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This knowledge enables the control of microbial growth that facilitates many of our interactions with microbes today. Many methods of control seek to eliminate harmful microbes from foods or equipment.
For example, high temperature is often used to kill microbes during cooking or through processes like pasteurization. In this way, potentially harmful microbes are broadly eliminated from the food product making it safe to consume and store.
Similarly, chemicals in disinfectants can damage or kill microbes broadly on surfaces. Alcohols like ethanol and isopropanol damage the cell membranes. Without this protective structure, microbes cannot control what enters or exits the cell. Subsequently, microbes cannot retain important nutrients and water.
Alternatively, hydrogen peroxide damages structures within the cell. As hydrogen peroxide decomposes, it forms molecules known as free radicals that damage proteins and DNA. Meanwhile, we also use soaps to physically remove microbes from surfaces. The chemical properties of soaps and physical force applied when wiping a surface dislodges the microbes.
When microbes cannot be completely eliminated from a material, such as food products that cannot be heated to high temperatures, measures can be taken to mitigate the growth of microbes. Recognizing how temperature impacts growth, supports the importance of refrigeration.
As mentioned, cold temperatures slow the growth of microbes, so refrigeration can delay the growth of microbes in these food products. As described above, microbes can replicate as quickly as every 20 minutes leading to visible growth within only a few hours.
At a lower temperature, the cells may divide only once every few hours and it will take multiple days to see visible growth. Alternatively, when we want to take advantage of microbes, we try to optimize the conditions for their growth. This is why yeasted dough is left at a warm temperature to allow the yeast to grow rapidly. If the dough is refrigerated, it takes much longer to rise. Similarly, to use E. Continuing to better understand microbial growth will help us live safely with the microbes in our community and make use of their unique capabilities.
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Click here for instructions on how to enable JavaScript in your browser. Skip to content by Molly Sargen figures by Molly Sargen and Nicholas Lue Microbes also known as microorganisms are everywhere: on surfaces we touch, in the air we breathe, and even inside us.
Figure 1: Microscopy reveals the intricate features of microbes. It takes at X magnification to see these organisms clearly with a microscope. Image sources: S. Figure 2: Features of a Microbial Cell. This diagram of a bacterial cell shows the essential features of a microbial cell including DNA, a cell membrane, and the essential components within the cell. This cell has a cell wall and also flagella an appendage some bacteria use for movement.
Mechanisms of microbial growth Microbial growth refers to an increase in number of cells rather than an increase in cell size.
Figure 3: The population increases exponentially as cells divide. Microbes with different shapes divide similarly. Figure 4: Some cells use budding to produce daughter cells. A parent cell produces small protrusions called buds. Factors affecting microbial growth All types of microbial growth are heavily impacted by environmental conditions.
Figure 5: Microbes grow well within a specific range of conditions for multiple environmental variables. Some microbes can tolerate a wide range of conditions, while others require a specific condition to grow well.
Most of the bacteria lack single or multiple enzymes involved in denitrification and known to be incomplete denitrifier, for example, most of the fungi and bacteria lack nitrous oxide reductase and thereby produce N 2 O as a final product. Therefore, incomplete denitrification results into emission of greenhouse gases. Sulfur-oxidizing prokaryotes are frequently thermophiles found in hot volcanic springs and near deep-sea thermal vents that are rich in H 2 S.
They may be acidophiles as well, because they acidify their own environment by the production of sulfuric acid. Since SO 4 and S may be used as electron acceptors for respiration, sulfate-reducing bacteria produce H 2 S during a process of anaerobic respiration analogous to denitrification.
The use of SO 4 as an electron acceptor is an obligatory process that takes place only in anaerobic environments. The process results in the distinctive odor of H 2 S in anaerobic bogs, soils, and sediments where it occurs. Sulfur is assimilated by bacteria and plants as SO 4 for use and reduction to sulfide.
Animals and bacteria can remove the sulfide group from proteins as a source of S during decomposition. These processes complete the sulfur cycle. Phosphorus is a critical element of various building blocks such as nucleic acids, e.
Phosphorus is a rare element in the environment because of its tendency to precipitate in the presence of divalent and trivalent cations at neutral and alkaline pH. Bacteria and fungi are able to biodegrade or detoxify substances through various ways; thereby, microbial processes are extensively used for bioremediation. Cost efficient, noninvasive, relatively passive, natural attenuation, treats soil and water.
Biodegradation abilities of indigenous microorganism, presence of metals and other inorganics, biodegradability of pollutants, chemical solubility, geological factor and pollutant distribution.
