ch11 - the diversity of bacteria and archaea

diversity of prokaryotes

• scientists just beginning to understand vast diversity of microbial life

• with better methods for detecting them right now, like metagenomics - detecting bacteria that we can’t grow in the lab

  • so many more out there that we didn’t even know existed before, and must be more than we’ve been able to detect

• only ~6000 of estimated million species of prokaryotes described

  • 950 genera

• majority have not been isolated

• new molecular techniques aiding in discovery, characterization

  • metagenomic and WGS: use the techniques to synthesize or sequence the whole genome of an organism, a prokaryote, without having to culture it in the lab first

• bcuz the organism is a result of the genes: when we look at the genome, we can characterize them based on their ability to break down or to use certain compounds as a source of nutrient, whether they’re able to do it or not

  • just from the genes we can make that prediction, even if it can’t be grown in the lab to test out

metabolic diversity of prokaryotes

prokaryotes are metabolically diverse

• metabolic diversity: ability to use different substances or chemicals as carbon and energy sources

  • need both of these in order to live for metabolism

• for higher organisms its limited but not for prokaryotes

  • one of the reasons why it allows microbes to live in more diverse environments than higher organisms

  • humans are quite limited to where they can live but not prokaryotes

    • prokaryotes inhabit almost every environment on and in the earth

    • those environments are providing it with a carbon and an energy source

the microbial world

all living things classified in one of three groups (domains)

organisms in each domain share certain properties

three domains: bacteria, archaea, eukarya

bacteria and archaea - prokaryotes

• all single celled organisms

• contain no nucleus or any membrane-bound organelles

• cytoplasm surrounded by rigid cell wall

archaea that thrive in extreme conditions

similarities to domain bacteria

• same shapes

• multiply through binary fission

• move by means of flagellum

differences from domain bacteria

• no peptidoglycan in cell wall, has pseudopeptidoglycan

• archaea thrive in extreme environments

  • high heat, acidity, alkalinity, salinity

  • 3 groups of archaea

    • methanogens are exception

    • methanogens: methane producing archaea/organisms

      • take CO2 and hydrogen from the environment and turn it into methane gas

    • extreme halophiles: live in extreme high salt environments

    • extreme thermophiles: love to live at very hot temperatures, some above boiling

domain bacteria

the most common type in causing human infections/diseases

• haven’t been able to find disease causing archaea

members are widely diverse

the most prominent features include

• single-celled

• specific shapes

  • rod shaped, spherical, and spiral

• rigid cell walls made of peptidoglycan

• multiply by binary fission

  • one cell divides into two (genetically identical)

• some are motile

  • move using flagella

microbial habitats

microbes live in every type of habitat that supports life (has all the required nutrients for growth - food and ability to withstand environment)

• extreme environments

• terrestrial environments (soil, air)

  • very high in the sky

  • some people have taken agar plates there, exposed it to it, closed it, incubated it → growth of microbes

  • all the water evaporated up there may have microbes in them

• aquatic environments (open sea, lakes, streams, ponds, marshes and wetlands, hot springs, arctic ice sheets)

• association with insects, plants, and animals

  • microbes can use these as habitats

extreme environments - hot and cold

hot:

• boiling pools

• hot springs

• hydrothermal vents - 120*C (250*F)

  • worms with bacteria in folds

  • TAQ dna polymerase for polymerase chain reactions - Thermus aquaticus

    • this enzyme wasn’t possible until the worm was discovered

cold:

• glaciers and snow fields

  • red bacteria - pigment allows for the bacteria to harvest energy from sunlight and make it photosynthetic (red pigment)

  • have to make own food to survive

• antarctic ice sheets - 12*C (10*F)

extreme environments - high salt

extreme halophiles

• Great Salt Lake, Dead Sea, soda lakes

  • most can grow in 5-32% NaCl

  • most higher microorganisms would not be able to survive living in this environment

• these microbes can: bacteria, algae, protozoa

  • most require 9% salt concentration

• Owens lake (Sierra Nevada)

  • reddish coloration due to salt-loving bacteria (halobacterium)

    • halophile that lives in this lake, and when it grows it produces the red color

extreme environments - alkaline and acidic

alkaline

• mono lake (california)

• alkaline, hypersaline

• anoxic, extremophiles

  • not much dissolved oxygen in it

• the organisms that live in here must be able to tolerate all of these environments in order to inhabit this lake

acidic

• sulfolobus

  • thrives in sulfur-rich, acidic hot springs and soils

  • contribute to acidity of the environment bcuz they use sulfur as a source of energy

