MICROBIAL ECOLOGY_2023_2024_LAAO- slides2 .pdf

Kwame Nkrumah University of Science & Technology, Kumasi, Ghana BIOL 252: MICROBIAL ECOLOGY 2023/2024 Name: Prof. (Mrs.)Linda Aurelia Ofori (PhD) Email: [email protected] /[email protected] Phone...

Kwame Nkrumah University of Science & Technology, Kumasi, Ghana BIOL 252: MICROBIAL ECOLOGY 2023/2024 Name: Prof. (Mrs.)Linda Aurelia Ofori (PhD) Email: [email protected] /[email protected] Phone Number: 0244220064  Recommended texts for further reading Introduction to Microbiology – Ingraham and Ingraham MICROBIOLOGY - Prescott, Harley and Klein Fundamentals of Microbiology – Frobisher Essential Microbiology – S. Hogg Any good Microbiology book Authentic Microbiology journals www.knust.edu.gh 6/23/24 2023/2024 1  Assessment Requirements ü Punctuality, Attendance ü Presentations (Group) Continuous ü Assignments (Individual and Group) Assessment ü Short Quizzes – Un/announced 30% ü Mid Semester Examination** ü Practical Assignments – Weekly ü End of Semester Examination 70% www.knust.edu.gh 6/23/24 2023/2024 2 2022/2023  Course Outline Natural Microbial Environments---done Microorganisms of Extreme environments-- done Strategies for survival---done Some important diseases ---- done Water and excreta-related diseases--- Biofilms Water Treatment Sewage Treatment www.knust.edu.gh 6/23/24 2023/2024 3  www.knust.edu.gh 6/23/24 2023/2024 4  Mode of transmission Uncooked or infected meat such as: -Fish (fish tapeworm) -Beef (beef tapeworm) -Pork (pork tapeworm) – Live in intestines – Symptoms Usually absent May include abdominal pain, fatigue, weight loss, diarrhea www.knust.edu.gh 6/23/24 2023/2024 5  Life cycle Hermaphrodites www.knust.edu.gh 6/23/24 2023/2024 6  Key factors for preventing Taeniases Consume well-cooked meat and fish www.knust.edu.gh 6/23/24 2023/2024 7  www.knust.edu.gh 6/23/24 2023/2024 8 2022/2023  www.knust.edu.gh 6/23/24 2023/2024 9  www.knust.edu.gh 6/23/24 2023/2024 10  Infections by Schistosoma haematobium, S. mansoni are frequent than those by S. japonicum and S. intercalatum Clinical: Each species give rise to specific clinical form, it depends on the parasite load üSchistosomiases (urinary): S. haematobium signs: haematuria, frequent and painful micturition evolution to fibrosis urethral. üSchistosomiases (intestinal): S. mansoni signs: bloody diarrhoea , abdominal pain, nauseas, vomit and it evolution liver fibrosis TRANSMISSION: By contact with the parasite when bathing or swimming in contaminated water. www.knust.edu.gh 6/23/24 2023/2024 11  Distribution www.knust.edu.gh 6/23/24 2023/2024 12 2022/2023  Life cycle www.knust.edu.gh 6/23/24 2023/2024 13 2022/2023  Presentations www.knust.edu.gh 6/23/24 2023/2024 14 2022/2023  www.knust.edu.gh 6/23/24 2023/2024 15 Key factors for preventing water-based diseases Safe water (drinking and domestic) supply Adequate drainage of stagnant waters Control snails Mass Drug Administrations www.knust.edu.gh 6/23/24 2023/2024 16  www.knust.edu.gh 6/23/24 2023/2024 17  www.knust.edu.gh 6/23/24 2023/2024 18  Insect vectors Transmission mechanisms Biting by mosquitoes, flies. Mosquitoes Transmitted by mosquitoes and Malaria, Dengue, sleeping flies sickness, Filariasis, yellow Bite near water fever. Breed in water Dirty environment www.knust.edu.gh 6/23/24 2023/2024 19  Malaria Pathogen: Plasmodium falciparum, vivax, malariae and ovale (Parasite) Vector: Mosquito Anopheles female (Anopheles gambiae complex) Clinical: üPainful muscles and joints, high fever with chills, headache, diarrhoea and vomiting, coma, death, anaemia Stagnant waters are the breeding place. www.knust.edu.gh 6/23/24 2023/2024 20  www.knust.edu.gh 6/23/24 2023/2024 21  www.knust.edu.gh 6/23/24 2023/2024 22  Yellow fever Pathogen: Virus (Flaviviridiae) Vector: Aedes aegypti Clinical: üFever, headache, myalgia, nausea, red eyes, jaundice. Breeds in stagnant waters. Only bites during daylight. www.knust.edu.gh 6/23/24 2023/2024 23  Lymphatic/Bancroftian Filariasis www.knust.edu.gh 6/23/24 2023/2024 24  Life cycle