Aquatic Microbiology (Marine Microbes) PDF

Aquatic microbiology (Marine Microbes) At the end of the study, the student will be able to understand and increase knowledge on marine microbes types and their examples water pollution and the indicator (biological and chemical)  Key Conc...

Aquatic microbiology (Marine Microbes) At the end of the study, the student will be able to understand and increase knowledge on marine microbes types and their examples water pollution and the indicator (biological and chemical)  Key Concepts Microbial life in the sea is extremely diverse, including members of all three domains of life as well as viruses. Marine virology is an emerging field of study, due to recognition of the critical role that viruses may play in population control of other microbes, in nutrient cycling, and in marine pathology.  Key Concepts Photosynthetic and chemosynthetic bacteria and archaeons are important primary producers in marine ecosystems. Heterotrophic bacteria, archaeons, and fungi play essential roles in recycling nutrients in the marine environment. Marine Viruses Virology—the study of viruses Viruses are diverse and are more abundant than any other organism in the sea Have significance for marine food webs, population biology and diseases of marine organisms Viruses of marine eukaryotic hosts first reported in the 1970s Reliable counts of marine viruses made in the 1980s  Lytic Cycle Infection Replication Lysis Lysogenic Cycle Stepped Art Fig. 6-3, p. 128  Marine Bacteria General characteristics ○ simple, prokaryotic organization: no nuclei or membrane-bound organelles, few genes, nonliving cell wall ○ reproduce asexually by binary fission ○ many shapes and sizes bacillus—rod shape coccus—spherical shape Spirillum – cork screw shape  Cyanobacteria species The unicellular cyanobacterium Synechocystis sp. Prochlorococcus spp. Nostoc punctiforme Calothrix spp.  Aerobic respiration CONSUMERS Oxygen Zooplankton Animals Aerobic Consumed by respiration Consumed by Die Wastes PRIMARY PRODUCERS DECOMPOSERS Photo-synthesi Chemo-sy Aerobic bacteria Anaerobic zers nthetic and fungi bacteria bacteria Die Cyanobacteria Phytoplankton Multicellular algae Plants Aerobic Consumed by metabolism Fermentation Nutrients released Nitrogen Sulfur Phosphorus Stepped Art Carbon dioxide Fig. 6-6, p. 131  Nutritional Types Cyanobacteria (blue-green bacteria) ❑ photosynthetic bacteria which are found in environments high in dissolved oxygen, and produce free oxygen ❑ store excess photosynthetic products as cyanophycean starch and oils ❑ primary photosynthetic pigments are chlorophyll a and chlorophyll b ❑ accessory pigments include carotenoids and phycobilins  Light energy Carbon dioxide (CO2) Oxygen Carbohydrates (CH2O)x (O2) Water (H2O) (a) Cyanobacteria – Free oxygen produced Light energy Carbon dioxide (CO2) Sulfate Carbohydrates (CH2O)x (SO42–) Hydrogen sulfide (H2S) (b) Purple and green bacteria – No free oxygen produced Stepped Art Fig. 6-8, p. 132 Nutritional Types (Cyanobacteria) Cyanobacteria (con’t) ○ chromatic adaptation—response of pigment composition to the quality of light in the sea ○ may exist as single cells or form dense mats held together by mucilage form associates called stromatolites—a coral-like mound of microbes that trap sediment and precipitate minerals in shallow tropical seas Nutritional Types Other photosynthetic bacteria ○ anaerobic green and purple sulfur and non-sulfur bacteria do not produce oxygen ○ the primary photosynthetic pigments are bacteriochlorophylls ○ sulfur bacteria are obligate anaerobes (tolerating no oxygen) ○ non-sulfur bacteria are facultative anaerobes (respiring when in low oxygen or in the dark and photosynthesizing anaerobically when in the presence of light)  Nutritional Types Chemosynthetic bacteria ○ use energy derived from chemical reactions that involve substances such as ammonium ion, sulfides and elemental sulfur, nitrites, hydrogen, and ferrous ion. ○ chemosynthesis is less efficient than photosynthesis, so rates of cell growth and division are slower. ○ found around hydrothermal vents and some shallower habitats where needed materials are available in abundance.  