective is now at hand to obtain molecular insights into these new metabolic properties. Several complete genome sequences were determined during the last few years from bacteria capable of anaerobic organic pollutant degradation. The ~4.7 Mb genome
of the facultative denitrifying Aromatoleum aromaticum strain EbN1 was the first to be determined for an anaerobic hydrocarbon degrader (using toluene
or ethylbenzene
as substrate
s). The genome sequence revealed about two dozen gene cluster
s (including several paralogs) coding for a complex catabolic network for anaerobic and aerobic degradation of aromatic compounds. The genome sequence forms the basis for current detailed studies on regulation of pathways and enzyme
structures. Further genomes of anaerobic hydrocarbon degrading bacteria were recently completed for the iron-reducing species Geobacter metallireducens (accession nr. NC_007517) and the perchlorate-reducing Dechloromonas aromatica (accession nr. NC_007298), but these are not yet evaluated in formal publications. Complete genomes were also determined for bacteria capable of anaerobic degradation of halogenated hydrocarbons by halorespiration
: the ~1.4 Mb genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides
sp. strain CBDB1 and the ~5.7 Mb genome of Desulfitobacterium hafniense strain Y51. Characteristic for all these bacteria is the presence of multiple paralogous genes for reductive dehalogenases, implicating a wider dehalogenating spectrum of the organisms than previously known. Moreover, genome sequences provided unprecedented insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.
Recently, it has become apparent that some organisms, including Desulfitobacterium chlororespirans, originally evaluated for halorespiration on chlorophenols, can also use certain brominated compounds, such as the herbicide bromoxynil
and its major metabolite as electron acceptors for growth. Iodinated compounds may be dehalogenated as well, though the process may not satisfy the need for an electron acceptor.
, or the amount of a substance that is physiochemically accessible to microorganism
s is a key factor in the efficient biodegradation
of pollutants. O'Loughlin et al. (2000) showed that, with the exception of kaolinite
clay, most soil clays and cation exchange resins attenuated biodegradation of 2-picoline by Arthrobacter
sp. strain R1, as a result of adsorption of the substrate to the clays. Chemotaxis
, or the directed movement of motile organisms towards or away from chemicals in the environment is an important physiological response that may contribute to effective catabolism of molecules in the environment. In addition, mechanisms for the intracellular accumulation of aromatic molecules via various transport mechanisms are also important.
oil contains aromatic compounds that are toxic for most life forms. Episodic and chronic pollution
of the environment by oil causes major ecological perturbations. Marine environments are especially vulnerable since oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult. In addition to pollution through human activities, about 250 million liters of petroleum enter the marine environment every year from natural seepages. Despite its toxicity, a considerable fraction of petroleum oil entering marine systems is eliminated by the hydrocarbon-degrading activities of microbial communities, in particular by a remarkable recently discovered group of specialists, the so-called hydrocarbonoclastic bacteria (HCB). Alcanivorax borkumensis was the first HCB to have its genome sequenced. In addition to hydrocarbons, crude oil often contains various heterocyclic compounds, such as pyridine, which appear to be degraded by similar, though separate mechanisms than hydrocarbons.
is a steroid highly abundant in the environment that plays a major role in the global carbon cycle. Many synthetic steroidic compounds like some sexual hormones frequently appear in municipal and industrial wastewaters, acting as environmental pollutants with strong metabolic activities negatively affecting the ecosystems. Since these compounds are common carbon sources for many different microorganisms their aerobic and anaerobic mineralization has been extensively studied. The interest of these studies lies on the biotechnological applications of sterol transforming enzymes for the industrial synthesis of sexual hormones and corticoids. Very recently the catabolism of cholesterol has acquired a high relevance because it is involved in the infectivity of Mycobacterium tuberculosis.
activities. Biotreatment, the processing of wastes using living organisms, is an environmentally friendly, relatively simple and cost-effective alternative to physico-chemical clean-up options. Confined environments, such as bioreactors, have been engineered to overcome the physical, chemical and biological limiting factors of biotreatment processes in highly controlled systems. The great versatility in the design of confined environments allows the treatment of a wide range of wastes under optimized conditions. To perform a correct assessment, it is necessary to consider various microorganisms having a variety of genome
s and expressed transcripts and proteins. A great number of analyses are often required. Using traditional genomic techniques, such assessments are limited and time-consuming. However, several high-throughput techniques originally developed for medical studies can be applied to assess biotreatment in confined environments.