www.knust.edu.gh 6/23/24 2023/2024 25  Extreme clinical presentation www.knust.edu.gh 6/23/24 2023/2024 26  Other insect vector-borne diseases Trypanosomiasis - spread by Tsetseflies Encephalitis - Japanese encephalitis – Culex (Mosquitoes) Onchocerciasis – Black fly Dengue - Aedes aegypti (Mosquitoes) www.knust.edu.gh 6/23/24 2023/2024 27  Key factors for preventing Insect vector diseases Adequate drainage of stagnant water Disposal of waste water Vector control www.knust.edu.gh 6/23/24 2023/2024 28  www.knust.edu.gh 6/23/24 2023/2024 29  www.knust.edu.gh 6/23/24 2023/2024 30  Diseases transmitted by rodents Hantavirus Pulmonary Syndrome Lassa fever Plague Rat-Bite Fever Salmonellosis Tularemia Hemorrhagic Fever with Renal Syndrome Leptospirosis www.knust.edu.gh 6/23/24 2023/2024 31  Bacterial disease that affects humans and animals Humans become infected through contact with water, food or soil containing urine from rats Occurs when swallowing contaminated food or water (vector) www.knust.edu.gh 6/23/24 2023/2024 32  Prevention and Control Keep rodent problems (rats, mice) under control. Wear protective clothing, especially footwear, if you must wade in flood waters or other areas that might be contaminated. Avoid contact with environments contaminated with animal urine. www.knust.edu.gh 6/23/24 2023/2024 33  BIOFILMS www.knust.edu.gh 6/23/24 2023/2024 34  Biofilms www.knust.edu.gh 6/23/24 2023/2024 35  Biofilms Slimy aggregates of microorganisms in which cells are stuck to each other and/or to a surface. They may form on living or non-living surfaces (rocks, leaves, water.) Complex aggregation of microorganisms often seen adhering to the surface of water. May initially consist of one bacteria type but later contain several bacteria. May include bacteria, protozoa, fungi, archaea and algae. www.knust.edu.gh 6/23/24 2023/2024 36 Biofilms provide: Nutrients for pathogens Microhabitats for growth Protection from biocides (increased resistance to detergents and antibiotics) such as chlorine and sunlight. www.knust.edu.gh 6/23/24 2023/2024 37  Mechanism of biofilm formation The formation of biofilm begins when free-floating microorganisms begin to pack themselves loosely together and attach to the surfaces through weak but reversible van der Waal’s forces. Over time, they are able to attach permanently (become irreversible) by producing extracellular polysaccharide or in some cases by means of specialised structures termed holdfasts or other cell adhesion structures like Pili, flagella and fimbriae. www.knust.edu.gh 6/23/24 2023/2024 38  Steps in Biofilm Development (5 stages) Stage 1 : Initial attachment; Stage 2 : Irreversible attachment; Stage 3 : Maturation I; Stage 4 : Maturation II; Stage 5 : Dispersion www.knust.edu.gh 6/23/24 2023/2024 39  Initial attachment: Aided by weak reversible van der Waals interactions between the cell surface and the substratum. Irreversible attachment: Development of micro-colonies which is promoted by the growth and division of the first attached cells Maturation I: Micro-colonies enlarge to form the first layer of cells covering the surface Maturation II: Multiple layers pile up and form a mature biofilm indicated by the presence of macro-colonies surrounded by water channels Dispersion: They spread and colonize other niches www.knust.edu.gh 6/23/24 2023/2024 40  Biofilm structure Thickness of biofilms depend on: Nutrient load of the surface Adsorptive surface Type of microbial community attached Fluid temperature Fluid velocity www.knust.edu.gh 6/23/24 2023/2024 41 Advantages of the “Biofilm mode of life” Provide defense – Physical forces – Phagocytosis – Penetration of antimicrobials Provide favorable micro-niches – Can attach to nutrient rich surfaces – Can attach to surface in flowing systems – Fixes bacteria to where nutrients are either in abundance or replenished www.knust.edu.gh 6/23/24 2023/2024 42 Advantages of the “Biofilm mode of life” Allow microbes to live in close proximity – Facilitates communication and cooperation – Can