Environmental Microbiology Lecture 1 PDF

Environmental Microbiology Lecture 1 MICROBES IN THE ENVIRONMENT Diverse and ubiquitous Differ from laboratory strains o Adapted to harsh/varied conditions 6 large groups o Fungi o Archaea o Bacteria o Virus o Algae...

Environmental Microbiology Lecture 1 MICROBES IN THE ENVIRONMENT Diverse and ubiquitous Differ from laboratory strains o Adapted to harsh/varied conditions 6 large groups o Fungi o Archaea o Bacteria o Virus o Algae o Protozoa VIRUSES Grouped on their own because they don’t really classify as living organisms Able to infect living organisms and cause diseases Small, obligate, intracellular parasites Species specific; most attention given to plant and animal viruses Major impact on public health (smallpox, influenza, SARS) Virion- complete virus particle consisting of an RNA or DNA core with a protein coat; extracellular infective form of a virus Viruses are smaller in size compared to bacteria: chlamydia is the largest virus, and polio is the smallest virus Basic structure: protein coat (capsid) and either RNA or DNA but NOT BOTH Can have genetic information going in both directions: DNA to RNA and RNA to DNA Some also have envelopes, spikes, tails and sheaths o Envelope (outer membrane) formed by budding from host cell Two types of capsid organizations o Helical o Icosahedron Viruses synthesize proteins by using the host machinery Viruses are incapable of movement outside of hosts; need a vehicle o Inside host they are living and replicating; outside host they are dormant Many transmission routes o Animal to human (rabies) o Human to human: direct aerosol (sneezing coughing)→ measles, mumps o Human to human: direct fecal-oral (did not wash hands after using washroom)→ enterovirus o Human to human: direct sexual and bloodborne → HIV and HBV o Human to arthropod (mosquito) to human→ Yellow Fever o Mother to fetus (Vertical) → HIV o Environmental Infection is via specific receptor sites on capsid or envelope  Generally viral infection of a cell interferes with the cell’s ability to function properly Types of viral infections: o Acute: happens instantly, period of illness directly associated with infection (rhinovirus), relatively short duration with rapid recovery o Chronic: infected calls survive for prolonged period while new viral particels are made o Latent: virus present but do not produce progeny; often cause initial disease, then remain dormant until reactivated (cold sores) o Asymptomatic: virus replicates without noticeable symptoms (mild common cold) o Oncogenic: alter function of host cell; results in malignant cancer cells (HPV) o Slow: prolonged incubation period followed by progressive disease (HIV), may not being with an acute period of viral multiplication Viroid: o Free RNA sequences able to reproduce in several hosts o Different from viruses ▪ No capsid- exist as free nucleic acid ▪ Low mw RNA than viral RNA ▪ RNA not translated (function and replication not well understood) ▪ Though to be quite distant from viruses phylogenetically ▪ Only known to infect plants Prions o Infections protein particles (no DNA/RNA) o Not sensitive to nucleases o Responsible for Creutzfeldt-Jakob disease in humans (BSE or “mad cow disease” in cattle) ▪ Prions are usually a normal part of the CNS, to create an infection the abnormal prion will come in contact with a normal prion and change its structure ▪ In 1999-2000 there was a huge outbreak of mad cow disease due to how cattles were raised. Cattles were fed left over parts of other cattles and this created prions to become abnormal and then it was consumed by humans that made them sick DOMAINS OF LIFE Bacteria→ prokaryote Archaea→ prokaryote Eukaryote Prokaryote are divided into 4 types (cell wall properties) o Gram positive: thick peptidoglycan layer, cell membrane, periplasmic space o Gram negative: thin peptidoglycan layer, extra outer membrane, periplasmic space o Mycoplasma (no cell wall) o Archaea (cell wall without peptidoglycan layer) BACTERIA Most common and ubiquitous organisms found on Earth Size: 0.5 – 3 micrometers Form colonies; different shapes Found in diverse and extreme environments Important effects on the environment o Drive the carbon and nitrogen cycle o Major role in climate change because its ability to produce methane gas Appendages o Flagellum: motility and attachment to surfaces o Fimbriae: cell attachment o Pili: mostly in gram negative, involved in conjugation o Type IV pili involved in twitching motility Cell envelope o Most consist of glycocalyx (EPS), cell wall and cell membrane Cell Protoplasm o Contains nucleoid (genetic material) o