BIO 123 | History & Scope of Microbial Ecology

Microbial Ecology vs. Environmental Microbiology

• Microbial ecology

  • Addressed the interactions between microbes and between microorganisms and higher forms of life

  • Singvhi et al. (2020): Interplay of human gut microbiome in health & wellness

    • There are microorganisms inside our body that influences human health

• Environmental microbiology

  • Study of processes in the environment mediated by microorganisms

  • Harms et al. (2011): Exploiting fungi for bioremediation of hazardous chemicals

    • Microorganisms influence the environmental processes occurring in aquatic, semiaquatic, & riparian habitats

T/F: There are subtle differences between environmental microbiology and microbial ecology but huge overlaps.

TRUE

Origin & Evolution of Microorganisms | Key idea

Microbes have developed mechanisms that allowed for their great ubiquity.

THEME 1 | Origin & Evolution of Microorganisms

Explain 4 mechanisms of bacteria that allowed for their great ubiquity

sdfs

1. Short life cycles with high mutation rates

   1. Short life cycles would mean higher reproductive rates > rapid reproduction process, probably due to being able to reproduce asexually

   2. High mutation rates increase their probability of acquiring a mutation that may confer favorable traits amongst their population and in their environment

2. Diverse metabolic plasticity

   1. Unlike humans who rely on cellular respiration for powering metabolic processes, bacteria have super diverse metabolisms, e.g., fermentation, anaerobic respiration, chemolithotrophy, photoautotrophy, etc.

3. Diversity and frequency of genetic transfer

   1. Diverse genetic transfer modes, such as

      1. Transformation: uptake of naked DNA from environment

      2. Transduction: transfer of genetic material via bacteriophages

      3. Conjugation: transfer of genetic material via direct contact

   2. that, in turn, allows them to have higher or more frequent rates of genetic transfer:

      1. which would also imply a higher probability of developing mutations that confer beneficial traits to a population, an example of which are:

4. Stress + resistance strategies

   1. Methicilin-resistant Staphylococcus aureus (MRSA)

      1. Prime example of how bacteria can acquire resistance via HGT

      2. What allowed these strains to be MR is their acquiring of a mecA gene, which encodes an altered penicillin-binding protein (PBP2a) with low affinity to B-lactam antibiotics, e.g., methicilin.

      3. Due to this low affinity of B-lactam antibiotics to PBP, it fails to inhibit the crosslinking of peptidoglycans for bacterial cell wall by the PBP. Thus, PBP can continue its cell wall synthesis function and the bacteria is able to resist methicilin.

T/F: Only prokaryotes are capable of horizontal gene transfer (HGT).

FALSE

While HGT is more common in prokaryotes, certain eukaryotes, such as fungi, plants, and even animals, can acquire genes from other organisms through mechanisms like viral infections, endosymbiosis, or direct transfer from other species. For example, parasitic plants can obtain genes from their host plants, and some eukaryotes acquire genes from bacteria, which can provide new functions.

T/F: Microbes have been adapting to climatic and geological changes that have occurred on Earth since the beginning of life, permeating equable habitats.

FALSE

Permeating varied habitats

T/F: All prokaryotes are unicellular.

TRUE

Biofilms, myxobacteria, and filamentous cyanobacteria, exhibit multicellular-like behavior or organized communities, but they are not technically multicellular in the same way that eukaryotic multicellular organisms are.

Taxonomic and Functional Diversity | Key idea

Microbes have a huge taxonomic and functional diversity in varied ecosystems.

THEME 2 | Taxonomic and Functional Diversity

Explain the huge taxonomic and functional diversity of microbes in varied ecosystems.

• Larsen et al. (2017)

  • All prokaryotic and eukaryotic unicellular microorganisms, even virus, are in the functional dimension of microbial ecology.

• Systematics of microorganisms is rapidly changing.

  • Wilson et al. 1992: Animals are dominant in diversity and numbers (dominant blue in pie chart)

  • Mora et al. 2011: With inclusion of invertebrates in Kingdom Animalia, the blue portion became more dominant.

  • Larson et al. 2017: With the discovery of more sophisticated techniques and shifting of analysis from phenotypes to genotypes, they discovered that microbes comprise 78% of diversity and density of all living organisms.

    • Excluding Archaea, which if added could easily double/rival that 78%

    • Excluding viruses, as these are not living things

    • In terms of sheer number, virus > bacteria > humans

• Raoult and Forterre (2008)

  • Proposed dividing biological entities into

    • Ribosome-encoding organisms (REO)

      • Bacteria, Archaea, Eukarya

      • Encodes their own ribosomes, machinery for protein synthesis

    • Capsid-encoding organisms (CEO)

      • Viruses of B,A,E

      • Can’t encode ribosomes, only have capsids (protein coats), must hijack host cell to replicate and metabolize

T/F: Viruses can encode their own ribosomes.

