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. Bacteria are present in most habitats on Earth, growing in soil, acidic hot springs, radioactive waste, water, and deep in the Earth's crust, as well as in organic matter and the live bodies of plants and animals, providing outstanding examples of mutualismin the digestive tracts of humans, termites and cockroaches. Bacteria are vital in recycling nutrients, with many steps in nutrient cycles depending on these organisms, such as the fixation of nitrogen from the atmosphere and putrefaction. In the biological communities surrounding hydrothermal vents and cold seeps, bacteria provide the nutrients needed to sustain life by converting dissolved compounds such as hydrogen sulphide and methane. The ability of bacteria to degrade a variety of organic compounds is remarkable and has been used in waste processing and bioremediation. Bacteria capable of digesting the hydrocarbons in petroleum are often used to clean up oil spills. Bacteria can also be used in the place of pesticides in the biological pest control. This commonly involves Bacillus thuringiensis (also called BT), a Gram-positive, soil dwelling bacterium. Subspecies of this bacteria are used as a Lepidopteran-specific insecticides under trade names such as Dipel and Thuricide. Because of their specificity, these pesticides are regarded as environmentally friendly, with little or no effect on humans, wildlife, pollinators and most other beneficial insects. Classification seeks to describe the diversity of bacterial species by naming and grouping organisms based on similarities. Bacteria can be classified on the basis of cell structure, cellular metabolism or on differences in cell components such as DNA, on fatty acids,

pigments, antigens and quinones.

The International

Committee

Systematic

Bacteriology (ICSB) maintains international rules for the naming of bacteria and taxonomic categories and for the ranking of them in the International Code of Nomenclature of Bacteria. The term "bacteria" was traditionally applied to all microscopic, single-cell prokaryotes. However, molecular systematics showed prokaryotic life to consist of two separate domains, originally called Eubacteria and Archaebacteria, but now called Bacteria and Archaea that evolved independently from an ancient common ancestor.The archaea and eukaryotes are more closely related to each other than either is to the bacteria. These two domains, along with

Eukarya, are the basis of the three-domain system, which is currently the most widely used classification system in microbiolology

Fig. Phylogenetic tree showing the diversity of bacteria, compared to other organisms. Eukaryotes are colored red, archaea green and bacteria blue. APPLICATIONS OF BACTERIA IN ENVIRONMENTAL BIOTECHNOLOGY WASTE TREATMENT Waste treatment refers to the activities required to ensure that waste has the least practicable impact on the environment. The three major groups of biological processes: aerobic, anaerobic, combination of aerobic and anaerobic can be run in combination or in sequence to offer greater levels of treatment Solid waste treatment technologies : composting.IncinerationLandfillRecyclingWindrow composting Alternative waste treatment technologies : Anaerobic digestion, Alcohol/ethanol production, Biodrying Mechanical biological treatment Compost is organic matter that has been decomposed and recycled as a fertilizer and soil

amendment. Compost is a key ingredient in organic farming. At the simplest level, the process of composting simply requires making a heap of wetted organic matter (leaves, food waste) and waiting for the materials to break down into soil after a period of weeks or months. Modern, methodical composting is a multi-step, closely monitored process with measured inputs of water,

air and carbon- and nitrogen-rich materials. The decomposition process is aided by shredding the plant matter, adding water and ensuring proper aeration by regularly turning the mixture. Worms and fungi further break up the material. Aerobic bacteria manage the chemical process by converting the inputs into heat, carbon dioxide and ammonium. The ammonium is further converted by bacteria into plant-nourishing nitrites and nitrates through the process