Chemosynthetic bacteria (in animal tissues, in water, and on rocks) Carbon dioxide (CO2) Produce Water (H2O) Elemental Carbohydrates sulfur (S) Hydrogen Carbon sulfide (H2S) dioxide (CO2) Carbon Hydrogen dioxide (CO2) sulfide (H2S) Animal community Stepped Art Magma (molten rock) Fig. 6-10, p. 134  Nutritional Types Heterotrophic bacteria ○ decomposers that obtain energy and materials from organic matter in their surroundings ○ return many chemicals to the marine environment through respiration and fermentation ○ populate the surface of organic particles suspended in the water by secreting mucilage (glue-like substance)  Symbiotic Bacteria Many bacteria have evolved symbiotic relationships with a variety of marine organisms Endosymbiotic theory ○ mitochondria, plastids & hydrogenosomes evolved as symbionts within other cells Chemosynthetic bacteria live within tube worms and clams Some deep-sea or nocturnal animals host helpful bioluminescent bacteria ○ photophores ○ embedded in the ink sacs of squid  Archaea General characteristics ○ small (0.1 to 15 micrometers) ○ prokaryotic ○ adapted to extreme environmental conditions: high and low temperatures, high salinities, low pH, and high pressure ○ formerly considered bacteria ○ differences from bacteria cell walls lack special sugar-amino acid compounds in bacterial cell walls cell membranes contain different lipids, which help stabilize them under extreme conditions  Archaea Nutritional Types ○ archaea includes photosynthesizers, chemosynthesizers and heterotrophs ○ most are methanogens: anaerobic organisms that metabolize organic matter for energy, producing methane as a waste product ○ halobacteria (photosynthetic), thrive at high salinities, trap light using bacteriorhodopsins, purple proteins  Archaea Hyperthermophiles ○ organisms that can survive at temperatures exceeding 100o C, such as near deep-sea vents ○ Potential for biomedical and industrial application  Eukarya Eukarya includes all organisms with eukaryotic cells Examples: ○ plants ○ animals ○ fungi ○ algae ○ single-celled animal-like protozoa  Fungi History of marine mycology ○ marine fungi first discovered in 1849 ○ marine fungi’s ecological role is difficult to evaluate; biomass needs to be quantified ○ important in marine ecosystems as decomposers, prey, pathogens and symbionts  Fungi General features of fungi ○ eukaryotes with cell walls of chitin ○ many are unicellular yeasts ○ filamentous fungi grow into long, multi-cellular filaments called hyphae that can branch to produce a tangled mass called a mycelium ○ heterotrohic decomposers that recycle organic material can digest lignin (major component of wood) Fungi General features of fungi (con’t) ○ store energy as glycogen ○ kingdom Fungi is divided into 4 phyla: Chytridiomycota (motile cells) Zygomycota (e.g. black bread mold) Basidiomycota (club fungi, e.g. mushrooms) Ascomycota (sac fungi) ○ in the sea, ascomycotes are the most diverse and abundant fungi Fungi Ecology and physiology of marine fungi ○ can be either obligately marine, requiring ocean or brakish water or facultatively marine (primarily of terrestrial or fresh water origin) ○ salinity is toxic to fungi, so they must devote energy to removing sodium ○ most marine fungi live on wood from land ○ some live on grass in salt marshes ○ others live on algae, mangroves or sand ○ fungi decompose the chitinous remains of dead crustaceans in open sea plankton communities  Maritime Lichens Lichens: mutualistic associations between a fungus and an alga ○ fungi are usually ascomycotes ○ algae are usually green or blue-green bacteria The fungus provides attachment, general structure, minerals, moisture The alga produces organic matter through photosynthesis Stramenophiles A diverse group of eukaryotic organisms unified by the nature of their cells’ 2 flagella The special flagella ○ 1 flagellum is a simple form, usually with a light-sensing body at the base; senses light ○ 2nd bears many mastigonemes (hair-like filaments) with a thickened base and a branching tip along the shaft; used for swimming Stramenophiles Heterokont: refers to the different form of the 2 flagella Ochrophytes: photosynthetic type that are usually golden brown ○ e.g. diatoms, silicoflagellates and brown algae Silicoflagellates Diatom Diatoms Extremely diverse and distinct members of marine phytoplankton Diatom structure ○ frustule—a two-part, box-shaped organic cell wall impregnated with silica ○ valve—one half of a frustule; 1 valve is larger and fits over the other like a box lid ○ 2 basic diatom shapes: radially symmetrical valves (generally planktonic) bilaterally symmetrical valves (generally benthic) Diatoms Locomotion in diatoms ○ some benthic diatoms move slowly by mucilage secretion from pores and grooves Reproduction in diatoms ○ asexual reproduction by fission each daughter cell gets 1 valve, and has to grow a 2nd, smaller one to complete frustule auxospore—daughter cell which casts off the small valve, increases in size, and secretes a new frustule of normal size (occurs when cell size reaches 50% of maximum)  Reproduction sexual and