s on pilot and even on industrial scale. Novel catalysts can be obtained from metagenomic libraries and DNA sequence
based approaches. Our increasing capabilities in adapting the catalysts to specific reactions and process requirements by rational and random mutagenesis
broadens the scope for application in the fine chemical industry, but also in the field of biodegradation
. In many cases, these catalysts need to be exploited in whole cell bioconversion
s or in fermentation
s, calling for system-wide approaches to understanding strain physiology and metabolism and rational approaches to the engineering of whole cells as they are increasingly put forward in the area of systems biotechnology
and synthetic biology.
and other moulds play an important role in these consortia because they are adept at recycling starches, hemicelluloses, celluloses, pectins and other sugar polymers. Some aspergilli are capable of degrading more refractory compounds such as fats, oils, chitin, and keratin. Maximum decomposition occurs when there is sufficient nitrogen, phosphorus and other essential inorganic nutrients. Fungi also provide food for many soil organisms.
For Aspergillus the process of degradation is the means of obtaining nutrients. When these moulds degrade human-made substrates, the process usually is called biodeterioration. Both paper and textiles (cotton, jute, and linen) are particularly vulnerable to Aspergillus degradation. Our artistic heritage is also subject to Aspergillus assault. To give but one example, after Florence in Italy flooded in 1969, 74% of the isolates from a damaged Ghirlandaio fresco in the Ognissanti church were Aspergillus versicolor.
Pollutant
A pollutant is a waste material that pollutes air, water or soil, and is the cause of pollution.Three factors determine the severity of a pollutant: its chemical nature, its concentration and its persistence. Some pollutants are biodegradable and therefore will not persist in the environment in the...
s has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments. These bioremediation
Bioremediation
Bioremediation is the use of microorganism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated...
and biotransformation
Biotransformation
Biotransformation is the chemical modification made by an organism on a chemical compound. If this modification ends in mineral compounds like CO2, NH4+, or H2O, the biotransformation is called mineralisation....
methods endeavour to harness the astonishing, naturally occurring ability of microbial xenobiotic metabolism
Xenobiotic metabolism
Xenobiotic metabolism is the set of metabolic pathways that modify the chemical structure of xenobiotics, which are compounds foreign to an organism's normal biochemistry, such as drugs and poisons...
to degrade, transform or accumulate a huge range of compounds including hydrocarbon
Hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons from which one hydrogen atom has been removed are functional groups, called hydrocarbyls....
s (e.g. oil), polychlorinated biphenyls (PCBs), polyaromatic hydrocarbons (PAHs), heterocyclic compounds (such as pyridine
Pyridine
Pyridine is a basic heterocyclic organic compound with the chemical formula C5H5N. It is structurally related to benzene, with one C-H group replaced by a nitrogen atom...
or quinoline
Quinoline
Quinoline is a heterocyclic aromatic organic compound. It has the formula C9H7N and is a colourless hygroscopic liquid with a strong odour. Aged samples, if exposed to light, become yellow and later brown...
), pharmaceutical substances, radionuclide
Radionuclide
A radionuclide is an atom with an unstable nucleus, which is a nucleus characterized by excess energy available to be imparted either to a newly created radiation particle within the nucleus or to an atomic electron. The radionuclide, in this process, undergoes radioactive decay, and emits gamma...
s and metals. Major methodological breakthroughs in recent years have enabled detailed genomic, metagenomic, proteomic, bioinformatic and other high-throughput analyses of environmentally relevant microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
s providing unprecedented insights into key biodegradative pathways and the ability of organisms to adapt to changing environmental conditions.
The elimination of a wide range of pollutants and wastes from the environment
Natural environment
The natural environment encompasses all living and non-living things occurring naturally on Earth or some region thereof. It is an environment that encompasses the interaction of all living species....
is an absolute requirement to promote a sustainable development of our society with low environmental impact. Biological processes play a major role in the removal of contaminants and they take advantage of the astonishing catabolic versatility of microorganisms to degrade or convert such compounds. New methodological breakthroughs in sequencing
Sequencing
In genetics and biochemistry, sequencing means to determine the primary structure of an unbranched biopolymer...
, genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
, proteomics
Proteomics
Proteomics is the large-scale study of proteins, particularly their structures and functions. Proteins are vital parts of living organisms, as they are the main components of the physiological metabolic pathways of cells. The term "proteomics" was first coined in 1997 to make an analogy with...
, bioinformatics
Bioinformatics
Bioinformatics is the application of computer science and information technology to the field of biology and medicine. Bioinformatics deals with algorithms, databases and information systems, web technologies, artificial intelligence and soft computing, information and computation theory, software...
and imaging are producing vast amounts of information. In the field of Environmental microbiology
Microbiology
Microbiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...
, genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
-based global studies open a new era providing unprecedented in silico views of metabolic and regulatory networks, as well as clues to the evolution of degradation pathways and to the molecular adaptation strategies to changing environmental conditions. Functional genomic and metagenomic approaches are increasing our understanding of the relative importance of different pathways and regulatory networks to carbon flux in particular environments and for particular compounds and they will certainly accelerate the development of bioremediation technologies and biotransformation processes.
Aerobic biodegradation of pollutants
The burgeoning amount of bacterial genomic data provides unparalleled opportunities for understanding the genetic and molecular bases of the degradation of organic pollutantPollutant
A pollutant is a waste material that pollutes air, water or soil, and is the cause of pollution.Three factors determine the severity of a pollutant: its chemical nature, its concentration and its persistence. Some pollutants are biodegradable and therefore will not persist in the environment in the...
s. Aromatic compounds are among the most recalcitrant of these pollutants and lessons can be learned from the recent genomic studies of Burkholderia xenovorans
Burkholderia xenovorans
Burkholderia xenovorans is a species of Proteobacteria.-Genomics:The genome of Burkholderia xenovorans is one of the largest bacterial genomes completely sequenced to date...
LB400 and Rhodococcus
Rhodococcus
Rhodococcus is a genus of aerobic, nonsporulating, nonmotile Gram-positive bacteria closely related to Mycobacteria and Corynebacteria. While a few species are pathogenic, most are benign and have been found to thrive in a broad range of environments, including soil, water, and eukaryotic cells...
sp. strain RHA1, two of the largest bacterial genomes completely sequenced to date. These studies have helped expand our understanding of bacterial catabolism
Catabolism
Catabolism is the set of metabolic pathways that break down molecules into smaller units and release energy. In catabolism, large molecules such as polysaccharides, lipids, nucleic acids and proteins are broken down into smaller units such as monosaccharides, fatty acids, nucleotides, and amino...
, non-catabolic physiological adaptation to organic compound
Organic compound
An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon. For historical reasons discussed below, a few types of carbon-containing compounds such as carbides, carbonates, simple oxides of carbon, and cyanides, as well as the...
s, and the evolution of large bacterial genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s. First, the metabolic pathway
Metabolic pathway
In biochemistry, metabolic pathways are series of chemical reactions occurring within a cell. In each pathway, a principal chemical is modified by a series of chemical reactions. Enzymes catalyze these reactions, and often require dietary minerals, vitamins, and other cofactors in order to function...
s from phylogenetically diverse isolates are very similar with respect to overall organization. Thus, as originally noted in pseudomonads, a large number of "peripheral aromatic" pathways funnel a range of natural and xenobiotic
Xenobiotic
A xenobiotic is a chemical which is found in an organism but which is not normally produced or expected to be present in it. It can also cover substances which are present in much higher concentrations than are usual...
compounds into a restricted number of "central aromatic" pathways. Nevertheless, these pathways are genetically organized in genus-specific fashions, as exemplified by the b-ketoadipate and Paa pathways. Comparative genomic studies further reveal that some pathways are more widespread than initially thought. Thus, the Box and Paa pathways illustrate the prevalence of non-oxygenolytic ring-cleavage strategies in aerobic aromatic degradation processes. Functional genomic studies have been useful in establishing that even organisms harboring high numbers of homologous enzymes seem to contain few examples of true redundancy. For example, the multiplicity of ring-cleaving dioxygenases in certain rhodococcal isolates may be attributed to the cryptic aromatic catabolism of different terpenoids and steroids. Finally, analyses have indicated that recent genetic flux appears to have played a more significant role in the evolution of some large genomes, such as LB400's, than others. However, the emerging trend is that the large gene repertoires of potent pollutant degraders such as LB400 and RHA1 have evolved principally through more ancient processes. That this is true in such phylogenetically diverse species is remarkable and further suggests the ancient origin of this catabolic capacity.
