Environmental microbiology
Encyclopedia
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 sediment
s covering the planet and can also include the animals and plants that inhabit these areas. Environmental microbiology also includes the study of microorganism
s that exist in artificial environments such as bioreactor
s.
Microbial life is amazingly diverse and microorganism
s literally cover the planet.
An average gram of soil contains approximately one billion (1,000,000,000) microbes representing probably several thousand species
. Microorganisms have special impact on the whole biosphere
. They are the backbone of ecosystem
s of the zones where light cannot approach. In such zones, chemosynthetic bacteria are present which provide energy and carbon to the other organisms there. Some microbes are decomposers which have ability to recycle the nutrients. Microbes have a special role in biogeochemical cycles. Microbes, especially bacteria, are of great importance because their symbiotic relationship (either positive, neutral, or negative) have special effects on the ecosystem.
Microorganisms are used for in-situ microbial biodegradation
or bioremediation
of domestic, agricultural and industrial wastes and subsurface pollution
in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste
depends on the nature of each contaminant. Since most sites typically have multiple pollutant types, the most effective approach to microbial biodegradation
is to use a mixture of bacterial species and strains, each specific to the biodegradation
of one or more types of contaminants. It is vital to monitor the composition of the indigenous and added bacteria in order to evaluate the activity level and to permit modifications of the nutrients and other conditions for optimizing the bioremediation process.
s, organophosphorus
compounds, alkane
s, PAH
s and PCB
s.
moisture effect in microbes
oil is toxic, and pollution
of the environment by oil causes major ecological concern. Oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult; much of the oil can, however, be eliminated by the hydrocarbon-degrading activities of microbial communities, in particular the hydrocarbonoclastic bacteria (HCB). These organisms can help remedy the ecological damage caused by oil pollution of marine habitats. HCB also have potential biotechnological applications in the areas of bioplastic
s and biocatalysis
.
, the processing of wastes using living organisms, is an environmentally friendly alternative to other options for treating waste material. Bioreactors have been designed to overcome the various limiting factors of biotreatment processes in highly controlled systems. This versatility in the design of bioreactors allows the treatment of a wide range of wastes under optimized conditions. It is vital to consider various microorganisms and a great number of analyses are often required.
and genomics
to environmental microbiology has led to the discovery of a huge complexity in natural communities of microbes. Diversity surveying, community fingerprinting and functional interrogation of natural populations have become common, enabled by a range of molecular and bioinformatics
techniques. Recent studies on the ecology of cyanobacteria have covered many habitats and have demonstrated that cyanobacterial communities tend to be habitat
-specific and that much genetic diversity is concealed among morphologically simple types. Molecular, bioinformatics, physiological and geochemical techniques have combined in the study of natural communities of these bacteria.
is common in many environments, with at least 50 species and 70 serogroups identified. Legionella
is commonly found in aquatic habitats where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans.
were once thought of as extremophile
s existing only in hostile environments but have since been found in all habitats and may contribute up to 20% of total biomass. Archaea are particularly common in the oceans, and the archaea in plankton
may be one of the most abundant groups of organisms on the planet. Archaea are subdivided into four phyla of which two, the Crenarchaeota and the Euryarchaeota, are most intensively studied.
of humans, where they are symbiotic and make up a portion of the gut flora
.
spores are common components of aerosols where they drift on air currents, dispersing themselves both short and long distances depending on environmental conditions. When the spores come in contact with a solid or liquid surface, they are deposited and if conditions of moisture are right, they germinate. The ability to disperse globally in air currents and to grow almost anywhere when appropriate food and water are available means that ubiquitous is among the most common adjectives used to describe these moulds.
. Another set of microbial reactions utilise the bioavailable nitrogen creating N2 and completing the cycle in a process called denitrification
. This crucial nutrient cycle has long been the subject of extensive research.
is a mutualistic process in which bacteria reside inside plants and reduce atmospheric nitrogen to ammonia. This ammonia can then be used by the plant for the synthesis of proteins and other nitrogen-containing compounds such as nucleic acids. The Gram-negative soil bacteria that carry out this process are collectively referred to as rhizobia
(from the Greek words Riza = Root and Bios = Life). The process of symbiotic nitrogen fixation is of agricultural and ecological significance because plants capable of nitrogen fixation do not need to compete for limited quantities of soil nitrogen, nor do they require expensive nitrogenous fertilizers that can be harmful to the environment.