Space requirement, extended treatment time, abiotic loss, mass transfer problem, bioavailability limitation. Rapid degradation, optimized environmental parameters, enhanced mass transfer, effective use of intoxicant and surfactants.
Heterotrophic microbes such as Pseudomonas , Sphingomonas , and Mycobacterium are known to be involved in oil degradation. Pseudomonas is one of well-studied bacteria capable of degrading alkanes, monoaromatics, naphthalene, and phenanthrene under aerobic conditions.
The hydrocarbon-degrading bacteria are dominant in soil contaminated with oil; however, higher concentration of hydrocarbons may deplete available nitrogen and phosphorus in that area since these elements are assimilated during biodegradation.
Microbes bacteria and fungi are able to degrade a range of biodegradable pesticides such as atrazine, which is degraded by a bacterium, e. Non-biodegradable pesticides, e. Some fungi having ability to degrade lignin, such as Phanerochaete chrysosporium , are able to degrade various contaminants such as pentachlorophenol and dioxin, and the best example are Zygomycetes that degraded various contaminants during wood-treating operation in Whakatane Thwaites et al.
Biodegradation of a contaminant depends upon its chemical structure and physical state since various contaminants, e. The ability for degradation also depends upon rare and novel structures and water solubility since less soluble compounds are difficult to degrade.
Additionally, poorly water-soluble or hydrophobic contaminants also readily bind to clay particles and, therefore, are easily available to microbes present in soil. These soil microbes utilize these contaminants as energy source, present at higher concentration, and these could be toxic for them, resulting into slow biodegradation. Biodegradation also involves a contact between contaminants and microbes. Some microbes, e.
Few microbes have evolved detoxification mechanisms during their exposure to heavy metals, e. One of the known examples is cadmium accumulation in agricultural soils in New Zealand due to extensive use of superphosphate fertilizer Loganathan et al. Due to metal toxicity, microbes have evolved few defense mechanisms such as metal sequestration, detoxification, and efflux of ions.
Bacteria sequester heavy metals through their binding with cell membrane, cell wall, and extracellular polysaccharides Harrison et al. Microbes may also detoxify toxic metals through reduction using various cellular enzymes, e.
Few gram-negative bacteria, e. Nowadays, the microbial ability to transform heavy metals is being extensively used as a tool for bioremediation.
Use substrates as a reducing agent by incorporating single oxygen atom, i. Incorporating two oxygen atoms to the substrate and resulting into aliphatic products. Ortho- and paradiphenols, aminophenols, polyphenols, polyamines, lignins, and aryldiamines. Bioremediation, food and paper industry, textile industry, cosmetics, synthetic chemistry, etc. Substrate oxidation using H 2 O 2 as a co-substrate and mediator like veratryl alcohol.
Bioremediation, food and paper industry, textile industry, pharmaceutical industry, etc. Catalyzes the electron transfer from an oxidizable substrate with reduction of complex I and II intermediates. Microbial oxidoreductases detoxify toxic xenobiotics such as phenolic compounds, produced from the decomposition of lignin through polymerization, copolymerization with other substances, or binding to humic substances.
Most of the metal-reducing bacteria reduce the radioactive metals into insoluble forms that appear as a precipitant with the help of an intermediate electron donor Leung The paper and pulp industry produces chlorinated phenolic compounds upon partial degradation of lignin during pulp bleaching process. These recalcitrant wastes are removed by the action of various fungal extracellular oxidoreductase enzymes such as laccase, manganese peroxidase, and lignin peroxidase that are released from fungal mycelium into their neighborhood environment.
The plants belonging to families such as Fabaceae, Gramineae, and Solanaceae release oxidoreductases, which are recruited in the oxidative degradation of certain soil constituents. Oxygenases fall into two major categories on the basis of number of oxygen atoms used during oxygenation: monooxygenases and dioxygenases.
Oxygenases mediate dehalogenation of halogenated pollutants, methanes, ethanes, and ethylenes through association with multifunctional enzymes Fetzner and Lingens Monooxygenases play an important role in bioremediation process as a biocatalyst due to their high selectivity and stereoselectivity on the wide range of substrates. Most of the monooxygenases are known to have cofactors but few act without them. Monooxygenases incorporate single atom of oxygen molecule into the substrate and are further classified into two subgroups based on the presence of cofactor.
P monooxygenases are heme-containing oxygenases, while flavin-dependent monooxygenases consist of flavin as a prosthetic group and require NADP or NADPH as a coenzyme. Monooxygenases catalyze desulfurization, dehalogenation, denitrification, ammonification, hydroxylation, and biotransformation of various aromatic and aliphatic compounds.