asexual diatom (video) Silicoflagellates Pelagophyceans – brown tides Most are coccolithophores with a surface coating of disc-shaped scales (coliths) of calcium carbonate ○ remains form calcereous oozes Asexual Reproduction Sexual Reproduction New cell Frustule formation Growth of the cell (auxospore) Zygote Gamete from another Gametes Mitosis formed Mitosis Gametes Cells’ division released Mitosis continues until cells become too Mitosis small to divide Stepped Art Fig. 6-19, p. 144  Other Ochrophytes Silicoflagellates ○ abundant in cold marine waters ○ basket-shaped external skeletons of silica which the cell wraps around ○ cell wraps around skeleton which appears internal  Other Ochrophytes Pelagophyceans ○ e.g. bloom-forming alga Aureococcus anophagefferens (non-toxic, coastal) responsible for “brown tides” ○ can block light from sea grasses or clog filter-feeding structures of molluscs. Aureococcus anophagefferens Labyrinthomorphs Spindle-shaped, mucous secreting osmotrophic cells Labyrinthulids (consists 13 species, no unique characters) ○ e.g. Labyrinthula zosterae, causes devastating eelgrass wasting disease  Thraustochytrids ○ planktonic and benthic decomposers ○ some are pathogens of shellfish ○ used to produce dietary supplements: oils extracted from some species are high in polyunsaturated omega-3 fatty acid docosahexaenoic acid (DHA)  Haptophytes Photosynthetic organisms with 2 simple flagella both used for locomotion Have haptonema: a unique structure arising from the cell surface between the 2 flagella, captures food  Most are coccolithophores with a surface coating of disc-shaped scales (coliths) of calcium carbonate ○ remains form calcereous oozes  Calcareous ooze is a calcium carbonate mud formed from the hard parts (tests) of the bodies of free-floating organisms. Once this mud has been deposited, it can be converted into stone by processes of compaction, cementation, and recrystallization. The main contributors to the ooze are coccolithophores and foraminifera. Coccolithophores are tiny single-celled organisms which cover themselves with tiny plates of calcite known as coccoliths. Foraminifera are also single-celled organisms.  Haptophytes Account for up to 40% of carbonate production in modern seas High reflectance of chalky coccolithophores and their production of dimethyl sulfide may have impact on global climate change The Seven Sisters, Sussex, England: a fine example of chalk Alveolates Recent re-grouping of several kinds of marine microbes Have membranous sacs (alveoli) beneath their cell membranes ○ pellicle: term for the cell surface if the combination of cell membrane and alveoli is complex (distinct from cell wall) Examples: ○ dinoflagellates ○ ciliates ○ apicomplexans (strictly parasitic) Alveolates Dinoflagellates ○ globular, unicellular (sometimes colonial) with 2 flagella ○ dinosporin: a unique chemical associated with the cellulose plates within the alveoli of dinoflagellates ○ Most are planktonic, some are benthic and others parasitic, also can be bioluminescent – Bioluminescent Bay, Puerto Rico Alveolates (Dinoflagellates) Harmful Algal Blooms (HABs) ○ occur when photosynthetic dinoflagellates undergo a population explosion ○ colors the water red, orange or brown ○ dinoflagellates that cause HABs produce toxins paralytic shellfish poisoning (PSP) occurs in humans who consume shellfish contaminated with these toxins toxins cannot be destroyed by cooking ○ oxygen content of the water may be reduced to deadly levels as bacteria decompose animals killed by dinoflagellate toxins Alveolates Ciliates ○ protozoans that bear cilia for locomotion and for gathering food membranelles—tufts or long rows of fused adjacent cilia cytostome—an organelle serving as a permanent site for phagocytosis of food ○ planktonic and benthic ○ major links in marine food chains ○ form symbiotic and parasitic relationships ○ reproduce asexually by binary fission and sexually by conjugation (nuclei transfer) Alveolates (Ciliates) Types of marine ciliates ○ scuticociliates (have a dense and uniform distribution of cilia on their body) ○ oligotrichs (have few cilia) tintinnids (usually lack body cilia and secrete an organic, loosely fitting shell, the lorica)  Ecological roles of marine ciliates ○ most are heterotrophs; some harbor autotrophic symbionts or chloroplasts ○ link hetero- and autotrophic blue-green bacteria to higher levels in the food chain Choanoflagellates Phylum of marine and freshwater flagellated cells that are more closely related to animals than any other group of one-celled microbes Unicellular or colonial ○ colonies may be stalked or embedded in