are a highly diverse group of protists, ranging from simple, unicellular organisms to complex, multicellular entities with a range of differentiated tissues and distinct organs. They are found among diverse aquatic ecosystems and play important roles by supplying carbon and energy as well as providing habitat to other members of the biological communities. Some algae cause significant environmental and health problems. There are three algal groups: the dinoflagellates, the diatoms and the haptophytes. their 3 main phylla are chlorophyta,rhodophyta and phaeophyta.
s are a group of mitochondrion
-lacking, binucleated flagellates found in anaerobic or micro-aerophilic environments. Most research on diplomonads has focused on Giardia
, which is a major cause of water-borne enteric disease in humans and other animals. The first diplomonad to have its genome sequenced was a Giardia isolate (WB) and the 11.7 million basepair genome is compact in structure and content with simplified basic cellular machineries and metabolism.
s. Presently, microbial tests are based essentially on time-consuming culture methods. However, newer enzymatic, immunological and genetic methods are being developed to replace and/or support classical approaches to microbial detection. Moreover, innovations in nanotechnology
and nanosciences are having a significant impact in biodiagnostics, where a number of nanoparticle-based assays and nanodevices have been introduced for biomolecular detection.
Molecular techniques based on genomics
, proteomics
and transcriptomics are rapidly growing as complete microbial genome sequences are becoming available, and advances are made in sequencing technology, analytical biochemistry, microfluidics and data analysis. While the clinical and food industries are increasingly adapting these techniques, there appear to be major challenges in detecting health-related microbes in source and treated drinking waters. This is due in part to the low density of pathogens in water, necessitating significant processing of large volume samples. From the vast panorama of available molecular techniques, some are finding a place in the water industry: Quantitative PCR, protein detection and immunological approaches, loop-mediated isothermal amplification (LAMP), microarrays.
) in response to signals in the intracellular and extracellular environment. The interaction of a signal with its receptor (usually a protein or RNA molecule) triggers a series of events that lead to reprogramming of cellular physiology, typically as a consequence of altered patterns of gene expression. In this way, the bacterial cell is able to mount appropriate and effective responses to changing physical and/or chemical environments. The versatility with which many bacteria adapt to environmental change underlies many important aspects of microbiology. For example, pathogens encounter multiple environments as they invade a host from the outside, and then progress through different sites within host tissues. There is growing evidence that pathogenic bacteria make use of physical and chemical cues to signal their presence in a suitable host, and need to adapt to the host environment in order to mount a successful infection. On the other hand, it should not be assumed that all signals to which bacteria must respond originate in the extracellular environment. For many species, even the cosseted life in a laboratory shake flask is 'stressful', in the sense that there is often a need to avoid or reverse the effects of harmful intermediates or by-products of metabolism. For example, all organisms that use dioxygen as a terminal electron acceptor have to deal with the reactive oxygen species
that arise as adventitious by-products of aerobic metabolism. In bacteria, multiple protein receptors for oxygen radicals have been described, which control the expression of genes encoding enzymes that detoxify oxygen radicals or repair the damage that they cause.
is the cultivation-independent analysis of the collective genomes of microbes within a given environment, using sequence- and function-based approaches. Metagenomic studies have revealed the vast size and richness of the microbial and viral world and demonstrated the phylogenetic diversity of various environments. Access to huge volume genomic sequence data from uncultured organisms has opened up many new avenues of research. Advances in the throughput of sequencing and screening technologies have greatly facilitated metagenomics research.
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....
. The environment in this case means the soil
Soil
Soil is a natural body consisting of layers of mineral constituents of variable thicknesses, which differ from the parent materials in their morphological, physical, chemical, and mineralogical characteristics...
, water
Water
Water is a chemical substance with the chemical formula H2O. A water molecule contains one oxygen and two hydrogen atoms connected by covalent bonds. Water is a liquid at ambient conditions, but it often co-exists on Earth with its solid state, ice, and gaseous state . Water also exists in a...
, air and sediment
Sediment
Sediment is naturally occurring material that is broken down by processes of weathering and erosion, and is subsequently transported by the action of fluids such as wind, water, or ice, and/or by the force of gravity acting on the particle itself....
s covering the planet and can also include the animals and plants that inhabit these areas. Environmental microbiology also includes the study of microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
s that exist in artificial environments such as bioreactor
Bioreactor
A bioreactor may refer to any manufactured or engineered device or system that supports a biologically active environment. In one case, a bioreactor is a vessel in which a chemical process is carried out which involves organisms or biochemically active substances derived from such organisms. This...
s.