Methane monooxygenase is the best-characterized monooxygenase involved in the degradation of various hydrocarbons. Monooxygenases exhibit differential activity in the presence or absence of oxygen. Monooxygenases catalyze oxidative dehalogenation under oxygen-rich conditions, whereas under low oxygen conditions, they catalyze reductive chlorination.
Microbial dioxygenases primarily oxidize aromatic compounds and are involved in bioremediation process. Aromatic hydrocarbon dioxygenases belong to Rieske non-heme iron oxygenase family and are involved in oxygenation of various substrates.
An example is naphthalene dioxygenase having Rieske 2Fe-2S cluster and mononuclear iron molecule in each alpha-subunit Dua et al. Laccases are the members of multicopper oxidase family, produced by certain plants, fungi, insects, and bacteria and catalyze oxidation of a wide range of phenolic and aromatic substrates.
Most of the microbes produce intra- and extracellular laccases, catalyzing the oxidation of aminophenols, polyphenols, ortho- or paradiphenols, lignins, aryl diamines, etc.
These enzymes act not only by oxidizing phenolic and methoxy-phenoic acids but also through their decarboxylation and demethylation. Laccases are also involved in depolymerization of lignin resulting into various phenols that are utilized by microorganisms. Microbial peroxidases catalyze oxidation of lignin and other phenolic compounds in the presence of hydrogen peroxide H 2 O 2 and a mediator.
Among all microbial peroxidases, lignin peroxidase LiP , manganese-dependent peroxidase MnP , and versatile peroxidase VP have shown potent activity to degrade toxic substances. Lignin peroxidases are heme-containing proteins secreted by white rot fungi during secondary metabolism and play an important role in degradation of lignin from plant cell wall. Manganese-dependent peroxidase is an extracellular heme-containing enzyme secreted by basidiomycete fungi.
VP exhibits broad substrate specificity and is able to oxidize substrates even in the absence of manganese as compared to other peroxidases.
Hence, bioremediation and biotechnological applications for industrial processing need efficient VP production. Microbial hydrolases play an important role in bioremediation process and act by disrupting chemical bonds in toxic compounds and thereby reduce their toxicity up to some extent.
These enzymes are readily available and do not need any cofactor for stereoselectivity. Some extracellular hydrolases such as amylases, proteases, lipases, DNases, and xylanases exhibit potential role in various sectors, e. Other hydrolases, e. Lipases are capable of degrading lipids e.
Recent reports suggest a close association of lipase with organic pollutants present in the soil, and its activity results into reduced hydrocarbon content in the contaminated soil. Microbial lipases are extensively used in industries since these enzymes catalyze various chemical reactions such as hydrolysis, esterification, alcoholysis, aminolysis, etc.
Lipase activity is an important indicator or parameter for testing hydrocarbon content present in the soil. Lipases are widely used in pharmaceutical, food, chemical, cosmetic, and paper industries, but the cost of their production limits their potent application in the industries. Cellulases convert cellulosic waste materials to glucose and have been implicated in intense research for bioremediation processes.
Some bacteria and fungi express extracellular cellulases, hemicellulases, and pectinases at very low levels, e. Cellulases are widely used in paper and pulp industry for ink removal during paper recycling, in ethanol production from cellulosic biomass, and in brewing industry to enhance juice release from fruit pulp. Proteases hydrolyze the proteinaceous substances in the atmosphere resulting from animal death, shedding, and molting of appendages, as a by-product of poultry, fishery, and leather industries.
Proteases are divided into two groups: exopeptidases and endopeptidases. Exopeptidases are further classified into aminopeptidases and carboxypeptidases depending on their site of cleavage either at N- or C-terminus of a peptide chain.
Endopeptidases are also grouped based on the position of active site such as serine endopeptidases, cysteine endopeptidases, aspartic endopeptidases, and metallopeptidases. Microbial proteases have been employed in cheese and detergent manufacturing industries since many years. Some proteases have been used in production of non-calorific artificial sweetener, e. Alkaline proteases are extensively used in leather industry for removal of hairs and parts on animal skin.
Some proteases are also used in combination with broad-spectrum antibiotics in the treatment of wounds, cuts, and burns. This means that there has to be a lot more organisms at the lower levels than at the upper levels. The number of organisms at each level makes a pyramid shape and is called a food pyramid. To better understand this energy loss, it is helpful to look at a food pyramid.
