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88 Cards in this Set

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how do we generally subdivide aquatic microbiology?

freshwater vs. marine types


still variable - different microhabitats for microbes (surface vs. deep)

marine habitats


intertidal zone

area of seashore that is submerged at high tide and exposed to air during low tide




harsh environment due to alternating moisture, heat, and oxgen exposure




includes:


neritic zone and pelagic zone

marine habitats


intertidal zone


neritic zone

water above continental shelf




sunlight reaches the bottom




diversity of producers

marine habitats


intertidal zones


pelagic zone/oceanic zone

deeper ocean with a larger water column

marine habitats


neuston zone

air-water inteface that extends less that a millimeter down




contains highest concentration of microbes with lots of algae, protists, and bacteria floating on the surface or utilizing surface tension




very high oxygen and light concentration

marine habitats


photic zone

a measurement of depth - goes down 100-200 meters




receives light = phytoplankton are abundant




oxygen levels decrease with depth

marine habitats


disphotic/twilight zone

receives faint or filtered sunlight = no photosynthesis is possible




cold water at high pressure




little microbial growth

marine habitats


aphotic/midnight zone

deep ocean with no light at all




intense pressure and near freezing




heterotrophic bacteria feed on org. matter that has fallen; lithotrophic bacteria feed on inorg. matter for energy




lots of bioluminescence occurs

marine habitats


benthic zone

ocean floor and its sediment




crushing pressure, almost no oxygen, temperature extremes (intense cold and geothermal vents)




lots of archaebacteria

what distinguishes freshwater from marine habitats and what are the major types of freshwater habitats?

freshwater habitats are defined by their relatively low salt concentrations - can accommodate microbes sensitive to high [salt]


variety:


- brackish estuaries: mix of fresh/salt water


- nutrient rich vs. poor lakes & ponds


- rivers & streams


- wetlands: includes swamps, bogs, marshes

lakes & ponds


how do we define the water column?

water column defined by aeration, depth, nutrient composition, and temperature

lakes & ponds


oligotrophic lakes

- clear, blue water




- deep, undisturbed lakes with dilute nutrient composition




- not a lot of microbial growth

lakes & ponds


oligotrophic lakes


major layers



- epilimnion: upper region


- thermocline: thin layer transition zone


- hypalimnion: lower region

lakes & ponds


oligotrophic lakes


epilimnion

upper region


- supports large # of oxygenic phototrophs (algae, cyanobacteria)


- warm, well oxygenated and mixed



lakes & ponds


oligotrophic lakes


thermocline

- thin layer between


- steep temperature transition zone that changes with the seasons


- cold beneath

lakes & ponds


oligotrophic lakes


hypalimnion

- lower region


- includes benthos (bottom)


- anoxic, cold water


- greater growth of anoxy. phototrophs, sulfur/sulfate bacteria, archae (alt e- used by lithotr.)

lakes & ponds


eutrophic lakes

- shallow, nutrient rich


- more plant / fish / microbial growth


- water = murky


- nutrients added from age, detergents, fertilizers, and sewage (N, P, org. pollutants)

lakes & ponds


eutrophic lakes


algal blooms

caused by extreme eutrophication


- increased nutrients = growth of more algae


- dying algae = heterotrophic bact. rapidly consuming & reproducing


- excessive hetero. depletes oxy. levels crucial for respiration




= lakes becomes either permanently or temporairly anoxic

rivers & streams





- relatively shallow, nutrient rich, better oxygenation (from constant movement)


- composition changes almost daily & more prone to widespread contamination


- microbial growth high from organic matter present = argicultural run off, industrial waste, sewage

wetlands



high levels of nutrient cycling:


- transition between terrestrial/aquatic


- helps protect inland/coastal from eutroph.


- lots of plants/roots, agricult. run off, decomp.




microbes:


- highly productive


- sulfate reducers, nitrogen fixers, methanogens, iron utilizers


- largely anaerobic because of roots

aquatic microbe


difficulties

- communication


- nutrient availability


- osmotic stress

aquatic microbe


difficulties


nutrient availability

sheer size of some bodies of water dilutes out many of the nutrients that are necessary for life



soutions: motility, scavenging enzymes

aquatic microbe


difficulties


communication

being too dispersed can negatively impact communication between microbes




solutions: biofilms onto substrates

aquatic microbe


difficulties


osmotic stress

freshwater microbes may be exposed to hypo. environments while marine microbes may be exposed to hyper. conditions




can cause lysis (=hypo.) or plasmolysis (=hyper.)

aquatic microbe


difficulties


osmotic stress


hypotonic conditions

adaptations:


- cell walls of bacteria and fungi prevent osmotic lysis


- protists and algae have contractile vacuoles (don't have cell walls)