Anaerobic biodegradation of pollutants
AnaerobicAnaerobic organism
An anaerobic organism or anaerobe is any organism that does not require oxygen for growth. It could possibly react negatively and may even die if oxygen is present...
microbial mineralization of recalcitrant organic pollutant
Pollutant
A pollutant is a waste material that pollutes air, water or soil, and is the cause of pollution.Three factors determine the severity of a pollutant: its chemical nature, its concentration and its persistence. Some pollutants are biodegradable and therefore will not persist in the environment in the...
s is of great environmental significance and involves intriguing novel biochemical reactions. In particular, hydrocarbon
Hydrocarbon
In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons from which one hydrogen atom has been removed are functional groups, called hydrocarbyls....
s and halogenated compounds have long been doubted to be degradable in the absence of oxygen, but the isolation of hitherto unknown anaerobic hydrocarbon-degrading and reductively dehalogenating bacteria
Bacteria
Bacteria are a large domain of prokaryotic microorganisms. Typically a few micrometres in length, bacteria have a wide range of shapes, ranging from spheres to rods and spirals...
during the last decades provided ultimate proof for these processes in nature. Many novel biochemical reactions were discovered enabling the respective metabolic pathways, but progress in the molecular understanding of these bacteria was rather slow, since genetic systems are not readily applicable for most of them. However, with the increasing application of genomics
Genomics
Genomics is a discipline in genetics concerning the study of the genomes of organisms. The field includes intensive efforts to determine the entire DNA sequence of organisms and fine-scale genetic mapping efforts. The field also includes studies of intragenomic phenomena such as heterosis,...
in the field of environmental microbiology
Environmental microbiology
Environmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
, a new and promising perspective is now at hand to obtain molecular insights into these new metabolic properties. Several complete genome sequences were determined during the last few years from bacteria capable of anaerobic organic pollutant degradation. The ~4.7 Mb genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
of the facultative denitrifying Aromatoleum aromaticum strain EbN1 was the first to be determined for an anaerobic hydrocarbon degrader (using toluene
Toluene
Toluene, formerly known as toluol, is a clear, water-insoluble liquid with the typical smell of paint thinners. It is a mono-substituted benzene derivative, i.e., one in which a single hydrogen atom from the benzene molecule has been replaced by a univalent group, in this case CH3.It is an aromatic...
or ethylbenzene
Ethylbenzene
Ethylbenzene is an organic compound with the formula C6H5CH2CH3. This aromatic hydrocarbon is important in the petrochemical industry as an intermediate in the production of styrene, which in turn is used for making polystyrene, a common plastic material....
as substrate
Substrate (chemistry)
In chemistry, a substrate is the chemical species being observed, which reacts with a reagent. This term is highly context-dependent. In particular, in biochemistry, an enzyme substrate is the material upon which an enzyme acts....
s). The genome sequence revealed about two dozen gene cluster
Gene cluster
A gene cluster is a set of two or more genes that serve to encode for the same or similar products. Because populations from a common ancestor tend to possess the same varieties of gene clusters, they are useful for tracing back recent evolutionary history...
s (including several paralogs) coding for a complex catabolic network for anaerobic and aerobic degradation of aromatic compounds. The genome sequence forms the basis for current detailed studies on regulation of pathways and enzyme
Enzyme
Enzymes are proteins that catalyze chemical reactions. In enzymatic reactions, the molecules at the beginning of the process, called substrates, are converted into different molecules, called products. Almost all chemical reactions in a biological cell need enzymes in order to occur at rates...
structures. Further genomes of anaerobic hydrocarbon degrading bacteria were recently completed for the iron-reducing species Geobacter metallireducens (accession nr. NC_007517) and the perchlorate-reducing Dechloromonas aromatica (accession nr. NC_007298), but these are not yet evaluated in formal publications. Complete genomes were also determined for bacteria capable of anaerobic degradation of halogenated hydrocarbons by halorespiration
Halorespiration
Halorespiration is the use of halogenated compounds as sources of energy. The halogen serves as terminal electron acceptor. It is also called dehalorespiration....
