BIO 123 | Microbial Diversity I: Domain Bacteria & Archaea

Describe microbial diversity

• Microorganisms account for majority of life on earth (>1 trillion in some estimates)

• Microbes possess diverse array of metabolic activities, which allows them to colonize virtually every habitat

• All 3 domains of life are dominated by microbial life present within

T/F: Only plants, animals, and fungi are macroorganisms.

TRUE

T/F: Microorganisms are dominant in all 3 domains of life.

TRUE

8 Challenges in Estimating Microbial Diversity

1. Strain concept

2. Changing phenotype

3. Functional role similarity

4. Horizontal gene transfer

5. Habitat specialization

6. Nonculturability

7. Defining a microorganism

Syphilis-causing bacterium

Treponema pallidum

Variety and variability of life

Diversity

T/F: Members of higher-level groups share fewer characteristics than those in lower-level groups.

TRUE

The more specific (the lower), the more characteristics they share.

As a general rule, _ is the smallest grouping of organisms possible.

species

_ is an exception to general rule that species is the smallest grouping of organisms possible

strain

When do you consider something a strain?

1. Small but permanent genetic difference

2. Antibiotic resistance (tricky bc they can get it thru HGT)

3. Need for a nutrient (thats not typically needed by species of that group)

4. Antigen presence

T/F: Unclassified bacteria is valuable bc it can contribute to overall similarities and differences that we don’t know of.

TRUE

T/F: Strains can be defined by a single nucleotide change, which may change the chromosomal structure of an organism.

TRUE

Explain

• Type strain: type specimen, a standard or reference specimen to which all classified strains should be close in terms of properties.

• Classified strains

• Undiscovered strains: unclassified

If animals have subspecies, plants have tribes, bacteria have _

strains

Explain why changing phenotype is a challenge in estimating microbial diversity

• Microorganisms are phenotypically indistinguishable or morphologically plastic.

• A single plate filled with white colonies can represent hundreds of different bacteria.

• Morphological characters of Talaromyces macrosporus differ per culture medium used.

Explain why functional role similarity is a challenge in estimating microbial diversity

• Distantly related organisms can fill equivalent functional roles in varied ecosystems.

• e.g., Kimchi from different areas have similar but not identical microbiomes, which suggests that different (sometimes even phylogenetically unrelated) microorganisms in a community perform the same fermentation role in that assemblage.

  • Lactococcus

  • Lactobacillus

  • Leuconostoc

  • Weisella

Explain how horizontal gene transfer poses challenge in estimating microbial diversity

• Microorganisms can exchange genes via HGT

• Comparative genomic analyses of closely related microbes that exhibit different phenotypes revealed distinct genome differences, which may have come from HGT.

• HGT

  • Transformation: uptake of naked DNA from environment (donor cell lyses)

  • Transduction: via bacteriophages

  • Conjugation: via direct contact

Explain how habitat specialization contributes to challenges in estimating microbial diversity

• The distribution of some species is restricted, making them rarer to sample.

• More heterogeneous or disturbed environments tend to be occupied by generalists

  • Filter: Interaction between taxa

• Specialists tend to develop more in homogeneous or constant environment and determined by natural selection

  • Abiotic factors: soil composition, pH, moisture

  • Biotic factors: presence of a host

T/F: Specialist species require more specific sampling techniques. If you can’t sample them, they will be very hard to classify.

TRUE

T/F: For microorganism to be classified, they have to be culturable.

TRUE

T/F: The more culturable microorganisms we have, the more we can sequence them, the more we can update databases.

TRUE

Explain how non-culturability is an issue in estimating microbial diversity.

• High proportions of microorganisms across most biomes remain uncultured.

• High proportions of microorganisms remain unculturable and can only be detected through high-throughput sequencing methods because we cannot perfectly replicate environmental conditions.

• Taxonomic assignments at 97% sequence similarities, we can only accurately identify >10% of most microorganisms due to limitations of sequenced barcodes in databases.

T/F: The classification of what belongs under “microbiology” is always in flux.

TRUE

T/F: Techniques in systematic differentiation, classification, and identification of prokaryotes and eukaryotes are different.

TRUE

T/F: Bacteria are ubiquitous, mostly free-living, and unicellular prokaryotic microorganisms.

