ch 7 - microbial ecology and growth

microbial nutrition

• process by which chemical compounds (nutrients) are acquired from the environment to sustain life

• bioelements = basic requirements for life (C Hopkins Ca Fe Mg Na Cl)

• essential nutrients = substance (element/compound) an organism must get from a source outside its cells (vitamins, minerals, amino acids)

  • macros are required in large quantities; play principle roles in cell structure and metabolism (proteins, carbs)

  • micronutrients or trace elements are required in small amounts; involved in enzyme function and maintenance of protein structure (manganese, zinc. nickel

bioelements

basic requirements for life (C Hopkins Ca Fe Mg Na Cl)

essential nutrients

substance an organism must get from a source outside its cells like vitamins, minerals, amino acids. there’s macros and micronutrients or trace elements

macronutrients

essential nutrients that play principal roles in cell structure and metabolism (proteins, carbohydrates) are required in large quantities

micronutrients

involved in enzyme function and maintenance of protein structure; (manganese, zinc, nickel) essential nutrients that are required in small amounts

organic nutrients

contain carbon and hydrogen atoms and are usually the products of living things

ex: methane (CH4, simplest organic compound), carbohydrates, lipids, proteins, and nucleic acids

inorganic nutrients

atom or molecule that contains a combination of atoms other than carbon and hydrogen

• ex: metals and their salts (magnesium sulfate, ferric nitrate, sodium phosphate),

• and GASES (oxygen, carbon dioxide)

• and WATER

chemical analysis of cell contents

• 70% water

• 97% of dry cell weight is organic compounds (proteins most prevalent)

• 96% of cell is composed of C H O P S N

  • oxygen is most abundant

essential biological nutrients

• carbon - produced by respiration and used in photosynthesis. found in cell walls and skeletons

• nitrogen - all organisms use NH3 to synthesize amino acids and nucleic acids

• oxygen - necessary for the metabolism of nutrients by aerobes

• hydrogen - H+ ions are the basis for transfers of cellular energy, maintain pH of cells, and water is the most abundant compound in cells

• phosphorus - in DNA, RNA, ATP (phosphodiester backbone of DNA, and phospholipids → stability to cell membrane

• sulfur - oxidized by some bacteria as an energy source. sulfhydryl from cysteine to form disulfide bonds → shape and stabilize proteins

carbon

• essential biological nutrient produced by respiration and used in photosynthesis. found in cell walls and skeletons

• carbon dioxide gas and carbonate (CO3²-)

• air is 0.036%

• sediments and soils

• living things

• co2 is produced by respiration and used in photosynthesis. CO3²- is found in cell walls and skeletons; organic compounds are essential to the structure and function of all organisms and VIRUSES (carbon compound capsule)

carbon dioxide; carbonate

• ___ is produced by respiration and used in photosynthesis. ___ is found in cell walls and skeletons; organic compounds are essential to the structure and function of all organisms and VIRUSES (carbon compound capsule)

nitrogen

• essential biological nutrients

• N2 gas (like 78% in atmosphere), NO2- (nitrite), NO3- (nitrate), NH3 (ammonia, nitrogen fixation), organic nitrogen (proteins and nucleic acid)

• all organisms use NH3 to synthesize amino acids and nucleic acids

• n2 gas is only available to certain microbes that fix it into other inorganic nitrogen compounds (no2-, no3-, NH3) which are the primary sources of nitrogen for algae, plants, and the majority of bacteria

• animals and protozoa require ORGANIC nitrogen

nitrogen fixation

A process occurring in certain bacteria in which atmospheric N₂ gas is converted to a form (NH₄) usable by plants.

