1 SBT413 Environmental microbiology Is the study of MO in relation to surrounding which influence their survival and ability to carry out

various activities. Habitat- a physical location ,where an organism is found and phys and chem xtics which affect its growth. Niche- the functional role of an organism within an habitat Categories of organism 1) Autochthonous- indigenous within a habitat, capable of survival and growth, successful growth and utilization of resources, exhibit adaptive features, 2) Allochthonous- foreign orgs in habitat n cant occupy, grown elsewhere, exhibit great variation in survival time, disappear quite rapidly (E. Coli), some may have adaptations like possessing spores to allow for grater survival time. Waste disposal- the removal of pathogenic orgs, organic residue, and other harmful ingredients from sewage b4 it is discharged into rivers, lakes and oceans. Sources of water 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. Ground water- reliable, constant temp, low pollution, high hardness, limited supply Dug well- shallow, undependable, often contaminated, inexpensive Drilled well- deeper, more dependable, less contaminated, moderately expensive, Spring- inexpensive, rarely available, often hard Surface water- unreliable, polluted, variable temp Rivers-turbid, highly polluted Lakes-lower turbidity than rivers, not widely available Reservoirs- Costly, variable quality, mayb polluted, eutrophication Rain water- soft water, uncontaminated, unreliable, difficulty in storage Cistern- stores rain water, may b polluted.

Water quality a) Physical- temp, turbidity, color harness, pH, metal preasence b) Biological- presence of pathogens, odour, taste from algal growth Importance of water purification 1. 2. 3. 4. 5. To increase water quality to accepted values Reduce bacterial content Eliminate undesirable physical and chemical properties Make water microbiologically safe Improve its utility

2 Water treatments are able to: i) ii) iii) iv) v) Remove pathogenic and potentially pathogenic MO Decrease turbidity Eliminate tastes and odour Eliminate nuisance chemicals eg Fe, Mn, Soften water for laundry

Stages of water purification 1. Sedimentation- water pumped to sedimentation basins, (sand, gravel, large particles removed). Essential wen water is turbid coz algal growth may occur causing odours and flavors. Pollution may also occur. 2. Coagulation- water subjected to coagulation chemicals(aluminum and iron) to form flocculent pptate which traps organisms, organic matter, and sediments and carry them out. Allowed to settle in basins for 6 hrs. 80% removed. 3. Filtration- Clarified water filtered to remove remaining suspended particles n microbes i) Slow sand filters- in small installations like resorts and private rural dwellings. Water pass through layers of sand 2-4ft deep. Top of sand filter will be clogged and must b removed and replaced with fresh sand ii) Rapid sand filters- large installations. Rate of water flow is kept high by maintaining a controlled height over the filter. When clogged, clarified by backwashing where water is plumbed back from bottom. iii) Pressure filtration- similar to 2 but water pumbed under high pressure. Used in swimos, industrial plants. 98-99.5% of total bacteria in raw water removed. 4. Chlorination- an oxidizing agent and reacts with organic matter. Causes death of MO, in 30 mins when sufficient. Reduces and eliminates most taste and odour producing compounds. Oxidizes FE, Mn compounds by forming pptates wich can then be removed. Added NaCl or CaOCl for small treatment, or as gas in large treatments. If there is high organic matter, sufficient Cl is added so that the excess can react with MO after it has reacted with the matter. Residual level= 0.2-0.6ppm. plant operator should always maintain and also use Ammonia. NH3 + Cl produce Chloramines> more effective agent, and leaves no chlorine taste 5. Softening- used for hard water. Removes CA and Mg salts by pptation, or ion exchange process. No microbiological benefit. 6. Fluoridation- add 1 ppm to final water. Fluoridated water is less subject to tooth decay. After final treatment to storage tanks where it flows to consumer through gravity. Tanks should be covered to avoid dirt from insects, birds, etc. Treatment o f small quantities at home 1. Boiling- 56-60 degrees for many hrs kills pathogens except spores 2. Filtration passed water though a drum/barrel filled with sand 3. Chlorinated also iodine