- transport ions out of the cell

aquatic microbe


difficulties


osmotic stress


hypertonic conditions

adaptations:


- microbes can produce a thick sugar layer that surrounds the membrane called the glycocalyx (capsule, matrix)


- limit flow of ions and water


- gram neg. bact. have protective LPS layer in cell wall


- some retain higher solute in cytosol

aquatic microbe


food webs

- can drastically alter chemistry of water around them


- can harm or kill any form of aquatic life and humans


- form base of all aquatic food webs


- include: cyanobacteria and phytoplankton

aquatic microbe


water quality

- aquatic decomposers living planktonically or within sediment (benthic) break down all organic wastes/dead organisms


- return nutrients back into the water


- recyle N, C, S for new producers


- excessive growth however = depletion of O2


*anoxic water = deadly to fish/plants

aquatic microbe


animal diseases

- Fibropspilloma-Associated: Turtle herpesvirus


- Ichthyophthirius multifilis: protozoa causes fish ich


- epidemics like red tide: algal bloom of Karenia brevis secrete neurotoxins that kill fish/marine mammals


- coral bleaching: bacterial infection

aquatic microbe


waterborne human pathogens

- most often due to contamination of drinking water




- causes: diarrhea, dysentary, severe fever (....meningitis, brain damage), liver inflammation/failure

aquatic microbe


waterborne human pathogens


E. coli - two strains

enterotoxigenic E. coli:


major cause of traveler's diarrhea




enterohemorrhagic E.coli:


causes hemorrhaging and kidney failure

aquatic microbe


waterborne human pathogens


Salmonella enteritidis

- causes self-limiting watery diarrhea for most


- enters water via sewage contamination or bird droppings

aquatic microbe


waterborne human pathogens


typhoid fever

- Salmonella typhi


- raw sewage contamination of drinking/bathing water ; can also spread via hands of infected individuals


- causes: sustained fever (+104F), brain damage rash, organ failure

aquatic microbe


waterborne human pathogens


vibrio cholerae

- causes: severe watery diarrhea and death w/in 1-2 days


- cholera toxin opens up Cl- ion channels


- spreads rapidly in countries with poor sanitation

aquatic microbe


waterborne human pathogens


Shigella & friends

shigella dysenteriae:


- similar to hemorrhagic E. coli cause they both cause fatal dysentary


- shiga toxin kills large number of intestinal cells = bloody diarrhea and shock

aquatic microbe


waterborne human pathogens


Campylobacter jejuni

- produces heavy diarrhea and some dysentary


- problematic for young kids, elderly, immunocompromised


- can spread beyond for these individuals

aquatic microbe


waterborne human pathogens


viruses

often naked - envelopes are unstable for long periods in water



aquatic microbe


waterborne human pathogens


rotavirus

- most common cause of diarrhea and vomiting in kids


- spread by exposure to contaminated objects / via water


- increased santiation does not help lower infection rates

aquatic microbe


waterborne human pathogens


hepatitis A vs. E

- common causes: jaundice, acute liver inflammation, fever, vomiting, diarrhea


- Hep A: spread by contact w/ contaminated item, and water, shellfish


- Hep E: spread via fecal contamination in water

aquatic microbe


waterborne human pathogens


poliomyelitis

- fecal contamination in water


- majority of those affected: no symptoms or minor diarrhea


- that 1%: virus goes to central nervous sys. and causes meningitis, seizures, paralysis, and death


- prevented with an oral vaccine - almost eradicated

aquatic microbe


waterborne human pathogens


norovirus

- mainly transmitted via food or fomites


- extremely contagious


- causes vomiting / diarrhea


- common in schools / daycares / cruises / restaurants

aquatic microbe


waterborne human pathogens


Giardia lamblia

- caused by flagellated protozoa


- contaminated water contains animal excreted cysts (can surve months)


- causes: diarrhea, weight loss, lactose intolerance

aquatic microbe


waterborne human pathogens


amoebic dysentery

- caused by Entamoeba histolytica (tissue-destruction) cysts


- from sewage contaminated drinking water


- trophozoite growth in intestine produces intense cramping and bloody diarrhea



aquatic microbe


waterborne human pathogens


Cryptosporidium

- commonly infects HIV patients (immunocompromised)


- fecal contamination of cysts in drinking or swimming water (can resist chlorine)


- causes: severe weight loss, diarrhea, respiratory illness

aquatic microbe


waterborne human pathogens


Schistosoma

- parasitic flatworm that spreads via freshwater snails


- can penetrate skin = children commonly affected


- causes: diarrhea, intestinal damage, liver/kidney development, bladder cancer, malnutrition, and negatively impact development

aquatic microbe


waterborne human pathogens


Ascaris lumbricoide

- parasitic roundworm most often spread through sewage contamination of drinking/crop water