FALSE

They are CEOs and often considered "biological entities" rather than living organisms because they lack the essential machinery (ribosomes) for autonomous life. They cannot carry out metabolic processes or replicate on their own and must hijack a host cell’s machinery to reproduce.

Roles in Ecosystem Functioning | Key idea

Microbes play major roles in the organization, functioning, and evolution of ecosystems.

Ecosystem functioning vs. Ecosystem services

• Ecosystem functioning refers to mechanisms and processes that sustain life in an ecosystem.

• Ecosystem services refers to the benefits derived by humans from an ecosystem.

THEME 4 | Roles in Ecosystem Functioning

Explain the microbes’ role in ecosystem functioning (4).

Microbial mass, metabolic diversity, and ecological adaptability allow microbes to:

1. Participate and control food web and trophic interactions

   1. In oceans, microorganisms drive food webs. They are the main producers.

   2. They influence food web dynamics by making nutrients available to other organisms.

2. Perform organic and mineral transformations

   1. Decomposing organic matter

   2. Can perform photosynthesis to convert CO2 into organic matter

   3. Nutrient cycling, especially nitrogen

      1. Nitrogen is limiting in many environments (and even us humans need it for nucleic acids, proteins)

      2. Humans can’t fix nitrogen, but microbes can (lightning also can).

3. Run biogeochemical cycles and systems

   1. Carbon cycle

      1. Decomposing organic matter

      2. Photoautotrophy

   2. Nitrogen cycle

      1. Nitrogen-fixing bacteria can convert atmospheric nitrogen into forms usable by plants.

4. Carry out synthesis and degradation reactions

   1. Mercury is highly volatile in air and when it gets deposited into bodies of water, it may be absorbed by tissues of fish and accumulate in their bodies.

   2. Bacteria can methylate mercury, producing methylmercury, which is a toxic and bioaccumulative form that can potentially pose threats to human and animal health.

   3. Bacteria can also degrade/demethylate mercury, mitigating its impact

   4. Some bacteria can also easily degrade oil spills

      1. Bioremediation

      2. Decomposition

T/F: Microorganisms participate in cloud formation.

TRUE

• For clouds to form, water vapor in atmosphere must condense into tiny water droplets. For these to condense, water vapor requires a surface to which it can adhere to called nucleation sites.

• Microorganisms release organic compounds, e.g., proteins and polysaccharides, which can serve as nucleation sites for droplets.

• Nitrogen-fixing bacteria influence formation of aerosols, which may also serve as nucleation sites.

Biotic Interactions | Key idea

Microorganisms interact with other microbes and all the other multicellular living organisms.

THEME 4 | Biotic interactions

Explain population dynamics, symbioses, and pathogenicity.

1. Population dynamics

   1. Populations of different microbes in various environments can form biofilms and microbial mats that provides these microbes greater access to nutrients and protection from predation and physicochemical disturbances.

2. Symbioses

   1. Mutualism

      1. Cows and microbes

         1. In cows, a symbiotic relationship with microorganisms allow these ruminants to digest a diet rich in fiber and low in protein (cellulose). Their rumen, in turn, provides a safe, substrate-rich environment for these microbes to proliferate.

      2. Squids and microbes

         1. Bacteria provides squids the light to help them camouflage, while squids provide bacteria with nutrients and protection (a safe habitat).

      3. Fungi and trees

         1. Ecto- and endomycorrhizae

            1. Fungi (mycorrhizae) extends roots of tree/plant, allowing for more efficient water and nutrient uptake

            2. Plant/tree, in turn, provides fungi with organic compounds

3. Pathogenicity

   1. Certain interactions between microorganisms and living organisms result in diseases (including crop and animal).

   2. Diarrheal diseases is second leading cause of death in children under 5yo and is responsible for deaths of 370,000 children in 2019 (WHO 2020).

Abiotic Interactions | Key idea

Differences in physical and chemical aspects of an environment affects microbes.

THEME 5 | Abiotic interactions

Explain presence/absence, spatial distribution, and growth & activity.

• Presence/absence

  • Most important environmental parameters interacting with microorganisms:

    • pH

    • pressure (temperature)

    • light intensity and wavelength

    • electron donor and acceptor concentration

• Spatial distribution

  • Interaction of microorganisms with natural surfaces must be considered because many of these microbes are not free-living in nature and attach to surfaces.