N2 + 6H+ (protons in water) → 2NH3 (bioavailable ammonia, is what cellulose degrader Cellumonas needs from Azotobacter)

oxygen

• essential biological nutrient

• O2, oxides (destructive to proteins), H2O

• air (20%), a major product of photosynthesis

• soil

• oxygen gas is necessary for the metabolism of nutrients by aerobes. oxygen is a significant element in organic compounds and inorganic

hydrogen

• essential biological nutrient

• H2, H2O, H2S (hydrogen sulfide - green and purple sulfur bacteria), CH4 (methanogen = archaea → climate change)

• waters, swamps (has methanogenic archaea), mud, volcanoes, vents

• water is the most abundant compound in cells and a solvent for metabolic reactions; gases are produced and used by bacteria and archaea; H+ ions are the basis for transfers of cellular energy and help maintain the pH of cells

water; gases; H+

____is the most abundant compound in cells and a solvent for metabolic reactions;

___ are produced and used by bacteria and archaea;

___ ions are the basis for transfers of cellular energy and help maintain the pH of cells

phosphorus

• essential biological nutrient

• PO4³- (phosphate)

• rocks, mineral deposits, soil (erosion of rocks into water, and soil is mostly weathered down rock)

• phosphate is a key component of DNA and RNA, is critical to the genetic makeup of cells and viruses; also found in ATP and NAD, where it takes part of the numerous metabolic reactions; its presence in phospholipids provides stability to cell membranes

phosphate; phospholipids

___ is a key component of DNA and RNA, is critical to the genetic makeup of cells and viruses; also found in ATP and NAD, where it takes part of the numerous metabolic reactions; its presence in ___provides stability to cell membranes

sulfur

• essential biological nutrient

• S, SO4²-, SH (sulfhydryl from cysteine - disulfide bonds in functional protein)

• mineral deposits, volcanic sediments, soil

• elemental sulfur (S) is oxidized by some bacteria as an energy source; sulfur is found in vitamin B1; sulfhydryl groups are part of cysteine where they from disulfide bonds that shape and stabilize proteins

carbon based sources of essential nutrients

• sources of the element carbon defines 2 basic nutritional types

• heterotroph = obtain carbon in an organic form such as proteins, carbs, lipids, and nucleic acids made by other living organisms

• autotroph = organism that uses CO2 (inorganic gas) as its carbon source

sulfur; cysteine

elemental ___ is oxidized by some bacteria as an energy source; sulfur is found in vitamin B1; sulfhydryl groups are part of ___ where they from disulfide bonds that shape and stabilize proteins

heterotroph

• = obtain carbon in an organic form such as proteins, carbs, lipids, and nucleic acids made by other living organisms

• some protozoa, all animals

• basidiomycota (fungi)

autotroph

• = organism that uses CO2 (inorganic gas) as its carbon source

• cyanobacteria, algae (phytoplankton), plants

phytoplankton

singe celled algae that photosynthesizes and is the bottom of the food chain as an auto troph

growth factors

• organic compounds that cannot be synthesized by an organism bc they lack the genetic and metabolic mechanisms to synthesize them

• must be provided as a nutrient for survival

• like essential amino acids and vitamins in plants and meat, which is why humans are omnivores

• evolutionarily supported by dentition (canines and flat teeth)

energy source

• the main determinants of nutritional type are carbon source=hetero or auto troph, but further break down into:

• chemotroph - gain energy from chemical compounds

• phototroph - gain energy thru photosynthesis

• bacteria are diverse bc are in all nutritional groups

chemotroph

• gain energy from chemical compounds

• chemo heterotroph - animals, bacteria

• chemo autotroph - bacteria only

phototroph

• gain energy thru photosynthesis

• photo hetero troph - bacteria only

• photo auto troph - plants, algae, fungi, bacteria

photoautotroph

• carbon source - autotroph / co2

• energy source - nonliving environment (sunlight)

• ex: photosynthetic organisms like cyanobacteria, plants, algae

• oxygenic photosynthesis and anoxygenic photosynthesis

chemoautotroph

• carbon source - autotroph / co2

• energy source - simple inorganic CHEMICALS

• ex: certain bacteria and archaea like methanogens and deep sea vent bacteria

• lithoautotrophs survive totally on inorganic substances

chemoheterotroph

• carbon source - heterotroph / organic carbon

• energy source - metabolic conversion of the nutrients from other organisms

• ex: protozoa, fungi, many bacteria, animals

• there’s saprobes and symbiotic microbes

saprobe

• carbon source - chemoheterotroph

• energy source - metabolize the organic matter from DEAD organisms

• = fungi, bacteria, some protozoa (decomposers)