: the ~1.4 Mb genomes of Dehalococcoides ethenogenes strain 195 and Dehalococcoides
Dehalococcoides
Dehalococcoides is a genus of bacteria within class Dehalococcoidetes that obtain energy via the oxidation of hydrogen gas and subsequent reductive dehalogenation of halogenated organic compounds.-Reductive dehalogenation:...
sp. strain CBDB1 and the ~5.7 Mb genome of Desulfitobacterium hafniense strain Y51. Characteristic for all these bacteria is the presence of multiple paralogous genes for reductive dehalogenases, implicating a wider dehalogenating spectrum of the organisms than previously known. Moreover, genome sequences provided unprecedented insights into the evolution of reductive dehalogenation and differing strategies for niche adaptation.
Recently, it has become apparent that some organisms, including Desulfitobacterium chlororespirans, originally evaluated for halorespiration on chlorophenols, can also use certain brominated compounds, such as the herbicide bromoxynil
Bromoxynil
Bromoxynil is a nitrile herbicide, trade names include Brominal, Bromotril, Bronate, Buctril, Certrol B, Litarol, M&B 10064, Merit, Pardner, Sabre, and Torch. It is used for post-emergent control of annual broadleaf weeds. It is especially effective in the control of weeds in cereal, corn,...
and its major metabolite as electron acceptors for growth. Iodinated compounds may be dehalogenated as well, though the process may not satisfy the need for an electron acceptor.
Bioavailability, chemotaxis, and transport of pollutants
BioavailabilityBioavailability
In pharmacology, bioavailability is a subcategory of absorption and is used to describe the fraction of an administered dose of unchanged drug that reaches the systemic circulation, one of the principal pharmacokinetic properties of drugs. By definition, when a medication is administered...
, or the amount of a substance that is physiochemically accessible to microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
s is a key factor in the efficient biodegradation
Biodegradation
Biodegradation or biotic degradation or biotic decomposition is the chemical dissolution of materials by bacteria or other biological means...
of pollutants. O'Loughlin et al. (2000) showed that, with the exception of kaolinite
Kaolinite
Kaolinite is a clay mineral, part of the group of industrial minerals, with the chemical composition Al2Si2O54. It is a layered silicate mineral, with one tetrahedral sheet linked through oxygen atoms to one octahedral sheet of alumina octahedra...
clay, most soil clays and cation exchange resins attenuated biodegradation of 2-picoline by Arthrobacter
Arthrobacter
Arthrobacter is a genus of bacteria that is commonly found in soil. All species in this genus are Gram-positive obligate aerobes that are rods during exponential growth and cocci in their stationary phase....
sp. strain R1, as a result of adsorption of the substrate to the clays. Chemotaxis
Chemotaxis
Chemotaxis is the phenomenon in which somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food by swimming towards the highest concentration of food molecules,...
, or the directed movement of motile organisms towards or away from chemicals in the environment is an important physiological response that may contribute to effective catabolism of molecules in the environment. In addition, mechanisms for the intracellular accumulation of aromatic molecules via various transport mechanisms are also important.