• Growth & activity

  • In natural systems, resources are limited and do not allow maximal growth and development of microbes, prompting their evolution of myriad survival mechanisms.

T/F: In natural systems, resources are infinite and allow maximal growth and development of microbes

FALSE

Resources are limited

Bioremediation & Other Activities | Key idea

Microbial ecology can provide solutions to many environmental problems.

THEME 6 | Bioremediation and other activities

Explain major drivers of global habitat degradation

Major Drivers of Global Habitat Degradation

isi

• Increase of world population

• Settlement of populations over extended range of biotopes

• Industrial development and production of more and more domestic and industrial wastes

How do we enhance metabolic properties of microorganisms to degrade most pollutants that affect our planet?

Bioremediation (there are microorganisms that accelerate degradation of oil spills, heavy metals, plastics, etc.)

How do we enhance metabolic properties of microorganisms to degrade most pollutants that affect our planet?

Bioremediation

Public Health Issues | Key idea

Microbial ecology can help in understanding public health issues from a broader view.

THEME 7 | Public Health Issues

Explain 3 public health problems

pfc

1. Production of safe drinking water and water resources

2. Food contamination and food safety

3. Changes in behavior of pathogens in environment

T/F: Microbiology existed before the invention of microscopes.

FALSE

Microbiology only existed after the invention of the microscope.

*Hans and Zacharias Janssen created the first microscope.

Who made the first known description of microorganisms?

English mathematician and natural historian, Robert Hooke

In Hooke’s book Micrographia, he illustrated many microscopic images, including _

fruiting structures of a mold using a compound microscope

Who is the first person to see bacteria in pepper-water using hand lens?

Dutch draper and amateur microscopist Antoni van Leeuwenhoek

_ constructed a simple microscope containing single lens (266x magnification) to examine various natural substances for microorganisms.

He wrote to Royal Society of London who made an English translation of his works. He observed '“animalcules” from sampling a drunk man’s teeth.

Antoni van Leeuwenhoek

Ridiculed rival of Leeuwenhoek, pioneer of protistology

Louis Joblot

_ was ridiculed for his imaginative portrayal of microscopic protists in his drawings

Louis Joblot

*Paramecium = 3rd photo from left

_ devoted much of his time to develop microscopes with which he described animalcules and other microscopic “snakes, fish, and eels,” which he observed in infused preparations of various plants or vinegar, and “the largest part is invisible to the ordinary scope of our eyes.”

Louis Joblot

He is the pioneer of the theory of microbial diseases

Ignaz Semmelweis

Ignaz Semmelweis imposed a new rule mandating handwashing with chlorine for doctors. This resulted in _

• The rate of deaths in his maternity ward dramatically declining—the first proof that cleansing hands could help prevent infection and death from puerperal fever.

_ studied fermentation, sterilization, disease and vaccination

Louis Pasteur

Louis Pasteur successfully disproved spontaneous generation in 1859 by showing _

The mechanics of spoilage with his swan-necked flasks, which showed that “vital essence” in their air did not cause putrefaction.

• 2 flasks (1 control, 1 experimental) with sterilized NB

• Exposed to open air

• For experimental, there was no microbial growth since while swan-neck design allowed entry of air, it prevented dust particles and microorganisms from reaching the NB

• For control, after breaking the swan-neck design, microbial growth was immediately observed, indicating that microorganisms from the air were responsible for the contamination

_ and his colleagues discovered that the rabies virus could be weakened or attenuated by drying the spinal cords of infected rabbits. This weakened virus was used to create a vaccine.

Pasteur

_ established postulates that would solidify the germ theory of diseases

Robert Koch

Koch’s 4 Postulates

1. The suspected pathogen must be present in all cases of disease and absent from healthy animals.

2. The disease organism must be isolated in pure culture.

3. Inoculation of sample of culture into a healthy, susceptible animal must produce the same disease.

4. The disease organism must now be recovered from the newly inoculated animal.

bacteriocins vs. antibiotics

While both serve to inhibit bacterial growth,

• Bacteriocins are naturally produced by bacteria, have narrow spectrum of activity, making it less likely to induce resistance

• Antibiotics can be naturally or synthetically produced and have wider spectrum of activity, but their overuse can lead to resistance

The first to observe interactions between microorganisms and develop antibiotics

Sir Alexander Fleming

In 1959, Fleming observed the inhibition of a culture of _ by contaminating mold, _.