Thus food web may create the capacity of coexistence which was responsible for species evolution and maintenance of microbial diversity. A relationship in which two dissimilar organisms symbionts live in close association with one another. A relationship between two species in which one is benefited and the other is not affected, neither negatively nor positively.
A relationship between two species in which one benefits parasite from the other host ; it usually involves some detriment to the host.
Agrobacterium radiobacter K84 and K Agrobacterium spp. Xanthomonas campestris pv. PGPR bacteria suppress the growth of pathogenic microbes by lowering iron availability through secretion of low molecular weight siderophores. These plant resistance systems are induced by signaling molecules, e. PGPR bacteria enhance the production of phytohormones e. These phytohormones play a critical role in root initiation, cell division, and cell growth. Auxin is most prominently secreted by Azospirillum spp.
Several commercial PGPRs support plant growth by several means such as bioprotectants, biostimulants, and biofertilizers. PGPR bacteria, e. Root-colonizing microbes are guided by chemical plant signal overlap. For example, plant flavonoids act as chemoattractants for nitrogen-fixing bacteria, mobile zoospores, and symbiotic fungi. During interaction of microbes with plant epidermis, plants secrete signal molecules in the form of flavonoids and flavones in the rhizosphere that drive the differentiation between pathogenic, associative, symbiotic, or neutralistic adaptation of microbes with the plants.
During this symbiotic relationship, plant root releases elicitors of nod gene expression, bacteria releases Nod factor, and plant root demonstrates ion flux, expresses nodulin proteins, and undergoes nodule morphogenesis. The plant supports metabolism of bacterial endosymbionts by providing a micro-aerobic environment for effective functioning of the oxygen-sensitive nitrogenase, encoded by bacterial nif genes and carbohydrates.
In return, bacteria fix atmospheric nitrogen for plants to meet their biological needs. The other diazotrophs such as Azotobacter , Azospirillum , as well as rhizosphere fungi and bacteria especially Pseudomonas and Bacillus also interact with Rhizobium affecting nodulation and nitrogen fixation and help in creating a beneficiary region where interacting microbes get benefit from additional nutrient resources.
Therefore, a mutualistic relationship exists between Azotobacter and Azospirillum where both interact with Rhizobium to improve plant growth, and these beneficiary effects are mainly attributed to improvements in root development, increase in water and mineral uptake by roots, the displacement of fungi and pathogenic bacteria, and, to lesser extent, biological nitrogen fixation Heath and Tiffin Nodule formation involves expression of rhizobia specific genes: bacterial genes nod genes and plant genes nodulin genes.
The component, enzymes, and their function are leghemoglobin protection against oxygen , nitrogenase N 2 fixation , glutamine synthetase N-detoxification , and uricase N-detoxification. They all belong to Glomales Zygomycetes. Initiation of interaction through germinating spores on plant plasma membrane. Formation of haustorium: penetration into plant cell intracellular arbuscules. Extracellular hyphae of the fungal species collect nutrients and transfer them to the fungus.
The association of mycorrhizal fungi with legumes has a great impact on root and shoot development and phosphorous uptake resulting in the enhancement of nodulation and nitrogen fixation. Benefited fungi activate the defense genes that encode defensin proteins and may produce the reactive oxygen species through NADH oxidase to protect crops against pathogenic microbes.
The yield of crop plants may increase four times higher with mycorrhizal fungi. Infectious diseases are caused by pathogenic microbes that attack and obtain their nutrition from the host they infect. A pathogen is a microorganism that has the potential to cause disease. An infection is the invasion and multiplication of pathogenic microbes in an individual or population. An infection does not always result in a disease.
Ability to cause disease is pathogenicity, whereas the degree of pathogenicity is known as virulence. To cause disease, a pathogen must gain an access to the host, adhere to host tissues, penetrate or evade host defense system, and damage the host either directly or indirectly by accumulation of microbial wastes. Trichophyton , Microsporum , and Epidermophyton. Mechanisms of pathogenesis determine the relationship between virulence and components of parasite fitness, such as transmission to new hosts and survival within the host.
By making explicit how the biochemical mechanisms of pathogenesis set the relations between parasite fitness and virulence, we expand the conceptual framework of parasite virulence to encompass many cases that are not addressed by the prior theories of virulence.
Human pathogens may enter into the host by different routes such as the mucous membranes, skin, and parental route and cause many diseases Table 3. Most microbes must enter through their preferred portal of entry in order to cause disease, whereas some can cause disease from many routes of entry. The likelihood of disease increases as the number of invading pathogens increases. Infectious dose ID 50 and lethal dose LD 50 are used to determine the number of microbes.