result in genetic exchange Nature’s default More than 99% of all microorganisms on earth prefer to live in biofilms www.knust.edu.gh 6/23/24 2023/2024 43  Economic importance of Biofilms Beneficial Biofilms Recycling of elements vital to life. These live in biofilm colonies on surfaces www.knust.edu.gh 6/23/24 2023/2024 44  Bioremediation The Microbes ‘eat up’ contaminants such as oil and organic matter www.knust.edu.gh 6/23/24 2023/2024 45  Water Treatment www.knust.edu.gh 6/23/24 2023/2024 46  Treatment of wastewater Biological treatment of wastewater could be improved by: – enhancing the production of flocculating biopolymers – improving the oxygen scavenging ability of beneficial floc- forming bacteria, and – using immobilized cells that can recover toxic metals from wastewater. www.knust.edu.gh 6/23/24 2023/2024 47  Anaerobic reactor (Bioreactor) The bioreactor contains a series of plastic hollow particle-like carriers on which a biofilm grows rapidly. The biofilm causes contaminants to decompose. www.knust.edu.gh 6/23/24 2023/2024 48  Anaerobic reactor The simplest anaerobic reactor is a septic tank, which separates domestic waste into a settling solid phase, a liquid effluent and floating scum layer In a completely mixed reaction, the minimum allowable time that solids must remain in a system is determined by the growth rate of methanogens which have a minimum doubling time of 3.3 days at 35oC. www.knust.edu.gh 6/23/24 2023/2024 49  Anaerobic reactor The incorporation of both aerobic and anaerobic degradation in the same bioreactor would require that the thickness of the biofilm be maintained such that the internal surfaces are anaerobic while the outer layer remains aerobic. www.knust.edu.gh 6/23/24 2023/2024 50  Anaerobic reactor Biofilms could facilitate nitrogen removal by promoting denitrification within the anaerobic zone and, nitrification on the aerobic surface. A microhabitat that possesses a range of redox potentials may also facilitate the breakdown of certain halogenated xenobiotics (e.g., DDT). www.knust.edu.gh 6/23/24 2023/2024 51  Microbial leaching - Bioleaching Process of metal extraction from low grade ore and mineral concentrate by the use of microorganisms Works by specific bacteria ‘eating’ the metal out of ore www.knust.edu.gh 6/23/24 2023/2024 52  Microbial fuel cell - MFC MFC: A bio- electrochemical system that drives an electric current by using bacteria and mimicking bacterial interactions found in nature. www.knust.edu.gh 6/23/24 2023/2024 53  Other Usefulness Use of bacteria and their products in wastewater treatment, bio-extraction and mining practices. The mining industry has exploited the ability of certain bacteria to accumulate metals intracellularly, particularly in the management of effluent treatment lagoons. Extracellular interactions between bacteria and metals are probably of greater importance to the integrity and ecology of the water distribution system. www.knust.edu.gh 6/23/24 2023/2024 54  Negative parts - Disadvantages www.knust.edu.gh 6/23/24 2023/2024 55  In natural environments…....... Biofilms grow virtually everywhere – Moisture – Nutrients – Surface Produce toxic alga blooms – Create O2 depleting zones in lakes, rivers and coastal environments www.knust.edu.gh 6/23/24 2023/2024 56  In industrial environments www.knust.edu.gh 6/23/24 2023/2024 57  Membrane fouling (Bio-fouling) Undesirable build up of biotic deposit on surfaces (membrane) Occurs: On the surfaces of living marine organisms In membrane systems such as membrane bioreactors In cooling water cycles of large industrial equipment and power stations In groundwater wells In the exterior and interior of ocean-laying pipes. www.knust.edu.gh 6/23/24 2023/2024 58  Biofilm effect in water system www.knust.edu.gh 6/23/24 2023/2024 59  Effect of biofilm in pipeline water distribution Affect turbidity Red (iron) and black (manganese) in H2O Increased frictional resistance Pipe corrosion Decreased aesthetic quality Failure to meet water quality criteria www.knust.edu.gh 