Plasmids: unique characteristics o Ribosomes: protein synthesis (70s unit) o Inclusion bodies (food storage) ACTINOMYCES Prokaryotes classified as bacteria Filamentous bacteria Morphologically similar to fungi; have elongated cells that branch into filaments (hyphae) o Fungi are eukaryotes o Actinomyces are prokaryotes classified as bacteria Actinomyces hyphae are much smaller than fungal hyphae o Under microscope actinomyces hyphae are thread like o Under microscope fungal hyphae are ribbon like INFORMATION EXCHANGE BETWEEN BACTERIA 1. Conjugation a. transferred in one direction (unilateral) b. donor needs to be alive and have F+ plasmid c. recipient needs to also be alive and have no plasmid d. donor will form sex pilus which will attach to recipient and pull it closer to form a cytoplasmic mating bridge where DNA will get transferred from donor to recipient 2. Transformation a. Donor is dead cell b. Recipient is alive  c. Donor cell is dead and degrades leaving free DNA; the recipient will pick up the free DNA and incorporate it into its own genome 3. Transduction a. Donor is a bacterial cell b. Recipient is a bacterial cell c. Vehicle transferring DNA from donor to recipient is a bacteriophage i. Bacteriophage: obligate, intracellular parasites, that will attach to host and take over the host machinery d. Bacterial cell from donor goes through the lytic cycle where the cell carries transducing phages (it finds the host to inject DNA but it cannot take over the host because they are missing viral DNA) BACTERIAL METABOLISM Oligotrophic: survive in nutrient-deficient environments o Deep surface soil, glacial and polar ice Copiotrophic: survive in nutrient-rich environments o Sewage, top soil Autotrophs: derive energy and C from inorganic sources C from CO2 o Photoautotrophs: carry out photosynthesis and obtain energy from sunlight (cyanobacteria) o Chemoautotrophs: obtain energy from oxidation of inorganic substances such as H2S, ammonia, and iron-bearing compounds (Nitrobacter) Heterotrophs: derive carbon from pre-formed organic compound that are broken down enzymatically o Chemoheterotrophs: energy derived from oxidation of organic compounds via respiration (E. coli) o Photoheterotrophs: derive energy from light and use organic compounds as a source of reducing power (eg green and purple sulfur bacteria) ARACHEA Morphologically similar to bacteria in size and shape Genetically and biochemically distant from bacteria Oldest life form on Earth Found in extreme and normal environments Some aspects of Archean structure and metabolism similar to bacteria Genetic transcription and translation more similar to eukaryotes FUNGI Eukaryotes and chemoheterotrophs Ubiquitous and diverse One of the largest organisms on Earth Found in fresh and marine water and soil Beneficial and adverse effects on the environment  Generally aerobic (except yeast, which can ferment, and zoosporic fungi in ruminant guts) Forms symbiotic relationships o Lichens: symbiotic relationship between fungus (Ascomycota) and green algae or cyanobacteria o Mycorrhiza: symbiotic relationship between a fungus and the roots of a vascular plant Fungi structure: o Yeast is unicellular o Mold is multicellular o Hyphae: long, branching filamentous structure ▪ Main mode of vegetative growth ▪ Collectively called a mycelium ▪ Can be septated (partitions) or non-septated (no partitions) o Eukaryotic cells with true nucleus and specialized organelles (Golgi apparatus, ribosome, mitochondria, ER, nucleolus, cell wall and storage vesicle) o Fungal cells lack flagella and other surface appendages o Contains glycocalyx (protection, attachment and signal reception) o Cell wall is rigid; distinct from prokaryotic cell wall; fungal cell wall contain chitin (provides strength and structure) 3 classifications of fungi 1. Molds: filamentous fungi (mycelia); undergo asexual or sexual reproduction, produces persistent spores (Penicillium) 2. Mushrooms: part of Basidiomycota; filamentous fungi producing large fruiting bodies (mushroom); undergo asexual or sexual reproduction; important decomposers 3. Yeasts: unicellular; can ferment under anaerobic conditions; do not produce spores; asexual reproduction via budding (Candida and Saccharomyces) ALGAE Eukaryotic, uni or multil cellular photosynthetic organisms Range in size from microscopic to macroscopic o Microalgae (microscope) vs macroalgae (macroscope) Blue-green algae is not an algae it is now known as a cyanobacteria Classification is based on the colour of photosynthetic pigments present (eg, red, green, brown algae) Structure of algae cell o Thin, rigid cell wall o Some contain