- can fill up intestines once infected


- causes: severe abdominal discomfort, malnutrition, lower IQ, larvae can spread to lungs and cause pneumonia

aquatic microbe


waterborne human pathogens


four forms of prevention

- boiling: very effective; costly for 3rd world


- disinfection: heavy metals, halogens


- filtration: charcoal, sand, ceramic, membrane


- UV light: destroys DNA in pathogens, expensive

aquatic microbe


beneficial uses

bioremediation and wastewater treatment:


natural aquatic decomp. amazing at degrading organic and chemical wastes




algae biofuels:


some species make long chain hydrocarbons that can be used as fuel without impacting climate; too expensive for widespread use

aeromicrobiology

study of microbes that are found suspended in the air




- called bioaerosols


- can be found on water droplet nuclei, attached to soil particles, or floating on dust

aeromicrobes


ability to travel

depends on size of microbe, what it's attached to, and the humidity of the air




- smaller the aerosol, longer it can remain suspended


- more humidity = aerosols fall faster to ground

aeromicrobes


difficulties of air travel

- air is not hospitable: dry, cold, UV radiation




- must have mechanisms for survival: endospores, fungal spores, capsules, cell walls

aeromicrobes


water cycle

airborne species high in the atmosphere make proteins that nucleate ice formation




there's good evidence that these microbes can nucleate the formation of clouds in upper atmosphere and help control the water cycle



aeromicrobes


airborne transmission

- launching of bioaerosols from source:


coughing, kicking up dirt, dusting


- transport via air movement:


dispersal from point A to point B via wind, air conditioning


- deposition onto a surface or in a person:


via gravity, diffusion, rain

aeromicrobes


plant disease

fungal diseases: dissemination of spores transmitted by wind


ex:


plant rust disease


downy mildew


leaf spot disease


blights

aeromicrobes


human-human disease

spread person-person via inhalation of contaminated aerosols (depends on size of droplet nuclei)


ex: rhinovirus, measles, tuberculosis, whooping cough, diphtheria

aeromicrobes


soil-human disease

some human pathogens spread via inhalation of contaminated soils or dust


- abundant endospores in the soil like botulism and anthrax (rare naturally, need lots of spores)


- Hantavirus acquired when dust containing mouse feces/urine is disturbed and inhaled

aeromicrobes


air-human disease

poor ventilation and high humidity levels in buildings can lead to major growth of mold / mildew / bacteria




constant inhalation can lead to allergy/asthma, pneumonia, & sick building syndrome (Legionnaires in Philly)

aeromicrobes


three stragies for prevention

- face masks: against personal aerosols


- HEPA filters: can remove bacteria / mold spores / some viruses


- UV light: destroys mold spores, located in some AC systems

biowarfare

intentional or threatened use of microbes or toxins from microbes to produce death, disease in humans, plants, animals




- can also be used to target food/water supplies


- goal is to induce mass hysteria (bioterrorism)

biowarfare


benefits to weaponization

- cheap mass production


- difficult to detect / easy to hide


- designed to effectively spread


- ease of genetic manipulation


- minimal technical experience required

biowarfare


early history


first use of bioterrorism - 1346

Caffa (Crimea) 1346


- bioweapons used before people knew how microbes caused disease


- Mongols were mass killed by bubonic plague outbreak while attacking Italian merchants


- during retreat, launched dead soldiers into city and plague broke out in the population, causing them to flee city

biowarefare


early history


1495

spanish put blood of leprosy patients into wine they sold to french




not effective at all because leprosy isn't spread via ingestion - takes ages to develop symptoms

biowarfare


early history


1763

british settlers give a bunch of smallpox infected blankets to the native americans




europeans exposed to smallpox as children = "vaccinated" while native americans susceptible to infection = 500,000 died

biowarfare


modern history


World War I

germans tried to infect livestock with glanders and anthrax spores to cause mass die-offs in farms and the army




didn't work for subsequent battles, but high rates of diseases in russia prevalent afterward

biowarfare


modern history


World War II

Japanese tested >25 agents on prisoners and civilians in infamous Unit 731 = killed thousands




used weapons on Manchuria China


- cholera/typhoid in wells, plague fleas dropped into major cities, anthrax dusting?