3 Microbial indicators of water pollution Xtics of indicator MO 1. 2. 3. 4. 5. They should be in water whenever the pathogenic MO are present They should b present in the water when there is real danger from pathogenc MO Should occur in greater numbers than pathogenic MO to provide a safety margin Should survive in the environment longer than potential pathogens Should be very easy to detect with high degree of reliability

Examples of indicator MO a) Fecal Streptococci eg i) Streptococcus faecalis human waste ii) S. Faecium human iii) S. bovis both human n other warm blooded iv) S. Equinus \\ Can grow in 45 degrees in presence of bile and conc NA Ozide, which are inhibitory to coliforms and gram negatives. Used to determine whether faecal pollution is from Humans or from other animals. Eg. Fcolifroms: Fs = 4: 1 (human) Fc: fs 0.6 : 1 (animals) b) Clostridium Perfrigens- gram positive spore forming. Indicates intermittent water pollution. Water heated to 70 degrees. Then streak a medium containing Fe2S. formation of black ferrous sulphide if present c) Coliforms- E. coli used which is universally present in human d tract. Its presence in water can be determined by simple procedures. Its the best. Standard methods of water analysis 1. Presumptive test-samples of water and dilutions from it are inoculated n tubes of a Lactose growth medium. Incubated for 24-48hrs. if gas is produced, considered to b positive presumptive test 2. Confirmed test- samples are streaked from positive tubes at the highest dilution onto plates containing a special agar (Eosine Methyline Blue)-lactose gar. E. coli produces acid from lactose and will form colonies of very dark color with metallic sheen due to acid accumulation. Consider a positive confirmed test 3. Completed test- typical E coli colonies are picked and innooculated into lactose broth. If gas is produced, further test are run to ensure that the MO isolated are typical gram negative nonsporulating rod and has certain biochemical properties xtics of E. coli.

4 Water sampling- taken directly from source, sterile bottles, tightly fitting stoppers. Allow water to run for 10 mins if sampling from water tap, hands must not touch the lips of stoppers, if its chlorinated then add sodium thiosulphate to dechlorinate, process as soon as btn 6-12 hrs, keep cool of stored for long, repeat in case of unusual results. Sewage treatment and disposal-Aims 1. Remove organic matter 2. Remove human pathogens 3. Remove toxic chemicals BOD and Enteric pollution Types of waste Domestic waste Slaughter house waste Piggery effluents Cattle shed effluents Vegetable processing plant BOD (mg/l) 200-600 1000-4000 25000 20000 200-5000

BOD-an index of organic pollution in water Methods of sewage treatment a) Primary sewage treatment- Relies on physical separation procedures to lower the BOD b) Secondary sewage treatment-Relies on microbiological biodegradation to lower the BOD c) Tertiary sewage treatment- Relies on chemical methods Types of sewage systems 1. Sanitary sewers- for waste from homes , business many industries 2. Storm sewers-for surface runoff . not polluted and can be discharged directly to streams without treatment 3. Combined sewers- all types of sewage. Undesirable during times of rain and floods. Many can pass without being treated . costly Composition of sewage 1. Domestic water-borne wastehuman waste and other waste 2. Industrial water-borne wasteacids, soils, grease , other waste from industries 3. Ground surface and atmospheric waters

5 PRIMARY SEWAG ETREATMENT- re4moves suspended solids in settling tanks/basins. Maybe subjected to anaerobic digestion or composting b4 final deposition to landfills. Low % is mineralized. Liquid portion can be subjected to further treatment or directly discharged. 70-805 0f BOD reduced.