Oil biodegradation
PetroleumPetroleum
Petroleum or crude oil is a naturally occurring, flammable liquid consisting of a complex mixture of hydrocarbons of various molecular weights and other liquid organic compounds, that are found in geologic formations beneath the Earth's surface. Petroleum is recovered mostly through oil drilling...
oil contains aromatic compounds that are toxic for most life forms. Episodic and chronic pollution
Pollution
Pollution is the introduction of contaminants into a natural environment that causes instability, disorder, harm or discomfort to the ecosystem i.e. physical systems or living organisms. Pollution can take the form of chemical substances or energy, such as noise, heat or light...
of the environment by oil causes major ecological perturbations. Marine environments are especially vulnerable since oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult. In addition to pollution through human activities, about 250 million liters of petroleum enter the marine environment every year from natural seepages. Despite its toxicity, a considerable fraction of petroleum oil entering marine systems is eliminated by the hydrocarbon-degrading activities of microbial communities, in particular by a remarkable recently discovered group of specialists, the so-called hydrocarbonoclastic bacteria (HCB). Alcanivorax borkumensis was the first HCB to have its genome sequenced. In addition to hydrocarbons, crude oil often contains various heterocyclic compounds, such as pyridine, which appear to be degraded by similar, though separate mechanisms than hydrocarbons.
Cholesterol biodegradation
CholesterolCholesterol
Cholesterol is a complex isoprenoid. Specifically, it is a waxy steroid of fat that is produced in the liver or intestines. It is used to produce hormones and cell membranes and is transported in the blood plasma of all mammals. It is an essential structural component of mammalian cell membranes...
is a steroid highly abundant in the environment that plays a major role in the global carbon cycle. Many synthetic steroidic compounds like some sexual hormones frequently appear in municipal and industrial wastewaters, acting as environmental pollutants with strong metabolic activities negatively affecting the ecosystems. Since these compounds are common carbon sources for many different microorganisms their aerobic and anaerobic mineralization has been extensively studied. The interest of these studies lies on the biotechnological applications of sterol transforming enzymes for the industrial synthesis of sexual hormones and corticoids. Very recently the catabolism of cholesterol has acquired a high relevance because it is involved in the infectivity of Mycobacterium tuberculosis.
Analysis of waste biotreatment
Sustainable development requires the promotion of environmental management and a constant search for new technologies to treat vast quantities of wastes generated by increasing anthropogenicAnthropogenic
Human impact on the environment or anthropogenic impact on the environment includes impacts on biophysical environments, biodiversity and other resources. The term anthropogenic designates an effect or object resulting from human activity. The term was first used in the technical sense by Russian...
activities. Biotreatment, the processing of wastes using living organisms, is an environmentally friendly, relatively simple and cost-effective alternative to physico-chemical clean-up options. Confined environments, such as bioreactors, have been engineered to overcome the physical, chemical and biological limiting factors of biotreatment processes in highly controlled systems. The great versatility in the design of confined environments allows the treatment of a wide range of wastes under optimized conditions. To perform a correct assessment, it is necessary to consider various microorganisms having a variety of genome
Genome
In modern molecular biology and genetics, the genome is the entirety of an organism's hereditary information. It is encoded either in DNA or, for many types of virus, in RNA. The genome includes both the genes and the non-coding sequences of the DNA/RNA....
s and expressed transcripts and proteins. A great number of analyses are often required. Using traditional genomic techniques, such assessments are limited and time-consuming. However, several high-throughput techniques originally developed for medical studies can be applied to assess biotreatment in confined environments.
Metabolic engineering and biocatalytic applications
The study of the fate of persistent organic chemicals in the environment has revealed a large reservoir of enzymatic reactions with a large potential in preparative organic synthesis, which has already been exploited for a number of oxygenaseOxygenase
An oxygenase is any enzyme that oxidizes a substrate by transferring the oxygen from molecular oxygen O2 to it. The oxygenases form a class of oxidoreductases; their EC number is EC 1.13 or EC 1.14....
s on pilot and even on industrial scale. Novel catalysts can be obtained from metagenomic libraries and DNA sequence
DNA sequence
The sequence or primary structure of a nucleic acid is the composition of atoms that make up the nucleic acid and the chemical bonds that bond those atoms. Because nucleic acids, such as DNA and RNA, are unbranched polymers, this specification is equivalent to specifying the sequence of...
based approaches. Our increasing capabilities in adapting the catalysts to specific reactions and process requirements by rational and random mutagenesis
Mutagenesis
Mutagenesis is a process by which the genetic information of an organism is changed in a stable manner, resulting in a mutation. It may occur spontaneously in nature, or as a result of exposure to mutagens. It can also be achieved experimentally using laboratory procedures...
broadens the scope for application in the fine chemical industry, but also in the field of biodegradation
Biodegradation
Biodegradation or biotic degradation or biotic decomposition is the chemical dissolution of materials by bacteria or other biological means...