- planned for US attack

biowarfare


modern history


Cold War

both USA and Soviets amassed literal tons of weaponized plague, smallpox, anthrax, many more




both documented tests on their own populations

biowarfare


traits of a good bioweapon

- cheap & stable


- easy to produce & disseminate to enemy


- high infectivity: low amount needed to cause reaction


- high virulence: causes quick disease in many individuals w/ high mortality rate


- no vaccines/treatments

biowarfare


offensive vs. defensive

offensive:


intent to kill or incapacitate human targets, livestock, or crops


- easier to target bodies of water/plots of land = harder to defend


- goal may be to cause mass hysteria/panic


safety of own army/population


- vaccines/prophyletic drugs; expert handling; regulated production



defensive:


Research and development of countermeasures


Biodetectors/widespread surveillance

biowarfare


offensive


four considerations

mode of dissemination:


- create entirely new agent: DNA tech allows new genome design


- genetic alteration of agent: increase antibiotic resistance / evade immunities or detection


- increase released stability: longer persistance = greater chance of infection


- size of aerosol: smaller = longer in air (anthrax)

biowarfare


defensive

goal is to prevent, track, contain bio attacks




concerned with:


- detection of infections agents in the air or water:


biodetectors like PANTHER


- research and development:


vaccines, new treatments, containment


- widespread surveillance:


clinicians and vets report unique cases

biotechnology


environmental definition

using biological agents and chemical, physical, and engineering processes to maintain, protect, and restore the environment




includes:


- bioremediation


- composting


- treatment and disposal of solid waste


- treatment of wastewater

biotechnology


landfills


goals and benefits



- oldest and most common


- goal's to fill solid waste compactly in small area that does not destroy surrounding soil/water


- fewer people needed, little mechanization, usually safer

biotechnology


landfills


bioreactors

the mechanization of landfills for a purpose

- add moisture and allow microbes to decompose waste


- larger volumes of waste could be treated and some economically beneficial products made like methane (can be used to power entire landfill)

biotechnology


landfills


design

- bottom consists of impenetrable (double plastic) liner with drainage layer of sand and gravel on top to prevent ground water contamination underneath - pipes w/in drainage layer to collect water and percolate through refuse


- refuse placed on top of liner/drainage and embedded with horizontal and vertical pipes that collect CO2 and CH4 gases


- final capplaced to limit water infiltration and encourage decomposition and gas collection

biotechnology


landfills


leachate

contaminated waste water collected by piping in drainage layer that is collected in tanks and processed

biotechnology


landfills


five phases

- adjustment period


- transition phase


- acidogenesis period


- methanogenesis period


- maturation period

biotechnology


landfills


five phases


adjustment period

1st step




- aerobic bacteria utilize trapped oxygen and decompose most carbons (CO2 + H2O)


- moisture will begin collecting


- continues until all the oxygen is used up



biotechnology


landfills


five phases


transition phase

2nd step



- anaerobic conditions begin to form


- causes transition to fermentation and the production of organic acids

biotechnology


landfills


five phases


acidogenesis period

3rd step




- acidogeneic bacteria ferment organic wastes, create high amounts organic acids


- pH drops significantly, heavy metals mobilized


- water added to promote growth of anaerobes


- leachate must be monitored



biotechnology


landfills


five phases


methanogenesis period

4th step




- alt. e- acceptors become limiting


- fermentation of organic acids increased by bacteria = methanogens (products are methane and CO2)


- pH moves towards neutrality


- peak methane gas production

biotechnology


landfills


five phases


maturation period

5th step



- available nutrient levels and gas levels drop


- continued slow decomp. will occur for years


- organics turn into humus like material


- decomp. can be sped up by added O2

biotechnology


landfills


biodegradation of synthetic solids

- take significantly longer than organic solids


- can stay in landfills for centuries


- difficult to balance creation of materials that last vs. environmental concerns

biotechnology


biodeterioration

utilizing newly developed materials that biodegrade more quickly through natural processes


- biodegradable plastics / packing peanuts

biotechnology


biofilms

- major form of biodeterioration


- form when proteins are deposited onto a substrate; bacteria/yeast begin colonization


- attached org. will secrete matrix of polysacc. to form stronger microbe-microbe interactions


- community will form as biochemical collaboration between species


- growth and maturation = more difficult to remove

biotechnology


biofilms


biodeterioriation

- cooling tower / drinking water facilities: can destroy imporant mechanical parts


- medical implants: catheters, heart valves, contacts; can cause infection/weaken material


- pipes: household, oil, municpal causing corrosion or blockages


- ship hulls: weaken structure and create greater drag = high fiel costs

biotechnology


biodeterioration


major forms

- biochemical


- mechanical damage/physical disruption


- soiling / fouling

biotechnology


biodeterioration


major forms


biochemical

assimilation:


microbe uses substrate as a carbon source - eats away at it




dissimilation:


microbe secretes acid or enzymes during metabolism - substrate destruction is indirect by-product

biotechnology


biodeterioration


major forms


soiling vs fouling

soiling:


simple presence of microbial growth or their by-products on an object makes it undesirable but functional


ex: shower curtains, moldy water bottle




fouling:


microbial presence doesn't damage object but makes it toxic to other living things or impairs its performance making it non-functional


ex: fungal spores releasing toxins into "bad" food