• Staphylococcus

• Penicilium notatum

Fleming’s discovery of antibiotics allowed us to think that _

• There are other ways microbes can be killed

• Bacteria can produce substances that kill other bacteria

The discovery of _ opened up a world smaller than bacteria and fungi

Viruses

_ was the first to demonstrate unfilterable infectious particles smaller than bacteria while studying tobacco mosaic virus (TMV)

Sergei Ivanovski

_ discovered the first oncovirus (1911), Rous Sarcoma Virus (RSV), which caused tumors in chickens

Peyton Rous

_ described bacteriophages, could not be observed until the discovery of electron microscope in 1939.

Felix Hubert d’Herelle

An area of uniform environmental conditions providing living space for a specific assemblage of plants and animals

Biotope

_ was the first to describe the “microbiology of natural biotopes”

Sergei Winogradsky

Winogradsky described 8 microorganisms using his Winogradsky column, which did not use a pure-culture strategy.

• Purple photosynthetic bacteria

• Sulfur-producing bacteria

• Anoxygenic phototrophic bacteria

• Sulfur-reducing bacteria

• Iron-oxiding bacteria

• Nitrifying bacteria

• Denitrifying bacteria

• Nitrogen-fixing bacteria

Nitrifying vs. Nitrogen-fixing vs. Denitrifying

• Nitrifying bacteria converts ammonia > nitrite > nitrate

• Nitrogen-fixing bacteria converts atmospheric nitrogen > ammonia (form usable by plants)

• Denitrifying bacteria converts nitrate/nitrate > nitrogen gas/nitrous oxide

T/F: Winogradsky’s experiment involved the use of a pure-culture strategy

FALSE

Sergei Winogradsky was the first to demonstrate the fundamental role of microbes in the _

transformation of mineral compounds through various metabolic processes and that allowed him to simultaneously grow different communities of bacteria along gradients of sulfur, light, O2.

T/F: In Winogradsky column, oxygen levels are highest at the surface and decrease toward the bottom of the column.

TRUE

T/F: Hydrogen sulfide concentrations are highest at the top of the column, where sulfate-reducing bacteria thrive, and decrease toward the bottom.

FALSE

Hydrogen sulfide concentrations are highest at the bottom of the column, where sulfate-reducing bacteria thrive, and decrease toward the top.

T/F: Winogradsky provided the framework for studying microbial ecology, specifically Monograph: Soil Microbiology: Problems & Methods

TRUE

Explain Monograph: Soil Microbiology: Problems & Methods

1. The study of pure cultures, while favorable bc it allows us to determine the microbes’ metabolic properties and mechanisms, does not mirror natural microbial life in the environment.

2. The diversity of microorganisms is profound and very few are culturable in lab conditions.

   1. What we currently know as diversity of microorganisms is just the culturable ones

3. Not all microorganisms are in an active state, which reflects their resistance to adverse conditions.

A technique used to increase the relative abundance of a specific microorganism in sample to make it easier to isolate and study them

Enrichment technique

Enrichment technique vs. culture method

• Enrichment technique: used when target microorganism is difficult to isolate directly due to low abundance or specific growth requirements.

• Culture method: used broadly to isolate, grow, and study microorganisms from various samples.

_ has contributed greatly to our understanding of biogeochemical cycles and microbial transformations on a global scale

Martinus Beijerinck

He was the first to describe viruses as reproducing entities different from other organisms

Beijerinck

He described biological nitrogen fixation

Beijerinck

_ showed the significant role of microorganisms in the recycling of elements and balance of ecosystems necessary for the maintenance of environmental quality and maintenance of life on Earth by _

• Beijerinck

• Developing enrichment techniques and culture methods

Microbial Ecology in the Present Time | Key idea

Unexplored aspects of microbial life, interactions, and metabolic activities are being shed light through technological advancements and contemporary discoveries.

Technological advancements and contemporary discoveries in modern microbial ecology

1. Environmental metagenomics

   1. Study genetic material recovered directly from environmental samples, without needing to culture organisms.

   2. Sequence everything from the sample and process it thru high throughput sequencing technologies (bioinformatics)

   3. Scientists can now explore questions related to:

      1. extent of diversity within naturally occurring microbial communities, and

      2. functional significance of that diversity

   4. Taxonomic composition bar plot illustrating phylum-level composition of microbial-mat samples

2. Biocomplexity

   1. Studies interactions among microbes and between microbes and their environment, emphasizing a whole ecosystem, rather than its parts, seeking to identify emergent properties that cannot be found in studies of individual components.

   2. Principal Coordinate Analysis plot containing 37,680 samples

Antibacterial substance secreted by bacteria

Bacteriocin

e.g., of emergent properties in bacteria

1. Biofilm formation

2. Quorum sensing

3. Swarming motility

Which subdivision of microbio does microbial ecology fall under?