CaCO3 or chitin o Diatoms contain silica → fossils o Some contain gelatinous capsule o Some have flagella o Chloroplasts→ chlorophyll A and others + xanthophyll  o Can reproduce sexually and asexually ▪ Binary fission more prevalent in microalgae Most significant impact in aqueous environment Basis of the aquatic food chain—phytoplankton (large floating communities of microscopic algae) Microalgae: unicellular, microscopic algae found in freshwater and marine systems o Used in nutraceuticals, cosmetics and animal feed o Source of biofuel Some produce toxins o (red tide): cause paralysis/death in humans. Caused by red algae that accumulate in shell fish which is then consumed by humans and causes them paralysis or death o Eutrophication: excess amounts of nutrients in the water which increases the number of algae present and they take over the water vapour and when they decompose they take up oxygen in the water and deprives aquatic organisms of oxygen and they die PROTOZOA Unicellular eukaryotes; some are visible with the naked eye (Amoeba) Adapted to a wide variety of environments, found in nearly all terrestrial and aquatic environments Free living or parasitic Most are heterotrophic- feed on bacteria, algae or other protozoa Both sexual and asexual reproduction o Mostly binary fission Structure: o No cell wall ▪ Cell rigidity is provided by gelatinous cytoplasmic material- ectoplasm o Wide range in size (5 micrometer to 1mm) o Vacuoles serve variety of functions ▪ Phagocytic: aid in digestion of food ▪ Contractile: aids in movement ▪ Secretory: aids with secretion of certain enzymes used in digestion of food 4 classifications Flagellates: flagella help them in movement Amoeboid: pseudopods use foot like movement Sporozoans: produce spore like characteristics Ciliates: have hair like structures that help in movement Encystment o Protozoa needs water to survive o Key features of protozoa is the ability to survive periods of desiccation (no water) by encystment  o Encystment: transformation into inactive, immobile, environmentally resistant cysts ▪ Can survive dry heat of 120 degrees Celsius, freezing in liquid N2 ▪ Cysts can be easily transported via air, water, aquatic birds or passage through intestinal tract o When conditions are favorable again, cyst walls are broken down in the process of excystation Beneficial roles of protozoa o Recycling nutrients; provide other microbes with nutrients from metabolic waste products; sustain MO population and increase decomposition rates o Sewage treatment: removal of particulate matter and reduction of bacteria via grazing o Direct contribution to food chain (nutrient source for higher consumers such as nematodes and crustaceans) Disease causing Protozoa o Malaria, sleeping sickness, giardiasis, and other illnesses o Often able to evade host immune system; survive in host and create chronic illness ▪ Toxoplasma: causes blindness, serious illness, or death in unborn fetuses o Transmission is often through ingestion or biting arthropods (mosquitoes) o Often enter in cyst form, once inside body excystation occurs EXTREMOPHILES Organisms that thrive in physically or geochemically extreme conditons o Extremely high or low temperatures (-40 to 122 degrees celcius) o pH (-3.6 to 13) o salinity (5M NaCl) o pressure (0.3atm to 1200 atm) o radiation (5000x gamma that is lethal to humans) Hyperthermophiles o Thrive in 60-130 degrees o Highest growth temperature 122 degrees M. kandleri ▪ Heat stable enzymes (amino acid substitution, high [chaperonin] maintain structure) ▪ Membranes rich in saturated fatty acids or lack fatty acids entirely (Archaea) Psychrophiles o Growth and reproduction in cold temperatures o Microbial activity at -40 degrees in sub-glacial aquatic environments ▪ “cold-active” enzymes ▪ Membranes have more unsaturated fatty acids (stay in fluid state) ▪ Cryoprotectants: protect them from freezing damage from the cold Acidophiles  o Thrive under highly acidic conditions (pH 1000atm) o Obligate barophiles cannot survive outside such environments (Halamonas salaria) requires 1000 atm and 3 degrees ▪ Enzymes fold (hence pressure doesn’t alter binding site) ▪ More unsaturated fatty acid on membranes ▪ Alteration of membrane composition to adjust permeability Radiation Tolerant o Can survive high dosage of radiation ▪ Deinococcus radiodurans can survive gamma-ray exposure at 5000X more than the lethal dosage to humans o Can be used to degrade nuclear waste ▪ Powerful DNA repair machinery ▪ Many copies of DNA repair gene ▪ Multiple copies of chromosomes in novel ring-like structure (4 compartments each with one copy of DNA)