• free living microorganisms that feed on organic detritus from dead organisms

  • opportunistic pathogen like candida

  • or facultative parasite (can survive independently or live as a parasite)

symbiotic microbes

• carbon source - chemoheterotroph

• energy source - obtain organic matter from LIVING organisms

• parasites, commensals, mutualistic microbes

• parasites = derive nutrients from host

• pathogens, some are obligate parasites

photoheterotroph

• carbon source - heterotroph / organic carbon

• energy source - sunlight or organic matter

• ex: green and purple photosynthetic (sulfur?) bacteria

oxygenic photosynthesis

• photoautotrophs have 2 diff kinds of photosynthesis

• plants, algae, and cyanobacteria

  • produce oxygen and use chlorophyll as the primary pigment

anoxygenic photosynthesis

• photoautotrophs have 2 diff kinds of photosynthesis

• green and purple sulfur bacteria

  • no oxygen but sulfur production, use BACTERIOCHLOROPHYL as pigment

• makes the bay stinky bc hydrogen sulfide

• bogs = swamp w no oxygen

anaerobic

methanogen, a kind of chemoautotroph (survive completely off of inorganic carbon substances) produces methane gas under what condition?

• such as in the digestive system

• cellulose from grazing on plants feeds methanogens

chemoorganotroph

• the majority of heterotrophs are this

• derive carbon and energy from ORGANIC compounds, that is, aerobic respiration (animals)

• saprobes = free living microorganisms that feed on organic detritus from dead organisms

  • opportunistic pathogen

  • facultative parasite (can live freely with or without a host)

• parasites = derive nutrients from host

  • pathogens

  • some are obligate parasites

niche

• totality of adaptations organisms make to their habitat

• environmental factors affect the function of metabolic enzymes:

  • temp, pH, oxygen requirements, osmotic pressure, barometric pressure

osmotic pressure

• osmophile -A microorganism that thrives in a medium having high osmotic pressure.

• hypotonic (low water concentration outside of cell, h2o moves into cell, cell swells up and lysis)

• hypertonic (high water concentration outside of cell, h2o moves out of cell, cell shrivels up)

• ppg in cell wall protects from osmotic pressure difference

osmophile

A microorganism that thrives in a medium having high osmotic pressure. meaning requires high concentration of salt (halophile) = archaea

• obligate halophile

barometric pressure

• evolved to survive at high pressure conditions

• cell wall of bacteria deals with pressure differential

• deep sea, deep ocean

3 cardinal temperatures

• the range of temps for microbial growth are expressed as ___ ;

• minimum temp

• maximum temp

• optimum temp

• bacteria have evolved to grow at our body temp, 37 C

• proteins have to be a specific shape for the enzyme, but change in pH and temp changes the protein shape

  • this is the crux of what kills bacteria

minimum

cardinal temp; lowest temp that permits a microbe’s growth and metabolism

maximum

cardinal temp = highest temp that permits a microbe’s growth and metabolism

optimum

cardinal temp that promotes the fastest rate of growth and metabolism

psychrophiles

optimum temp Below 15 C and capable of growth at 0 C

mesophile

optimum temp btwn 20 and 40 C, most human pathogens (moderate temp range)

thermophile

optimum temp is >45 C

ex: archaeans. such as in yellowstone park

• increase pressure (bp of water) doesn’t boil - deep thermal vents

catalase; superoxide dismutase

• these are developed enzymes that neutralize the toxic chemicals that oxygen transforms into (singlet oxygen 1O2, superoxide ion O2-, peroxide H2O2, and hydroxyl radicals OH-)

• catalase + = aerobic and catalase - = anaerobe

• if a microbe is not capable of dealing with toxic oxygen, it is forced to live in oxygen free habitats

aerobe

• utilizes oxygen and can detoxify it

• (catalase + and also has superoxide dismutase maybe)

• obligate aerobe - cannot grow without oxygen

• facultative anaerobe - utilizes oxygen but can also grow in its absence (microbial antagonism, like E. coli)

• microaerophile - requires only a small amount of oxygen, like in high altitudes

obligate aerobe

• cannot grow without oxygen

facultative anaerobe

• utilizes oxygen but can also grow in its absence (microbial antagonism, like E. coli)

microaerophile

• requires only a small amount of oxygen, like in high altitudes

anaerobe

• does not utilize oxygen (look at catalase test)