Microbial life is amazingly diverse and microorganism
Microorganism
A microorganism or microbe is a microscopic organism that comprises either a single cell , cell clusters, or no cell at all...
s literally cover the planet.
An average gram of soil contains approximately one billion (1,000,000,000) microbes representing probably several thousand species
Species
In biology, a species is one of the basic units of biological classification and a taxonomic rank. A species is often defined as a group of organisms capable of interbreeding and producing fertile offspring. While in many cases this definition is adequate, more precise or differing measures are...
. Microorganisms have special impact on the whole biosphere
Biosphere
The biosphere is the global sum of all ecosystems. It can also be called the zone of life on Earth, a closed and self-regulating system...
. They are the backbone of ecosystem
Ecosystem
An ecosystem is a biological environment consisting of all the organisms living in a particular area, as well as all the nonliving , physical components of the environment with which the organisms interact, such as air, soil, water and sunlight....
s of the zones where light cannot approach. In such zones, chemosynthetic bacteria are present which provide energy and carbon to the other organisms there. Some microbes are decomposers which have ability to recycle the nutrients. Microbes have a special role in biogeochemical cycles. Microbes, especially bacteria, are of great importance because their symbiotic relationship (either positive, neutral, or negative) have special effects on the ecosystem.
Microorganisms are used for in-situ microbial biodegradation
Microbial biodegradation
Interest in the microbial biodegradation of pollutants has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments...
or 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...
of domestic, agricultural and industrial wastes and subsurface 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...
in soils, sediments and marine environments. The ability of each microorganism to degrade toxic waste
Toxic waste
Toxic waste is waste material that can cause death or injury to living creatures. It spreads quite easily and can contaminate lakes and rivers. The term is often used interchangeably with “hazardous waste”, or discarded material that can pose a long-term risk to health or environment.Toxic waste...
depends on the nature of each contaminant. Since most sites typically have multiple pollutant types, the most effective approach to microbial biodegradation
Microbial biodegradation
Interest in the microbial biodegradation of pollutants has intensified in recent years as humanity strives to find sustainable ways to clean up contaminated environments...
is to use a mixture of bacterial species and strains, each specific to the biodegradation
Biodegradation
Biodegradation or biotic degradation or biotic decomposition is the chemical dissolution of materials by bacteria or other biological means...
of one or more types of contaminants. It is vital to monitor the composition of the indigenous and added bacteria in order to evaluate the activity level and to permit modifications of the nutrients and other conditions for optimizing the bioremediation process.
Biodegradation of pollutants
Microbial biodegradation of pollutants plays a pivotal role in the bioremediation of contaminated soil and groundwater sites. Such pollutants include chloroethenes, steroidSteroid
A steroid is a type of organic compound that contains a characteristic arrangement of four cycloalkane rings that are joined to each other. Examples of steroids include the dietary fat cholesterol, the sex hormones estradiol and testosterone, and the anti-inflammatory drug dexamethasone.The core...
s, organophosphorus
Organophosphorus
Organophosphorus compounds are degradable organic compounds containing carbon–phosphorus bonds , used primarily in pest control as an alternative to chlorinated hydrocarbons that persist in the environment...
compounds, alkane
Alkane
Alkanes are chemical compounds that consist only of hydrogen and carbon atoms and are bonded exclusively by single bonds without any cycles...
s, PAH
Polycyclic aromatic hydrocarbon
Polycyclic aromatic hydrocarbons , also known as poly-aromatic hydrocarbons or polynuclear aromatic hydrocarbons, are potent atmospheric pollutants that consist of fused aromatic rings and do not contain heteroatoms or carry substituents. Naphthalene is the simplest example of a PAH...
s and PCB
Polychlorinated biphenyl
Polychlorinated biphenyls are a class of organic compounds with 2 to 10 chlorine atoms attached to biphenyl, which is a molecule composed of two benzene rings. The chemical formula for PCBs is C12H10-xClx...
s.
moisture effect in microbes
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 is toxic, and 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 concern. Oil spills of coastal regions and the open sea are poorly containable and mitigation is difficult; much of the oil can, however, be eliminated by the hydrocarbon-degrading activities of microbial communities, in particular the hydrocarbonoclastic bacteria (HCB). These organisms can help remedy the ecological damage caused by oil pollution of marine habitats. HCB also have potential biotechnological applications in the areas of bioplastic
Bioplastic
Bioplastics are a form of plastics derived from renewable biomass sources, such as vegetable fats and oils, corn starch, pea starch, or microbiota, rather than fossil-fuel plastics which are derived from petroleum...
s and biocatalysis
Biocatalysis
Biocatalysis is the use of natural catalysts, such as protein enzymes, to perform chemical transformations on organic compounds. Both enzymes that have been more or less isolated and enzymes still residing inside living cells are employed for this task....