  • oxidize sulfur to sulfuric acid (very acidic)

  • require pH between 1-6

  • grow above 50*C to 85*C

aquatic environments

lack steady nutrient supply

• sheathed bacteria form chains of cells within tube

  • the sheath bacteria live together in the structure called the sheath

  • sheaths protect, help bacteria attach to solid objects, and helps them share nutrients in the sheath

  • gram-negative Sphaerotilus, Leptothrix are found a lot and are very long strings of cells that do these things

• prosthecate bacteria

  • have extensions that provide increased surface area for nutrient absorption, some allow attachment

  • caulobacter

    • when the two cells divide, the daughter cell has the flagella and will swim away from the mother cell, so that there’s no competition with the mother cell

    • when the daughter cell is ready to reproduce, it will lose the flagella and will produce something called a stalk and holdfast

      • stalk: extension

    • holdfast allows for it to stick itself somewhere on a surface with nutrients and settles down there using the nutrients to reproduce

    • only then will the cell reproduce

    • and when it produces a daughter cell, the daughter cell will swim away and when the daughter cell is ready to reproduce, it will do the same thing again

bacteria that prey on other bacteria

• Bdellovibrio

  • highly motile gram-negative curved rods

  • prey on E. coli and other gram-negatives

  • for example: when bdellovibrio infects E. coli, it will get through the outer membrane and into the periplasm (gram - bacteria have a large periplasmic space)

  • when it gets into the periplasmic space it will start feeding on the gram negative bacteria, starts breaking it down

  • then it will grow and then reproduce

  • once its done it will lyse the cell and releases all the progeny/offspring

  • then they can go on and feed on other gram - bacteria

animals as habitats

bodies provide a variety of ecological habitats for bacteria

• skin

  • typically dry, salty, inhospitable to many microbes

  • so only bacteria that can tolerate these environments stay and grow

  • Staphylococcal species: significant component of skin flora

    • s epidermidis and s aureus

• mucous membranes

  • respiratory, genitourinary, intestinal tracts

    • Bacteroides - mouth, most abundant in the GI, and genital tracts

    • Bifidobacterium - GI tract (breastfed babies)

association with animals

humans: some of the normal bacterial flora (human microbiome), the bacteria vary/are diverse

• the more diverse your microbiome is, the better it is for you

• when you take antibiotics and it destroys some of them and the diversity decreases, it could lead to some types of illnesses and more vulnerable to infections

bioluminescent bacteria: Photobacterium, Vibrio

• these can form symbiotic or mutualistic relationships with certain fish, squid

  • benefits both the animal and the bacteria

• help with camouflage, confuse predators and prey

• establish relationships with other animals for food and protection

• fish: flashlight fish

  • called that because it has an organ that holds the bacteria on both sides, it starts to glow and offers light for the fish when it goes deeper in the ocean

  • it gives the bacteria protection and they can have all the food they want from the fish, the fish benefits as well because there’s a built in flashlight → mutualistic symbiosis

association with insects

insects

• ants that live in associations with fungi

  • they want the fungus to grow so they’re taking care of it so it can grow on a particular substrate and the fungus will break down that substrate into a form that the ants can use as a source of food

  • like us using bacteria to make yogurt

• aphids that live in association with bacteria

  • has a mutualistic association with bacteria

  • in the gut of this aphid it has a big organ that houses the bacteria

  • this insect feeds on plant sap - rich in sugar but very low in amino acids or other nitrogenous compounds

  • how will an insect that feeds only on sap survive?

    • they survive because of the bacteria

    • it makes all the essential nutrients that they need, including amino acids for the insect

    • we know that cuz when we feed it antibiotic it kills the bacteria

    • these insects don’t live for long after that and never reproduce

association with plants

plants

• bacteria that associate with plants

  • Agrobacterium - plant pathogen

    • not a good bacterium for plants

    • produces plant tumors to gain nutrient from the plant (often fatal to plant)

  • Rhizobium

    • have a mutually beneficial relationship with plants (legumes)

    • infects the hair roots of plants, specifically the legumes

      • like peas, beans, alfalfa, clover

    • and when they infect it, it will initiate the formation of a structure called the root nodule

    • these nodules on the hair roots are where the bacteria is

    • open it up and we see bacteria

    • the bacteria are doing a very important thing for the plant which is nitrogen fixation

    • nitrogen fixation used as a nutrient source for plant

      • results in formation of ammonia which can be converted to nitrate (basically fertilizer for the plant)

    • will grow faster with Rhizobium