• obligate anaerobe = lacks the enzymes to detoxify oxygen, so it can’t survive in an oxygen environment

• aerotolerant anaerobes - do not utilize oxygen but can survive and grow in its presence

obligate anaerobe

• lacks the enzymes to detoxify oxygen, so it can’t survive in an oxygen environment

aerotolerant anaerobes

• do not utilize oxygen but can survive and grow in its presence

thioglycollate

• test

• cultures with reducing media that contain an O2- removing chemical such as ___ can help determine the o2 requirements of a microbe

• relative position of growth of bacteria differ in o2 requirements in such culture media provides some indication of their adaptations to O2 use

• oxygen gradient = aerobic bacteria at top (21% oxygen), anaerobic at bottom (0% oxygen)

capnophile

• grows best at higher CO2 tensions (5%) than normally present in atmosphere

  • tends to be anaerobic, a lot can be pathogenic and enteric bc need higher CO2

• compare to MOST microbes, which require SOME CO2 in their metabolism

neutrophil

• effect of pH

• majority of microorganisms grow at a pH btwn 6-8

acidophil

• effects of pH

• grow at extreme acid pH

alkalinophile

• effects of pH

• grow at extreme alkaline pH

obligate halophile

• while most microbes exist under hypotonic or isotonic conditions (lower solute concentration outside of cell, or equal, repectively)

• __ __ grow optimally in solutions of 25% NaCl but require at least 9% NaCl (salt lakes, ponds)

• ex: halobacterium, halococcus, both archaea

• a kind of osmophile

obligate halophiles

halobacterium and halococcus are what kind of archaea (hint - osmotic pressure)

osmotolerant

• do not require high concentration of solute (most microbes exist under hypotonic or isotonic conditions)

• facultative halophiles - remarkably resistant to salt

• ex: staphylococcus aureus (MSA is selective for this bc of 7.5% NaCl)

facultative halophile

remarkably resistant to salt

ex: staphylococcus aureus on MSA (7.5% NaCl)

barophile

• deep sea vent bacteria

• can survive under extreme pressure and will rupture if exposed to normal atmospheric pressure

water

• an environmental factor

• only dormant, dehydrated cell stages (ie endospores, cysts) tolerate extreme drying bc of the inactivity of their enzymes

ecological associations

• microbial associations = symbiotic or nonsymbiotic

• symbiotic - organisms live in close nutritional relationships; required by one or both members

  • mutualism, commensalism, parasitism

symbiotic relationship

• organisms live in close nutritional relationships; required by one or both members

mutualism

• sort of symbiotic relationship

• obligatory, dependent; both members benefit

• require each other - like probiotic bacteria

commensal relationship

• sort of unequal symbiotic relationship

• one partner benefits; other member is unharmed (or doesn’t even know)

• ex: micrococcus luteus in belly button

• haemophilus absorb required growth factors given off by staphylococcus

parasitism relationship

• sort of symbiotic relationship

• microbe invades sterile regions of host, occupies its tissues and cells, causing some degree of damage

• ex: all viruses (obligate intercellular parasite) that invade cells and take over their function

• malaria

nonsymbiotic relationship

• organisms are free-living; relationships not required for survival

• syntrophy: members cooperate and share nutrients

• amensalism: some members are inhibited or destroyed by others

syntrophy

• free living, nonsymbiotic

• members cooperate and share nutrients (crossfeeding)

• like a 50 year marriage, a couple that doesn’t need each other but get along well

• azotobacter and cellulomonas

amensalism

• free living nonsymbiotic

• some members are inhibited or destroyed by others

• like evil roommate that likes to piss you off

• ANTIBIOSIS

nonobligate mutualism

• type of mutualistic symbiotic relationship, both members benefit

• organisms interact at the cellular level for mutual benefit, but they can be separated and live apart

• ciliophoran euplotes engulfs algae but absorbs the nutrients they release and shelters them

obligate mutualism

• kind of mutualistic symbiotic relationship

• can not be separated and live apart

• ex: trichonympha living in gut of termite

• rhizobium bacteria living on the root nodules in certain plants (nitrogen fixation)