SECONDARY SEWAGE TREATMENT- The dissolved organic matter are mineralized and converted to removable solids. 80-90% of BOD reduced. Accom[plihed using various devices. a) Oxidation of ponds or lagoons/stabilization of ponds- heterotrophic bacteria degraded sewage organic natter. Used in rural. Proliferation of algal popns produce oxygen in lagoons thus replenishing the bacteria hence continued decomposition. b) Trickling filter system-simple, relatively inexpensive film flow type. Sewage distributed by a revolving sprinkler over a bed of porous material. Sewage slowly evaporates through porous bed and effluent collected at the bottom. The porous material is coated with dense slimy material composed of Zooglea, Ramigera, and similar bacteria. Bacteria incl Beggiatoa alba, Sphaeroticus natans, Achromobacter Spp, Flavobacterium spp, Zooglea spp. Aeration occurs passively, sewage may pass two other filters or re-circulated till they reach acceptable levels, allow sloughed off biomass to settle before discharge. Simple, inexpensive. However, nutrient overload reduces aeration, cold temperatures reduces effectiveness. c) Activated slime-preferable over trickling system. d) Chlorination Role of MO in microbial film 1. Slime forming bacteria- provide basis of the fluid and carry out initial oxidation 2. Filamentous bacteria and fungi- live in association with slime producers. help maintain film structure. Oxidize organic matter. 3. Protozoa- eat bacteria and fungi keeping the film from becoming thick 4. Invertebrate animals- rotifers and nemas. Eat protozoa 5. Autotrophic bacteria- oxidize NH3 and H2S liberated during decomposition ADVANCED TREATMENT METHODS 1. Coagulation sedimentation- chemicals such as alum and lime are added to the effluents causing the formation of clumps and flocs. The treated water is held in sedimentation tanks until flocs settle and then discharged when clarified. 2. Adsorption- Effluents passed over a bed of material that will adsorb to chemicals dissolved in water. The adsorbent is activated carbon granules and removes 98% of dissolved organic matter. Removes non-biodegradable chemicals hence pass through conventional plants 3. Elecrodialysis-Effluent passes thro one side of plastic membrane that is permeable to salts. A current generated across the membrane causes salts to pass across the membrane and water left behind is depleted of salts.

6 4. Reverse osmosis- the effluent is forced under pressure down one side of a plastic membrane that is permeable to water than to dissolved substances. Pressure causes water to pass thro the membrane and is collected and is collected on the other side in a relatively pure state. 5. Chemical oxidation pure O2 or O3 is used to oxidize organic matter. Its a pure chemical process. Water is now clean for drinking.

HYDROECOSPHERE Limnetic- fresh water habitats Estuarine- found at th einteface btn fresh and marine ecosystem Lentic- standing fresh water eg ponds lakes Lotic- moving fresh water eg rivers Neuston- the layer of organism growing at the interface btn air and water Eg algae, bacteria and protozoa. 1. Bacteria- Pseudomionas, Caulobacter, Nevskia, Hyphomicrobium, Achromobacter, Alcaligenes, Brevibacterium, Micrococcus, Leptothrix 2. Cyanobacteria- Anabaena, Microcystis, Aphanizomenon 3. Fungi- filamentous Cladosporium, Yeasts, 4. Algal- Codosiga, Navincula, Botrydiopsis 5. Protozoa- Diffulgia, Vorticella, Arcella, Codonosigna FRESH WATER BACTERIA Flavobacterium, Achromobacter, Brevibacterium, Micrococcus, Bacillus, Pseudomonas, Nocardia, Streptomyces, Micromonospora, Cytophaga, Spirillum, Vibrio Stalked bacteria- Caulobacteria, Hyphomicrobium (submerged) CyanobacteriaYeast- Torulopsis, Candida, Rhodotorula, Cryptococcus Algae- Chlorophycophyta, Eugleno, Phaeo, Chryso, Crypto, Pyrrho, Rhodo, Protozoa- Paramecium, Vorticella, Stentor, Didinium. INTERACTION BETWEEN MO 1. Competition 2. Symbiosis/mutualism- obligatory and benefits booth organisms.eg