TRUE

Gold standard for prokaryote classification

Gene sequence, not morphology (but it could be something that comes out phenotypically)

Enumerate the 10 key characteristics of bacteria

1. Cell type

   1. Prokaryotic, peptidoglycan wall, S-layer, glycocalyx

2. Size

   1. 0.5-5 um to 2 cm (Theomargarita magnifica)

3. Habitat & ecology

   1. Ubiquitous, almost all habitats, extreme environments

4. Morphology

   1. Unicellular, diverse but with several common forms (cocci, bacilli) and patterns of association (streptococci)

   2. Multicellular forms: aggregates of Myxobacteria, filaments of Actinomycetes, hyphae of Streptomyces, biofilm and microbial mat formations

5. Metabolism

   1. Great metabolic diversity

   2. Classified based on energy source, carbon source used for growth, electron donors used

6. Growth & reproduction

   1. Binary fission common, other types are present (budding, fruiting bodies, etc.)

7. Genetics

   1. Single circular chromosome, plasmid, HGT

8. Behavior & communication

   1. Flagellar motility in many, pili, bioluminescence, quorom sensing, chemo-, photo-, magneto, and energy taxis

9. Interactions

   1. Commensals, predators, mutualists, pathogens

10. Significance

    1. Food and beverage, detergents and enzymes, biotechnology, medicine, bioremediation, pest-control, biogeochemical cycles, etc.

T/F: At species level, 97% genetic similarity is required. Meanwhile, at strain level, 99% genetic similarity is needed.

TRUE

Explain how domain bacteria has constantly changing phyla

• There is much consideration to the definition and number of bacterial phyla

• Much debate to the definition of phylum in domain bacteria

• Common definition: monophyletic lineages sharing ~75% or less of 16s rRNA genes with other phyla

  • There may be up 1300 bacteria phyla existing

• Almost 72% of all bacterial phyla remain “candidates,” i.e., they have no culturable representatives.

• 41 phyla accepted by List of Prokaryotic names with Standing in Nomenclature (LSPN)

  • 89 phyla recognized in SILVA database

  • 30 phyla have culturable representatives

• 90% of all culture bacteria belong to either

  • Bacteroidetes, Proteobacteria, Actinobacteria, Tenericutes, Firmicutes

Almost _ of all bacterial phyla remain “candidates,” meaning they have no culturable representatives

72%

Basis for phylum classification in microbiology

Genetics

• The largest and most metabolically diverse bacterial phylum

• With most cultured members in record

• More than 1/3 of characterized species are found in this group

• Constitutes bacteria of medical, industrial, agricultural significance

• All gram-negative, with very few metabolism NOT occurring this group

• 6 classes: Alpha, Beta, Gamma, Delta, Epsilon, Zeta

PROTEOBACTERIA

• Second largest class of bacteria

• >1000 described species with extensive functional diversity

• Most species are obligate/facultative aerobes and many are oligotrophic (can grow in environments w very low nutrient concentrations)

• 10 well characterized orders

  • Rhizobiales

    • Rhizobium: root commensal

  • Rickettsiales

    • Rickettsia lysing human cell

  • Rhodobacterales

    • Nitrobacter oxidizes NO2- to NO3-

  • Rhodospirillales

  • Caudobacterales

    • Acetobacter produces acetic acid industrially

  • Sphingomonadales

    • degrades aromatic organics, performs degradation

Alphaproteobacteria

• Third largest class of bacteria

• ~500 described species with extensive functional diversity

• Broad variety of metabolic activities from obligate parasite to living in oligotrophic ground water

• 6 major orders

  • Burkholderiales

  • Hydrogenophilales

  • Methylophilales

  • Neisseriales

  • Nitrosomonadales

  • Rhodocyclales

    • Zoogloea ramigera degrades carbon, causes flocculation of wastewater treatment

    • Neisseria has pathogenic species (Gonorrhea, Meningitis)

    • Nitrospira are ammonia-oxidizing bacteria

Betaproteobacteria

Alphaproteobacteria that degrades aromatic organics, performs degradation

Sphingomonas

Alphaproteo oxidizes NO2 to NO3

Nitrobacter

Alphaproteo produces acetic acid industrially

Acetobacter

Alphaproteo lysing human cell

Rickettsia

Betaproteo that degrades carbon, causes flocculation of wastewater treatments

Zoogloea ramigera

Betaproteo with pathogenic species causing Gonorrhea, Meningitis

Neisseria

Betaproteo that are important ammonia-oxidizing bacteria

Nitrospira

• Largest, most diverse, most culturable bacterial class, most studied, most media formulated with it in mind

• Nearly half of characterized species in phylum (>1500)

• Rapidly grow in lab media, can be isolated in wide diversity of habitats

• Many are pathogenic to animals, humans, plants

• 15 major orders but most well-characterized are

  • Enterobacteriales

    • Shigella dysenteriae invades epithelial cells and can cause bacillary dysentery