• coral reefs and dinoflagellate (= coral bleaching)

ocean acidification

why are dinoflagellates leaving the coral reefs? dinoflagellates photosynthesize and give coral sugar (nutrients = color), when dinoflagellate leaves, coral bleaching occurs and it dies

commensalism

• haemophilus grows in satellite colonies around staphylococcus in blood agar

• haemophilus benefits and staphylococcus isn’t greatly affected

parasitic

• rickettsia (rocky mountain fever) and epidemic typhus use the host’s nutrients to reproduce

• chlamydia relies on host cell for ATP

• host is harmed by parasite that is dependent and benefits from host

crossfeeding

aka syntrophy, where microbes sharing a habitat feed off substances released by other organism. a nonsymbiotic association

• azotobacter releases NH4 that feeds cellulomonas. cellulomonas degrades cellulose that feeds azotobacter

antibiosis

aka amensalism - one member of an association produces a substance that harms or kills another (antagonism, competition)

carbon fixation

6H2O + 6CO2 → C6H12O6 + 6O2

taking inorganic carbon, plant makes it bioavailable/organic

zone of inhibition

• zone w no growth where antibiotic inhibits undesirable fungus

• antifungal compound → basis behind antibiotics (come from microbes)

• antibiosis by an actinomycete against a pathogenic fungus (antibiosis = antagonism, amensalism)

biofilms

• result when organisms attach to a substrate by some form of extracellular matrix that binds them together in complex, organized layers

• dominate the structure of most natural environments on earth

• communicate and cooperate in the formation and function = quorum sensing

quorum sensing

• specific number of microbes used for a function, and they sense each other and start a task

• diff kinds of microbes can alter gene expression to cooperate with other bacteria

biofilm formation

1. free swimming cells lose their motility and settle down onto a surface or substrate

2. cells synthesize an adhesive MATRIX that holds them tightly to substrate

3. when biofilm grows to a certain density (quorum), the cells release inducer molecules that can coordinate a response

4. enlargement of one cell to show genetic induction. inducer molecule stimulates expression of a particular gene and synthesis of a protein product, such as an enzyme

5. cells secrete their enzymes in unison to digest food particles

synergistic relationship

• microbial compounds/organisms

• microbes work together to produce a function

• antibiotics. enhancers

levels of microbial growth

• cellular level where microbes increase with size, and increase in population

• division of bacterial cells is mainly through binary fission

binary fission

• parent cell enlarges, duplicates its chromosome, and forms a central transverse septum dividing the cell into two identical daughter cells

• 1 parent cell elongates, replicates chromosome → chromosome division and septation →completion of cell compartments → result is 2 identical daughter cells

doubling time

• time required for a complete fission cycle is called the generation time or ___

• each new fission cycle increases the population by a factor of 2 = exponential growth

• can vary from minutes to days.

• generally 20-30 mins for a new gen

• growth curve for a bacteria is logarithmic

calculate population size

• Nf = (Ni) 2^N

• Nf = total number of cells inthe population

• Ni = starting number of cells

• exponent N denotes generation time

  • ex: N hours has passed, so use Nx2 for 2 generations every hour

population growth curve

• populations in lab studies typically display a predictable pattern over time called ?

• stages:

• 1. lag phase = flat period of adjustment, enlargement; little growth

• 2. exponential growth phase= period of maximum growth when cells have adequate nutrients and a favorable environment

• 3. stationary phase = rate of cell growth equals rate of cell death caused by depleted nutrients and o2, excretion of organic acids and pollutants

• 4. death phase = as limiting factors intensify, cells die exponentially

lag phase

• first stage of pop growth curve

• flat period of adjustment, enlargement; little growth

exponential growth phase

• 2nd phase of population growth curve

• a period of max growth when cells have adequate nutrients and a favorable environment

stationary phase

• 3rd phase of pop growth curve

• rate of cell growth = rate of cell death, caused by depleted nutrients and O2, excretion of organic acids and pollutants

death phase

• 4th stage of pop growth factor

• as limiting factors intensify, cells die exponentially

turbidometry

• most simple method of analyzing population growth

• degree of cloudiness, turbidity, of the nutrient culture media reflects the relative population size

enumeration

• method of analyzing pop growth

• viable colony count

• direct cell count = manually or automated counting the number of cells in a sample microscopically