microbes can be both harmful and helpful
if the pathogen is highly contagious or relatively unstudied, it may require containment at biosafety level 3 or 4 (BSL-3 or BSL-4)
the use of polymerase chain reaction has been helpful to detect small amount of DNA traces of blood or of fossilized bones
microbes are diverse in form and lifestyle - typically microscopic with exceptions
all kinds of life host viruses, some of which have preferences for a particular environment
they can consist of just a singular cell unit and have a genome used to reproduce its species
they acquire food, gain energy to build themselves and respond to environmental change
they evolve rapidly
microbial cells can range in sizes from 5 mm to <0.2 um
examples of diverse microbes that contradict the traditional definition
super-size microbial cells
can be seen by the unaided human eye (page 4)
microbial populations and communities
formation of complex multicellular assemblages like biofilm and fruiting bodies
two examples of multicellular organisms that require observation under a microscope but are not considered a microbe are mites and tardigrades
viruses
a noncellular particle containing genetic material that takes over the metabolism of a cell to generate more virus particles
the three domains of life: bacteria, archaea, and eukaryota
microbial genomes are sequenced
the use of advanced microscopy and sequencing of genome allowed for further insight to microbes
the genome reveals how the microbe grows and associates with other species
we can trace ancestry and close relatives to a species & potential evolution paths
metagenome: the sum of genomes of all members of a community of organisms
microbes and human history summarized
microbial disease devastates human populations
bubonic plague point in case wiped out 1/3 of Europe’s population
in the nineteenth century, tuberculosis was out here claiming many lives (and resistant strands of it are still present today)
influenza had a head count of a number larger than those killed in WWI
AIDS also be out here, killing about 35 million
COVID, the star of the show, killed 6 million deaths (hold your applause)
medical statistics & health disparities
Florence Nightingale recognized the significance of disease in warfare
founded the science of medial statistics and devised the “polar are chart” to represent mortality rates by certain causes
prompted the improvement of living conditions and standards of army hospitals
medical statistics bring insight to disparities that racial and ethnic groups face
caused by racism, lack of access to quality health care, and lower socioeconomic status
microscopes reveal the microbial world
Robert Hooke observes the microscopic world by building a compound microscope and published his drawings of the microbes he observed in Micrographia
Antonie van Leeuwenhoek observes bacteria with a single lens
grinded lens strength until he produced a lens stronger than Hooke’s
founded the fundamental idea that heat kills microbes
spontaneous generation
a theory that was supported in the 18th century due to the fact that the process seemed similar to the way chemicals changed during a reaction
Redi’s experiment of maggots found in decaying meat supported the theory of being the offspring of flies
argued against spontaneous generation
Spallanzani further warranted the opposition by showing that a sealed flask of meat broth that was sterilized failed to grow microbes
noticed that microbes appeared in pairs (asexual reproduction - parents)
demonstrated cell fission, a process of new cells forming by the splitting of preexisting cells
Pasteur’s experiments proved the theory that microbes did not arise by spontaneous generation (wasn’t believe yet though)
studied mirror chemistry & chirality
discovered that some organisms do not need oxygen to appear - one of the key components of why Spallanzani’s findings were rejected
used a swan neck flask that allowed air passage but prevented particle contamination to experiment
Tyndall performed Pasteur’s experiment but had heat-resistant bacteria, endospores, within his solution of hay infusion
the spore can only be killed by multiple rounds of boiling and resting
the invention of the autoclave gave way to a more efficient way to reduce microbial contamination by using steam pressure
life origins
components of early life included the following:
anoxic conditions (no oxygen)
presence of heat in the form of lightening or electrical discharge and ultraviolet rays
organic molecules that have a strong tendency to donate electrons
when a stimulation is run to test the necessary components of early Earth, it was found that amino acids were produced
medical microbiology
Koch devised the first scientific basis for the germ theory of disease
he studied anthrax because it took a toll on agriculture and livestock longevity
the pathogen can survive for an extended period of time in dormant conditions and in a desiccated endospore form
demonstrated the principle of the chain of infection which illustrated the transmission of a disease
Koch & his colleagues used this newfound information to apply to a dormant disease that had been quite deadly: tuberculosis
by following a series of steps from a starting stock of inoculated serum, they found that M. tuberculosis causes tuberculosis
Julius Richard Petri invented the Petri dish
Angelina Hesse recommended her husband use solidified agar in the petri dish as a gelling agent to remain intact at high temperatures
Koch’s postulates
because some organisms like intracellular pathogens and viruses cannot be grown in pure culture, Koch developed a set of criteria for establishing a causative link between an infectious agent and a disease
these postulates can be used to determine whether a given strain of microbes cause a disease
there are exceptions though, like Lyme disease, where the organism does not necessarily meet each criteria requirement
one difficulty with many human diseases is the absence of an animal host that exhibits the same disease
the two species may not show the same range of symptoms when inoculated which presents a limitation to testing and application
immunization can prevent the potential to get disease
it was found that the deliberate inoculation of individuals with the disease that was killing everyone proved to decrease the spread of disease
during a period outside the host, the virus becomes attenuated - it loses some of its molecular structure required for infection