6/23/24 2023/2024 60  www.knust.edu.gh 6/23/24 2023/2024 61  Microbe-metal interactions Unfavourable interactions include transformation and mobilization of toxic metals and corrosion. Within the water distribution system, a number of toxic metals are likely to be present, including lead from old piping and solder, copper from piping, zinc from corrosion inhibitors and other components from steel piping, fitments and weldments. www.knust.edu.gh 6/23/24 2023/2024 62  Three processes can be considered of paramount importance. – Interaction between bacterial cell walls and metals – Interaction between bacterial extracellular materials and metals – Production of acids and other corrosive metabolites. www.knust.edu.gh 6/23/24 2023/2024 63  Bio-corrosion www.knust.edu.gh 6/23/24 2023/2024 64  Bio-corrosion They promote corrosion of metallic surfaces Accelerate the corrosion of the pipes themselves, and initiate degradation of submerged objects such as offshore oil rigs, boats and shoreline installations. www.knust.edu.gh 6/23/24 2023/2024 65  When water comes into contact with metal piping and O2 is introduced, microorganisms attach themselves to the metal surface and form a biofilm composed of bacteria, algae and other microorganisms. This type of corrosion is called Microbiologically Influenced Corrosion (MIC) MIC can spread so quickly and cause pinhole leaks in piping that lead to inefficiency, poor performance and ultimately, failure of a system. www.knust.edu.gh 6/23/24 2023/2024 66  Bio-corrosion Responsible for off-flavours; Discoloured water; Harbour pathogens such as Legionella species; Increase the chlorine demand and provide a site/sites for the regrowth of coliforms. www.knust.edu.gh 6/23/24 2023/2024 67  Tubercle formation Tubercles develop from chemical or biological deposition of iron and manganese oxides to form deposits or concretions on a metal surface These deposits may block flow within the pipe and may substantially reduce efficiency and discolour the water www.knust.edu.gh 6/23/24 2023/2024 68  Microbial deterioration of wastewater systems and other concrete structures Major city sewerage systems (concrete) have been very badly damaged by acid deterioration, often known as sewer crown corrosion The microbiology is dependent on the Sulphur cycle www.knust.edu.gh 6/23/24 2023/2024 69  Sewer crown corrosion www.knust.edu.gh 6/23/24 2023/2024 70  Sewer crown corrosion CO2 and H2S (products of sewage decomposition) react with the damp concrete surfaces to form carbonates and calcium sulphate. As a result the surface pH of the concrete drops from approximately 12.5 to about 8.5. Hydrogen sulphide is partially oxidized in air to form thiosulphuric and polythionic acids. These in turn lower the pH further to approximately 7.5. Below pH 10 a number of different bacteria oxidize thiosulphate and polythionates to sulphate. The pH continues to decline and at about 5, Thiobacillus thiooxidans oxidizes elemental sulphur to sulphuric acid. The final pH can reach 0.6 (Acidic) www.knust.edu.gh 6/23/24 2023/2024 71  Biofilms in water supply systems Interactions between anthropogenic and natural systems result in the development of unique microbiological ecosystems E.g. Iron tubercle formation on water distribution and cooling pipes and the corrosion due to sulphur in concrete sewers. The common denominator is the use of source water www.knust.edu.gh 6/23/24 2023/2024 72  A source water (fresh, brackish, or marine), contains a community of bacteria, fungi, protozoa, algae, and higher invertebrates that initially contaminate and may thrive in the anthropogenic system. The implications of this initial contamination include: – Natural microbial population development in piping systems, storage tanks and cooling systems etc., may result in biofouling, odour problems, health risks and bio-corrosion (direct consequences of microbial film formation on the surface of pipes) www.knust.edu.gh 6/23/24 2023/2024 73  Biofilms and Human Health Bacterial cells within biofilms are controlled by