.
Waste biotreatment
BiotreatmentBiotreatment
Biotreatment is the processing of waste or hazardous substance using living organisms such as bacteria, fungi or protozoa. It is an environmentally friendly, relatively simple and cost-effective alternative to physico-chemical clean-up options....
, the processing of wastes using living organisms, is an environmentally friendly alternative to other options for treating waste material. Bioreactors have been designed to overcome the various limiting factors of biotreatment processes in highly controlled systems. This versatility in the design of bioreactors allows the treatment of a wide range of wastes under optimized conditions. It is vital to consider various microorganisms and a great number of analyses are often required.
Wastewater treatment
Wastewater treatment processes are geared towards one purpose: cleaning up water. Recent application of molecular techniques is unveiling the microbial composition and architecture of the complex communities involved in the treatment processes. It is now recognized that wastewater processes harbor a vast variety of microorganisms most of which are yet-to-be cultured, hence uncharacterized. Metagenomic technology is being used to study the diversity, structure and functions of microbial communities in nitrifying processes, anaerobic ammonia oxidation processes and methane fermenting processes.Environmental genomics of cyanobacteria
The application of molecular biologyMolecular biology
Molecular biology is the branch of biology that deals with the molecular basis of biological activity. This field overlaps with other areas of biology and chemistry, particularly genetics and biochemistry...
and 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,...
to environmental microbiology has led to the discovery of a huge complexity in natural communities of microbes. Diversity surveying, community fingerprinting and functional interrogation of natural populations have become common, enabled by a range of molecular and 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...
techniques. Recent studies on the ecology of cyanobacteria have covered many habitats and have demonstrated that cyanobacterial communities tend to be habitat
Habitat
* Habitat , a place where a species lives and grows*Human habitat, a place where humans live, work or play** Space habitat, a space station intended as a permanent settlement...
-specific and that much genetic diversity is concealed among morphologically simple types. Molecular, bioinformatics, physiological and geochemical techniques have combined in the study of natural communities of these bacteria.
Corynebacteria
Corynebacteria are a diverse group Gram-positive bacteria found in a range of different ecological niches such as soil, vegetables, sewage, skin, and cheese smear. Some, such as Corynebacterium diphtheriae, are important pathogens while others, such as Corynebacterium glutamicum, are of immense industrial importance. C. glutamicum is one of the biotechnologically most important bacterial species with an annual production of more than two million tons of amino acids, mainly L-glutamate and L-lysine.Legionella
LegionellaLegionella
Legionella is a pathogenic Gram negative bacterium, including species that cause legionellosis or Legionnaires' disease, most notably L. pneumophila. It may be readily visualized with a silver stain....
is common in many environments, with at least 50 species and 70 serogroups identified. Legionella
Legionella
Legionella is a pathogenic Gram negative bacterium, including species that cause legionellosis or Legionnaires' disease, most notably L. pneumophila. It may be readily visualized with a silver stain....
is commonly found in aquatic habitats where its ability to survive and to multiply within different protozoa equips the bacterium to be transmissible and pathogenic to humans.
Archaea
Originally, ArchaeaArchaea
The Archaea are a group of single-celled microorganisms. A single individual or species from this domain is called an archaeon...
were once thought of as extremophile
Extremophile
An extremophile is an organism that thrives in physically or geochemically extreme conditions that are detrimental to most life on Earth. In contrast, organisms that live in more moderate environments may be termed mesophiles or neutrophiles...
s existing only in hostile environments but have since been found in all habitats and may contribute up to 20% of total biomass. Archaea are particularly common in the oceans, and the archaea in plankton
Plankton
Plankton are any drifting organisms that inhabit the pelagic zone of oceans, seas, or bodies of fresh water. That is, plankton are defined by their ecological niche rather than phylogenetic or taxonomic classification...
may be one of the most abundant groups of organisms on the planet. Archaea are subdivided into four phyla of which two, the Crenarchaeota and the Euryarchaeota, are most intensively studied.