of nitrification. Compost can be rich in nutrients. It is used in gardens, landscaping, horticulture, and agriculture. The compost itself is beneficial for the land in many ways, including as a soil conditioner, a fertilizer, addition of vital humus or humic acids, and as a natural pesticide for soil. In ecosystems, compost is useful for erosion control, land and stream reclamation, wetland construction, and as landfill cover . Organic ingredients intended for composting can alternatively be used to generate biogas through anaerobic digestion. A landfill site is a site for the disposal of waste materials by burial and is the oldest form of waste treatment. Historically, landfills have been the most common methods of organized waste disposal and remain so in many places around the world. Landfills may include internal waste disposal sites (where a producer of waste carries out their own waste disposal at the place of production) as well as sites used by many producers. Many landfills are also used for waste management purposes, such as the temporary storage, consolidation and transfer, or processing of waste material (sorting, treatment, or recycling). A landfill also may refer to ground that has been filled in with rocks instead of waste materials, so that it can be used for a specific purpose, such as for building houses. Unless they are stabilized, these areas may experience severe shaking or liquefaction of the ground in a large earthquake. Anaerobic digestion is particularly suited to organic material, and is commonly used for effluent and sewage treatment. Anaerobic digestion, a simple process, can greatly reduce the amount of organic matter which might otherwise be destined to be dumped at sea, dumped in landfills, or burnt in incinerators.

Anaerobic

digestion is

series

of

processes

in

which microorganisms break

down biodegradable material in the absence of oxygen. It is used for industrial or domestic purposes to manage waste and/or to release energy. The digestion process begins with bacterial hydrolysis of the input materials to break down insoluble organic polymers, such as carbohydrates, and make them available for other bacteria. Acidogenic bacteria then convert the sugars and amino acids into carbon

dioxide, hydrogen, ammonia, and organic acids. Acetogenic bacteria then convert these resulting organic acids into acetic acid, along with additional ammonia, hydrogen, and carbon dioxide. Finally, methanogens convert these products to methane and carbon dioxide. In fact, the methanogenic archaea populations play an indispensable role in anaerobic wastewater treatments. It is used as part of the process to treat biodegradable waste and sewage sludge. As part of an integrated waste management system, anaerobic digestion reduces the emission of landfill gas into the atmosphere. Anaerobic digesters can also be fed with purpose-grown energy crops, such as maize. Anaerobic digestion is widely used as a source of renewable energy. The process produces a biogas, consisting of methane,carbon dioxide and traces of other contaminant gases. This biogas can be used directly as cooking fuel, in combined heat and power gas engines or upgraded to natural gas-quality biomethane. The use of biogas as a fuel helps to replace fossil fuels. The nutrient-rich digestate also produced can be used as fertilizer. Many microorganisms are involved in the process of anaerobic digestion, including acetic acidforming bacteria (acetogens) and methane-forming archaea (methanogens). These organisms feed upon the initial feedstock, which undergoes a number of different processes, converting it to intermediate molecules, including sugars, hydrogen, and acetic acid, before finally being converted to biogas. Different species of bacteria are able to survive at different temperature ranges. Ones living optimally at temperatures between 35 and 40 C are called mesophiles or mesophilic bacteria. Some of the bacteria can survive at the hotter and more hostile conditions of 55 to 60 C; these are called thermophiles or thermophilic bacteria. Methanogens come from the domain of archaea. This family includes species that can grow in the hostile conditions of hydrothermal vents, so are

more resistant to heat, and can, therefore, operate at high temperatures, a property unique to thermophiles. As with aerobic systems, the bacteria, the growing and reproducing microorganisms within anaerobic systems, require a source of elemental oxygen to survive, but in anaerobic systems, there is an absence of gaseous oxygen. Gaseous oxygen is prevented from entering the system through physical containment in sealed tanks. Anaerobes access oxygen from sources other than the surrounding air, which can be the organic material itself or may be supplied by inorganic oxides from within the input material. When the oxygen source in an anaerobic system is derived from the organic material itself, the 'intermediate' end products are

primarily alcohols, aldehydes, and organic acids, plus carbon dioxide. In the presence of specialised methanogens, the intermediates are converted to the 'final' end products of methane, carbon dioxide, and trace levels of hydrogen sulfide.In an anaerobic system, the majority of the chemical energy contained within the starting material is released by methanogenic bacteria as methane. Populations of anaerobic microorganisms typically take a significant period of time to establish themselves to be fully effective. Therefore, common practice is to introduce anaerobic microorganisms from materials with existing populations, a process known as "seeding" the digesters, typically accomplished with the addition of sewage sludge or cattle slurry. Process stages