the immune system Contamination of medical devices – Artificial surfaces such as medical implants = sites for development of biofilms containing pathogenic microorganisms – Major source of nosocomial infections – Responsible for over 65% of infections treated in the developed world www.knust.edu.gh 6/23/24 2023/2024 74  Human Health www.knust.edu.gh 6/23/24 2023/2024 75  Medical implants Medical devices implanted in the body: Catheters: tubes used to conduct fluids in or out of the body Prosthetic devices www.knust.edu.gh 6/23/24 2023/2024 76  Dental plaque A yellowish biofilm that builds up on the teeth The microbial composition changes from one that is primarily gram-positive to a structure filled with gram-negative anaerobes Microorganisms that form the biofilm are almost entirely bacteria (mainly Streptococcus mutans, S. mitis, S. sobrinus) Anaerobes include Fusobacterium and Actinobacteria www.knust.edu.gh 6/23/24 2023/2024 77  Biofilms are also present on the teeth of most animals as dental plaque, where they may become responsible for tooth decay and gum disease Dental plaque is biofilm (usually of a clear color) that builds up on the teeth If not removed regularly, it can lead to dental cavities (caries) or peridontal problems (such as gingivitis) www.knust.edu.gh 6/23/24 2023/2024 78 Factors: The shape of the teeth is important. Dogs are highly resistant to tooth decay because the shape of their teeth does not favor retention of food. Diets high in sugars are especially cariogenic because lactic acid bacteria ferment the sugars to lactic acid, which causes decalcification of the enamel of the tooth. Once breakdown of the hard tissue has begun, proteolysis of the matrix of the tooth enamel occurs through the action of proteolytic enzymes released by bacteria. www.knust.edu.gh 6/23/24 2023/2024 79 Two microorganisms that have been implicated in dental caries are: Streptococcus sobrinus and S. mutans, both lactic acid producing bacteria. S. sobrinus is able to colonize smooth surfaces because of its specific affinity for salivary glycoproteins and this organism is probably the primary organisms involved in decay of smooth surfaces. S. mutans is found predominantly in crevices and small fissures www.knust.edu.gh 6/23/24 2023/2024 80  Improper removal of plaque causes a build up of calculus (dark yellow color) near the gums on almost all the teeth. www.knust.edu.gh 6/23/24 2023/2024 81  Eye and biofilms Contact lenses and contact lens storage cases Intraocular lenses Suture material www.knust.edu.gh 6/23/24 2023/2024 82  Biofilms – Food industry www.knust.edu.gh 6/23/24 2023/2024 83  www.knust.edu.gh 6/23/24 2023/2024 84  www.knust.edu.gh 6/23/24 2023/2024 85  Food Industry Biofilms are found on food processing vessels etc., where the bacteria adhere tenaciously resisting removal by washing and also gaining protection from the common disinfectants, which cannot easily penetrate the polysaccharide matrix. Biofilms on floors and counters can make sanitation difficult in food preparation areas www.knust.edu.gh 6/23/24 2023/2024 86  Biofilm Issues Protection from washing and sanitization E. coli- 2400x more resistant to chlorine in biofilm Bacteria more resistant to removal by washing Inclusion in a biofilm appears to select for bacterial phenotypes more resistant to biocides. www.knust.edu.gh 6/23/24 2023/2024 87  Petroleum Industry Biofilms can help eliminate petroleum oil from contaminated oceans or marine systems The oil is eliminated by the hydrocarbon-degrading activities of microbial communities, in particular by a remarkable recently discovered group of specialists, the so-called hydrocarbonoclastic bacteria (HCB) www.knust.edu.gh 6/23/24 2023/2024 88  Visualisation of Biofilms Confocal laser scanning microscopy used to determine the location of GFP E. coli painted onto lettuce Other enteropathogens can be examined Other methods: eg Molecular- based methods GFP E. coli on Lettuce observed using confocal laser scanning microscopy www.knust.edu.gh 6/23/24 2023/2024 89