the act of variolation led to vaccination, the inoculation from cowpox lesions
molecular components of pathogens generate immunity
Pasteur’s bitch ass recognized the significance of attenuation and extended the principle to other pathogens
the method to attenuate a strain depended on the pathogen present though heat treatment or aging for periods of time were the most effective approaches
vaccines today are constructed by molecular cloning of certain parts of pathogens
antiseptics and antibiotics
mortality rates are affected whether proper precautions are taken to prevent the spread of disease like sanitizing one’s hands after dissecting a cadaver
Lister found that carbolic acid was the most successful antiseptic agent to treat wounds and surgical instruments
sterilization processes became implemented to prevent the spread of pathogens and developed aseptic environments for surgery
in search for an antibiotic, it was found that microbes themselves produce antibiotic compounds
Alexander Fleming had accidentally discovered penicillin when he was culturing Staphylococcus
indiscriminate and broad use of common antibiotics has led to resistance of certain strains of major pathogens to those antibiotics & less effective
discovery of viruses
Ivanovsky had a porcelain filter that blocked known microbes from passing through
the agent of transmission to the disease he was observing wasn’t a microbe but an infectious noncellular particle
viruses consist of a helical tube of protein subunits containing its genetic material coiled within
Environment and ecology
Winogradsky columns are a wetland ecosystem model that maintain layers of niches for certain organisms to thrive in
at the top of the column, the conditions are rich in oxygen and usually house cyanobacteria and other photosynthetic organisms that require water, sunlight, and oxygen to metabolize
at the bottom of the column, the conditions are anoxic and sulfate rich; this layer houses sulfate-reducing bacteria
microbes cycle the many minerals essential for life like atmospheric nitrogen and oxygen
Earth’s ecology is microbial ecology since microbes can be found 3 km deep into Earth’s crust and 15 km out into the stratosphere
environmental microbes support ecosystems
in sewage, ammonia is oxidized by donating electrons to oxygen and in turn form nitrate; nitrate formation can be eliminated by antibacterial treatment
subclassification of microbes to be lithotrophs (rock-consuming)
Winogradsky cultured nitrifiers on inorganic solution containing silica gel and ammonia
an example of enrichment culture which is the selective growth media that support certain classes microbial metabolism
some microorganisms play roles in geochemical cycling processes like the nitrogen-cycle, the oxygen-cycle and the phosphorus cycle
extremophiles are set as a priority to study since they have valuable applications in industry and bioremediation purposes
these would include microbes that have the ability to digest toxic wastes or withstand extreme temperatures as well as extreme salinity or acidic environments
microbial endosymbiosis with plants and animals
endosymbiosis is the partnership of a host organism with its associated endosymbionts
endosymbiotic microbes make essential nutritional contributions to host animals and plants
nitrogen-fixing bacteria rhizobia within the root nodules of legume plants
invertebrates like hydras and corals harbor endosymbiotic phototrophs that provide products of photosynthesis in return for protection and nutrients
cattle and livestock have digestive bacteria that help them break down cellulose and other plant polymers
some intestinal bacteria grow as biofilms; play major roles in all ecosystems and within human body parts
all multicellular organisms have microbiota
microbial life on other plants
proposed by Oro due to prior experimentation, he theorized that the first chemical of life could have come from outer space and potentially carried by comets
rovers sent to Mars are exploring the presence or absence of water, organic compounds and other pieces of evidence of microbial life
the microbial family tree
Linnaeus classified every organism into his works by Kingdom, Phylum, Class, Order, Family, Genus, Species; Woese organized three addtional categories termed domains
bacteria, archaea, eukarya
challenges that biologist faced when tasked with naming microbes
the resolution of the light microscope revealed little more than the outward shape of microbial cells
vastly different kinds of microbes looked more or less alike
this challenge was overcome as advances were made in biochemistry and microscopy
microbes did not readily fit the classic definition of a species
they reproduced asexually, it was not a group of organisms that copulated
when they do exchange genes, they may do so with related strains or with distantly related species
the most useful classification defines relatedness on the basis of similarity of DNA sequence since it was believed there was a shorter divergence time from a common ancestor with more gene likeliness
taxonomists categorized organisms by only two classes: plant or animal
this was contradicting to the lifestyle, cell, structure, and biochemistry of those that could not fit those refined definitions
Haeckel proposed that microscopic organisms constituted a third kind of life that he termed Monera
this class was then further categorized by Copeland; Monera consisted of prokaryotes and eukaryotes
archaea differ from bacteria and eukaryotes
usually live in extreme environments like deep sea heat vents or salt pools
archaea are intermediates to bacteria and eukarya
they are prokaryotic like bacteria
they have gene expression machinery similar to eukarya
eukaryotes evolved through endosymbiosis
the major cellular components of plants and animals are chloroplasts and mitochondria which have double-membranes and have their own chromosomes
it is theorized that eukaryotes evolved by merging with bacteria to form composite cells by intracellular endosymbiosis, in which one cell internalizes another that grows within it
in the case of those two organelles, they were capable of independent existence
this theory was controversial because it implied a polyphyletic ancestry of living species
this was contradictory to the long-held assumption that species evolve only by divergence from a common ancestor