The key process stages of anaerobic digestion There are four key biological and chemical stages of anaerobic digestion: 1. Hydrolysis 2. Acidogenesis 3. Acetogenesis 4. Methanogenesis In most cases, biomass is made up of large organic polymers. For the bacteria in anaerobic digesters to access the energy potential of the material, these chains must first be broken down into their smaller constituent parts. These constituent parts, or monomers, such as sugars, are readily available to other bacteria. The process of breaking these chains and dissolving the smaller molecules into solution is called hydrolysis. Therefore, hydrolysis of these highmolecular-weight polymeric components is the necessary first step in anaerobic

digestion.Through hydrolysis the complex organic molecules are broken down into simple sugars, amino acids, and fatty acids. Acetate and hydrogen produced in the first stages can be used directly by methanogens. Other molecules, such as volatile fatty acids (VFAs) with a chain length greater than that of acetate must first be catabolised into compounds that can be directly used by methanogens. The biological process of acidogenesis results in further breakdown of the remaining components by acidogenic (fermentative) bacteria. Here, VFAs are created, along with ammonia, carbon dioxide, and hydrogen sulfide, as well as other byproducts. The process of acidogenesis is similar to the way milk sours. The third stage of anaerobic digestion is acetogenesis. Here, simple molecules created through the acidogenesis phase are further digested by acetogens to produce largely acetic acid, as well as carbon dioxide and hydrogen. The terminal stage of anaerobic digestion is the biological process of methanogenesis. Here, methanogens use the intermediate products of the preceding stages and convert them into methane, carbon dioxide, and water. These components make up the majority of the biogas emitted from the system. Methanogenesis is sensitive to both high and low pHs and occurs

between pH 6.5 and pH 8.The remaining, indigestible material the microbes cannot use and any dead bacterial remains constitute the digestate. A simplified generic chemical equation for the overall processes outlined above is as follows: C6H12O6 3CO2 + 3CH4 Methanogenesis or biomethanation is the formation of methane by microbes known

as methanogens. Organisms capable of producing methane have been identified only from the domain Archaea, a group phylogenetically distinct from both eukaryotes and bacteria,

although many live in close association with anaerobic bacteria. The production of methane is an important and widespread form of microbial metabolism. In most environments, it is the final step in the decomposition of biomass. Recently, some experiments have suggested that leaf tissues of living plants emit methane. Other research has indicated that the plants are not actually generating methane; they are just absorbing methane from the soil and then emitting it through their leaf tissues.There may still be some unknown mechanism by which plants produce methane, but that is by no means certain. Methanogenesis in microbes is a form of anaerobic respiration. Methanogens do not use oxygen to respire; in fact, oxygen inhibits the growth of methanogens. The terminal electron acceptor in methanogenesis is not oxygen, but carbon. The carbon can occur in a small number of organic compounds, all with low molecular weights. The two best described pathways involve the use of carbon dioxide and acetic acid as terminal electron acceptors: CO2 + 4 H2 CH4 + 2H2O CH3COOH CH4 + CO2 However, methanogenesis has been shown to use carbon from other small organic compounds, such as formic acid (formate), methanol, methylamines, dimethyl sulfide, and methanethiol. Activated sludge is a process for treating sewage and industrial wastewaters using air and a biological floc composed of bacteria and protozoans. he process involves air or oxygen being introduced into a mixture of primary treated or screened sewage or industrial wastewater (called wastewater from now on) combined with organisms to develop a biological floc which reduces the organic content of the sewage. This material, which in healthy sludge is a brown floc, is largely composed of saprotrophic bacteria but also has an important protozoan flora mainly

composed of amoebae, Spirotrichs, Peritrichs including Vorticellids and a range of other filter feeding species. Other important constituents include motile and sedentary Rotifers. In poorly managed activated sludge, a range of mucilaginous filamentous bacteria can develop including Sphaerotilus natans which produces a sludge that is difficult to settle and can result in the sludge blanket decanting over the weirs in the settlement tank to severely contaminate the final effluent quality. This material is often described as sewage fungus but true fungal communities are relatively uncommon. The combination of wastewater and biological mass is commonly known as mixed liquor. In all activated sludge plants, once the wastewater has received sufficient treatment, excess mixed liquor is discharged into settling tanks and the treated supernatant is run off to undergo further treatment before discharge. Part of the settled material, the sludge, is returned to the head of the aeration system to re-seed the new wastewater entering the tank. This fraction of the floc is called return activated sludge (R.A.S.). Excess sludge is called surplus activated sludge(S.A.S.) or waste activated sludge(W.A.S). S.A.S is removed from the treatment process to keep the ratio of biomass to food supplied in the wastewater in balance. S.A.S is stored in sludge tanks and is further treated by digestion, either under anaerobic or aerobic conditions prior to disposal. Many sewage treatment plants use axial flow pumps to transfer nitrified mixed liquor from the aeration zone to the anoxic zone for denitrification. These pumps are often referred to as internal mixed liquor recycle pumps (IMLR pumps). The raw sewage, the RAS, and the nitrified mixed liquor are mixed by submersible mixers in the anoxic zones in order to achieve denitrification.