7 Lichens-btw algae and fungi. Algae uses light to produce organic cmpds. Fungi provides protection , minerals, transport, provides growth fctors. Algae may be cyanobact or chlorophycophyta. Green algae Trebouxia, and cyano Nostoc ii) Endosymbionts of protozoa- Paramecium ca host numerous cells of Chlorella in its cytoplasm. Algae provides organic carbon while protozoa provides protection, motility and CO2, growth factors. Protozoa can have 50-100 algal cells. NB: protozoa can also host bacterial endosymbionts and they appear to boost the nutritional requirements. Eg Blastocrithidia and crithidia provide hemin. Protozoa provides protection, motility, n nutrients. iii) Relationship btn lysogenic phage and bacterial populations- phage genetic info incorporated to that of bacteria. This provides a survival mechanism for the phage in a dormant state for long time. Bacterial popns harbouring lysigenic phage acquire competitive advantage over those that donot have and acts towards them in a lytic manner. iv) Relationship between leguminous plants and nitrogen fixing bacteria- eg Bradyrhizobium, Rhizobium, Sinorhizobium, Azorhizobium, Mesorhizobuim. Form relationship with legumes. Rhizobium forms with Phaseolus vulgaris, Bradyrhizobium from with Vigna radiata (green grams), Vigna unguiculata (cow pea), Cajanus Cajan (Pigeon pea). 3. Commensalism eg a) Modification of habitat-when the popn of facultative anaerobes utilizes oxygen and lowers oxygen tension thus creating a habitat suitable for obligate anaerobes b) Production of growth factors-Flavobacterium brevis secretecysteine used by Legionella pneumiphilla in acquatic habitats. No effect on FC. c) Transformation of insoluble compounds to soluble compounds methane produced by bacterial popn in sediments can benefit methane oxidizing popn in the overlying water column. d) Conversion of organic molecules by one popn into substrate of the other- fungi produce extracellular enzymes that convert complex polymeric cpds eg cellulose to glucose. This will benefit MO that donot have the enzymes e) Removal or utilization of toxic material- oxidation of H@S by Begggiatoa is an example of detoxification and benefits H2S sensitive MO 4. Synergism- eg i) Streptococcus faecalia and E.coli. neither can convert Arginine to putrescine. But when working 2getha, S. Faecalis >arginine to ornithine, while E. coli firther converts it to putrescence. Have to work together. ii) One orgs supllis growth factor for the other eg in a minimal medial. Arabinosus ans S. faecalis can grow torether but not alone. S. faecalis requires folic acid produced by Lactobacillus. L requires phenylalanine produced by streptococcus iii) Cyclohehane degraded by mixed popns of Nocardia and pseudomionas but not either. Nocardia degrades it producing growth factors for pseudomonas, which in turn provides biotin. i)

8 5. Neutralism lack of interaction. Cant occur btn ogrs having sam eioverlapping functional role in a community. Occurs to those who are sparstically distant, outside their natural habitats, frozen food ATMOECOSPHERE Troposphere Stratosphere Ionosphere

Xenospheres- spores whose main function is dispersion Adaptation of xenospores 1. 2. 3. 4. 5. 6. 7. Metabolically less active Produced in high numbers Have extremely thick walls Pigmented to protect against radiation Relatively small in size n low density Contain gas vacuoles Refractile to reduce amount of radiation

ENVIRONMENTAL FCATORS WHICH INFLUENCE GROWTH 1. Chemical factors 2. Physical factors Effects of chemicals 1. Beneficial 2. Negative effect 3. No effect Nutrients- compounds taken up by a MO in order to satisfy their biosynthetic raw materials and energy eg i) Water Water activity 0.9 0.85 0.75 0.6

bacteria lactobacillus staphylococcus halobacterium

fungi fusarium Penicilium aspergillus sacharromyces

9 ii) Biosynthetic raw materials 1. C, H, O- from simple carbohydrates, polyhydric alcohols, AA, lipids, HC 2. NitrogenGrowth factors Factors affecting requirement of a growth factor 1. Oxygen supply- mucor rouxii requires biotin n thiamin ein anaerobic conditions 2. pH 3. temperature for incubation 4. chemical composition of the environment Inorganic nutrients 1. Macronutrient- Mg, Zn, K, Fe, Mn, Na, Cl, ions 2. Micronutrient Co, NI, Mo, Se, , Va. Oxygen Hydrogen ions Physical factors 1. Temperature 2. Radiation Cosmic rays and x-rays Uv radiation- chain linkage, intrastrand cross linking, formation of DNA-protein linkages. Nb::: photo reactivation an dark repair system. Visible radiation IR radiation

iii)

iv)

v) vi) vii)

Factors determining microbial distribution of the soil 1. 2. 3. 4. 5. Nature of soil particles Response to soil aeration Ph of soil Temperature Nutrient status