Clavibacter michiganensis pv. Pseudomonas syringae pv. Pratylenchus coffeae and Helicotylenchus multicinctus. In sum, it may be said that microbes play a significant role to maintain our environmental sustainability by maintaining biogeochemical and nutrient cycles. Microbes protect our environment from hazardous compounds by using a technique known as bioremediation and keeping our environment healthy.
This chapter also provides evidences to explore PGPRs in sustainable agriculture to improve productivity and other environmental prospects. Therefore, current agricultural practices need to be improved through use of biopesticides and biofertilizers in order to minimize environmental and health problems. Skip to main content Skip to sections. This service is more advanced with JavaScript available.
Advertisement Hide. Chapter First Online: 15 October Download chapter PDF. Together, they make up all the components of our planet, both living and nonliving.
Earth produces everything it needs to ensure the survival and growth of its residents. Environment is defined as the circumstances or conditions that surround an organism or group of organisms. Environment is the complex of social or cultural conditions that affects an individual or community. Since humans inhabit the natural world as well as the built or technological, social, and cultural world, all constitute an important part of our environment.
Open image in new window. Photosynthesis is the basis of energy economy of all, but a few specific ecosystem and ecosystem dynamics are based in how organisms share food resources. In fact one of the major properties of an ecosystem is its productivity, the amount of biomass produced in a given area during a given period of time.
The rate of production of food creates a linked series of feeding known as food chain, whereas when individual food chains become interconnected, they form food web. Their cell sizes typically range from 0. Both exist in various cell shapes, e. Their DNA is found free in the cell cytoplasm and lack a true nuclear envelope, and the genome is mainly composed of single double-stranded DNA molecule with smaller DNA elements known as plasmids.
The size of bacterial genome typically ranges from four to six million nucleotides in length and enable to code 3,—4, genes. A bacterial cell envelope is composed of two layers, the inner layer is cell membrane made of phospholipids and the outer layer is cell wall made of proteins, carbohydrates, and lipids, but its composition varies based on the type of organism.
Most of the microbes move through flagella whiplike extensions from the cell and file filaments, e. The pili enable them to attach with each other or to soil particles.
Additionally these pili are also involved in transfer of genetic material between bacterial cells, known as conjugation. These microbes usually reproduce asexually, e. On the basis of gram staining, bacteria are of two types: gram positive and gram negative; both vary in cell structure and physiology Fig. Bacteria and archaea both require carbon as building blocks of their cellular materials and energy to drive the reactions involved in cell biosynthesis and metabolism. Most of the bacteria utilize oxygen, whereas some bacteria and archaea grow anaerobically by using alternative electron acceptors, e.
Norman Pace and colleagues in found that microorganisms could be identified in naturally occurring microbial populations without culturing them Hugenholtz et al.
These specific primers may differentiate among various microbial communities at level of different domains such as Bacteria, Eukarya, and Archaea or phylum e.
However, a range of approaches could be adopted in order to separate and sequence the rRNA genes. The advanced high-throughput DNA sequencing now allows the identification of each individual in thousands of samples within a short duration Caporaso et al.
Once we compare these rRNA gene sequences from cultivated species using various online databases, e. Phylogenetic information sometimes also provides details about the physiology, e.
Microorganisms avail carbon for living organisms and for themselves as well through extracting it from nonliving sources. In aquatic habitats, microbes convert carbon anaerobically, present at oxygen-free zones such as deep mud of lakes and ponds.
Carbon dioxide CO 2 is the most common form of carbon that enters into a carbon cycle. CO 2 is a water-soluble gas present in the atmosphere. Plants and photosynthetic alga use CO 2 during photosynthesis to synthesize carbohydrates. Additionally chemoautotrophs such as archaea and bacteria also utilize CO 2 to synthesize sugars. This carbon, present in the form of sugar, is further processed through a chain of reactions during respiration known as tricarboxylic acid cycle resulting into energy.
Microbes may also use carbon under anaerobic conditions to produce energy through a process called as fermentation. Some microbes execute anaerobic or fermentative degradation of organic compounds into organic acids and some gases, e. Methanogens are able to use that hydrogen to reduce CO 2 into methane under strict anaerobic conditions Fig. In order to complete cycle, methane-oxidizing bacteria, e. Other microbes such as green and purple sulfur bacteria participate in carbon cycle by degrading hydrogen sulfide H 2 S into compounds having carbon during energy production see in reaction.
Some bacteria, e.
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