BIOFERTILIZER A biofertilizer is a substance which contains living microorganisms which, when applied to seed, plant surfaces, or soil, colonizes the rhizosphere or the interior of the plant and promotes growth by increasing the supply or availability of primary nutrients to the host plant. Biofertilizers add nutrients through the natural processes of nitrogen fixation,

solubilizing phosphorus, and stimulating plant growth through the synthesis of growthpromoting substances. Bio-fertilizers can be expected to reduce the use of chemical fertilizers and pesticides. The microorganisms in bio-fertilizers restore the soil's natural nutrient cycle and build soil organic matter. Through the use of bio-fertilizers, healthy plants can be grown, while enhancing the sustainability and the health of the soil. Since they play several roles, a preferred scientific term for such beneficial bacteria is "plant-growth promoting rhizobacteria" (PGPR). Therefore, they are extremely advantageous in enriching soil fertility and fulfilling plant nutrient requirements by supplying the organic nutrients through microorganism and their byproducts. Hence, bio-fertilizers do not contain any chemicals which are harmful to the living soil. Bio-fertilizers are eco-friendly organic agro-input and more cost-effective than chemical fertilizers. Bio-fertilizers such as Rhizobium, Azotobacter, Azospirillum and blue green algae (BGA) have been in use a long time. Rhizobium inoculant is used for leguminous crops. Azotobacter can be used with crops like wheat, maize, mustard, cotton, potato and other vegetable crops. Azospirillum inoculations wheat. Blue are green recommended algae belonging mainly to a

for sorghum, millets, maize, sugarcane and

general cyanobacteria genus, Nostoc or Anabaena or Tolypothrix or Aulosira, fix atmospheric nitrogen and are used as inoculations for paddy crop grown both under upland and low-land conditions. Anabaena in association with water fern Azolla contributes nitrogen up to 60 kg/ha/season and also enriches soils with organic matter. Other types of bacteria, so-called phosphate-solubilizing bacteria, such as Pantoea

agglomerans strain P5 or Pseudomonas putida strain P13, are able to solubilize the insoluble phosphate from organic and inorganic phosphate sources. In fact, due to immobilization of phosphate by mineral ions such as Fe, Al and Ca or organic acids, the rate of available phosphate (Pi) in soil is well below plant needs. In addition, chemical Pi fertilizers are also immobilized in

the soil, immediately, so that less than 20 percent of added fertilizer is absorbed by plants. Therefore, reduction in Pi resources, on one hand, and environmental pollutions resulting from both production and applications of chemical Pi fertilizer, on the other hand, have already demanded the use of new generation of phosphate fertilizers globally known as phosphatesolubilizing bacteria or phosphate bio-fertilizers. Benefits of using biofertilizers: 1. Since a bio-fertilizer is technically living, it can symbiotically associate with plant roots. Involved microorganisms could readily and safely convert complex organic material in simple compounds, so that plants are easily taken up. Microorganism function is in long duration, causing improvement of the soil fertility. It maintains the natural habitat of the soil. It increases crop yield by 20-30%, replaces chemical nitrogen and phosphorus by 25%, and stimulates plant growth. It can also provide protection against drought and some soil-borne diseases. 2. Bio-fertilizers are cost-effective relative to chemical fertilizers. They have lower manufacturing costs, especially regarding nitrogen and phosphorus use. 3. It is environmentally friendly in that it not only prevents damaging the natural source but also helps to some extent cleanse the plant from precipitated chemical fertilizers. BIOPESTICIDES Biopesticides include "naturally occurring substances that control pests (biochemical pesticides), microorganisms that control pests (microbial pesticides), and pesticidal substances produced by plants containing added genetic material (plant-incorporated protectants) or PIPs." Biopesticides are biochemical pesticides that are naturally occurring substances that control pests by nontoxic mechanisms. Conventional pesticides, by contrast, are generally synthetic materials that directly kill or inactivate the pests. For example, a plant in the presence of chitosan will naturally induce systemic resistance (ISR) to allow the plant to defend itself against disease, pathogens and pests. Biopesticides are considered eco-friendly and easy to use. Biopesticides are key components of integrated pest management (IPM) programmes, and are receiving much practical attention as a means to reduce the load of synthetic chemical products being used to control plant diseases. Bacillus thuringiensis (or Bt) is a Gram-positive, soil-dwelling bacterium, commonly used as