a gelatinous mass ○ cell often surrounded by a lorica of siliceous rods; flagellum is surrounded by a funnel-shaped collar of microvilli Highly efficient consumers of bacteria Water Pollution What is water pollution? Water pollution can be defined as the contamination of a stream, river, lake, ocean or any other stretch of water, depleting water quality and making it toxic for the environment and humans. (Solar Impulse Foundation, 2020)  Types of water pollution Organic pollution due to microorganisms - bacteria and viruses - present in the water, generated by excrement, animal and vegetable waste Chemical pollution generated by the nitrates and phosphates of pesticides, human and animal drugs, household products, heavy metals, acids and hydrocarbons used in industries (Solar Impulse Foundation, 2020) What are the sources of water pollution? Unsurprisingly, human activity is primarily responsible for water pollution, even if natural phenomenon - such as landslides and floods - can also contribute to degrade the water quality. (Solar Impulse Foundation, 2020) Types and Sources of Water Pollution Point sources Nonpoint sources Water Do (ppm) at 20˚C Biological Quality Good oxygen demand Slightly 8-9 polluted 6.7-8 Water quality Moderately polluted 4.5-6.7 Heavily polluted Below 4.5 Gravely polluted Below 4 Pg. 535  Point and Nonpoint Sources NONPOINT SOURCES Rural homes Urban streets Cropland Animal feedlot Suburban POINT development SOURCES Factory Wastewater treatment plant Water pollution Bacteria,Viruses,Protozoa, Parasitic worms Oxygen demanding substances Inorganic plant nutrients Organic chemicals Sediment or suspended matter Thermal pollution Genetic pollution Biological Magnification Water 0.000002 ppm Herring gull 124 ppm Phytoplankton 0.0025 ppm Herring gull eggs 124 ppm Zooplankton Lake trout 0.123 ppm 4.83 ppm Rainbow smelt 1.04 ppm  Pollution of Streams Oxygen sag curve Fig. 20-5  Pollution of Lakes Discharge of untreated Eutrophication municipal sewage Nitrogen compounds (nitrates and phosphates) produced by cars and factories Natural runoff Discharge of (nitrates and detergents phosphates ( phosphates) Manure runoff From feedlots (nitrates and Discharge of treated Phosphates, municipal sewage ammonia) (primary and secondary treatment: nitrates and phosphates) Runoff from streets, lawns, and construction Lake ecosystem lots (nitrates and nutrient overload phosphates) and breakdown of chemical cycling Runoff and erosion Dissolving of (from from cultivation, nitrogen oxides mining, construction, (from internal combustion and poor land use) engines and furnaces) Fig.22.7, p. 499 Solutions to better water quality Drainage Area Management Plans Agriculture plots 1987 Water Quality Act  Groundwater Pollution: Causes Hazardous waste injection well Pesticides Coal strip De-icing Buried gasoline mine runoff road salt and solvent tank Pumping Cesspool Gasoline septic tank well station Waste lagoon Water pumping Sewer well Landfill Accidental Leakage from faulty spills casing uifer q Discharge ra w ate r sh ife d fre r a qu Confined aquifer ine a t e f con shw Un f r e Groundwater ined nf flow Co Fig. 20-11 Groundwater Pollution Prevention Monitoring aquifers Strictly regulating hazardous waste disposal Storing hazardous materials above ground Industry Cities Urban sprawl Nitrogen oxides Toxic metals Bacteria and viruses Construction sites from autos and and oil from from Sediments are washed into smokestacks, streets and sewers and septic waterways, choking fish and plants, toxic chemicals, parking lots tanks contaminate clouding waters, and blocking and heavy metals in pollute waters; shellfish beds sunlight. effluents flow into bays and estuaries. Farms Runoff of pesticides, manure, and fertilizers adds toxins and excess nitrogen and phosphorus. Red tides Closed Excess nitrogen causes shellfish beds explosive growth of toxicmicroscopic algae, Closed poisoning fish and beach marine mammals. Oxygen-depleted zone Toxic sediments Chemicals and toxic metals contaminate shellfish beds, kill spawning fish, and accumulate in the tissues of bottom feeders. Oxygen-depleted zone Healthy zone Sedimentation and algae Clear, oxygen-rich overgrowth reduce sunlight, waters promote growth Fig. 20-15 kill beneficial sea grasses, use of plankton and sea grasses, up oxygen, and degrade habitat. and support fish. Fig. 21-10, p. 505 Reducing Water Pollution through Sewage Treatment Primary and Secondary sewage treatment. Figure 20-19 Global Outlook: Stream Pollution in Developing Countries Water in many of central China's rivers are greenish black from uncontrolled pollution by thousands of