. In many cases, these catalysts need to be exploited in whole cell bioconversion
Bioconversion
The term Bioconversion, also known as biotransformation refers to the use of live organisms often microorganisms to carry out a chemical reaction that is more costly or not feasible nonbiologically. These organisms converts a substance to a chemically modified form. An example is the industrial...
s or in fermentation
Fermentation (biochemistry)
Fermentation is the process of extracting energy from the oxidation of organic compounds, such as carbohydrates, using an endogenous electron acceptor, which is usually an organic compound. In contrast, respiration is where electrons are donated to an exogenous electron acceptor, such as oxygen,...
s, calling for system-wide approaches to understanding strain physiology and metabolism and rational approaches to the engineering of whole cells as they are increasingly put forward in the area of systems biotechnology
Biotechnology
Biotechnology is a field of applied biology that involves the use of living organisms and bioprocesses in engineering, technology, medicine and other fields requiring bioproducts. Biotechnology also utilizes these products for manufacturing purpose...
and synthetic biology.
Fungal biodegradation
In the ecosystem, different substrates are attacked at different rates by consortia of organisms from different kingdoms. AspergillusAspergillus
Aspergillus is a genus consisting of several hundred mold species found in various climates worldwide. Aspergillus was first catalogued in 1729 by the Italian priest and biologist Pier Antonio Micheli...
and other moulds play an important role in these consortia because they are adept at recycling starches, hemicelluloses, celluloses, pectins and other sugar polymers. Some aspergilli are capable of degrading more refractory compounds such as fats, oils, chitin, and keratin. Maximum decomposition occurs when there is sufficient nitrogen, phosphorus and other essential inorganic nutrients. Fungi also provide food for many soil organisms.
For Aspergillus the process of degradation is the means of obtaining nutrients. When these moulds degrade human-made substrates, the process usually is called biodeterioration. Both paper and textiles (cotton, jute, and linen) are particularly vulnerable to Aspergillus degradation. Our artistic heritage is also subject to Aspergillus assault. To give but one example, after Florence in Italy flooded in 1969, 74% of the isolates from a damaged Ghirlandaio fresco in the Ognissanti church were Aspergillus versicolor.
See also
- BiodegradationBiodegradationBiodegradation or biotic degradation or biotic decomposition is the chemical dissolution of materials by bacteria or other biological means...
- BioremediationBioremediationBioremediation is the use of microorganism metabolism to remove pollutants. Technologies can be generally classified as in situ or ex situ. In situ bioremediation involves treating the contaminated material at the site, while ex situ involves the removal of the contaminated material to be treated...
- BiotransformationBiotransformationBiotransformation is the chemical modification made by an organism on a chemical compound. If this modification ends in mineral compounds like CO2, NH4+, or H2O, the biotransformation is called mineralisation....
- BioavailabilityBioavailabilityIn pharmacology, bioavailability is a subcategory of absorption and is used to describe the fraction of an administered dose of unchanged drug that reaches the systemic circulation, one of the principal pharmacokinetic properties of drugs. By definition, when a medication is administered...
- ChemotaxisChemotaxisChemotaxis is the phenomenon in which somatic cells, bacteria, and other single-cell or multicellular organisms direct their movements according to certain chemicals in their environment. This is important for bacteria to find food by swimming towards the highest concentration of food molecules,...
- MicrobiologyMicrobiologyMicrobiology is the study of microorganisms, which are defined as any microscopic organism that comprises either a single cell , cell clusters or no cell at all . This includes eukaryotes, such as fungi and protists, and prokaryotes...
- Environmental microbiologyEnvironmental microbiologyEnvironmental microbiology is the study of the composition and physiology of microbial communities in the environment. The environment in this case means the soil, water, air and sediments covering the planet and can also include the animals and plants that inhabit these areas...
- Industrial microbiologyIndustrial microbiologyIndustrial microbiology or microbial biotechnology encompasses the use of microorganisms in the manufacture of food or industrial products. The use of microorganisms for the production of food, either human or animal, is often considered a branch of food microbiology...