Lactobacillus
Lactobacillus species are found in the environment mainly associated with plant material. They are also found in the gastrointestinal tractGastrointestinal tract
The human gastrointestinal tract refers to the stomach and intestine, and sometimes to all the structures from the mouth to the anus. ....
of humans, where they are symbiotic and make up a portion of the gut flora
Gut flora
Gut flora consists of microorganisms that live in the digestive tracts of animals and is the largest reservoir of human flora. In this context, gut is synonymous with intestinal, and flora with microbiota and microflora....
.
Aspergillus
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...
spores are common components of aerosols where they drift on air currents, dispersing themselves both short and long distances depending on environmental conditions. When the spores come in contact with a solid or liquid surface, they are deposited and if conditions of moisture are right, they germinate. The ability to disperse globally in air currents and to grow almost anywhere when appropriate food and water are available means that ubiquitous is among the most common adjectives used to describe these moulds.
Microbial nitrogen cycling
Microorganisms that convert gaseous nitrogen (N2) to a form suitable for use by living organisms are pivotal for life on earth. This process is called nitrogen fixationNitrogen fixation
Nitrogen fixation is the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia . This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g., nucleotides for DNA and RNA and...
. Another set of microbial reactions utilise the bioavailable nitrogen creating N2 and completing the cycle in a process called denitrification
Denitrification
Denitrification is a microbially facilitated process of nitrate reduction that may ultimately produce molecular nitrogen through a series of intermediate gaseous nitrogen oxide products....
. This crucial nutrient cycle has long been the subject of extensive research.
Rhizobia
Symbiotic nitrogen fixationNitrogen fixation
Nitrogen fixation is the natural process, either biological or abiotic, by which nitrogen in the atmosphere is converted into ammonia . This process is essential for life because fixed nitrogen is required to biosynthesize the basic building blocks of life, e.g., nucleotides for DNA and RNA and...
is a mutualistic process in which bacteria reside inside plants and reduce atmospheric nitrogen to ammonia. This ammonia can then be used by the plant for the synthesis of proteins and other nitrogen-containing compounds such as nucleic acids. The Gram-negative soil bacteria that carry out this process are collectively referred to as rhizobia
Rhizobia
Rhizobia are soil bacteria that fix nitrogen after becoming established inside root nodules of legumes . Rhizobia require a plant host; they cannot independently fix nitrogen...
(from the Greek words Riza = Root and Bios = Life). The process of symbiotic nitrogen fixation is of agricultural and ecological significance because plants capable of nitrogen fixation do not need to compete for limited quantities of soil nitrogen, nor do they require expensive nitrogenous fertilizers that can be harmful to the environment.
Microalgae
AlgaeAlgae
Algae are a large and diverse group of simple, typically autotrophic organisms, ranging from unicellular to multicellular forms, such as the giant kelps that grow to 65 meters in length. They are photosynthetic like plants, and "simple" because their tissues are not organized into the many...
are a highly diverse group of protists, ranging from simple, unicellular organisms to complex, multicellular entities with a range of differentiated tissues and distinct organs. They are found among diverse aquatic ecosystems and play important roles by supplying carbon and energy as well as providing habitat to other members of the biological communities. Some algae cause significant environmental and health problems. There are three algal groups: the dinoflagellates, the diatoms and the haptophytes. their 3 main phylla are chlorophyta,rhodophyta and phaeophyta.
Anaerobic protozoa
DiplomonadDiplomonad
The diplomonads are a group of flagellates, most of which are parasitic. They include most notably Giardia lamblia, which causes giardiasis in humans...
s are a group of mitochondrion
Mitochondrion
In cell biology, a mitochondrion is a membrane-enclosed organelle found in most eukaryotic cells. These organelles range from 0.5 to 1.0 micrometers in diameter...
-lacking, binucleated flagellates found in anaerobic or micro-aerophilic environments. Most research on diplomonads has focused on Giardia
Giardia
Giardia is a genus of anaerobic flagellated protozoan parasites of the phylum Metamonada in the supergroup "Excavata" that colonise and reproduce in the small intestines of several vertebrates, causing giardiasis, commonly known as Beaver fever...
, which is a major cause of water-borne enteric disease in humans and other animals. The first diplomonad to have its genome sequenced was a Giardia isolate (WB) and the 11.7 million basepair genome is compact in structure and content with simplified basic cellular machineries and metabolism.