Basic research microbio > by process

Which subdivision of microbio does environmental microbio fall under?

Applied microbio > environmental

Study & Scope of Modern Microbial Ecology | Key idea

Pasteur, Koch, and other early microbiologists were generalists. Developments in S&T allowed more specialized fields to be developed, including microbial ecology.

Understanding the development of microbial ecology entails _

understanding the timeline of Earth’s development and how microbes evolved with it

Sum of chemical processes carried out by living organisms necessary to maintain life

Metabolism

Many molecules constituting cellular structures and energy used to power reactions are obtained via _

Metabolism

Type of metabolism that involves breaking down of larger molecules that, in turn, releases useful form of energy + lost heat, and produces small molecules

Catabolism

Type of metabolism that creates larger molecules from smaller precursor molecules by using energy

Anabolism

Volume of bacterial cell, percent compostion

• 2×10^-12 cm³

• 70% H2O

• 30% chemical — macromolecules

  • 15% proteins, 6% RNA, 2% polysaccharide, 1 % DNA

Electron transfers that allow some energy to be captured and stored for cell use

Redox reactions

(+)
Loss of electrons
Loss of hydrogen
Loss of energy
Gain of oxygen
Exothermic, exergonic

Oxidation

(-)
Gain of electrons
Gain of hydrogen
Gain of energy
Loss of oxygen
Endothermic, endergonic

Reduction

arrange in increasing oxidation potential

formic acid, methanol, carbon dioxide, formaldehyde, methane

carbon dioxide < formic acid < formaldehyde < methanol < methane

methane has the highest oxidation potential bc it has the highest potential to lose high number of hydrogen/electrons (currently in low oxidation state)

arrange in increasing oxidation state

formic acid, methanol, carbon dioxide, formaldehyde, methane

methane (-4) < methanol (-2)< formaldehyde (0) < formic acid (+2) < carbon dioxide (+4)

CO2 has the highest oxidation state because it has lost the most electrons.

arrange in increasing reduction potential

formic acid, methanol, carbon dioxide, formaldehyde, methane

methane < methanol < formaldehyde < formic acid < carbon dioxide

Carbon dioxide has highest reduction potential bc it has highest potential to gain hydrogen/electrons

arrange in increasing reduction state

formic acid, methanol, carbon dioxide, formaldehyde, methane

carbon dioxide < formic acid < formaldehyde < methanol < methane

Methane has highest reduction state because it is highly reduced, i.e., gained most hydrogen/electrons

reduced or oxidized?

NADH

Reduced

reduced or oxidized?

NAD+

Oxidized

reduced or oxidized?

FAD

Oxidized

reduced or oxidized?

FADH2

Reduced

3 activated energy carriers during Krebs

1. NADPH

2. NADH

3. FADH2

A reducing agent reduces an entity by _

oxidizing itself (undergoing oxidation)

RA loses electron for the other entity to gain it or become reduced.
LEORA: Reducing agent loses electrons (undergoes oxidation)

An oxidizing agent induces oxidation by _

reducing itself (undergoing reduction)

OA oxidizes entity by gaining/hogging its electrons to themselves
GEROA: Oxidizing agent gains electrons

Oxidizing agent for catabolism

NAD+

Reducing agent for anabolism

NADPH

T/F: The evolution of microbial life is tied to the development of the Earth. Anabolic and catabolic pathways were patterned on the available molecules present.

TRUE

Arrange ff. in sequence (how they appeared on earth)

vascular plants, eukarya, animals, mammals, cyanobacteria, phototrophic bacteria, bacteria & archaea, humans

1. Bacteria & Archaea (3.9 bya)

2. Phototrophic bacteria (No oxygen)

3. Cyanobacteria (Oxygenated atmosphere)

4. Eukarya (Oxygen present onwards)

5. Animals

6. Vascular plants

7. mammals

8. Humans

Earth dates back to _

4.6 bya

Type of photosynthesis that uses alternative electron donors, e.g., hydrogen sulfide (H2S), instead of H2O and bc there’s no splitting of water, there’s also no production of oxygen.

Anoxygenic photosynthesis

_ focuses on material production, which requires carbon/nitrogen source to occur.

Anabolism

_ metabolism involves synthesizing cellular materials from precursor molecules

Anabolic

Cellular materials produced from anabolism are used for _

• Growth

• Reproduction

• Repair of cellular structures

_ focused on energy production, which requires energy source to occur.

Catabolism