  • Pseudomonadales

    • Pseudomonas aeruginosa can readily colonize surfaces and cause hospital nosocomial infections

  • Vibrionales

    • Vibrio parahaemolyticus inhabits marine habitats and causes gastroenteritis

Gammaproteobacteria

Gammaproteo inhabiting marine habitats, causes gastroenteritis

Vibrio parahaemolyticus

Gammaproteo readily colonizing surfaces, causes hospital nosocomial infections

Pseudomonas aeruginosa

Gammaproteo invading epithelial cells, causes bacillary dysentery

Shigella dysenteriae

3 classes under proteobacteria containing least number of species and functional diversity

Delta-, Epsilon-, Zetaproteobacteria

Proteobacteria

• Oxidizes H2S produced by sulfate- and sulfur-reducers

Epsilonproteobacteria

Proteobacteria that contains only 1 characterized species, iron oxidizer Mariprofundus ferrooxydans, but 28 potential others

Zetaproteobacteria

Proteobacteria mostly sulfate- and sulfur-reducing, dissimilative iron-reducing, bacterial predators

Deltaproteobacteria

Causative agents of gastroenteritis, gastritis

Helicobacter, Campylobacter

Common sulfate-reducing microbes

Desulfovibrio, Deltaproteobacteria

Produces mineralized twisted stalks of iron due to Fe oxidation

Mariprofundus ferrooxydans

_ combined contain nearly 50% of all characterized species

Firmicutes, Tenericutes, Actinobacteria

Actinobacteria include _, which is a huge group of primarily filamentous soil bacteria with high C+G concentrations in DNA

Actinomycetes

High C+G conc > higher melting point in DNA bc C+G has 3 H bonds as opposed to A+T (2 H bonds) > important when classifying

_ lacks cell wall, e.g., _ that cannot synthesize peptidoglycan

• Tenericutes

• Mycoplasma (lack of cell wall contributes to their being highly infectious)

_ includes endospore-forming bacteria, lactic-acid producing bacteria, and other groups, with low C+G concentrations in their DNA

Firmicutes

• Bacillales, Clostridiales

• Lactobacillales

3 classes under Firmicutes

Lactobacillales, Bacillales, Clostridiales

2 classes under Tenericutes

Mycoplasmatales, Entomoplasmatales

3 classes under Actinobacteria

Actinomycetales, Bifidobacteriales, Coriobacteriales

Firmicutes important in plant food fermentation

Leuconostoc mesenteroides

Firmicutes used in cheese fermentations to produce flavor

Streptococcus thermophilus

Firmicutes extensively studied as cell factory for protein products

Lactococcus lactis

Firmicutes used commonly in making yoghurts

Lactobacillus delbrueckii subsp. Bulgaricus

Class under Firmicutes containing industrially significant lactic acid bacteria

Lactobacillales

Genera of bacteria composed of aerotolerant obligate fermenters important to various industries

Lactic Acid Bacteria (LAB) group

T/F: All lactic acid bacteria produce lactic acid as major or sole fermentation product and, thus, can be divided into:

• Homofermentive (only produce lactic acid)

• Heterofermentive (produce lactic acid, as well as smth else, e.g., ethanol, propionic acid)

TRUE

T/F: Most LABs can obtain energy only from sugar fermentation which expands the habitats where they are isolated.

FALSE

Most LABs can obtain energy only from sugar fermentation which restricts habitats where they are isolated.

T/F: Many members of Clostridiales and Bacillales do not form spores.

TRUE

3 examples of nonspore-forming genera

1. Listeria

2. Staphylococcus

3. Sarcinia

• Facultative aerobe that can grow fermentatively

• Can tolerate drying and high salt concentrations

• Common commensals in animals, humans but can cause serious illness (MRSA)

Staphylococcus

• Found widely in soil, opportunistic pathogen

• Common cause of foodborne illness

• Transmitted through ready-to-eat food, e.g., cheese, sausages, which are cold-tolerant

Listeria

• Obligate anaerobes that divide in 3 perpendicular planes to create packets for 8 or more cells

• Can be isolated from soil, mud, feces, stomach contents due to its extreme acid tolerance

Sarcina, e.g., Sarcinia ventriculi in mucosa of gastric ulcer patient

T/F: All endospore-forming bacteria are Gram-negative species of Bacillales or Clostridiales

FALSE

Gram-positive species of Bacillales, Clostridiales (BLUE to PURPLE)

