Bio 301 - Ch 1 Book Notes

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