Water microbiology
An adequate supply of safe drinking water is one of the major prerequisites for a healthy life, but waterborne diseases are still a major cause of death in many parts of the world, particularly in young children, the elderly, or those with compromised immune systems. As the epidemiology of waterborne diseases is changing, there is a growing global public health concern about new and reemerging infectious diseases that are occurring through a complex interaction of social, economic, evolutionary, and ecological factors. An important challenge is therefore the rapid, specific and sensitive detection of waterborne pathogenPathogen
A pathogen gignomai "I give birth to") or infectious agent — colloquially, a germ — is a microbe or microorganism such as a virus, bacterium, prion, or fungus that causes disease in its animal or plant host...
s. Presently, microbial tests are based essentially on time-consuming culture methods. However, newer enzymatic, immunological and genetic methods are being developed to replace and/or support classical approaches to microbial detection. Moreover, innovations in nanotechnology
Nanotechnology
Nanotechnology is the study of manipulating matter on an atomic and molecular scale. Generally, nanotechnology deals with developing materials, devices, or other structures possessing at least one dimension sized from 1 to 100 nanometres...
and nanosciences are having a significant impact in biodiagnostics, where a number of nanoparticle-based assays and nanodevices have been introduced for biomolecular detection.
Molecular techniques based on 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...
and transcriptomics are rapidly growing as complete microbial genome sequences are becoming available, and advances are made in sequencing technology, analytical biochemistry, microfluidics and data analysis. While the clinical and food industries are increasingly adapting these techniques, there appear to be major challenges in detecting health-related microbes in source and treated drinking waters. This is due in part to the low density of pathogens in water, necessitating significant processing of large volume samples. From the vast panorama of available molecular techniques, some are finding a place in the water industry: Quantitative PCR, protein detection and immunological approaches, loop-mediated isothermal amplification (LAMP), microarrays.
Sensory mechanisms
Bacteria have evolved abilities to regulate aspects of their behaviour (such as gene expressionGene expression
Gene expression is the process by which information from a gene is used in the synthesis of a functional gene product. These products are often proteins, but in non-protein coding genes such as ribosomal RNA , transfer RNA or small nuclear RNA genes, the product is a functional RNA...
) in response to signals in the intracellular and extracellular environment. The interaction of a signal with its receptor (usually a protein or RNA molecule) triggers a series of events that lead to reprogramming of cellular physiology, typically as a consequence of altered patterns of gene expression. In this way, the bacterial cell is able to mount appropriate and effective responses to changing physical and/or chemical environments. The versatility with which many bacteria adapt to environmental change underlies many important aspects of microbiology. For example, pathogens encounter multiple environments as they invade a host from the outside, and then progress through different sites within host tissues. There is growing evidence that pathogenic bacteria make use of physical and chemical cues to signal their presence in a suitable host, and need to adapt to the host environment in order to mount a successful infection. On the other hand, it should not be assumed that all signals to which bacteria must respond originate in the extracellular environment. For many species, even the cosseted life in a laboratory shake flask is 'stressful', in the sense that there is often a need to avoid or reverse the effects of harmful intermediates or by-products of metabolism. For example, all organisms that use dioxygen as a terminal electron acceptor have to deal with the reactive oxygen species
Reactive oxygen species
Reactive oxygen species are chemically reactive molecules containing oxygen. Examples include oxygen ions and peroxides. Reactive oxygen species are highly reactive due to the presence of unpaired valence shell electrons....
that arise as adventitious by-products of aerobic metabolism. In bacteria, multiple protein receptors for oxygen radicals have been described, which control the expression of genes encoding enzymes that detoxify oxygen radicals or repair the damage that they cause.
Metagenomics
MetagenomicsMetagenomics
Metagenomics is the study of metagenomes, genetic material recovered directly from environmental samples. The broad field may also be referred to as environmental genomics, ecogenomics or community genomics. Traditional microbiology and microbial genome sequencing rely upon cultivated clonal cultures...
is the cultivation-independent analysis of the collective genomes of microbes within a given environment, using sequence- and function-based approaches. Metagenomic studies have revealed the vast size and richness of the microbial and viral world and demonstrated the phylogenetic diversity of various environments. Access to huge volume genomic sequence data from uncultured organisms has opened up many new avenues of research. Advances in the throughput of sequencing and screening technologies have greatly facilitated metagenomics research.