3 spore-forming genera

1. Bacillus, Paenibacillus

2. Clostridium

3. Sporosarcina

Spore-forming genera that produces extracellular enzymes that break biopolymers, produces antibiotics during stationary phase, produces toxic insecticidal proteins

Bacillus, Paenibacillus

Spore-forming genera whose cells are cocci not rods; catabolizes urea into ammonia, raising soil pH; uniquely cultured until pH 10

Sporosarcina

Spore-forming genera that lives in anoxic pockets of soil, lacks respiratory chain, uses substrate-level phosphorylation

• Produces butyric acid, acetone, butanol from sugars and polymers, e.g., cellulose

• Ferment amino acids

• Produce toxins deadly to humans, e.g., C. tetani, botulinum, perfringens

Clostridium

_ could cause muscular contractions strong enough to break bones (backbreaker disease)

Tetanus

_ produces insecticidal parasporal protein (X)

Bacillus thuringiensis

T/F: Bacillus and Paenibacillus become highly active in producing enzymes BEFORE entering sporulation stage.

TRUE

This increase in enzyme production helps in breaking down organic matter in their environment, which is beneficial for nutrient acquisition and survival.

T/F: Stressful conditions induce Bacillus & Paenibacillus to enter a specific growth phase where antibiotic production is triggered.

TRUE

Antibiotic production is a defense mechanism to reduce competition, particularly during periods when resources are very limited.

Normally, Agrobacterium AT has pathogenic DNA that causes a type of disease in plant called _

Crown gall disease

Explain how we make BT corn, rice, etc.

1. Isolate gene encoding insecticidal parasporal protein from BT

2. Insert BT gene into plasmid

3. Transform plasmid into Agrobacterium tumefaciens (AT)

4. Infect plant cells with transformed Agrobacterium AT cells

Agrobacterium tumefaciens causes a type of plant disease known as crown gall, which results from the insertion of its own DNA into the plant's genome. Scientists exploit this mechanism by replacing the pathogenic DNA with the BT gene.

C. tetani vs. C. botulinum

• Tetani: continuous muscle contractions, spasms

• Botulinum: continuous muscle relaxation, paralysis

Dormant, tough, asexual, nonreproductive structures that have high and wide ranging tolerance to harsh climactic conditions. Its production require genes not acquired via HGT.

Endospore

T/F: Production of endospores require genes acquired via HGT

FALSE

Production of endospores require genes NOT acquired via HGT

Single class under Tenericutes lacking bacterial cell wall

Mollicutes

• Latin for soft

• Lacks cell walls due to adaptation of living as symbionts, intracellular pathogens

• Some of the smallest microbes

Mollicutes

Mollicutes genera

• Most well-characterized genus

• Sterols in cell membrane for protection against osmotic lysis

• Lipoglycans for added protection, adherence to surfaces

• Have varied growth morphology in media

Mycoplasma

_ (TEM) has varied growth morphology: coccoid, hyphae-like elements

Mycoplasma mycoides

_ detected in hemolymph of Drosophila pseudoobscura, causing it to bear only female progeny

Spiroplasma sp.

Mollicutes genera

• Helical, spiral-shaped

• Lacks flagella but have rotary, screw motion

• Commonly found in gut of insects, internal tissues of plant

Spiroplasma

_ have been detected in plants, suggesting that a large group of plant-associated Mycoplasma may exist

Mycoplasma-like organisms

Phylum rod-shaped to filamentous, primarily aerobic, common inhabitants of soil and plant materials

• Many members are commensals, except Mycobacterium, which has pathogenic members

• Some members are economically significant as producers of antibiotics or fermented dairy products

• Contains 9 orders but most species belong to Actinomycetales (Gram-positive, anaerobic, have “mycelia”)

Actinobacteria

Actinobacteria species

• Have unusual filamentous branching growth pattern

Actinomyces israelii

Actinobacteria species

• Have critical role in acne formation

Propionibacterium acnes

Actinobacteria species

• Isolated from AIDS patient

Mycobacterium avium

Colonies of _ and other soil bacteria in casein-starch agar plate

Streptomyces

• Have an unusual method of cell division

• Gram-positive, aerobic, nonmotile, rod-shaped organisms; irregularly shaped, club-shaped, v-shaped cell arrangement during growth

• V-shaped cells arise from snapping division, where outer layer of cell wall of diving cell lyses while inner layer remains fused

Coryneform bacteria

Main genera of coryneform bacteria

• Corynebacterium, composed of animal & plant pathogens, saprophytes

• Arthrobacter, nutritionally versatile & stress-resistant microorganisms