factories. Figure 20-7 Case Study: India’s Ganges River: Religion, Poverty, and Health Religious beliefs, cultural traditions, poverty, and a large population interact to cause severe pollution of the Ganges River in India. Very little of the sewage is treated. Hindu believe in cremating the dead to free the soul and throwing the ashes in the holy Ganges. Some are too poor to afford the wood to fully cremate. Decomposing bodies promote disease and depletes DO. Case Study: India’s Ganges River: Religion, Poverty, and Health Daily, more than 1 million Hindus in India bathe, drink from, or carry out religious ceremonies in the highly polluted Ganges River. Biological indicator Characteristics of a Useful Indicator Useful for all water types Always present when pathogens are present Not present in the absence of the pathogen Correlated with degree of pollution More easily detectable than a pathogen Survive longer than the pathogen Not dangerous to work with Bacterial-Indicator Organisms Common Groups Coliforms Total coliforms Fecal coliforms Escherichia coli Streptococci fecal streptococci Enterococci Spore Formers Clostridium perfringens Indicator Organisms General coliforms – indicate water in contact with plant or animal life (universally present) Fecal coliforms – mammal or bird feces in water Enterococcus bacteria (type of fecal streptococci)– feces from warm blooded animals in water These are not what generally make people sick Problems With the Coliform Indicator Test False Positives False Negatives Enterobacter areogenes Salmonella typhi Some Factors Affecting Ratio of Indicator Organisms to Pathogens Feces from human populations with higher infection rates are of greater concern All treatment methods and environmental conditions affect pathogens and indicators differently - Chlorinated water may have zero indicators and pathogens, but loaded with viruses. - Pathogens can “hide” from treatment inside suspended solids. The ratio of indictors to actual pathogens is not fixed Direct Tests For Pathogens Involves selective cultivation to large numbers ❑ Time consuming ❑ Expensive ❑ Potentially dangerous to lab personnel Molecular tests ❑ Require testing for each pathogen ❑ Expensive ❑ Require expertise  HOW TO PREVENT….? Always wash your hand before handling food especially and after using toilet Wash your fruits and vegetable before use as it contain harmful chemicals and microbes. Don’t drink water from river, lakes and ponds. Try to adopt healthy and good hygiene as possible Chemical Indicator  A chemical indicator is a substance that undergoes a distinct observable change when conditions in its solution change. This could be a color change, precipitate formation, bubble formation, temperature change, or other measurable quality Another type of indicator that may be encountered in chemistry and other sciences is a pointer or light on a device or instrument, which may show pressure, volume, temperature, etc. or the condition of a piece of equipment (e.g., power on/off, available memory space). Litmus Paper and the Litmus Test  Examples of Indicators A pH indicator changes color over a narrow range of pH values in solution. There are many different pH indicators, which display different colors and act between certain pH limits. A classic example is litmus paper. Blue litmus paper turns red when it's exposed to acidic conditions, while red litmus paper turns blue under basic conditions. Fluorescein is a type of adsorption indicator. The dye is used to detect the completed reaction of the silver ion with chloride. Once sufficient silver is added to precipitate chloride as silver chloride, excess silver is adsorbed onto the surface. Fluorescein combines with adsorbed silver to produce a color change from greenish-yellow to red.  Other types of fluorescent indicators are designed to bond to selected molecules. The fluorescence signals the presence of the target species. A similar technique is used to label molecules with radioisotopes. An indicator may be used to identify the endpoint of a titration. This may involve the appearance or disappearance of a color. Indicators may indicate the presence or absence of a molecule of interest. For example, lead tests, pregnancy tests, and nitrate tests all employ indicators.  Desirable Qualities of a Chemical Indicator To be useful, chemical indicators must be both sensitive and easily detectable Another important quality is that the indicator doesn't change the conditions of the sample. Source: Helmenstine, Anne Marie, Ph.D. "What Is a Chemical Indicator?" ThoughtCo, Aug. 26, 2020, thoughtco.com/definition-of-indicator-605239. THANK YOU