a biological pesticide; alternatively, the Cry toxin may be extracted and used as a pesticide. B.thuringiensis also occurs naturally in the gut of caterpillars of various types of moths and butterflies, as well as on the dark surfaces of plants. During sporulation, many Bt strains produce crystal proteins (proteinaceous inclusions), called -endotoxins, that

have insecticidal action. This has led to their use as insecticides, and more recently to genetically modified crops using Bt genes BIOSENSORS A biosensor is an analytical device that combines a biological sensing element with a transducer to produce a signalproportional to the analyte concentration. This signal can result from a change in protons concentration, release or uptake of gases, light emission, absorption and so forth, brought about by the metabolism of the target compound by the biological recognition element. The transducer converts thisbiological signal into a measurable response such as current, potential or absorption of light through electrochemical or optical means, which can be further amplied, processed and stored for later analysis .Biomolecules such as enzymes, antibodies, receptors, organelles and microorganisms as well as animal and plant cells or tissues have been used as biological sensing elements. Among these, microorganisms offer advantages of ability to detect a wide range of chemical substances, amenability to genetic modication, and broad operating pH and temperature range, making them ideal as biological sensing materials. A microbial biosensor is an analytical device that couples microorganisms with a transducer to enable rapid, accurate and sensitive detection of target analytes in elds as diverse as medicine, environmental monitoring, defense, food processing and safety. The earlier microbial biosensors used the respiratory and metabolic functions of the microorganisms to detect a substance that is either a substrate or an inhibitor of these processes. Recently, genetically engineered microorganisms based on fusing of the lux, gfp or lacZ gene reporters to an inducible gene promoter have been widely applied to assay toxicity and bioavailability. Microorganisms have been integrated with a variety of transducers such as amperometric, potentiometric, calorimetric, conductimetric, colorimetric, luminescence and uorescence toconstruct biosensor device.

Electrochemical microbial biosensor There are three types of electrochemical microbial biosensors: amperometric, potentiometric, and conductometric . Amperometric microbial biosensor Amperometric microbial biosensor operates at xed potential with respect to a reference electrode and involves the detection of the current generated by the oxidation or reduction of species at the surface of the electrode. Amperometric microbial biosensors have been widely developed for the determination of biochemical oxygen demand (BOD) for the measurement of biodegradable organic pollutants in aqueous samples. The conventional standard method for the determination of BOD measures the microorganisms oxygen consumption/respiration over a period of 5 days and is reported as BOD5. The microbial strains used as biological sensing element include Torulopsis candida , Trichosporon cutaneum , Pseudomonas putida , Klebsiella oxytoca , Bacillus subtilis [36,37], Arxula adeninivorans LS3 , Serratia marcescens LSY4 , Pseudomonas sp. , P. uorescens , P. putida SG10 , Thermophilic bacteria , Hansennula anomala. Potentiometric microbial biosensor Conventional potentiometric microbial biosensors consist of an ion-selective electrode (pH, ammonium, chloride and so on) or a gas-sensing electrode (pCO2 and pNH3) coated with animmobilized microbe layer. Target Organophosphates Penicillin Flat Urea Microorganism Flavobacteium sp. Recombinant E coli Bacillus sp Transducer type pH electrode pH electrode NH4+ ion selective electrode

Trichloroethylene

P. aeruginosa JI104

Chloride ion selective

Optical microbial biosensor The modulation in optical properties such as UVvis absorption, bio- and chemi-luminescence, reectance and uorescence brought by the interaction of the biocatalyst with the target analyte is the basis for optical microbial biosensors. Bioluminescence is associated with the emission of light by living microorganisms and it plays a very important role in realtime process monitoring. The bacterial luminescence lux gene has been widely applied as a reporter either in an inducible or constitutive manner. Fluorescent materials and green uorescent protein have been extensively used in the construction of uorescent biosensor. Green uorescence protein-based biosensor like bioluminescent reporter lux gene, gfp gene coding for the green uorescent protein (GFP) has also been widely applied as reporters and fused to the host gene that allows reporter activity to be examined in individual cells.

Fig. P. uorescens Target Ni2+ and Co2+ Bioavailable mercury Microorganism Ralstonia eutropha AE2515 Transducer type Luminescence

E. coli HMS174 harboring Luminescence mer-lux plasmid pRB27 or pRB28

Bioavailable copper

P. uorescens DF57 with a Luminescence Tn5::luxAB promoter probe transposon

Pollution- induced stress

P. uorescens pUCD607

Luminescence

Bioavailable iron

Recombinant

Pseudomonas Fluorescence

syringae carrying gfp gene BOD P. putida and optical ber Fluorescence sensor

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 elsewhere. Some examples of bioremediation technologies are bioventing, bioleaching , bioreactor , composting , bioaugmentation , rhizofiltration, and biostimulation. Bioremediation can occur on its own (natural attenuation or intrinsic bioremediation) or can be spurred on via the addition of fertilizers to increase the bioavailability within the medium (biostimulation). Recent advancements have also proven successful via the addition of matched microbe strains to the medium to enhance the resident microbe population's ability to break down contaminants. Microorganisms used to perform the function of bioremediation are known as bioremediators

Table: Bacteria involved in environmental remediation.

Microbes Type cocci Shape spherical shape Bacteria bacilli rods Bacillius subtilis Example Streptococcus Abilities hydrocarbon-degrading bacteria heavy oil degrade dairy industry waste (whey) degrade crude oil bioremediation of chlorpyrifos-contaminated soil

Spiral forms

Vibrio cholera Spirillum volutans

heavy metals

sheated bacteria

(gram-

Sphaeratilus

reduce iron to ferric hydroxide (Sphaeratilus natans, Crenothrix) reduce manganese to manganese oxide (Leptothrix) found in polluted streams and wastewater treatment plants

negative rods Leptothrix that become Crenothrix flagellated)

ptalked bacteria flagellated

Caulobacter Gallionella

aerobic, aquatic environments with low organic content G. ferruginea, present in iron rich waters and oxidizes Fe2+ to Fe3+.can be formed in water distribution systems

budding bacteria

filaments or hyphae

Hyphomicrobium

soil

and

aquatic

environments

requires one-carbon compounds to grow (e.g.methanol)

gliding bacteria

filamentous (gramnegative)

Beggiatoa Thiothrix

oxidize H2S to S

bdellovibrio

flagellated (predatory)

B. bacteriovorus

grow independently on complex organic media

actinomycetes

filamentous (grampositive) mycelial growth

Micromonospora Streptomyces Nocordia (Gordonia)

most are strict aerobes found in water, wastewater treatment plants, soils (neutral and alkaline) degrade polysaccharides (starch,cellulose),

hydrocarbons, lignin can produce antibiotics (streptomycin,

tetracycline, chloramphenicol) Gordonia is a significant constituent

of foams in activated sludge units cyanobacteria (blue-green algae) unicellular, colonial filamentous organisms or Anabaena prokaryotic organisms able to fix nitrogen have a high resistance to extreme environmental conditions (temperature, dessication) so that are found in desert soil and hot springs responsible for algal blooms in lakes and other aquatic environments some are quite toxic Archea crenarchaeotes euryarchaeotes korarchaeotes (more closely related to eukaryotes than to bacteria) extremophyles Thermophiles Hyperthermophil es Psychrophiles Acidophiles Alkaliphiles halophiles prokaryotic cells use organic

compounds as a source of carbon and energy (organotrophs) use CO2 as a carbon source (chemoautothrophs)